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2022
	Tran, Hoang-Dai; Shin, Min-Kyoung; Denman, Charlotte; Han, Run-Run; Kuhn, Bernd; Arbuthnott, Gordon; Jo, Junghyun Generation of Human Striatal-Midbrain Assembloids From Human Pluripotent Stem Cells to Model Alpha-Synuclein Propagation Journal Article Sneak Peek - Cell Press, 2022. Abstract \| Links \| BibTeX \| Tags: MaxOne, Organoids @article{Tran2022, title = {Generation of Human Striatal-Midbrain Assembloids From Human Pluripotent Stem Cells to Model Alpha-Synuclein Propagation}, author = {Hoang-Dai Tran and Min-Kyoung Shin and Charlotte Denman and Run-Run Han and Bernd Kuhn and Gordon Arbuthnott and Junghyun Jo}, url = {https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4288935}, doi = {http://dx.doi.org/10.2139/ssrn.4288935}, year = {2022}, date = {2022-12-05}, journal = {Sneak Peek - Cell Press}, abstract = {Animal models of the pathology of Parkinson’s disease (PD) have provided most of the treatments to date, but the disease is restricted to human patients. In vitro models using human pluripotent stem cell-derived neural organoids have provided improved access to study PD etiology. Here, we generated human striatal and midbrain organoids and assembled both regionalized neural organoids to form human striatal-midbrain assembloids (hSMAs), mimicking a part of basal ganglia. Both the nigrostriatal and striatonigral pathways are present and electrophysiologically active in the hSMAs. hSMA development in the presence of increased alpha-synuclein (α-syn) from SNCA overexpression, induced nigrostriatal system damage, which is typical of the disease. Using the α-syn-mKO2 reporter and bimolecular fluorescence complementation system, we demonstrated that fluorescent α-syn is transported from the striatal area tothe dopaminergic (DA) neurons of the midbrain area. Furthermore, insoluble α-syn aggregated over time in DA neurons similar to Lewy bodies in human patients. Such assembloids are a compelling new platform to develop novel PD therapeutic strategies.}, keywords = {MaxOne, Organoids}, pubstate = {published}, tppubtype = {article} } Close Animal models of the pathology of Parkinson’s disease (PD) have provided most of the treatments to date, but the disease is restricted to human patients. In vitro models using human pluripotent stem cell-derived neural organoids have provided improved access to study PD etiology. Here, we generated human striatal and midbrain organoids and assembled both regionalized neural organoids to form human striatal-midbrain assembloids (hSMAs), mimicking a part of basal ganglia. Both the nigrostriatal and striatonigral pathways are present and electrophysiologically active in the hSMAs. hSMA development in the presence of increased alpha-synuclein (α-syn) from SNCA overexpression, induced nigrostriatal system damage, which is typical of the disease. Using the α-syn-mKO2 reporter and bimolecular fluorescence complementation system, we demonstrated that fluorescent α-syn is transported from the striatal area tothe dopaminergic (DA) neurons of the midbrain area. Furthermore, insoluble α-syn aggregated over time in DA neurons similar to Lewy bodies in human patients. Such assembloids are a compelling new platform to develop novel PD therapeutic strategies. Close https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4288935 doi:http://dx.doi.org/10.2139/ssrn.4288935 Close
	Akarca, Danyal; Dunn, Alexander W E; Hornauer, Philipp J; Ronchi, Silvia; Fiscella, Michele; Wang, Congwei; Terrigno, Marco; Jagasia, Ravi; Vértes, Petra E; Mierau, Susanna B; Paulsen, Ole; Eglen, Stephen J; Hierlemann, Andreas; Astle, Duncan E; Schröter, Manuel Homophilic wiring principles underpin neuronal network topology in vitro Journal Article BioRxiv, 2022. Abstract \| Links \| BibTeX \| Tags: MaxOne, MaxTwo, MEA Technology @article{Akarca2022, title = {Homophilic wiring principles underpin neuronal network topology in vitro}, author = {Danyal Akarca and Alexander W. E. Dunn and Philipp J. Hornauer and Silvia Ronchi and Michele Fiscella and Congwei Wang and Marco Terrigno and Ravi Jagasia and Petra E. Vértes and Susanna B. Mierau and Ole Paulsen and Stephen J. Eglen and Andreas Hierlemann and Duncan E. Astle and Manuel Schröter}, url = {https://www.biorxiv.org/content/10.1101/2022.03.09.483605v2.abstract}, doi = {https://doi.org/10.1101/2022.03.09.483605}, year = {2022}, date = {2022-12-01}, journal = {BioRxiv}, abstract = {Economic efficiency has been a popular explanation for how networks self-organize within the developing nervous system. However, the precise nature of the economic negotiations governing this putative organizational principle remains unclear. Here, we address this question further by combining large-scale electrophysiological recordings, to characterize the functional connectivity of developing neuronal networks in vitro, with a generative modeling approach capable of simulating network formation. We find that the best fitting model uses a homophilic generative wiring principle in which neurons form connections to other neurons which are spatially proximal and have similar connectivity patterns to themselves. Homophilic generative models outperform more canonical models in which neurons wire depending upon their spatial proximity either alone or in combination with the extent of their local connectivity. This homophily-based mechanism for neuronal network emergence accounts for a wide range of observations that are described, but not sufficiently explained, by traditional analyses of network topology. Using rodent and human monolayer and organoid cultures, we show that homophilic generative mechanisms can accurately recapitulate the topology of emerging cellular functional connectivity, representing an important wiring principle and determining factor of neuronal network formation in vitro.}, keywords = {MaxOne, MaxTwo, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close Economic efficiency has been a popular explanation for how networks self-organize within the developing nervous system. However, the precise nature of the economic negotiations governing this putative organizational principle remains unclear. Here, we address this question further by combining large-scale electrophysiological recordings, to characterize the functional connectivity of developing neuronal networks in vitro, with a generative modeling approach capable of simulating network formation. We find that the best fitting model uses a homophilic generative wiring principle in which neurons form connections to other neurons which are spatially proximal and have similar connectivity patterns to themselves. Homophilic generative models outperform more canonical models in which neurons wire depending upon their spatial proximity either alone or in combination with the extent of their local connectivity. This homophily-based mechanism for neuronal network emergence accounts for a wide range of observations that are described, but not sufficiently explained, by traditional analyses of network topology. Using rodent and human monolayer and organoid cultures, we show that homophilic generative mechanisms can accurately recapitulate the topology of emerging cellular functional connectivity, representing an important wiring principle and determining factor of neuronal network formation in vitro. Close https://www.biorxiv.org/content/10.1101/2022.03.09.483605v2.abstract doi:https://doi.org/10.1101/2022.03.09.483605 Close
	Habibollahi, Forough; Khajehnejad, Moein; Gaurav, Amitesh; Kagan, Brett Joseph Biological Neurons vs Deep Reinforcement Learning: Sample efficiency in a simulated game-world Conference 2022. Abstract \| Links \| BibTeX \| Tags: Machine Learning, MaxOne @conference{Habibollahi2022, title = {Biological Neurons vs Deep Reinforcement Learning: Sample efficiency in a simulated game-world }, author = {Forough Habibollahi and Moein Khajehnejad and Amitesh Gaurav and Brett Joseph Kagan}, url = {https://openreview.net/forum?id=N5qLXpc7HQy}, year = {2022}, date = {2022-11-28}, journal = {OpenReview.net}, abstract = {How do synthetic biological systems and artificial neural networks compete in their performance in a game environment? Reinforcement learning has undergone significant advances, however remains behind biological neural intelligence in terms of sample efficiency. Yet most biological systems are significantly more complicated than most algorithms. Here we compare the inherent intelligence of in vitro biological neuronal networks to state-of-the-art deep reinforcement learning algorithms in the arcade game 'pong'. We employed DishBrain, a system that embodies in vitro neural networks with in silico computation using a high-density multielectrode array. We compared the learning curve and the performance of these biological systems against time-matched learning from DQN, A2C, and PPO algorithms. Agents were implemented in a reward-based environment of the `Pong' game. Key learning characteristics of the deep reinforcement learning agents were tested with those of the biological neuronal cultures in the same game environment. We find that even these very simple biological cultures typically outperform deep reinforcement learning systems in terms of various game performance characteristics, such as the average rally length implying a higher sample efficiency. Furthermore, the human cell cultures proved to have the overall highest relative improvement in the average number of hits in a rally when comparing the initial 5 minutes and the last 15 minutes of each designed gameplay session. }, keywords = {Machine Learning, MaxOne}, pubstate = {published}, tppubtype = {conference} } Close How do synthetic biological systems and artificial neural networks compete in their performance in a game environment? Reinforcement learning has undergone significant advances, however remains behind biological neural intelligence in terms of sample efficiency. Yet most biological systems are significantly more complicated than most algorithms. Here we compare the inherent intelligence of in vitro biological neuronal networks to state-of-the-art deep reinforcement learning algorithms in the arcade game 'pong'. We employed DishBrain, a system that embodies in vitro neural networks with in silico computation using a high-density multielectrode array. We compared the learning curve and the performance of these biological systems against time-matched learning from DQN, A2C, and PPO algorithms. Agents were implemented in a reward-based environment of the `Pong' game. Key learning characteristics of the deep reinforcement learning agents were tested with those of the biological neuronal cultures in the same game environment. We find that even these very simple biological cultures typically outperform deep reinforcement learning systems in terms of various game performance characteristics, such as the average rally length implying a higher sample efficiency. Furthermore, the human cell cultures proved to have the overall highest relative improvement in the average number of hits in a rally when comparing the initial 5 minutes and the last 15 minutes of each designed gameplay session. Close https://openreview.net/forum?id=N5qLXpc7HQy Close
	McSweeney, Danny; Gabriel, Rafael; Jin, Kang; Pang, Zhiping P; Aronow, Bruce; and Pak, ChangHui CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons Journal Article iScience, 2022. Abstract \| Links \| BibTeX \| Tags: 2D Neuronal Culture, CMOS, CRISPR, HD-MEA, MaxOne, Synapses @article{McSweeney2022b, title = {CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons}, author = {Danny McSweeney and Rafael Gabriel and Kang Jin and Zhiping P. Pang and Bruce Aronow and and ChangHui Pak}, url = {https://www.cell.com/iscience/fulltext/S2589-0042(22)01459-6?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2589004222014596%3Fshowall%3Dtrue}, doi = {https://doi.org/10.1016/j.isci.2022.105187}, year = {2022}, date = {2022-10-21}, journal = {iScience}, abstract = {Loss-of-function (LOF) mutations in CASK cause severe developmental pheno- types, including microcephaly with pontine and cerebellar hypoplasia, X-linked in- tellectual disability, and autism. Unraveling the pathological mechanisms of CASK-related disorders has been challenging owing to limited human cellular models to study the dynamic roles of this molecule during neuronal maturation and synapse development. Here, we investigate cell-autonomous functions of CASK in cortical excitatory induced neurons (iNs) generated from CASK knockout (KO) isogenic human embryonic stem cells (hESCs) using gene expression, mor- phometrics, and electrophysiology. While immature CASK KO iNs show robust neuronal outgrowth, mature CASK KO iNs display severe defects in syn- aptic transmission and synchronized network activity without compromising neuronal morphology and synapse numbers. In the developing human cortical excitatory neurons, CASK functions to promote both structural integrity and establishment of cortical excitatory neuronal networks. These results lay the foundation for future studies identifying suppressors of such phenotypes rele- vant to human patients.}, keywords = {2D Neuronal Culture, CMOS, CRISPR, HD-MEA, MaxOne, Synapses}, pubstate = {published}, tppubtype = {article} } Close Loss-of-function (LOF) mutations in CASK cause severe developmental pheno- types, including microcephaly with pontine and cerebellar hypoplasia, X-linked in- tellectual disability, and autism. Unraveling the pathological mechanisms of CASK-related disorders has been challenging owing to limited human cellular models to study the dynamic roles of this molecule during neuronal maturation and synapse development. Here, we investigate cell-autonomous functions of CASK in cortical excitatory induced neurons (iNs) generated from CASK knockout (KO) isogenic human embryonic stem cells (hESCs) using gene expression, mor- phometrics, and electrophysiology. While immature CASK KO iNs show robust neuronal outgrowth, mature CASK KO iNs display severe defects in syn- aptic transmission and synchronized network activity without compromising neuronal morphology and synapse numbers. In the developing human cortical excitatory neurons, CASK functions to promote both structural integrity and establishment of cortical excitatory neuronal networks. These results lay the foundation for future studies identifying suppressors of such phenotypes rele- vant to human patients. Close https://www.cell.com/iscience/fulltext/S2589-0042(22)01459-6?_returnURL=https%3A[...] doi:https://doi.org/10.1016/j.isci.2022.105187 Close
	Kagan, Brett J; Kitchen, Andy C; Tran, Nhi T; Habibollahi, Forough; Khajehnejad, Moein; Parker, Bradyn J; Bhat, Anjali; Rollo, Ben; Razi, Adeel; Friston, Karl J In vitro neurons learn and exhibit sentience when embodied in a simulated game-world Journal Article Neuron, 2022. Abstract \| Links \| BibTeX \| Tags: 2D Neuronal Culture, Activity Scan Assay, closed loop stimulation, HD-MEA, IPSC, MaxOne, MEA Metrics, MEA Technology, Primary Neuronal Cell Culture @article{Kagan2022, title = {In vitro neurons learn and exhibit sentience when embodied in a simulated game-world}, author = {Brett J. Kagan and Andy C. Kitchen and Nhi T. Tran and Forough Habibollahi and Moein Khajehnejad and Bradyn J. Parker and Anjali Bhat and Ben Rollo and Adeel Razi and Karl J Friston }, url = {https://www.cell.com/neuron/fulltext/S0896-6273(22)00806-6?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0896627322008066%3Fshowall%3Dtrue}, doi = {https://doi.org/10.1016/j.neuron.2022.09.001}, year = {2022}, date = {2022-10-12}, journal = {Neuron}, abstract = {Integrating neurons into digital systems may enable performance infeasible with silicon alone. Here, we develop DishBrain, a system that harnesses the inherent adaptive computation of neurons in a structured environment. In vitro neural networks from human or rodent origins are integrated with in silico computing via a high-density multielectrode array. Through electrophysiological stimulation and recording, cultures are embedded in a simulated game-world, mimicking the arcade game “Pong.” Applying implications from the theory of active inference via the free energy principle, we find apparent learning within five minutes of real-time gameplay not observed in control conditions. Further experiments demonstrate the importance of closed-loop structured feedback in eliciting learning over time. Cultures display the ability to self-organize activity in a goal-directed manner in response to sparse sensory information about the consequences of their actions, which we term synthetic biological intelligence. Future applications may provide further insights into the cellular correlates of intelligence.}, keywords = {2D Neuronal Culture, Activity Scan Assay, closed loop stimulation, HD-MEA, IPSC, MaxOne, MEA Metrics, MEA Technology, Primary Neuronal Cell Culture}, pubstate = {published}, tppubtype = {article} } Close Integrating neurons into digital systems may enable performance infeasible with silicon alone. Here, we develop DishBrain, a system that harnesses the inherent adaptive computation of neurons in a structured environment. In vitro neural networks from human or rodent origins are integrated with in silico computing via a high-density multielectrode array. Through electrophysiological stimulation and recording, cultures are embedded in a simulated game-world, mimicking the arcade game “Pong.” Applying implications from the theory of active inference via the free energy principle, we find apparent learning within five minutes of real-time gameplay not observed in control conditions. Further experiments demonstrate the importance of closed-loop structured feedback in eliciting learning over time. Cultures display the ability to self-organize activity in a goal-directed manner in response to sparse sensory information about the consequences of their actions, which we term synthetic biological intelligence. Future applications may provide further insights into the cellular correlates of intelligence. Close https://www.cell.com/neuron/fulltext/S0896-6273(22)00806-6?_returnURL=https%3A%2[...] doi:https://doi.org/10.1016/j.neuron.2022.09.001 Close
	Habibey, Rouhollah; Striebel, Johannes; Schmieder, Felix; Czarske, Jürgen; Busskamp, Volker Long-term morphological and functional dynamics of human stem cell-derived neuronal networks on high-density micro-electrode arrays Journal Article Frontiers in Neuroscience, 2022. Abstract \| Links \| BibTeX \| Tags: 2D Neuronal Culture, CMOS, HD-MEA, IPSC, MaxOne, MEA Metrics, Modeling, Spike Sorting @article{Habibey2022, title = {Long-term morphological and functional dynamics of human stem cell-derived neuronal networks on high-density micro-electrode arrays}, author = {Rouhollah Habibey and Johannes Striebel and Felix Schmieder and Jürgen Czarske and Volker Busskamp}, url = {https://www.frontiersin.org/articles/10.3389/fnins.2022.951964/full}, doi = {10.3389/fnins.2022.951964}, year = {2022}, date = {2022-10-04}, journal = {Frontiers in Neuroscience}, abstract = {Comprehensive electrophysiological characterizations of human induced pluripotent stem cell (hiPSC)-derived neuronal networks are essential to determine to what extent these in vitro models recapitulate the functional features of in vivo neuronal circuits. High-density micro-electrode arrays (HD-MEAs) offer non-invasive recording with the best spatial and temporal resolution possible to date. For 3 months, we tracked the morphology and activity features of developing networks derived from a transgenic hiPSC line in which neurogenesis is inducible by neurogenic transcription factor overexpression. Our morphological data revealed large-scale structural changes from homogeneously distributed neurons in the first month to the formation of neuronal clusters over time. This led to a constant shift in position of neuronal cells and clusters on HD-MEAs and corresponding changes in spatial distribution of the network activity maps. Network activity appeared as scarce action potentials (APs), evolved as local bursts with longer duration and changed to network-wide synchronized bursts with higher frequencies but shorter duration over time, resembling the emerging burst features found in the developing human brain. Instantaneous firing rate data indicated that the fraction of fast spiking neurons (150–600 Hz) increases sharply after 63 days post induction (dpi). Inhibition of glutamatergic synapses erased burst features from network activity profiles and confirmed the presence of mature excitatory neurotransmission. The application of GABAergic receptor antagonists profoundly changed the bursting profile of the network at 120 dpi. This indicated a GABAergic switch from excitatory to inhibitory neurotransmission during circuit development and maturation. Our results suggested that an emerging GABAergic system at older culture ages is involved in regulating spontaneous network bursts. In conclusion, our data showed that long-term and continuous microscopy and electrophysiology readouts are crucial for a meaningful characterization of morphological and functional maturation in stem cell-derived human networks. Most importantly, assessing the level and duration of functional maturation is key to subject these human neuronal circuits on HD-MEAs for basic and biomedical applications.}, keywords = {2D Neuronal Culture, CMOS, HD-MEA, IPSC, MaxOne, MEA Metrics, Modeling, Spike Sorting}, pubstate = {published}, tppubtype = {article} } Close Comprehensive electrophysiological characterizations of human induced pluripotent stem cell (hiPSC)-derived neuronal networks are essential to determine to what extent these in vitro models recapitulate the functional features of in vivo neuronal circuits. High-density micro-electrode arrays (HD-MEAs) offer non-invasive recording with the best spatial and temporal resolution possible to date. For 3 months, we tracked the morphology and activity features of developing networks derived from a transgenic hiPSC line in which neurogenesis is inducible by neurogenic transcription factor overexpression. Our morphological data revealed large-scale structural changes from homogeneously distributed neurons in the first month to the formation of neuronal clusters over time. This led to a constant shift in position of neuronal cells and clusters on HD-MEAs and corresponding changes in spatial distribution of the network activity maps. Network activity appeared as scarce action potentials (APs), evolved as local bursts with longer duration and changed to network-wide synchronized bursts with higher frequencies but shorter duration over time, resembling the emerging burst features found in the developing human brain. Instantaneous firing rate data indicated that the fraction of fast spiking neurons (150–600 Hz) increases sharply after 63 days post induction (dpi). Inhibition of glutamatergic synapses erased burst features from network activity profiles and confirmed the presence of mature excitatory neurotransmission. The application of GABAergic receptor antagonists profoundly changed the bursting profile of the network at 120 dpi. This indicated a GABAergic switch from excitatory to inhibitory neurotransmission during circuit development and maturation. Our results suggested that an emerging GABAergic system at older culture ages is involved in regulating spontaneous network bursts. In conclusion, our data showed that long-term and continuous microscopy and electrophysiology readouts are crucial for a meaningful characterization of morphological and functional maturation in stem cell-derived human networks. Most importantly, assessing the level and duration of functional maturation is key to subject these human neuronal circuits on HD-MEAs for basic and biomedical applications. Close https://www.frontiersin.org/articles/10.3389/fnins.2022.951964/full doi:10.3389/fnins.2022.951964 Close
	Kumar, Sreedhar S; Gänswein, Tobias; Buccino, Alessio P; Xue, Xiaohan; Bartram, Julian; Emmenegger, Vishalini; Hierlemann, Andreas Tracking axon initial segment plasticity using high-density microelectrode arrays: A computational study Journal Article Frontiers in Neuroinformatics, 2022. Abstract \| Links \| BibTeX \| Tags: CMOS, HD-MEA, MEA Technology @article{Kumar2022, title = {Tracking axon initial segment plasticity using high-density microelectrode arrays: A computational study}, author = {Sreedhar S. Kumar and Tobias Gänswein and Alessio P. Buccino and Xiaohan Xue and Julian Bartram and Vishalini Emmenegger and Andreas Hierlemann}, url = {https://www.frontiersin.org/articles/10.3389/fninf.2022.957255/full}, doi = {10.3389/fninf.2022.957255}, year = {2022}, date = {2022-10-03}, journal = {Frontiers in Neuroinformatics}, abstract = {Despite being composed of highly plastic neurons with extensive positive feedback, the nervous system maintains stable overall function. To keep activity within bounds, it relies on a set of negative feedback mechanisms that can induce stabilizing adjustments and that are collectively termed “homeostatic plasticity.” Recently, a highly excitable microdomain, located at the proximal end of the axon—the axon initial segment (AIS)—was found to exhibit structural modifications in response to activity perturbations. Though AIS plasticity appears to serve a homeostatic purpose, many aspects governing its expression and its functional role in regulating neuronal excitability remain elusive. A central challenge in studying the phenomenon is the rich heterogeneity of its expression (distal/proximal relocation, shortening, lengthening) and the variability of its functional role. A potential solution is to track AISs of a large number of neurons over time and attempt to induce structural plasticity in them. To this end, a promising approach is to use extracellular electrophysiological readouts to track a large number of neurons at high spatiotemporal resolution by means of high-density microelectrode arrays (HD-MEAs). However, an analysis framework that reliably identifies specific activity signatures that uniquely map on to underlying microstructural changes is missing. In this study, we assessed the feasibility of such a task and used the distal relocation of the AIS as an exemplary problem. We used sophisticated computational models to systematically explore the relationship between incremental changes in AIS positions and the specific consequences observed in simulated extracellular field potentials. An ensemble of feature changes in the extracellular fields that reliably characterize AIS plasticity was identified. We trained models that could detect these signatures with remarkable accuracy. Based on these findings, we propose a hybrid analysis framework that could potentially enable high-throughput experimental studies of activity-dependent AIS plasticity using HD-MEAs.}, keywords = {CMOS, HD-MEA, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close Despite being composed of highly plastic neurons with extensive positive feedback, the nervous system maintains stable overall function. To keep activity within bounds, it relies on a set of negative feedback mechanisms that can induce stabilizing adjustments and that are collectively termed “homeostatic plasticity.” Recently, a highly excitable microdomain, located at the proximal end of the axon—the axon initial segment (AIS)—was found to exhibit structural modifications in response to activity perturbations. Though AIS plasticity appears to serve a homeostatic purpose, many aspects governing its expression and its functional role in regulating neuronal excitability remain elusive. A central challenge in studying the phenomenon is the rich heterogeneity of its expression (distal/proximal relocation, shortening, lengthening) and the variability of its functional role. A potential solution is to track AISs of a large number of neurons over time and attempt to induce structural plasticity in them. To this end, a promising approach is to use extracellular electrophysiological readouts to track a large number of neurons at high spatiotemporal resolution by means of high-density microelectrode arrays (HD-MEAs). However, an analysis framework that reliably identifies specific activity signatures that uniquely map on to underlying microstructural changes is missing. In this study, we assessed the feasibility of such a task and used the distal relocation of the AIS as an exemplary problem. We used sophisticated computational models to systematically explore the relationship between incremental changes in AIS positions and the specific consequences observed in simulated extracellular field potentials. An ensemble of feature changes in the extracellular fields that reliably characterize AIS plasticity was identified. We trained models that could detect these signatures with remarkable accuracy. Based on these findings, we propose a hybrid analysis framework that could potentially enable high-throughput experimental studies of activity-dependent AIS plasticity using HD-MEAs. Close https://www.frontiersin.org/articles/10.3389/fninf.2022.957255/full doi:10.3389/fninf.2022.957255 Close
	Lee, Jihyun; Gänswein, Tobias; Ulusan, Hasan; Emmenegger, Vishalini; Saguner, Ardan M; Duru, Firat; and Hierlemann, Andreas Repeated and On-Demand Intracellular Recordings of Cardiomyocytes Derived from Human Induced Pluripotent Stem Cells Journal Article ACS Sensors, 2022. Abstract \| Links \| BibTeX \| Tags: Cardiomyocytes, CMOS, HD-MEA, MaxOne, MEA Technology @article{Lee2022, title = {Repeated and On-Demand Intracellular Recordings of Cardiomyocytes Derived from Human Induced Pluripotent Stem Cells}, author = {Jihyun Lee and Tobias Gänswein and Hasan Ulusan and Vishalini Emmenegger and Ardan M. Saguner and Firat Duru and and Andreas Hierlemann}, url = {https://pubs.acs.org/doi/10.1021/acssensors.2c01678}, doi = {https://doi.org/10.1021/acssensors.2c01678}, year = {2022}, date = {2022-09-27}, journal = {ACS Sensors}, abstract = {Pharmaceutical compounds may have cardiotoxic properties, triggering potentially life-threatening arrhythmi- as. To investigate proarrhythmic effects of drugs, the patch clamp technique has been used as the gold standard for charac- terizing the electrophysiology of cardiomyocytes in vitro. However, the applicability of this technology for drug screening is limited, as it is complex to use and features low throughput. Recent studies have demonstrated that 3D-nanostructured electrodes enable to obtain intracellular signals from many cardiomyocytes in parallel; however, the tedious electrode fab- rication and limited measurement duration still remain major issues for cardiotoxicity testing. Here, we demonstrate how porous Pt-black electrodes, arranged in high-density microelectrode arrays, can be used to record intracellular-like signals of cardiomyocytes at large-scale repeatedly over an extended period of time. The developed technique, which yields highly parallelized electroporations by using stimulation voltages around 1 Volt peak-to-peak amplitude, enabled intracellular-like recordings at high success rates without causing significant alteration in key electrophysiological features. In a proof of concept study, we investigated electrophysiological modulations induced by two clinically applied drugs, nifedipine and quinidine. As the obtained results were in good agreement with previously published data, we are confident that the devel- oped technique has the potential to be routinely used in in vitro platforms for cardiotoxicity screening.}, keywords = {Cardiomyocytes, CMOS, HD-MEA, MaxOne, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close Pharmaceutical compounds may have cardiotoxic properties, triggering potentially life-threatening arrhythmi- as. To investigate proarrhythmic effects of drugs, the patch clamp technique has been used as the gold standard for charac- terizing the electrophysiology of cardiomyocytes in vitro. However, the applicability of this technology for drug screening is limited, as it is complex to use and features low throughput. Recent studies have demonstrated that 3D-nanostructured electrodes enable to obtain intracellular signals from many cardiomyocytes in parallel; however, the tedious electrode fab- rication and limited measurement duration still remain major issues for cardiotoxicity testing. Here, we demonstrate how porous Pt-black electrodes, arranged in high-density microelectrode arrays, can be used to record intracellular-like signals of cardiomyocytes at large-scale repeatedly over an extended period of time. The developed technique, which yields highly parallelized electroporations by using stimulation voltages around 1 Volt peak-to-peak amplitude, enabled intracellular-like recordings at high success rates without causing significant alteration in key electrophysiological features. In a proof of concept study, we investigated electrophysiological modulations induced by two clinically applied drugs, nifedipine and quinidine. As the obtained results were in good agreement with previously published data, we are confident that the devel- oped technique has the potential to be routinely used in in vitro platforms for cardiotoxicity screening. Close https://pubs.acs.org/doi/10.1021/acssensors.2c01678 doi:https://doi.org/10.1021/acssensors.2c01678 Close
	Al-Absi, Abdel-Rahman; Thambiappaa, Sakeerthi Kethees; Khanc, Ahmad Raza; Glerup, Simon; Sanchez, Connie; Landau, Anne M; Nyengaard, Jens R Df(h22q11)/+ mouse model exhibits reduced binding levels of GABAA receptors and structural and functional dysregulation in the inhibitory and excitatory networks of hippocampus Journal Article Molecular and Cellular Neuroscience, 2022. Abstract \| Links \| BibTeX \| Tags: Brain Slice, CMOS, HD-MEA, MaxOne @article{Al-Absi2022, title = {Df(h22q11)/+ mouse model exhibits reduced binding levels of GABAA receptors and structural and functional dysregulation in the inhibitory and excitatory networks of hippocampus}, author = {Abdel-Rahman Al-Absi and Sakeerthi Kethees Thambiappaa and Ahmad Raza Khanc and Simon Glerup and Connie Sanchez and Anne M. Landau and Jens R. Nyengaard}, url = {https://www.sciencedirect.com/science/article/pii/S1044743122000756?via%3Dihub}, doi = {https://doi.org/10.1016/j.mcn.2022.103769}, year = {2022}, date = {2022-08-18}, journal = {Molecular and Cellular Neuroscience}, abstract = {The 22q11.2 hemizygous deletion confers high risk for multiple neurodevelopmental disorders. Inhibitory signaling, largely regulated through GABAA receptors, is suggested to serve a multitude of brain functions that are disrupted in the 22q11.2 deletion syndrome. We investigated the putative deficit of GABAA receptors and the potential substrates contributing to the inhibitory and excitatory dysregulations in hippocampal networks of the Df(h22q11)/+ mouse model of the 22q11.2 hemizygous deletion. The Df(h22q11)/+ mice exhibited impairments in several hippocampus-related functional domains, represented by impaired spatial memory and sensory gating functions. Autoradiography using the [3H]muscimol tracer revealed a significant reduction in GABAA receptor binding in the CA1 and CA3 subregions, together with a loss of GAD67+ interneurons in CA1 of Df(h22q11)/+ mice. Furthermore, electro- physiology recordings exhibited significantly higher neuronal activity in CA3, in response to the GABAA receptor antagonist, bicuculline, as compared with wild type mice. Density and volume of dendritic spines in pyramidal neurons were reduced and Sholl analysis also showed a reduction in the complexity of basal dendritic tree in CA1 and CA3 subregions of Df(h22q11)/+ mice. Overall, our findings demonstrate that hemizygous deletion in the 22q11.2 locus leads to dysregulations in the inhibitory circuits, involving reduced binding levels of GABAA receptors, in addition to functional and structural modulations of the excitatory networks of hippocampus.}, keywords = {Brain Slice, CMOS, HD-MEA, MaxOne}, pubstate = {published}, tppubtype = {article} } Close The 22q11.2 hemizygous deletion confers high risk for multiple neurodevelopmental disorders. Inhibitory signaling, largely regulated through GABAA receptors, is suggested to serve a multitude of brain functions that are disrupted in the 22q11.2 deletion syndrome. We investigated the putative deficit of GABAA receptors and the potential substrates contributing to the inhibitory and excitatory dysregulations in hippocampal networks of the Df(h22q11)/+ mouse model of the 22q11.2 hemizygous deletion. The Df(h22q11)/+ mice exhibited impairments in several hippocampus-related functional domains, represented by impaired spatial memory and sensory gating functions. Autoradiography using the [3H]muscimol tracer revealed a significant reduction in GABAA receptor binding in the CA1 and CA3 subregions, together with a loss of GAD67+ interneurons in CA1 of Df(h22q11)/+ mice. Furthermore, electro- physiology recordings exhibited significantly higher neuronal activity in CA3, in response to the GABAA receptor antagonist, bicuculline, as compared with wild type mice. Density and volume of dendritic spines in pyramidal neurons were reduced and Sholl analysis also showed a reduction in the complexity of basal dendritic tree in CA1 and CA3 subregions of Df(h22q11)/+ mice. Overall, our findings demonstrate that hemizygous deletion in the 22q11.2 locus leads to dysregulations in the inhibitory circuits, involving reduced binding levels of GABAA receptors, in addition to functional and structural modulations of the excitatory networks of hippocampus. Close https://www.sciencedirect.com/science/article/pii/S1044743122000756?via%3Dihub doi:https://doi.org/10.1016/j.mcn.2022.103769 Close
	Buccino Alessio Paolo; Damart, Tanguy; Bartram Julian; Mandge Darshan; Xue Xiaohan; Zbili Mickael; Gänswein Tobias; Jaquier Aurélien; Emmenegger Vishalini; Markram Henry; Hierlemann Andreas; Van Geit Werner. A multi-modal fitting approach to construct single-neuron models with patch clamp and high-density microelectrode arrays Journal Article bioRxiv, 2022. Abstract \| Links \| BibTeX \| Tags: 2D Neuronal Culture, Activity Scan Assay, Axon Tracking Assay, HD-MEA, MaxOne, Other Tissues, Publication, Stimulation Assay @article{Buccino2022, title = {A multi-modal fitting approach to construct single-neuron models with patch clamp and high-density microelectrode arrays}, author = {Buccino, Alessio Paolo; Damart, Tanguy; Bartram, Julian; Mandge, Darshan; Xue, Xiaohan; Zbili, Mickael; Gänswein, Tobias; Jaquier, Aurélien; Emmenegger, Vishalini; Markram, Henry; Hierlemann, Andreas; Van Geit, Werner.}, doi = {https://doi.org/10.1101/2022.08.03.502468}, year = {2022}, date = {2022-08-11}, journal = {bioRxiv}, abstract = {In computational neuroscience, multicompartment models are among the most biophysically realistic representations of single neurons. Constructing such models usually involves the use of the patch-clamp technique to record somatic voltage signals under different experimental conditions. The experimental data are then used to fit the many parameters of the model. While patching of the soma is currently the gold-standard approach to build multicompartment models, several studies have also evidenced a richness of dynamics in dendritic and axonal sections. Recording from the soma alone makes it hard to observe and correctly parameterize the activity of non-somatic compartments. In order to provide a richer set of data as input to multicompartment models, we here investigate the combination of somatic patch-clamp recordings with recordings of high-density micro-electrode arrays (HD-MEAs). HD-MEAs enable the observation of extracellular potentials and neural activity of neuronal compartments at sub-cellular resolution. In this work, we introduce a novel framework to combine patch-clamp and HD-MEA data to construct multicompartment models. We first validate our method on a ground-truth model with known parameters and show that the use of features extracted from extracellular signals, in addition to intracellular ones, yields models enabling better fits than using intracellular features alone. We also demonstrate our procedure using experimental data by constructing cell models from in vitro cell cultures. The proposed multi-modal fitting procedure has the potential to augment the modeling efforts of the computational neuroscience community and to provide the field with neuronal models that are more realistic and can be better validated. Author Summary Multicompartment models are one of the most biophysically detailed representations of single neurons. The vast majority of these models are built using experimental data from somatic recordings. However, neurons are much more than just their soma and one needs recordings from distal neurites to build an accurate model. In this article, we combine the patch-clamp technique with extracellular high-density microelectrode arrays (HD-MEAs) to compensate this shortcoming. In fact, HD-MEAs readouts allow one to record the neuronal signal in the entire axonal arbor. We show that the proposed multi-modal strategy is superior to the use of patch clamp alone using an existing model as ground-truth. Finally, we show an application of this strategy on experimental data from cultured neurons.}, keywords = {2D Neuronal Culture, Activity Scan Assay, Axon Tracking Assay, HD-MEA, MaxOne, Other Tissues, Publication, Stimulation Assay}, pubstate = {published}, tppubtype = {article} } Close In computational neuroscience, multicompartment models are among the most biophysically realistic representations of single neurons. Constructing such models usually involves the use of the patch-clamp technique to record somatic voltage signals under different experimental conditions. The experimental data are then used to fit the many parameters of the model. While patching of the soma is currently the gold-standard approach to build multicompartment models, several studies have also evidenced a richness of dynamics in dendritic and axonal sections. Recording from the soma alone makes it hard to observe and correctly parameterize the activity of non-somatic compartments. In order to provide a richer set of data as input to multicompartment models, we here investigate the combination of somatic patch-clamp recordings with recordings of high-density micro-electrode arrays (HD-MEAs). HD-MEAs enable the observation of extracellular potentials and neural activity of neuronal compartments at sub-cellular resolution. In this work, we introduce a novel framework to combine patch-clamp and HD-MEA data to construct multicompartment models. We first validate our method on a ground-truth model with known parameters and show that the use of features extracted from extracellular signals, in addition to intracellular ones, yields models enabling better fits than using intracellular features alone. We also demonstrate our procedure using experimental data by constructing cell models from in vitro cell cultures. The proposed multi-modal fitting procedure has the potential to augment the modeling efforts of the computational neuroscience community and to provide the field with neuronal models that are more realistic and can be better validated. Author Summary Multicompartment models are one of the most biophysically detailed representations of single neurons. The vast majority of these models are built using experimental data from somatic recordings. However, neurons are much more than just their soma and one needs recordings from distal neurites to build an accurate model. In this article, we combine the patch-clamp technique with extracellular high-density microelectrode arrays (HD-MEAs) to compensate this shortcoming. In fact, HD-MEAs readouts allow one to record the neuronal signal in the entire axonal arbor. We show that the proposed multi-modal strategy is superior to the use of patch clamp alone using an existing model as ground-truth. Finally, we show an application of this strategy on experimental data from cultured neurons. Close doi:https://doi.org/10.1101/2022.08.03.502468 Close
	Xue, Xiaohan; Buccino, Alessio Paolo; Kumar, Sreedhar Saseendran; Hierlemann, Andreas; Bartram, Julian Inferring monosynaptic connections from paired dendritic spine Ca2+ imaging and large-scale recording of extracellular spiking Journal Article Journal of Neural Engineering, 2022. Abstract \| Links \| BibTeX \| Tags: 2D Neuronal Culture, Activity Assay, HD-MEA, MaxOne, Network Assay, Primary Neuronal Cell Culture, Publication @article{Xue2022b, title = {Inferring monosynaptic connections from paired dendritic spine Ca2+ imaging and large-scale recording of extracellular spiking}, author = {Xiaohan Xue and Alessio Paolo Buccino and Sreedhar Saseendran Kumar and Andreas Hierlemann and Julian Bartram}, doi = {https://doi.org/10.1088/1741-2552/ac8765}, year = {2022}, date = {2022-08-11}, journal = {Journal of Neural Engineering}, abstract = {Techniques to identify monosynaptic connections between neurons have been vital for neuroscience research, facilitating important advancements concerning network topology, synaptic plasticity, and synaptic integration, among others. Here, we introduce a novel approach to identify and monitor monosynaptic connections using high-resolution dendritic spine Ca2+ imaging combined with simultaneous large-scale recording of extracellular electrical activity by means of high-density microelectrode arrays (HD-MEAs). We introduce an easily adoptable analysis pipeline that associates the imaged spine with its presynaptic unit and test it on in vitro recordings. The method is further validated and optimized by simulating synaptically-evoked spine Ca2+ transients based on measured spike trains in order to obtain simulated ground-truth connections. The proposed approach offers unique advantages as i) it can be used to identify monosynaptic connections with an accurate localization of the synapse within the dendritic tree, ii) it provides precise information of presynaptic spiking, and iii) postsynaptic spine Ca2+ signals and, finally, iv) the non-invasive nature of the proposed method allows for long-term measurements. The analysis toolkit together with the rich data sets that were acquired are made publicly available for further exploration by the research community.}, keywords = {2D Neuronal Culture, Activity Assay, HD-MEA, MaxOne, Network Assay, Primary Neuronal Cell Culture, Publication}, pubstate = {published}, tppubtype = {article} } Close Techniques to identify monosynaptic connections between neurons have been vital for neuroscience research, facilitating important advancements concerning network topology, synaptic plasticity, and synaptic integration, among others. Here, we introduce a novel approach to identify and monitor monosynaptic connections using high-resolution dendritic spine Ca2+ imaging combined with simultaneous large-scale recording of extracellular electrical activity by means of high-density microelectrode arrays (HD-MEAs). We introduce an easily adoptable analysis pipeline that associates the imaged spine with its presynaptic unit and test it on in vitro recordings. The method is further validated and optimized by simulating synaptically-evoked spine Ca2+ transients based on measured spike trains in order to obtain simulated ground-truth connections. The proposed approach offers unique advantages as i) it can be used to identify monosynaptic connections with an accurate localization of the synapse within the dendritic tree, ii) it provides precise information of presynaptic spiking, and iii) postsynaptic spine Ca2+ signals and, finally, iv) the non-invasive nature of the proposed method allows for long-term measurements. The analysis toolkit together with the rich data sets that were acquired are made publicly available for further exploration by the research community. Close doi:https://doi.org/10.1088/1741-2552/ac8765 Close
	Sharf Tal; Molen, Tjitse; Glasauer Stella; Guzman Elmer; Buccino Alessio; Luna Gabriel; Cheng Zhuowei; Audouard Morgane; Ranasinghe Kamalini; Kudo Kiwamu; Nagarajan Srikantan; Tovar Kenneth; Petzold Linda; Hierlemann Andreas; Hansma Paul; ; Kosik, Kenneth; Functional neuronal circuitry and oscillatory dynamics in human brain organoids Journal Article Nature Communications, 2022. Abstract \| Links \| BibTeX \| Tags: MaxOne, Neuronal Networks, Organoids @article{Sharf2022, title = {Functional neuronal circuitry and oscillatory dynamics in human brain organoids}, author = {Sharf, Tal; Molen, Tjitse; Glasauer, Stella; Guzman, Elmer; Buccino, Alessio; Luna, Gabriel; Cheng, Zhuowei; Audouard, Morgane; Ranasinghe, Kamalini; Kudo, Kiwamu; Nagarajan, Srikantan; Tovar, Kenneth; Petzold, Linda; Hierlemann, Andreas; Hansma, Paul; and Kosik, Kenneth; }, doi = {https://doi.org/10.1038/s41467-022-32115-4}, year = {2022}, date = {2022-07-29}, journal = {Nature Communications}, abstract = {Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiology of neuronal circuits within organoids remains under-explored. With high-density CMOS microelectrode arrays and shank electrodes, we captured spontaneous extracellular activity from brain organoids derived from human induced pluripotent stem cells. We inferred functional connectivity from spike timing, revealing a large number of weak connections within a skeleton of significantly fewer strong connections. A benzodiazepine increased the uniformity of firing patterns and decreased the relative fraction of weakly connected edges. Our analysis of the local field potential demonstrate that brain organoids contain neuronal assemblies of sufficient size and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug action, and the effects of external stimuli upon neuronal networks.}, keywords = {MaxOne, Neuronal Networks, Organoids}, pubstate = {published}, tppubtype = {article} } Close Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiology of neuronal circuits within organoids remains under-explored. With high-density CMOS microelectrode arrays and shank electrodes, we captured spontaneous extracellular activity from brain organoids derived from human induced pluripotent stem cells. We inferred functional connectivity from spike timing, revealing a large number of weak connections within a skeleton of significantly fewer strong connections. A benzodiazepine increased the uniformity of firing patterns and decreased the relative fraction of weakly connected edges. Our analysis of the local field potential demonstrate that brain organoids contain neuronal assemblies of sufficient size and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug action, and the effects of external stimuli upon neuronal networks. Close doi:https://doi.org/10.1038/s41467-022-32115-4 Close
	Idrees, Saad; Baumann, Matthias-Philipp; Korympidou, Maria M; Schubert, Timm; Kling, Alexandra; Franke, Katrin; Hafed, Ziad M; Franke, Felix; Münch, Thomas A Suppression without inhibition: how retinal computation contributes to saccadic suppression Journal Article Communications Biology, 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, MaxOne, Retina @article{Idrees2022, title = {Suppression without inhibition: how retinal computation contributes to saccadic suppression}, author = {Saad Idrees and Matthias-Philipp Baumann and Maria M. Korympidou and Timm Schubert and Alexandra Kling and Katrin Franke and Ziad M. Hafed and Felix Franke and Thomas A. Münch }, url = {https://www.nature.com/articles/s42003-022-03526-2}, year = {2022}, date = {2022-07-12}, journal = {Communications Biology}, abstract = {Visual perception remains stable across saccadic eye movements, despite the concurrent strongly disruptive visual flow. This stability is partially associated with a reduction in visual sensitivity, known as saccadic suppression, which already starts in the retina with reduced ganglion cell sensitivity. However, the retinal circuit mechanisms giving rise to such sup- pression remain unknown. Here, we describe these mechanisms using electrophysiology in mouse, pig, and macaque retina, 2-photon calcium imaging, computational modeling, and human psychophysics. We find that sequential stimuli, like those that naturally occur during saccades, trigger three independent suppressive mechanisms in the retina. The main mechanism is triggered by contrast-reversing sequential stimuli and originates within the receptive field center of ganglion cells. It does not involve inhibition or other known sup- pressive mechanisms like saturation or adaptation. Instead, it relies on temporal filtering of the inherently slow response of cone photoreceptors coupled with downstream non- linearities. Two further mechanisms of suppression are present predominantly in ON ganglion cells and originate in the receptive field surround, highlighting another disparity between ON and OFF ganglion cells. The mechanisms uncovered here likely play a role in shaping the retinal output following eye movements and other natural viewing conditions where sequential stimulation is ubiquitous.}, keywords = {HD-MEA, MaxOne, Retina}, pubstate = {published}, tppubtype = {article} } Close Visual perception remains stable across saccadic eye movements, despite the concurrent strongly disruptive visual flow. This stability is partially associated with a reduction in visual sensitivity, known as saccadic suppression, which already starts in the retina with reduced ganglion cell sensitivity. However, the retinal circuit mechanisms giving rise to such sup- pression remain unknown. Here, we describe these mechanisms using electrophysiology in mouse, pig, and macaque retina, 2-photon calcium imaging, computational modeling, and human psychophysics. We find that sequential stimuli, like those that naturally occur during saccades, trigger three independent suppressive mechanisms in the retina. The main mechanism is triggered by contrast-reversing sequential stimuli and originates within the receptive field center of ganglion cells. It does not involve inhibition or other known sup- pressive mechanisms like saturation or adaptation. Instead, it relies on temporal filtering of the inherently slow response of cone photoreceptors coupled with downstream non- linearities. Two further mechanisms of suppression are present predominantly in ON ganglion cells and originate in the receptive field surround, highlighting another disparity between ON and OFF ganglion cells. The mechanisms uncovered here likely play a role in shaping the retinal output following eye movements and other natural viewing conditions where sequential stimulation is ubiquitous. Close https://www.nature.com/articles/s42003-022-03526-2 Close
	Wang, F; Li, S; Wang, T Y; Lopez, G A; Antoshechkin, I; Chou, T F P97/VCP ATPase inhibitors can rescue p97 mutation-linked motor neuron degeneration Journal Article Brain Communications, 2022. Abstract \| Links \| BibTeX \| Tags: MaxTwo @article{Wang2022, title = {P97/VCP ATPase inhibitors can rescue p97 mutation-linked motor neuron degeneration}, author = {F. Wang and S. Li and T. Y. Wang and G. A. Lopez and I. Antoshechkin and T.F. Chou}, url = {https://academic.oup.com/braincomms/article/4/4/fcac176/6632805}, doi = {https://doi.org/10.1093/braincomms/fcac176}, year = {2022}, date = {2022-07-06}, journal = {Brain Communications}, abstract = {Mutations in p97/VCP cause two motor neuron diseases: inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia and familial amyotrophic lateral sclerosis. How p97 mutations lead to motor neuron degeneration is, however, unknown. Here we used patient-derived induced pluripotent stem cells to generate p97 mutant motor neurons. We reduced the genetic background variation by comparing mutant motor neurons to its isogenic wild type lines. Proteomic analysis reveals that p97R155H/+ motor neurons upregulate several cell cycle proteins at Day 14, but this effect diminishes by Day 20. Molecular changes linked to delayed cell cycle exit are observed in p97 mutant motor neurons. We also find that two p97 inhibitors, CB-5083 and NMS-873, restore some dysregulated protein levels. In addition, two p97 inhibitors and a food and drug administration-approved cyclin-dependent kinase 4/6 inhibitor, Abemaciclib, can rescue motor neuron death. Overall, we successfully used iPSC-derived motor neurons, identified dysregulated proteome and transcriptome and showed that p97 inhibitors rescue phenotypes in this disease model.}, keywords = {MaxTwo}, pubstate = {published}, tppubtype = {article} } Close Mutations in p97/VCP cause two motor neuron diseases: inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia and familial amyotrophic lateral sclerosis. How p97 mutations lead to motor neuron degeneration is, however, unknown. Here we used patient-derived induced pluripotent stem cells to generate p97 mutant motor neurons. We reduced the genetic background variation by comparing mutant motor neurons to its isogenic wild type lines. Proteomic analysis reveals that p97R155H/+ motor neurons upregulate several cell cycle proteins at Day 14, but this effect diminishes by Day 20. Molecular changes linked to delayed cell cycle exit are observed in p97 mutant motor neurons. We also find that two p97 inhibitors, CB-5083 and NMS-873, restore some dysregulated protein levels. In addition, two p97 inhibitors and a food and drug administration-approved cyclin-dependent kinase 4/6 inhibitor, Abemaciclib, can rescue motor neuron death. Overall, we successfully used iPSC-derived motor neurons, identified dysregulated proteome and transcriptome and showed that p97 inhibitors rescue phenotypes in this disease model. Close https://academic.oup.com/braincomms/article/4/4/fcac176/6632805 doi:https://doi.org/10.1093/braincomms/fcac176 Close
	Schröter Manuel; Wang, Congwei; Terrigno Marco; Hornauer Philipp; Huang Ziqiang; Jagasia Ravi; Hierlemann Andreas Functional imaging of brain organoids using high-density microelectrode arrays Journal Article MRS Bulletin, 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, MaxOne, MaxTwo, Organoids @article{Schroter2022, title = {Functional imaging of brain organoids using high-density microelectrode arrays}, author = {Schröter, Manuel; Wang, Congwei; Terrigno, Marco; Hornauer, Philipp; Huang, Ziqiang; Jagasia, Ravi; Hierlemann, Andreas}, url = {https://link.springer.com/article/10.1557/s43577-022-00282-w}, year = {2022}, date = {2022-06-30}, journal = {MRS Bulletin}, abstract = {Studies have provided evidence that human cerebral organoids (hCOs) recapitulate fundamental milestones of early brain development, but many important questions regarding their functionality and electrophysiological properties persist. High-density microelectrode arrays (HD-MEAs) represent an attractive analysis platform to perform functional studies of neuronal networks at the cellular and network scale. Here, we use HD-MEAs to derive large-scale electrophysiological recordings from sliced hCOs. We record the activity of hCO slices over several weeks and probe observed neuronal dynamics pharmacologically. Moreover, we present results on how the obtained recordings can be spike-sorted and subsequently studied across scales. For example, we show how to track single neurons across several days on the HD-MEA and how to infer axonal action potential velocities. We also infer putative functional connectivity from hCO recordings. The introduced methodology will contribute to a better understanding of developing neuronal networks in brain organoids and provide new means for their functional characterization.}, keywords = {HD-MEA, MaxOne, MaxTwo, Organoids}, pubstate = {published}, tppubtype = {article} } Close Studies have provided evidence that human cerebral organoids (hCOs) recapitulate fundamental milestones of early brain development, but many important questions regarding their functionality and electrophysiological properties persist. High-density microelectrode arrays (HD-MEAs) represent an attractive analysis platform to perform functional studies of neuronal networks at the cellular and network scale. Here, we use HD-MEAs to derive large-scale electrophysiological recordings from sliced hCOs. We record the activity of hCO slices over several weeks and probe observed neuronal dynamics pharmacologically. Moreover, we present results on how the obtained recordings can be spike-sorted and subsequently studied across scales. For example, we show how to track single neurons across several days on the HD-MEA and how to infer axonal action potential velocities. We also infer putative functional connectivity from hCO recordings. The introduced methodology will contribute to a better understanding of developing neuronal networks in brain organoids and provide new means for their functional characterization. Close https://link.springer.com/article/10.1557/s43577-022-00282-w Close
	Xu, Jax H; Yao, Yao; Yao, Fenyong; Chen, Jiehui; Li, Meishi; Xianfa, ; Yang, ; Li, Sheng; Lu, Fangru; Hu, Ping; He, Shuijin; Peng, Guangdun; Jing, Naihe Generation of functional posterior spinal motor neurons from hPSCs-derived human spinal cord neural progenitor cells Journal Article BioRxiv, 2022. Abstract \| Links \| BibTeX \| Tags: 2D Neuronal Culture, CMOS, HD-MEA, IPSC, MaxOne @article{Xu2022, title = {Generation of functional posterior spinal motor neurons from hPSCs-derived human spinal cord neural progenitor cells}, author = {Jax H. Xu and Yao Yao and Fenyong Yao and Jiehui Chen and Meishi Li and Xianfa and Yang and Sheng Li and Fangru Lu and Ping Hu and Shuijin He and Guangdun Peng and Naihe Jing}, url = {https://www.biorxiv.org/content/10.1101/2022.06.26.495599v1}, doi = {https://doi.org/10.1101/2022.06.26.495599}, year = {2022}, date = {2022-06-27}, journal = {BioRxiv}, abstract = {Spinal motor neurons deficiency results in a series of devastating disorders such as amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA) and spinal cord injury (SCI). These disorders are currently incurable, while human pluripotent stem cells (hPSCs)-derived spinal motor neurons are promising but suffered from low-efficiency, functional immaturity and lacks of posterior cellular identity. In this study, we have established human spinal cord neural progenitor cells (hSCNPCs) via hPSCs differentiated neuromesodermal progenitors (NMPs) and demonstrated the hSCNPCs can be continuously expanded up to 40 passages. hSCNPCs can be rapidly differentiated into posterior spinal motor neurons with high efficiency. The functional maturity has been examined in detail. Moreover, a co-culture scheme which is compatible for both neural and muscular differentiation is developed to mimic the neuromuscular junction (NMJ) formation in vitro. Together, these studies highlight the potential avenues for generating clinically relevant spinal motor neurons and modeling neuromuscular diseases through our defined hSCNPCs.}, keywords = {2D Neuronal Culture, CMOS, HD-MEA, IPSC, MaxOne}, pubstate = {published}, tppubtype = {article} } Close Spinal motor neurons deficiency results in a series of devastating disorders such as amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA) and spinal cord injury (SCI). These disorders are currently incurable, while human pluripotent stem cells (hPSCs)-derived spinal motor neurons are promising but suffered from low-efficiency, functional immaturity and lacks of posterior cellular identity. In this study, we have established human spinal cord neural progenitor cells (hSCNPCs) via hPSCs differentiated neuromesodermal progenitors (NMPs) and demonstrated the hSCNPCs can be continuously expanded up to 40 passages. hSCNPCs can be rapidly differentiated into posterior spinal motor neurons with high efficiency. The functional maturity has been examined in detail. Moreover, a co-culture scheme which is compatible for both neural and muscular differentiation is developed to mimic the neuromuscular junction (NMJ) formation in vitro. Together, these studies highlight the potential avenues for generating clinically relevant spinal motor neurons and modeling neuromuscular diseases through our defined hSCNPCs. Close https://www.biorxiv.org/content/10.1101/2022.06.26.495599v1 doi:https://doi.org/10.1101/2022.06.26.495599 Close
	Sommer Daniel ; Rajkumar, Sandeep; Seidel Mira; Aly Amr; Ludolph Albert; Ho Ritchie; Boeckers Tobias; Catanese Alberto. Aging-Dependent Altered Transcriptional Programs Underlie Activity Impairments in Human C9orf72-Mutant Motor Neurons Journal Article Frontiers in Molecular Neuroscience, 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, MaxOne, Neuronal Networks @article{Sommer2022, title = {Aging-Dependent Altered Transcriptional Programs Underlie Activity Impairments in Human C9orf72-Mutant Motor Neurons}, author = {Sommer, Daniel ; Rajkumar, Sandeep; Seidel, Mira; Aly, Amr; Ludolph, Albert; Ho, Ritchie; Boeckers, Tobias; Catanese, Alberto.}, url = {https://www.frontiersin.org/articles/10.3389/fnmol.2022.894230/full}, year = {2022}, date = {2022-06-14}, journal = {Frontiers in Molecular Neuroscience}, abstract = {Amyotrophic Lateral Sclerosis (ALS) is an incurable neurodegenerative disease characterized by dysfunction and loss of upper and lower motor neurons (MN). Despite several studies identifying drastic alterations affecting synaptic composition and functionality in different experimental models, the specific contribution of impaired activity to the neurodegenerative processes observed in ALS-related MN remains controversial. In particular, contrasting lines of evidence have shown both hyper- as well as hypoexcitability as driving pathomechanisms characterizing this specific neuronal population. In this study, we combined high definition multielectrode array (HD-MEA) techniques with transcriptomic analysis to longitudinally monitor and untangle the activity-dependent alterations arising in human C9orf72-mutant MN. We found a time-dependent reduction of neuronal activity in ALSC9orf72 cultures occurring as synaptic contacts undergo maturation and matched by a significant loss of mutant MN upon aging. Notably, ALS-related neurons displayed reduced network synchronicity most pronounced at later stages of culture, suggesting synaptic imbalance. In concordance with the HD-MEA data, transcriptomic analysis revealed an early up-regulation of synaptic terms in ALSC9orf72 MN, whose expression was decreased in aged cultures. In addition, treatment of older mutant cells with Apamin, a K+ channel blocker previously shown to be neuroprotective in ALS, rescued the time-dependent loss of firing properties observed in ALSC9orf72 MN as well as the expression of maturity-related synaptic genes. All in all, this study broadens the understanding of how impaired synaptic activity contributes to MN degeneration in ALS by correlating electrophysiological alterations to aging-dependent transcriptional programs. }, keywords = {HD-MEA, MaxOne, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Amyotrophic Lateral Sclerosis (ALS) is an incurable neurodegenerative disease characterized by dysfunction and loss of upper and lower motor neurons (MN). Despite several studies identifying drastic alterations affecting synaptic composition and functionality in different experimental models, the specific contribution of impaired activity to the neurodegenerative processes observed in ALS-related MN remains controversial. In particular, contrasting lines of evidence have shown both hyper- as well as hypoexcitability as driving pathomechanisms characterizing this specific neuronal population. In this study, we combined high definition multielectrode array (HD-MEA) techniques with transcriptomic analysis to longitudinally monitor and untangle the activity-dependent alterations arising in human C9orf72-mutant MN. We found a time-dependent reduction of neuronal activity in ALSC9orf72 cultures occurring as synaptic contacts undergo maturation and matched by a significant loss of mutant MN upon aging. Notably, ALS-related neurons displayed reduced network synchronicity most pronounced at later stages of culture, suggesting synaptic imbalance. In concordance with the HD-MEA data, transcriptomic analysis revealed an early up-regulation of synaptic terms in ALSC9orf72 MN, whose expression was decreased in aged cultures. In addition, treatment of older mutant cells with Apamin, a K+ channel blocker previously shown to be neuroprotective in ALS, rescued the time-dependent loss of firing properties observed in ALSC9orf72 MN as well as the expression of maturity-related synaptic genes. All in all, this study broadens the understanding of how impaired synaptic activity contributes to MN degeneration in ALS by correlating electrophysiological alterations to aging-dependent transcriptional programs. Close https://www.frontiersin.org/articles/10.3389/fnmol.2022.894230/full Close
	Cheng, Zhuowei; Guzman, Elmer; van der Molen, Tjitse; Sharf, Tal; Hansma, Paul K; Kosik, Kenneth S; Petzold, Linda; Tovar, Kenneth R Automated detection of extracellular action potentials from single neurons Journal Article bioRxiv, 2022. Abstract \| Links \| BibTeX \| Tags: Action Potential, HD-MEA, MaxOne @article{Cheng2023, title = {Automated detection of extracellular action potentials from single neurons}, author = {Zhuowei Cheng and Elmer Guzman and Tjitse van der Molen and Tal Sharf and Paul K. Hansma and Kenneth S Kosik and Linda Petzold and Kenneth R Tovar}, url = {https://www.biorxiv.org/content/10.1101/2022.06.06.494896v1.abstract}, doi = {https://doi.org/10.1101/2022.06.06.494896}, year = {2022}, date = {2022-06-06}, journal = {bioRxiv}, abstract = {Multi-electrode arrays (MEAs) non-invasively record extracellular action potentials (eAPs, also known as spikes) from hundreds of neurons simultaneously. However, because extracellular electrodes sample from the local electrical field, each electrode can detect eAPs from multiple nearby neurons. Interpreting spike trains at individual electrodes of high-density arrays requires spike sorting, a computational process which groups eAPs from single ’units’ based on assumptions of how spike waveforms correlate with different neuronal sources. Additionally, when experimental conditions result in changes to eAP waveforms, spike sorting routines may have difficulty correlating eAPs from multiple neurons at single electrodes before and after such waveform changes. We present here a novel, empirical method for unambiguously isolating eAPs from individual, uniquely identifiable neurons, based on automated multi- point detection of action potential propagation. This method is insensitive to changes in eAP waveform morphology because it makes no assumptions about the relationship between spike waveform and neuronal source. Our algorithm for automated detection of action potential propagation produces a ’fingerprint’ that uniquely identifies those spikes from each neuron. By unambiguously isolating eAPs from multiple neurons in each recording, on a range of platforms and experimental preparations, our method now enables high-content screening with contemporary MEAs. We outline the limitations and strengths of propagation-based isolation of eAPs from single neurons and propose how our automated method complements spike sorting and could be adapted to in vivo use.}, keywords = {Action Potential, HD-MEA, MaxOne}, pubstate = {published}, tppubtype = {article} } Close Multi-electrode arrays (MEAs) non-invasively record extracellular action potentials (eAPs, also known as spikes) from hundreds of neurons simultaneously. However, because extracellular electrodes sample from the local electrical field, each electrode can detect eAPs from multiple nearby neurons. Interpreting spike trains at individual electrodes of high-density arrays requires spike sorting, a computational process which groups eAPs from single ’units’ based on assumptions of how spike waveforms correlate with different neuronal sources. Additionally, when experimental conditions result in changes to eAP waveforms, spike sorting routines may have difficulty correlating eAPs from multiple neurons at single electrodes before and after such waveform changes. We present here a novel, empirical method for unambiguously isolating eAPs from individual, uniquely identifiable neurons, based on automated multi- point detection of action potential propagation. This method is insensitive to changes in eAP waveform morphology because it makes no assumptions about the relationship between spike waveform and neuronal source. Our algorithm for automated detection of action potential propagation produces a ’fingerprint’ that uniquely identifies those spikes from each neuron. By unambiguously isolating eAPs from multiple neurons in each recording, on a range of platforms and experimental preparations, our method now enables high-content screening with contemporary MEAs. We outline the limitations and strengths of propagation-based isolation of eAPs from single neurons and propose how our automated method complements spike sorting and could be adapted to in vivo use. Close https://www.biorxiv.org/content/10.1101/2022.06.06.494896v1.abstract doi:https://doi.org/10.1101/2022.06.06.494896 Close
	Noh Seungmin ; Jeon, Sungwoong; Kim Eunhee; Oh Untaek; Park Danbi; Park Sun Hwa; Kim Sung Won; Pané Salvador; Nelson Bradley; Kim Jin-young; Choi Hongsoo; A Biodegradable Magnetic Microrobot Based on Gelatin Methacrylate for Precise Delivery of Stem Cells with Mass Production Capability Journal Article Small, 2022. Abstract \| Links \| BibTeX \| Tags: MaxOne @article{Noh2022, title = {A Biodegradable Magnetic Microrobot Based on Gelatin Methacrylate for Precise Delivery of Stem Cells with Mass Production Capability}, author = {Noh, Seungmin ; Jeon, Sungwoong; Kim, Eunhee; Oh, Untaek; Park, Danbi; Park, Sun Hwa; Kim, Sung Won; Pané, Salvador; Nelson, Bradley; Kim, Jin-young; Choi, Hongsoo;}, url = {https://onlinelibrary.wiley.com/doi/10.1002/smll.202107888}, doi = {10.1002/smll.202107888}, year = {2022}, date = {2022-05-23}, journal = {Small}, abstract = {A great deal of research has focused on small-scale robots for biomedical applications and minimally invasive delivery of therapeutics (e.g., cells, drugs, and genes) to a target area. Conventional fabrication methods, such as two-photon polymerization, can be used to build sophisticated micro- and nanorobots, but the long fabrication cycle for a single microrobot has limited its practical use. This study proposes a biodegradable spherical gelatin methacrylate (GelMA) microrobot for mass production in a microfluidic channel. The proposed microrobot is fabricated in a flow-focusing droplet generator by shearing a mixture of GelMA, photoinitiator, and superparamagnetic iron oxide nanoparticles (SPIONs) with a mixture of oil and surfactant. Human nasal turbinate stem cells (hNTSCs) are loaded on the GelMA microrobot, and the hNTSC-loaded microrobot shows precise rolling motion in response to an external rotating magnetic field. The microrobot is enzymatically degraded by collagenase, and released hNTSCs are proliferated and differentiated into neuronal cells. In addition, the feasibility of the GelMA microrobot as a cell therapeutic delivery system is investigated by measuring electrophysiological activity on a multielectrode array. Such a versatile and fully biodegradable microrobot has the potential for targeted stem cell delivery, proliferation, and differentiation for stem cell-based therapy.}, keywords = {MaxOne}, pubstate = {published}, tppubtype = {article} } Close A great deal of research has focused on small-scale robots for biomedical applications and minimally invasive delivery of therapeutics (e.g., cells, drugs, and genes) to a target area. Conventional fabrication methods, such as two-photon polymerization, can be used to build sophisticated micro- and nanorobots, but the long fabrication cycle for a single microrobot has limited its practical use. This study proposes a biodegradable spherical gelatin methacrylate (GelMA) microrobot for mass production in a microfluidic channel. The proposed microrobot is fabricated in a flow-focusing droplet generator by shearing a mixture of GelMA, photoinitiator, and superparamagnetic iron oxide nanoparticles (SPIONs) with a mixture of oil and surfactant. Human nasal turbinate stem cells (hNTSCs) are loaded on the GelMA microrobot, and the hNTSC-loaded microrobot shows precise rolling motion in response to an external rotating magnetic field. The microrobot is enzymatically degraded by collagenase, and released hNTSCs are proliferated and differentiated into neuronal cells. In addition, the feasibility of the GelMA microrobot as a cell therapeutic delivery system is investigated by measuring electrophysiological activity on a multielectrode array. Such a versatile and fully biodegradable microrobot has the potential for targeted stem cell delivery, proliferation, and differentiation for stem cell-based therapy. Close https://onlinelibrary.wiley.com/doi/10.1002/smll.202107888 doi:10.1002/smll.202107888 Close
	Sato Yuya; Yamamoto, Hideaki; Kato Hideyuki; Tanii Takashi; Sato Shigeo; Hirano-Iwata Ayumi Microfluidic cell engineering on high-density microelectrode arrays for assessing structure-function relationships in living neuronal networks Journal Article 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, MaxOne, Neuronal Networks @article{Sato2022, title = {Microfluidic cell engineering on high-density microelectrode arrays for assessing structure-function relationships in living neuronal networks}, author = {Sato, Yuya; Yamamoto, Hideaki; Kato, Hideyuki; Tanii, Takashi; Sato, Shigeo; Hirano-Iwata, Ayumi}, url = {https://arxiv.org/abs/2205.04342}, year = {2022}, date = {2022-05-11}, abstract = {Neuronal networks in dissociated culture combined with cell engineering technology offer a pivotal platform to constructively explore the relationship between structure and function in living neuronal networks. Here, we fabricated defined neuronal networks possessing a modular architecture on high-density microelectrode arrays (HD-MEAs), a state-of-the-art electrophysiological tool for recording neural activity with high spatial and temporal resolutions. We first established a surface coating protocol using a cell-permissive hydrogel to stably attach polydimethylsiloxane microfluidic film on the HD-MEA. We then recorded the spontaneous neural activity of the engineered neuronal network, which revealed an important portrait of the engineered neuronal network--modular architecture enhances functional complexity by reducing the excessive neural correlation between spatially segregated modules. The results of this study highlight the impact of HD-MEA recordings combined with cell engineering technologies as a novel tool in neuroscience to constructively assess the structure-function relationships in neuronal networks.}, keywords = {HD-MEA, MaxOne, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Neuronal networks in dissociated culture combined with cell engineering technology offer a pivotal platform to constructively explore the relationship between structure and function in living neuronal networks. Here, we fabricated defined neuronal networks possessing a modular architecture on high-density microelectrode arrays (HD-MEAs), a state-of-the-art electrophysiological tool for recording neural activity with high spatial and temporal resolutions. We first established a surface coating protocol using a cell-permissive hydrogel to stably attach polydimethylsiloxane microfluidic film on the HD-MEA. We then recorded the spontaneous neural activity of the engineered neuronal network, which revealed an important portrait of the engineered neuronal network--modular architecture enhances functional complexity by reducing the excessive neural correlation between spatially segregated modules. The results of this study highlight the impact of HD-MEA recordings combined with cell engineering technologies as a novel tool in neuroscience to constructively assess the structure-function relationships in neuronal networks. Close https://arxiv.org/abs/2205.04342 Close
	Shimba Kenta; Asahina, Takahiro; Sakai Koji; Kotani Kiyoshi; Jimbo Yasuhiko Recording Saltatory Conduction Along Sensory Axons Using a High-Density Microelectrode Array Journal Article Frontiers in Neuroscience, 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, MaxOne, Neuronal cell culture @article{Shimba2022, title = {Recording Saltatory Conduction Along Sensory Axons Using a High-Density Microelectrode Array}, author = {Shimba, Kenta; Asahina, Takahiro; Sakai, Koji; Kotani, Kiyoshi; Jimbo, Yasuhiko}, url = {https://www.frontiersin.org/articles/10.3389/fnins.2022.854637/full}, year = {2022}, date = {2022-04-18}, journal = {Frontiers in Neuroscience}, abstract = {In bottom-up neuroscience, questions on neural information processing are addressed by engineering small but reproducible biological neural networks of defined network topology in vitro. The network topology can be controlled by culturing neurons within polydimethylsiloxane (PDMS) microstructures that are combined with microelectrode arrays (MEAs) for electric access to the network. However, currently used glass MEAs are limited to 256 electrodes and pose a limitation to the spatial resolution as well as the design of more complex microstructures. The use of high density complementary metal-oxide-semiconductor (CMOS) MEAs greatly increases the spatial resolution, enabling sub-cellular readout and stimulation of neurons in defined neural networks. Unfortunately, the non-planar surface of CMOS MEAs complicates the attachment of PDMS microstructures. To overcome the problem of axons escaping the microstructures through the ridges of the CMOS MEA, we stamp-transferred a thin film of hexane-diluted PDMS onto the array such that the PDMS filled the ridges at the contact surface of the microstructures without clogging the axon guidance channels. This method resulted in 23 % of structurally fully connected but sealed networks on the CMOS MEA of which about 45 % showed spiking activity in all channels. Moreover, we provide an impedance-based method to visualize the exact location of the microstructures on the MEA and show that our method can confine axonal growth within the PDMS microstructures. Finally, the high spatial resolution of the CMOS MEA enabled us to show that action potentials follow the unidirectional topology of our circular multi-node microstructure.}, keywords = {HD-MEA, MaxOne, Neuronal cell culture}, pubstate = {published}, tppubtype = {article} } Close In bottom-up neuroscience, questions on neural information processing are addressed by engineering small but reproducible biological neural networks of defined network topology in vitro. The network topology can be controlled by culturing neurons within polydimethylsiloxane (PDMS) microstructures that are combined with microelectrode arrays (MEAs) for electric access to the network. However, currently used glass MEAs are limited to 256 electrodes and pose a limitation to the spatial resolution as well as the design of more complex microstructures. The use of high density complementary metal-oxide-semiconductor (CMOS) MEAs greatly increases the spatial resolution, enabling sub-cellular readout and stimulation of neurons in defined neural networks. Unfortunately, the non-planar surface of CMOS MEAs complicates the attachment of PDMS microstructures. To overcome the problem of axons escaping the microstructures through the ridges of the CMOS MEA, we stamp-transferred a thin film of hexane-diluted PDMS onto the array such that the PDMS filled the ridges at the contact surface of the microstructures without clogging the axon guidance channels. This method resulted in 23 % of structurally fully connected but sealed networks on the CMOS MEA of which about 45 % showed spiking activity in all channels. Moreover, we provide an impedance-based method to visualize the exact location of the microstructures on the MEA and show that our method can confine axonal growth within the PDMS microstructures. Finally, the high spatial resolution of the CMOS MEA enabled us to show that action potentials follow the unidirectional topology of our circular multi-node microstructure. Close https://www.frontiersin.org/articles/10.3389/fnins.2022.854637/full Close
	Hornauer Philipp; Prack, Gustavo; Anastasi Nadia; Ronchi Silvia; Kim Taehoon; Donner Christian; Fiscella Michele; Borgwardt Karsten; Taylor Verdon; Jagasia Ravi; Roqueiro Damian; Hierlemann Andreas; Downregulating α-synuclein in iPSC-derived dopaminergic neurons mimics 2 electrophysiological phenotype of the A53T mutation Journal Article bioRxiv, 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, MaxOne, Neuronal cell culture @article{Hornauer2022, title = {Downregulating α-synuclein in iPSC-derived dopaminergic neurons mimics 2 electrophysiological phenotype of the A53T mutation}, author = {Hornauer, Philipp; Prack, Gustavo; Anastasi, Nadia; Ronchi, Silvia; Kim, Taehoon; Donner, Christian; Fiscella, Michele; Borgwardt, Karsten; Taylor, Verdon; Jagasia, Ravi; Roqueiro, Damian; Hierlemann, Andreas;}, url = {https://www.biorxiv.org/content/10.1101/2022.03.31.486582v1.full}, year = {2022}, date = {2022-04-01}, journal = {bioRxiv}, abstract = {Parkinson’s disease (PD) is a common debilitating neurodegenerative disorder, characterized by a progressive loss of dopaminergic (DA) neurons. Mutations, gene dosage increase, and single nucleotide polymorphisms in the α-synuclein-encoding gene SNCA either cause or increase the risk for PD. However, neither the function of α-synuclein in health and disease, nor its role throughout development is fully understood. Here, we introduce DeePhys, a new tool that allows for data-driven functional phenotyping of neuronal cell lines by combining electrophysiological features inferred from high-density microelectrode array (HD-MEA) recordings with a robust machine learning workflow. We apply DeePhys to human induced pluripotent stem cell (iPSC)-derived DA neuron-astrocyte co-cultures harboring the prominent SNCA mutation A53T and an isogenic control line. Moreover, we demonstrate how DeePhys can facilitate the assessment of cellular and network-level electrophysiological features to build functional phenotypes and to evaluate potential treatment interventions. We find that electrophysiological features across all scales proved to be highly specific for the A53T phenotype, enabled to predict the genotype and age of individual cultures with high accuracy, and revealed a mutant-like phenotype after downregulation of α-synuclein.}, keywords = {HD-MEA, MaxOne, Neuronal cell culture}, pubstate = {published}, tppubtype = {article} } Close Parkinson’s disease (PD) is a common debilitating neurodegenerative disorder, characterized by a progressive loss of dopaminergic (DA) neurons. Mutations, gene dosage increase, and single nucleotide polymorphisms in the α-synuclein-encoding gene SNCA either cause or increase the risk for PD. However, neither the function of α-synuclein in health and disease, nor its role throughout development is fully understood. Here, we introduce DeePhys, a new tool that allows for data-driven functional phenotyping of neuronal cell lines by combining electrophysiological features inferred from high-density microelectrode array (HD-MEA) recordings with a robust machine learning workflow. We apply DeePhys to human induced pluripotent stem cell (iPSC)-derived DA neuron-astrocyte co-cultures harboring the prominent SNCA mutation A53T and an isogenic control line. Moreover, we demonstrate how DeePhys can facilitate the assessment of cellular and network-level electrophysiological features to build functional phenotypes and to evaluate potential treatment interventions. We find that electrophysiological features across all scales proved to be highly specific for the A53T phenotype, enabled to predict the genotype and age of individual cultures with high accuracy, and revealed a mutant-like phenotype after downregulation of α-synuclein. Close https://www.biorxiv.org/content/10.1101/2022.03.31.486582v1.full Close
	Sawada, Haruto; Wake, Naoki; Sasabuchi, Kazuhiro; Takamatsu, Jun; Takahashi, Hirokazu; Ikeuchi, Katsushi Design strategies for controlling neuron-connected robots using reinforcement learning Journal Article arXiv, 2022. Abstract \| Links \| BibTeX \| Tags: Machine Learning, MaxOne, Stimulation @article{Sawada2022, title = {Design strategies for controlling neuron-connected robots using reinforcement learning}, author = {Haruto Sawada and Naoki Wake and Kazuhiro Sasabuchi and Jun Takamatsu and Hirokazu Takahashi and Katsushi Ikeuchi}, url = {https://arxiv.org/abs/2203.15290}, doi = {https://doi.org/10.48550/arXiv.2203.15290}, year = {2022}, date = {2022-03-29}, journal = {arXiv}, abstract = {Despite the growing interest in robot control utilizing the computation of biological neurons, context-dependent behavior by neuron-connected robots remains a challenge. Context-dependent behavior here is defined as behavior that is not the result of a simple sensory-motor coupling, but rather based on an understanding of the task goal. This paper proposes design principles for training neuron-connected robots based on task goals to achieve context-dependent behavior. First, we employ deep reinforcement learning (RL) to enable training that accounts for goal achievements. Second, we propose a neuron simulator as a probability distribution based on recorded neural data, aiming to represent physiologically valid neural dynamics while avoiding complex modeling with high computational costs. Furthermore, we propose to update the simulators during the training to bridge the gap between the simulation and the real settings. The experiments showed that the robot gradually learned context-dependent behaviors in pole balancing and robot navigation tasks. Moreover, the learned policies were valid for neural simulators based on novel neural data, and the task performance increased by updating the simulators during training. These results suggest the effectiveness of the proposed design principle for the context-dependent behavior of neuron-connected robots.}, keywords = {Machine Learning, MaxOne, Stimulation}, pubstate = {published}, tppubtype = {article} } Close Despite the growing interest in robot control utilizing the computation of biological neurons, context-dependent behavior by neuron-connected robots remains a challenge. Context-dependent behavior here is defined as behavior that is not the result of a simple sensory-motor coupling, but rather based on an understanding of the task goal. This paper proposes design principles for training neuron-connected robots based on task goals to achieve context-dependent behavior. First, we employ deep reinforcement learning (RL) to enable training that accounts for goal achievements. Second, we propose a neuron simulator as a probability distribution based on recorded neural data, aiming to represent physiologically valid neural dynamics while avoiding complex modeling with high computational costs. Furthermore, we propose to update the simulators during the training to bridge the gap between the simulation and the real settings. The experiments showed that the robot gradually learned context-dependent behaviors in pole balancing and robot navigation tasks. Moreover, the learned policies were valid for neural simulators based on novel neural data, and the task performance increased by updating the simulators during training. These results suggest the effectiveness of the proposed design principle for the context-dependent behavior of neuron-connected robots. Close https://arxiv.org/abs/2203.15290 doi:https://doi.org/10.48550/arXiv.2203.15290 Close
	Duru Jens; Küchler, Joël; Ihle Stephan Forró Csaba; Bernardi Aeneas; Girardin Sophie; Hengsteler Julian; Wheeler Stephen; János; Ruff Tobias; J ; Vörös Engineered Biological Neural Networks on High Density CMOS Microelectrode Arrays Journal Article 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, MaxOne, Neuronal Networks @article{Duru2022, title = {Engineered Biological Neural Networks on High Density CMOS Microelectrode Arrays}, author = {Duru, Jens; Küchler, Joël; Ihle, Stephan J.;, Forró, Csaba; Bernardi, Aeneas; Girardin, Sophie; Hengsteler, Julian; Wheeler, Stephen; Vörös, János; Ruff, Tobias;}, url = {https://www.frontiersin.org/articles/10.3389/fnins.2022.829884/full}, year = {2022}, date = {2022-02-21}, abstract = {In bottom-up neuroscience, questions on neural information processing are addressed by engineering small but reproducible biological neural networks of defined network topology in vitro. The network topology can be controlled by culturing neurons within polydimethylsiloxane (PDMS) microstructures that are combined with microelectrode arrays (MEAs) for electric access to the network. However, currently used glass MEAs are limited to 256 electrodes and pose a limitation to the spatial resolution as well as the design of more complex microstructures. The use of high density complementary metal-oxide-semiconductor (CMOS) MEAs greatly increases the spatial resolution, enabling sub-cellular readout and stimulation of neurons in defined neural networks. Unfortunately, the non-planar surface of CMOS MEAs complicates the attachment of PDMS microstructures. To overcome the problem of axons escaping the microstructures through the ridges of the CMOS MEA, we stamp-transferred a thin film of hexane-diluted PDMS onto the array such that the PDMS filled the ridges at the contact surface of the microstructures without clogging the axon guidance channels. This method resulted in 23 % of structurally fully connected but sealed networks on the CMOS MEA of which about 45 % showed spiking activity in all channels. Moreover, we provide an impedance-based method to visualize the exact location of the microstructures on the MEA and show that our method can confine axonal growth within the PDMS microstructures. Finally, the high spatial resolution of the CMOS MEA enabled us to show that action potentials follow the unidirectional topology of our circular multi-node microstructure.}, keywords = {HD-MEA, MaxOne, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close In bottom-up neuroscience, questions on neural information processing are addressed by engineering small but reproducible biological neural networks of defined network topology in vitro. The network topology can be controlled by culturing neurons within polydimethylsiloxane (PDMS) microstructures that are combined with microelectrode arrays (MEAs) for electric access to the network. However, currently used glass MEAs are limited to 256 electrodes and pose a limitation to the spatial resolution as well as the design of more complex microstructures. The use of high density complementary metal-oxide-semiconductor (CMOS) MEAs greatly increases the spatial resolution, enabling sub-cellular readout and stimulation of neurons in defined neural networks. Unfortunately, the non-planar surface of CMOS MEAs complicates the attachment of PDMS microstructures. To overcome the problem of axons escaping the microstructures through the ridges of the CMOS MEA, we stamp-transferred a thin film of hexane-diluted PDMS onto the array such that the PDMS filled the ridges at the contact surface of the microstructures without clogging the axon guidance channels. This method resulted in 23 % of structurally fully connected but sealed networks on the CMOS MEA of which about 45 % showed spiking activity in all channels. Moreover, we provide an impedance-based method to visualize the exact location of the microstructures on the MEA and show that our method can confine axonal growth within the PDMS microstructures. Finally, the high spatial resolution of the CMOS MEA enabled us to show that action potentials follow the unidirectional topology of our circular multi-node microstructure. Close https://www.frontiersin.org/articles/10.3389/fnins.2022.829884/full Close
	Xue, Xiaohan ; Buccino, Alessio Paolo ; Kumar, Sreedhar Saseendran ; Hierlemann, Andreas ; Bartram, Julian Inferring monosynaptic connections from paired dendritic spine Ca2+ imaging and large-scale recording of extracellular spiking Journal Article bioRxiv, 2022. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Neuronal Networks @article{Xue2022, title = {Inferring monosynaptic connections from paired dendritic spine Ca2+ imaging and large-scale recording of extracellular spiking}, author = {Xue, Xiaohan and Buccino, Alessio Paolo and Kumar, Sreedhar Saseendran and Hierlemann, Andreas and Bartram, Julian}, doi = {10.1101/2022.02.16.480643}, year = {2022}, date = {2022-02-16}, journal = {bioRxiv}, abstract = {Techniques to identify monosynaptic connections between neurons have been vital for neuroscience research, facilitating important advancements concerning network topology, synaptic plasticity, and synaptic integration, among others. Here, we introduce a novel approach to identify and monitor monosynaptic connections using high-resolution dendritic spine Ca2+ imaging combined with simultaneous large-scale recording of extracellular electrical activity by means of high-density microelectrode arrays (HD-MEAs). We introduce an easily adoptable analysis pipeline that associates the imaged spine with its presynaptic unit and test it on in vitro recordings. The method is further validated and optimized by simulating synaptically-evoked spine Ca2+ transients based on measured spike trains in order to obtain simulated ground-truth connections. The proposed approach offers unique advantages as i) it can be used to identify monosynaptic connections with an accurate localization of the synapse within the dendritic tree, ii) it provides precise information of presynaptic spiking, and iii) postsynaptic spine Ca2+ signals and, finally, iv) the non-invasive nature of the proposed method allows for long-term measurements. The analysis toolkit together with the rich data sets that were acquired are made publicly available for further exploration by the research community.}, keywords = {ETH-CMOS-MEA, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Techniques to identify monosynaptic connections between neurons have been vital for neuroscience research, facilitating important advancements concerning network topology, synaptic plasticity, and synaptic integration, among others. Here, we introduce a novel approach to identify and monitor monosynaptic connections using high-resolution dendritic spine Ca2+ imaging combined with simultaneous large-scale recording of extracellular electrical activity by means of high-density microelectrode arrays (HD-MEAs). We introduce an easily adoptable analysis pipeline that associates the imaged spine with its presynaptic unit and test it on in vitro recordings. The method is further validated and optimized by simulating synaptically-evoked spine Ca2+ transients based on measured spike trains in order to obtain simulated ground-truth connections. The proposed approach offers unique advantages as i) it can be used to identify monosynaptic connections with an accurate localization of the synapse within the dendritic tree, ii) it provides precise information of presynaptic spiking, and iii) postsynaptic spine Ca2+ signals and, finally, iv) the non-invasive nature of the proposed method allows for long-term measurements. The analysis toolkit together with the rich data sets that were acquired are made publicly available for further exploration by the research community. Close doi:10.1101/2022.02.16.480643 Close
	McSweeney, Danny; Gabriel, Rafael; Jin, Kang; Pang, Zhiping P; Aronow, Bruce; Pak, ChangHui Loss of Neurodevelopmental Gene CASK Disrupts Neural Connectivity in Human Cortical Excitatory Neurons Journal Article BioRxiv, 2022. Abstract \| Links \| BibTeX \| Tags: IPSC, MaxOne, Neuronal Networks @article{McSweeney2022, title = {Loss of Neurodevelopmental Gene CASK Disrupts Neural Connectivity in Human Cortical Excitatory Neurons}, author = {Danny McSweeney and Rafael Gabriel and Kang Jin and Zhiping P. Pang and Bruce Aronow and ChangHui Pak}, url = {https://doi.org/10.1101/2022.02.14.480404}, doi = {10.1101/2022.02.14.480404}, year = {2022}, date = {2022-02-15}, journal = {BioRxiv}, abstract = {Loss-of-function (LOF) mutations in CASK cause severe developmental phenotypes, including microcephaly with pontine and cerebellar hypoplasia, X-linked intellectual disability, and autism. Unraveling the pathogenesis of CASK-related disorders has been challenging due to limited human cellular models to study the dynamic roles of this molecule during neuronal and synapse development. Here, we generated CASK knockout (KO) isogenic cell lines from human embryonic stem cells (hESCs) using CRISPR/Cas9 and examined gene expression, morphometrics and synaptic function of induced neuronal cells during development. While young (immature) CASK KO neurons show robust neuronal outgrowth, mature CASK KO neurons displayed severe defects in synaptic transmission and synchronized burst activity without compromising neuronal morphology and synapse numbers. In developing human cortical neurons, CASK functions to promote both structural integrity and establishment of cortical excitatory neuronal networks. These results lay the foundation for future studies identifying suppressors of such phenotypes relevant to human patients.}, keywords = {IPSC, MaxOne, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Loss-of-function (LOF) mutations in CASK cause severe developmental phenotypes, including microcephaly with pontine and cerebellar hypoplasia, X-linked intellectual disability, and autism. Unraveling the pathogenesis of CASK-related disorders has been challenging due to limited human cellular models to study the dynamic roles of this molecule during neuronal and synapse development. Here, we generated CASK knockout (KO) isogenic cell lines from human embryonic stem cells (hESCs) using CRISPR/Cas9 and examined gene expression, morphometrics and synaptic function of induced neuronal cells during development. While young (immature) CASK KO neurons show robust neuronal outgrowth, mature CASK KO neurons displayed severe defects in synaptic transmission and synchronized burst activity without compromising neuronal morphology and synapse numbers. In developing human cortical neurons, CASK functions to promote both structural integrity and establishment of cortical excitatory neuronal networks. These results lay the foundation for future studies identifying suppressors of such phenotypes relevant to human patients. Close https://doi.org/10.1101/2022.02.14.480404 doi:10.1101/2022.02.14.480404 Close
	Paulsen, Bruna; Velasco, Silvia; Kedaigle, Amanda J; Pigoni, Martina; Quadrato, Giorgia; Deo, Anthony J; Adiconis, Xian; Uzquiano, Ana; Sartore, Rafaela; Yang, Sung Min; Simmons, Sean K; Symvoulidis, Panagiotis; Kim, Kwanho; Tsafou, Kalliopi; Podury, Archana; Abbate, Catherine; Tucewicz, Ashley; Smith, Samantha N; Albanese, Alexandre; Barrett, Lindy; Sanjana, Neville E; Shi, Xi; Chung, Kwanghun; Lage, Kasper; Boyden, Edward S; andJoshua Levin, Aviv Regev Z; Arlotta, Paola Autism genes converge on asynchronous development of shared neuron classes Journal Article Nature, 602 , pp. 268–273, 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, MaxOne, Organoids @article{Paulsen2022, title = {Autism genes converge on asynchronous development of shared neuron classes}, author = {Bruna Paulsen and Silvia Velasco and Amanda J. Kedaigle and Martina Pigoni and Giorgia Quadrato and Anthony J. Deo and Xian Adiconis and Ana Uzquiano and Rafaela Sartore and Sung Min Yang and Sean K. Simmons and Panagiotis Symvoulidis and Kwanho Kim and Kalliopi Tsafou and Archana Podury and Catherine Abbate and Ashley Tucewicz and Samantha N. Smith and Alexandre Albanese and Lindy Barrett and Neville E. Sanjana and Xi Shi and Kwanghun Chung and Kasper Lage and Edward S. Boyden and Aviv Regev andJoshua Z. Levin and Paola Arlotta }, url = {https://www.nature.com/articles/s41586-021-04358-6}, doi = {10.1038/s41586-021-04358-6}, year = {2022}, date = {2022-02-02}, journal = {Nature}, volume = {602}, pages = {268–273}, abstract = {Genetic risk for autism spectrum disorder (ASD) is associated with hundreds of genes spanning a wide range of biological functions1,2,3,4,5,6. The alterations in the human brain resulting from mutations in these genes remain unclear. Furthermore, their phenotypic manifestation varies across individuals7,8. Here we used organoid models of the human cerebral cortex to identify cell-type-specific developmental abnormalities that result from haploinsufficiency in three ASD risk genes—SUV420H1 (also known as KMT5B), ARID1B and CHD8—in multiple cell lines from different donors, using single-cell RNA-sequencing (scRNA-seq) analysis of more than 745,000 cells and proteomic analysis of individual organoids, to identify phenotypic convergence. Each of the three mutations confers asynchronous development of two main cortical neuronal lineages—γ-aminobutyric-acid-releasing (GABAergic) neurons and deep-layer excitatory projection neurons—but acts through largely distinct molecular pathways. Although these phenotypes are consistent across cell lines, their expressivity is influenced by the individual genomic context, in a manner that is dependent on both the risk gene and the developmental defect. Calcium imaging in intact organoids shows that these early-stage developmental changes are followed by abnormal circuit activity. This research uncovers cell-type-specific neurodevelopmental abnormalities that are shared across ASD risk genes and are finely modulated by human genomic context, finding convergence in the neurobiological basis of how different risk genes contribute to ASD pathology.}, keywords = {HD-MEA, MaxOne, Organoids}, pubstate = {published}, tppubtype = {article} } Close Genetic risk for autism spectrum disorder (ASD) is associated with hundreds of genes spanning a wide range of biological functions1,2,3,4,5,6. The alterations in the human brain resulting from mutations in these genes remain unclear. Furthermore, their phenotypic manifestation varies across individuals7,8. Here we used organoid models of the human cerebral cortex to identify cell-type-specific developmental abnormalities that result from haploinsufficiency in three ASD risk genes—SUV420H1 (also known as KMT5B), ARID1B and CHD8—in multiple cell lines from different donors, using single-cell RNA-sequencing (scRNA-seq) analysis of more than 745,000 cells and proteomic analysis of individual organoids, to identify phenotypic convergence. Each of the three mutations confers asynchronous development of two main cortical neuronal lineages—γ-aminobutyric-acid-releasing (GABAergic) neurons and deep-layer excitatory projection neurons—but acts through largely distinct molecular pathways. Although these phenotypes are consistent across cell lines, their expressivity is influenced by the individual genomic context, in a manner that is dependent on both the risk gene and the developmental defect. Calcium imaging in intact organoids shows that these early-stage developmental changes are followed by abnormal circuit activity. This research uncovers cell-type-specific neurodevelopmental abnormalities that are shared across ASD risk genes and are finely modulated by human genomic context, finding convergence in the neurobiological basis of how different risk genes contribute to ASD pathology. Close https://www.nature.com/articles/s41586-021-04358-6 doi:10.1038/s41586-021-04358-6 Close
	McCready, Fraser P; Gordillo-Sampedro, Sara; Pradeepan, Kartik; Martinez-Trujillo, Julio; Ellis, James Multielectrode Arrays for Functional Phenotyping of Neurons from Induced Pluripotent Stem Cell Models of Neurodevelopmental Disorders Journal Article Biology, 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, IPSC, MaxOne, MEA Technology @article{McCready2022, title = {Multielectrode Arrays for Functional Phenotyping of Neurons from Induced Pluripotent Stem Cell Models of Neurodevelopmental Disorders}, author = {Fraser P. McCready and Sara Gordillo-Sampedro and Kartik Pradeepan and Julio Martinez-Trujillo and James Ellis}, url = {https://www.mdpi.com/2079-7737/11/2/316}, doi = {10.3390/biology11020316}, year = {2022}, date = {2022-01-11}, journal = {Biology}, abstract = {In vitro multielectrode array (MEA) systems are increasingly used as higher-throughput platforms for functional phenotyping studies of neurons in induced pluripotent stem cell (iPSC) disease models. While MEA systems generate large amounts of spatiotemporal activity data from networks of iPSC-derived neurons, the downstream analysis and interpretation of such high-dimensional data often pose a significant challenge to researchers. In this review, we examine how MEA technology is currently deployed in iPSC modeling studies of neurodevelopmental disorders. We first highlight the strengths of in vitro MEA technology by reviewing the history of its development and the original scientific questions MEAs were intended to answer. Methods of generating patient iPSCderived neurons and astrocytes for MEA co-cultures are summarized. We then discuss challenges associated with MEA data analysis in a disease modeling context, and present novel computational methods used to better interpret network phenotyping data. We end by suggesting best practices for presenting MEA data in research publications, and propose that the creation of a public MEA data repository to enable collaborative data sharing would be of great benefit to the iPSC disease modeling community.}, keywords = {HD-MEA, IPSC, MaxOne, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close In vitro multielectrode array (MEA) systems are increasingly used as higher-throughput platforms for functional phenotyping studies of neurons in induced pluripotent stem cell (iPSC) disease models. While MEA systems generate large amounts of spatiotemporal activity data from networks of iPSC-derived neurons, the downstream analysis and interpretation of such high-dimensional data often pose a significant challenge to researchers. In this review, we examine how MEA technology is currently deployed in iPSC modeling studies of neurodevelopmental disorders. We first highlight the strengths of in vitro MEA technology by reviewing the history of its development and the original scientific questions MEAs were intended to answer. Methods of generating patient iPSCderived neurons and astrocytes for MEA co-cultures are summarized. We then discuss challenges associated with MEA data analysis in a disease modeling context, and present novel computational methods used to better interpret network phenotyping data. We end by suggesting best practices for presenting MEA data in research publications, and propose that the creation of a public MEA data repository to enable collaborative data sharing would be of great benefit to the iPSC disease modeling community. Close https://www.mdpi.com/2079-7737/11/2/316 doi:10.3390/biology11020316 Close
2021
	Hruska-Plochan, Marian; Betz, Katharina M; Ronchi, Silvia; Wiersma, Vera I; Maniecka, Zuzanna; Hock, Eva-Maria; Laferriere, Florent; Sahadevan, Sonu; Hoop, Vanessa; Delvendahl, Igor; Panatta, Martina; van der Bourg, Alexander; Bohaciakova, Dasa; Frontzek, Karl; Aguzzi, Adriano; Lashley, Tammaryn; Robinson, Mark D; Karayannis, Theofanis; Mueller, Martin; Hierlemann, Andreas; Polymenidou, Magdalini Human neural networks with sparse TDP-43 pathology reveal NPTX2 misregulation in ALS/FTLD Journal Article BioRxiv, 2021. Abstract \| Links \| BibTeX \| Tags: Inhibitory Neurons, MEA Technology, Neuronal Networks @article{Hruska-Plochan2021, title = {Human neural networks with sparse TDP-43 pathology reveal NPTX2 misregulation in ALS/FTLD}, author = {Marian Hruska-Plochan and Katharina M. Betz and Silvia Ronchi and Vera I. Wiersma and Zuzanna Maniecka and Eva-Maria Hock and Florent Laferriere and Sonu Sahadevan and Vanessa Hoop and Igor Delvendahl and Martina Panatta and Alexander van der Bourg and Dasa Bohaciakova and Karl Frontzek and Adriano Aguzzi and Tammaryn Lashley and Mark D. Robinson and Theofanis Karayannis and Martin Mueller and Andreas Hierlemann and Magdalini Polymenidou}, url = {https://doi.org/10.1101/2021.12.08.471089}, doi = {10.1101/2021.12.08.471089}, year = {2021}, date = {2021-12-09}, journal = {BioRxiv}, abstract = {Human cellular models of neurodegeneration require reproducibility and longevity, which is necessary for simulating these age-dependent diseases. Such systems are particularly needed for TDP-43 proteinopathies1,2, which involve human-specific mechanisms3–6 that cannot be directly studied in animal models. To explore the emergence and consequences of TDP-43 pathologies, we generated iPSC-derived, colony morphology neural stem cells (iCoMoNSCs) via manual selection of neural precursors7. Single-cell transcriptomics (scRNA-seq) and comparison to independent NSCs8, showed that iCoMoNSCs are uniquely homogenous and self-renewing. Differentiated iCoMoNSCs formed a self-organized multicellular system consisting of synaptically connected and electrophysiologically active neurons, which matured into long-lived functional networks. Neuronal and glial maturation in iCoMoNSC-derived cultures was similar to that of cortical organoids9. Overexpression of wild-type TDP-43 in a minority of iCoMoNSC-derived neurons led to progressive fragmentation and aggregation, resulting in loss of function and neurotoxicity. scRNA-seq revealed a novel set of misregulated RNA targets coinciding in both TDP-43 overexpressing neurons and patient brains exhibiting loss of nuclear TDP-43. The strongest misregulated target encoded for the synaptic protein NPTX2, which was consistently misaccumulated in ALS and FTLD patient neurons with TDP-43 pathology. Our work directly links TDP-43 misregulation and NPTX2 accumulation, thereby highlighting a new pathway of neurotoxicity.}, keywords = {Inhibitory Neurons, MEA Technology, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Human cellular models of neurodegeneration require reproducibility and longevity, which is necessary for simulating these age-dependent diseases. Such systems are particularly needed for TDP-43 proteinopathies1,2, which involve human-specific mechanisms3–6 that cannot be directly studied in animal models. To explore the emergence and consequences of TDP-43 pathologies, we generated iPSC-derived, colony morphology neural stem cells (iCoMoNSCs) via manual selection of neural precursors7. Single-cell transcriptomics (scRNA-seq) and comparison to independent NSCs8, showed that iCoMoNSCs are uniquely homogenous and self-renewing. Differentiated iCoMoNSCs formed a self-organized multicellular system consisting of synaptically connected and electrophysiologically active neurons, which matured into long-lived functional networks. Neuronal and glial maturation in iCoMoNSC-derived cultures was similar to that of cortical organoids9. Overexpression of wild-type TDP-43 in a minority of iCoMoNSC-derived neurons led to progressive fragmentation and aggregation, resulting in loss of function and neurotoxicity. scRNA-seq revealed a novel set of misregulated RNA targets coinciding in both TDP-43 overexpressing neurons and patient brains exhibiting loss of nuclear TDP-43. The strongest misregulated target encoded for the synaptic protein NPTX2, which was consistently misaccumulated in ALS and FTLD patient neurons with TDP-43 pathology. Our work directly links TDP-43 misregulation and NPTX2 accumulation, thereby highlighting a new pathway of neurotoxicity. Close https://doi.org/10.1101/2021.12.08.471089 doi:10.1101/2021.12.08.471089 Close
	Kagan, Brett J; Kitchen, Andy C; Tran, Nhi T; Parker, Bradyn J; Bhat, Anjali; Rollo, Ben; Razi, Adeel; Friston, Karl J In vitro neurons learn and exhibit sentience when embodied in a simulated game-world Journal Article bioRxiv, 2021. Abstract \| Links \| BibTeX \| Tags: 2D Neuronal Culture, Activity Scan Assay, closed loop stimulation, HD-MEA, In-Vitro, IPSC, MaxOne, MEA Technology, Network Assay, Neuronal Networks, Primary Neuronal Cell Culture, Stimulation @article{Kagan2021b, title = {In vitro neurons learn and exhibit sentience when embodied in a simulated game-world}, author = {Brett J. Kagan and Andy C. Kitchen and Nhi T. Tran and Bradyn J. Parker and Anjali Bhat and Ben Rollo and Adeel Razi and Karl J. Friston}, url = {https://www.biorxiv.org/content/10.1101/2021.12.02.471005v2}, doi = {10.1101/2021.12.02.471005}, year = {2021}, date = {2021-12-03}, journal = {bioRxiv}, abstract = {Integrating neurons into digital systems to leverage their innate intelligence may enable performance infeasible with silicon alone, along with providing insight into the cellular origin of intelligence. We developed DishBrain, a system which exhibits natural intelligence by harnessing the inherent adaptive computation of neurons in a structured environment. In vitro neural networks from human or rodent origins, are integrated with in silico computing via high-density multielectrode array. Through electrophysiological stimulation and recording, cultures were embedded in a simulated game-world, mimicking the arcade game ‘Pong’. Applying a previously untestable theory of active inference via the Free Energy Principle, we found that learning was apparent within five minutes of real-time gameplay, not observed in control conditions. Further experiments demonstrate the importance of closed-loop structured feedback in eliciting learning over time. Cultures display the ability to self-organise in a goal-directed manner in response to sparse sensory information about the consequences of their actions.}, keywords = {2D Neuronal Culture, Activity Scan Assay, closed loop stimulation, HD-MEA, In-Vitro, IPSC, MaxOne, MEA Technology, Network Assay, Neuronal Networks, Primary Neuronal Cell Culture, Stimulation}, pubstate = {published}, tppubtype = {article} } Close Integrating neurons into digital systems to leverage their innate intelligence may enable performance infeasible with silicon alone, along with providing insight into the cellular origin of intelligence. We developed DishBrain, a system which exhibits natural intelligence by harnessing the inherent adaptive computation of neurons in a structured environment. In vitro neural networks from human or rodent origins, are integrated with in silico computing via high-density multielectrode array. Through electrophysiological stimulation and recording, cultures were embedded in a simulated game-world, mimicking the arcade game ‘Pong’. Applying a previously untestable theory of active inference via the Free Energy Principle, we found that learning was apparent within five minutes of real-time gameplay, not observed in control conditions. Further experiments demonstrate the importance of closed-loop structured feedback in eliciting learning over time. Cultures display the ability to self-organise in a goal-directed manner in response to sparse sensory information about the consequences of their actions. Close https://www.biorxiv.org/content/10.1101/2021.12.02.471005v2 doi:10.1101/2021.12.02.471005 Close
	Kubota, Tomoyuki; Takahashi, Hirokazu; and Nakajima, Kohei Unifying framework for information processing in stochastically driven dynamical systems Journal Article Physical Review Research, 2021. Abstract \| Links \| BibTeX \| Tags: 2D Neuronal Culture, HD-MEA, MaxOne, Primary Neuronal Cell Culture, Stimulation @article{Kubota2023, title = {Unifying framework for information processing in stochastically driven dynamical systems}, author = {Tomoyuki Kubota and Hirokazu Takahashi and and Kohei Nakajima}, url = {https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.3.043135}, doi = {https://doi.org/10.1103/PhysRevResearch.3.043135}, year = {2021}, date = {2021-11-23}, journal = {Physical Review Research}, abstract = {A dynamical system is an information processing apparatus that encodes input streams from the external environment to its state and processes them through state transitions. The information processing capacity (IPC) is an excellent tool that comprehensively evaluates these processed inputs, providing details of unknown information processing in black box systems; however, this measure can be applied only to time-invariant systems. This paper extends the applicable range to time-variant systems and further reveals that the IPC is equivalent to coefficients of polynomial chaos (PC) expansion in more general dynamical systems. To achieve this objective, we tackle three issues. First, we establish a connection between the IPC for time-invariant systems and PC expansion, which is a type of polynomial expansion using orthogonal functions of input history as bases. We prove that the IPC corresponds to the squared norm of the coefficient vector of the basis in the PC expansion. Second, we show that an input following an arbitrary distribution can be used for the IPC, removing previous restrictions to specific input distributions. Third, we extend the conventional orthogonal bases to functions of both time and input history and propose the IPC for time-variant systems. To show the significance of our approach, we demonstrate that our measure can reveal information representations in not only machine learning networks but also a real, cultured neural network. Our generalized measure paves the way for unveiling the information processing capabilities of a wide variety of physical dynamics which have been left behind in nature.}, keywords = {2D Neuronal Culture, HD-MEA, MaxOne, Primary Neuronal Cell Culture, Stimulation}, pubstate = {published}, tppubtype = {article} } Close A dynamical system is an information processing apparatus that encodes input streams from the external environment to its state and processes them through state transitions. The information processing capacity (IPC) is an excellent tool that comprehensively evaluates these processed inputs, providing details of unknown information processing in black box systems; however, this measure can be applied only to time-invariant systems. This paper extends the applicable range to time-variant systems and further reveals that the IPC is equivalent to coefficients of polynomial chaos (PC) expansion in more general dynamical systems. To achieve this objective, we tackle three issues. First, we establish a connection between the IPC for time-invariant systems and PC expansion, which is a type of polynomial expansion using orthogonal functions of input history as bases. We prove that the IPC corresponds to the squared norm of the coefficient vector of the basis in the PC expansion. Second, we show that an input following an arbitrary distribution can be used for the IPC, removing previous restrictions to specific input distributions. Third, we extend the conventional orthogonal bases to functions of both time and input history and propose the IPC for time-variant systems. To show the significance of our approach, we demonstrate that our measure can reveal information representations in not only machine learning networks but also a real, cultured neural network. Our generalized measure paves the way for unveiling the information processing capabilities of a wide variety of physical dynamics which have been left behind in nature. Close https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.3.043135 doi:https://doi.org/10.1103/PhysRevResearch.3.043135 Close
	Sharf, Tal; van der Molen, Tjitse; Glasauer, Stella M K; Guzman, Elmer; Buccino, Alessio P; Luna, Gabriel; Cheng, Zhouwei; Audouard, Morgane; Ranasinghe, Kamalini G; Kudo, Kiwamu; Nagarajan, Srikantan S; Tovar, Kenneth R; Petzold, Linda R; Hierlemann, Andreas; Hansma, Paul K; Kosik, Kenneth S Human brain organoid networks Journal Article bioRxiv, 2021. Abstract \| Links \| BibTeX \| Tags: 3D Culture, Activity Scan Assay, HD-MEA, IPSC, MaxOne, MEA Technology, Organoids, Slices, Spike Sorting @article{Sharf2021b, title = {Human brain organoid networks}, author = {Tal Sharf and Tjitse van der Molen and Stella M.K. Glasauer and Elmer Guzman and Alessio P. Buccino and Gabriel Luna and Zhouwei Cheng and Morgane Audouard and Kamalini G. Ranasinghe and Kiwamu Kudo and Srikantan S. Nagarajan and Kenneth R. Tovar and Linda R. Petzold and Andreas Hierlemann and Paul K. Hansma and Kenneth S. Kosik}, url = {https://www.biorxiv.org/content/10.1101/2021.01.28.428643v2}, doi = {10.1101/2021.01.28.428643}, year = {2021}, date = {2021-09-23}, journal = {bioRxiv}, abstract = {Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiological behavior of neuronal circuits within organoids remains relatively under-explored. With high-density CMOS microelectrode arrays (26,400 electrodes) and shank electrodes (960 electrodes), we probed broadband and three-dimensional extracellular field recordings generated by spontaneous activity of human brain organoids. These recordings simultaneously captured local field potentials (LFPs) and single-unit activity extracted through spike sorting. From spiking activity, we estimated a directed functional connectivity graph of synchronous neural network activity, which showed a large number of weak functional connections enmeshed within a network skeleton of significantly fewer strong connections. Treatment of the organoid with a benzodiazepine induced a reproducible signature response that shortened the inter-burst intervals, increased the uniformity of the firing pattern within each burst and decreased the population of weakly connected edges. Simultaneously examining the spontaneous LFPs and their phase alignment to spiking showed that spike bursts were coherent with theta oscillations in the LFPs. Our results demonstrate that human brain organoids have self-organized neuronal assemblies of sufficient size, cellular orientation, and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug mechanisms, and the effects of external stimuli upon neuronal networks.}, keywords = {3D Culture, Activity Scan Assay, HD-MEA, IPSC, MaxOne, MEA Technology, Organoids, Slices, Spike Sorting}, pubstate = {published}, tppubtype = {article} } Close Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiological behavior of neuronal circuits within organoids remains relatively under-explored. With high-density CMOS microelectrode arrays (26,400 electrodes) and shank electrodes (960 electrodes), we probed broadband and three-dimensional extracellular field recordings generated by spontaneous activity of human brain organoids. These recordings simultaneously captured local field potentials (LFPs) and single-unit activity extracted through spike sorting. From spiking activity, we estimated a directed functional connectivity graph of synchronous neural network activity, which showed a large number of weak functional connections enmeshed within a network skeleton of significantly fewer strong connections. Treatment of the organoid with a benzodiazepine induced a reproducible signature response that shortened the inter-burst intervals, increased the uniformity of the firing pattern within each burst and decreased the population of weakly connected edges. Simultaneously examining the spontaneous LFPs and their phase alignment to spiking showed that spike bursts were coherent with theta oscillations in the LFPs. Our results demonstrate that human brain organoids have self-organized neuronal assemblies of sufficient size, cellular orientation, and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug mechanisms, and the effects of external stimuli upon neuronal networks. Close https://www.biorxiv.org/content/10.1101/2021.01.28.428643v2 doi:10.1101/2021.01.28.428643 Close
	Schenke, Maren; Prause, Hélène-Christine; Bergforth, Wiebke; Przykopanski, Adina Human-Relevant Sensitivity of iPSC-Derived Human Motor Neurons to BoNT/A1 and B1 Journal Article toxins, 2021. Abstract \| Links \| BibTeX \| Tags: MaxOne @article{Schenke2021, title = {Human-Relevant Sensitivity of iPSC-Derived Human Motor Neurons to BoNT/A1 and B1}, author = {Maren Schenke and Hélène-Christine Prause and Wiebke Bergforth and Adina Przykopanski}, url = {https://www.mdpi.com/2072-6651/13/8/585}, doi = {https://doi.org/10.3390/toxins13080585}, year = {2021}, date = {2021-08-22}, journal = {toxins}, abstract = {The application of botulinum neurotoxins (BoNTs) for medical treatments necessitates a potency quantification of these lethal bacterial toxins, resulting in the use of a large number of test animals. Available alternative methods are limited in their relevance, as they are based on rodent cells or neuroblastoma cell lines or applicable for single toxin serotypes only. Here, human motor neurons (MNs), which are the physiological target of BoNTs, were generated from induced pluripotent stem cells (iPSCs) and compared to the neuroblastoma cell line SiMa, which is often used in cell-based assays for BoNT potency determination. In comparison with the mouse bioassay, human MNs exhibit a superior sensitivity to the BoNT serotypes A1 and B1 at levels that are reflective of human sensitivity. SiMa cells were able to detect BoNT/A1, but with much lower sensitivity than human MNs and appear unsuitable to detect any BoNT/B1 activity. The MNs used for these experiments were generated according to three differentiation protocols, which resulted in distinct sensitivity levels. Molecular parameters such as receptor protein concentration and electrical activity of the MNs were analyzed, but are not predictive for BoNT sensitivity. These results show that human MNs from several sources should be considered in BoNT testing and that human MNs are a physiologically relevant model, which could be used to optimize current BoNT potency testing.}, keywords = {MaxOne}, pubstate = {published}, tppubtype = {article} } Close The application of botulinum neurotoxins (BoNTs) for medical treatments necessitates a potency quantification of these lethal bacterial toxins, resulting in the use of a large number of test animals. Available alternative methods are limited in their relevance, as they are based on rodent cells or neuroblastoma cell lines or applicable for single toxin serotypes only. Here, human motor neurons (MNs), which are the physiological target of BoNTs, were generated from induced pluripotent stem cells (iPSCs) and compared to the neuroblastoma cell line SiMa, which is often used in cell-based assays for BoNT potency determination. In comparison with the mouse bioassay, human MNs exhibit a superior sensitivity to the BoNT serotypes A1 and B1 at levels that are reflective of human sensitivity. SiMa cells were able to detect BoNT/A1, but with much lower sensitivity than human MNs and appear unsuitable to detect any BoNT/B1 activity. The MNs used for these experiments were generated according to three differentiation protocols, which resulted in distinct sensitivity levels. Molecular parameters such as receptor protein concentration and electrical activity of the MNs were analyzed, but are not predictive for BoNT sensitivity. These results show that human MNs from several sources should be considered in BoNT testing and that human MNs are a physiologically relevant model, which could be used to optimize current BoNT potency testing. Close https://www.mdpi.com/2072-6651/13/8/585 doi:https://doi.org/10.3390/toxins13080585 Close
	Sundberg, Maria; Pinson, Hannah; Smith, Richard S; Winden, Kellen D; Venugopal, Pooja; Tai, Derek J C; Gusella, James F; Talkowski, Michael E; Walsh, Christopher A; Tegmark, Max; Sahin, Mustafa 16p11.2 deletion is associated with hyperactivation of human iPSC-derived dopaminergic neuron networks and is rescued by RHOA inhibition in vitro Journal Article Nature Communications, 12 (2897 ), 2021. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, IPSC, MaxOne @article{Sundberg2021, title = {16p11.2 deletion is associated with hyperactivation of human iPSC-derived dopaminergic neuron networks and is rescued by RHOA inhibition in vitro}, author = {Maria Sundberg and Hannah Pinson and Richard S. Smith and Kellen D. Winden and Pooja Venugopal and Derek J. C. Tai and James F. Gusella and Michael E. Talkowski and Christopher A. Walsh and Max Tegmark and Mustafa Sahin }, url = {https://www.nature.com/articles/s41467-021-23113-z}, doi = {10.1038/s41467-021-23113-z}, year = {2021}, date = {2021-05-18}, journal = {Nature Communications}, volume = {12}, number = {2897 }, abstract = {Reciprocal copy number variations (CNVs) of 16p11.2 are associated with a wide spectrum of neuropsychiatric and neurodevelopmental disorders. Here, we use human induced pluripotent stem cells (iPSCs)-derived dopaminergic (DA) neurons carrying CNVs of 16p11.2 duplication (16pdup) and 16p11.2 deletion (16pdel), engineered using CRISPR-Cas9. We show that 16pdel iPSC-derived DA neurons have increased soma size and synaptic marker expression compared to isogenic control lines, while 16pdup iPSC-derived DA neurons show deficits in neuronal differentiation and reduced synaptic marker expression. The 16pdel iPSC-derived DA neurons have impaired neurophysiological properties. The 16pdel iPSC-derived DA neuronal networks are hyperactive and have increased bursting in culture compared to controls. We also show that the expression of RHOA is increased in the 16pdel iPSC-derived DA neurons and that treatment with a specific RHOA-inhibitor, Rhosin, rescues the network activity of the 16pdel iPSC-derived DA neurons. Our data suggest that 16p11.2 deletion-associated iPSC-derived DA neuron hyperactivation can be rescued by RHOA inhibition.}, keywords = {ETH-CMOS-MEA, IPSC, MaxOne}, pubstate = {published}, tppubtype = {article} } Close Reciprocal copy number variations (CNVs) of 16p11.2 are associated with a wide spectrum of neuropsychiatric and neurodevelopmental disorders. Here, we use human induced pluripotent stem cells (iPSCs)-derived dopaminergic (DA) neurons carrying CNVs of 16p11.2 duplication (16pdup) and 16p11.2 deletion (16pdel), engineered using CRISPR-Cas9. We show that 16pdel iPSC-derived DA neurons have increased soma size and synaptic marker expression compared to isogenic control lines, while 16pdup iPSC-derived DA neurons show deficits in neuronal differentiation and reduced synaptic marker expression. The 16pdel iPSC-derived DA neurons have impaired neurophysiological properties. The 16pdel iPSC-derived DA neuronal networks are hyperactive and have increased bursting in culture compared to controls. We also show that the expression of RHOA is increased in the 16pdel iPSC-derived DA neurons and that treatment with a specific RHOA-inhibitor, Rhosin, rescues the network activity of the 16pdel iPSC-derived DA neurons. Our data suggest that 16p11.2 deletion-associated iPSC-derived DA neuron hyperactivation can be rescued by RHOA inhibition. Close https://www.nature.com/articles/s41467-021-23113-z doi:10.1038/s41467-021-23113-z Close
	Kajiwara Motoki; Nomura, Ritsuki; Goetze Felix; Kawabata Masanori; Isomura Yoshikazu; Akutsu Tatsuya; Shimono Masanori; Inhibitory neurons exhibit high controlling ability in the cortical microconnectome Journal Article PLOS Computational Biology, 2021. Abstract \| Links \| BibTeX \| Tags: Brain Slice, MaxOne @article{Kajiwara2021, title = {Inhibitory neurons exhibit high controlling ability in the cortical microconnectome}, author = {Kajiwara, Motoki; Nomura, Ritsuki; Goetze, Felix; Kawabata, Masanori; Isomura, Yoshikazu; Akutsu, Tatsuya; Shimono, Masanori; }, url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008846}, year = {2021}, date = {2021-04-08}, journal = {PLOS Computational Biology}, abstract = {The brain is a network system in which excitatory and inhibitory neurons keep activity bal- anced in the highly non-random connectivity pattern of the microconnectome. It is well known that the relative percentage of inhibitory neurons is much smaller than excitatory neu- rons in the cortex. So, in general, how inhibitory neurons can keep the balance with the sur- rounding excitatory neurons is an important question. There is much accumulated knowledge about this fundamental question. This study quantitatively evaluated the rela- tively higher functional contribution of inhibitory neurons in terms of not only properties of individual neurons, such as firing rate, but also in terms of topological mechanisms and con- trolling ability on other excitatory neurons. We combined simultaneous electrical recording (~2.5 hours) of ~1000 neurons in vitro, and quantitative evaluation of neuronal interactions including excitatory-inhibitory categorization. This study accurately defined recording brain anatomical targets, such as brain regions and cortical layers, by inter-referring MRI and immunostaining recordings. The interaction networks enabled us to quantify topological influence of individual neurons, in terms of controlling ability to other neurons. Especially, the result indicated that highly influential inhibitory neurons show higher controlling ability of other neurons than excitatory neurons, and are relatively often distributed in deeper layers of the cortex. Furthermore, the neurons having high controlling ability are more effectively limited in number than central nodes of k-cores, and these neurons also participate in more clustered motifs. In summary, this study suggested that the high controlling ability of inhibi- tory neurons is a key mechanism to keep balance with a large number of other excitatory neurons beyond simple higher firing rate. Application of the selection method of limited important neurons would be also applicable for the ability to effectively and selectively stimu- late E/I imbalanced disease states.}, keywords = {Brain Slice, MaxOne}, pubstate = {published}, tppubtype = {article} } Close The brain is a network system in which excitatory and inhibitory neurons keep activity bal- anced in the highly non-random connectivity pattern of the microconnectome. It is well known that the relative percentage of inhibitory neurons is much smaller than excitatory neu- rons in the cortex. So, in general, how inhibitory neurons can keep the balance with the sur- rounding excitatory neurons is an important question. There is much accumulated knowledge about this fundamental question. This study quantitatively evaluated the rela- tively higher functional contribution of inhibitory neurons in terms of not only properties of individual neurons, such as firing rate, but also in terms of topological mechanisms and con- trolling ability on other excitatory neurons. We combined simultaneous electrical recording (~2.5 hours) of ~1000 neurons in vitro, and quantitative evaluation of neuronal interactions including excitatory-inhibitory categorization. This study accurately defined recording brain anatomical targets, such as brain regions and cortical layers, by inter-referring MRI and immunostaining recordings. The interaction networks enabled us to quantify topological influence of individual neurons, in terms of controlling ability to other neurons. Especially, the result indicated that highly influential inhibitory neurons show higher controlling ability of other neurons than excitatory neurons, and are relatively often distributed in deeper layers of the cortex. Furthermore, the neurons having high controlling ability are more effectively limited in number than central nodes of k-cores, and these neurons also participate in more clustered motifs. In summary, this study suggested that the high controlling ability of inhibi- tory neurons is a key mechanism to keep balance with a large number of other excitatory neurons beyond simple higher firing rate. Application of the selection method of limited important neurons would be also applicable for the ability to effectively and selectively stimu- late E/I imbalanced disease states. Close https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008846 Close
	Yuan, Xinyue; Hierlemann, Andreas; Frey, Urs Extracellular Recording of Entire Neural Networks Using a Dual-Mode Microelectrode Array With 19,584 Electrodes and High SNR Journal Article IEEE, 2021. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, MEA Technology @article{Yuan2021, title = {Extracellular Recording of Entire Neural Networks Using a Dual-Mode Microelectrode Array With 19,584 Electrodes and High SNR}, author = {Xinyue Yuan and Andreas Hierlemann and Urs Frey}, url = {https://ieeexplore.ieee.org/document/9385387}, doi = {10.1109/JSSC.2021.3066043}, year = {2021}, date = {2021-03-24}, journal = {IEEE}, abstract = {Electrophysiological research on neural networks and their activity focuses on the recording and analysis of large data sets that include information of thousands of neurons. CMOS microelectrode arrays (MEAs) feature thousands of electrodes at a spatial resolution on the scale of single cells and are, therefore, ideal tools to support neural-network research. Moreover, they offer high spatio-temporal resolution and signal-to-noise ratio (SNR) to capture all features and subcellular-resolution details of neuronal signaling. Here, we present a dual-mode (DM) MEA, which enables simultaneous: 1) full-frame readout from all electrodes and 2) high-SNR readout from an arbitrarily selectable subset of electrodes. The DM-MEA includes 19,584 electrodes, 19,584 full-frame recording channels with noise levels of 10.4 μVrms in the action potential (AP) frequency band (300 Hz-5 kHz), 246 low-noise recording channels with noise levels of 3.0 μVrms in the AP band and eight stimulation units. The capacity to simultaneously perform full-frame and high-SNR recordings endows the presented DM-MEA with great flexibility for various applications in neuroscience and pharmacology.}, keywords = {ETH-CMOS-MEA, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close Electrophysiological research on neural networks and their activity focuses on the recording and analysis of large data sets that include information of thousands of neurons. CMOS microelectrode arrays (MEAs) feature thousands of electrodes at a spatial resolution on the scale of single cells and are, therefore, ideal tools to support neural-network research. Moreover, they offer high spatio-temporal resolution and signal-to-noise ratio (SNR) to capture all features and subcellular-resolution details of neuronal signaling. Here, we present a dual-mode (DM) MEA, which enables simultaneous: 1) full-frame readout from all electrodes and 2) high-SNR readout from an arbitrarily selectable subset of electrodes. The DM-MEA includes 19,584 electrodes, 19,584 full-frame recording channels with noise levels of 10.4 μVrms in the action potential (AP) frequency band (300 Hz-5 kHz), 246 low-noise recording channels with noise levels of 3.0 μVrms in the AP band and eight stimulation units. The capacity to simultaneously perform full-frame and high-SNR recordings endows the presented DM-MEA with great flexibility for various applications in neuroscience and pharmacology. Close https://ieeexplore.ieee.org/document/9385387 doi:10.1109/JSSC.2021.3066043 Close
	Ronchi, Silvia; Buccino, Alessio Paolo; Prack, Gustavo; Kumar, Sreedhar Saseendran; Schröter, Manuel; Fiscella, Michele; Hierlemann, Andreas Microelectrode Arrays: Electrophysiological Phenotype Characterization of Human iPSC-Derived Neuronal Cell Lines by Means of High-Density Microelectrode Arrays Journal Article Advanced Biology, 5 (3), 2021. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, IPSC @article{Ronchi2021, title = {Microelectrode Arrays: Electrophysiological Phenotype Characterization of Human iPSC-Derived Neuronal Cell Lines by Means of High-Density Microelectrode Arrays}, author = {Silvia Ronchi and Alessio Paolo Buccino and Gustavo Prack and Sreedhar Saseendran Kumar and Manuel Schröter and Michele Fiscella and Andreas Hierlemann}, url = {https://onlinelibrary.wiley.com/doi/10.1002/adbi.202000223}, doi = {10.1002/adbi.202000223}, year = {2021}, date = {2021-03-17}, journal = {Advanced Biology}, volume = {5}, number = {3}, abstract = {In article number 2000223, Silvia Ronchi, Michele Fiscella, and co-workers show neurons plated on a high-density microelectrode array. The small electrode size and the tight spacing between the 26 400 electrodes enable functional extracellular electrophysiological characterization of neurons across scales, from subcellular-resolution features, like axons and dendrites, through individual neuronal cells to entire networks.}, keywords = {ETH-CMOS-MEA, IPSC}, pubstate = {published}, tppubtype = {article} } Close In article number 2000223, Silvia Ronchi, Michele Fiscella, and co-workers show neurons plated on a high-density microelectrode array. The small electrode size and the tight spacing between the 26 400 electrodes enable functional extracellular electrophysiological characterization of neurons across scales, from subcellular-resolution features, like axons and dendrites, through individual neuronal cells to entire networks. Close https://onlinelibrary.wiley.com/doi/10.1002/adbi.202000223 doi:10.1002/adbi.202000223 Close
	Sharf, Tal; van der Molen, Tjitse; Guzman, Elmer; Glasauer, Stella M K; Luna, Gabriel; Cheng, Zhouwei; Audouard, Morgane; Ranasinghe, Kamalini G; Kudo, Kiwamu; Nagarajan, Srikantan S; Tovar, Kenneth R; Petzold, Linda R; Hansma, Paul K; Kosik, Kenneth S Intrinsic network activity in human brain organoids Journal Article BioRxiv, 2021. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Neuronal Networks, Organoids @article{Sharf2021, title = {Intrinsic network activity in human brain organoids}, author = {Tal Sharf and Tjitse van der Molen and Elmer Guzman and Stella M.K. Glasauer and Gabriel Luna and Zhouwei Cheng and Morgane Audouard and Kamalini G. Ranasinghe and Kiwamu Kudo and Srikantan S. Nagarajan and Kenneth R. Tovar and Linda R. Petzold and Paul K. Hansma and Kenneth S. Kosik}, url = {https://www.biorxiv.org/content/10.1101/2021.01.28.428643v1}, doi = {10.1101/2021.01.28.428643}, year = {2021}, date = {2021-01-28}, journal = {BioRxiv}, abstract = {Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiological behavior of neuronal circuits within organoids remains relatively under-explored. With high-density CMOS microelectrode arrays and shank electrodes, we probed broadband and three-dimensional spontaneous activity of human brain organoids. These recordings simultaneously captured local field potentials (LFPs) and single unit activity. From spiking activity, we estimated a directed functional connectivity graph of synchronous neural network activity which showed a large number of weak functional connections enmeshed within a network skeleton of significantly fewer strong connections. Increasing the intrinsic inhibitory tone with a benzodiazepine altered the functional network graph of the organoid by suppressing the network skeleton. Simultaneously examining the spontaneous LFPs and their phase alignment to spiking showed that spike bursts were coherent with theta oscillations in the LFPs. An ensemble of spikes phase-locked to theta frequency oscillations were strongly interconnected as a sub-network within the larger network in which they were embedded. Our results demonstrate that human brain organoids have self-organized neuronal assemblies of sufficient size, cellular orientation, and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug mechanisms, and the effects of external stimuli upon neuronal networks.}, keywords = {ETH-CMOS-MEA, Neuronal Networks, Organoids}, pubstate = {published}, tppubtype = {article} } Close Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiological behavior of neuronal circuits within organoids remains relatively under-explored. With high-density CMOS microelectrode arrays and shank electrodes, we probed broadband and three-dimensional spontaneous activity of human brain organoids. These recordings simultaneously captured local field potentials (LFPs) and single unit activity. From spiking activity, we estimated a directed functional connectivity graph of synchronous neural network activity which showed a large number of weak functional connections enmeshed within a network skeleton of significantly fewer strong connections. Increasing the intrinsic inhibitory tone with a benzodiazepine altered the functional network graph of the organoid by suppressing the network skeleton. Simultaneously examining the spontaneous LFPs and their phase alignment to spiking showed that spike bursts were coherent with theta oscillations in the LFPs. An ensemble of spikes phase-locked to theta frequency oscillations were strongly interconnected as a sub-network within the larger network in which they were embedded. Our results demonstrate that human brain organoids have self-organized neuronal assemblies of sufficient size, cellular orientation, and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug mechanisms, and the effects of external stimuli upon neuronal networks. Close https://www.biorxiv.org/content/10.1101/2021.01.28.428643v1 doi:10.1101/2021.01.28.428643 Close
2020
	Idrees, Saad; Münch, Thomas A Different contrast encoding in ON and OFF visual pathways Journal Article BioRxiv, 2020. Abstract \| Links \| BibTeX \| Tags: MaxOne, Retina @article{Idrees2020b, title = {Different contrast encoding in ON and OFF visual pathways}, author = {Saad Idrees and Thomas A. Münch }, url = {https://www.biorxiv.org/content/10.1101/2020.11.25.398230v1}, doi = {10.1101/2020.11.25.398230}, year = {2020}, date = {2020-11-26}, journal = {BioRxiv}, abstract = {Subjective visual experience builds on sensory encoding of light reflected by different objects in our environment. Most retinal ganglion cells encode changes in light intensity, quantified as contrast, rather than the absolute intensity. Mathematically, contrast is often defined as a relative change in light intensity. Activity in the visual system and perceptual responses are usually explained with such definitions of contrast. Here, for the first time, we explicitly explored how contrast is actually represented in the visual system. Using mouse retina electrophysiology, we show that response strength of OFF retinal ganglion cells does not represent relative, but absolute changes in light intensity. ON RGC response strength is governed by a combination of absolute and relative change in light intensity. This is true for a wide range of ambient light levels, at least from scotopic to high mesopic regimes. Consequently, light decrements and increments are represented asymmetrically in the retina, which may explain the asymmetries in responses to negative and positive contrast observed throughout the visual system. These findings may help to more thoroughly design and interpret vision science studies where responses are driven by contrast of the visual stimuli.}, keywords = {MaxOne, Retina}, pubstate = {published}, tppubtype = {article} } Close Subjective visual experience builds on sensory encoding of light reflected by different objects in our environment. Most retinal ganglion cells encode changes in light intensity, quantified as contrast, rather than the absolute intensity. Mathematically, contrast is often defined as a relative change in light intensity. Activity in the visual system and perceptual responses are usually explained with such definitions of contrast. Here, for the first time, we explicitly explored how contrast is actually represented in the visual system. Using mouse retina electrophysiology, we show that response strength of OFF retinal ganglion cells does not represent relative, but absolute changes in light intensity. ON RGC response strength is governed by a combination of absolute and relative change in light intensity. This is true for a wide range of ambient light levels, at least from scotopic to high mesopic regimes. Consequently, light decrements and increments are represented asymmetrically in the retina, which may explain the asymmetries in responses to negative and positive contrast observed throughout the visual system. These findings may help to more thoroughly design and interpret vision science studies where responses are driven by contrast of the visual stimuli. Close https://www.biorxiv.org/content/10.1101/2020.11.25.398230v1 doi:10.1101/2020.11.25.398230 Close
	Battaglia, Chiara R; Cursano, Silvia; Calzia, Enrico; Catanese, Alberto; Boeckers, Tobias M Corticotropin-releasing hormone (CRH) alters mitochondrial morphology and function by activating the NF-kB-DRP1 axis in hippocampal neurons Journal Article Cell Death & Disease, 2020. Abstract \| Links \| BibTeX \| Tags: MaxTwo @article{Battaglia2020, title = {Corticotropin-releasing hormone (CRH) alters mitochondrial morphology and function by activating the NF-kB-DRP1 axis in hippocampal neurons}, author = {Chiara R. Battaglia and Silvia Cursano and Enrico Calzia and Alberto Catanese and Tobias M. Boeckers }, url = {https://www.nature.com/articles/s41419-020-03204-3}, doi = {https://doi.org/10.1038/s41419-020-03204-3}, year = {2020}, date = {2020-11-23}, journal = {Cell Death & Disease}, abstract = {Neuronal stress-adaptation combines multiple molecular responses. We have previously reported that thorax trauma induces a transient loss of hippocampal excitatory synapses mediated by the local release of the stress-related hormone corticotropin-releasing hormone (CRH). Since a physiological synaptic activity relies also on mitochondrial functionality, we investigated the direct involvement of mitochondria in the (mal)-adaptive changes induced by the activation of neuronal CRH receptors 1 (CRHR1). We observed, in vivo and in vitro, a significant shift of mitochondrial dynamics towards fission, which correlated with increased swollen mitochondria and aberrant cristae. These morphological changes, which are associated with increased NF-kB activity and nitric oxide concentrations, correlated with a pronounced reduction of mitochondrial activity. However, ATP availability was unaltered, suggesting that neurons maintain a physiological energy metabolism to preserve them from apoptosis under CRH exposure. Our findings demonstrate that stress-induced CRHR1 activation leads to strong, but reversible, modifications of mitochondrial dynamics and morphology. These alterations are accompanied by bioenergetic defects and the reduction of neuronal activity, which are linked to increased intracellular oxidative stress, and to the activation of the NF-kB/c-Abl/DRP1 axis. }, keywords = {MaxTwo}, pubstate = {published}, tppubtype = {article} } Close Neuronal stress-adaptation combines multiple molecular responses. We have previously reported that thorax trauma induces a transient loss of hippocampal excitatory synapses mediated by the local release of the stress-related hormone corticotropin-releasing hormone (CRH). Since a physiological synaptic activity relies also on mitochondrial functionality, we investigated the direct involvement of mitochondria in the (mal)-adaptive changes induced by the activation of neuronal CRH receptors 1 (CRHR1). We observed, in vivo and in vitro, a significant shift of mitochondrial dynamics towards fission, which correlated with increased swollen mitochondria and aberrant cristae. These morphological changes, which are associated with increased NF-kB activity and nitric oxide concentrations, correlated with a pronounced reduction of mitochondrial activity. However, ATP availability was unaltered, suggesting that neurons maintain a physiological energy metabolism to preserve them from apoptosis under CRH exposure. Our findings demonstrate that stress-induced CRHR1 activation leads to strong, but reversible, modifications of mitochondrial dynamics and morphology. These alterations are accompanied by bioenergetic defects and the reduction of neuronal activity, which are linked to increased intracellular oxidative stress, and to the activation of the NF-kB/c-Abl/DRP1 axis. Close https://www.nature.com/articles/s41419-020-03204-3 doi:https://doi.org/10.1038/s41419-020-03204-3 Close
	Ricci, Chiara; Frey, Urs; Obien, Marie Engelene J MAPSYNE: Miniaturized micropipette system combined with high-density microelectrode arrays for automated manipulation of neuronal networks in-vitro Journal Article IEEE, 2020. Abstract \| Links \| BibTeX \| Tags: Activity Scan Assay, HD-MEA, MaxOne, MEA Technology @article{Ricci2020, title = {MAPSYNE: Miniaturized micropipette system combined with high-density microelectrode arrays for automated manipulation of neuronal networks in-vitro}, author = {Chiara Ricci and Urs Frey and Marie Engelene J. Obien}, url = {https://ieeexplore.ieee.org/document/9175797/}, doi = {10.1109/EMBC44109.2020.9175797}, year = {2020}, date = {2020-10-08}, journal = {IEEE}, abstract = {We present MAPSYNE, a miniaturized and automated system combining a high-density microelectrode array (HD-MEA) and a movable micropipette for studying, monitoring, and perturbing neurons in vitro. The system involves an all-electrical approach to automatically move a glass micropipette towards a target location on the HD-MEA surface, without the need for a microscope. Two methods of performing blind navigation are employed, (i) stop-measure-go approach wherein the pipette moves for a predefined distance before measuring its location then the process is repeated until the pipette reaches its destination, and (ii) predictive approach wherein the pipette is continuously tracked and moved. This automated system can be applied for unsupervised single-cell manipulation of neurons in a network, such as electroporation and local delivery of compounds.}, keywords = {Activity Scan Assay, HD-MEA, MaxOne, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close We present MAPSYNE, a miniaturized and automated system combining a high-density microelectrode array (HD-MEA) and a movable micropipette for studying, monitoring, and perturbing neurons in vitro. The system involves an all-electrical approach to automatically move a glass micropipette towards a target location on the HD-MEA surface, without the need for a microscope. Two methods of performing blind navigation are employed, (i) stop-measure-go approach wherein the pipette moves for a predefined distance before measuring its location then the process is repeated until the pipette reaches its destination, and (ii) predictive approach wherein the pipette is continuously tracked and moved. This automated system can be applied for unsupervised single-cell manipulation of neurons in a network, such as electroporation and local delivery of compounds. Close https://ieeexplore.ieee.org/document/9175797/ doi:10.1109/EMBC44109.2020.9175797 Close
	Yuan, Xinyue; Schröter, Manuel; Obien, Marie Engelene J; Fiscella, Michele; Gong, Wei; Kikuchi, Tetsuhiro; Odawara, Aoi; Noji, Shuhei; Suzuki, Ikuro; Takahashi, Jun; Hierlemann, Andreas; Frey, Urs Versatile live-cell activity analysis platform for characterization of neuronal dynamics at single-cell and network level Journal Article Nature Communications, 11 (4854), 2020. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, MEA Technology @article{Yuan2020, title = {Versatile live-cell activity analysis platform for characterization of neuronal dynamics at single-cell and network level}, author = {Xinyue Yuan and Manuel Schröter and Marie Engelene J. Obien and Michele Fiscella and Wei Gong and Tetsuhiro Kikuchi and Aoi Odawara and Shuhei Noji and Ikuro Suzuki and Jun Takahashi and Andreas Hierlemann and Urs Frey}, url = {https://www.nature.com/articles/s41467-020-18620-4#citeas}, doi = {10.1038/s41467-020-18620-4}, year = {2020}, date = {2020-09-25}, journal = {Nature Communications}, volume = {11}, number = {4854}, abstract = {Chronic imaging of neuronal networks in vitro has provided fundamental insights into mechanisms underlying neuronal function. Current labeling and optical imaging methods, however, cannot be used for continuous and long-term recordings of the dynamics and evolution of neuronal networks, as fluorescent indicators can cause phototoxicity. Here, we introduce a versatile platform for label-free, comprehensive and detailed electrophysiological live-cell imaging of various neurogenic cells and tissues over extended time scales. We report on a dual-mode high-density microelectrode array, which can simultaneously record in (i) full-frame mode with 19,584 recording sites and (ii) high-signal-to-noise mode with 246 channels. We set out to demonstrate the capabilities of this platform with recordings from primary and iPSC-derived neuronal cultures and tissue preparations over several weeks, providing detailed morpho-electrical phenotypic parameters at subcellular, cellular and network level. Moreover, we develop reliable analysis tools, which drastically increase the throughput to infer axonal morphology and conduction speed.}, keywords = {ETH-CMOS-MEA, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close Chronic imaging of neuronal networks in vitro has provided fundamental insights into mechanisms underlying neuronal function. Current labeling and optical imaging methods, however, cannot be used for continuous and long-term recordings of the dynamics and evolution of neuronal networks, as fluorescent indicators can cause phototoxicity. Here, we introduce a versatile platform for label-free, comprehensive and detailed electrophysiological live-cell imaging of various neurogenic cells and tissues over extended time scales. We report on a dual-mode high-density microelectrode array, which can simultaneously record in (i) full-frame mode with 19,584 recording sites and (ii) high-signal-to-noise mode with 246 channels. We set out to demonstrate the capabilities of this platform with recordings from primary and iPSC-derived neuronal cultures and tissue preparations over several weeks, providing detailed morpho-electrical phenotypic parameters at subcellular, cellular and network level. Moreover, we develop reliable analysis tools, which drastically increase the throughput to infer axonal morphology and conduction speed. Close https://www.nature.com/articles/s41467-020-18620-4#citeas doi:10.1038/s41467-020-18620-4 Close
	Kim, Eunhee; Jeon, Sungwoong; An, Hyun-Kyu; Mehrnoosh Kianpour, Seong-Woon Yu ; Kim, Jin-young; Rah, Jong-Cheol; Choi, Hongsoo A magnetically actuated microrobot for targeted neural cell delivery and selective connection of neural networks Journal Article Science Advances, 6 (39), 2020. Abstract \| Links \| BibTeX \| Tags: microrobot, Neuronal Networks @article{Kim2020, title = {A magnetically actuated microrobot for targeted neural cell delivery and selective connection of neural networks}, author = {Eunhee Kim and Sungwoong Jeon and Hyun-Kyu An and Mehrnoosh Kianpour, Seong-Woon Yu and Jin-young Kim and Jong-Cheol Rah and Hongsoo Choi}, url = {https://advances.sciencemag.org/content/6/39/eabb5696}, doi = {10.1126/sciadv.abb5696}, year = {2020}, date = {2020-09-25}, journal = {Science Advances}, volume = {6}, number = {39}, abstract = {There has been a great deal of interest in the development of technologies for actively manipulating neural networks in vitro, providing natural but simplified environments in a highly reproducible manner in which to study brain function and related diseases. Platforms for these in vitro neural networks require precise and selective neural connections at the target location, with minimal external influences, and measurement of neural activity to determine how neurons communicate. Here, we report a neuron-loaded microrobot for selective connection of neural networks via precise delivery to a gap between two neural clusters by an external magnetic field. In addition, the extracellular action potential was propagated from one cluster to the other through the neurons on the microrobot. The proposed technique shows the potential for use in experiments to understand how neurons communicate in the neural network by actively connecting neural clusters.}, keywords = {microrobot, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close There has been a great deal of interest in the development of technologies for actively manipulating neural networks in vitro, providing natural but simplified environments in a highly reproducible manner in which to study brain function and related diseases. Platforms for these in vitro neural networks require precise and selective neural connections at the target location, with minimal external influences, and measurement of neural activity to determine how neurons communicate. Here, we report a neuron-loaded microrobot for selective connection of neural networks via precise delivery to a gap between two neural clusters by an external magnetic field. In addition, the extracellular action potential was propagated from one cluster to the other through the neurons on the microrobot. The proposed technique shows the potential for use in experiments to understand how neurons communicate in the neural network by actively connecting neural clusters. Close https://advances.sciencemag.org/content/6/39/eabb5696 doi:10.1126/sciadv.abb5696 Close
	Cowan, Cameron S; Renner, Magdalena; Gennaro, Martina De; Gross-Scherf, Brigitte; Goldblum, David; Hou, Yanyan; Munz, Martin; Rodrigues, Tiago M; Krol, Jacek; Szikra, Tamas; Cuttat, Rachel; Waldt, Annick; Papasaikas, Panagiotis; Diggelmann, Roland; Patino-Alvarez, Claudia P; Galliker, Patricia; Spirig, Stefan E; Pavlinic, Dinko; Gerber-Hollbach, Nadine; Schuierer, Sven; Srdanovic, Aldin; Balogh, Marton; Panero, Riccardo; Kusnyerik, Akos; Szabo, Arnold; Stadler, Michael B; Orgül, Selim; Picelli, Simone; Hasler, Pascal W; Hierlemann, Andreas; Scholl, Hendrik P N; Roma, Guglielmo; Nigsch, Florian; Roska, Botond Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution Journal Article CellPress, 182 , pp. 1623–1640, 2020. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Organoids @article{Cowan2020, title = {Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution}, author = {Cameron S. Cowan and Magdalena Renner and Martina De Gennaro and Brigitte Gross-Scherf and David Goldblum and Yanyan Hou and Martin Munz and Tiago M. Rodrigues and Jacek Krol and Tamas Szikra and Rachel Cuttat and Annick Waldt and Panagiotis Papasaikas and Roland Diggelmann and Claudia P. Patino-Alvarez and Patricia Galliker and Stefan E. Spirig and Dinko Pavlinic and Nadine Gerber-Hollbach and Sven Schuierer and Aldin Srdanovic and Marton Balogh and Riccardo Panero and Akos Kusnyerik and Arnold Szabo and Michael B. Stadler and Selim Orgül and Simone Picelli and Pascal W. Hasler and Andreas Hierlemann and Hendrik P.N. Scholl and Guglielmo Roma and Florian Nigsch and Botond Roska}, url = {https://www.cell.com/cell/fulltext/S0092-8674(20)31004-7?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867420310047%3Fshowall%3Dtrue}, doi = {10.1016/j.cell.2020.08.013}, year = {2020}, date = {2020-09-17}, journal = {CellPress}, volume = {182}, pages = { 1623–1640}, abstract = {Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed light-sensitive human retinal organoids with multiple nuclear and synaptic layers and functional synapses. We sequenced the RNA of 285,441 single cells from these organoids at seven developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas, and performed histochemistry. Cell types in organoids matured in vitro to a stable “developed” state at a rate similar to human retina development in vivo. Transcriptomes of organoid cell types converged toward the transcriptomes of adult peripheral retinal cell types. Expression of disease-associated genes was cell-type-specific in adult retina, and cell-type specificity was retained in organoids. We implicate unexpected cell types in diseases such as macular degeneration. This resource identifies cellular targets for studying disease mechanisms in organoids and for targeted repair in human retinas.}, keywords = {ETH-CMOS-MEA, Organoids}, pubstate = {published}, tppubtype = {article} } Close Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed light-sensitive human retinal organoids with multiple nuclear and synaptic layers and functional synapses. We sequenced the RNA of 285,441 single cells from these organoids at seven developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas, and performed histochemistry. Cell types in organoids matured in vitro to a stable “developed” state at a rate similar to human retina development in vivo. Transcriptomes of organoid cell types converged toward the transcriptomes of adult peripheral retinal cell types. Expression of disease-associated genes was cell-type-specific in adult retina, and cell-type specificity was retained in organoids. We implicate unexpected cell types in diseases such as macular degeneration. This resource identifies cellular targets for studying disease mechanisms in organoids and for targeted repair in human retinas. Close https://www.cell.com/cell/fulltext/S0092-8674(20)31004-7?_returnURL=https%3A%2F%[...] doi:10.1016/j.cell.2020.08.013 Close
	Ronchi, Silvia; Buccino, Alessio Paolo; Prack, Gustavo; Kumar, Sreedhar Saseendran; Schröter, Manuel; Fiscella, Michele; Hierlemann, Andreas Electrophysiological Phenotype Characterization of Human iPSC-Derived Neuronal Cell Lines by Means of High-Density Microelectrode Arrays Journal Article BioRxiv, 2020. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, IPSC @article{Ronchi2020, title = {Electrophysiological Phenotype Characterization of Human iPSC-Derived Neuronal Cell Lines by Means of High-Density Microelectrode Arrays}, author = {Silvia Ronchi and Alessio Paolo Buccino and Gustavo Prack and Sreedhar Saseendran Kumar and Manuel Schröter and Michele Fiscella and Andreas Hierlemann }, url = {https://www.biorxiv.org/content/10.1101/2020.09.02.271403v1}, doi = {10.1101/2020.09.02.271403}, year = {2020}, date = {2020-09-02}, journal = {BioRxiv}, abstract = {Recent advances in the field of cellular reprogramming have opened a route to study the fundamental mechanisms underlying common neurological disorders. High-density microelectrode-arrays (HD-MEAs) provide unprecedented means to study neuronal physiology at different scales, ranging from network through single-neuron to subcellular features. In this work, we used HD-MEAs in vitro to characterize and compare human induced-pluripotent-stem-cell (iPSC)-derived dopaminergic and motor neurons, including isogenic neuronal lines modeling Parkinson’s disease and amyotrophic lateral sclerosis. We established reproducible electrophysiological network, single-cell and subcellular metrics, which were used for phenotype characterization and drug testing. Metrics such as burst shapes and axonal velocity enabled the distinction of healthy and diseased neurons. The HD-MEA metrics could also be used to detect the effects of dosing the drug retigabine to human motor neurons. Finally, we showed that the ability to detect drug effects and the observed culture-to-culture variability critically depend on the number of available recording electrodes}, keywords = {ETH-CMOS-MEA, IPSC}, pubstate = {published}, tppubtype = {article} } Close Recent advances in the field of cellular reprogramming have opened a route to study the fundamental mechanisms underlying common neurological disorders. High-density microelectrode-arrays (HD-MEAs) provide unprecedented means to study neuronal physiology at different scales, ranging from network through single-neuron to subcellular features. In this work, we used HD-MEAs in vitro to characterize and compare human induced-pluripotent-stem-cell (iPSC)-derived dopaminergic and motor neurons, including isogenic neuronal lines modeling Parkinson’s disease and amyotrophic lateral sclerosis. We established reproducible electrophysiological network, single-cell and subcellular metrics, which were used for phenotype characterization and drug testing. Metrics such as burst shapes and axonal velocity enabled the distinction of healthy and diseased neurons. The HD-MEA metrics could also be used to detect the effects of dosing the drug retigabine to human motor neurons. Finally, we showed that the ability to detect drug effects and the observed culture-to-culture variability critically depend on the number of available recording electrodes Close https://www.biorxiv.org/content/10.1101/2020.09.02.271403v1 doi:10.1101/2020.09.02.271403 Close
	Al-Absi, Abdel-Rahman; Qvist, Per; Okujeni, Samora; Khan, Ahmad Raza; Glerup, Simon; Sanchez, Connie; Nyengaard, Jens R Layers II/III of Prefrontal Cortex in Df(h22q11)/+ Mouse Model of the 22q11.2 Deletion Display Loss of Parvalbumin Interneurons and Modulation of Neuronal Morphology and Excitability Journal Article Molecular Neurobiology, 2020. Abstract \| Links \| BibTeX \| Tags: MaxOne, Slices @article{Al-Absi2020, title = {Layers II/III of Prefrontal Cortex in Df(h22q11)/+ Mouse Model of the 22q11.2 Deletion Display Loss of Parvalbumin Interneurons and Modulation of Neuronal Morphology and Excitability}, author = {Abdel-Rahman Al-Absi and Per Qvist and Samora Okujeni and Ahmad Raza Khan and Simon Glerup and Connie Sanchez and Jens R. Nyengaard }, url = {https://link.springer.com/article/10.1007/s12035-020-02067-1}, doi = {https://doi.org/10.1007/s12035-020-02067-1}, year = {2020}, date = {2020-08-20}, journal = {Molecular Neurobiology}, abstract = {The 22q11.2 deletion has been identified as a risk factor for multiple neurodevelopmental disorders. Behavioral and cognitive impairments are common among carriers of the 22q11.2 deletion. Parvalbumin expressing (PV+) interneurons provide perisomatic inhibition of excitatory neuronal circuits through GABAA receptors, and a deficit of PV+ inhibitory circuits may underlie a multitude of the behavioral and functional deficits in the 22q11.2 deletion syndrome. We investigated putative deficits of PV+ inhibitory circuits and the associated molecular, morphological, and functional alterations in the prefrontal cortex (PFC) of the Df(h22q11)/+ mouse model of the 22q11.2 hemizygous deletion. We detected a significant decrease in the number of PV+ interneurons in layers II/III of PFC in Df(h22q11)/+ mice together with a reduction in the mRNA and protein levels of GABAA (α3), a PV+ putative postsynaptic receptor subunit. Pyramidal neurons from the same layers further experienced morphological reorganizations of spines and dendrites. Accordingly, a decrease in the levels of the postsynaptic density protein 95 (PSD95) and a higher neuronal activity in response to the GABAA antagonist bicuculline were measured in these layers in PFC of Df(h22q11)/+ mice compared with their wild-type littermates. Our study shows that a hemizygotic deletion of the 22q11.2 locus leads to deficit in the GABAergic control of network activity and involves molecular and morphological changes in both the inhibitory and excitatory synapses of parvalbumin interneurons and pyramidal neurons specifically in layers II/III PFC.}, keywords = {MaxOne, Slices}, pubstate = {published}, tppubtype = {article} } Close The 22q11.2 deletion has been identified as a risk factor for multiple neurodevelopmental disorders. Behavioral and cognitive impairments are common among carriers of the 22q11.2 deletion. Parvalbumin expressing (PV+) interneurons provide perisomatic inhibition of excitatory neuronal circuits through GABAA receptors, and a deficit of PV+ inhibitory circuits may underlie a multitude of the behavioral and functional deficits in the 22q11.2 deletion syndrome. We investigated putative deficits of PV+ inhibitory circuits and the associated molecular, morphological, and functional alterations in the prefrontal cortex (PFC) of the Df(h22q11)/+ mouse model of the 22q11.2 hemizygous deletion. We detected a significant decrease in the number of PV+ interneurons in layers II/III of PFC in Df(h22q11)/+ mice together with a reduction in the mRNA and protein levels of GABAA (α3), a PV+ putative postsynaptic receptor subunit. Pyramidal neurons from the same layers further experienced morphological reorganizations of spines and dendrites. Accordingly, a decrease in the levels of the postsynaptic density protein 95 (PSD95) and a higher neuronal activity in response to the GABAA antagonist bicuculline were measured in these layers in PFC of Df(h22q11)/+ mice compared with their wild-type littermates. Our study shows that a hemizygotic deletion of the 22q11.2 locus leads to deficit in the GABAergic control of network activity and involves molecular and morphological changes in both the inhibitory and excitatory synapses of parvalbumin interneurons and pyramidal neurons specifically in layers II/III PFC. Close https://link.springer.com/article/10.1007/s12035-020-02067-1 doi:https://doi.org/10.1007/s12035-020-02067-1 Close
	Bandarabadi, Mojtaba; Vassalli, Anne; Tafti, Mehdi Sleep as a default state of cortical and subcortical networks Journal Article Current Opinion in Physiology, 15 , pp. 60-67, 2020. Abstract \| Links \| BibTeX \| Tags: Neuronal Networks, Review, Sleep @article{Bandarabadi2020, title = {Sleep as a default state of cortical and subcortical networks}, author = {Mojtaba Bandarabadi and Anne Vassalli and Mehdi Tafti}, url = {https://www.sciencedirect.com/science/article/pii/S2468867319301907?via%3Dihub}, doi = {10.1016/j.cophys.2019.12.004}, year = {2020}, date = {2020-06-20}, journal = {Current Opinion in Physiology}, volume = {15}, pages = {60-67}, abstract = {Sleep has been conceptualized as ‘activity-dependent’, hence a response to prior waking experience, and proposed to be ‘the price the brain pays for plasticity during wakefulness’. We here propose that at the level of neuronal networks, particularly those arising from isolated embryonic thalamocortical cells maintained in culture, it represents a default mode of functioning. We show that cell assemblies in ex vivo cultures express powerful sleep specific patterns of oscillatory activity, as well as metabolic and molecular signatures of the sleep state. We summarize recent evidences that support our hypothesis and discuss potential applications of developing ex vivo sleep models to answer open questions in the field.}, keywords = {Neuronal Networks, Review, Sleep}, pubstate = {published}, tppubtype = {article} } Close Sleep has been conceptualized as ‘activity-dependent’, hence a response to prior waking experience, and proposed to be ‘the price the brain pays for plasticity during wakefulness’. We here propose that at the level of neuronal networks, particularly those arising from isolated embryonic thalamocortical cells maintained in culture, it represents a default mode of functioning. We show that cell assemblies in ex vivo cultures express powerful sleep specific patterns of oscillatory activity, as well as metabolic and molecular signatures of the sleep state. We summarize recent evidences that support our hypothesis and discuss potential applications of developing ex vivo sleep models to answer open questions in the field. Close https://www.sciencedirect.com/science/article/pii/S2468867319301907?via%3Dihub doi:10.1016/j.cophys.2019.12.004 Close
	Masumori, Atsushi; Sinapayen, Lana; Maruyama, Norihiro; Mita, Takeshi; Bakkum, Douglas J; Frey, Urs; Takahashi, Hirokazu; Ikegami, Takashi Neural Autopoiesis: Organizing Self-Boundaries by Stimulus Avoidance in Biological and Artificial Neural Networks Journal Article Artificial Life, 26 (1), pp. 130-151, 2020, ISSN: 1064-5462. Abstract \| Links \| BibTeX \| Tags: Neuronal Networks @article{Masumori2020, title = {Neural Autopoiesis: Organizing Self-Boundaries by Stimulus Avoidance in Biological and Artificial Neural Networks}, author = {Atsushi Masumori and Lana Sinapayen and Norihiro Maruyama and Takeshi Mita and Douglas J. Bakkum and Urs Frey and Hirokazu Takahashi and Takashi Ikegami}, url = {https://www.mitpressjournals.org/doi/full/10.1162/artl_a_00314}, doi = {10.1162/artl_a_00314}, issn = {1064-5462}, year = {2020}, date = {2020-04-28}, journal = {Artificial Life}, volume = {26}, number = {1}, pages = {130-151}, abstract = {Living organisms must actively maintain themselves in order to continue existing. Autopoiesis is a key concept in the study of living organisms, where the boundaries of the organism are not static but dynamically regulated by the system itself. To study the autonomous regulation of a self-boundary, we focus on neural homeodynamic responses to environmental changes using both biological and artificial neural networks. Previous studies showed that embodied cultured neural networks and spiking neural networks with spike-timing dependent plasticity (STDP) learn an action as they avoid stimulation from outside. In this article, as a result of our experiments using embodied cultured neurons, we find that there is also a second property allowing the network to avoid stimulation: If the agent cannot learn an action to avoid the external stimuli, it tends to decrease the stimulus-evoked spikes, as if to ignore the uncontrollable input. We also show such a behavior is reproduced by spiking neural networks with asymmetric STDP. We consider that these properties are to be regarded as autonomous regulation of self and nonself for the network, in which a controllable neuron is regarded as self, and an uncontrollable neuron is regarded as nonself. Finally, we introduce neural autopoiesis by proposing the principle of stimulus avoidance.}, keywords = {Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Living organisms must actively maintain themselves in order to continue existing. Autopoiesis is a key concept in the study of living organisms, where the boundaries of the organism are not static but dynamically regulated by the system itself. To study the autonomous regulation of a self-boundary, we focus on neural homeodynamic responses to environmental changes using both biological and artificial neural networks. Previous studies showed that embodied cultured neural networks and spiking neural networks with spike-timing dependent plasticity (STDP) learn an action as they avoid stimulation from outside. In this article, as a result of our experiments using embodied cultured neurons, we find that there is also a second property allowing the network to avoid stimulation: If the agent cannot learn an action to avoid the external stimuli, it tends to decrease the stimulus-evoked spikes, as if to ignore the uncontrollable input. We also show such a behavior is reproduced by spiking neural networks with asymmetric STDP. We consider that these properties are to be regarded as autonomous regulation of self and nonself for the network, in which a controllable neuron is regarded as self, and an uncontrollable neuron is regarded as nonself. Finally, we introduce neural autopoiesis by proposing the principle of stimulus avoidance. Close https://www.mitpressjournals.org/doi/full/10.1162/artl_a_00314 doi:10.1162/artl_a_00314 Close
	Idrees, Saad; Baumann, Matthias P; Franke, Felix; Münch, Thomas A; Hafed, Ziad M Perceptual saccadic suppression starts in the retina Journal Article Nature Communications, 11 (1977), 2020. Links \| BibTeX \| Tags: ETH-CMOS-MEA, MaxOne, Retina @article{Idrees2020, title = {Perceptual saccadic suppression starts in the retina}, author = {Saad Idrees and Matthias P. Baumann and Felix Franke and Thomas A. Münch and Ziad M. Hafed}, url = {https://www.nature.com/articles/s41467-020-15890-w}, doi = {10.1038/s41467-020-15890-w}, year = {2020}, date = {2020-04-24}, journal = {Nature Communications}, volume = {11}, number = {1977}, keywords = {ETH-CMOS-MEA, MaxOne, Retina}, pubstate = {published}, tppubtype = {article} } Close https://www.nature.com/articles/s41467-020-15890-w doi:10.1038/s41467-020-15890-w Close
	Obaid, Abdulmalik; Hanna, Mina-Elrahb; Wu, Yu-Wei; Kollo, Mihaly; Racz, Romeo; Angle, Matthew R; Muller, Jan; Brackbill, Nora; Wray, William; Franke, Felix; Chichilnski, E J; Hierlemann, Andreas; Ding, Jun B; Schaefer, Andreas T; Melosh, Nicholas A Massively parallel microwire arrays integrated withCMOS chips for neural recording Journal Article Science Advances, 2020. Abstract \| Links \| BibTeX \| Tags: Electrodes, ETH-CMOS-MEA @article{Obaid2020, title = {Massively parallel microwire arrays integrated withCMOS chips for neural recording}, author = {Abdulmalik Obaid and Mina-Elrahb Hanna and Yu-Wei Wu and Mihaly Kollo and Romeo Racz and Matthew R Angle and Jan Muller and Nora Brackbill and William Wray and Felix Franke and E J Chichilnski and Andreas Hierlemann and Jun B. Ding and Andreas T. Schaefer and Nicholas A. Melosh}, url = {https://advances.sciencemag.org/content/6/12/eaay2789}, doi = {10.1126/sciadv.aay2789}, year = {2020}, date = {2020-03-20}, journal = {Science Advances}, abstract = {Multi-channel electrical recordings of neural activity in the brain is an increasingly powerful method revealing new aspects of neural communication, computation, and prosthetics. However, while planar silicon-based CMOS devices in conventional electronics scale rapidly, neural interface devices have not kept pace. Here, we present a new strategy to interface silicon-based chips with three-dimensional microwire arrays, providing the link between rapidly-developing electronics and high density neural interfaces. The system consists of a bundle of microwires mated to large-scale microelectrode arrays, such as camera chips. This system has excellent recording performance, demonstrated via single unit and local-field potential recordings in isolated retina and in the motor cortex or striatum of awake moving mice. The modular design enables a variety of microwire types and sizes to be integrated with different types of pixel arrays, connecting the rapid progress of commercial multiplexing, digitisation and data acquisition hardware together with a three-dimensional neural interface.}, keywords = {Electrodes, ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close Multi-channel electrical recordings of neural activity in the brain is an increasingly powerful method revealing new aspects of neural communication, computation, and prosthetics. However, while planar silicon-based CMOS devices in conventional electronics scale rapidly, neural interface devices have not kept pace. Here, we present a new strategy to interface silicon-based chips with three-dimensional microwire arrays, providing the link between rapidly-developing electronics and high density neural interfaces. The system consists of a bundle of microwires mated to large-scale microelectrode arrays, such as camera chips. This system has excellent recording performance, demonstrated via single unit and local-field potential recordings in isolated retina and in the motor cortex or striatum of awake moving mice. The modular design enables a variety of microwire types and sizes to be integrated with different types of pixel arrays, connecting the rapid progress of commercial multiplexing, digitisation and data acquisition hardware together with a three-dimensional neural interface. Close https://advances.sciencemag.org/content/6/12/eaay2789 doi:10.1126/sciadv.aay2789 Close

243 entries « ‹ 3 of 5 › »

Selected Publications

High-resolution CMOS MEA platform to study neurons at subcellular, cellular, and network levels

Presenting measurements of neuronal preparations with a novel CMOS-based microelectrode array at high-spatiotemporal-resolution on subcellular, cellular, and network level.

J. Müller, M. Ballini, P. Livi, Y. Chen, M. Radivojevic, A. Shadmani, V. Viswam, I. L. Jones, M. Fiscella, R. Diggelmann, A. Stettler, U. Frey, D. J. Bakkum, and A. Hierlemann, “High-resolution CMOS MEA platform to study neurons at subcellular, cellular, and network levels,” Lab Chip, vol. 15, no. 13, pp. 2767–2780, May 2015.

Revealing Neuronal Function through Microelectrode Array Recordings

Reviewing the current understanding of microelectrode signals and the techniques for analyzing them, with focus on the ongoing advancements in microelectrode technology (in vivo and in vitro) and recent advanced microelectrode array measurement methods that facilitate the understanding of single neurons and network function.

M. E. J. Obien, K. Deligkaris, T. Bullmann, D. J. Bakkum, and U. Frey, “Revealing Neuronal Function through Microelectrode Array Recordings,” Front. Neurosci., 8:423, Jan 2015.

A 1024-Channel CMOS Microelectrode Array With 26,400 Electrodes for Recording and Stimulation of Electrogenic Cells In Vitro

A high-resolution CMOS-based microelectrode array featuring 1,024 low-noise readout channels, 26,400 electrodes at a density of 3,265 electrodes per mm², including on-chip 10bit ADCs and consuming only 75 mW.

M. Ballini, J. Muller, P. Livi, Y. Chen, U. Frey, A. Stettler, A. Shadmani, V. Viswam, I. L. Jones, D. Jackel, M. Radivojevic, M. K. Lewandowska, W. Gong, M. Fiscella, D. J. Bakkum, F. Heer, and A. Hierlemann, “A 1024-Channel CMOS Microelectrode Array With 26,400 Electrodes for Recording and Stimulation of Electrogenic Cells In Vitro,” IEEE Journal of Solid-State Circuits, vol. 49, no. 11, pp. 2705-2719, 2014.

Tracking axonal action potential propagation on a high-density microelectrode array across hundreds of sites

Demonstrating a method to electrically visualize action potential propagation on axons and revealing
large variations in velocity.

D. J. Bakkum, U. Frey, M. Radivojevic, T. L. Russell, J. Muller, M. Fiscella, H. Takahashi, and A. Hierlemann, “Tracking axonal action potential propagation on a high-density microelectrode array across hundreds of sites,” Nature Communications, 4:2181, Jul 2013.

Microelectronic System for High-Resolution Mapping of Extracellular Electric Fields Applied to Brain Slices

Recording and modeling extracellular action potentials of Purkinje cells at subcellular resolution.

U. Frey, U. Egert, F. Heer, S. Hafizovic, and A. Hierlemann, “Microelectronic System for High-Resolution Mapping of Extracellular Electric Fields Applied to Brain Slices,” Biosensors and Bioelectronics, vol. 24, no. 7, pp. 2191-2198, 2009.

Modulation of Cardiomyocyte Electrical Properties Using Regulated Bone Morphogenetic Protein-2 Expression

Controlling BMP-2 expression to modulate the electrophysiological properties of cardiomyocytes using an HD-MEA for detailed monitoring.

C. D. Sanchez-Bustamante, U. Frey, J. M. Kelm, A. Hierlemann, and M. Fussenegger,
“Modulation of Cardiomyocyte Electrical Properties Using Regulated Bone Morphogenetic Protein-2 Expression,” Tissue Engineering Part A, vol. 14, no. 12, pp. 1969-1988, 2008.

2022
	Tran, Hoang-Dai; Shin, Min-Kyoung; Denman, Charlotte; Han, Run-Run; Kuhn, Bernd; Arbuthnott, Gordon; Jo, Junghyun Generation of Human Striatal-Midbrain Assembloids From Human Pluripotent Stem Cells to Model Alpha-Synuclein Propagation Journal Article Sneak Peek - Cell Press, 2022. Abstract \| Links \| BibTeX \| Tags: MaxOne, Organoids @article{Tran2022, title = {Generation of Human Striatal-Midbrain Assembloids From Human Pluripotent Stem Cells to Model Alpha-Synuclein Propagation}, author = {Hoang-Dai Tran and Min-Kyoung Shin and Charlotte Denman and Run-Run Han and Bernd Kuhn and Gordon Arbuthnott and Junghyun Jo}, url = {https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4288935}, doi = {http://dx.doi.org/10.2139/ssrn.4288935}, year = {2022}, date = {2022-12-05}, journal = {Sneak Peek - Cell Press}, abstract = {Animal models of the pathology of Parkinson’s disease (PD) have provided most of the treatments to date, but the disease is restricted to human patients. In vitro models using human pluripotent stem cell-derived neural organoids have provided improved access to study PD etiology. Here, we generated human striatal and midbrain organoids and assembled both regionalized neural organoids to form human striatal-midbrain assembloids (hSMAs), mimicking a part of basal ganglia. Both the nigrostriatal and striatonigral pathways are present and electrophysiologically active in the hSMAs. hSMA development in the presence of increased alpha-synuclein (α-syn) from SNCA overexpression, induced nigrostriatal system damage, which is typical of the disease. Using the α-syn-mKO2 reporter and bimolecular fluorescence complementation system, we demonstrated that fluorescent α-syn is transported from the striatal area tothe dopaminergic (DA) neurons of the midbrain area. Furthermore, insoluble α-syn aggregated over time in DA neurons similar to Lewy bodies in human patients. Such assembloids are a compelling new platform to develop novel PD therapeutic strategies.}, keywords = {MaxOne, Organoids}, pubstate = {published}, tppubtype = {article} } Close Animal models of the pathology of Parkinson’s disease (PD) have provided most of the treatments to date, but the disease is restricted to human patients. In vitro models using human pluripotent stem cell-derived neural organoids have provided improved access to study PD etiology. Here, we generated human striatal and midbrain organoids and assembled both regionalized neural organoids to form human striatal-midbrain assembloids (hSMAs), mimicking a part of basal ganglia. Both the nigrostriatal and striatonigral pathways are present and electrophysiologically active in the hSMAs. hSMA development in the presence of increased alpha-synuclein (α-syn) from SNCA overexpression, induced nigrostriatal system damage, which is typical of the disease. Using the α-syn-mKO2 reporter and bimolecular fluorescence complementation system, we demonstrated that fluorescent α-syn is transported from the striatal area tothe dopaminergic (DA) neurons of the midbrain area. Furthermore, insoluble α-syn aggregated over time in DA neurons similar to Lewy bodies in human patients. Such assembloids are a compelling new platform to develop novel PD therapeutic strategies. Close https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4288935 doi:http://dx.doi.org/10.2139/ssrn.4288935 Close
	Akarca, Danyal; Dunn, Alexander W E; Hornauer, Philipp J; Ronchi, Silvia; Fiscella, Michele; Wang, Congwei; Terrigno, Marco; Jagasia, Ravi; Vértes, Petra E; Mierau, Susanna B; Paulsen, Ole; Eglen, Stephen J; Hierlemann, Andreas; Astle, Duncan E; Schröter, Manuel Homophilic wiring principles underpin neuronal network topology in vitro Journal Article BioRxiv, 2022. Abstract \| Links \| BibTeX \| Tags: MaxOne, MaxTwo, MEA Technology @article{Akarca2022, title = {Homophilic wiring principles underpin neuronal network topology in vitro}, author = {Danyal Akarca and Alexander W. E. Dunn and Philipp J. Hornauer and Silvia Ronchi and Michele Fiscella and Congwei Wang and Marco Terrigno and Ravi Jagasia and Petra E. Vértes and Susanna B. Mierau and Ole Paulsen and Stephen J. Eglen and Andreas Hierlemann and Duncan E. Astle and Manuel Schröter}, url = {https://www.biorxiv.org/content/10.1101/2022.03.09.483605v2.abstract}, doi = {https://doi.org/10.1101/2022.03.09.483605}, year = {2022}, date = {2022-12-01}, journal = {BioRxiv}, abstract = {Economic efficiency has been a popular explanation for how networks self-organize within the developing nervous system. However, the precise nature of the economic negotiations governing this putative organizational principle remains unclear. Here, we address this question further by combining large-scale electrophysiological recordings, to characterize the functional connectivity of developing neuronal networks in vitro, with a generative modeling approach capable of simulating network formation. We find that the best fitting model uses a homophilic generative wiring principle in which neurons form connections to other neurons which are spatially proximal and have similar connectivity patterns to themselves. Homophilic generative models outperform more canonical models in which neurons wire depending upon their spatial proximity either alone or in combination with the extent of their local connectivity. This homophily-based mechanism for neuronal network emergence accounts for a wide range of observations that are described, but not sufficiently explained, by traditional analyses of network topology. Using rodent and human monolayer and organoid cultures, we show that homophilic generative mechanisms can accurately recapitulate the topology of emerging cellular functional connectivity, representing an important wiring principle and determining factor of neuronal network formation in vitro.}, keywords = {MaxOne, MaxTwo, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close Economic efficiency has been a popular explanation for how networks self-organize within the developing nervous system. However, the precise nature of the economic negotiations governing this putative organizational principle remains unclear. Here, we address this question further by combining large-scale electrophysiological recordings, to characterize the functional connectivity of developing neuronal networks in vitro, with a generative modeling approach capable of simulating network formation. We find that the best fitting model uses a homophilic generative wiring principle in which neurons form connections to other neurons which are spatially proximal and have similar connectivity patterns to themselves. Homophilic generative models outperform more canonical models in which neurons wire depending upon their spatial proximity either alone or in combination with the extent of their local connectivity. This homophily-based mechanism for neuronal network emergence accounts for a wide range of observations that are described, but not sufficiently explained, by traditional analyses of network topology. Using rodent and human monolayer and organoid cultures, we show that homophilic generative mechanisms can accurately recapitulate the topology of emerging cellular functional connectivity, representing an important wiring principle and determining factor of neuronal network formation in vitro. Close https://www.biorxiv.org/content/10.1101/2022.03.09.483605v2.abstract doi:https://doi.org/10.1101/2022.03.09.483605 Close
	Habibollahi, Forough; Khajehnejad, Moein; Gaurav, Amitesh; Kagan, Brett Joseph Biological Neurons vs Deep Reinforcement Learning: Sample efficiency in a simulated game-world Conference 2022. Abstract \| Links \| BibTeX \| Tags: Machine Learning, MaxOne @conference{Habibollahi2022, title = {Biological Neurons vs Deep Reinforcement Learning: Sample efficiency in a simulated game-world }, author = {Forough Habibollahi and Moein Khajehnejad and Amitesh Gaurav and Brett Joseph Kagan}, url = {https://openreview.net/forum?id=N5qLXpc7HQy}, year = {2022}, date = {2022-11-28}, journal = {OpenReview.net}, abstract = {How do synthetic biological systems and artificial neural networks compete in their performance in a game environment? Reinforcement learning has undergone significant advances, however remains behind biological neural intelligence in terms of sample efficiency. Yet most biological systems are significantly more complicated than most algorithms. Here we compare the inherent intelligence of in vitro biological neuronal networks to state-of-the-art deep reinforcement learning algorithms in the arcade game 'pong'. We employed DishBrain, a system that embodies in vitro neural networks with in silico computation using a high-density multielectrode array. We compared the learning curve and the performance of these biological systems against time-matched learning from DQN, A2C, and PPO algorithms. Agents were implemented in a reward-based environment of the `Pong' game. Key learning characteristics of the deep reinforcement learning agents were tested with those of the biological neuronal cultures in the same game environment. We find that even these very simple biological cultures typically outperform deep reinforcement learning systems in terms of various game performance characteristics, such as the average rally length implying a higher sample efficiency. Furthermore, the human cell cultures proved to have the overall highest relative improvement in the average number of hits in a rally when comparing the initial 5 minutes and the last 15 minutes of each designed gameplay session. }, keywords = {Machine Learning, MaxOne}, pubstate = {published}, tppubtype = {conference} } Close How do synthetic biological systems and artificial neural networks compete in their performance in a game environment? Reinforcement learning has undergone significant advances, however remains behind biological neural intelligence in terms of sample efficiency. Yet most biological systems are significantly more complicated than most algorithms. Here we compare the inherent intelligence of in vitro biological neuronal networks to state-of-the-art deep reinforcement learning algorithms in the arcade game 'pong'. We employed DishBrain, a system that embodies in vitro neural networks with in silico computation using a high-density multielectrode array. We compared the learning curve and the performance of these biological systems against time-matched learning from DQN, A2C, and PPO algorithms. Agents were implemented in a reward-based environment of the `Pong' game. Key learning characteristics of the deep reinforcement learning agents were tested with those of the biological neuronal cultures in the same game environment. We find that even these very simple biological cultures typically outperform deep reinforcement learning systems in terms of various game performance characteristics, such as the average rally length implying a higher sample efficiency. Furthermore, the human cell cultures proved to have the overall highest relative improvement in the average number of hits in a rally when comparing the initial 5 minutes and the last 15 minutes of each designed gameplay session. Close https://openreview.net/forum?id=N5qLXpc7HQy Close
	McSweeney, Danny; Gabriel, Rafael; Jin, Kang; Pang, Zhiping P; Aronow, Bruce; and Pak, ChangHui CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons Journal Article iScience, 2022. Abstract \| Links \| BibTeX \| Tags: 2D Neuronal Culture, CMOS, CRISPR, HD-MEA, MaxOne, Synapses @article{McSweeney2022b, title = {CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons}, author = {Danny McSweeney and Rafael Gabriel and Kang Jin and Zhiping P. Pang and Bruce Aronow and and ChangHui Pak}, url = {https://www.cell.com/iscience/fulltext/S2589-0042(22)01459-6?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2589004222014596%3Fshowall%3Dtrue}, doi = {https://doi.org/10.1016/j.isci.2022.105187}, year = {2022}, date = {2022-10-21}, journal = {iScience}, abstract = {Loss-of-function (LOF) mutations in CASK cause severe developmental pheno- types, including microcephaly with pontine and cerebellar hypoplasia, X-linked in- tellectual disability, and autism. Unraveling the pathological mechanisms of CASK-related disorders has been challenging owing to limited human cellular models to study the dynamic roles of this molecule during neuronal maturation and synapse development. Here, we investigate cell-autonomous functions of CASK in cortical excitatory induced neurons (iNs) generated from CASK knockout (KO) isogenic human embryonic stem cells (hESCs) using gene expression, mor- phometrics, and electrophysiology. While immature CASK KO iNs show robust neuronal outgrowth, mature CASK KO iNs display severe defects in syn- aptic transmission and synchronized network activity without compromising neuronal morphology and synapse numbers. In the developing human cortical excitatory neurons, CASK functions to promote both structural integrity and establishment of cortical excitatory neuronal networks. These results lay the foundation for future studies identifying suppressors of such phenotypes rele- vant to human patients.}, keywords = {2D Neuronal Culture, CMOS, CRISPR, HD-MEA, MaxOne, Synapses}, pubstate = {published}, tppubtype = {article} } Close Loss-of-function (LOF) mutations in CASK cause severe developmental pheno- types, including microcephaly with pontine and cerebellar hypoplasia, X-linked in- tellectual disability, and autism. Unraveling the pathological mechanisms of CASK-related disorders has been challenging owing to limited human cellular models to study the dynamic roles of this molecule during neuronal maturation and synapse development. Here, we investigate cell-autonomous functions of CASK in cortical excitatory induced neurons (iNs) generated from CASK knockout (KO) isogenic human embryonic stem cells (hESCs) using gene expression, mor- phometrics, and electrophysiology. While immature CASK KO iNs show robust neuronal outgrowth, mature CASK KO iNs display severe defects in syn- aptic transmission and synchronized network activity without compromising neuronal morphology and synapse numbers. In the developing human cortical excitatory neurons, CASK functions to promote both structural integrity and establishment of cortical excitatory neuronal networks. These results lay the foundation for future studies identifying suppressors of such phenotypes rele- vant to human patients. Close https://www.cell.com/iscience/fulltext/S2589-0042(22)01459-6?_returnURL=https%3A[...] doi:https://doi.org/10.1016/j.isci.2022.105187 Close
	Kagan, Brett J; Kitchen, Andy C; Tran, Nhi T; Habibollahi, Forough; Khajehnejad, Moein; Parker, Bradyn J; Bhat, Anjali; Rollo, Ben; Razi, Adeel; Friston, Karl J In vitro neurons learn and exhibit sentience when embodied in a simulated game-world Journal Article Neuron, 2022. Abstract \| Links \| BibTeX \| Tags: 2D Neuronal Culture, Activity Scan Assay, closed loop stimulation, HD-MEA, IPSC, MaxOne, MEA Metrics, MEA Technology, Primary Neuronal Cell Culture @article{Kagan2022, title = {In vitro neurons learn and exhibit sentience when embodied in a simulated game-world}, author = {Brett J. Kagan and Andy C. Kitchen and Nhi T. Tran and Forough Habibollahi and Moein Khajehnejad and Bradyn J. Parker and Anjali Bhat and Ben Rollo and Adeel Razi and Karl J Friston }, url = {https://www.cell.com/neuron/fulltext/S0896-6273(22)00806-6?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0896627322008066%3Fshowall%3Dtrue}, doi = {https://doi.org/10.1016/j.neuron.2022.09.001}, year = {2022}, date = {2022-10-12}, journal = {Neuron}, abstract = {Integrating neurons into digital systems may enable performance infeasible with silicon alone. Here, we develop DishBrain, a system that harnesses the inherent adaptive computation of neurons in a structured environment. In vitro neural networks from human or rodent origins are integrated with in silico computing via a high-density multielectrode array. Through electrophysiological stimulation and recording, cultures are embedded in a simulated game-world, mimicking the arcade game “Pong.” Applying implications from the theory of active inference via the free energy principle, we find apparent learning within five minutes of real-time gameplay not observed in control conditions. Further experiments demonstrate the importance of closed-loop structured feedback in eliciting learning over time. Cultures display the ability to self-organize activity in a goal-directed manner in response to sparse sensory information about the consequences of their actions, which we term synthetic biological intelligence. Future applications may provide further insights into the cellular correlates of intelligence.}, keywords = {2D Neuronal Culture, Activity Scan Assay, closed loop stimulation, HD-MEA, IPSC, MaxOne, MEA Metrics, MEA Technology, Primary Neuronal Cell Culture}, pubstate = {published}, tppubtype = {article} } Close Integrating neurons into digital systems may enable performance infeasible with silicon alone. Here, we develop DishBrain, a system that harnesses the inherent adaptive computation of neurons in a structured environment. In vitro neural networks from human or rodent origins are integrated with in silico computing via a high-density multielectrode array. Through electrophysiological stimulation and recording, cultures are embedded in a simulated game-world, mimicking the arcade game “Pong.” Applying implications from the theory of active inference via the free energy principle, we find apparent learning within five minutes of real-time gameplay not observed in control conditions. Further experiments demonstrate the importance of closed-loop structured feedback in eliciting learning over time. Cultures display the ability to self-organize activity in a goal-directed manner in response to sparse sensory information about the consequences of their actions, which we term synthetic biological intelligence. Future applications may provide further insights into the cellular correlates of intelligence. Close https://www.cell.com/neuron/fulltext/S0896-6273(22)00806-6?_returnURL=https%3A%2[...] doi:https://doi.org/10.1016/j.neuron.2022.09.001 Close
	Habibey, Rouhollah; Striebel, Johannes; Schmieder, Felix; Czarske, Jürgen; Busskamp, Volker Long-term morphological and functional dynamics of human stem cell-derived neuronal networks on high-density micro-electrode arrays Journal Article Frontiers in Neuroscience, 2022. Abstract \| Links \| BibTeX \| Tags: 2D Neuronal Culture, CMOS, HD-MEA, IPSC, MaxOne, MEA Metrics, Modeling, Spike Sorting @article{Habibey2022, title = {Long-term morphological and functional dynamics of human stem cell-derived neuronal networks on high-density micro-electrode arrays}, author = {Rouhollah Habibey and Johannes Striebel and Felix Schmieder and Jürgen Czarske and Volker Busskamp}, url = {https://www.frontiersin.org/articles/10.3389/fnins.2022.951964/full}, doi = {10.3389/fnins.2022.951964}, year = {2022}, date = {2022-10-04}, journal = {Frontiers in Neuroscience}, abstract = {Comprehensive electrophysiological characterizations of human induced pluripotent stem cell (hiPSC)-derived neuronal networks are essential to determine to what extent these in vitro models recapitulate the functional features of in vivo neuronal circuits. High-density micro-electrode arrays (HD-MEAs) offer non-invasive recording with the best spatial and temporal resolution possible to date. For 3 months, we tracked the morphology and activity features of developing networks derived from a transgenic hiPSC line in which neurogenesis is inducible by neurogenic transcription factor overexpression. Our morphological data revealed large-scale structural changes from homogeneously distributed neurons in the first month to the formation of neuronal clusters over time. This led to a constant shift in position of neuronal cells and clusters on HD-MEAs and corresponding changes in spatial distribution of the network activity maps. Network activity appeared as scarce action potentials (APs), evolved as local bursts with longer duration and changed to network-wide synchronized bursts with higher frequencies but shorter duration over time, resembling the emerging burst features found in the developing human brain. Instantaneous firing rate data indicated that the fraction of fast spiking neurons (150–600 Hz) increases sharply after 63 days post induction (dpi). Inhibition of glutamatergic synapses erased burst features from network activity profiles and confirmed the presence of mature excitatory neurotransmission. The application of GABAergic receptor antagonists profoundly changed the bursting profile of the network at 120 dpi. This indicated a GABAergic switch from excitatory to inhibitory neurotransmission during circuit development and maturation. Our results suggested that an emerging GABAergic system at older culture ages is involved in regulating spontaneous network bursts. In conclusion, our data showed that long-term and continuous microscopy and electrophysiology readouts are crucial for a meaningful characterization of morphological and functional maturation in stem cell-derived human networks. Most importantly, assessing the level and duration of functional maturation is key to subject these human neuronal circuits on HD-MEAs for basic and biomedical applications.}, keywords = {2D Neuronal Culture, CMOS, HD-MEA, IPSC, MaxOne, MEA Metrics, Modeling, Spike Sorting}, pubstate = {published}, tppubtype = {article} } Close Comprehensive electrophysiological characterizations of human induced pluripotent stem cell (hiPSC)-derived neuronal networks are essential to determine to what extent these in vitro models recapitulate the functional features of in vivo neuronal circuits. High-density micro-electrode arrays (HD-MEAs) offer non-invasive recording with the best spatial and temporal resolution possible to date. For 3 months, we tracked the morphology and activity features of developing networks derived from a transgenic hiPSC line in which neurogenesis is inducible by neurogenic transcription factor overexpression. Our morphological data revealed large-scale structural changes from homogeneously distributed neurons in the first month to the formation of neuronal clusters over time. This led to a constant shift in position of neuronal cells and clusters on HD-MEAs and corresponding changes in spatial distribution of the network activity maps. Network activity appeared as scarce action potentials (APs), evolved as local bursts with longer duration and changed to network-wide synchronized bursts with higher frequencies but shorter duration over time, resembling the emerging burst features found in the developing human brain. Instantaneous firing rate data indicated that the fraction of fast spiking neurons (150–600 Hz) increases sharply after 63 days post induction (dpi). Inhibition of glutamatergic synapses erased burst features from network activity profiles and confirmed the presence of mature excitatory neurotransmission. The application of GABAergic receptor antagonists profoundly changed the bursting profile of the network at 120 dpi. This indicated a GABAergic switch from excitatory to inhibitory neurotransmission during circuit development and maturation. Our results suggested that an emerging GABAergic system at older culture ages is involved in regulating spontaneous network bursts. In conclusion, our data showed that long-term and continuous microscopy and electrophysiology readouts are crucial for a meaningful characterization of morphological and functional maturation in stem cell-derived human networks. Most importantly, assessing the level and duration of functional maturation is key to subject these human neuronal circuits on HD-MEAs for basic and biomedical applications. Close https://www.frontiersin.org/articles/10.3389/fnins.2022.951964/full doi:10.3389/fnins.2022.951964 Close
	Kumar, Sreedhar S; Gänswein, Tobias; Buccino, Alessio P; Xue, Xiaohan; Bartram, Julian; Emmenegger, Vishalini; Hierlemann, Andreas Tracking axon initial segment plasticity using high-density microelectrode arrays: A computational study Journal Article Frontiers in Neuroinformatics, 2022. Abstract \| Links \| BibTeX \| Tags: CMOS, HD-MEA, MEA Technology @article{Kumar2022, title = {Tracking axon initial segment plasticity using high-density microelectrode arrays: A computational study}, author = {Sreedhar S. Kumar and Tobias Gänswein and Alessio P. Buccino and Xiaohan Xue and Julian Bartram and Vishalini Emmenegger and Andreas Hierlemann}, url = {https://www.frontiersin.org/articles/10.3389/fninf.2022.957255/full}, doi = {10.3389/fninf.2022.957255}, year = {2022}, date = {2022-10-03}, journal = {Frontiers in Neuroinformatics}, abstract = {Despite being composed of highly plastic neurons with extensive positive feedback, the nervous system maintains stable overall function. To keep activity within bounds, it relies on a set of negative feedback mechanisms that can induce stabilizing adjustments and that are collectively termed “homeostatic plasticity.” Recently, a highly excitable microdomain, located at the proximal end of the axon—the axon initial segment (AIS)—was found to exhibit structural modifications in response to activity perturbations. Though AIS plasticity appears to serve a homeostatic purpose, many aspects governing its expression and its functional role in regulating neuronal excitability remain elusive. A central challenge in studying the phenomenon is the rich heterogeneity of its expression (distal/proximal relocation, shortening, lengthening) and the variability of its functional role. A potential solution is to track AISs of a large number of neurons over time and attempt to induce structural plasticity in them. To this end, a promising approach is to use extracellular electrophysiological readouts to track a large number of neurons at high spatiotemporal resolution by means of high-density microelectrode arrays (HD-MEAs). However, an analysis framework that reliably identifies specific activity signatures that uniquely map on to underlying microstructural changes is missing. In this study, we assessed the feasibility of such a task and used the distal relocation of the AIS as an exemplary problem. We used sophisticated computational models to systematically explore the relationship between incremental changes in AIS positions and the specific consequences observed in simulated extracellular field potentials. An ensemble of feature changes in the extracellular fields that reliably characterize AIS plasticity was identified. We trained models that could detect these signatures with remarkable accuracy. Based on these findings, we propose a hybrid analysis framework that could potentially enable high-throughput experimental studies of activity-dependent AIS plasticity using HD-MEAs.}, keywords = {CMOS, HD-MEA, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close Despite being composed of highly plastic neurons with extensive positive feedback, the nervous system maintains stable overall function. To keep activity within bounds, it relies on a set of negative feedback mechanisms that can induce stabilizing adjustments and that are collectively termed “homeostatic plasticity.” Recently, a highly excitable microdomain, located at the proximal end of the axon—the axon initial segment (AIS)—was found to exhibit structural modifications in response to activity perturbations. Though AIS plasticity appears to serve a homeostatic purpose, many aspects governing its expression and its functional role in regulating neuronal excitability remain elusive. A central challenge in studying the phenomenon is the rich heterogeneity of its expression (distal/proximal relocation, shortening, lengthening) and the variability of its functional role. A potential solution is to track AISs of a large number of neurons over time and attempt to induce structural plasticity in them. To this end, a promising approach is to use extracellular electrophysiological readouts to track a large number of neurons at high spatiotemporal resolution by means of high-density microelectrode arrays (HD-MEAs). However, an analysis framework that reliably identifies specific activity signatures that uniquely map on to underlying microstructural changes is missing. In this study, we assessed the feasibility of such a task and used the distal relocation of the AIS as an exemplary problem. We used sophisticated computational models to systematically explore the relationship between incremental changes in AIS positions and the specific consequences observed in simulated extracellular field potentials. An ensemble of feature changes in the extracellular fields that reliably characterize AIS plasticity was identified. We trained models that could detect these signatures with remarkable accuracy. Based on these findings, we propose a hybrid analysis framework that could potentially enable high-throughput experimental studies of activity-dependent AIS plasticity using HD-MEAs. Close https://www.frontiersin.org/articles/10.3389/fninf.2022.957255/full doi:10.3389/fninf.2022.957255 Close
	Lee, Jihyun; Gänswein, Tobias; Ulusan, Hasan; Emmenegger, Vishalini; Saguner, Ardan M; Duru, Firat; and Hierlemann, Andreas Repeated and On-Demand Intracellular Recordings of Cardiomyocytes Derived from Human Induced Pluripotent Stem Cells Journal Article ACS Sensors, 2022. Abstract \| Links \| BibTeX \| Tags: Cardiomyocytes, CMOS, HD-MEA, MaxOne, MEA Technology @article{Lee2022, title = {Repeated and On-Demand Intracellular Recordings of Cardiomyocytes Derived from Human Induced Pluripotent Stem Cells}, author = {Jihyun Lee and Tobias Gänswein and Hasan Ulusan and Vishalini Emmenegger and Ardan M. Saguner and Firat Duru and and Andreas Hierlemann}, url = {https://pubs.acs.org/doi/10.1021/acssensors.2c01678}, doi = {https://doi.org/10.1021/acssensors.2c01678}, year = {2022}, date = {2022-09-27}, journal = {ACS Sensors}, abstract = {Pharmaceutical compounds may have cardiotoxic properties, triggering potentially life-threatening arrhythmi- as. To investigate proarrhythmic effects of drugs, the patch clamp technique has been used as the gold standard for charac- terizing the electrophysiology of cardiomyocytes in vitro. However, the applicability of this technology for drug screening is limited, as it is complex to use and features low throughput. Recent studies have demonstrated that 3D-nanostructured electrodes enable to obtain intracellular signals from many cardiomyocytes in parallel; however, the tedious electrode fab- rication and limited measurement duration still remain major issues for cardiotoxicity testing. Here, we demonstrate how porous Pt-black electrodes, arranged in high-density microelectrode arrays, can be used to record intracellular-like signals of cardiomyocytes at large-scale repeatedly over an extended period of time. The developed technique, which yields highly parallelized electroporations by using stimulation voltages around 1 Volt peak-to-peak amplitude, enabled intracellular-like recordings at high success rates without causing significant alteration in key electrophysiological features. In a proof of concept study, we investigated electrophysiological modulations induced by two clinically applied drugs, nifedipine and quinidine. As the obtained results were in good agreement with previously published data, we are confident that the devel- oped technique has the potential to be routinely used in in vitro platforms for cardiotoxicity screening.}, keywords = {Cardiomyocytes, CMOS, HD-MEA, MaxOne, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close Pharmaceutical compounds may have cardiotoxic properties, triggering potentially life-threatening arrhythmi- as. To investigate proarrhythmic effects of drugs, the patch clamp technique has been used as the gold standard for charac- terizing the electrophysiology of cardiomyocytes in vitro. However, the applicability of this technology for drug screening is limited, as it is complex to use and features low throughput. Recent studies have demonstrated that 3D-nanostructured electrodes enable to obtain intracellular signals from many cardiomyocytes in parallel; however, the tedious electrode fab- rication and limited measurement duration still remain major issues for cardiotoxicity testing. Here, we demonstrate how porous Pt-black electrodes, arranged in high-density microelectrode arrays, can be used to record intracellular-like signals of cardiomyocytes at large-scale repeatedly over an extended period of time. The developed technique, which yields highly parallelized electroporations by using stimulation voltages around 1 Volt peak-to-peak amplitude, enabled intracellular-like recordings at high success rates without causing significant alteration in key electrophysiological features. In a proof of concept study, we investigated electrophysiological modulations induced by two clinically applied drugs, nifedipine and quinidine. As the obtained results were in good agreement with previously published data, we are confident that the devel- oped technique has the potential to be routinely used in in vitro platforms for cardiotoxicity screening. Close https://pubs.acs.org/doi/10.1021/acssensors.2c01678 doi:https://doi.org/10.1021/acssensors.2c01678 Close
	Al-Absi, Abdel-Rahman; Thambiappaa, Sakeerthi Kethees; Khanc, Ahmad Raza; Glerup, Simon; Sanchez, Connie; Landau, Anne M; Nyengaard, Jens R Df(h22q11)/+ mouse model exhibits reduced binding levels of GABAA receptors and structural and functional dysregulation in the inhibitory and excitatory networks of hippocampus Journal Article Molecular and Cellular Neuroscience, 2022. Abstract \| Links \| BibTeX \| Tags: Brain Slice, CMOS, HD-MEA, MaxOne @article{Al-Absi2022, title = {Df(h22q11)/+ mouse model exhibits reduced binding levels of GABAA receptors and structural and functional dysregulation in the inhibitory and excitatory networks of hippocampus}, author = {Abdel-Rahman Al-Absi and Sakeerthi Kethees Thambiappaa and Ahmad Raza Khanc and Simon Glerup and Connie Sanchez and Anne M. Landau and Jens R. Nyengaard}, url = {https://www.sciencedirect.com/science/article/pii/S1044743122000756?via%3Dihub}, doi = {https://doi.org/10.1016/j.mcn.2022.103769}, year = {2022}, date = {2022-08-18}, journal = {Molecular and Cellular Neuroscience}, abstract = {The 22q11.2 hemizygous deletion confers high risk for multiple neurodevelopmental disorders. Inhibitory signaling, largely regulated through GABAA receptors, is suggested to serve a multitude of brain functions that are disrupted in the 22q11.2 deletion syndrome. We investigated the putative deficit of GABAA receptors and the potential substrates contributing to the inhibitory and excitatory dysregulations in hippocampal networks of the Df(h22q11)/+ mouse model of the 22q11.2 hemizygous deletion. The Df(h22q11)/+ mice exhibited impairments in several hippocampus-related functional domains, represented by impaired spatial memory and sensory gating functions. Autoradiography using the [3H]muscimol tracer revealed a significant reduction in GABAA receptor binding in the CA1 and CA3 subregions, together with a loss of GAD67+ interneurons in CA1 of Df(h22q11)/+ mice. Furthermore, electro- physiology recordings exhibited significantly higher neuronal activity in CA3, in response to the GABAA receptor antagonist, bicuculline, as compared with wild type mice. Density and volume of dendritic spines in pyramidal neurons were reduced and Sholl analysis also showed a reduction in the complexity of basal dendritic tree in CA1 and CA3 subregions of Df(h22q11)/+ mice. Overall, our findings demonstrate that hemizygous deletion in the 22q11.2 locus leads to dysregulations in the inhibitory circuits, involving reduced binding levels of GABAA receptors, in addition to functional and structural modulations of the excitatory networks of hippocampus.}, keywords = {Brain Slice, CMOS, HD-MEA, MaxOne}, pubstate = {published}, tppubtype = {article} } Close The 22q11.2 hemizygous deletion confers high risk for multiple neurodevelopmental disorders. Inhibitory signaling, largely regulated through GABAA receptors, is suggested to serve a multitude of brain functions that are disrupted in the 22q11.2 deletion syndrome. We investigated the putative deficit of GABAA receptors and the potential substrates contributing to the inhibitory and excitatory dysregulations in hippocampal networks of the Df(h22q11)/+ mouse model of the 22q11.2 hemizygous deletion. The Df(h22q11)/+ mice exhibited impairments in several hippocampus-related functional domains, represented by impaired spatial memory and sensory gating functions. Autoradiography using the [3H]muscimol tracer revealed a significant reduction in GABAA receptor binding in the CA1 and CA3 subregions, together with a loss of GAD67+ interneurons in CA1 of Df(h22q11)/+ mice. Furthermore, electro- physiology recordings exhibited significantly higher neuronal activity in CA3, in response to the GABAA receptor antagonist, bicuculline, as compared with wild type mice. Density and volume of dendritic spines in pyramidal neurons were reduced and Sholl analysis also showed a reduction in the complexity of basal dendritic tree in CA1 and CA3 subregions of Df(h22q11)/+ mice. Overall, our findings demonstrate that hemizygous deletion in the 22q11.2 locus leads to dysregulations in the inhibitory circuits, involving reduced binding levels of GABAA receptors, in addition to functional and structural modulations of the excitatory networks of hippocampus. Close https://www.sciencedirect.com/science/article/pii/S1044743122000756?via%3Dihub doi:https://doi.org/10.1016/j.mcn.2022.103769 Close
	Buccino Alessio Paolo; Damart, Tanguy; Bartram Julian; Mandge Darshan; Xue Xiaohan; Zbili Mickael; Gänswein Tobias; Jaquier Aurélien; Emmenegger Vishalini; Markram Henry; Hierlemann Andreas; Van Geit Werner. A multi-modal fitting approach to construct single-neuron models with patch clamp and high-density microelectrode arrays Journal Article bioRxiv, 2022. Abstract \| Links \| BibTeX \| Tags: 2D Neuronal Culture, Activity Scan Assay, Axon Tracking Assay, HD-MEA, MaxOne, Other Tissues, Publication, Stimulation Assay @article{Buccino2022, title = {A multi-modal fitting approach to construct single-neuron models with patch clamp and high-density microelectrode arrays}, author = {Buccino, Alessio Paolo; Damart, Tanguy; Bartram, Julian; Mandge, Darshan; Xue, Xiaohan; Zbili, Mickael; Gänswein, Tobias; Jaquier, Aurélien; Emmenegger, Vishalini; Markram, Henry; Hierlemann, Andreas; Van Geit, Werner.}, doi = {https://doi.org/10.1101/2022.08.03.502468}, year = {2022}, date = {2022-08-11}, journal = {bioRxiv}, abstract = {In computational neuroscience, multicompartment models are among the most biophysically realistic representations of single neurons. Constructing such models usually involves the use of the patch-clamp technique to record somatic voltage signals under different experimental conditions. The experimental data are then used to fit the many parameters of the model. While patching of the soma is currently the gold-standard approach to build multicompartment models, several studies have also evidenced a richness of dynamics in dendritic and axonal sections. Recording from the soma alone makes it hard to observe and correctly parameterize the activity of non-somatic compartments. In order to provide a richer set of data as input to multicompartment models, we here investigate the combination of somatic patch-clamp recordings with recordings of high-density micro-electrode arrays (HD-MEAs). HD-MEAs enable the observation of extracellular potentials and neural activity of neuronal compartments at sub-cellular resolution. In this work, we introduce a novel framework to combine patch-clamp and HD-MEA data to construct multicompartment models. We first validate our method on a ground-truth model with known parameters and show that the use of features extracted from extracellular signals, in addition to intracellular ones, yields models enabling better fits than using intracellular features alone. We also demonstrate our procedure using experimental data by constructing cell models from in vitro cell cultures. The proposed multi-modal fitting procedure has the potential to augment the modeling efforts of the computational neuroscience community and to provide the field with neuronal models that are more realistic and can be better validated. Author Summary Multicompartment models are one of the most biophysically detailed representations of single neurons. The vast majority of these models are built using experimental data from somatic recordings. However, neurons are much more than just their soma and one needs recordings from distal neurites to build an accurate model. In this article, we combine the patch-clamp technique with extracellular high-density microelectrode arrays (HD-MEAs) to compensate this shortcoming. In fact, HD-MEAs readouts allow one to record the neuronal signal in the entire axonal arbor. We show that the proposed multi-modal strategy is superior to the use of patch clamp alone using an existing model as ground-truth. Finally, we show an application of this strategy on experimental data from cultured neurons.}, keywords = {2D Neuronal Culture, Activity Scan Assay, Axon Tracking Assay, HD-MEA, MaxOne, Other Tissues, Publication, Stimulation Assay}, pubstate = {published}, tppubtype = {article} } Close In computational neuroscience, multicompartment models are among the most biophysically realistic representations of single neurons. Constructing such models usually involves the use of the patch-clamp technique to record somatic voltage signals under different experimental conditions. The experimental data are then used to fit the many parameters of the model. While patching of the soma is currently the gold-standard approach to build multicompartment models, several studies have also evidenced a richness of dynamics in dendritic and axonal sections. Recording from the soma alone makes it hard to observe and correctly parameterize the activity of non-somatic compartments. In order to provide a richer set of data as input to multicompartment models, we here investigate the combination of somatic patch-clamp recordings with recordings of high-density micro-electrode arrays (HD-MEAs). HD-MEAs enable the observation of extracellular potentials and neural activity of neuronal compartments at sub-cellular resolution. In this work, we introduce a novel framework to combine patch-clamp and HD-MEA data to construct multicompartment models. We first validate our method on a ground-truth model with known parameters and show that the use of features extracted from extracellular signals, in addition to intracellular ones, yields models enabling better fits than using intracellular features alone. We also demonstrate our procedure using experimental data by constructing cell models from in vitro cell cultures. The proposed multi-modal fitting procedure has the potential to augment the modeling efforts of the computational neuroscience community and to provide the field with neuronal models that are more realistic and can be better validated. Author Summary Multicompartment models are one of the most biophysically detailed representations of single neurons. The vast majority of these models are built using experimental data from somatic recordings. However, neurons are much more than just their soma and one needs recordings from distal neurites to build an accurate model. In this article, we combine the patch-clamp technique with extracellular high-density microelectrode arrays (HD-MEAs) to compensate this shortcoming. In fact, HD-MEAs readouts allow one to record the neuronal signal in the entire axonal arbor. We show that the proposed multi-modal strategy is superior to the use of patch clamp alone using an existing model as ground-truth. Finally, we show an application of this strategy on experimental data from cultured neurons. Close doi:https://doi.org/10.1101/2022.08.03.502468 Close
	Xue, Xiaohan; Buccino, Alessio Paolo; Kumar, Sreedhar Saseendran; Hierlemann, Andreas; Bartram, Julian Inferring monosynaptic connections from paired dendritic spine Ca2+ imaging and large-scale recording of extracellular spiking Journal Article Journal of Neural Engineering, 2022. Abstract \| Links \| BibTeX \| Tags: 2D Neuronal Culture, Activity Assay, HD-MEA, MaxOne, Network Assay, Primary Neuronal Cell Culture, Publication @article{Xue2022b, title = {Inferring monosynaptic connections from paired dendritic spine Ca2+ imaging and large-scale recording of extracellular spiking}, author = {Xiaohan Xue and Alessio Paolo Buccino and Sreedhar Saseendran Kumar and Andreas Hierlemann and Julian Bartram}, doi = {https://doi.org/10.1088/1741-2552/ac8765}, year = {2022}, date = {2022-08-11}, journal = {Journal of Neural Engineering}, abstract = {Techniques to identify monosynaptic connections between neurons have been vital for neuroscience research, facilitating important advancements concerning network topology, synaptic plasticity, and synaptic integration, among others. Here, we introduce a novel approach to identify and monitor monosynaptic connections using high-resolution dendritic spine Ca2+ imaging combined with simultaneous large-scale recording of extracellular electrical activity by means of high-density microelectrode arrays (HD-MEAs). We introduce an easily adoptable analysis pipeline that associates the imaged spine with its presynaptic unit and test it on in vitro recordings. The method is further validated and optimized by simulating synaptically-evoked spine Ca2+ transients based on measured spike trains in order to obtain simulated ground-truth connections. The proposed approach offers unique advantages as i) it can be used to identify monosynaptic connections with an accurate localization of the synapse within the dendritic tree, ii) it provides precise information of presynaptic spiking, and iii) postsynaptic spine Ca2+ signals and, finally, iv) the non-invasive nature of the proposed method allows for long-term measurements. The analysis toolkit together with the rich data sets that were acquired are made publicly available for further exploration by the research community.}, keywords = {2D Neuronal Culture, Activity Assay, HD-MEA, MaxOne, Network Assay, Primary Neuronal Cell Culture, Publication}, pubstate = {published}, tppubtype = {article} } Close Techniques to identify monosynaptic connections between neurons have been vital for neuroscience research, facilitating important advancements concerning network topology, synaptic plasticity, and synaptic integration, among others. Here, we introduce a novel approach to identify and monitor monosynaptic connections using high-resolution dendritic spine Ca2+ imaging combined with simultaneous large-scale recording of extracellular electrical activity by means of high-density microelectrode arrays (HD-MEAs). We introduce an easily adoptable analysis pipeline that associates the imaged spine with its presynaptic unit and test it on in vitro recordings. The method is further validated and optimized by simulating synaptically-evoked spine Ca2+ transients based on measured spike trains in order to obtain simulated ground-truth connections. The proposed approach offers unique advantages as i) it can be used to identify monosynaptic connections with an accurate localization of the synapse within the dendritic tree, ii) it provides precise information of presynaptic spiking, and iii) postsynaptic spine Ca2+ signals and, finally, iv) the non-invasive nature of the proposed method allows for long-term measurements. The analysis toolkit together with the rich data sets that were acquired are made publicly available for further exploration by the research community. Close doi:https://doi.org/10.1088/1741-2552/ac8765 Close
	Sharf Tal; Molen, Tjitse; Glasauer Stella; Guzman Elmer; Buccino Alessio; Luna Gabriel; Cheng Zhuowei; Audouard Morgane; Ranasinghe Kamalini; Kudo Kiwamu; Nagarajan Srikantan; Tovar Kenneth; Petzold Linda; Hierlemann Andreas; Hansma Paul; ; Kosik, Kenneth; Functional neuronal circuitry and oscillatory dynamics in human brain organoids Journal Article Nature Communications, 2022. Abstract \| Links \| BibTeX \| Tags: MaxOne, Neuronal Networks, Organoids @article{Sharf2022, title = {Functional neuronal circuitry and oscillatory dynamics in human brain organoids}, author = {Sharf, Tal; Molen, Tjitse; Glasauer, Stella; Guzman, Elmer; Buccino, Alessio; Luna, Gabriel; Cheng, Zhuowei; Audouard, Morgane; Ranasinghe, Kamalini; Kudo, Kiwamu; Nagarajan, Srikantan; Tovar, Kenneth; Petzold, Linda; Hierlemann, Andreas; Hansma, Paul; and Kosik, Kenneth; }, doi = {https://doi.org/10.1038/s41467-022-32115-4}, year = {2022}, date = {2022-07-29}, journal = {Nature Communications}, abstract = {Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiology of neuronal circuits within organoids remains under-explored. With high-density CMOS microelectrode arrays and shank electrodes, we captured spontaneous extracellular activity from brain organoids derived from human induced pluripotent stem cells. We inferred functional connectivity from spike timing, revealing a large number of weak connections within a skeleton of significantly fewer strong connections. A benzodiazepine increased the uniformity of firing patterns and decreased the relative fraction of weakly connected edges. Our analysis of the local field potential demonstrate that brain organoids contain neuronal assemblies of sufficient size and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug action, and the effects of external stimuli upon neuronal networks.}, keywords = {MaxOne, Neuronal Networks, Organoids}, pubstate = {published}, tppubtype = {article} } Close Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiology of neuronal circuits within organoids remains under-explored. With high-density CMOS microelectrode arrays and shank electrodes, we captured spontaneous extracellular activity from brain organoids derived from human induced pluripotent stem cells. We inferred functional connectivity from spike timing, revealing a large number of weak connections within a skeleton of significantly fewer strong connections. A benzodiazepine increased the uniformity of firing patterns and decreased the relative fraction of weakly connected edges. Our analysis of the local field potential demonstrate that brain organoids contain neuronal assemblies of sufficient size and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug action, and the effects of external stimuli upon neuronal networks. Close doi:https://doi.org/10.1038/s41467-022-32115-4 Close
	Idrees, Saad; Baumann, Matthias-Philipp; Korympidou, Maria M; Schubert, Timm; Kling, Alexandra; Franke, Katrin; Hafed, Ziad M; Franke, Felix; Münch, Thomas A Suppression without inhibition: how retinal computation contributes to saccadic suppression Journal Article Communications Biology, 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, MaxOne, Retina @article{Idrees2022, title = {Suppression without inhibition: how retinal computation contributes to saccadic suppression}, author = {Saad Idrees and Matthias-Philipp Baumann and Maria M. Korympidou and Timm Schubert and Alexandra Kling and Katrin Franke and Ziad M. Hafed and Felix Franke and Thomas A. Münch }, url = {https://www.nature.com/articles/s42003-022-03526-2}, year = {2022}, date = {2022-07-12}, journal = {Communications Biology}, abstract = {Visual perception remains stable across saccadic eye movements, despite the concurrent strongly disruptive visual flow. This stability is partially associated with a reduction in visual sensitivity, known as saccadic suppression, which already starts in the retina with reduced ganglion cell sensitivity. However, the retinal circuit mechanisms giving rise to such sup- pression remain unknown. Here, we describe these mechanisms using electrophysiology in mouse, pig, and macaque retina, 2-photon calcium imaging, computational modeling, and human psychophysics. We find that sequential stimuli, like those that naturally occur during saccades, trigger three independent suppressive mechanisms in the retina. The main mechanism is triggered by contrast-reversing sequential stimuli and originates within the receptive field center of ganglion cells. It does not involve inhibition or other known sup- pressive mechanisms like saturation or adaptation. Instead, it relies on temporal filtering of the inherently slow response of cone photoreceptors coupled with downstream non- linearities. Two further mechanisms of suppression are present predominantly in ON ganglion cells and originate in the receptive field surround, highlighting another disparity between ON and OFF ganglion cells. The mechanisms uncovered here likely play a role in shaping the retinal output following eye movements and other natural viewing conditions where sequential stimulation is ubiquitous.}, keywords = {HD-MEA, MaxOne, Retina}, pubstate = {published}, tppubtype = {article} } Close Visual perception remains stable across saccadic eye movements, despite the concurrent strongly disruptive visual flow. This stability is partially associated with a reduction in visual sensitivity, known as saccadic suppression, which already starts in the retina with reduced ganglion cell sensitivity. However, the retinal circuit mechanisms giving rise to such sup- pression remain unknown. Here, we describe these mechanisms using electrophysiology in mouse, pig, and macaque retina, 2-photon calcium imaging, computational modeling, and human psychophysics. We find that sequential stimuli, like those that naturally occur during saccades, trigger three independent suppressive mechanisms in the retina. The main mechanism is triggered by contrast-reversing sequential stimuli and originates within the receptive field center of ganglion cells. It does not involve inhibition or other known sup- pressive mechanisms like saturation or adaptation. Instead, it relies on temporal filtering of the inherently slow response of cone photoreceptors coupled with downstream non- linearities. Two further mechanisms of suppression are present predominantly in ON ganglion cells and originate in the receptive field surround, highlighting another disparity between ON and OFF ganglion cells. The mechanisms uncovered here likely play a role in shaping the retinal output following eye movements and other natural viewing conditions where sequential stimulation is ubiquitous. Close https://www.nature.com/articles/s42003-022-03526-2 Close
	Wang, F; Li, S; Wang, T Y; Lopez, G A; Antoshechkin, I; Chou, T F P97/VCP ATPase inhibitors can rescue p97 mutation-linked motor neuron degeneration Journal Article Brain Communications, 2022. Abstract \| Links \| BibTeX \| Tags: MaxTwo @article{Wang2022, title = {P97/VCP ATPase inhibitors can rescue p97 mutation-linked motor neuron degeneration}, author = {F. Wang and S. Li and T. Y. Wang and G. A. Lopez and I. Antoshechkin and T.F. Chou}, url = {https://academic.oup.com/braincomms/article/4/4/fcac176/6632805}, doi = {https://doi.org/10.1093/braincomms/fcac176}, year = {2022}, date = {2022-07-06}, journal = {Brain Communications}, abstract = {Mutations in p97/VCP cause two motor neuron diseases: inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia and familial amyotrophic lateral sclerosis. How p97 mutations lead to motor neuron degeneration is, however, unknown. Here we used patient-derived induced pluripotent stem cells to generate p97 mutant motor neurons. We reduced the genetic background variation by comparing mutant motor neurons to its isogenic wild type lines. Proteomic analysis reveals that p97R155H/+ motor neurons upregulate several cell cycle proteins at Day 14, but this effect diminishes by Day 20. Molecular changes linked to delayed cell cycle exit are observed in p97 mutant motor neurons. We also find that two p97 inhibitors, CB-5083 and NMS-873, restore some dysregulated protein levels. In addition, two p97 inhibitors and a food and drug administration-approved cyclin-dependent kinase 4/6 inhibitor, Abemaciclib, can rescue motor neuron death. Overall, we successfully used iPSC-derived motor neurons, identified dysregulated proteome and transcriptome and showed that p97 inhibitors rescue phenotypes in this disease model.}, keywords = {MaxTwo}, pubstate = {published}, tppubtype = {article} } Close Mutations in p97/VCP cause two motor neuron diseases: inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia and familial amyotrophic lateral sclerosis. How p97 mutations lead to motor neuron degeneration is, however, unknown. Here we used patient-derived induced pluripotent stem cells to generate p97 mutant motor neurons. We reduced the genetic background variation by comparing mutant motor neurons to its isogenic wild type lines. Proteomic analysis reveals that p97R155H/+ motor neurons upregulate several cell cycle proteins at Day 14, but this effect diminishes by Day 20. Molecular changes linked to delayed cell cycle exit are observed in p97 mutant motor neurons. We also find that two p97 inhibitors, CB-5083 and NMS-873, restore some dysregulated protein levels. In addition, two p97 inhibitors and a food and drug administration-approved cyclin-dependent kinase 4/6 inhibitor, Abemaciclib, can rescue motor neuron death. Overall, we successfully used iPSC-derived motor neurons, identified dysregulated proteome and transcriptome and showed that p97 inhibitors rescue phenotypes in this disease model. Close https://academic.oup.com/braincomms/article/4/4/fcac176/6632805 doi:https://doi.org/10.1093/braincomms/fcac176 Close
	Schröter Manuel; Wang, Congwei; Terrigno Marco; Hornauer Philipp; Huang Ziqiang; Jagasia Ravi; Hierlemann Andreas Functional imaging of brain organoids using high-density microelectrode arrays Journal Article MRS Bulletin, 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, MaxOne, MaxTwo, Organoids @article{Schroter2022, title = {Functional imaging of brain organoids using high-density microelectrode arrays}, author = {Schröter, Manuel; Wang, Congwei; Terrigno, Marco; Hornauer, Philipp; Huang, Ziqiang; Jagasia, Ravi; Hierlemann, Andreas}, url = {https://link.springer.com/article/10.1557/s43577-022-00282-w}, year = {2022}, date = {2022-06-30}, journal = {MRS Bulletin}, abstract = {Studies have provided evidence that human cerebral organoids (hCOs) recapitulate fundamental milestones of early brain development, but many important questions regarding their functionality and electrophysiological properties persist. High-density microelectrode arrays (HD-MEAs) represent an attractive analysis platform to perform functional studies of neuronal networks at the cellular and network scale. Here, we use HD-MEAs to derive large-scale electrophysiological recordings from sliced hCOs. We record the activity of hCO slices over several weeks and probe observed neuronal dynamics pharmacologically. Moreover, we present results on how the obtained recordings can be spike-sorted and subsequently studied across scales. For example, we show how to track single neurons across several days on the HD-MEA and how to infer axonal action potential velocities. We also infer putative functional connectivity from hCO recordings. The introduced methodology will contribute to a better understanding of developing neuronal networks in brain organoids and provide new means for their functional characterization.}, keywords = {HD-MEA, MaxOne, MaxTwo, Organoids}, pubstate = {published}, tppubtype = {article} } Close Studies have provided evidence that human cerebral organoids (hCOs) recapitulate fundamental milestones of early brain development, but many important questions regarding their functionality and electrophysiological properties persist. High-density microelectrode arrays (HD-MEAs) represent an attractive analysis platform to perform functional studies of neuronal networks at the cellular and network scale. Here, we use HD-MEAs to derive large-scale electrophysiological recordings from sliced hCOs. We record the activity of hCO slices over several weeks and probe observed neuronal dynamics pharmacologically. Moreover, we present results on how the obtained recordings can be spike-sorted and subsequently studied across scales. For example, we show how to track single neurons across several days on the HD-MEA and how to infer axonal action potential velocities. We also infer putative functional connectivity from hCO recordings. The introduced methodology will contribute to a better understanding of developing neuronal networks in brain organoids and provide new means for their functional characterization. Close https://link.springer.com/article/10.1557/s43577-022-00282-w Close
	Xu, Jax H; Yao, Yao; Yao, Fenyong; Chen, Jiehui; Li, Meishi; Xianfa, ; Yang, ; Li, Sheng; Lu, Fangru; Hu, Ping; He, Shuijin; Peng, Guangdun; Jing, Naihe Generation of functional posterior spinal motor neurons from hPSCs-derived human spinal cord neural progenitor cells Journal Article BioRxiv, 2022. Abstract \| Links \| BibTeX \| Tags: 2D Neuronal Culture, CMOS, HD-MEA, IPSC, MaxOne @article{Xu2022, title = {Generation of functional posterior spinal motor neurons from hPSCs-derived human spinal cord neural progenitor cells}, author = {Jax H. Xu and Yao Yao and Fenyong Yao and Jiehui Chen and Meishi Li and Xianfa and Yang and Sheng Li and Fangru Lu and Ping Hu and Shuijin He and Guangdun Peng and Naihe Jing}, url = {https://www.biorxiv.org/content/10.1101/2022.06.26.495599v1}, doi = {https://doi.org/10.1101/2022.06.26.495599}, year = {2022}, date = {2022-06-27}, journal = {BioRxiv}, abstract = {Spinal motor neurons deficiency results in a series of devastating disorders such as amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA) and spinal cord injury (SCI). These disorders are currently incurable, while human pluripotent stem cells (hPSCs)-derived spinal motor neurons are promising but suffered from low-efficiency, functional immaturity and lacks of posterior cellular identity. In this study, we have established human spinal cord neural progenitor cells (hSCNPCs) via hPSCs differentiated neuromesodermal progenitors (NMPs) and demonstrated the hSCNPCs can be continuously expanded up to 40 passages. hSCNPCs can be rapidly differentiated into posterior spinal motor neurons with high efficiency. The functional maturity has been examined in detail. Moreover, a co-culture scheme which is compatible for both neural and muscular differentiation is developed to mimic the neuromuscular junction (NMJ) formation in vitro. Together, these studies highlight the potential avenues for generating clinically relevant spinal motor neurons and modeling neuromuscular diseases through our defined hSCNPCs.}, keywords = {2D Neuronal Culture, CMOS, HD-MEA, IPSC, MaxOne}, pubstate = {published}, tppubtype = {article} } Close Spinal motor neurons deficiency results in a series of devastating disorders such as amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA) and spinal cord injury (SCI). These disorders are currently incurable, while human pluripotent stem cells (hPSCs)-derived spinal motor neurons are promising but suffered from low-efficiency, functional immaturity and lacks of posterior cellular identity. In this study, we have established human spinal cord neural progenitor cells (hSCNPCs) via hPSCs differentiated neuromesodermal progenitors (NMPs) and demonstrated the hSCNPCs can be continuously expanded up to 40 passages. hSCNPCs can be rapidly differentiated into posterior spinal motor neurons with high efficiency. The functional maturity has been examined in detail. Moreover, a co-culture scheme which is compatible for both neural and muscular differentiation is developed to mimic the neuromuscular junction (NMJ) formation in vitro. Together, these studies highlight the potential avenues for generating clinically relevant spinal motor neurons and modeling neuromuscular diseases through our defined hSCNPCs. Close https://www.biorxiv.org/content/10.1101/2022.06.26.495599v1 doi:https://doi.org/10.1101/2022.06.26.495599 Close
	Sommer Daniel ; Rajkumar, Sandeep; Seidel Mira; Aly Amr; Ludolph Albert; Ho Ritchie; Boeckers Tobias; Catanese Alberto. Aging-Dependent Altered Transcriptional Programs Underlie Activity Impairments in Human C9orf72-Mutant Motor Neurons Journal Article Frontiers in Molecular Neuroscience, 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, MaxOne, Neuronal Networks @article{Sommer2022, title = {Aging-Dependent Altered Transcriptional Programs Underlie Activity Impairments in Human C9orf72-Mutant Motor Neurons}, author = {Sommer, Daniel ; Rajkumar, Sandeep; Seidel, Mira; Aly, Amr; Ludolph, Albert; Ho, Ritchie; Boeckers, Tobias; Catanese, Alberto.}, url = {https://www.frontiersin.org/articles/10.3389/fnmol.2022.894230/full}, year = {2022}, date = {2022-06-14}, journal = {Frontiers in Molecular Neuroscience}, abstract = {Amyotrophic Lateral Sclerosis (ALS) is an incurable neurodegenerative disease characterized by dysfunction and loss of upper and lower motor neurons (MN). Despite several studies identifying drastic alterations affecting synaptic composition and functionality in different experimental models, the specific contribution of impaired activity to the neurodegenerative processes observed in ALS-related MN remains controversial. In particular, contrasting lines of evidence have shown both hyper- as well as hypoexcitability as driving pathomechanisms characterizing this specific neuronal population. In this study, we combined high definition multielectrode array (HD-MEA) techniques with transcriptomic analysis to longitudinally monitor and untangle the activity-dependent alterations arising in human C9orf72-mutant MN. We found a time-dependent reduction of neuronal activity in ALSC9orf72 cultures occurring as synaptic contacts undergo maturation and matched by a significant loss of mutant MN upon aging. Notably, ALS-related neurons displayed reduced network synchronicity most pronounced at later stages of culture, suggesting synaptic imbalance. In concordance with the HD-MEA data, transcriptomic analysis revealed an early up-regulation of synaptic terms in ALSC9orf72 MN, whose expression was decreased in aged cultures. In addition, treatment of older mutant cells with Apamin, a K+ channel blocker previously shown to be neuroprotective in ALS, rescued the time-dependent loss of firing properties observed in ALSC9orf72 MN as well as the expression of maturity-related synaptic genes. All in all, this study broadens the understanding of how impaired synaptic activity contributes to MN degeneration in ALS by correlating electrophysiological alterations to aging-dependent transcriptional programs. }, keywords = {HD-MEA, MaxOne, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Amyotrophic Lateral Sclerosis (ALS) is an incurable neurodegenerative disease characterized by dysfunction and loss of upper and lower motor neurons (MN). Despite several studies identifying drastic alterations affecting synaptic composition and functionality in different experimental models, the specific contribution of impaired activity to the neurodegenerative processes observed in ALS-related MN remains controversial. In particular, contrasting lines of evidence have shown both hyper- as well as hypoexcitability as driving pathomechanisms characterizing this specific neuronal population. In this study, we combined high definition multielectrode array (HD-MEA) techniques with transcriptomic analysis to longitudinally monitor and untangle the activity-dependent alterations arising in human C9orf72-mutant MN. We found a time-dependent reduction of neuronal activity in ALSC9orf72 cultures occurring as synaptic contacts undergo maturation and matched by a significant loss of mutant MN upon aging. Notably, ALS-related neurons displayed reduced network synchronicity most pronounced at later stages of culture, suggesting synaptic imbalance. In concordance with the HD-MEA data, transcriptomic analysis revealed an early up-regulation of synaptic terms in ALSC9orf72 MN, whose expression was decreased in aged cultures. In addition, treatment of older mutant cells with Apamin, a K+ channel blocker previously shown to be neuroprotective in ALS, rescued the time-dependent loss of firing properties observed in ALSC9orf72 MN as well as the expression of maturity-related synaptic genes. All in all, this study broadens the understanding of how impaired synaptic activity contributes to MN degeneration in ALS by correlating electrophysiological alterations to aging-dependent transcriptional programs. Close https://www.frontiersin.org/articles/10.3389/fnmol.2022.894230/full Close
	Cheng, Zhuowei; Guzman, Elmer; van der Molen, Tjitse; Sharf, Tal; Hansma, Paul K; Kosik, Kenneth S; Petzold, Linda; Tovar, Kenneth R Automated detection of extracellular action potentials from single neurons Journal Article bioRxiv, 2022. Abstract \| Links \| BibTeX \| Tags: Action Potential, HD-MEA, MaxOne @article{Cheng2023, title = {Automated detection of extracellular action potentials from single neurons}, author = {Zhuowei Cheng and Elmer Guzman and Tjitse van der Molen and Tal Sharf and Paul K. Hansma and Kenneth S Kosik and Linda Petzold and Kenneth R Tovar}, url = {https://www.biorxiv.org/content/10.1101/2022.06.06.494896v1.abstract}, doi = {https://doi.org/10.1101/2022.06.06.494896}, year = {2022}, date = {2022-06-06}, journal = {bioRxiv}, abstract = {Multi-electrode arrays (MEAs) non-invasively record extracellular action potentials (eAPs, also known as spikes) from hundreds of neurons simultaneously. However, because extracellular electrodes sample from the local electrical field, each electrode can detect eAPs from multiple nearby neurons. Interpreting spike trains at individual electrodes of high-density arrays requires spike sorting, a computational process which groups eAPs from single ’units’ based on assumptions of how spike waveforms correlate with different neuronal sources. Additionally, when experimental conditions result in changes to eAP waveforms, spike sorting routines may have difficulty correlating eAPs from multiple neurons at single electrodes before and after such waveform changes. We present here a novel, empirical method for unambiguously isolating eAPs from individual, uniquely identifiable neurons, based on automated multi- point detection of action potential propagation. This method is insensitive to changes in eAP waveform morphology because it makes no assumptions about the relationship between spike waveform and neuronal source. Our algorithm for automated detection of action potential propagation produces a ’fingerprint’ that uniquely identifies those spikes from each neuron. By unambiguously isolating eAPs from multiple neurons in each recording, on a range of platforms and experimental preparations, our method now enables high-content screening with contemporary MEAs. We outline the limitations and strengths of propagation-based isolation of eAPs from single neurons and propose how our automated method complements spike sorting and could be adapted to in vivo use.}, keywords = {Action Potential, HD-MEA, MaxOne}, pubstate = {published}, tppubtype = {article} } Close Multi-electrode arrays (MEAs) non-invasively record extracellular action potentials (eAPs, also known as spikes) from hundreds of neurons simultaneously. However, because extracellular electrodes sample from the local electrical field, each electrode can detect eAPs from multiple nearby neurons. Interpreting spike trains at individual electrodes of high-density arrays requires spike sorting, a computational process which groups eAPs from single ’units’ based on assumptions of how spike waveforms correlate with different neuronal sources. Additionally, when experimental conditions result in changes to eAP waveforms, spike sorting routines may have difficulty correlating eAPs from multiple neurons at single electrodes before and after such waveform changes. We present here a novel, empirical method for unambiguously isolating eAPs from individual, uniquely identifiable neurons, based on automated multi- point detection of action potential propagation. This method is insensitive to changes in eAP waveform morphology because it makes no assumptions about the relationship between spike waveform and neuronal source. Our algorithm for automated detection of action potential propagation produces a ’fingerprint’ that uniquely identifies those spikes from each neuron. By unambiguously isolating eAPs from multiple neurons in each recording, on a range of platforms and experimental preparations, our method now enables high-content screening with contemporary MEAs. We outline the limitations and strengths of propagation-based isolation of eAPs from single neurons and propose how our automated method complements spike sorting and could be adapted to in vivo use. Close https://www.biorxiv.org/content/10.1101/2022.06.06.494896v1.abstract doi:https://doi.org/10.1101/2022.06.06.494896 Close
	Noh Seungmin ; Jeon, Sungwoong; Kim Eunhee; Oh Untaek; Park Danbi; Park Sun Hwa; Kim Sung Won; Pané Salvador; Nelson Bradley; Kim Jin-young; Choi Hongsoo; A Biodegradable Magnetic Microrobot Based on Gelatin Methacrylate for Precise Delivery of Stem Cells with Mass Production Capability Journal Article Small, 2022. Abstract \| Links \| BibTeX \| Tags: MaxOne @article{Noh2022, title = {A Biodegradable Magnetic Microrobot Based on Gelatin Methacrylate for Precise Delivery of Stem Cells with Mass Production Capability}, author = {Noh, Seungmin ; Jeon, Sungwoong; Kim, Eunhee; Oh, Untaek; Park, Danbi; Park, Sun Hwa; Kim, Sung Won; Pané, Salvador; Nelson, Bradley; Kim, Jin-young; Choi, Hongsoo;}, url = {https://onlinelibrary.wiley.com/doi/10.1002/smll.202107888}, doi = {10.1002/smll.202107888}, year = {2022}, date = {2022-05-23}, journal = {Small}, abstract = {A great deal of research has focused on small-scale robots for biomedical applications and minimally invasive delivery of therapeutics (e.g., cells, drugs, and genes) to a target area. Conventional fabrication methods, such as two-photon polymerization, can be used to build sophisticated micro- and nanorobots, but the long fabrication cycle for a single microrobot has limited its practical use. This study proposes a biodegradable spherical gelatin methacrylate (GelMA) microrobot for mass production in a microfluidic channel. The proposed microrobot is fabricated in a flow-focusing droplet generator by shearing a mixture of GelMA, photoinitiator, and superparamagnetic iron oxide nanoparticles (SPIONs) with a mixture of oil and surfactant. Human nasal turbinate stem cells (hNTSCs) are loaded on the GelMA microrobot, and the hNTSC-loaded microrobot shows precise rolling motion in response to an external rotating magnetic field. The microrobot is enzymatically degraded by collagenase, and released hNTSCs are proliferated and differentiated into neuronal cells. In addition, the feasibility of the GelMA microrobot as a cell therapeutic delivery system is investigated by measuring electrophysiological activity on a multielectrode array. Such a versatile and fully biodegradable microrobot has the potential for targeted stem cell delivery, proliferation, and differentiation for stem cell-based therapy.}, keywords = {MaxOne}, pubstate = {published}, tppubtype = {article} } Close A great deal of research has focused on small-scale robots for biomedical applications and minimally invasive delivery of therapeutics (e.g., cells, drugs, and genes) to a target area. Conventional fabrication methods, such as two-photon polymerization, can be used to build sophisticated micro- and nanorobots, but the long fabrication cycle for a single microrobot has limited its practical use. This study proposes a biodegradable spherical gelatin methacrylate (GelMA) microrobot for mass production in a microfluidic channel. The proposed microrobot is fabricated in a flow-focusing droplet generator by shearing a mixture of GelMA, photoinitiator, and superparamagnetic iron oxide nanoparticles (SPIONs) with a mixture of oil and surfactant. Human nasal turbinate stem cells (hNTSCs) are loaded on the GelMA microrobot, and the hNTSC-loaded microrobot shows precise rolling motion in response to an external rotating magnetic field. The microrobot is enzymatically degraded by collagenase, and released hNTSCs are proliferated and differentiated into neuronal cells. In addition, the feasibility of the GelMA microrobot as a cell therapeutic delivery system is investigated by measuring electrophysiological activity on a multielectrode array. Such a versatile and fully biodegradable microrobot has the potential for targeted stem cell delivery, proliferation, and differentiation for stem cell-based therapy. Close https://onlinelibrary.wiley.com/doi/10.1002/smll.202107888 doi:10.1002/smll.202107888 Close
	Sato Yuya; Yamamoto, Hideaki; Kato Hideyuki; Tanii Takashi; Sato Shigeo; Hirano-Iwata Ayumi Microfluidic cell engineering on high-density microelectrode arrays for assessing structure-function relationships in living neuronal networks Journal Article 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, MaxOne, Neuronal Networks @article{Sato2022, title = {Microfluidic cell engineering on high-density microelectrode arrays for assessing structure-function relationships in living neuronal networks}, author = {Sato, Yuya; Yamamoto, Hideaki; Kato, Hideyuki; Tanii, Takashi; Sato, Shigeo; Hirano-Iwata, Ayumi}, url = {https://arxiv.org/abs/2205.04342}, year = {2022}, date = {2022-05-11}, abstract = {Neuronal networks in dissociated culture combined with cell engineering technology offer a pivotal platform to constructively explore the relationship between structure and function in living neuronal networks. Here, we fabricated defined neuronal networks possessing a modular architecture on high-density microelectrode arrays (HD-MEAs), a state-of-the-art electrophysiological tool for recording neural activity with high spatial and temporal resolutions. We first established a surface coating protocol using a cell-permissive hydrogel to stably attach polydimethylsiloxane microfluidic film on the HD-MEA. We then recorded the spontaneous neural activity of the engineered neuronal network, which revealed an important portrait of the engineered neuronal network--modular architecture enhances functional complexity by reducing the excessive neural correlation between spatially segregated modules. The results of this study highlight the impact of HD-MEA recordings combined with cell engineering technologies as a novel tool in neuroscience to constructively assess the structure-function relationships in neuronal networks.}, keywords = {HD-MEA, MaxOne, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Neuronal networks in dissociated culture combined with cell engineering technology offer a pivotal platform to constructively explore the relationship between structure and function in living neuronal networks. Here, we fabricated defined neuronal networks possessing a modular architecture on high-density microelectrode arrays (HD-MEAs), a state-of-the-art electrophysiological tool for recording neural activity with high spatial and temporal resolutions. We first established a surface coating protocol using a cell-permissive hydrogel to stably attach polydimethylsiloxane microfluidic film on the HD-MEA. We then recorded the spontaneous neural activity of the engineered neuronal network, which revealed an important portrait of the engineered neuronal network--modular architecture enhances functional complexity by reducing the excessive neural correlation between spatially segregated modules. The results of this study highlight the impact of HD-MEA recordings combined with cell engineering technologies as a novel tool in neuroscience to constructively assess the structure-function relationships in neuronal networks. Close https://arxiv.org/abs/2205.04342 Close
	Shimba Kenta; Asahina, Takahiro; Sakai Koji; Kotani Kiyoshi; Jimbo Yasuhiko Recording Saltatory Conduction Along Sensory Axons Using a High-Density Microelectrode Array Journal Article Frontiers in Neuroscience, 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, MaxOne, Neuronal cell culture @article{Shimba2022, title = {Recording Saltatory Conduction Along Sensory Axons Using a High-Density Microelectrode Array}, author = {Shimba, Kenta; Asahina, Takahiro; Sakai, Koji; Kotani, Kiyoshi; Jimbo, Yasuhiko}, url = {https://www.frontiersin.org/articles/10.3389/fnins.2022.854637/full}, year = {2022}, date = {2022-04-18}, journal = {Frontiers in Neuroscience}, abstract = {In bottom-up neuroscience, questions on neural information processing are addressed by engineering small but reproducible biological neural networks of defined network topology in vitro. The network topology can be controlled by culturing neurons within polydimethylsiloxane (PDMS) microstructures that are combined with microelectrode arrays (MEAs) for electric access to the network. However, currently used glass MEAs are limited to 256 electrodes and pose a limitation to the spatial resolution as well as the design of more complex microstructures. The use of high density complementary metal-oxide-semiconductor (CMOS) MEAs greatly increases the spatial resolution, enabling sub-cellular readout and stimulation of neurons in defined neural networks. Unfortunately, the non-planar surface of CMOS MEAs complicates the attachment of PDMS microstructures. To overcome the problem of axons escaping the microstructures through the ridges of the CMOS MEA, we stamp-transferred a thin film of hexane-diluted PDMS onto the array such that the PDMS filled the ridges at the contact surface of the microstructures without clogging the axon guidance channels. This method resulted in 23 % of structurally fully connected but sealed networks on the CMOS MEA of which about 45 % showed spiking activity in all channels. Moreover, we provide an impedance-based method to visualize the exact location of the microstructures on the MEA and show that our method can confine axonal growth within the PDMS microstructures. Finally, the high spatial resolution of the CMOS MEA enabled us to show that action potentials follow the unidirectional topology of our circular multi-node microstructure.}, keywords = {HD-MEA, MaxOne, Neuronal cell culture}, pubstate = {published}, tppubtype = {article} } Close In bottom-up neuroscience, questions on neural information processing are addressed by engineering small but reproducible biological neural networks of defined network topology in vitro. The network topology can be controlled by culturing neurons within polydimethylsiloxane (PDMS) microstructures that are combined with microelectrode arrays (MEAs) for electric access to the network. However, currently used glass MEAs are limited to 256 electrodes and pose a limitation to the spatial resolution as well as the design of more complex microstructures. The use of high density complementary metal-oxide-semiconductor (CMOS) MEAs greatly increases the spatial resolution, enabling sub-cellular readout and stimulation of neurons in defined neural networks. Unfortunately, the non-planar surface of CMOS MEAs complicates the attachment of PDMS microstructures. To overcome the problem of axons escaping the microstructures through the ridges of the CMOS MEA, we stamp-transferred a thin film of hexane-diluted PDMS onto the array such that the PDMS filled the ridges at the contact surface of the microstructures without clogging the axon guidance channels. This method resulted in 23 % of structurally fully connected but sealed networks on the CMOS MEA of which about 45 % showed spiking activity in all channels. Moreover, we provide an impedance-based method to visualize the exact location of the microstructures on the MEA and show that our method can confine axonal growth within the PDMS microstructures. Finally, the high spatial resolution of the CMOS MEA enabled us to show that action potentials follow the unidirectional topology of our circular multi-node microstructure. Close https://www.frontiersin.org/articles/10.3389/fnins.2022.854637/full Close
	Hornauer Philipp; Prack, Gustavo; Anastasi Nadia; Ronchi Silvia; Kim Taehoon; Donner Christian; Fiscella Michele; Borgwardt Karsten; Taylor Verdon; Jagasia Ravi; Roqueiro Damian; Hierlemann Andreas; Downregulating α-synuclein in iPSC-derived dopaminergic neurons mimics 2 electrophysiological phenotype of the A53T mutation Journal Article bioRxiv, 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, MaxOne, Neuronal cell culture @article{Hornauer2022, title = {Downregulating α-synuclein in iPSC-derived dopaminergic neurons mimics 2 electrophysiological phenotype of the A53T mutation}, author = {Hornauer, Philipp; Prack, Gustavo; Anastasi, Nadia; Ronchi, Silvia; Kim, Taehoon; Donner, Christian; Fiscella, Michele; Borgwardt, Karsten; Taylor, Verdon; Jagasia, Ravi; Roqueiro, Damian; Hierlemann, Andreas;}, url = {https://www.biorxiv.org/content/10.1101/2022.03.31.486582v1.full}, year = {2022}, date = {2022-04-01}, journal = {bioRxiv}, abstract = {Parkinson’s disease (PD) is a common debilitating neurodegenerative disorder, characterized by a progressive loss of dopaminergic (DA) neurons. Mutations, gene dosage increase, and single nucleotide polymorphisms in the α-synuclein-encoding gene SNCA either cause or increase the risk for PD. However, neither the function of α-synuclein in health and disease, nor its role throughout development is fully understood. Here, we introduce DeePhys, a new tool that allows for data-driven functional phenotyping of neuronal cell lines by combining electrophysiological features inferred from high-density microelectrode array (HD-MEA) recordings with a robust machine learning workflow. We apply DeePhys to human induced pluripotent stem cell (iPSC)-derived DA neuron-astrocyte co-cultures harboring the prominent SNCA mutation A53T and an isogenic control line. Moreover, we demonstrate how DeePhys can facilitate the assessment of cellular and network-level electrophysiological features to build functional phenotypes and to evaluate potential treatment interventions. We find that electrophysiological features across all scales proved to be highly specific for the A53T phenotype, enabled to predict the genotype and age of individual cultures with high accuracy, and revealed a mutant-like phenotype after downregulation of α-synuclein.}, keywords = {HD-MEA, MaxOne, Neuronal cell culture}, pubstate = {published}, tppubtype = {article} } Close Parkinson’s disease (PD) is a common debilitating neurodegenerative disorder, characterized by a progressive loss of dopaminergic (DA) neurons. Mutations, gene dosage increase, and single nucleotide polymorphisms in the α-synuclein-encoding gene SNCA either cause or increase the risk for PD. However, neither the function of α-synuclein in health and disease, nor its role throughout development is fully understood. Here, we introduce DeePhys, a new tool that allows for data-driven functional phenotyping of neuronal cell lines by combining electrophysiological features inferred from high-density microelectrode array (HD-MEA) recordings with a robust machine learning workflow. We apply DeePhys to human induced pluripotent stem cell (iPSC)-derived DA neuron-astrocyte co-cultures harboring the prominent SNCA mutation A53T and an isogenic control line. Moreover, we demonstrate how DeePhys can facilitate the assessment of cellular and network-level electrophysiological features to build functional phenotypes and to evaluate potential treatment interventions. We find that electrophysiological features across all scales proved to be highly specific for the A53T phenotype, enabled to predict the genotype and age of individual cultures with high accuracy, and revealed a mutant-like phenotype after downregulation of α-synuclein. Close https://www.biorxiv.org/content/10.1101/2022.03.31.486582v1.full Close
	Sawada, Haruto; Wake, Naoki; Sasabuchi, Kazuhiro; Takamatsu, Jun; Takahashi, Hirokazu; Ikeuchi, Katsushi Design strategies for controlling neuron-connected robots using reinforcement learning Journal Article arXiv, 2022. Abstract \| Links \| BibTeX \| Tags: Machine Learning, MaxOne, Stimulation @article{Sawada2022, title = {Design strategies for controlling neuron-connected robots using reinforcement learning}, author = {Haruto Sawada and Naoki Wake and Kazuhiro Sasabuchi and Jun Takamatsu and Hirokazu Takahashi and Katsushi Ikeuchi}, url = {https://arxiv.org/abs/2203.15290}, doi = {https://doi.org/10.48550/arXiv.2203.15290}, year = {2022}, date = {2022-03-29}, journal = {arXiv}, abstract = {Despite the growing interest in robot control utilizing the computation of biological neurons, context-dependent behavior by neuron-connected robots remains a challenge. Context-dependent behavior here is defined as behavior that is not the result of a simple sensory-motor coupling, but rather based on an understanding of the task goal. This paper proposes design principles for training neuron-connected robots based on task goals to achieve context-dependent behavior. First, we employ deep reinforcement learning (RL) to enable training that accounts for goal achievements. Second, we propose a neuron simulator as a probability distribution based on recorded neural data, aiming to represent physiologically valid neural dynamics while avoiding complex modeling with high computational costs. Furthermore, we propose to update the simulators during the training to bridge the gap between the simulation and the real settings. The experiments showed that the robot gradually learned context-dependent behaviors in pole balancing and robot navigation tasks. Moreover, the learned policies were valid for neural simulators based on novel neural data, and the task performance increased by updating the simulators during training. These results suggest the effectiveness of the proposed design principle for the context-dependent behavior of neuron-connected robots.}, keywords = {Machine Learning, MaxOne, Stimulation}, pubstate = {published}, tppubtype = {article} } Close Despite the growing interest in robot control utilizing the computation of biological neurons, context-dependent behavior by neuron-connected robots remains a challenge. Context-dependent behavior here is defined as behavior that is not the result of a simple sensory-motor coupling, but rather based on an understanding of the task goal. This paper proposes design principles for training neuron-connected robots based on task goals to achieve context-dependent behavior. First, we employ deep reinforcement learning (RL) to enable training that accounts for goal achievements. Second, we propose a neuron simulator as a probability distribution based on recorded neural data, aiming to represent physiologically valid neural dynamics while avoiding complex modeling with high computational costs. Furthermore, we propose to update the simulators during the training to bridge the gap between the simulation and the real settings. The experiments showed that the robot gradually learned context-dependent behaviors in pole balancing and robot navigation tasks. Moreover, the learned policies were valid for neural simulators based on novel neural data, and the task performance increased by updating the simulators during training. These results suggest the effectiveness of the proposed design principle for the context-dependent behavior of neuron-connected robots. Close https://arxiv.org/abs/2203.15290 doi:https://doi.org/10.48550/arXiv.2203.15290 Close
	Duru Jens; Küchler, Joël; Ihle Stephan Forró Csaba; Bernardi Aeneas; Girardin Sophie; Hengsteler Julian; Wheeler Stephen; János; Ruff Tobias; J ; Vörös Engineered Biological Neural Networks on High Density CMOS Microelectrode Arrays Journal Article 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, MaxOne, Neuronal Networks @article{Duru2022, title = {Engineered Biological Neural Networks on High Density CMOS Microelectrode Arrays}, author = {Duru, Jens; Küchler, Joël; Ihle, Stephan J.;, Forró, Csaba; Bernardi, Aeneas; Girardin, Sophie; Hengsteler, Julian; Wheeler, Stephen; Vörös, János; Ruff, Tobias;}, url = {https://www.frontiersin.org/articles/10.3389/fnins.2022.829884/full}, year = {2022}, date = {2022-02-21}, abstract = {In bottom-up neuroscience, questions on neural information processing are addressed by engineering small but reproducible biological neural networks of defined network topology in vitro. The network topology can be controlled by culturing neurons within polydimethylsiloxane (PDMS) microstructures that are combined with microelectrode arrays (MEAs) for electric access to the network. However, currently used glass MEAs are limited to 256 electrodes and pose a limitation to the spatial resolution as well as the design of more complex microstructures. The use of high density complementary metal-oxide-semiconductor (CMOS) MEAs greatly increases the spatial resolution, enabling sub-cellular readout and stimulation of neurons in defined neural networks. Unfortunately, the non-planar surface of CMOS MEAs complicates the attachment of PDMS microstructures. To overcome the problem of axons escaping the microstructures through the ridges of the CMOS MEA, we stamp-transferred a thin film of hexane-diluted PDMS onto the array such that the PDMS filled the ridges at the contact surface of the microstructures without clogging the axon guidance channels. This method resulted in 23 % of structurally fully connected but sealed networks on the CMOS MEA of which about 45 % showed spiking activity in all channels. Moreover, we provide an impedance-based method to visualize the exact location of the microstructures on the MEA and show that our method can confine axonal growth within the PDMS microstructures. Finally, the high spatial resolution of the CMOS MEA enabled us to show that action potentials follow the unidirectional topology of our circular multi-node microstructure.}, keywords = {HD-MEA, MaxOne, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close In bottom-up neuroscience, questions on neural information processing are addressed by engineering small but reproducible biological neural networks of defined network topology in vitro. The network topology can be controlled by culturing neurons within polydimethylsiloxane (PDMS) microstructures that are combined with microelectrode arrays (MEAs) for electric access to the network. However, currently used glass MEAs are limited to 256 electrodes and pose a limitation to the spatial resolution as well as the design of more complex microstructures. The use of high density complementary metal-oxide-semiconductor (CMOS) MEAs greatly increases the spatial resolution, enabling sub-cellular readout and stimulation of neurons in defined neural networks. Unfortunately, the non-planar surface of CMOS MEAs complicates the attachment of PDMS microstructures. To overcome the problem of axons escaping the microstructures through the ridges of the CMOS MEA, we stamp-transferred a thin film of hexane-diluted PDMS onto the array such that the PDMS filled the ridges at the contact surface of the microstructures without clogging the axon guidance channels. This method resulted in 23 % of structurally fully connected but sealed networks on the CMOS MEA of which about 45 % showed spiking activity in all channels. Moreover, we provide an impedance-based method to visualize the exact location of the microstructures on the MEA and show that our method can confine axonal growth within the PDMS microstructures. Finally, the high spatial resolution of the CMOS MEA enabled us to show that action potentials follow the unidirectional topology of our circular multi-node microstructure. Close https://www.frontiersin.org/articles/10.3389/fnins.2022.829884/full Close
	Xue, Xiaohan ; Buccino, Alessio Paolo ; Kumar, Sreedhar Saseendran ; Hierlemann, Andreas ; Bartram, Julian Inferring monosynaptic connections from paired dendritic spine Ca2+ imaging and large-scale recording of extracellular spiking Journal Article bioRxiv, 2022. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Neuronal Networks @article{Xue2022, title = {Inferring monosynaptic connections from paired dendritic spine Ca2+ imaging and large-scale recording of extracellular spiking}, author = {Xue, Xiaohan and Buccino, Alessio Paolo and Kumar, Sreedhar Saseendran and Hierlemann, Andreas and Bartram, Julian}, doi = {10.1101/2022.02.16.480643}, year = {2022}, date = {2022-02-16}, journal = {bioRxiv}, abstract = {Techniques to identify monosynaptic connections between neurons have been vital for neuroscience research, facilitating important advancements concerning network topology, synaptic plasticity, and synaptic integration, among others. Here, we introduce a novel approach to identify and monitor monosynaptic connections using high-resolution dendritic spine Ca2+ imaging combined with simultaneous large-scale recording of extracellular electrical activity by means of high-density microelectrode arrays (HD-MEAs). We introduce an easily adoptable analysis pipeline that associates the imaged spine with its presynaptic unit and test it on in vitro recordings. The method is further validated and optimized by simulating synaptically-evoked spine Ca2+ transients based on measured spike trains in order to obtain simulated ground-truth connections. The proposed approach offers unique advantages as i) it can be used to identify monosynaptic connections with an accurate localization of the synapse within the dendritic tree, ii) it provides precise information of presynaptic spiking, and iii) postsynaptic spine Ca2+ signals and, finally, iv) the non-invasive nature of the proposed method allows for long-term measurements. The analysis toolkit together with the rich data sets that were acquired are made publicly available for further exploration by the research community.}, keywords = {ETH-CMOS-MEA, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Techniques to identify monosynaptic connections between neurons have been vital for neuroscience research, facilitating important advancements concerning network topology, synaptic plasticity, and synaptic integration, among others. Here, we introduce a novel approach to identify and monitor monosynaptic connections using high-resolution dendritic spine Ca2+ imaging combined with simultaneous large-scale recording of extracellular electrical activity by means of high-density microelectrode arrays (HD-MEAs). We introduce an easily adoptable analysis pipeline that associates the imaged spine with its presynaptic unit and test it on in vitro recordings. The method is further validated and optimized by simulating synaptically-evoked spine Ca2+ transients based on measured spike trains in order to obtain simulated ground-truth connections. The proposed approach offers unique advantages as i) it can be used to identify monosynaptic connections with an accurate localization of the synapse within the dendritic tree, ii) it provides precise information of presynaptic spiking, and iii) postsynaptic spine Ca2+ signals and, finally, iv) the non-invasive nature of the proposed method allows for long-term measurements. The analysis toolkit together with the rich data sets that were acquired are made publicly available for further exploration by the research community. Close doi:10.1101/2022.02.16.480643 Close
	McSweeney, Danny; Gabriel, Rafael; Jin, Kang; Pang, Zhiping P; Aronow, Bruce; Pak, ChangHui Loss of Neurodevelopmental Gene CASK Disrupts Neural Connectivity in Human Cortical Excitatory Neurons Journal Article BioRxiv, 2022. Abstract \| Links \| BibTeX \| Tags: IPSC, MaxOne, Neuronal Networks @article{McSweeney2022, title = {Loss of Neurodevelopmental Gene CASK Disrupts Neural Connectivity in Human Cortical Excitatory Neurons}, author = {Danny McSweeney and Rafael Gabriel and Kang Jin and Zhiping P. Pang and Bruce Aronow and ChangHui Pak}, url = {https://doi.org/10.1101/2022.02.14.480404}, doi = {10.1101/2022.02.14.480404}, year = {2022}, date = {2022-02-15}, journal = {BioRxiv}, abstract = {Loss-of-function (LOF) mutations in CASK cause severe developmental phenotypes, including microcephaly with pontine and cerebellar hypoplasia, X-linked intellectual disability, and autism. Unraveling the pathogenesis of CASK-related disorders has been challenging due to limited human cellular models to study the dynamic roles of this molecule during neuronal and synapse development. Here, we generated CASK knockout (KO) isogenic cell lines from human embryonic stem cells (hESCs) using CRISPR/Cas9 and examined gene expression, morphometrics and synaptic function of induced neuronal cells during development. While young (immature) CASK KO neurons show robust neuronal outgrowth, mature CASK KO neurons displayed severe defects in synaptic transmission and synchronized burst activity without compromising neuronal morphology and synapse numbers. In developing human cortical neurons, CASK functions to promote both structural integrity and establishment of cortical excitatory neuronal networks. These results lay the foundation for future studies identifying suppressors of such phenotypes relevant to human patients.}, keywords = {IPSC, MaxOne, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Loss-of-function (LOF) mutations in CASK cause severe developmental phenotypes, including microcephaly with pontine and cerebellar hypoplasia, X-linked intellectual disability, and autism. Unraveling the pathogenesis of CASK-related disorders has been challenging due to limited human cellular models to study the dynamic roles of this molecule during neuronal and synapse development. Here, we generated CASK knockout (KO) isogenic cell lines from human embryonic stem cells (hESCs) using CRISPR/Cas9 and examined gene expression, morphometrics and synaptic function of induced neuronal cells during development. While young (immature) CASK KO neurons show robust neuronal outgrowth, mature CASK KO neurons displayed severe defects in synaptic transmission and synchronized burst activity without compromising neuronal morphology and synapse numbers. In developing human cortical neurons, CASK functions to promote both structural integrity and establishment of cortical excitatory neuronal networks. These results lay the foundation for future studies identifying suppressors of such phenotypes relevant to human patients. Close https://doi.org/10.1101/2022.02.14.480404 doi:10.1101/2022.02.14.480404 Close
	Paulsen, Bruna; Velasco, Silvia; Kedaigle, Amanda J; Pigoni, Martina; Quadrato, Giorgia; Deo, Anthony J; Adiconis, Xian; Uzquiano, Ana; Sartore, Rafaela; Yang, Sung Min; Simmons, Sean K; Symvoulidis, Panagiotis; Kim, Kwanho; Tsafou, Kalliopi; Podury, Archana; Abbate, Catherine; Tucewicz, Ashley; Smith, Samantha N; Albanese, Alexandre; Barrett, Lindy; Sanjana, Neville E; Shi, Xi; Chung, Kwanghun; Lage, Kasper; Boyden, Edward S; andJoshua Levin, Aviv Regev Z; Arlotta, Paola Autism genes converge on asynchronous development of shared neuron classes Journal Article Nature, 602 , pp. 268–273, 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, MaxOne, Organoids @article{Paulsen2022, title = {Autism genes converge on asynchronous development of shared neuron classes}, author = {Bruna Paulsen and Silvia Velasco and Amanda J. Kedaigle and Martina Pigoni and Giorgia Quadrato and Anthony J. Deo and Xian Adiconis and Ana Uzquiano and Rafaela Sartore and Sung Min Yang and Sean K. Simmons and Panagiotis Symvoulidis and Kwanho Kim and Kalliopi Tsafou and Archana Podury and Catherine Abbate and Ashley Tucewicz and Samantha N. Smith and Alexandre Albanese and Lindy Barrett and Neville E. Sanjana and Xi Shi and Kwanghun Chung and Kasper Lage and Edward S. Boyden and Aviv Regev andJoshua Z. Levin and Paola Arlotta }, url = {https://www.nature.com/articles/s41586-021-04358-6}, doi = {10.1038/s41586-021-04358-6}, year = {2022}, date = {2022-02-02}, journal = {Nature}, volume = {602}, pages = {268–273}, abstract = {Genetic risk for autism spectrum disorder (ASD) is associated with hundreds of genes spanning a wide range of biological functions1,2,3,4,5,6. The alterations in the human brain resulting from mutations in these genes remain unclear. Furthermore, their phenotypic manifestation varies across individuals7,8. Here we used organoid models of the human cerebral cortex to identify cell-type-specific developmental abnormalities that result from haploinsufficiency in three ASD risk genes—SUV420H1 (also known as KMT5B), ARID1B and CHD8—in multiple cell lines from different donors, using single-cell RNA-sequencing (scRNA-seq) analysis of more than 745,000 cells and proteomic analysis of individual organoids, to identify phenotypic convergence. Each of the three mutations confers asynchronous development of two main cortical neuronal lineages—γ-aminobutyric-acid-releasing (GABAergic) neurons and deep-layer excitatory projection neurons—but acts through largely distinct molecular pathways. Although these phenotypes are consistent across cell lines, their expressivity is influenced by the individual genomic context, in a manner that is dependent on both the risk gene and the developmental defect. Calcium imaging in intact organoids shows that these early-stage developmental changes are followed by abnormal circuit activity. This research uncovers cell-type-specific neurodevelopmental abnormalities that are shared across ASD risk genes and are finely modulated by human genomic context, finding convergence in the neurobiological basis of how different risk genes contribute to ASD pathology.}, keywords = {HD-MEA, MaxOne, Organoids}, pubstate = {published}, tppubtype = {article} } Close Genetic risk for autism spectrum disorder (ASD) is associated with hundreds of genes spanning a wide range of biological functions1,2,3,4,5,6. The alterations in the human brain resulting from mutations in these genes remain unclear. Furthermore, their phenotypic manifestation varies across individuals7,8. Here we used organoid models of the human cerebral cortex to identify cell-type-specific developmental abnormalities that result from haploinsufficiency in three ASD risk genes—SUV420H1 (also known as KMT5B), ARID1B and CHD8—in multiple cell lines from different donors, using single-cell RNA-sequencing (scRNA-seq) analysis of more than 745,000 cells and proteomic analysis of individual organoids, to identify phenotypic convergence. Each of the three mutations confers asynchronous development of two main cortical neuronal lineages—γ-aminobutyric-acid-releasing (GABAergic) neurons and deep-layer excitatory projection neurons—but acts through largely distinct molecular pathways. Although these phenotypes are consistent across cell lines, their expressivity is influenced by the individual genomic context, in a manner that is dependent on both the risk gene and the developmental defect. Calcium imaging in intact organoids shows that these early-stage developmental changes are followed by abnormal circuit activity. This research uncovers cell-type-specific neurodevelopmental abnormalities that are shared across ASD risk genes and are finely modulated by human genomic context, finding convergence in the neurobiological basis of how different risk genes contribute to ASD pathology. Close https://www.nature.com/articles/s41586-021-04358-6 doi:10.1038/s41586-021-04358-6 Close
	McCready, Fraser P; Gordillo-Sampedro, Sara; Pradeepan, Kartik; Martinez-Trujillo, Julio; Ellis, James Multielectrode Arrays for Functional Phenotyping of Neurons from Induced Pluripotent Stem Cell Models of Neurodevelopmental Disorders Journal Article Biology, 2022. Abstract \| Links \| BibTeX \| Tags: HD-MEA, IPSC, MaxOne, MEA Technology @article{McCready2022, title = {Multielectrode Arrays for Functional Phenotyping of Neurons from Induced Pluripotent Stem Cell Models of Neurodevelopmental Disorders}, author = {Fraser P. McCready and Sara Gordillo-Sampedro and Kartik Pradeepan and Julio Martinez-Trujillo and James Ellis}, url = {https://www.mdpi.com/2079-7737/11/2/316}, doi = {10.3390/biology11020316}, year = {2022}, date = {2022-01-11}, journal = {Biology}, abstract = {In vitro multielectrode array (MEA) systems are increasingly used as higher-throughput platforms for functional phenotyping studies of neurons in induced pluripotent stem cell (iPSC) disease models. While MEA systems generate large amounts of spatiotemporal activity data from networks of iPSC-derived neurons, the downstream analysis and interpretation of such high-dimensional data often pose a significant challenge to researchers. In this review, we examine how MEA technology is currently deployed in iPSC modeling studies of neurodevelopmental disorders. We first highlight the strengths of in vitro MEA technology by reviewing the history of its development and the original scientific questions MEAs were intended to answer. Methods of generating patient iPSCderived neurons and astrocytes for MEA co-cultures are summarized. We then discuss challenges associated with MEA data analysis in a disease modeling context, and present novel computational methods used to better interpret network phenotyping data. We end by suggesting best practices for presenting MEA data in research publications, and propose that the creation of a public MEA data repository to enable collaborative data sharing would be of great benefit to the iPSC disease modeling community.}, keywords = {HD-MEA, IPSC, MaxOne, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close In vitro multielectrode array (MEA) systems are increasingly used as higher-throughput platforms for functional phenotyping studies of neurons in induced pluripotent stem cell (iPSC) disease models. While MEA systems generate large amounts of spatiotemporal activity data from networks of iPSC-derived neurons, the downstream analysis and interpretation of such high-dimensional data often pose a significant challenge to researchers. In this review, we examine how MEA technology is currently deployed in iPSC modeling studies of neurodevelopmental disorders. We first highlight the strengths of in vitro MEA technology by reviewing the history of its development and the original scientific questions MEAs were intended to answer. Methods of generating patient iPSCderived neurons and astrocytes for MEA co-cultures are summarized. We then discuss challenges associated with MEA data analysis in a disease modeling context, and present novel computational methods used to better interpret network phenotyping data. We end by suggesting best practices for presenting MEA data in research publications, and propose that the creation of a public MEA data repository to enable collaborative data sharing would be of great benefit to the iPSC disease modeling community. Close https://www.mdpi.com/2079-7737/11/2/316 doi:10.3390/biology11020316 Close
2021
	Hruska-Plochan, Marian; Betz, Katharina M; Ronchi, Silvia; Wiersma, Vera I; Maniecka, Zuzanna; Hock, Eva-Maria; Laferriere, Florent; Sahadevan, Sonu; Hoop, Vanessa; Delvendahl, Igor; Panatta, Martina; van der Bourg, Alexander; Bohaciakova, Dasa; Frontzek, Karl; Aguzzi, Adriano; Lashley, Tammaryn; Robinson, Mark D; Karayannis, Theofanis; Mueller, Martin; Hierlemann, Andreas; Polymenidou, Magdalini Human neural networks with sparse TDP-43 pathology reveal NPTX2 misregulation in ALS/FTLD Journal Article BioRxiv, 2021. Abstract \| Links \| BibTeX \| Tags: Inhibitory Neurons, MEA Technology, Neuronal Networks @article{Hruska-Plochan2021, title = {Human neural networks with sparse TDP-43 pathology reveal NPTX2 misregulation in ALS/FTLD}, author = {Marian Hruska-Plochan and Katharina M. Betz and Silvia Ronchi and Vera I. Wiersma and Zuzanna Maniecka and Eva-Maria Hock and Florent Laferriere and Sonu Sahadevan and Vanessa Hoop and Igor Delvendahl and Martina Panatta and Alexander van der Bourg and Dasa Bohaciakova and Karl Frontzek and Adriano Aguzzi and Tammaryn Lashley and Mark D. Robinson and Theofanis Karayannis and Martin Mueller and Andreas Hierlemann and Magdalini Polymenidou}, url = {https://doi.org/10.1101/2021.12.08.471089}, doi = {10.1101/2021.12.08.471089}, year = {2021}, date = {2021-12-09}, journal = {BioRxiv}, abstract = {Human cellular models of neurodegeneration require reproducibility and longevity, which is necessary for simulating these age-dependent diseases. Such systems are particularly needed for TDP-43 proteinopathies1,2, which involve human-specific mechanisms3–6 that cannot be directly studied in animal models. To explore the emergence and consequences of TDP-43 pathologies, we generated iPSC-derived, colony morphology neural stem cells (iCoMoNSCs) via manual selection of neural precursors7. Single-cell transcriptomics (scRNA-seq) and comparison to independent NSCs8, showed that iCoMoNSCs are uniquely homogenous and self-renewing. Differentiated iCoMoNSCs formed a self-organized multicellular system consisting of synaptically connected and electrophysiologically active neurons, which matured into long-lived functional networks. Neuronal and glial maturation in iCoMoNSC-derived cultures was similar to that of cortical organoids9. Overexpression of wild-type TDP-43 in a minority of iCoMoNSC-derived neurons led to progressive fragmentation and aggregation, resulting in loss of function and neurotoxicity. scRNA-seq revealed a novel set of misregulated RNA targets coinciding in both TDP-43 overexpressing neurons and patient brains exhibiting loss of nuclear TDP-43. The strongest misregulated target encoded for the synaptic protein NPTX2, which was consistently misaccumulated in ALS and FTLD patient neurons with TDP-43 pathology. Our work directly links TDP-43 misregulation and NPTX2 accumulation, thereby highlighting a new pathway of neurotoxicity.}, keywords = {Inhibitory Neurons, MEA Technology, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Human cellular models of neurodegeneration require reproducibility and longevity, which is necessary for simulating these age-dependent diseases. Such systems are particularly needed for TDP-43 proteinopathies1,2, which involve human-specific mechanisms3–6 that cannot be directly studied in animal models. To explore the emergence and consequences of TDP-43 pathologies, we generated iPSC-derived, colony morphology neural stem cells (iCoMoNSCs) via manual selection of neural precursors7. Single-cell transcriptomics (scRNA-seq) and comparison to independent NSCs8, showed that iCoMoNSCs are uniquely homogenous and self-renewing. Differentiated iCoMoNSCs formed a self-organized multicellular system consisting of synaptically connected and electrophysiologically active neurons, which matured into long-lived functional networks. Neuronal and glial maturation in iCoMoNSC-derived cultures was similar to that of cortical organoids9. Overexpression of wild-type TDP-43 in a minority of iCoMoNSC-derived neurons led to progressive fragmentation and aggregation, resulting in loss of function and neurotoxicity. scRNA-seq revealed a novel set of misregulated RNA targets coinciding in both TDP-43 overexpressing neurons and patient brains exhibiting loss of nuclear TDP-43. The strongest misregulated target encoded for the synaptic protein NPTX2, which was consistently misaccumulated in ALS and FTLD patient neurons with TDP-43 pathology. Our work directly links TDP-43 misregulation and NPTX2 accumulation, thereby highlighting a new pathway of neurotoxicity. Close https://doi.org/10.1101/2021.12.08.471089 doi:10.1101/2021.12.08.471089 Close
	Kagan, Brett J; Kitchen, Andy C; Tran, Nhi T; Parker, Bradyn J; Bhat, Anjali; Rollo, Ben; Razi, Adeel; Friston, Karl J In vitro neurons learn and exhibit sentience when embodied in a simulated game-world Journal Article bioRxiv, 2021. Abstract \| Links \| BibTeX \| Tags: 2D Neuronal Culture, Activity Scan Assay, closed loop stimulation, HD-MEA, In-Vitro, IPSC, MaxOne, MEA Technology, Network Assay, Neuronal Networks, Primary Neuronal Cell Culture, Stimulation @article{Kagan2021b, title = {In vitro neurons learn and exhibit sentience when embodied in a simulated game-world}, author = {Brett J. Kagan and Andy C. Kitchen and Nhi T. Tran and Bradyn J. Parker and Anjali Bhat and Ben Rollo and Adeel Razi and Karl J. Friston}, url = {https://www.biorxiv.org/content/10.1101/2021.12.02.471005v2}, doi = {10.1101/2021.12.02.471005}, year = {2021}, date = {2021-12-03}, journal = {bioRxiv}, abstract = {Integrating neurons into digital systems to leverage their innate intelligence may enable performance infeasible with silicon alone, along with providing insight into the cellular origin of intelligence. We developed DishBrain, a system which exhibits natural intelligence by harnessing the inherent adaptive computation of neurons in a structured environment. In vitro neural networks from human or rodent origins, are integrated with in silico computing via high-density multielectrode array. Through electrophysiological stimulation and recording, cultures were embedded in a simulated game-world, mimicking the arcade game ‘Pong’. Applying a previously untestable theory of active inference via the Free Energy Principle, we found that learning was apparent within five minutes of real-time gameplay, not observed in control conditions. Further experiments demonstrate the importance of closed-loop structured feedback in eliciting learning over time. Cultures display the ability to self-organise in a goal-directed manner in response to sparse sensory information about the consequences of their actions.}, keywords = {2D Neuronal Culture, Activity Scan Assay, closed loop stimulation, HD-MEA, In-Vitro, IPSC, MaxOne, MEA Technology, Network Assay, Neuronal Networks, Primary Neuronal Cell Culture, Stimulation}, pubstate = {published}, tppubtype = {article} } Close Integrating neurons into digital systems to leverage their innate intelligence may enable performance infeasible with silicon alone, along with providing insight into the cellular origin of intelligence. We developed DishBrain, a system which exhibits natural intelligence by harnessing the inherent adaptive computation of neurons in a structured environment. In vitro neural networks from human or rodent origins, are integrated with in silico computing via high-density multielectrode array. Through electrophysiological stimulation and recording, cultures were embedded in a simulated game-world, mimicking the arcade game ‘Pong’. Applying a previously untestable theory of active inference via the Free Energy Principle, we found that learning was apparent within five minutes of real-time gameplay, not observed in control conditions. Further experiments demonstrate the importance of closed-loop structured feedback in eliciting learning over time. Cultures display the ability to self-organise in a goal-directed manner in response to sparse sensory information about the consequences of their actions. Close https://www.biorxiv.org/content/10.1101/2021.12.02.471005v2 doi:10.1101/2021.12.02.471005 Close
	Kubota, Tomoyuki; Takahashi, Hirokazu; and Nakajima, Kohei Unifying framework for information processing in stochastically driven dynamical systems Journal Article Physical Review Research, 2021. Abstract \| Links \| BibTeX \| Tags: 2D Neuronal Culture, HD-MEA, MaxOne, Primary Neuronal Cell Culture, Stimulation @article{Kubota2023, title = {Unifying framework for information processing in stochastically driven dynamical systems}, author = {Tomoyuki Kubota and Hirokazu Takahashi and and Kohei Nakajima}, url = {https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.3.043135}, doi = {https://doi.org/10.1103/PhysRevResearch.3.043135}, year = {2021}, date = {2021-11-23}, journal = {Physical Review Research}, abstract = {A dynamical system is an information processing apparatus that encodes input streams from the external environment to its state and processes them through state transitions. The information processing capacity (IPC) is an excellent tool that comprehensively evaluates these processed inputs, providing details of unknown information processing in black box systems; however, this measure can be applied only to time-invariant systems. This paper extends the applicable range to time-variant systems and further reveals that the IPC is equivalent to coefficients of polynomial chaos (PC) expansion in more general dynamical systems. To achieve this objective, we tackle three issues. First, we establish a connection between the IPC for time-invariant systems and PC expansion, which is a type of polynomial expansion using orthogonal functions of input history as bases. We prove that the IPC corresponds to the squared norm of the coefficient vector of the basis in the PC expansion. Second, we show that an input following an arbitrary distribution can be used for the IPC, removing previous restrictions to specific input distributions. Third, we extend the conventional orthogonal bases to functions of both time and input history and propose the IPC for time-variant systems. To show the significance of our approach, we demonstrate that our measure can reveal information representations in not only machine learning networks but also a real, cultured neural network. Our generalized measure paves the way for unveiling the information processing capabilities of a wide variety of physical dynamics which have been left behind in nature.}, keywords = {2D Neuronal Culture, HD-MEA, MaxOne, Primary Neuronal Cell Culture, Stimulation}, pubstate = {published}, tppubtype = {article} } Close A dynamical system is an information processing apparatus that encodes input streams from the external environment to its state and processes them through state transitions. The information processing capacity (IPC) is an excellent tool that comprehensively evaluates these processed inputs, providing details of unknown information processing in black box systems; however, this measure can be applied only to time-invariant systems. This paper extends the applicable range to time-variant systems and further reveals that the IPC is equivalent to coefficients of polynomial chaos (PC) expansion in more general dynamical systems. To achieve this objective, we tackle three issues. First, we establish a connection between the IPC for time-invariant systems and PC expansion, which is a type of polynomial expansion using orthogonal functions of input history as bases. We prove that the IPC corresponds to the squared norm of the coefficient vector of the basis in the PC expansion. Second, we show that an input following an arbitrary distribution can be used for the IPC, removing previous restrictions to specific input distributions. Third, we extend the conventional orthogonal bases to functions of both time and input history and propose the IPC for time-variant systems. To show the significance of our approach, we demonstrate that our measure can reveal information representations in not only machine learning networks but also a real, cultured neural network. Our generalized measure paves the way for unveiling the information processing capabilities of a wide variety of physical dynamics which have been left behind in nature. Close https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.3.043135 doi:https://doi.org/10.1103/PhysRevResearch.3.043135 Close
	Sharf, Tal; van der Molen, Tjitse; Glasauer, Stella M K; Guzman, Elmer; Buccino, Alessio P; Luna, Gabriel; Cheng, Zhouwei; Audouard, Morgane; Ranasinghe, Kamalini G; Kudo, Kiwamu; Nagarajan, Srikantan S; Tovar, Kenneth R; Petzold, Linda R; Hierlemann, Andreas; Hansma, Paul K; Kosik, Kenneth S Human brain organoid networks Journal Article bioRxiv, 2021. Abstract \| Links \| BibTeX \| Tags: 3D Culture, Activity Scan Assay, HD-MEA, IPSC, MaxOne, MEA Technology, Organoids, Slices, Spike Sorting @article{Sharf2021b, title = {Human brain organoid networks}, author = {Tal Sharf and Tjitse van der Molen and Stella M.K. Glasauer and Elmer Guzman and Alessio P. Buccino and Gabriel Luna and Zhouwei Cheng and Morgane Audouard and Kamalini G. Ranasinghe and Kiwamu Kudo and Srikantan S. Nagarajan and Kenneth R. Tovar and Linda R. Petzold and Andreas Hierlemann and Paul K. Hansma and Kenneth S. Kosik}, url = {https://www.biorxiv.org/content/10.1101/2021.01.28.428643v2}, doi = {10.1101/2021.01.28.428643}, year = {2021}, date = {2021-09-23}, journal = {bioRxiv}, abstract = {Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiological behavior of neuronal circuits within organoids remains relatively under-explored. With high-density CMOS microelectrode arrays (26,400 electrodes) and shank electrodes (960 electrodes), we probed broadband and three-dimensional extracellular field recordings generated by spontaneous activity of human brain organoids. These recordings simultaneously captured local field potentials (LFPs) and single-unit activity extracted through spike sorting. From spiking activity, we estimated a directed functional connectivity graph of synchronous neural network activity, which showed a large number of weak functional connections enmeshed within a network skeleton of significantly fewer strong connections. Treatment of the organoid with a benzodiazepine induced a reproducible signature response that shortened the inter-burst intervals, increased the uniformity of the firing pattern within each burst and decreased the population of weakly connected edges. Simultaneously examining the spontaneous LFPs and their phase alignment to spiking showed that spike bursts were coherent with theta oscillations in the LFPs. Our results demonstrate that human brain organoids have self-organized neuronal assemblies of sufficient size, cellular orientation, and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug mechanisms, and the effects of external stimuli upon neuronal networks.}, keywords = {3D Culture, Activity Scan Assay, HD-MEA, IPSC, MaxOne, MEA Technology, Organoids, Slices, Spike Sorting}, pubstate = {published}, tppubtype = {article} } Close Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiological behavior of neuronal circuits within organoids remains relatively under-explored. With high-density CMOS microelectrode arrays (26,400 electrodes) and shank electrodes (960 electrodes), we probed broadband and three-dimensional extracellular field recordings generated by spontaneous activity of human brain organoids. These recordings simultaneously captured local field potentials (LFPs) and single-unit activity extracted through spike sorting. From spiking activity, we estimated a directed functional connectivity graph of synchronous neural network activity, which showed a large number of weak functional connections enmeshed within a network skeleton of significantly fewer strong connections. Treatment of the organoid with a benzodiazepine induced a reproducible signature response that shortened the inter-burst intervals, increased the uniformity of the firing pattern within each burst and decreased the population of weakly connected edges. Simultaneously examining the spontaneous LFPs and their phase alignment to spiking showed that spike bursts were coherent with theta oscillations in the LFPs. Our results demonstrate that human brain organoids have self-organized neuronal assemblies of sufficient size, cellular orientation, and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug mechanisms, and the effects of external stimuli upon neuronal networks. Close https://www.biorxiv.org/content/10.1101/2021.01.28.428643v2 doi:10.1101/2021.01.28.428643 Close
	Schenke, Maren; Prause, Hélène-Christine; Bergforth, Wiebke; Przykopanski, Adina Human-Relevant Sensitivity of iPSC-Derived Human Motor Neurons to BoNT/A1 and B1 Journal Article toxins, 2021. Abstract \| Links \| BibTeX \| Tags: MaxOne @article{Schenke2021, title = {Human-Relevant Sensitivity of iPSC-Derived Human Motor Neurons to BoNT/A1 and B1}, author = {Maren Schenke and Hélène-Christine Prause and Wiebke Bergforth and Adina Przykopanski}, url = {https://www.mdpi.com/2072-6651/13/8/585}, doi = {https://doi.org/10.3390/toxins13080585}, year = {2021}, date = {2021-08-22}, journal = {toxins}, abstract = {The application of botulinum neurotoxins (BoNTs) for medical treatments necessitates a potency quantification of these lethal bacterial toxins, resulting in the use of a large number of test animals. Available alternative methods are limited in their relevance, as they are based on rodent cells or neuroblastoma cell lines or applicable for single toxin serotypes only. Here, human motor neurons (MNs), which are the physiological target of BoNTs, were generated from induced pluripotent stem cells (iPSCs) and compared to the neuroblastoma cell line SiMa, which is often used in cell-based assays for BoNT potency determination. In comparison with the mouse bioassay, human MNs exhibit a superior sensitivity to the BoNT serotypes A1 and B1 at levels that are reflective of human sensitivity. SiMa cells were able to detect BoNT/A1, but with much lower sensitivity than human MNs and appear unsuitable to detect any BoNT/B1 activity. The MNs used for these experiments were generated according to three differentiation protocols, which resulted in distinct sensitivity levels. Molecular parameters such as receptor protein concentration and electrical activity of the MNs were analyzed, but are not predictive for BoNT sensitivity. These results show that human MNs from several sources should be considered in BoNT testing and that human MNs are a physiologically relevant model, which could be used to optimize current BoNT potency testing.}, keywords = {MaxOne}, pubstate = {published}, tppubtype = {article} } Close The application of botulinum neurotoxins (BoNTs) for medical treatments necessitates a potency quantification of these lethal bacterial toxins, resulting in the use of a large number of test animals. Available alternative methods are limited in their relevance, as they are based on rodent cells or neuroblastoma cell lines or applicable for single toxin serotypes only. Here, human motor neurons (MNs), which are the physiological target of BoNTs, were generated from induced pluripotent stem cells (iPSCs) and compared to the neuroblastoma cell line SiMa, which is often used in cell-based assays for BoNT potency determination. In comparison with the mouse bioassay, human MNs exhibit a superior sensitivity to the BoNT serotypes A1 and B1 at levels that are reflective of human sensitivity. SiMa cells were able to detect BoNT/A1, but with much lower sensitivity than human MNs and appear unsuitable to detect any BoNT/B1 activity. The MNs used for these experiments were generated according to three differentiation protocols, which resulted in distinct sensitivity levels. Molecular parameters such as receptor protein concentration and electrical activity of the MNs were analyzed, but are not predictive for BoNT sensitivity. These results show that human MNs from several sources should be considered in BoNT testing and that human MNs are a physiologically relevant model, which could be used to optimize current BoNT potency testing. Close https://www.mdpi.com/2072-6651/13/8/585 doi:https://doi.org/10.3390/toxins13080585 Close
	Sundberg, Maria; Pinson, Hannah; Smith, Richard S; Winden, Kellen D; Venugopal, Pooja; Tai, Derek J C; Gusella, James F; Talkowski, Michael E; Walsh, Christopher A; Tegmark, Max; Sahin, Mustafa 16p11.2 deletion is associated with hyperactivation of human iPSC-derived dopaminergic neuron networks and is rescued by RHOA inhibition in vitro Journal Article Nature Communications, 12 (2897 ), 2021. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, IPSC, MaxOne @article{Sundberg2021, title = {16p11.2 deletion is associated with hyperactivation of human iPSC-derived dopaminergic neuron networks and is rescued by RHOA inhibition in vitro}, author = {Maria Sundberg and Hannah Pinson and Richard S. Smith and Kellen D. Winden and Pooja Venugopal and Derek J. C. Tai and James F. Gusella and Michael E. Talkowski and Christopher A. Walsh and Max Tegmark and Mustafa Sahin }, url = {https://www.nature.com/articles/s41467-021-23113-z}, doi = {10.1038/s41467-021-23113-z}, year = {2021}, date = {2021-05-18}, journal = {Nature Communications}, volume = {12}, number = {2897 }, abstract = {Reciprocal copy number variations (CNVs) of 16p11.2 are associated with a wide spectrum of neuropsychiatric and neurodevelopmental disorders. Here, we use human induced pluripotent stem cells (iPSCs)-derived dopaminergic (DA) neurons carrying CNVs of 16p11.2 duplication (16pdup) and 16p11.2 deletion (16pdel), engineered using CRISPR-Cas9. We show that 16pdel iPSC-derived DA neurons have increased soma size and synaptic marker expression compared to isogenic control lines, while 16pdup iPSC-derived DA neurons show deficits in neuronal differentiation and reduced synaptic marker expression. The 16pdel iPSC-derived DA neurons have impaired neurophysiological properties. The 16pdel iPSC-derived DA neuronal networks are hyperactive and have increased bursting in culture compared to controls. We also show that the expression of RHOA is increased in the 16pdel iPSC-derived DA neurons and that treatment with a specific RHOA-inhibitor, Rhosin, rescues the network activity of the 16pdel iPSC-derived DA neurons. Our data suggest that 16p11.2 deletion-associated iPSC-derived DA neuron hyperactivation can be rescued by RHOA inhibition.}, keywords = {ETH-CMOS-MEA, IPSC, MaxOne}, pubstate = {published}, tppubtype = {article} } Close Reciprocal copy number variations (CNVs) of 16p11.2 are associated with a wide spectrum of neuropsychiatric and neurodevelopmental disorders. Here, we use human induced pluripotent stem cells (iPSCs)-derived dopaminergic (DA) neurons carrying CNVs of 16p11.2 duplication (16pdup) and 16p11.2 deletion (16pdel), engineered using CRISPR-Cas9. We show that 16pdel iPSC-derived DA neurons have increased soma size and synaptic marker expression compared to isogenic control lines, while 16pdup iPSC-derived DA neurons show deficits in neuronal differentiation and reduced synaptic marker expression. The 16pdel iPSC-derived DA neurons have impaired neurophysiological properties. The 16pdel iPSC-derived DA neuronal networks are hyperactive and have increased bursting in culture compared to controls. We also show that the expression of RHOA is increased in the 16pdel iPSC-derived DA neurons and that treatment with a specific RHOA-inhibitor, Rhosin, rescues the network activity of the 16pdel iPSC-derived DA neurons. Our data suggest that 16p11.2 deletion-associated iPSC-derived DA neuron hyperactivation can be rescued by RHOA inhibition. Close https://www.nature.com/articles/s41467-021-23113-z doi:10.1038/s41467-021-23113-z Close
	Kajiwara Motoki; Nomura, Ritsuki; Goetze Felix; Kawabata Masanori; Isomura Yoshikazu; Akutsu Tatsuya; Shimono Masanori; Inhibitory neurons exhibit high controlling ability in the cortical microconnectome Journal Article PLOS Computational Biology, 2021. Abstract \| Links \| BibTeX \| Tags: Brain Slice, MaxOne @article{Kajiwara2021, title = {Inhibitory neurons exhibit high controlling ability in the cortical microconnectome}, author = {Kajiwara, Motoki; Nomura, Ritsuki; Goetze, Felix; Kawabata, Masanori; Isomura, Yoshikazu; Akutsu, Tatsuya; Shimono, Masanori; }, url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008846}, year = {2021}, date = {2021-04-08}, journal = {PLOS Computational Biology}, abstract = {The brain is a network system in which excitatory and inhibitory neurons keep activity bal- anced in the highly non-random connectivity pattern of the microconnectome. It is well known that the relative percentage of inhibitory neurons is much smaller than excitatory neu- rons in the cortex. So, in general, how inhibitory neurons can keep the balance with the sur- rounding excitatory neurons is an important question. There is much accumulated knowledge about this fundamental question. This study quantitatively evaluated the rela- tively higher functional contribution of inhibitory neurons in terms of not only properties of individual neurons, such as firing rate, but also in terms of topological mechanisms and con- trolling ability on other excitatory neurons. We combined simultaneous electrical recording (~2.5 hours) of ~1000 neurons in vitro, and quantitative evaluation of neuronal interactions including excitatory-inhibitory categorization. This study accurately defined recording brain anatomical targets, such as brain regions and cortical layers, by inter-referring MRI and immunostaining recordings. The interaction networks enabled us to quantify topological influence of individual neurons, in terms of controlling ability to other neurons. Especially, the result indicated that highly influential inhibitory neurons show higher controlling ability of other neurons than excitatory neurons, and are relatively often distributed in deeper layers of the cortex. Furthermore, the neurons having high controlling ability are more effectively limited in number than central nodes of k-cores, and these neurons also participate in more clustered motifs. In summary, this study suggested that the high controlling ability of inhibi- tory neurons is a key mechanism to keep balance with a large number of other excitatory neurons beyond simple higher firing rate. Application of the selection method of limited important neurons would be also applicable for the ability to effectively and selectively stimu- late E/I imbalanced disease states.}, keywords = {Brain Slice, MaxOne}, pubstate = {published}, tppubtype = {article} } Close The brain is a network system in which excitatory and inhibitory neurons keep activity bal- anced in the highly non-random connectivity pattern of the microconnectome. It is well known that the relative percentage of inhibitory neurons is much smaller than excitatory neu- rons in the cortex. So, in general, how inhibitory neurons can keep the balance with the sur- rounding excitatory neurons is an important question. There is much accumulated knowledge about this fundamental question. This study quantitatively evaluated the rela- tively higher functional contribution of inhibitory neurons in terms of not only properties of individual neurons, such as firing rate, but also in terms of topological mechanisms and con- trolling ability on other excitatory neurons. We combined simultaneous electrical recording (~2.5 hours) of ~1000 neurons in vitro, and quantitative evaluation of neuronal interactions including excitatory-inhibitory categorization. This study accurately defined recording brain anatomical targets, such as brain regions and cortical layers, by inter-referring MRI and immunostaining recordings. The interaction networks enabled us to quantify topological influence of individual neurons, in terms of controlling ability to other neurons. Especially, the result indicated that highly influential inhibitory neurons show higher controlling ability of other neurons than excitatory neurons, and are relatively often distributed in deeper layers of the cortex. Furthermore, the neurons having high controlling ability are more effectively limited in number than central nodes of k-cores, and these neurons also participate in more clustered motifs. In summary, this study suggested that the high controlling ability of inhibi- tory neurons is a key mechanism to keep balance with a large number of other excitatory neurons beyond simple higher firing rate. Application of the selection method of limited important neurons would be also applicable for the ability to effectively and selectively stimu- late E/I imbalanced disease states. Close https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008846 Close
	Yuan, Xinyue; Hierlemann, Andreas; Frey, Urs Extracellular Recording of Entire Neural Networks Using a Dual-Mode Microelectrode Array With 19,584 Electrodes and High SNR Journal Article IEEE, 2021. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, MEA Technology @article{Yuan2021, title = {Extracellular Recording of Entire Neural Networks Using a Dual-Mode Microelectrode Array With 19,584 Electrodes and High SNR}, author = {Xinyue Yuan and Andreas Hierlemann and Urs Frey}, url = {https://ieeexplore.ieee.org/document/9385387}, doi = {10.1109/JSSC.2021.3066043}, year = {2021}, date = {2021-03-24}, journal = {IEEE}, abstract = {Electrophysiological research on neural networks and their activity focuses on the recording and analysis of large data sets that include information of thousands of neurons. CMOS microelectrode arrays (MEAs) feature thousands of electrodes at a spatial resolution on the scale of single cells and are, therefore, ideal tools to support neural-network research. Moreover, they offer high spatio-temporal resolution and signal-to-noise ratio (SNR) to capture all features and subcellular-resolution details of neuronal signaling. Here, we present a dual-mode (DM) MEA, which enables simultaneous: 1) full-frame readout from all electrodes and 2) high-SNR readout from an arbitrarily selectable subset of electrodes. The DM-MEA includes 19,584 electrodes, 19,584 full-frame recording channels with noise levels of 10.4 μVrms in the action potential (AP) frequency band (300 Hz-5 kHz), 246 low-noise recording channels with noise levels of 3.0 μVrms in the AP band and eight stimulation units. The capacity to simultaneously perform full-frame and high-SNR recordings endows the presented DM-MEA with great flexibility for various applications in neuroscience and pharmacology.}, keywords = {ETH-CMOS-MEA, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close Electrophysiological research on neural networks and their activity focuses on the recording and analysis of large data sets that include information of thousands of neurons. CMOS microelectrode arrays (MEAs) feature thousands of electrodes at a spatial resolution on the scale of single cells and are, therefore, ideal tools to support neural-network research. Moreover, they offer high spatio-temporal resolution and signal-to-noise ratio (SNR) to capture all features and subcellular-resolution details of neuronal signaling. Here, we present a dual-mode (DM) MEA, which enables simultaneous: 1) full-frame readout from all electrodes and 2) high-SNR readout from an arbitrarily selectable subset of electrodes. The DM-MEA includes 19,584 electrodes, 19,584 full-frame recording channels with noise levels of 10.4 μVrms in the action potential (AP) frequency band (300 Hz-5 kHz), 246 low-noise recording channels with noise levels of 3.0 μVrms in the AP band and eight stimulation units. The capacity to simultaneously perform full-frame and high-SNR recordings endows the presented DM-MEA with great flexibility for various applications in neuroscience and pharmacology. Close https://ieeexplore.ieee.org/document/9385387 doi:10.1109/JSSC.2021.3066043 Close
	Ronchi, Silvia; Buccino, Alessio Paolo; Prack, Gustavo; Kumar, Sreedhar Saseendran; Schröter, Manuel; Fiscella, Michele; Hierlemann, Andreas Microelectrode Arrays: Electrophysiological Phenotype Characterization of Human iPSC-Derived Neuronal Cell Lines by Means of High-Density Microelectrode Arrays Journal Article Advanced Biology, 5 (3), 2021. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, IPSC @article{Ronchi2021, title = {Microelectrode Arrays: Electrophysiological Phenotype Characterization of Human iPSC-Derived Neuronal Cell Lines by Means of High-Density Microelectrode Arrays}, author = {Silvia Ronchi and Alessio Paolo Buccino and Gustavo Prack and Sreedhar Saseendran Kumar and Manuel Schröter and Michele Fiscella and Andreas Hierlemann}, url = {https://onlinelibrary.wiley.com/doi/10.1002/adbi.202000223}, doi = {10.1002/adbi.202000223}, year = {2021}, date = {2021-03-17}, journal = {Advanced Biology}, volume = {5}, number = {3}, abstract = {In article number 2000223, Silvia Ronchi, Michele Fiscella, and co-workers show neurons plated on a high-density microelectrode array. The small electrode size and the tight spacing between the 26 400 electrodes enable functional extracellular electrophysiological characterization of neurons across scales, from subcellular-resolution features, like axons and dendrites, through individual neuronal cells to entire networks.}, keywords = {ETH-CMOS-MEA, IPSC}, pubstate = {published}, tppubtype = {article} } Close In article number 2000223, Silvia Ronchi, Michele Fiscella, and co-workers show neurons plated on a high-density microelectrode array. The small electrode size and the tight spacing between the 26 400 electrodes enable functional extracellular electrophysiological characterization of neurons across scales, from subcellular-resolution features, like axons and dendrites, through individual neuronal cells to entire networks. Close https://onlinelibrary.wiley.com/doi/10.1002/adbi.202000223 doi:10.1002/adbi.202000223 Close
	Sharf, Tal; van der Molen, Tjitse; Guzman, Elmer; Glasauer, Stella M K; Luna, Gabriel; Cheng, Zhouwei; Audouard, Morgane; Ranasinghe, Kamalini G; Kudo, Kiwamu; Nagarajan, Srikantan S; Tovar, Kenneth R; Petzold, Linda R; Hansma, Paul K; Kosik, Kenneth S Intrinsic network activity in human brain organoids Journal Article BioRxiv, 2021. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Neuronal Networks, Organoids @article{Sharf2021, title = {Intrinsic network activity in human brain organoids}, author = {Tal Sharf and Tjitse van der Molen and Elmer Guzman and Stella M.K. Glasauer and Gabriel Luna and Zhouwei Cheng and Morgane Audouard and Kamalini G. Ranasinghe and Kiwamu Kudo and Srikantan S. Nagarajan and Kenneth R. Tovar and Linda R. Petzold and Paul K. Hansma and Kenneth S. Kosik}, url = {https://www.biorxiv.org/content/10.1101/2021.01.28.428643v1}, doi = {10.1101/2021.01.28.428643}, year = {2021}, date = {2021-01-28}, journal = {BioRxiv}, abstract = {Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiological behavior of neuronal circuits within organoids remains relatively under-explored. With high-density CMOS microelectrode arrays and shank electrodes, we probed broadband and three-dimensional spontaneous activity of human brain organoids. These recordings simultaneously captured local field potentials (LFPs) and single unit activity. From spiking activity, we estimated a directed functional connectivity graph of synchronous neural network activity which showed a large number of weak functional connections enmeshed within a network skeleton of significantly fewer strong connections. Increasing the intrinsic inhibitory tone with a benzodiazepine altered the functional network graph of the organoid by suppressing the network skeleton. Simultaneously examining the spontaneous LFPs and their phase alignment to spiking showed that spike bursts were coherent with theta oscillations in the LFPs. An ensemble of spikes phase-locked to theta frequency oscillations were strongly interconnected as a sub-network within the larger network in which they were embedded. Our results demonstrate that human brain organoids have self-organized neuronal assemblies of sufficient size, cellular orientation, and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug mechanisms, and the effects of external stimuli upon neuronal networks.}, keywords = {ETH-CMOS-MEA, Neuronal Networks, Organoids}, pubstate = {published}, tppubtype = {article} } Close Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiological behavior of neuronal circuits within organoids remains relatively under-explored. With high-density CMOS microelectrode arrays and shank electrodes, we probed broadband and three-dimensional spontaneous activity of human brain organoids. These recordings simultaneously captured local field potentials (LFPs) and single unit activity. From spiking activity, we estimated a directed functional connectivity graph of synchronous neural network activity which showed a large number of weak functional connections enmeshed within a network skeleton of significantly fewer strong connections. Increasing the intrinsic inhibitory tone with a benzodiazepine altered the functional network graph of the organoid by suppressing the network skeleton. Simultaneously examining the spontaneous LFPs and their phase alignment to spiking showed that spike bursts were coherent with theta oscillations in the LFPs. An ensemble of spikes phase-locked to theta frequency oscillations were strongly interconnected as a sub-network within the larger network in which they were embedded. Our results demonstrate that human brain organoids have self-organized neuronal assemblies of sufficient size, cellular orientation, and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug mechanisms, and the effects of external stimuli upon neuronal networks. Close https://www.biorxiv.org/content/10.1101/2021.01.28.428643v1 doi:10.1101/2021.01.28.428643 Close
2020
	Idrees, Saad; Münch, Thomas A Different contrast encoding in ON and OFF visual pathways Journal Article BioRxiv, 2020. Abstract \| Links \| BibTeX \| Tags: MaxOne, Retina @article{Idrees2020b, title = {Different contrast encoding in ON and OFF visual pathways}, author = {Saad Idrees and Thomas A. Münch }, url = {https://www.biorxiv.org/content/10.1101/2020.11.25.398230v1}, doi = {10.1101/2020.11.25.398230}, year = {2020}, date = {2020-11-26}, journal = {BioRxiv}, abstract = {Subjective visual experience builds on sensory encoding of light reflected by different objects in our environment. Most retinal ganglion cells encode changes in light intensity, quantified as contrast, rather than the absolute intensity. Mathematically, contrast is often defined as a relative change in light intensity. Activity in the visual system and perceptual responses are usually explained with such definitions of contrast. Here, for the first time, we explicitly explored how contrast is actually represented in the visual system. Using mouse retina electrophysiology, we show that response strength of OFF retinal ganglion cells does not represent relative, but absolute changes in light intensity. ON RGC response strength is governed by a combination of absolute and relative change in light intensity. This is true for a wide range of ambient light levels, at least from scotopic to high mesopic regimes. Consequently, light decrements and increments are represented asymmetrically in the retina, which may explain the asymmetries in responses to negative and positive contrast observed throughout the visual system. These findings may help to more thoroughly design and interpret vision science studies where responses are driven by contrast of the visual stimuli.}, keywords = {MaxOne, Retina}, pubstate = {published}, tppubtype = {article} } Close Subjective visual experience builds on sensory encoding of light reflected by different objects in our environment. Most retinal ganglion cells encode changes in light intensity, quantified as contrast, rather than the absolute intensity. Mathematically, contrast is often defined as a relative change in light intensity. Activity in the visual system and perceptual responses are usually explained with such definitions of contrast. Here, for the first time, we explicitly explored how contrast is actually represented in the visual system. Using mouse retina electrophysiology, we show that response strength of OFF retinal ganglion cells does not represent relative, but absolute changes in light intensity. ON RGC response strength is governed by a combination of absolute and relative change in light intensity. This is true for a wide range of ambient light levels, at least from scotopic to high mesopic regimes. Consequently, light decrements and increments are represented asymmetrically in the retina, which may explain the asymmetries in responses to negative and positive contrast observed throughout the visual system. These findings may help to more thoroughly design and interpret vision science studies where responses are driven by contrast of the visual stimuli. Close https://www.biorxiv.org/content/10.1101/2020.11.25.398230v1 doi:10.1101/2020.11.25.398230 Close
	Battaglia, Chiara R; Cursano, Silvia; Calzia, Enrico; Catanese, Alberto; Boeckers, Tobias M Corticotropin-releasing hormone (CRH) alters mitochondrial morphology and function by activating the NF-kB-DRP1 axis in hippocampal neurons Journal Article Cell Death & Disease, 2020. Abstract \| Links \| BibTeX \| Tags: MaxTwo @article{Battaglia2020, title = {Corticotropin-releasing hormone (CRH) alters mitochondrial morphology and function by activating the NF-kB-DRP1 axis in hippocampal neurons}, author = {Chiara R. Battaglia and Silvia Cursano and Enrico Calzia and Alberto Catanese and Tobias M. Boeckers }, url = {https://www.nature.com/articles/s41419-020-03204-3}, doi = {https://doi.org/10.1038/s41419-020-03204-3}, year = {2020}, date = {2020-11-23}, journal = {Cell Death & Disease}, abstract = {Neuronal stress-adaptation combines multiple molecular responses. We have previously reported that thorax trauma induces a transient loss of hippocampal excitatory synapses mediated by the local release of the stress-related hormone corticotropin-releasing hormone (CRH). Since a physiological synaptic activity relies also on mitochondrial functionality, we investigated the direct involvement of mitochondria in the (mal)-adaptive changes induced by the activation of neuronal CRH receptors 1 (CRHR1). We observed, in vivo and in vitro, a significant shift of mitochondrial dynamics towards fission, which correlated with increased swollen mitochondria and aberrant cristae. These morphological changes, which are associated with increased NF-kB activity and nitric oxide concentrations, correlated with a pronounced reduction of mitochondrial activity. However, ATP availability was unaltered, suggesting that neurons maintain a physiological energy metabolism to preserve them from apoptosis under CRH exposure. Our findings demonstrate that stress-induced CRHR1 activation leads to strong, but reversible, modifications of mitochondrial dynamics and morphology. These alterations are accompanied by bioenergetic defects and the reduction of neuronal activity, which are linked to increased intracellular oxidative stress, and to the activation of the NF-kB/c-Abl/DRP1 axis. }, keywords = {MaxTwo}, pubstate = {published}, tppubtype = {article} } Close Neuronal stress-adaptation combines multiple molecular responses. We have previously reported that thorax trauma induces a transient loss of hippocampal excitatory synapses mediated by the local release of the stress-related hormone corticotropin-releasing hormone (CRH). Since a physiological synaptic activity relies also on mitochondrial functionality, we investigated the direct involvement of mitochondria in the (mal)-adaptive changes induced by the activation of neuronal CRH receptors 1 (CRHR1). We observed, in vivo and in vitro, a significant shift of mitochondrial dynamics towards fission, which correlated with increased swollen mitochondria and aberrant cristae. These morphological changes, which are associated with increased NF-kB activity and nitric oxide concentrations, correlated with a pronounced reduction of mitochondrial activity. However, ATP availability was unaltered, suggesting that neurons maintain a physiological energy metabolism to preserve them from apoptosis under CRH exposure. Our findings demonstrate that stress-induced CRHR1 activation leads to strong, but reversible, modifications of mitochondrial dynamics and morphology. These alterations are accompanied by bioenergetic defects and the reduction of neuronal activity, which are linked to increased intracellular oxidative stress, and to the activation of the NF-kB/c-Abl/DRP1 axis. Close https://www.nature.com/articles/s41419-020-03204-3 doi:https://doi.org/10.1038/s41419-020-03204-3 Close
	Ricci, Chiara; Frey, Urs; Obien, Marie Engelene J MAPSYNE: Miniaturized micropipette system combined with high-density microelectrode arrays for automated manipulation of neuronal networks in-vitro Journal Article IEEE, 2020. Abstract \| Links \| BibTeX \| Tags: Activity Scan Assay, HD-MEA, MaxOne, MEA Technology @article{Ricci2020, title = {MAPSYNE: Miniaturized micropipette system combined with high-density microelectrode arrays for automated manipulation of neuronal networks in-vitro}, author = {Chiara Ricci and Urs Frey and Marie Engelene J. Obien}, url = {https://ieeexplore.ieee.org/document/9175797/}, doi = {10.1109/EMBC44109.2020.9175797}, year = {2020}, date = {2020-10-08}, journal = {IEEE}, abstract = {We present MAPSYNE, a miniaturized and automated system combining a high-density microelectrode array (HD-MEA) and a movable micropipette for studying, monitoring, and perturbing neurons in vitro. The system involves an all-electrical approach to automatically move a glass micropipette towards a target location on the HD-MEA surface, without the need for a microscope. Two methods of performing blind navigation are employed, (i) stop-measure-go approach wherein the pipette moves for a predefined distance before measuring its location then the process is repeated until the pipette reaches its destination, and (ii) predictive approach wherein the pipette is continuously tracked and moved. This automated system can be applied for unsupervised single-cell manipulation of neurons in a network, such as electroporation and local delivery of compounds.}, keywords = {Activity Scan Assay, HD-MEA, MaxOne, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close We present MAPSYNE, a miniaturized and automated system combining a high-density microelectrode array (HD-MEA) and a movable micropipette for studying, monitoring, and perturbing neurons in vitro. The system involves an all-electrical approach to automatically move a glass micropipette towards a target location on the HD-MEA surface, without the need for a microscope. Two methods of performing blind navigation are employed, (i) stop-measure-go approach wherein the pipette moves for a predefined distance before measuring its location then the process is repeated until the pipette reaches its destination, and (ii) predictive approach wherein the pipette is continuously tracked and moved. This automated system can be applied for unsupervised single-cell manipulation of neurons in a network, such as electroporation and local delivery of compounds. Close https://ieeexplore.ieee.org/document/9175797/ doi:10.1109/EMBC44109.2020.9175797 Close
	Yuan, Xinyue; Schröter, Manuel; Obien, Marie Engelene J; Fiscella, Michele; Gong, Wei; Kikuchi, Tetsuhiro; Odawara, Aoi; Noji, Shuhei; Suzuki, Ikuro; Takahashi, Jun; Hierlemann, Andreas; Frey, Urs Versatile live-cell activity analysis platform for characterization of neuronal dynamics at single-cell and network level Journal Article Nature Communications, 11 (4854), 2020. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, MEA Technology @article{Yuan2020, title = {Versatile live-cell activity analysis platform for characterization of neuronal dynamics at single-cell and network level}, author = {Xinyue Yuan and Manuel Schröter and Marie Engelene J. Obien and Michele Fiscella and Wei Gong and Tetsuhiro Kikuchi and Aoi Odawara and Shuhei Noji and Ikuro Suzuki and Jun Takahashi and Andreas Hierlemann and Urs Frey}, url = {https://www.nature.com/articles/s41467-020-18620-4#citeas}, doi = {10.1038/s41467-020-18620-4}, year = {2020}, date = {2020-09-25}, journal = {Nature Communications}, volume = {11}, number = {4854}, abstract = {Chronic imaging of neuronal networks in vitro has provided fundamental insights into mechanisms underlying neuronal function. Current labeling and optical imaging methods, however, cannot be used for continuous and long-term recordings of the dynamics and evolution of neuronal networks, as fluorescent indicators can cause phototoxicity. Here, we introduce a versatile platform for label-free, comprehensive and detailed electrophysiological live-cell imaging of various neurogenic cells and tissues over extended time scales. We report on a dual-mode high-density microelectrode array, which can simultaneously record in (i) full-frame mode with 19,584 recording sites and (ii) high-signal-to-noise mode with 246 channels. We set out to demonstrate the capabilities of this platform with recordings from primary and iPSC-derived neuronal cultures and tissue preparations over several weeks, providing detailed morpho-electrical phenotypic parameters at subcellular, cellular and network level. Moreover, we develop reliable analysis tools, which drastically increase the throughput to infer axonal morphology and conduction speed.}, keywords = {ETH-CMOS-MEA, MEA Technology}, pubstate = {published}, tppubtype = {article} } Close Chronic imaging of neuronal networks in vitro has provided fundamental insights into mechanisms underlying neuronal function. Current labeling and optical imaging methods, however, cannot be used for continuous and long-term recordings of the dynamics and evolution of neuronal networks, as fluorescent indicators can cause phototoxicity. Here, we introduce a versatile platform for label-free, comprehensive and detailed electrophysiological live-cell imaging of various neurogenic cells and tissues over extended time scales. We report on a dual-mode high-density microelectrode array, which can simultaneously record in (i) full-frame mode with 19,584 recording sites and (ii) high-signal-to-noise mode with 246 channels. We set out to demonstrate the capabilities of this platform with recordings from primary and iPSC-derived neuronal cultures and tissue preparations over several weeks, providing detailed morpho-electrical phenotypic parameters at subcellular, cellular and network level. Moreover, we develop reliable analysis tools, which drastically increase the throughput to infer axonal morphology and conduction speed. Close https://www.nature.com/articles/s41467-020-18620-4#citeas doi:10.1038/s41467-020-18620-4 Close
	Kim, Eunhee; Jeon, Sungwoong; An, Hyun-Kyu; Mehrnoosh Kianpour, Seong-Woon Yu ; Kim, Jin-young; Rah, Jong-Cheol; Choi, Hongsoo A magnetically actuated microrobot for targeted neural cell delivery and selective connection of neural networks Journal Article Science Advances, 6 (39), 2020. Abstract \| Links \| BibTeX \| Tags: microrobot, Neuronal Networks @article{Kim2020, title = {A magnetically actuated microrobot for targeted neural cell delivery and selective connection of neural networks}, author = {Eunhee Kim and Sungwoong Jeon and Hyun-Kyu An and Mehrnoosh Kianpour, Seong-Woon Yu and Jin-young Kim and Jong-Cheol Rah and Hongsoo Choi}, url = {https://advances.sciencemag.org/content/6/39/eabb5696}, doi = {10.1126/sciadv.abb5696}, year = {2020}, date = {2020-09-25}, journal = {Science Advances}, volume = {6}, number = {39}, abstract = {There has been a great deal of interest in the development of technologies for actively manipulating neural networks in vitro, providing natural but simplified environments in a highly reproducible manner in which to study brain function and related diseases. Platforms for these in vitro neural networks require precise and selective neural connections at the target location, with minimal external influences, and measurement of neural activity to determine how neurons communicate. Here, we report a neuron-loaded microrobot for selective connection of neural networks via precise delivery to a gap between two neural clusters by an external magnetic field. In addition, the extracellular action potential was propagated from one cluster to the other through the neurons on the microrobot. The proposed technique shows the potential for use in experiments to understand how neurons communicate in the neural network by actively connecting neural clusters.}, keywords = {microrobot, Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close There has been a great deal of interest in the development of technologies for actively manipulating neural networks in vitro, providing natural but simplified environments in a highly reproducible manner in which to study brain function and related diseases. Platforms for these in vitro neural networks require precise and selective neural connections at the target location, with minimal external influences, and measurement of neural activity to determine how neurons communicate. Here, we report a neuron-loaded microrobot for selective connection of neural networks via precise delivery to a gap between two neural clusters by an external magnetic field. In addition, the extracellular action potential was propagated from one cluster to the other through the neurons on the microrobot. The proposed technique shows the potential for use in experiments to understand how neurons communicate in the neural network by actively connecting neural clusters. Close https://advances.sciencemag.org/content/6/39/eabb5696 doi:10.1126/sciadv.abb5696 Close
	Cowan, Cameron S; Renner, Magdalena; Gennaro, Martina De; Gross-Scherf, Brigitte; Goldblum, David; Hou, Yanyan; Munz, Martin; Rodrigues, Tiago M; Krol, Jacek; Szikra, Tamas; Cuttat, Rachel; Waldt, Annick; Papasaikas, Panagiotis; Diggelmann, Roland; Patino-Alvarez, Claudia P; Galliker, Patricia; Spirig, Stefan E; Pavlinic, Dinko; Gerber-Hollbach, Nadine; Schuierer, Sven; Srdanovic, Aldin; Balogh, Marton; Panero, Riccardo; Kusnyerik, Akos; Szabo, Arnold; Stadler, Michael B; Orgül, Selim; Picelli, Simone; Hasler, Pascal W; Hierlemann, Andreas; Scholl, Hendrik P N; Roma, Guglielmo; Nigsch, Florian; Roska, Botond Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution Journal Article CellPress, 182 , pp. 1623–1640, 2020. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, Organoids @article{Cowan2020, title = {Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution}, author = {Cameron S. Cowan and Magdalena Renner and Martina De Gennaro and Brigitte Gross-Scherf and David Goldblum and Yanyan Hou and Martin Munz and Tiago M. Rodrigues and Jacek Krol and Tamas Szikra and Rachel Cuttat and Annick Waldt and Panagiotis Papasaikas and Roland Diggelmann and Claudia P. Patino-Alvarez and Patricia Galliker and Stefan E. Spirig and Dinko Pavlinic and Nadine Gerber-Hollbach and Sven Schuierer and Aldin Srdanovic and Marton Balogh and Riccardo Panero and Akos Kusnyerik and Arnold Szabo and Michael B. Stadler and Selim Orgül and Simone Picelli and Pascal W. Hasler and Andreas Hierlemann and Hendrik P.N. Scholl and Guglielmo Roma and Florian Nigsch and Botond Roska}, url = {https://www.cell.com/cell/fulltext/S0092-8674(20)31004-7?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867420310047%3Fshowall%3Dtrue}, doi = {10.1016/j.cell.2020.08.013}, year = {2020}, date = {2020-09-17}, journal = {CellPress}, volume = {182}, pages = { 1623–1640}, abstract = {Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed light-sensitive human retinal organoids with multiple nuclear and synaptic layers and functional synapses. We sequenced the RNA of 285,441 single cells from these organoids at seven developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas, and performed histochemistry. Cell types in organoids matured in vitro to a stable “developed” state at a rate similar to human retina development in vivo. Transcriptomes of organoid cell types converged toward the transcriptomes of adult peripheral retinal cell types. Expression of disease-associated genes was cell-type-specific in adult retina, and cell-type specificity was retained in organoids. We implicate unexpected cell types in diseases such as macular degeneration. This resource identifies cellular targets for studying disease mechanisms in organoids and for targeted repair in human retinas.}, keywords = {ETH-CMOS-MEA, Organoids}, pubstate = {published}, tppubtype = {article} } Close Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed light-sensitive human retinal organoids with multiple nuclear and synaptic layers and functional synapses. We sequenced the RNA of 285,441 single cells from these organoids at seven developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas, and performed histochemistry. Cell types in organoids matured in vitro to a stable “developed” state at a rate similar to human retina development in vivo. Transcriptomes of organoid cell types converged toward the transcriptomes of adult peripheral retinal cell types. Expression of disease-associated genes was cell-type-specific in adult retina, and cell-type specificity was retained in organoids. We implicate unexpected cell types in diseases such as macular degeneration. This resource identifies cellular targets for studying disease mechanisms in organoids and for targeted repair in human retinas. Close https://www.cell.com/cell/fulltext/S0092-8674(20)31004-7?_returnURL=https%3A%2F%[...] doi:10.1016/j.cell.2020.08.013 Close
	Ronchi, Silvia; Buccino, Alessio Paolo; Prack, Gustavo; Kumar, Sreedhar Saseendran; Schröter, Manuel; Fiscella, Michele; Hierlemann, Andreas Electrophysiological Phenotype Characterization of Human iPSC-Derived Neuronal Cell Lines by Means of High-Density Microelectrode Arrays Journal Article BioRxiv, 2020. Abstract \| Links \| BibTeX \| Tags: ETH-CMOS-MEA, IPSC @article{Ronchi2020, title = {Electrophysiological Phenotype Characterization of Human iPSC-Derived Neuronal Cell Lines by Means of High-Density Microelectrode Arrays}, author = {Silvia Ronchi and Alessio Paolo Buccino and Gustavo Prack and Sreedhar Saseendran Kumar and Manuel Schröter and Michele Fiscella and Andreas Hierlemann }, url = {https://www.biorxiv.org/content/10.1101/2020.09.02.271403v1}, doi = {10.1101/2020.09.02.271403}, year = {2020}, date = {2020-09-02}, journal = {BioRxiv}, abstract = {Recent advances in the field of cellular reprogramming have opened a route to study the fundamental mechanisms underlying common neurological disorders. High-density microelectrode-arrays (HD-MEAs) provide unprecedented means to study neuronal physiology at different scales, ranging from network through single-neuron to subcellular features. In this work, we used HD-MEAs in vitro to characterize and compare human induced-pluripotent-stem-cell (iPSC)-derived dopaminergic and motor neurons, including isogenic neuronal lines modeling Parkinson’s disease and amyotrophic lateral sclerosis. We established reproducible electrophysiological network, single-cell and subcellular metrics, which were used for phenotype characterization and drug testing. Metrics such as burst shapes and axonal velocity enabled the distinction of healthy and diseased neurons. The HD-MEA metrics could also be used to detect the effects of dosing the drug retigabine to human motor neurons. Finally, we showed that the ability to detect drug effects and the observed culture-to-culture variability critically depend on the number of available recording electrodes}, keywords = {ETH-CMOS-MEA, IPSC}, pubstate = {published}, tppubtype = {article} } Close Recent advances in the field of cellular reprogramming have opened a route to study the fundamental mechanisms underlying common neurological disorders. High-density microelectrode-arrays (HD-MEAs) provide unprecedented means to study neuronal physiology at different scales, ranging from network through single-neuron to subcellular features. In this work, we used HD-MEAs in vitro to characterize and compare human induced-pluripotent-stem-cell (iPSC)-derived dopaminergic and motor neurons, including isogenic neuronal lines modeling Parkinson’s disease and amyotrophic lateral sclerosis. We established reproducible electrophysiological network, single-cell and subcellular metrics, which were used for phenotype characterization and drug testing. Metrics such as burst shapes and axonal velocity enabled the distinction of healthy and diseased neurons. The HD-MEA metrics could also be used to detect the effects of dosing the drug retigabine to human motor neurons. Finally, we showed that the ability to detect drug effects and the observed culture-to-culture variability critically depend on the number of available recording electrodes Close https://www.biorxiv.org/content/10.1101/2020.09.02.271403v1 doi:10.1101/2020.09.02.271403 Close
	Al-Absi, Abdel-Rahman; Qvist, Per; Okujeni, Samora; Khan, Ahmad Raza; Glerup, Simon; Sanchez, Connie; Nyengaard, Jens R Layers II/III of Prefrontal Cortex in Df(h22q11)/+ Mouse Model of the 22q11.2 Deletion Display Loss of Parvalbumin Interneurons and Modulation of Neuronal Morphology and Excitability Journal Article Molecular Neurobiology, 2020. Abstract \| Links \| BibTeX \| Tags: MaxOne, Slices @article{Al-Absi2020, title = {Layers II/III of Prefrontal Cortex in Df(h22q11)/+ Mouse Model of the 22q11.2 Deletion Display Loss of Parvalbumin Interneurons and Modulation of Neuronal Morphology and Excitability}, author = {Abdel-Rahman Al-Absi and Per Qvist and Samora Okujeni and Ahmad Raza Khan and Simon Glerup and Connie Sanchez and Jens R. Nyengaard }, url = {https://link.springer.com/article/10.1007/s12035-020-02067-1}, doi = {https://doi.org/10.1007/s12035-020-02067-1}, year = {2020}, date = {2020-08-20}, journal = {Molecular Neurobiology}, abstract = {The 22q11.2 deletion has been identified as a risk factor for multiple neurodevelopmental disorders. Behavioral and cognitive impairments are common among carriers of the 22q11.2 deletion. Parvalbumin expressing (PV+) interneurons provide perisomatic inhibition of excitatory neuronal circuits through GABAA receptors, and a deficit of PV+ inhibitory circuits may underlie a multitude of the behavioral and functional deficits in the 22q11.2 deletion syndrome. We investigated putative deficits of PV+ inhibitory circuits and the associated molecular, morphological, and functional alterations in the prefrontal cortex (PFC) of the Df(h22q11)/+ mouse model of the 22q11.2 hemizygous deletion. We detected a significant decrease in the number of PV+ interneurons in layers II/III of PFC in Df(h22q11)/+ mice together with a reduction in the mRNA and protein levels of GABAA (α3), a PV+ putative postsynaptic receptor subunit. Pyramidal neurons from the same layers further experienced morphological reorganizations of spines and dendrites. Accordingly, a decrease in the levels of the postsynaptic density protein 95 (PSD95) and a higher neuronal activity in response to the GABAA antagonist bicuculline were measured in these layers in PFC of Df(h22q11)/+ mice compared with their wild-type littermates. Our study shows that a hemizygotic deletion of the 22q11.2 locus leads to deficit in the GABAergic control of network activity and involves molecular and morphological changes in both the inhibitory and excitatory synapses of parvalbumin interneurons and pyramidal neurons specifically in layers II/III PFC.}, keywords = {MaxOne, Slices}, pubstate = {published}, tppubtype = {article} } Close The 22q11.2 deletion has been identified as a risk factor for multiple neurodevelopmental disorders. Behavioral and cognitive impairments are common among carriers of the 22q11.2 deletion. Parvalbumin expressing (PV+) interneurons provide perisomatic inhibition of excitatory neuronal circuits through GABAA receptors, and a deficit of PV+ inhibitory circuits may underlie a multitude of the behavioral and functional deficits in the 22q11.2 deletion syndrome. We investigated putative deficits of PV+ inhibitory circuits and the associated molecular, morphological, and functional alterations in the prefrontal cortex (PFC) of the Df(h22q11)/+ mouse model of the 22q11.2 hemizygous deletion. We detected a significant decrease in the number of PV+ interneurons in layers II/III of PFC in Df(h22q11)/+ mice together with a reduction in the mRNA and protein levels of GABAA (α3), a PV+ putative postsynaptic receptor subunit. Pyramidal neurons from the same layers further experienced morphological reorganizations of spines and dendrites. Accordingly, a decrease in the levels of the postsynaptic density protein 95 (PSD95) and a higher neuronal activity in response to the GABAA antagonist bicuculline were measured in these layers in PFC of Df(h22q11)/+ mice compared with their wild-type littermates. Our study shows that a hemizygotic deletion of the 22q11.2 locus leads to deficit in the GABAergic control of network activity and involves molecular and morphological changes in both the inhibitory and excitatory synapses of parvalbumin interneurons and pyramidal neurons specifically in layers II/III PFC. Close https://link.springer.com/article/10.1007/s12035-020-02067-1 doi:https://doi.org/10.1007/s12035-020-02067-1 Close
	Bandarabadi, Mojtaba; Vassalli, Anne; Tafti, Mehdi Sleep as a default state of cortical and subcortical networks Journal Article Current Opinion in Physiology, 15 , pp. 60-67, 2020. Abstract \| Links \| BibTeX \| Tags: Neuronal Networks, Review, Sleep @article{Bandarabadi2020, title = {Sleep as a default state of cortical and subcortical networks}, author = {Mojtaba Bandarabadi and Anne Vassalli and Mehdi Tafti}, url = {https://www.sciencedirect.com/science/article/pii/S2468867319301907?via%3Dihub}, doi = {10.1016/j.cophys.2019.12.004}, year = {2020}, date = {2020-06-20}, journal = {Current Opinion in Physiology}, volume = {15}, pages = {60-67}, abstract = {Sleep has been conceptualized as ‘activity-dependent’, hence a response to prior waking experience, and proposed to be ‘the price the brain pays for plasticity during wakefulness’. We here propose that at the level of neuronal networks, particularly those arising from isolated embryonic thalamocortical cells maintained in culture, it represents a default mode of functioning. We show that cell assemblies in ex vivo cultures express powerful sleep specific patterns of oscillatory activity, as well as metabolic and molecular signatures of the sleep state. We summarize recent evidences that support our hypothesis and discuss potential applications of developing ex vivo sleep models to answer open questions in the field.}, keywords = {Neuronal Networks, Review, Sleep}, pubstate = {published}, tppubtype = {article} } Close Sleep has been conceptualized as ‘activity-dependent’, hence a response to prior waking experience, and proposed to be ‘the price the brain pays for plasticity during wakefulness’. We here propose that at the level of neuronal networks, particularly those arising from isolated embryonic thalamocortical cells maintained in culture, it represents a default mode of functioning. We show that cell assemblies in ex vivo cultures express powerful sleep specific patterns of oscillatory activity, as well as metabolic and molecular signatures of the sleep state. We summarize recent evidences that support our hypothesis and discuss potential applications of developing ex vivo sleep models to answer open questions in the field. Close https://www.sciencedirect.com/science/article/pii/S2468867319301907?via%3Dihub doi:10.1016/j.cophys.2019.12.004 Close
	Masumori, Atsushi; Sinapayen, Lana; Maruyama, Norihiro; Mita, Takeshi; Bakkum, Douglas J; Frey, Urs; Takahashi, Hirokazu; Ikegami, Takashi Neural Autopoiesis: Organizing Self-Boundaries by Stimulus Avoidance in Biological and Artificial Neural Networks Journal Article Artificial Life, 26 (1), pp. 130-151, 2020, ISSN: 1064-5462. Abstract \| Links \| BibTeX \| Tags: Neuronal Networks @article{Masumori2020, title = {Neural Autopoiesis: Organizing Self-Boundaries by Stimulus Avoidance in Biological and Artificial Neural Networks}, author = {Atsushi Masumori and Lana Sinapayen and Norihiro Maruyama and Takeshi Mita and Douglas J. Bakkum and Urs Frey and Hirokazu Takahashi and Takashi Ikegami}, url = {https://www.mitpressjournals.org/doi/full/10.1162/artl_a_00314}, doi = {10.1162/artl_a_00314}, issn = {1064-5462}, year = {2020}, date = {2020-04-28}, journal = {Artificial Life}, volume = {26}, number = {1}, pages = {130-151}, abstract = {Living organisms must actively maintain themselves in order to continue existing. Autopoiesis is a key concept in the study of living organisms, where the boundaries of the organism are not static but dynamically regulated by the system itself. To study the autonomous regulation of a self-boundary, we focus on neural homeodynamic responses to environmental changes using both biological and artificial neural networks. Previous studies showed that embodied cultured neural networks and spiking neural networks with spike-timing dependent plasticity (STDP) learn an action as they avoid stimulation from outside. In this article, as a result of our experiments using embodied cultured neurons, we find that there is also a second property allowing the network to avoid stimulation: If the agent cannot learn an action to avoid the external stimuli, it tends to decrease the stimulus-evoked spikes, as if to ignore the uncontrollable input. We also show such a behavior is reproduced by spiking neural networks with asymmetric STDP. We consider that these properties are to be regarded as autonomous regulation of self and nonself for the network, in which a controllable neuron is regarded as self, and an uncontrollable neuron is regarded as nonself. Finally, we introduce neural autopoiesis by proposing the principle of stimulus avoidance.}, keywords = {Neuronal Networks}, pubstate = {published}, tppubtype = {article} } Close Living organisms must actively maintain themselves in order to continue existing. Autopoiesis is a key concept in the study of living organisms, where the boundaries of the organism are not static but dynamically regulated by the system itself. To study the autonomous regulation of a self-boundary, we focus on neural homeodynamic responses to environmental changes using both biological and artificial neural networks. Previous studies showed that embodied cultured neural networks and spiking neural networks with spike-timing dependent plasticity (STDP) learn an action as they avoid stimulation from outside. In this article, as a result of our experiments using embodied cultured neurons, we find that there is also a second property allowing the network to avoid stimulation: If the agent cannot learn an action to avoid the external stimuli, it tends to decrease the stimulus-evoked spikes, as if to ignore the uncontrollable input. We also show such a behavior is reproduced by spiking neural networks with asymmetric STDP. We consider that these properties are to be regarded as autonomous regulation of self and nonself for the network, in which a controllable neuron is regarded as self, and an uncontrollable neuron is regarded as nonself. Finally, we introduce neural autopoiesis by proposing the principle of stimulus avoidance. Close https://www.mitpressjournals.org/doi/full/10.1162/artl_a_00314 doi:10.1162/artl_a_00314 Close
	Idrees, Saad; Baumann, Matthias P; Franke, Felix; Münch, Thomas A; Hafed, Ziad M Perceptual saccadic suppression starts in the retina Journal Article Nature Communications, 11 (1977), 2020. Links \| BibTeX \| Tags: ETH-CMOS-MEA, MaxOne, Retina @article{Idrees2020, title = {Perceptual saccadic suppression starts in the retina}, author = {Saad Idrees and Matthias P. Baumann and Felix Franke and Thomas A. Münch and Ziad M. Hafed}, url = {https://www.nature.com/articles/s41467-020-15890-w}, doi = {10.1038/s41467-020-15890-w}, year = {2020}, date = {2020-04-24}, journal = {Nature Communications}, volume = {11}, number = {1977}, keywords = {ETH-CMOS-MEA, MaxOne, Retina}, pubstate = {published}, tppubtype = {article} } Close https://www.nature.com/articles/s41467-020-15890-w doi:10.1038/s41467-020-15890-w Close
	Obaid, Abdulmalik; Hanna, Mina-Elrahb; Wu, Yu-Wei; Kollo, Mihaly; Racz, Romeo; Angle, Matthew R; Muller, Jan; Brackbill, Nora; Wray, William; Franke, Felix; Chichilnski, E J; Hierlemann, Andreas; Ding, Jun B; Schaefer, Andreas T; Melosh, Nicholas A Massively parallel microwire arrays integrated withCMOS chips for neural recording Journal Article Science Advances, 2020. Abstract \| Links \| BibTeX \| Tags: Electrodes, ETH-CMOS-MEA @article{Obaid2020, title = {Massively parallel microwire arrays integrated withCMOS chips for neural recording}, author = {Abdulmalik Obaid and Mina-Elrahb Hanna and Yu-Wei Wu and Mihaly Kollo and Romeo Racz and Matthew R Angle and Jan Muller and Nora Brackbill and William Wray and Felix Franke and E J Chichilnski and Andreas Hierlemann and Jun B. Ding and Andreas T. Schaefer and Nicholas A. Melosh}, url = {https://advances.sciencemag.org/content/6/12/eaay2789}, doi = {10.1126/sciadv.aay2789}, year = {2020}, date = {2020-03-20}, journal = {Science Advances}, abstract = {Multi-channel electrical recordings of neural activity in the brain is an increasingly powerful method revealing new aspects of neural communication, computation, and prosthetics. However, while planar silicon-based CMOS devices in conventional electronics scale rapidly, neural interface devices have not kept pace. Here, we present a new strategy to interface silicon-based chips with three-dimensional microwire arrays, providing the link between rapidly-developing electronics and high density neural interfaces. The system consists of a bundle of microwires mated to large-scale microelectrode arrays, such as camera chips. This system has excellent recording performance, demonstrated via single unit and local-field potential recordings in isolated retina and in the motor cortex or striatum of awake moving mice. The modular design enables a variety of microwire types and sizes to be integrated with different types of pixel arrays, connecting the rapid progress of commercial multiplexing, digitisation and data acquisition hardware together with a three-dimensional neural interface.}, keywords = {Electrodes, ETH-CMOS-MEA}, pubstate = {published}, tppubtype = {article} } Close Multi-channel electrical recordings of neural activity in the brain is an increasingly powerful method revealing new aspects of neural communication, computation, and prosthetics. However, while planar silicon-based CMOS devices in conventional electronics scale rapidly, neural interface devices have not kept pace. Here, we present a new strategy to interface silicon-based chips with three-dimensional microwire arrays, providing the link between rapidly-developing electronics and high density neural interfaces. The system consists of a bundle of microwires mated to large-scale microelectrode arrays, such as camera chips. This system has excellent recording performance, demonstrated via single unit and local-field potential recordings in isolated retina and in the motor cortex or striatum of awake moving mice. The modular design enables a variety of microwire types and sizes to be integrated with different types of pixel arrays, connecting the rapid progress of commercial multiplexing, digitisation and data acquisition hardware together with a three-dimensional neural interface. Close https://advances.sciencemag.org/content/6/12/eaay2789 doi:10.1126/sciadv.aay2789 Close

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