日本語
繁體中文
简体中文
English
Publications
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.
All Publications
| 1. | Kasuba, Krishna Chaitanya; Buccino, Alessio Paolo; Bartram, Julian; Gaub, Benjamin M; Fauser, Felix J; Ronchi, Silvia; Kumar, Sreedhar Saseendran; Geissler, Sydney; Nava, Michele M; Hierlemann, Andreas; Müller, Daniel J: Mechanical stimulation and electrophysiological monitoring at subcellular resolution reveals differential mechanosensation of neurons within networks. In: Nature Nanotechnology, 2024. (Type: Journal Article | Abstract | Links | BibTeX) @article{Kasuba2024, title = {Mechanical stimulation and electrophysiological monitoring at subcellular resolution reveals differential mechanosensation of neurons within networks}, author = {Krishna Chaitanya Kasuba and Alessio Paolo Buccino and Julian Bartram and Benjamin M. Gaub and Felix J. Fauser and Silvia Ronchi and Sreedhar Saseendran Kumar and Sydney Geissler and Michele M. Nava and Andreas Hierlemann and Daniel J. Müller }, url = {https://www.nature.com/articles/s41565-024-01609-1}, doi = {10.1038/s41565-024-01609-1}, year = {2024}, date = {2024-02-20}, journal = {Nature Nanotechnology}, abstract = {A growing consensus that the brain is a mechanosensitive organ is driving the need for tools that mechanically stimulate and simultaneously record the electrophysiological response of neurons within neuronal networks. Here we introduce a synchronized combination of atomic force microscopy, high-density microelectrode array and fluorescence microscopy to monitor neuronal networks and to mechanically characterize and stimulate individual neurons at piconewton force sensitivity and nanometre precision while monitoring their electrophysiological activity at subcellular spatial and millisecond temporal resolution. No correlation is found between mechanical stiffness and electrophysiological activity of neuronal compartments. Furthermore, spontaneously active neurons show exceptional functional resilience to static mechanical compression of their soma. However, application of fast transient (∼500 ms) mechanical stimuli to the neuronal soma can evoke action potentials, which depend on the anchoring of neuronal membrane and actin cytoskeleton. Neurons show higher responsivity, including bursts of action potentials, to slower transient mechanical stimuli (∼60 s). Moreover, transient and repetitive application of the same compression modulates the neuronal firing rate. Seemingly, neuronal networks can differentiate and respond to specific characteristics of mechanical stimulation. Ultimately, the developed multiparametric tool opens the door to explore manifold nanomechanobiological responses of neuronal systems and new ways of mechanical control.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A growing consensus that the brain is a mechanosensitive organ is driving the need for tools that mechanically stimulate and simultaneously record the electrophysiological response of neurons within neuronal networks. Here we introduce a synchronized combination of atomic force microscopy, high-density microelectrode array and fluorescence microscopy to monitor neuronal networks and to mechanically characterize and stimulate individual neurons at piconewton force sensitivity and nanometre precision while monitoring their electrophysiological activity at subcellular spatial and millisecond temporal resolution. No correlation is found between mechanical stiffness and electrophysiological activity of neuronal compartments. Furthermore, spontaneously active neurons show exceptional functional resilience to static mechanical compression of their soma. However, application of fast transient (∼500 ms) mechanical stimuli to the neuronal soma can evoke action potentials, which depend on the anchoring of neuronal membrane and actin cytoskeleton. Neurons show higher responsivity, including bursts of action potentials, to slower transient mechanical stimuli (∼60 s). Moreover, transient and repetitive application of the same compression modulates the neuronal firing rate. Seemingly, neuronal networks can differentiate and respond to specific characteristics of mechanical stimulation. Ultimately, the developed multiparametric tool opens the door to explore manifold nanomechanobiological responses of neuronal systems and new ways of mechanical control. |
| 2. | Hruska-Plochan, Marian; Wiersma, Vera I; Betz, Katharina M; Mallona, Izaskun; Ronchi, Silvia; Maniecka, Zuzanna; Hock, Eva-Maria; Tantardini, Elena; Laferriere, Florent; Sahadevan, Sonu; Hoop, Vanessa; Delvendahl, Igor; Pérez-Berlanga, Manuela; Gatta, Beatrice; Panatta, Martina; van der Bourg, Alexander; Bohaciakova, Dasa; Sharma, Puneet; Vos, Laura De; Frontzek, Karl; Aguzzi, Adriano; Lashley, Tammaryn; Robinson, Mark D; Karayannis, Theofanis; Mueller, Martin; Hierlemann, Andreas; Polymenidou, Magdalini: A model of human neural networks reveals NPTX2 pathology in ALS and FTLD. In: Nature, 2024. (Type: Journal Article | Abstract | Links | BibTeX) @article{Hruska-Plochan2024, title = {A model of human neural networks reveals NPTX2 pathology in ALS and FTLD}, author = {Marian Hruska-Plochan and Vera I. Wiersma and Katharina M. Betz and Izaskun Mallona and Silvia Ronchi and Zuzanna Maniecka and Eva-Maria Hock and Elena Tantardini and Florent Laferriere and Sonu Sahadevan and Vanessa Hoop and Igor Delvendahl and Manuela Pérez-Berlanga and Beatrice Gatta and Martina Panatta and Alexander van der Bourg and Dasa Bohaciakova and Puneet Sharma and Laura De Vos 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://www.nature.com/articles/s41586-024-07042-7}, doi = {10.1038/s41586-024-07042-7}, year = {2024}, date = {2024-02-14}, journal = {Nature}, abstract = {Human cellular models of neurodegeneration require reproducibility and longevity, which is necessary for simulating age-dependent diseases. Such systems are particularly needed for TDP-43 proteinopathies1, which involve human-specific mechanisms that cannot be directly studied in animal models. Here, to explore the emergence and consequences of TDP-43 pathologies, we generated induced pluripotent stem cell-derived, colony morphology neural stem cells (iCoMoNSCs) via manual selection of neural precursors. Single-cell transcriptomics and comparison to independent neural stem cells 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 (which we designate iNets). Neuronal and glial maturation in iNets was similar to that of cortical organoids. Overexpression of wild-type TDP-43 in a minority of neurons within iNets led to progressive fragmentation and aggregation of the protein, resulting in a partial loss of function and neurotoxicity. Single-cell transcriptomics revealed a novel set of misregulated RNA targets in TDP-43-overexpressing neurons and in patients with TDP-43 proteinopathies exhibiting a loss of nuclear TDP-43. The strongest misregulated target encoded the synaptic protein NPTX2, the levels of which are controlled by TDP-43 binding on its 3′ untranslated region. When NPTX2 was overexpressed in iNets, it exhibited neurotoxicity, whereas correcting NPTX2 misregulation partially rescued neurons from TDP-43-induced neurodegeneration. Notably, NPTX2 was consistently misaccumulated in neurons from patients with amyotrophic lateral sclerosis and frontotemporal lobar degeneration with TDP-43 pathology. Our work directly links TDP-43 misregulation and NPTX2 accumulation, thereby revealing a TDP-43-dependent pathway of neurotoxicity.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Human cellular models of neurodegeneration require reproducibility and longevity, which is necessary for simulating age-dependent diseases. Such systems are particularly needed for TDP-43 proteinopathies1, which involve human-specific mechanisms that cannot be directly studied in animal models. Here, to explore the emergence and consequences of TDP-43 pathologies, we generated induced pluripotent stem cell-derived, colony morphology neural stem cells (iCoMoNSCs) via manual selection of neural precursors. Single-cell transcriptomics and comparison to independent neural stem cells 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 (which we designate iNets). Neuronal and glial maturation in iNets was similar to that of cortical organoids. Overexpression of wild-type TDP-43 in a minority of neurons within iNets led to progressive fragmentation and aggregation of the protein, resulting in a partial loss of function and neurotoxicity. Single-cell transcriptomics revealed a novel set of misregulated RNA targets in TDP-43-overexpressing neurons and in patients with TDP-43 proteinopathies exhibiting a loss of nuclear TDP-43. The strongest misregulated target encoded the synaptic protein NPTX2, the levels of which are controlled by TDP-43 binding on its 3′ untranslated region. When NPTX2 was overexpressed in iNets, it exhibited neurotoxicity, whereas correcting NPTX2 misregulation partially rescued neurons from TDP-43-induced neurodegeneration. Notably, NPTX2 was consistently misaccumulated in neurons from patients with amyotrophic lateral sclerosis and frontotemporal lobar degeneration with TDP-43 pathology. Our work directly links TDP-43 misregulation and NPTX2 accumulation, thereby revealing a TDP-43-dependent pathway of neurotoxicity. |
| 3. | Hornauer, Philipp; Prack, Gustavo; Anastasi, Nadia; Ronchi, Silvia; Kim, Taehoon; Donner, Christian; Fiscella, Michele; Borgwardt, Karsten; Taylor, Verdon; Jagasia, Ravi; Roqueiro, Damian; Hierlemann, Andreas; Schröter, Manuel: DeePhys: A machine learning–assisted platform for electrophysiological phenotyping of human neuronal networks. In: Stem Cell Reports, 2024. (Type: Journal Article | Abstract | Links | BibTeX) @article{Hornauer2024, title = {DeePhys: A machine learning–assisted platform for electrophysiological phenotyping of human neuronal networks}, author = {Philipp Hornauer and Gustavo Prack and Nadia Anastasi and Silvia Ronchi and Taehoon Kim and Christian Donner and Michele Fiscella and Karsten Borgwardt and Verdon Taylor and Ravi Jagasia and Damian Roqueiro and Andreas Hierlemann and Manuel Schröter}, url = {https://www.sciencedirect.com/science/article/pii/S2213671123005015}, doi = {10.1016/j.stemcr.2023.12.008}, year = {2024}, date = {2024-01-25}, journal = {Stem Cell Reports}, abstract = {Reproducible functional assays to study in vitro neuronal networks represent an important cornerstone in the quest to develop physiologically relevant cellular models of human diseases. Here, we introduce DeePhys, a MATLAB-based analysis tool for data-driven functional phenotyping of in vitro neuronal cultures recorded by high-density microelectrode arrays. DeePhys is a modular workflow that offers a range of techniques to extract features from spike-sorted data, allowing for the examination of functional phenotypes both at the individual cell and network levels, as well as across development. In addition, DeePhys incorporates the capability to integrate novel features and to use machine-learning-assisted approaches, which facilitates a comprehensive evaluation of pharmacological interventions. To illustrate its practical application, we apply DeePhys to human induced pluripotent stem cell–derived dopaminergic neurons obtained from both patients and healthy individuals and showcase how DeePhys enables phenotypic screenings.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Reproducible functional assays to study in vitro neuronal networks represent an important cornerstone in the quest to develop physiologically relevant cellular models of human diseases. Here, we introduce DeePhys, a MATLAB-based analysis tool for data-driven functional phenotyping of in vitro neuronal cultures recorded by high-density microelectrode arrays. DeePhys is a modular workflow that offers a range of techniques to extract features from spike-sorted data, allowing for the examination of functional phenotypes both at the individual cell and network levels, as well as across development. In addition, DeePhys incorporates the capability to integrate novel features and to use machine-learning-assisted approaches, which facilitates a comprehensive evaluation of pharmacological interventions. To illustrate its practical application, we apply DeePhys to human induced pluripotent stem cell–derived dopaminergic neurons obtained from both patients and healthy individuals and showcase how DeePhys enables phenotypic screenings. |
| 4. | Cai, Hongwei; Ao, Zheng; Tian, Chunhui; Wu, Zhuhao; Liu, Hongcheng; Tchieu, Jason; Gu, Mingxia; Mackie, Ken; Guo, Feng: Brain organoid reservoir computing for artificial intelligence. In: Nature Electronics, 2023. (Type: Journal Article | Abstract | Links | BibTeX) @article{Cai2023b, title = {Brain organoid reservoir computing for artificial intelligence}, author = {Hongwei Cai and Zheng Ao and Chunhui Tian and Zhuhao Wu and Hongcheng Liu and Jason Tchieu and Mingxia Gu and Ken Mackie and Feng Guo }, url = {https://www.nature.com/articles/s41928-023-01069-w}, doi = {10.1038/s41928-023-01069-w}, year = {2023}, date = {2023-12-11}, journal = {Nature Electronics}, abstract = {Brain-inspired computing hardware aims to emulate the structure and working principles of the brain and could be used to address current limitations in artificial intelligence technologies. However, brain-inspired silicon chips are still limited in their ability to fully mimic brain function as most examples are built on digital electronic principles. Here we report an artificial intelligence hardware approach that uses adaptive reservoir computation of biological neural networks in a brain organoid. In this approach—which is termed Brainoware—computation is performed by sending and receiving information from the brain organoid using a high-density multielectrode array. By applying spatiotemporal electrical stimulation, nonlinear dynamics and fading memory properties are achieved, as well as unsupervised learning from training data by reshaping the organoid functional connectivity. We illustrate the practical potential of this technique by using it for speech recognition and nonlinear equation prediction in a reservoir computing framework.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Brain-inspired computing hardware aims to emulate the structure and working principles of the brain and could be used to address current limitations in artificial intelligence technologies. However, brain-inspired silicon chips are still limited in their ability to fully mimic brain function as most examples are built on digital electronic principles. Here we report an artificial intelligence hardware approach that uses adaptive reservoir computation of biological neural networks in a brain organoid. In this approach—which is termed Brainoware—computation is performed by sending and receiving information from the brain organoid using a high-density multielectrode array. By applying spatiotemporal electrical stimulation, nonlinear dynamics and fading memory properties are achieved, as well as unsupervised learning from training data by reshaping the organoid functional connectivity. We illustrate the practical potential of this technique by using it for speech recognition and nonlinear equation prediction in a reservoir computing framework. |
| 5. | Ryu, Seungmi; Weber, Claire; Chu, Pei-Hsuan; Ernest, Ben; Jovanovic, Vukasin M; Deng, Tao; Slamecka, Jaroslav; Hong, Hyenjong; Jethmalani, Yogita; Baskir, Hannah M; Inman, Jason; Braisted, John; Hirst, Marissa B; Simeonov, Anton; Voss, Ty C; Tristan, Carlos A; Singeç, Ilyas: Stress-free cell aggregation by using the CEPT cocktail enhances embryoid body and organoid fitness. In: Biofabrication, 2023. (Type: Journal Article | Abstract | Links | BibTeX) @article{Ryu2023, title = {Stress-free cell aggregation by using the CEPT cocktail enhances embryoid body and organoid fitness}, author = {Seungmi Ryu and Claire Weber and Pei-Hsuan Chu and Ben Ernest and Vukasin M Jovanovic and Tao Deng and Jaroslav Slamecka and Hyenjong Hong and Yogita Jethmalani and Hannah M Baskir and Jason Inman and John Braisted and Marissa B Hirst and Anton Simeonov and Ty C Voss and Carlos A Tristan and Ilyas Singeç}, url = {https://dx.doi.org/10.1088/1758-5090/ad0d13}, doi = {10.1088/1758-5090/ad0d13}, year = {2023}, date = {2023-12-11}, journal = {Biofabrication}, abstract = {Embryoid bodies (EBs) and self-organizing organoids derived from human pluripotent stem cells (hPSCs) recapitulate tissue development in a dish and hold great promise for disease modeling and drug development. However, current protocols are hampered by cellular stress and apoptosis during cell aggregation, resulting in variability and impaired cell differentiation. Here, we demonstrate that EBs and various organoid models (e.g., brain, gut, kidney) can be optimized by using the small molecule cocktail named CEPT (chroman 1, emricasan, polyamines, trans-ISRIB), a polypharmacological approach that ensures cytoprotection and cell survival. Application of CEPT for just 24 h during cell aggregation has long-lasting consequences affecting morphogenesis, gene expression, cellular differentiation, and organoid function. Various qualification methods confirmed that CEPT treatment enhanced experimental reproducibility and consistently improved EB and organoid fitness as compared to the widely used ROCK inhibitor Y-27632. Collectively, we discovered that stress-free cell aggregation and superior cell survival in the presence of CEPT are critical quality control determinants that establish a robust foundation for bioengineering complex tissue and organ models.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Embryoid bodies (EBs) and self-organizing organoids derived from human pluripotent stem cells (hPSCs) recapitulate tissue development in a dish and hold great promise for disease modeling and drug development. However, current protocols are hampered by cellular stress and apoptosis during cell aggregation, resulting in variability and impaired cell differentiation. Here, we demonstrate that EBs and various organoid models (e.g., brain, gut, kidney) can be optimized by using the small molecule cocktail named CEPT (chroman 1, emricasan, polyamines, trans-ISRIB), a polypharmacological approach that ensures cytoprotection and cell survival. Application of CEPT for just 24 h during cell aggregation has long-lasting consequences affecting morphogenesis, gene expression, cellular differentiation, and organoid function. Various qualification methods confirmed that CEPT treatment enhanced experimental reproducibility and consistently improved EB and organoid fitness as compared to the widely used ROCK inhibitor Y-27632. Collectively, we discovered that stress-free cell aggregation and superior cell survival in the presence of CEPT are critical quality control determinants that establish a robust foundation for bioengineering complex tissue and organ models. |
| 6. | Elliott, Matthew A T; Schweiger, Hunter E; Robbins, Ash; Vera-Choqqueccota, Samira; Ehrlich, Drew; Hernandez, Sebastian; Voitiuk, Kateryna; Geng, Jinghui; Sevetson, Jess L; Core, Cordero; Rosen, Yohei M; Teodorescu, Mircea; Wagner, Nico O; Haussler, David; Mostajo-Radji, Mohammed A: Internet-Connected Cortical Organoids for Project-Based Stem Cell and Neuroscience Education. In: eNeuro, 2023. (Type: Journal Article | Abstract | Links | BibTeX) @article{Elliott2023, title = {Internet-Connected Cortical Organoids for Project-Based Stem Cell and Neuroscience Education}, author = {Matthew A. T. Elliott and Hunter E. Schweiger and Ash Robbins and Samira Vera-Choqqueccota and Drew Ehrlich and Sebastian Hernandez and Kateryna Voitiuk and Jinghui Geng and Jess L. Sevetson and Cordero Core and Yohei M. Rosen and Mircea Teodorescu and Nico O. Wagner and David Haussler and Mohammed A. Mostajo-Radji}, url = {https://www.eneuro.org/lookup/doi/10.1523/ENEURO.0308-23.2023}, doi = {10.1523/ENEURO.0308-23.2023}, year = {2023}, date = {2023-11-28}, journal = {eNeuro}, abstract = {The introduction of Internet-connected technologies to the classroom has the potential to revolutionize STEM education by allowing students to perform experiments in complex models that are unattainable in traditional teaching laboratories. By connecting laboratory equipment to the cloud, we introduce students to experimentation in pluripotent stem cell (PSC)-derived cortical organoids in two different settings: using microscopy to monitor organoid growth in an introductory tissue culture course and using high-density (HD) multielectrode arrays (MEAs) to perform neuronal stimulation and recording in an advanced neuroscience mathematics course. We demonstrate that this approach develops interest in stem cell and neuroscience in the students of both courses. All together, we propose cloud technologies as an effective and scalable approach for complex project-based university training.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The introduction of Internet-connected technologies to the classroom has the potential to revolutionize STEM education by allowing students to perform experiments in complex models that are unattainable in traditional teaching laboratories. By connecting laboratory equipment to the cloud, we introduce students to experimentation in pluripotent stem cell (PSC)-derived cortical organoids in two different settings: using microscopy to monitor organoid growth in an introductory tissue culture course and using high-density (HD) multielectrode arrays (MEAs) to perform neuronal stimulation and recording in an advanced neuroscience mathematics course. We demonstrate that this approach develops interest in stem cell and neuroscience in the students of both courses. All together, we propose cloud technologies as an effective and scalable approach for complex project-based university training. |
| 7. | Kobayashi, Toki; Shimba, Kenta; Kotani, Kiyoshi; Jimbo, Yasuhiko: Measuring and Inducing the Plasticity of Single-Neuron Scale at Multiple Points. ISSS Xplore, 2023. (Type: Conference | Abstract | Links | BibTeX) @conference{Kobayashi2023, title = {Measuring and Inducing the Plasticity of Single-Neuron Scale at Multiple Points}, author = {Toki Kobayashi and Kenta Shimba and Kiyoshi Kotani and Yasuhiko Jimbo}, url = {https://ieeexplore.ieee.org/abstract/document/10322076}, doi = {10.1109/BMEiCON60347.2023.10322076}, year = {2023}, date = {2023-11-22}, journal = {IEEE Xplore}, publisher = {ISSS Xplore}, abstract = {Information processing in the brain is supported by the plasticity of the connections of neurons in biological neuronal networks. There is a gap between our understanding on plasticity of individual connections and that of the neuronal networks. Here, we aimed to induce and measure plasticity at the connections of individual neurons and at the network level. We achieved inducing plasticity with a combination of single cell stimulation by optogenetics and high-resolution extracellular potentials recording by high-density microelectrode array. Spike timing plasticity in a single neuron was successfully measured. Although we also tried to induce synaptic potentiation by tetanus stimulation, no significant change was observed. In the future, we will investigate how the plasticity of individual connections changes dynamics of entire network.}, keywords = {}, pubstate = {published}, tppubtype = {conference} } Information processing in the brain is supported by the plasticity of the connections of neurons in biological neuronal networks. There is a gap between our understanding on plasticity of individual connections and that of the neuronal networks. Here, we aimed to induce and measure plasticity at the connections of individual neurons and at the network level. We achieved inducing plasticity with a combination of single cell stimulation by optogenetics and high-resolution extracellular potentials recording by high-density microelectrode array. Spike timing plasticity in a single neuron was successfully measured. Although we also tried to induce synaptic potentiation by tetanus stimulation, no significant change was observed. In the future, we will investigate how the plasticity of individual connections changes dynamics of entire network. |
| 8. | Tamatani, Chie; Shimba, Kenta; andYasuhiko Jimbo, Kiyoshi Kotani: Activity- and Spatial-dependent Variations in Axonal Conduction Recorded from Microtunnel Electrodes. IEEE Xplore, 2023. (Type: Conference | Abstract | Links | BibTeX) @conference{Tamatani2023, title = {Activity- and Spatial-dependent Variations in Axonal Conduction Recorded from Microtunnel Electrodes}, author = {Chie Tamatani and Kenta Shimba and Kiyoshi Kotani andYasuhiko Jimbo }, url = {https://ieeexplore.ieee.org/abstract/document/10321980}, doi = {10.1109/BMEiCON60347.2023.10321980}, year = {2023}, date = {2023-11-22}, publisher = {IEEE Xplore}, abstract = {Axons are not simple transmission cables in neuronal networks, but they are directly involved in information processing. We developed a novel culture device that aims to assess axonal conduction properties. The microdevice consists of microtunnels directly fabricated on high-density microelectrode array. Neuron growth and axon isolation were confirmed by immunofluorescent staining and neural activity recording. Several dozens of electrodes were detected from each tunnel and signals had enough S/N ratio to handle each spike event. Activity- and spatial-dependent variations in conduction velocity were observed. These results suggest that our microdevice is feasible to study axonal information processing.}, keywords = {}, pubstate = {published}, tppubtype = {conference} } Axons are not simple transmission cables in neuronal networks, but they are directly involved in information processing. We developed a novel culture device that aims to assess axonal conduction properties. The microdevice consists of microtunnels directly fabricated on high-density microelectrode array. Neuron growth and axon isolation were confirmed by immunofluorescent staining and neural activity recording. Several dozens of electrodes were detected from each tunnel and signals had enough S/N ratio to handle each spike event. Activity- and spatial-dependent variations in conduction velocity were observed. These results suggest that our microdevice is feasible to study axonal information processing. |
| 9. | Sawada, Tomoyo; Barbosa, André R; Araujo, Bruno; McCord, Alejandra E; D’Ignazio, Laura; Benjamin, Kynon J M; Sheehan, Bonna; Zabolocki, Michael; Feltrin, Arthur; Arora, Ria; Brandtjen, Anna C; Kleinman, Joel E; Hyde, Thomas M; Bardy, Cedric; Weinberger, Daniel R; Paquola, Apuã C M; Erwin, Jennifer A: Recapitulation of Perturbed Striatal Gene Expression Dynamics of Donor’s Brains With Ventral Forebrain Organoids Derived From the Same Individuals With Schizophrenia. In: American Journal of Psychiatry, 2023, ISSN: 0002-953X. (Type: Journal Article | Abstract | Links | BibTeX) @article{Tomoyo2023, title = {Recapitulation of Perturbed Striatal Gene Expression Dynamics of Donor’s Brains With Ventral Forebrain Organoids Derived From the Same Individuals With Schizophrenia}, author = {Tomoyo Sawada and André R. Barbosa and Bruno Araujo and Alejandra E. McCord and Laura D’Ignazio and Kynon J.M. Benjamin and Bonna Sheehan and Michael Zabolocki and Arthur Feltrin and Ria Arora and Anna C. Brandtjen and Joel E. Kleinman and Thomas M. Hyde and Cedric Bardy and Daniel R. Weinberger and Apuã C.M. Paquola and Jennifer A. Erwin}, url = {https://ajp.psychiatryonline.org/doi/10.1176/appi.ajp.20220723}, doi = {10.1176/appi.ajp.20220723}, issn = {0002-953X}, year = {2023}, date = {2023-11-02}, journal = {American Journal of Psychiatry}, abstract = {Objective: Schizophrenia is a brain disorder that originates during neurodevelopment and has complex genetic and environmental etiologies. Despite decades of clinical evidence of altered striatal function in affected patients, studies examining its cellular and molecular mechanisms in humans are limited. To explore neurodevelopmental alterations in the striatum associated with schizophrenia, the authors established a method for the differentiation of induced pluripotent stem cells (iPSCs) into ventral forebrain organoids (VFOs). Methods: VFOs were generated from postmortem dural fibroblast–derived iPSCs of four individuals with schizophrenia and four neurotypical control individuals for whom postmortem caudate genotypes and transcriptomic data were profiled in the BrainSeq neurogenomics consortium. Individuals were selected such that the two groups had nonoverlapping schizophrenia polygenic risk scores (PRSs). Results: Single-cell RNA sequencing analyses of VFOs revealed differences in developmental trajectory between schizophrenia and control individuals in which inhibitory neuronal cells from the patients exhibited accelerated maturation. Furthermore, upregulated genes in inhibitory neurons in schizophrenia VFOs showed a significant overlap with upregulated genes in postmortem caudate tissue of individuals with schizophrenia compared with control individuals, including the donors of the iPSC cohort. Conclusions: The findings suggest that striatal neurons derived from high-PRS individuals with schizophrenia carry abnormalities that originated during early brain development and that the VFO model can recapitulate disease-relevant cell type–specific neurodevelopmental phenotypes in a dish.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Objective: Schizophrenia is a brain disorder that originates during neurodevelopment and has complex genetic and environmental etiologies. Despite decades of clinical evidence of altered striatal function in affected patients, studies examining its cellular and molecular mechanisms in humans are limited. To explore neurodevelopmental alterations in the striatum associated with schizophrenia, the authors established a method for the differentiation of induced pluripotent stem cells (iPSCs) into ventral forebrain organoids (VFOs). Methods: VFOs were generated from postmortem dural fibroblast–derived iPSCs of four individuals with schizophrenia and four neurotypical control individuals for whom postmortem caudate genotypes and transcriptomic data were profiled in the BrainSeq neurogenomics consortium. Individuals were selected such that the two groups had nonoverlapping schizophrenia polygenic risk scores (PRSs). Results: Single-cell RNA sequencing analyses of VFOs revealed differences in developmental trajectory between schizophrenia and control individuals in which inhibitory neuronal cells from the patients exhibited accelerated maturation. Furthermore, upregulated genes in inhibitory neurons in schizophrenia VFOs showed a significant overlap with upregulated genes in postmortem caudate tissue of individuals with schizophrenia compared with control individuals, including the donors of the iPSC cohort. Conclusions: The findings suggest that striatal neurons derived from high-PRS individuals with schizophrenia carry abnormalities that originated during early brain development and that the VFO model can recapitulate disease-relevant cell type–specific neurodevelopmental phenotypes in a dish. |
| 10. | Duru, Jens; Rüfenacht, Arielle; Löhle, Josephine; Pozzi, Marcello; Forró, Csaba; Ledermann, Linus; Bernardi, Aeneas; Matter, Michael; Renia, André; Simona, Benjamin; Tringides, Christina M; Bernhard, Stéphane; Ihle, Stephan J; Hengsteler, Julian; Maurer, Benedikt; Zhanga, Xinyu; Nakatsuka, Nako: Driving electrochemical reactions at the microscale using CMOS microelectrode arrays. In: Lab on a Chip, 2023, ISSN: 1473-0189. (Type: Journal Article | Abstract | Links | BibTeX) @article{Duru2023c, title = {Driving electrochemical reactions at the microscale using CMOS microelectrode arrays}, author = {Jens Duru and Arielle Rüfenacht and Josephine Löhle and Marcello Pozzi and Csaba Forró and Linus Ledermann and Aeneas Bernardi and Michael Matter and André Renia and Benjamin Simona and Christina M. Tringides and Stéphane Bernhard and Stephan J. Ihle and Julian Hengsteler and Benedikt Maurer and Xinyu Zhanga and Nako Nakatsuka}, url = {https://pubs.rsc.org/en/content/articlelanding/2023/lc/d3lc00630a}, doi = {10.1039/D3LC00630A}, issn = {1473-0189}, year = {2023}, date = {2023-10-30}, journal = {Lab on a Chip}, abstract = {Precise control of pH values at electrode interfaces enables the systematic investigation of pH-dependent processes by electrochemical means. In this work, we employed high-density complementary metal-oxide-semiconductor (CMOS) microelectrode arrays (MEAs) as miniaturized systems to induce and confine electrochemical reactions in areas corresponding to the pitch of single electrodes (17.5 μm). First, we present a strategy for generating localized pH patterns on the surface of the CMOS MEA with unprecedented spatial resolution. Leveraging the versatile routing capabilities of the switch matrix beneath the CMOS MEA, we created arbitrary combinations of anodic and cathodic electrodes and hence pH patterns. Moreover, we utilized the system to produce polymeric surface patterns by additive and subtractive methods. For additive patterning, we controlled the in situ formation of polydopamine at the microelectrode surface through oxidation of free dopamine above a threshold pH > 8.5. For subtractive patterning, we removed cell-adhesive poly-L-lysine from the electrode surface and backfilled the voids with antifouling polymers. Such polymers were chosen to provide a proof-of-concept application of controlling neuronal growth via electrochemically-induced patterns on the CMOS MEA surface. Importantly, our platform is compatible with commercially available high-density MEAs and requires no custom equipment, rendering the findings generalizable and accessible.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Precise control of pH values at electrode interfaces enables the systematic investigation of pH-dependent processes by electrochemical means. In this work, we employed high-density complementary metal-oxide-semiconductor (CMOS) microelectrode arrays (MEAs) as miniaturized systems to induce and confine electrochemical reactions in areas corresponding to the pitch of single electrodes (17.5 μm). First, we present a strategy for generating localized pH patterns on the surface of the CMOS MEA with unprecedented spatial resolution. Leveraging the versatile routing capabilities of the switch matrix beneath the CMOS MEA, we created arbitrary combinations of anodic and cathodic electrodes and hence pH patterns. Moreover, we utilized the system to produce polymeric surface patterns by additive and subtractive methods. For additive patterning, we controlled the in situ formation of polydopamine at the microelectrode surface through oxidation of free dopamine above a threshold pH > 8.5. For subtractive patterning, we removed cell-adhesive poly-L-lysine from the electrode surface and backfilled the voids with antifouling polymers. Such polymers were chosen to provide a proof-of-concept application of controlling neuronal growth via electrochemically-induced patterns on the CMOS MEA surface. Importantly, our platform is compatible with commercially available high-density MEAs and requires no custom equipment, rendering the findings generalizable and accessible. |
| 11. | Kelley, Matt R; Chipman, Laura B; Asano, Shoh; Knott, Matthew; Howard, Samantha T; Berg, Allison P: Potentiating NaV1.1 in Dravet syndrome patient iPSC-derived GABAergic neurons increases neuronal firing frequency and decreases network synchrony. In: bioRxiv, 2023. (Type: Journal Article | Abstract | Links | BibTeX) @article{Kelley2023, title = {Potentiating NaV1.1 in Dravet syndrome patient iPSC-derived GABAergic neurons increases neuronal firing frequency and decreases network synchrony}, author = {Matt R Kelley and Laura B Chipman and Shoh Asano and Matthew Knott and Samantha T Howard and Allison P Berg}, url = {https://www.biorxiv.org/content/10.1101/2023.09.28.559990v1}, doi = {10.1101/2023.09.28.559990}, year = {2023}, date = {2023-09-29}, journal = {bioRxiv}, abstract = {Dravet syndrome is a developmental and epileptic encephalopathy characterized by seizures, behavioral abnormalities, developmental deficits, and elevated risk of sudden unexpected death in epilepsy (SUDEP). Most patient cases are caused by de novo loss-of-function mutations in the gene SCN1A, causing a haploinsufficiency of the alpha subunit of the voltage-gated sodium channel NaV1.1. Within the brain, NaV1.1 is primarily localized to the axons of inhibitory neurons, and decreased NaV1.1 function is hypothesized to reduce GABAergic inhibitory neurotransmission within the brain, driving neuronal network hyperexcitability and subsequent pathology. We have developed a human in vitro model of Dravet syndrome using differentiated neurons derived from patient iPSC and enriched for GABA expressing neurons. Neurons were plated on high definition multielectrode arrays (HD-MEAs), permitting recordings from the same cultures over the 7-weeks duration of study at the network, single cell, and subcellular resolution. Using this capability, we characterized the features of axonal morphology and physiology. Neurons developed increased spiking activity and synchronous network bursting. Recordings were processed through a spike sorting pipeline for curation of single unit activity and to assess the effects of pharmacological treatments. At 7-weeks, the application of the GABAAR receptor agonist muscimol eliminated network bursting, indicating the presence of GABAergic neurotransmission. To identify the role of NaV1.1 on neuronal and network activity, cultures were treated with a dose-response of the NaV1.1 potentiator δ-theraphotoxin-Hm1a. This resulted in a strong increase in firing rates of putative GABAergic neurons, an increase in the intraburst firing rate, and eliminated network bursting. These results validate that potentiation of NaV1.1 in Dravet patient iPSC-derived neurons results in decreased firing synchrony in neuronal networks through increased GABAergic neuron activity and support the use of human neurons and HD-MEAs as viable high-throughput electrophysiological platform to enable therapeutic discovery.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Dravet syndrome is a developmental and epileptic encephalopathy characterized by seizures, behavioral abnormalities, developmental deficits, and elevated risk of sudden unexpected death in epilepsy (SUDEP). Most patient cases are caused by de novo loss-of-function mutations in the gene SCN1A, causing a haploinsufficiency of the alpha subunit of the voltage-gated sodium channel NaV1.1. Within the brain, NaV1.1 is primarily localized to the axons of inhibitory neurons, and decreased NaV1.1 function is hypothesized to reduce GABAergic inhibitory neurotransmission within the brain, driving neuronal network hyperexcitability and subsequent pathology. We have developed a human in vitro model of Dravet syndrome using differentiated neurons derived from patient iPSC and enriched for GABA expressing neurons. Neurons were plated on high definition multielectrode arrays (HD-MEAs), permitting recordings from the same cultures over the 7-weeks duration of study at the network, single cell, and subcellular resolution. Using this capability, we characterized the features of axonal morphology and physiology. Neurons developed increased spiking activity and synchronous network bursting. Recordings were processed through a spike sorting pipeline for curation of single unit activity and to assess the effects of pharmacological treatments. At 7-weeks, the application of the GABAAR receptor agonist muscimol eliminated network bursting, indicating the presence of GABAergic neurotransmission. To identify the role of NaV1.1 on neuronal and network activity, cultures were treated with a dose-response of the NaV1.1 potentiator δ-theraphotoxin-Hm1a. This resulted in a strong increase in firing rates of putative GABAergic neurons, an increase in the intraburst firing rate, and eliminated network bursting. These results validate that potentiation of NaV1.1 in Dravet patient iPSC-derived neurons results in decreased firing synchrony in neuronal networks through increased GABAergic neuron activity and support the use of human neurons and HD-MEAs as viable high-throughput electrophysiological platform to enable therapeutic discovery. |
| 12. | Metto, Abigael C; Telgkamp, Petra; McLane-Svoboda, Autumn K; Gilad, Assaf A; Pelled, Galit: Closed-loop neurostimulation via expression of magnetogenetics-sensitive protein in inhibitory neurons leads to reduction of seizure activity in a rat model of epilepsy. In: Brain Research, 2023. (Type: Journal Article | Abstract | Links | BibTeX) @article{Metto2023, title = {Closed-loop neurostimulation via expression of magnetogenetics-sensitive protein in inhibitory neurons leads to reduction of seizure activity in a rat model of epilepsy}, author = {Abigael C. Metto and Petra Telgkamp and Autumn K. McLane-Svoboda and Assaf A. Gilad and Galit Pelled}, url = {https://www.sciencedirect.com/science/article/pii/S0006899323003621}, doi = {https://doi.org/10.1016/j.brainres.2023.148591}, year = {2023}, date = {2023-09-24}, journal = {Brain Research}, abstract = {On-demand neurostimulation has shown success in epilepsy patients with pharmacoresistant seizures. Seizures produce magnetic fields that can be recorded using magnetoencephalography. We developed a new closed-loop approach to control seizure activity based on magnetogenetics using the electromagnetic perceptive gene (EPG) that encodes a protein that responds to magnetic fields. The EPG transgene was expressed in inhibitory interneurons under the hDlx promoter and kainic acid was used to induce acute seizures. In vivo electrophysiological signals were recorded. We found that hDlx EPG rats exhibited a significant delay in the onset of first seizure (1142.72 ± 186.35 s) compared to controls (644.03 ± 15.06 s) and significantly less seizures (4.11 ± 1.03) compared to controls (8.33 ± 1.58). These preliminary findings suggest that on-demand activation of EPG expressed in inhibitory interneurons suppresses seizure activity, and magnetogenetics via EPG may be an effective strategy to alleviate seizure severity in a closed-loop, and cell-specific fashion.}, keywords = {}, pubstate = {published}, tppubtype = {article} } On-demand neurostimulation has shown success in epilepsy patients with pharmacoresistant seizures. Seizures produce magnetic fields that can be recorded using magnetoencephalography. We developed a new closed-loop approach to control seizure activity based on magnetogenetics using the electromagnetic perceptive gene (EPG) that encodes a protein that responds to magnetic fields. The EPG transgene was expressed in inhibitory interneurons under the hDlx promoter and kainic acid was used to induce acute seizures. In vivo electrophysiological signals were recorded. We found that hDlx EPG rats exhibited a significant delay in the onset of first seizure (1142.72 ± 186.35 s) compared to controls (644.03 ± 15.06 s) and significantly less seizures (4.11 ± 1.03) compared to controls (8.33 ± 1.58). These preliminary findings suggest that on-demand activation of EPG expressed in inhibitory interneurons suppresses seizure activity, and magnetogenetics via EPG may be an effective strategy to alleviate seizure severity in a closed-loop, and cell-specific fashion. |
| 13. | Silverman, Jill L; Fenton, Timothy; Haouchine, Olivia; Hallam, Elizabeth; Smith, Emily; Jackson, Kiya; Rahbarian, Darlene; Canales, Cesar; Adhikari, Anna; Nord, Alex; Ben-Shalom, Roy: Hyperexcitability and translational phenotypes in a preclinical model of SYNGAP1mutations. In: Research Square, 2023. (Type: Journal Article | Abstract | Links | BibTeX) @article{Silverman2023, title = {Hyperexcitability and translational phenotypes in a preclinical model of SYNGAP1mutations}, author = {Jill L. Silverman and Timothy Fenton and Olivia Haouchine and Elizabeth Hallam and Emily Smith and Kiya Jackson and Darlene Rahbarian and Cesar Canales and Anna Adhikari and Alex Nord and Roy Ben-Shalom}, url = {https://www.researchsquare.com/article/rs-3246655/v1}, doi = {https://doi.org/10.21203/rs.3.rs-3246655/v1}, year = {2023}, date = {2023-09-13}, journal = {Research Square}, abstract = {SYNGAP1is a critical gene for neuronal development, synaptic structure, and function. Although rare, the disruption of SYNGAP1directly causes a genetically identi able neurodevelopmental disorder (NDD) called SYNGAP1-related intellectual disability. Without functional SynGAP1 protein, patients present with intellectual disability, motor impairments, and epilepsy. Previous work using mouse models with a variety of germline and conditional mutations has helped delineate SynGAP1’s critical roles in neuronal structure and function, as well as key biochemical signaling pathways essential to synapse integrity. Homozygous loss of SYNGAP1is embryonically lethal. Heterozygous mutations of SynGAP1result in a broad range of phenotypes including increased locomotor activity, impaired working spatial memory, impaired cued fear memory, and increased stereotypic behavior. Ourinvivofunctional data, using the original germline mutation mouse line from the Huganir laboratory, corroborated robust hyperactivity and learning and memory de cits. Here, we describe impairments in the translational biomarker domain of sleep, characterized using neurophysiological data collected with wireless telemetric electroencephalography (EEG). We discoveredSyngap1+/− mice exhibited elevated spike trains in both number and duration, in addition to elevated power, most notably in the delta power band. Primary neurons fromSyngap1+/− mice displayed increased network ring activity, greater spikes per burst, and shorter inter-burst intervals between peaks using high density micro-electrode arrays (HD-MEA). This work is translational, innovative, and highly signi cant as it outlines functional impairments in Syngap1mutant mice. Simultaneously, the work utilized untethered, wireless neurophysiology that can discover potential biomarkers of Syngap1RID, for clinical trials, as it has done with other NDDs. Our work is substantial forward progress toward translational work for SynGAP1R-ID as it bridges in-vitroelectrophysiological neuronal activity and function with invivoneurophysiological brain activity and function. These data elucidate multiple quantitative, translational biomarkers invivoand invitrofor the development of treatments for SYNGAP1-related intellectual disability.}, keywords = {}, pubstate = {published}, tppubtype = {article} } SYNGAP1is a critical gene for neuronal development, synaptic structure, and function. Although rare, the disruption of SYNGAP1directly causes a genetically identi able neurodevelopmental disorder (NDD) called SYNGAP1-related intellectual disability. Without functional SynGAP1 protein, patients present with intellectual disability, motor impairments, and epilepsy. Previous work using mouse models with a variety of germline and conditional mutations has helped delineate SynGAP1’s critical roles in neuronal structure and function, as well as key biochemical signaling pathways essential to synapse integrity. Homozygous loss of SYNGAP1is embryonically lethal. Heterozygous mutations of SynGAP1result in a broad range of phenotypes including increased locomotor activity, impaired working spatial memory, impaired cued fear memory, and increased stereotypic behavior. Ourinvivofunctional data, using the original germline mutation mouse line from the Huganir laboratory, corroborated robust hyperactivity and learning and memory de cits. Here, we describe impairments in the translational biomarker domain of sleep, characterized using neurophysiological data collected with wireless telemetric electroencephalography (EEG). We discoveredSyngap1+/− mice exhibited elevated spike trains in both number and duration, in addition to elevated power, most notably in the delta power band. Primary neurons fromSyngap1+/− mice displayed increased network ring activity, greater spikes per burst, and shorter inter-burst intervals between peaks using high density micro-electrode arrays (HD-MEA). This work is translational, innovative, and highly signi cant as it outlines functional impairments in Syngap1mutant mice. Simultaneously, the work utilized untethered, wireless neurophysiology that can discover potential biomarkers of Syngap1RID, for clinical trials, as it has done with other NDDs. Our work is substantial forward progress toward translational work for SynGAP1R-ID as it bridges in-vitroelectrophysiological neuronal activity and function with invivoneurophysiological brain activity and function. These data elucidate multiple quantitative, translational biomarkers invivoand invitrofor the development of treatments for SYNGAP1-related intellectual disability. |
| 14. | Habibollahi, Forough; Kagan, Brett J; Burkitt, Anthony N; French, Chris: Critical dynamics arise during structured information presentation within embodied in vitro neuronal networks. In: Nature Communications, 2023. (Type: Journal Article | Abstract | Links | BibTeX) @article{Habibollahi2023, title = {Critical dynamics arise during structured information presentation within embodied in vitro neuronal networks}, author = {Forough Habibollahi and Brett J. Kagan and Anthony N. Burkitt and Chris French }, url = {https://www.nature.com/articles/s41467-023-41020-3}, doi = {https://doi.org/10.1038/s41467-023-41020-3}, year = {2023}, date = {2023-08-30}, journal = {Nature Communications}, abstract = {Understanding how brains process information is an incredibly difficult task. Amongst the metrics characterising information processing in the brain, observations of dynamic near-critical states have generated significant interest. However, theoretical and experimental limitations associated with human and animal models have precluded a definite answer about when and why neural criticality arises with links from attention, to cognition, and even to consciousness. To explore this topic, we used an in vitro neural network of cortical neurons that was trained to play a simplified game of ‘Pong’ to demonstrate Synthetic Biological Intelligence (SBI). We demonstrate that critical dynamics emerge when neural networks receive task-related structured sensory input, reorganizing the system to a near-critical state. Additionally, better task performance correlated with proximity to critical dynamics. However, criticality alone is insufficient for a neuronal network to demonstrate learning in the absence of additional information regarding the consequences of previous actions. These findings offer compelling support that neural criticality arises as a base feature of incoming structured information processing without the need for higher order cognition.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Understanding how brains process information is an incredibly difficult task. Amongst the metrics characterising information processing in the brain, observations of dynamic near-critical states have generated significant interest. However, theoretical and experimental limitations associated with human and animal models have precluded a definite answer about when and why neural criticality arises with links from attention, to cognition, and even to consciousness. To explore this topic, we used an in vitro neural network of cortical neurons that was trained to play a simplified game of ‘Pong’ to demonstrate Synthetic Biological Intelligence (SBI). We demonstrate that critical dynamics emerge when neural networks receive task-related structured sensory input, reorganizing the system to a near-critical state. Additionally, better task performance correlated with proximity to critical dynamics. However, criticality alone is insufficient for a neuronal network to demonstrate learning in the absence of additional information regarding the consequences of previous actions. These findings offer compelling support that neural criticality arises as a base feature of incoming structured information processing without the need for higher order cognition. |
| 15. | Duru, Jens; Maurer, Benedikt; Doran, Ciara Giles; Jelitto, Robert; Küchler, Joël; Ihle, Stephan J; Ruff, Tobias; John, Robert; Genocchi, Barbara; Vörös, János: Investigation of the input-output relationship of engineered neural networks using high-density microelectrode arrays. In: Biosensors and Bioelectronics, 2023. (Type: Journal Article | Abstract | Links | BibTeX) @article{Duru2023b, title = {Investigation of the input-output relationship of engineered neural networks using high-density microelectrode arrays}, author = {Jens Duru and Benedikt Maurer and Ciara Giles Doran and Robert Jelitto and Joël Küchler and Stephan J. Ihle and Tobias Ruff and Robert John and Barbara Genocchi and János Vörös }, url = {https://www.sciencedirect.com/science/article/pii/S095656632300533X?via%3Dihub}, doi = {https://doi.org/10.1016/j.bios.2023.115591}, year = {2023}, date = {2023-08-18}, journal = {Biosensors and Bioelectronics}, abstract = {Bottom-up neuroscience utilizes small, engineered biological neural networks to study neuronal activity in systems of reduced complexity. We present a platform that establishes up to six independent networks formed by primary rat neurons on planar complementary metal–oxide–semiconductor (CMOS) microelectrode arrays (MEAs). We introduce an approach that allows repetitive stimulation and recording of network activity at any of the over 700 electrodes underlying a network. We demonstrate that the continuous application of a repetitive super-threshold stimulus yields a reproducible network answer within a 15 ms post-stimulus window. This response can be tracked with high spatiotemporal resolution across the whole extent of the network. Moreover, we show that the location of the stimulation plays a significant role in the networks' early response to the stimulus. By applying a stimulation pattern to all network-underlying electrodes in sequence, the sensitivity of the whole network to the stimulus can be visualized. We demonstrate that microchannels reduce the voltage stimulation threshold and induce the strongest network response. By varying the stimulation amplitude and frequency we reveal discrete network transition points. Finally, we introduce vector fields to follow stimulation-induced spike propagation pathways within the network. Overall we show that our defined neural networks on CMOS MEAs enable us to elicit highly reproducible activity patterns that can be precisely modulated by stimulation amplitude, stimulation frequency and the site of stimulation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Bottom-up neuroscience utilizes small, engineered biological neural networks to study neuronal activity in systems of reduced complexity. We present a platform that establishes up to six independent networks formed by primary rat neurons on planar complementary metal–oxide–semiconductor (CMOS) microelectrode arrays (MEAs). We introduce an approach that allows repetitive stimulation and recording of network activity at any of the over 700 electrodes underlying a network. We demonstrate that the continuous application of a repetitive super-threshold stimulus yields a reproducible network answer within a 15 ms post-stimulus window. This response can be tracked with high spatiotemporal resolution across the whole extent of the network. Moreover, we show that the location of the stimulation plays a significant role in the networks' early response to the stimulus. By applying a stimulation pattern to all network-underlying electrodes in sequence, the sensitivity of the whole network to the stimulus can be visualized. We demonstrate that microchannels reduce the voltage stimulation threshold and induce the strongest network response. By varying the stimulation amplitude and frequency we reveal discrete network transition points. Finally, we introduce vector fields to follow stimulation-induced spike propagation pathways within the network. Overall we show that our defined neural networks on CMOS MEAs enable us to elicit highly reproducible activity patterns that can be precisely modulated by stimulation amplitude, stimulation frequency and the site of stimulation. |
| 16. | Yamamoto, Hideaki; Hirano-Iwata, Ayumi; Sato, Shigeo: Microfluidic technologies for reconstituting neuronal network functions in vitro. In: JSAP Review, 2023. (Type: Journal Article | Abstract | Links | BibTeX) @article{Yamamoto2023, title = {Microfluidic technologies for reconstituting neuronal network functions in vitro}, author = {Hideaki Yamamoto and Ayumi Hirano-Iwata and Shigeo Sato}, url = {https://www.jstage.jst.go.jp/article/oubutsu/92/5/92_278/_article/-char/en}, doi = {10.11470/oubutsu.92.5_278}, year = {2023}, date = {2023-07-06}, journal = {JSAP Review}, abstract = {The structure and function of complex neuronal networks in the brain can be partially reconstituted in vitro by integrating cell culture and microfluidic device technologies. In this report, we review our recent studies on developing microfluidic devices to reconstitute small neuronal networks bearing a modular structure, which is a canonical structure found in the nervous systems of animals. We also describe the process of recording functional activity from the reconstituted neuronal networks. These fundamental technologies offer novel tools for investigating structure–function relationships in living neuronal networks and exploring the physical basis of biological computing in the brain.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The structure and function of complex neuronal networks in the brain can be partially reconstituted in vitro by integrating cell culture and microfluidic device technologies. In this report, we review our recent studies on developing microfluidic devices to reconstitute small neuronal networks bearing a modular structure, which is a canonical structure found in the nervous systems of animals. We also describe the process of recording functional activity from the reconstituted neuronal networks. These fundamental technologies offer novel tools for investigating structure–function relationships in living neuronal networks and exploring the physical basis of biological computing in the brain. |
| 17. | Zhao, Eric T; Hull, Jacob M; Hemed, Nofar Mintz; Ulusan, Hasan; Bartram, Julian; Zhang, Anqi; Wang, Pingyu; Pham, Albert; Silvia Ronchi, John Huguenard R; Hierlemann, Andreas; Melosh, Nicholas A: A CMOS-based highly scalable flexible neural electrode interface. In: Science Advances, 2023. (Type: Journal Article | Abstract | Links | BibTeX) @article{Zhao2023, title = {A CMOS-based highly scalable flexible neural electrode interface}, author = {Eric T. Zhao and Jacob M. Hull and Nofar Mintz Hemed and Hasan Ulusan and Julian Bartram and Anqi Zhang and Pingyu Wang and Albert Pham and Silvia Ronchi, John R. Huguenard and Andreas Hierlemann and Nicholas A. Melosh}, url = {https://www.science.org/doi/10.1126/sciadv.adf9524}, doi = {DOI: 10.1126/sciadv.adf9524}, year = {2023}, date = {2023-06-07}, journal = {Science Advances}, abstract = {Perception, thoughts, and actions are encoded by the coordinated activity of large neuronal populations spread over large areas. However, existing electrophysiological devices are limited by their scalability in capturing this cortex-wide activity. Here, we developed an electrode connector based on an ultra-conformable thin-film electrode array that self-assembles onto silicon microelectrode arrays enabling multithousand channel counts at a millimeter scale. The interconnects are formed using microfabricated electrode pads suspended by thin support arms, termed Flex2Chip. Capillary-assisted assembly drives the pads to deform toward the chip surface, and van der Waals forces maintain this deformation, establishing Ohmic contact. Flex2Chip arrays successfully measured extracellular action potentials ex vivo and resolved micrometer scale seizure propagation trajectories in epileptic mice. We find that seizure dynamics in absence epilepsy in the Scn8a+/− model do not have constant propagation trajectories.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Perception, thoughts, and actions are encoded by the coordinated activity of large neuronal populations spread over large areas. However, existing electrophysiological devices are limited by their scalability in capturing this cortex-wide activity. Here, we developed an electrode connector based on an ultra-conformable thin-film electrode array that self-assembles onto silicon microelectrode arrays enabling multithousand channel counts at a millimeter scale. The interconnects are formed using microfabricated electrode pads suspended by thin support arms, termed Flex2Chip. Capillary-assisted assembly drives the pads to deform toward the chip surface, and van der Waals forces maintain this deformation, establishing Ohmic contact. Flex2Chip arrays successfully measured extracellular action potentials ex vivo and resolved micrometer scale seizure propagation trajectories in epileptic mice. We find that seizure dynamics in absence epilepsy in the Scn8a+/− model do not have constant propagation trajectories. |
| 18. | Girardi, Gregory; Zumpano, Danielle; Goshi, Noah; Raybould, Helen; Seker, Erkin: Cultured Vagal Afferent Neurons as Sensors for Intestinal Effector Molecules. In: biosensors, 2023. (Type: Journal Article | Abstract | Links | BibTeX) @article{Girardi2023, title = {Cultured Vagal Afferent Neurons as Sensors for Intestinal Effector Molecules}, author = {Gregory Girardi and Danielle Zumpano and Noah Goshi and Helen Raybould and Erkin Seker}, url = {https://www.mdpi.com/2079-6374/13/6/601}, doi = {10.3390/bios13060601}, year = {2023}, date = {2023-05-31}, journal = {biosensors}, abstract = {The gut–brain axis embodies the bi-directional communication between the gastrointestinal tract and the central nervous system (CNS), where vagal afferent neurons (VANs) serve as sensors for a variety of gut-derived signals. The gut is colonized by a large and diverse population of microorganisms that communicate via small (effector) molecules, which also act on the VAN terminals situated in the gut viscera and consequently influence many CNS processes. However, the convoluted in vivo environment makes it difficult to study the causative impact of the effector molecules on VAN activation or desensitization. Here, we report on a VAN culture and its proof-of-principle demonstration as a cell-based sensor to monitor the influence of gastrointestinal effector molecules on neuronal behavior. We initially compared the effect of surface coatings (poly-L-lysine vs. Matrigel) and culture media composition (serum vs. growth factor supplement) on neurite growth as a surrogate of VAN regeneration following tissue harvesting, where the Matrigel coating, but not the media composition, played a significant role in the increased neurite growth. We then used both live-cell calcium imaging and extracellular electrophysiological recordings to show that the VANs responded to classical effector molecules of endogenous and exogenous origin (cholecystokinin serotonin and capsaicin) in a complex fashion. We expect this study to enable platforms for screening various effector molecules and their influence on VAN activity, assessed by their information-rich electrophysiological fingerprints.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The gut–brain axis embodies the bi-directional communication between the gastrointestinal tract and the central nervous system (CNS), where vagal afferent neurons (VANs) serve as sensors for a variety of gut-derived signals. The gut is colonized by a large and diverse population of microorganisms that communicate via small (effector) molecules, which also act on the VAN terminals situated in the gut viscera and consequently influence many CNS processes. However, the convoluted in vivo environment makes it difficult to study the causative impact of the effector molecules on VAN activation or desensitization. Here, we report on a VAN culture and its proof-of-principle demonstration as a cell-based sensor to monitor the influence of gastrointestinal effector molecules on neuronal behavior. We initially compared the effect of surface coatings (poly-L-lysine vs. Matrigel) and culture media composition (serum vs. growth factor supplement) on neurite growth as a surrogate of VAN regeneration following tissue harvesting, where the Matrigel coating, but not the media composition, played a significant role in the increased neurite growth. We then used both live-cell calcium imaging and extracellular electrophysiological recordings to show that the VANs responded to classical effector molecules of endogenous and exogenous origin (cholecystokinin serotonin and capsaicin) in a complex fashion. We expect this study to enable platforms for screening various effector molecules and their influence on VAN activity, assessed by their information-rich electrophysiological fingerprints. |
| 19. | Bartram, Julian; Franke, Felix; Kumar, Sreedhar Saseendran; Buccino, Alessio Paolo; Xue, Xiaohan; Gänswein, Tobias; Schröter, Manuel; Kim, Taehoon; Kasuba, Krishna Chaitanya; Hierlemann, Andreas: Parallel reconstruction of the excitatory and inhibitory inputs received by single neurons reveals the synaptic basis of recurrent spiking. In: eLife, 2023. (Type: Journal Article | Abstract | Links | BibTeX) @article{Bartram2023b, title = {Parallel reconstruction of the excitatory and inhibitory inputs received by single neurons reveals the synaptic basis of recurrent spiking}, author = {Julian Bartram and Felix Franke and Sreedhar Saseendran Kumar and Alessio Paolo Buccino and Xiaohan Xue and Tobias Gänswein and Manuel Schröter and Taehoon Kim and Krishna Chaitanya Kasuba and Andreas Hierlemann}, url = {https://elifesciences.org/reviewed-preprints/86820}, doi = {10.7554/eLife.86820}, year = {2023}, date = {2023-05-17}, journal = {eLife}, abstract = {Self-sustained recurrent activity in cortical networks is thought to be important for multiple crucial processes, including circuit development and homeostasis. Yet, the precise relationship between the synaptic input patterns and the spiking output of individual neurons remains largely unresolved. Here, we developed, validated and applied a novel in vitro experimental platform and analytical procedures that provide – for individual neurons – simultaneous excitatory and inhibitory synaptic activity estimates during recurrent network activity. Our approach combines whole-network high-density microelectrode array (HD-MEA) recordings from rat neuronal cultures with patch clamping and enables a comprehensive mapping and characterization of active incoming connections to single postsynaptic neurons. We found that, during network states with excitation(E)-inhibition(I) balance, postsynaptic spiking coincided precisely with the maxima of fast fluctuations in the input E/I ratio. These spike-associated E/I ratio escalations were largely due to a rapid bidirectional change in synaptic inhibition that was modulated by the network-activity level. Our approach also uncovered the underlying circuit architecture and we show that individual neurons received a few key inhibitory connections – often from special hub neurons – that were instrumental in controlling postsynaptic spiking. Balanced network theory predicts dynamical regimes governed by small and rapid input fluctuation and featuring a fast neuronal responsiveness. Our findings – obtained in self-organized neuronal cultures – suggest that the emergence of these favorable regimes and associated network architectures is an inherent property of cortical networks in general.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Self-sustained recurrent activity in cortical networks is thought to be important for multiple crucial processes, including circuit development and homeostasis. Yet, the precise relationship between the synaptic input patterns and the spiking output of individual neurons remains largely unresolved. Here, we developed, validated and applied a novel in vitro experimental platform and analytical procedures that provide – for individual neurons – simultaneous excitatory and inhibitory synaptic activity estimates during recurrent network activity. Our approach combines whole-network high-density microelectrode array (HD-MEA) recordings from rat neuronal cultures with patch clamping and enables a comprehensive mapping and characterization of active incoming connections to single postsynaptic neurons. We found that, during network states with excitation(E)-inhibition(I) balance, postsynaptic spiking coincided precisely with the maxima of fast fluctuations in the input E/I ratio. These spike-associated E/I ratio escalations were largely due to a rapid bidirectional change in synaptic inhibition that was modulated by the network-activity level. Our approach also uncovered the underlying circuit architecture and we show that individual neurons received a few key inhibitory connections – often from special hub neurons – that were instrumental in controlling postsynaptic spiking. Balanced network theory predicts dynamical regimes governed by small and rapid input fluctuation and featuring a fast neuronal responsiveness. Our findings – obtained in self-organized neuronal cultures – suggest that the emergence of these favorable regimes and associated network architectures is an inherent property of cortical networks in general. |
| 20. | Duru, Jens; Maurer, Benedikt; Doran, Ciara Giles; Jelitto, Robert; Küchler, Joël; Ihle, Stephan J; Ruff, Tobias; John, Robert; Genocchi, Barbara; Vörös, János: Investigation of the input-output relationship of engineered neural networks using high-density microelectrode arrays. In: SSRN, 2023. (Type: Journal Article | Abstract | Links | BibTeX) @article{Duru2023, title = {Investigation of the input-output relationship of engineered neural networks using high-density microelectrode arrays}, author = {Jens Duru and Benedikt Maurer and Ciara Giles Doran and Robert Jelitto and Joël Küchler and Stephan J. Ihle and Tobias Ruff and Robert John and Barbara Genocchi and János Vörös}, url = {https://www.ssrn.com/abstract=4427959}, doi = {DOI: 10.2139/ssrn.4427959}, year = {2023}, date = {2023-04-24}, journal = {SSRN}, abstract = {Bottom-up neuroscience utilizes small, engineered biological neural networks to study neuronal activity in systems of reduced complexity. We present a platform that establishes up to six independent networks formed by primary rat neurons on planar complementary metal–oxide–semiconductor (CMOS) microelectrode arrays (MEAs). We introduce an approach that allows repetitive stimulation and recording of network activity at any of the over 700 electrodes underlying a network. We demonstrate that the continuous application of a repetitive super-threshold stimulus yields a reproducible network answer within a 15 ms post-stimulus window. This response can be tracked with high spatiotemporal resolution across the whole extent of the network. Moreover, we show that the location of the stimulation plays a significant role in the networks’ early response to the stimulus. By applying a stimulation pattern to all network-underlying electrodes in sequence, the sensitivity of the whole network to the stimulus can be visualized. We demonstrate that microchannels reduce the voltage stimulation threshold and induce the strongest network response. By varying the stimulation amplitude and frequency we reveal discrete network transition points. Finally, we introduce vector fields to follow stimulation-induced spike propagation pathways within the network. Overall we show that our defined neural networks on CMOS MEAs enable us to elicit highly reproducible activity patterns that can be precisely modulated by stimulation amplitude, stimulation frequency and the site of stimulation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Bottom-up neuroscience utilizes small, engineered biological neural networks to study neuronal activity in systems of reduced complexity. We present a platform that establishes up to six independent networks formed by primary rat neurons on planar complementary metal–oxide–semiconductor (CMOS) microelectrode arrays (MEAs). We introduce an approach that allows repetitive stimulation and recording of network activity at any of the over 700 electrodes underlying a network. We demonstrate that the continuous application of a repetitive super-threshold stimulus yields a reproducible network answer within a 15 ms post-stimulus window. This response can be tracked with high spatiotemporal resolution across the whole extent of the network. Moreover, we show that the location of the stimulation plays a significant role in the networks’ early response to the stimulus. By applying a stimulation pattern to all network-underlying electrodes in sequence, the sensitivity of the whole network to the stimulus can be visualized. We demonstrate that microchannels reduce the voltage stimulation threshold and induce the strongest network response. By varying the stimulation amplitude and frequency we reveal discrete network transition points. Finally, we introduce vector fields to follow stimulation-induced spike propagation pathways within the network. Overall we show that our defined neural networks on CMOS MEAs enable us to elicit highly reproducible activity patterns that can be precisely modulated by stimulation amplitude, stimulation frequency and the site of stimulation. |
Kasuba, Krishna Chaitanya; Buccino, Alessio Paolo; Bartram, Julian; Gaub, Benjamin M; Fauser, Felix J; Ronchi, Silvia; Kumar, Sreedhar Saseendran; Geissler, Sydney; Nava, Michele M; Hierlemann, Andreas; Müller, Daniel J Nature Nanotechnology, 2024. Abstract | Links | BibTeX | タグ: Action Potential, Brain Slice, HD-MEA, MaxOne, Primary Neuronal Cell Culture, Spike Sorting Hruska-Plochan, Marian; Wiersma, Vera I; Betz, Katharina M; Mallona, Izaskun; Ronchi, Silvia; Maniecka, Zuzanna; Hock, Eva-Maria; Tantardini, Elena; Laferriere, Florent; Sahadevan, Sonu; Hoop, Vanessa; Delvendahl, Igor; Pérez-Berlanga, Manuela; Gatta, Beatrice; Panatta, Martina; van der Bourg, Alexander; Bohaciakova, Dasa; Sharma, Puneet; Vos, Laura De; Frontzek, Karl; Aguzzi, Adriano; Lashley, Tammaryn; Robinson, Mark D; Karayannis, Theofanis; Mueller, Martin; Hierlemann, Andreas; Polymenidou, Magdalini A model of human neural networks reveals NPTX2 pathology in ALS and FTLD Journal Article Nature, 2024. Abstract | Links | BibTeX | タグ: Activity Scan Assay, HD-MEA, IPSC, MaxOne, MEA Technology, Network Assay, Primary Neuronal Cell Culture, Spike Sorting Hornauer, Philipp; Prack, Gustavo; Anastasi, Nadia; Ronchi, Silvia; Kim, Taehoon; Donner, Christian; Fiscella, Michele; Borgwardt, Karsten; Taylor, Verdon; Jagasia, Ravi; Roqueiro, Damian; Hierlemann, Andreas; Schröter, Manuel DeePhys: A machine learning–assisted platform for electrophysiological phenotyping of human neuronal networks Journal Article Stem Cell Reports, 2024. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, HD-MEA, IPSC, MaxOne, MEA Technology, Spike Sorting Cai, Hongwei; Ao, Zheng; Tian, Chunhui; Wu, Zhuhao; Liu, Hongcheng; Tchieu, Jason; Gu, Mingxia; Mackie, Ken; Guo, Feng Brain organoid reservoir computing for artificial intelligence Journal Article Nature Electronics, 2023. Abstract | Links | BibTeX | タグ: 3D Culture, HD-MEA, Machine Learning, MaxOne, MEA Technology, Organoids, Stimulation Ryu, Seungmi; Weber, Claire; Chu, Pei-Hsuan; Ernest, Ben; Jovanovic, Vukasin M; Deng, Tao; Slamecka, Jaroslav; Hong, Hyenjong; Jethmalani, Yogita; Baskir, Hannah M; Inman, Jason; Braisted, John; Hirst, Marissa B; Simeonov, Anton; Voss, Ty C; Tristan, Carlos A; Singeç, Ilyas Stress-free cell aggregation by using the CEPT cocktail enhances embryoid body and organoid fitness Journal Article Biofabrication, 2023. Abstract | Links | BibTeX | タグ: 3D Culture, Activity Scan Assay, HD-MEA, MEA Technology, Organoids Elliott, Matthew A T; Schweiger, Hunter E; Robbins, Ash; Vera-Choqqueccota, Samira; Ehrlich, Drew; Hernandez, Sebastian; Voitiuk, Kateryna; Geng, Jinghui; Sevetson, Jess L; Core, Cordero; Rosen, Yohei M; Teodorescu, Mircea; Wagner, Nico O; Haussler, David; Mostajo-Radji, Mohammed A Internet-Connected Cortical Organoids for Project-Based Stem Cell and Neuroscience Education Journal Article eNeuro, 2023. Abstract | Links | BibTeX | タグ: 3D Culture, Activity Scan Assay, HD-MEA, IPSC, MaxOne, MEA Technology, Organoids, Spike Sorting, Stimulation Kobayashi, Toki; Shimba, Kenta; Kotani, Kiyoshi; Jimbo, Yasuhiko Measuring and Inducing the Plasticity of Single-Neuron Scale at Multiple Points Conference ISSS Xplore, 2023. Abstract | Links | BibTeX | タグ: HD-MEA, MaxOne, Primary Neuronal Cell Culture, Stimulation Tamatani, Chie; Shimba, Kenta; andYasuhiko Jimbo, Kiyoshi Kotani Activity- and Spatial-dependent Variations in Axonal Conduction Recorded from Microtunnel Electrodes Conference IEEE Xplore, 2023. Abstract | Links | BibTeX | タグ: HD-MEA, MaxOne Sawada, Tomoyo; Barbosa, André R; Araujo, Bruno; McCord, Alejandra E; D’Ignazio, Laura; Benjamin, Kynon J M; Sheehan, Bonna; Zabolocki, Michael; Feltrin, Arthur; Arora, Ria; Brandtjen, Anna C; Kleinman, Joel E; Hyde, Thomas M; Bardy, Cedric; Weinberger, Daniel R; Paquola, Apuã C M; Erwin, Jennifer A American Journal of Psychiatry, 2023, ISSN: 0002-953X. Abstract | Links | BibTeX | タグ: 3D Culture, Activity Scan Assay, HD-MEA, MaxTwo, Network Assay, Organoids Duru, Jens; Rüfenacht, Arielle; Löhle, Josephine; Pozzi, Marcello; Forró, Csaba; Ledermann, Linus; Bernardi, Aeneas; Matter, Michael; Renia, André; Simona, Benjamin; Tringides, Christina M; Bernhard, Stéphane; Ihle, Stephan J; Hengsteler, Julian; Maurer, Benedikt; Zhanga, Xinyu; Nakatsuka, Nako Driving electrochemical reactions at the microscale using CMOS microelectrode arrays Journal Article Lab on a Chip, 2023, ISSN: 1473-0189. Abstract | Links | BibTeX | タグ: HD-MEA, MaxOne, Primary Neuronal Cell Culture, Stimulation Kelley, Matt R; Chipman, Laura B; Asano, Shoh; Knott, Matthew; Howard, Samantha T; Berg, Allison P bioRxiv, 2023. Abstract | Links | BibTeX | タグ: Activity Scan Assay, Axon Tracking Assay, HD-MEA, IPSC, MaxTwo, MEA Technology, Network Assay, Spike Sorting Metto, Abigael C; Telgkamp, Petra; McLane-Svoboda, Autumn K; Gilad, Assaf A; Pelled, Galit Brain Research, 2023. Abstract | Links | BibTeX | タグ: 3D Culture, closed loop stimulation, HD-MEA, MaxOne, Slices Silverman, Jill L; Fenton, Timothy; Haouchine, Olivia; Hallam, Elizabeth; Smith, Emily; Jackson, Kiya; Rahbarian, Darlene; Canales, Cesar; Adhikari, Anna; Nord, Alex; Ben-Shalom, Roy Hyperexcitability and translational phenotypes in a preclinical model of SYNGAP1mutations Journal Article Research Square, 2023. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, Activity Scan Assay, HD-MEA, MaxOne, Network Assay, Primary Neuronal Cell Culture Habibollahi, Forough; Kagan, Brett J; Burkitt, Anthony N; French, Chris Critical dynamics arise during structured information presentation within embodied in vitro neuronal networks Journal Article Nature Communications, 2023. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, HD-MEA, IPSC, MaxOne, MEA Metrics, MEA Technology, Primary Neuronal Cell Culture Duru, Jens; Maurer, Benedikt; Doran, Ciara Giles; Jelitto, Robert; Küchler, Joël; Ihle, Stephan J; Ruff, Tobias; John, Robert; Genocchi, Barbara; Vörös, János Investigation of the input-output relationship of engineered neural networks using high-density microelectrode arrays Journal Article Biosensors and Bioelectronics, 2023. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, HD-MEA, MaxOne, Stimulation Yamamoto, Hideaki; Hirano-Iwata, Ayumi; Sato, Shigeo Microfluidic technologies for reconstituting neuronal network functions in vitro Journal Article JSAP Review, 2023. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, HD-MEA, MaxOne, MEA Technology, Microfluidics Zhao, Eric T; Hull, Jacob M; Hemed, Nofar Mintz; Ulusan, Hasan; Bartram, Julian; Zhang, Anqi; Wang, Pingyu; Pham, Albert; Silvia Ronchi, John Huguenard R; Hierlemann, Andreas; Melosh, Nicholas A A CMOS-based highly scalable flexible neural electrode interface Journal Article Science Advances, 2023. Abstract | Links | BibTeX | タグ: 3D Culture, HD-MEA, MaxOne, Other Tissues, Slices Girardi, Gregory; Zumpano, Danielle; Goshi, Noah; Raybould, Helen; Seker, Erkin Cultured Vagal Afferent Neurons as Sensors for Intestinal Effector Molecules Journal Article biosensors, 2023. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, HD-MEA, MaxOne, MEA Technology, Primary Neuronal Cell Culture Bartram, Julian; Franke, Felix; Kumar, Sreedhar Saseendran; Buccino, Alessio Paolo; Xue, Xiaohan; Gänswein, Tobias; Schröter, Manuel; Kim, Taehoon; Kasuba, Krishna Chaitanya; Hierlemann, Andreas Parallel reconstruction of the excitatory and inhibitory inputs received by single neurons reveals the synaptic basis of recurrent spiking Journal Article eLife, 2023. Abstract | Links | BibTeX | タグ: HD-MEA, MaxOne, MEA Metrics, MEA Technology, Modeling, Primary Neuronal Cell Culture, Spike Sorting Duru, Jens; Maurer, Benedikt; Doran, Ciara Giles; Jelitto, Robert; Küchler, Joël; Ihle, Stephan J; Ruff, Tobias; John, Robert; Genocchi, Barbara; Vörös, János Investigation of the input-output relationship of engineered neural networks using high-density microelectrode arrays Journal Article SSRN, 2023. Abstract | Links | BibTeX | タグ: HD-MEA, MaxOne, MEA Technology, Primary Neuronal Cell Culture, Spike Sorting, Stimulation Xu, He Jax; Yao, Yao; Yao, Fenyong; Chen, Jiehui; Li, Meishi; Yang, Xianfa; 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 Cell Regeneration, 2023. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, Activity Scan Assay, Axon Tracking Assay, HD-MEA, IPSC, MaxOne, MEA Technology, Network Assay, Organoids Cai, Hongwei; Ao, Zheng; Tian, Chunhui; Wu, Zhuhao; Liu, Hongcheng; Tchieu, Jason; Gu, Mingxia; Mackie, Ken; and Guo, Feng Brain Organoid Computing for Artificial Intelligence Journal Article bioRxiv, 2023. Abstract | Links | BibTeX | タグ: HD-MEA, Machine Learning, MaxOne, MEA Technology, Modeling, Organoids, Stimulation Qian, Junming; Guan, Xiaonan; Xie, Bing; Xu, Chuanyun; Niu, Jacqueline; Tang, Xin; Li, Charles H; Colecraft, Henry M; Jaenisch, Rudolf; Liu, Shawn X Multiplex epigenome editing of MECP2 to rescue Rett syndrome neurons Journal Article Science Translational Medicine, 2023. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, HD-MEA, IPSC, MaxTwo, MEA Technology Bartram, Julian; Franke, Felix; Kumar, Sreedhar Saseendran; Buccino, Alessio Paolo; Xue, Xiaohan; Gänswein, Tobias; Schröter, Manuel; Kim, Taehoon; Kasuba, Krishna Chaitanya; Hierlemann, Andreas Parallel reconstruction of the excitatory and inhibitory inputs received by single neurons reveals the synaptic basis of recurrent spiking Journal Article bioRxiv, 2023. Abstract | Links | BibTeX | タグ: CMOS, HD-MEA, Modeling, Primary Neuronal Cell Culture, Spike Sorting Han, Xiaobo; Matsuda, Naoki; Ishibashi, Yuto; Odawara, Aoi; Takahashi, Sayuri; Tooi, Norie; Kinoshita, Koshi; Suzuki, Ikuro A functional neuron maturation device provides convenient application on microelectrode array for neural network measurement Journal Article Biomaterials Research, 2022. Abstract | Links | BibTeX | タグ: HD-MEA, IPSC, MaxOne, Neuronal cell culture, Organoids, Primary Neuronal Cell Culture 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 | タグ: 2D Neuronal Culture, CMOS, CRISPR, HD-MEA, MaxOne, Synapses 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 | タグ: CMOS, HD-MEA, IPSC, MaxOne, Primary Neuronal Cell Culture 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 | タグ: 2D Neuronal Culture, CMOS, HD-MEA, IPSC, MaxOne, MEA Metrics, Modeling, Spike Sorting 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 | タグ: CMOS, HD-MEA, MEA Technology 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 | タグ: Cardiomyocytes, CMOS, HD-MEA, MaxOne, MEA Technology Al-Absi, Abdel-Rahman; Thambiappaa, Sakeerthi Kethees; Khanc, Ahmad Raza; Glerup, Simon; Sanchez, Connie; Landau, Anne M; Nyengaard, Jens R Molecular and Cellular Neuroscience, 2022. Abstract | Links | BibTeX | タグ: Brain Slice, CMOS, HD-MEA, MaxOne 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 | タグ: 2D Neuronal Culture, Activity Scan Assay, Axon Tracking Assay, HD-MEA, MaxOne, Other Tissues, Publication, Stimulation Assay 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 | タグ: 2D Neuronal Culture, Activity Assay, HD-MEA, MaxOne, Network Assay, Primary Neuronal Cell Culture, Publication 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 | タグ: HD-MEA, MaxOne, Retina 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 | タグ: HD-MEA, MaxOne, MaxTwo, Organoids 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 | タグ: 2D Neuronal Culture, CMOS, HD-MEA, IPSC, MaxOne 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 | タグ: HD-MEA, MaxOne, Neuronal Networks 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 | タグ: Action Potential, HD-MEA, MaxOne 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 | タグ: HD-MEA, MaxOne, Neuronal Networks 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 | タグ: HD-MEA, MaxOne, Neuronal cell culture 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 | タグ: HD-MEA, MaxOne, Neuronal cell culture 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 | タグ: HD-MEA, MaxOne, Neuronal Networks 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 | タグ: HD-MEA, MaxOne, Organoids 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 | タグ: 2D Neuronal Culture, HD-MEA, MaxOne, Primary Neuronal Cell Culture, Stimulation Ricci, Chiara; Frey, Urs; Obien, Marie Engelene J IEEE, 2020. Abstract | Links | BibTeX | タグ: Activity Scan Assay, HD-MEA, MaxOne, MEA Technology Shimba, Kenta; Asahina, Takahiro; Sakai, Koji; JImbo, Yasuhiko; Kotani, Kiyoshi Evaluation of Conduction Properties of Sensory Axons with High-Density Microelectrode Array Conference 2019. Abstract | Links | BibTeX | タグ: HD-MEA Bullmann Torsten; Radivojevic, Milos; Huber Stefan Deligkaris Kosmas; Hierlemann Andreas; Frey Urs T: Large-Scale Mapping of Axonal Arbors Using High-Density Microelectrode Arrays Journal Article Frontiers in Cellular Neuroscience , 13 , 2019, ISSN: 1662-5102. Abstract | Links | BibTeX | タグ: Axonal Arbors, HD-MEA Mita, Takeshi; Bakkum, Douglas J; Frey, Urs; Hierlemann, Andreas; Kanzaki, Ryohei; Takahashi, Hirokazu IEEJ Transactions on Electronics, Information and Systems, 139 (5), pp. 615-624, 2019, ISSN: 1348-8155. Abstract | Links | BibTeX | タグ: Action Potential, HD-MEA Emmenegger, Vishalini; Obien, Marie Engelene J; Franke, Felix; Hierlemann, Andreas Technologies to Study Action Potential Propagation With a Focus on HD-MEAs Journal Article Frontiers in Cellular Neuroscience, 13 , pp. 1-11, 2019, ISSN: 1662-5102 . Abstract | Links | BibTeX | タグ: Action Potential, HD-MEA Viswam, Vijay; Bounik, Raziyeh; Shadmani, Amir; Dragas, Jelena; Urwyler, Cedar; Boos, Julia Alicia; Obien, Marie Engelene J; Muller, Jan; Chen, Yihui; Hierlemann, Andreas Impedance Spectroscopy and Electrophysiological Imaging of Cells With a High-Density CMOS Microelectrode Array System Journal Article IEEE Transactions on Biomedical Circuits and Systems, 12 (6), pp. 1356-1368, 2018, ISSN: 1932-4545. Abstract | Links | BibTeX | タグ: HD-MEA
2024
title = {Mechanical stimulation and electrophysiological monitoring at subcellular resolution reveals differential mechanosensation of neurons within networks},
author = {Krishna Chaitanya Kasuba and Alessio Paolo Buccino and Julian Bartram and Benjamin M. Gaub and Felix J. Fauser and Silvia Ronchi and Sreedhar Saseendran Kumar and Sydney Geissler and Michele M. Nava and Andreas Hierlemann and Daniel J. Müller },
url = {https://www.nature.com/articles/s41565-024-01609-1},
doi = {10.1038/s41565-024-01609-1},
year = {2024},
date = {2024-02-20},
journal = {Nature Nanotechnology},
abstract = {A growing consensus that the brain is a mechanosensitive organ is driving the need for tools that mechanically stimulate and simultaneously record the electrophysiological response of neurons within neuronal networks. Here we introduce a synchronized combination of atomic force microscopy, high-density microelectrode array and fluorescence microscopy to monitor neuronal networks and to mechanically characterize and stimulate individual neurons at piconewton force sensitivity and nanometre precision while monitoring their electrophysiological activity at subcellular spatial and millisecond temporal resolution. No correlation is found between mechanical stiffness and electrophysiological activity of neuronal compartments. Furthermore, spontaneously active neurons show exceptional functional resilience to static mechanical compression of their soma. However, application of fast transient (∼500 ms) mechanical stimuli to the neuronal soma can evoke action potentials, which depend on the anchoring of neuronal membrane and actin cytoskeleton. Neurons show higher responsivity, including bursts of action potentials, to slower transient mechanical stimuli (∼60 s). Moreover, transient and repetitive application of the same compression modulates the neuronal firing rate. Seemingly, neuronal networks can differentiate and respond to specific characteristics of mechanical stimulation. Ultimately, the developed multiparametric tool opens the door to explore manifold nanomechanobiological responses of neuronal systems and new ways of mechanical control.},
keywords = {Action Potential, Brain Slice, HD-MEA, MaxOne, Primary Neuronal Cell Culture, Spike Sorting},
pubstate = {published},
tppubtype = {article}
}
title = {A model of human neural networks reveals NPTX2 pathology in ALS and FTLD},
author = {Marian Hruska-Plochan and Vera I. Wiersma and Katharina M. Betz and Izaskun Mallona and Silvia Ronchi and Zuzanna Maniecka and Eva-Maria Hock and Elena Tantardini and Florent Laferriere and Sonu Sahadevan and Vanessa Hoop and Igor Delvendahl and Manuela Pérez-Berlanga and Beatrice Gatta and Martina Panatta and Alexander van der Bourg and Dasa Bohaciakova and Puneet Sharma and Laura De Vos 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://www.nature.com/articles/s41586-024-07042-7},
doi = {10.1038/s41586-024-07042-7},
year = {2024},
date = {2024-02-14},
journal = {Nature},
abstract = {Human cellular models of neurodegeneration require reproducibility and longevity, which is necessary for simulating age-dependent diseases. Such systems are particularly needed for TDP-43 proteinopathies1, which involve human-specific mechanisms that cannot be directly studied in animal models. Here, to explore the emergence and consequences of TDP-43 pathologies, we generated induced pluripotent stem cell-derived, colony morphology neural stem cells (iCoMoNSCs) via manual selection of neural precursors. Single-cell transcriptomics and comparison to independent neural stem cells 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 (which we designate iNets). Neuronal and glial maturation in iNets was similar to that of cortical organoids. Overexpression of wild-type TDP-43 in a minority of neurons within iNets led to progressive fragmentation and aggregation of the protein, resulting in a partial loss of function and neurotoxicity. Single-cell transcriptomics revealed a novel set of misregulated RNA targets in TDP-43-overexpressing neurons and in patients with TDP-43 proteinopathies exhibiting a loss of nuclear TDP-43. The strongest misregulated target encoded the synaptic protein NPTX2, the levels of which are controlled by TDP-43 binding on its 3′ untranslated region. When NPTX2 was overexpressed in iNets, it exhibited neurotoxicity, whereas correcting NPTX2 misregulation partially rescued neurons from TDP-43-induced neurodegeneration. Notably, NPTX2 was consistently misaccumulated in neurons from patients with amyotrophic lateral sclerosis and frontotemporal lobar degeneration with TDP-43 pathology. Our work directly links TDP-43 misregulation and NPTX2 accumulation, thereby revealing a TDP-43-dependent pathway of neurotoxicity.},
keywords = {Activity Scan Assay, HD-MEA, IPSC, MaxOne, MEA Technology, Network Assay, Primary Neuronal Cell Culture, Spike Sorting},
pubstate = {published},
tppubtype = {article}
}
title = {DeePhys: A machine learning–assisted platform for electrophysiological phenotyping of human neuronal networks},
author = {Philipp Hornauer and Gustavo Prack and Nadia Anastasi and Silvia Ronchi and Taehoon Kim and Christian Donner and Michele Fiscella and Karsten Borgwardt and Verdon Taylor and Ravi Jagasia and Damian Roqueiro and Andreas Hierlemann and Manuel Schröter},
url = {https://www.sciencedirect.com/science/article/pii/S2213671123005015},
doi = {10.1016/j.stemcr.2023.12.008},
year = {2024},
date = {2024-01-25},
journal = {Stem Cell Reports},
abstract = {Reproducible functional assays to study in vitro neuronal networks represent an important cornerstone in the quest to develop physiologically relevant cellular models of human diseases. Here, we introduce DeePhys, a MATLAB-based analysis tool for data-driven functional phenotyping of in vitro neuronal cultures recorded by high-density microelectrode arrays. DeePhys is a modular workflow that offers a range of techniques to extract features from spike-sorted data, allowing for the examination of functional phenotypes both at the individual cell and network levels, as well as across development. In addition, DeePhys incorporates the capability to integrate novel features and to use machine-learning-assisted approaches, which facilitates a comprehensive evaluation of pharmacological interventions. To illustrate its practical application, we apply DeePhys to human induced pluripotent stem cell–derived dopaminergic neurons obtained from both patients and healthy individuals and showcase how DeePhys enables phenotypic screenings.},
keywords = {2D Neuronal Culture, HD-MEA, IPSC, MaxOne, MEA Technology, Spike Sorting},
pubstate = {published},
tppubtype = {article}
}
2023
title = {Brain organoid reservoir computing for artificial intelligence},
author = {Hongwei Cai and Zheng Ao and Chunhui Tian and Zhuhao Wu and Hongcheng Liu and Jason Tchieu and Mingxia Gu and Ken Mackie and Feng Guo },
url = {https://www.nature.com/articles/s41928-023-01069-w},
doi = {10.1038/s41928-023-01069-w},
year = {2023},
date = {2023-12-11},
journal = {Nature Electronics},
abstract = {Brain-inspired computing hardware aims to emulate the structure and working principles of the brain and could be used to address current limitations in artificial intelligence technologies. However, brain-inspired silicon chips are still limited in their ability to fully mimic brain function as most examples are built on digital electronic principles. Here we report an artificial intelligence hardware approach that uses adaptive reservoir computation of biological neural networks in a brain organoid. In this approach—which is termed Brainoware—computation is performed by sending and receiving information from the brain organoid using a high-density multielectrode array. By applying spatiotemporal electrical stimulation, nonlinear dynamics and fading memory properties are achieved, as well as unsupervised learning from training data by reshaping the organoid functional connectivity. We illustrate the practical potential of this technique by using it for speech recognition and nonlinear equation prediction in a reservoir computing framework.},
keywords = {3D Culture, HD-MEA, Machine Learning, MaxOne, MEA Technology, Organoids, Stimulation},
pubstate = {published},
tppubtype = {article}
}
title = {Stress-free cell aggregation by using the CEPT cocktail enhances embryoid body and organoid fitness},
author = {Seungmi Ryu and Claire Weber and Pei-Hsuan Chu and Ben Ernest and Vukasin M Jovanovic and Tao Deng and Jaroslav Slamecka and Hyenjong Hong and Yogita Jethmalani and Hannah M Baskir and Jason Inman and John Braisted and Marissa B Hirst and Anton Simeonov and Ty C Voss and Carlos A Tristan and Ilyas Singeç},
url = {https://dx.doi.org/10.1088/1758-5090/ad0d13},
doi = {10.1088/1758-5090/ad0d13},
year = {2023},
date = {2023-12-11},
journal = {Biofabrication},
abstract = {Embryoid bodies (EBs) and self-organizing organoids derived from human pluripotent stem cells (hPSCs) recapitulate tissue development in a dish and hold great promise for disease modeling and drug development. However, current protocols are hampered by cellular stress and apoptosis during cell aggregation, resulting in variability and impaired cell differentiation. Here, we demonstrate that EBs and various organoid models (e.g., brain, gut, kidney) can be optimized by using the small molecule cocktail named CEPT (chroman 1, emricasan, polyamines, trans-ISRIB), a polypharmacological approach that ensures cytoprotection and cell survival. Application of CEPT for just 24 h during cell aggregation has long-lasting consequences affecting morphogenesis, gene expression, cellular differentiation, and organoid function. Various qualification methods confirmed that CEPT treatment enhanced experimental reproducibility and consistently improved EB and organoid fitness as compared to the widely used ROCK inhibitor Y-27632. Collectively, we discovered that stress-free cell aggregation and superior cell survival in the presence of CEPT are critical quality control determinants that establish a robust foundation for bioengineering complex tissue and organ models.},
keywords = {3D Culture, Activity Scan Assay, HD-MEA, MEA Technology, Organoids},
pubstate = {published},
tppubtype = {article}
}
title = {Internet-Connected Cortical Organoids for Project-Based Stem Cell and Neuroscience Education},
author = {Matthew A. T. Elliott and Hunter E. Schweiger and Ash Robbins and Samira Vera-Choqqueccota and Drew Ehrlich and Sebastian Hernandez and Kateryna Voitiuk and Jinghui Geng and Jess L. Sevetson and Cordero Core and Yohei M. Rosen and Mircea Teodorescu and Nico O. Wagner and David Haussler and Mohammed A. Mostajo-Radji},
url = {https://www.eneuro.org/lookup/doi/10.1523/ENEURO.0308-23.2023},
doi = {10.1523/ENEURO.0308-23.2023},
year = {2023},
date = {2023-11-28},
journal = {eNeuro},
abstract = {The introduction of Internet-connected technologies to the classroom has the potential to revolutionize STEM education by allowing students to perform experiments in complex models that are unattainable in traditional teaching laboratories. By connecting laboratory equipment to the cloud, we introduce students to experimentation in pluripotent stem cell (PSC)-derived cortical organoids in two different settings: using microscopy to monitor organoid growth in an introductory tissue culture course and using high-density (HD) multielectrode arrays (MEAs) to perform neuronal stimulation and recording in an advanced neuroscience mathematics course. We demonstrate that this approach develops interest in stem cell and neuroscience in the students of both courses. All together, we propose cloud technologies as an effective and scalable approach for complex project-based university training.},
keywords = {3D Culture, Activity Scan Assay, HD-MEA, IPSC, MaxOne, MEA Technology, Organoids, Spike Sorting, Stimulation},
pubstate = {published},
tppubtype = {article}
}
title = {Measuring and Inducing the Plasticity of Single-Neuron Scale at Multiple Points},
author = {Toki Kobayashi and Kenta Shimba and Kiyoshi Kotani and Yasuhiko Jimbo},
url = {https://ieeexplore.ieee.org/abstract/document/10322076},
doi = {10.1109/BMEiCON60347.2023.10322076},
year = {2023},
date = {2023-11-22},
journal = {IEEE Xplore},
publisher = {ISSS Xplore},
abstract = {Information processing in the brain is supported by the plasticity of the connections of neurons in biological neuronal networks. There is a gap between our understanding on plasticity of individual connections and that of the neuronal networks. Here, we aimed to induce and measure plasticity at the connections of individual neurons and at the network level. We achieved inducing plasticity with a combination of single cell stimulation by optogenetics and high-resolution extracellular potentials recording by high-density microelectrode array. Spike timing plasticity in a single neuron was successfully measured. Although we also tried to induce synaptic potentiation by tetanus stimulation, no significant change was observed. In the future, we will investigate how the plasticity of individual connections changes dynamics of entire network.},
keywords = {HD-MEA, MaxOne, Primary Neuronal Cell Culture, Stimulation},
pubstate = {published},
tppubtype = {conference}
}
title = {Activity- and Spatial-dependent Variations in Axonal Conduction Recorded from Microtunnel Electrodes},
author = {Chie Tamatani and Kenta Shimba and Kiyoshi Kotani andYasuhiko Jimbo
},
url = {https://ieeexplore.ieee.org/abstract/document/10321980},
doi = {10.1109/BMEiCON60347.2023.10321980},
year = {2023},
date = {2023-11-22},
publisher = {IEEE Xplore},
abstract = {Axons are not simple transmission cables in neuronal networks, but they are directly involved in information processing. We developed a novel culture device that aims to assess axonal conduction properties. The microdevice consists of microtunnels directly fabricated on high-density microelectrode array. Neuron growth and axon isolation were confirmed by immunofluorescent staining and neural activity recording. Several dozens of electrodes were detected from each tunnel and signals had enough S/N ratio to handle each spike event. Activity- and spatial-dependent variations in conduction velocity were observed. These results suggest that our microdevice is feasible to study axonal information processing.},
keywords = {HD-MEA, MaxOne},
pubstate = {published},
tppubtype = {conference}
}
title = {Recapitulation of Perturbed Striatal Gene Expression Dynamics of Donor’s Brains With Ventral Forebrain Organoids Derived From the Same Individuals With Schizophrenia},
author = {Tomoyo Sawada and André R. Barbosa and Bruno Araujo and Alejandra E. McCord and Laura D’Ignazio and Kynon J.M. Benjamin and Bonna Sheehan and Michael Zabolocki and Arthur Feltrin and Ria Arora and Anna C. Brandtjen and Joel E. Kleinman and Thomas M. Hyde and Cedric Bardy and Daniel R. Weinberger and Apuã C.M. Paquola and Jennifer A. Erwin},
url = {https://ajp.psychiatryonline.org/doi/10.1176/appi.ajp.20220723},
doi = {10.1176/appi.ajp.20220723},
issn = {0002-953X},
year = {2023},
date = {2023-11-02},
journal = {American Journal of Psychiatry},
abstract = {Objective:
Schizophrenia is a brain disorder that originates during neurodevelopment and has complex genetic and environmental etiologies. Despite decades of clinical evidence of altered striatal function in affected patients, studies examining its cellular and molecular mechanisms in humans are limited. To explore neurodevelopmental alterations in the striatum associated with schizophrenia, the authors established a method for the differentiation of induced pluripotent stem cells (iPSCs) into ventral forebrain organoids (VFOs).
Methods:
VFOs were generated from postmortem dural fibroblast–derived iPSCs of four individuals with schizophrenia and four neurotypical control individuals for whom postmortem caudate genotypes and transcriptomic data were profiled in the BrainSeq neurogenomics consortium. Individuals were selected such that the two groups had nonoverlapping schizophrenia polygenic risk scores (PRSs).
Results:
Single-cell RNA sequencing analyses of VFOs revealed differences in developmental trajectory between schizophrenia and control individuals in which inhibitory neuronal cells from the patients exhibited accelerated maturation. Furthermore, upregulated genes in inhibitory neurons in schizophrenia VFOs showed a significant overlap with upregulated genes in postmortem caudate tissue of individuals with schizophrenia compared with control individuals, including the donors of the iPSC cohort.
Conclusions:
The findings suggest that striatal neurons derived from high-PRS individuals with schizophrenia carry abnormalities that originated during early brain development and that the VFO model can recapitulate disease-relevant cell type–specific neurodevelopmental phenotypes in a dish.},
keywords = {3D Culture, Activity Scan Assay, HD-MEA, MaxTwo, Network Assay, Organoids},
pubstate = {published},
tppubtype = {article}
}
Schizophrenia is a brain disorder that originates during neurodevelopment and has complex genetic and environmental etiologies. Despite decades of clinical evidence of altered striatal function in affected patients, studies examining its cellular and molecular mechanisms in humans are limited. To explore neurodevelopmental alterations in the striatum associated with schizophrenia, the authors established a method for the differentiation of induced pluripotent stem cells (iPSCs) into ventral forebrain organoids (VFOs).
Methods:
VFOs were generated from postmortem dural fibroblast–derived iPSCs of four individuals with schizophrenia and four neurotypical control individuals for whom postmortem caudate genotypes and transcriptomic data were profiled in the BrainSeq neurogenomics consortium. Individuals were selected such that the two groups had nonoverlapping schizophrenia polygenic risk scores (PRSs).
Results:
Single-cell RNA sequencing analyses of VFOs revealed differences in developmental trajectory between schizophrenia and control individuals in which inhibitory neuronal cells from the patients exhibited accelerated maturation. Furthermore, upregulated genes in inhibitory neurons in schizophrenia VFOs showed a significant overlap with upregulated genes in postmortem caudate tissue of individuals with schizophrenia compared with control individuals, including the donors of the iPSC cohort.
Conclusions:
The findings suggest that striatal neurons derived from high-PRS individuals with schizophrenia carry abnormalities that originated during early brain development and that the VFO model can recapitulate disease-relevant cell type–specific neurodevelopmental phenotypes in a dish.
title = {Driving electrochemical reactions at the microscale using CMOS microelectrode arrays},
author = {Jens Duru and Arielle Rüfenacht and Josephine Löhle and Marcello Pozzi and Csaba Forró and Linus Ledermann and Aeneas Bernardi and Michael Matter and André Renia and Benjamin Simona and Christina M. Tringides and Stéphane Bernhard and Stephan J. Ihle and Julian Hengsteler and Benedikt Maurer and Xinyu Zhanga and Nako Nakatsuka},
url = {https://pubs.rsc.org/en/content/articlelanding/2023/lc/d3lc00630a},
doi = {10.1039/D3LC00630A},
issn = {1473-0189},
year = {2023},
date = {2023-10-30},
journal = {Lab on a Chip},
abstract = {Precise control of pH values at electrode interfaces enables the systematic investigation of pH-dependent processes by electrochemical means. In this work, we employed high-density complementary metal-oxide-semiconductor (CMOS) microelectrode arrays (MEAs) as miniaturized systems to induce and confine electrochemical reactions in areas corresponding to the pitch of single electrodes (17.5 μm). First, we present a strategy for generating localized pH patterns on the surface of the CMOS MEA with unprecedented spatial resolution. Leveraging the versatile routing capabilities of the switch matrix beneath the CMOS MEA, we created arbitrary combinations of anodic and cathodic electrodes and hence pH patterns. Moreover, we utilized the system to produce polymeric surface patterns by additive and subtractive methods. For additive patterning, we controlled the in situ formation of polydopamine at the microelectrode surface through oxidation of free dopamine above a threshold pH > 8.5. For subtractive patterning, we removed cell-adhesive poly-L-lysine from the electrode surface and backfilled the voids with antifouling polymers. Such polymers were chosen to provide a proof-of-concept application of controlling neuronal growth via electrochemically-induced patterns on the CMOS MEA surface. Importantly, our platform is compatible with commercially available high-density MEAs and requires no custom equipment, rendering the findings generalizable and accessible.},
keywords = {HD-MEA, MaxOne, Primary Neuronal Cell Culture, Stimulation},
pubstate = {published},
tppubtype = {article}
}
title = {Potentiating NaV1.1 in Dravet syndrome patient iPSC-derived GABAergic neurons increases neuronal firing frequency and decreases network synchrony},
author = {Matt R Kelley and Laura B Chipman and Shoh Asano and Matthew Knott and Samantha T Howard and Allison P Berg},
url = {https://www.biorxiv.org/content/10.1101/2023.09.28.559990v1},
doi = {10.1101/2023.09.28.559990},
year = {2023},
date = {2023-09-29},
journal = {bioRxiv},
abstract = {Dravet syndrome is a developmental and epileptic encephalopathy characterized by seizures, behavioral abnormalities, developmental deficits, and elevated risk of sudden unexpected death in epilepsy (SUDEP). Most patient cases are caused by de novo loss-of-function mutations in the gene SCN1A, causing a haploinsufficiency of the alpha subunit of the voltage-gated sodium channel NaV1.1. Within the brain, NaV1.1 is primarily localized to the axons of inhibitory neurons, and decreased NaV1.1 function is hypothesized to reduce GABAergic inhibitory neurotransmission within the brain, driving neuronal network hyperexcitability and subsequent pathology. We have developed a human in vitro model of Dravet syndrome using differentiated neurons derived from patient iPSC and enriched for GABA expressing neurons. Neurons were plated on high definition multielectrode arrays (HD-MEAs), permitting recordings from the same cultures over the 7-weeks duration of study at the network, single cell, and subcellular resolution. Using this capability, we characterized the features of axonal morphology and physiology. Neurons developed increased spiking activity and synchronous network bursting. Recordings were processed through a spike sorting pipeline for curation of single unit activity and to assess the effects of pharmacological treatments. At 7-weeks, the application of the GABAAR receptor agonist muscimol eliminated network bursting, indicating the presence of GABAergic neurotransmission. To identify the role of NaV1.1 on neuronal and network activity, cultures were treated with a dose-response of the NaV1.1 potentiator δ-theraphotoxin-Hm1a. This resulted in a strong increase in firing rates of putative GABAergic neurons, an increase in the intraburst firing rate, and eliminated network bursting. These results validate that potentiation of NaV1.1 in Dravet patient iPSC-derived neurons results in decreased firing synchrony in neuronal networks through increased GABAergic neuron activity and support the use of human neurons and HD-MEAs as viable high-throughput electrophysiological platform to enable therapeutic discovery.},
keywords = {Activity Scan Assay, Axon Tracking Assay, HD-MEA, IPSC, MaxTwo, MEA Technology, Network Assay, Spike Sorting},
pubstate = {published},
tppubtype = {article}
}
title = {Closed-loop neurostimulation via expression of magnetogenetics-sensitive protein in inhibitory neurons leads to reduction of seizure activity in a rat model of epilepsy},
author = {Abigael C. Metto and Petra Telgkamp and Autumn K. McLane-Svoboda and Assaf A. Gilad and Galit Pelled},
url = {https://www.sciencedirect.com/science/article/pii/S0006899323003621},
doi = {https://doi.org/10.1016/j.brainres.2023.148591},
year = {2023},
date = {2023-09-24},
journal = {Brain Research},
abstract = {On-demand neurostimulation has shown success in epilepsy patients with pharmacoresistant seizures. Seizures produce magnetic fields that can be recorded using magnetoencephalography. We developed a new closed-loop approach to control seizure activity based on magnetogenetics using the electromagnetic perceptive gene (EPG) that encodes a protein that responds to magnetic fields. The EPG transgene was expressed in inhibitory interneurons under the hDlx promoter and kainic acid was used to induce acute seizures. In vivo electrophysiological signals were recorded. We found that hDlx EPG rats exhibited a significant delay in the onset of first seizure (1142.72 ± 186.35 s) compared to controls (644.03 ± 15.06 s) and significantly less seizures (4.11 ± 1.03) compared to controls (8.33 ± 1.58). These preliminary findings suggest that on-demand activation of EPG expressed in inhibitory interneurons suppresses seizure activity, and magnetogenetics via EPG may be an effective strategy to alleviate seizure severity in a closed-loop, and cell-specific fashion.},
keywords = {3D Culture, closed loop stimulation, HD-MEA, MaxOne, Slices},
pubstate = {published},
tppubtype = {article}
}
title = {Hyperexcitability and translational phenotypes in a preclinical model of SYNGAP1mutations},
author = {Jill L. Silverman and Timothy Fenton and Olivia Haouchine and Elizabeth Hallam and Emily Smith and Kiya Jackson and Darlene Rahbarian and Cesar Canales and Anna Adhikari and Alex Nord and Roy Ben-Shalom},
url = {https://www.researchsquare.com/article/rs-3246655/v1},
doi = {https://doi.org/10.21203/rs.3.rs-3246655/v1},
year = {2023},
date = {2023-09-13},
journal = {Research Square},
abstract = {SYNGAP1is a critical gene for neuronal development, synaptic structure, and function. Although rare, the disruption of SYNGAP1directly causes a genetically identi able neurodevelopmental disorder (NDD) called SYNGAP1-related intellectual disability. Without functional SynGAP1 protein, patients present with intellectual disability, motor impairments, and epilepsy. Previous work using mouse models with a variety of germline and conditional mutations has helped delineate SynGAP1’s critical roles in neuronal structure and function, as well as key biochemical signaling pathways essential to synapse integrity. Homozygous loss of SYNGAP1is embryonically lethal. Heterozygous mutations of SynGAP1result in a broad range of phenotypes including increased locomotor activity, impaired working spatial memory, impaired cued fear memory, and increased stereotypic behavior. Ourinvivofunctional data, using the original germline mutation mouse line from the Huganir laboratory, corroborated robust hyperactivity and learning and memory de cits. Here, we describe impairments in the translational biomarker domain of sleep, characterized using neurophysiological data collected with wireless telemetric electroencephalography (EEG). We discoveredSyngap1+/− mice exhibited elevated spike trains in both number and duration, in addition to elevated power, most notably in the delta power band. Primary neurons fromSyngap1+/− mice displayed increased network ring activity, greater spikes per burst, and shorter inter-burst intervals between peaks using high density micro-electrode arrays (HD-MEA). This work is translational, innovative, and highly signi cant as it outlines functional impairments in Syngap1mutant mice. Simultaneously, the work utilized untethered, wireless neurophysiology that can discover potential biomarkers of Syngap1RID, for clinical trials, as it has done with other NDDs. Our work is substantial forward progress toward translational work for SynGAP1R-ID as it bridges in-vitroelectrophysiological neuronal activity and function with invivoneurophysiological brain activity and function. These data elucidate multiple quantitative, translational biomarkers invivoand invitrofor the development of treatments for SYNGAP1-related intellectual disability.},
keywords = {2D Neuronal Culture, Activity Scan Assay, HD-MEA, MaxOne, Network Assay, Primary Neuronal Cell Culture},
pubstate = {published},
tppubtype = {article}
}
title = {Critical dynamics arise during structured information presentation within embodied in vitro neuronal networks},
author = {Forough Habibollahi and Brett J. Kagan and Anthony N. Burkitt and Chris French },
url = {https://www.nature.com/articles/s41467-023-41020-3},
doi = {https://doi.org/10.1038/s41467-023-41020-3},
year = {2023},
date = {2023-08-30},
journal = {Nature Communications},
abstract = {Understanding how brains process information is an incredibly difficult task. Amongst the metrics characterising information processing in the brain, observations of dynamic near-critical states have generated significant interest. However, theoretical and experimental limitations associated with human and animal models have precluded a definite answer about when and why neural criticality arises with links from attention, to cognition, and even to consciousness. To explore this topic, we used an in vitro neural network of cortical neurons that was trained to play a simplified game of ‘Pong’ to demonstrate Synthetic Biological Intelligence (SBI). We demonstrate that critical dynamics emerge when neural networks receive task-related structured sensory input, reorganizing the system to a near-critical state. Additionally, better task performance correlated with proximity to critical dynamics. However, criticality alone is insufficient for a neuronal network to demonstrate learning in the absence of additional information regarding the consequences of previous actions. These findings offer compelling support that neural criticality arises as a base feature of incoming structured information processing without the need for higher order cognition.},
keywords = {2D Neuronal Culture, HD-MEA, IPSC, MaxOne, MEA Metrics, MEA Technology, Primary Neuronal Cell Culture},
pubstate = {published},
tppubtype = {article}
}
title = {Investigation of the input-output relationship of engineered neural networks using high-density microelectrode arrays},
author = {Jens Duru and Benedikt Maurer and Ciara Giles Doran and Robert Jelitto and Joël Küchler and Stephan J. Ihle and Tobias Ruff and Robert John and Barbara Genocchi and János Vörös
},
url = {https://www.sciencedirect.com/science/article/pii/S095656632300533X?via%3Dihub},
doi = {https://doi.org/10.1016/j.bios.2023.115591},
year = {2023},
date = {2023-08-18},
journal = {Biosensors and Bioelectronics},
abstract = {Bottom-up neuroscience utilizes small, engineered biological neural networks to study neuronal activity in systems of reduced complexity. We present a platform that establishes up to six independent networks formed by primary rat neurons on planar complementary metal–oxide–semiconductor (CMOS) microelectrode arrays (MEAs). We introduce an approach that allows repetitive stimulation and recording of network activity at any of the over 700 electrodes underlying a network. We demonstrate that the continuous application of a repetitive super-threshold stimulus yields a reproducible network answer within a 15 ms post-stimulus window. This response can be tracked with high spatiotemporal resolution across the whole extent of the network. Moreover, we show that the location of the stimulation plays a significant role in the networks' early response to the stimulus. By applying a stimulation pattern to all network-underlying electrodes in sequence, the sensitivity of the whole network to the stimulus can be visualized. We demonstrate that microchannels reduce the voltage stimulation threshold and induce the strongest network response. By varying the stimulation amplitude and frequency we reveal discrete network transition points. Finally, we introduce vector fields to follow stimulation-induced spike propagation pathways within the network. Overall we show that our defined neural networks on CMOS MEAs enable us to elicit highly reproducible activity patterns that can be precisely modulated by stimulation amplitude, stimulation frequency and the site of stimulation.},
keywords = {2D Neuronal Culture, HD-MEA, MaxOne, Stimulation},
pubstate = {published},
tppubtype = {article}
}
title = {Microfluidic technologies for reconstituting neuronal network functions in vitro},
author = {Hideaki Yamamoto and Ayumi Hirano-Iwata and Shigeo Sato},
url = {https://www.jstage.jst.go.jp/article/oubutsu/92/5/92_278/_article/-char/en},
doi = {10.11470/oubutsu.92.5_278},
year = {2023},
date = {2023-07-06},
journal = {JSAP Review},
abstract = {The structure and function of complex neuronal networks in the brain can be partially reconstituted in vitro by integrating cell culture and microfluidic device technologies. In this report, we review our recent studies on developing microfluidic devices to reconstitute small neuronal networks bearing a modular structure, which is a canonical structure found in the nervous systems of animals. We also describe the process of recording functional activity from the reconstituted neuronal networks. These fundamental technologies offer novel tools for investigating structure–function relationships in living neuronal networks and exploring the physical basis of biological computing in the brain.},
keywords = {2D Neuronal Culture, HD-MEA, MaxOne, MEA Technology, Microfluidics},
pubstate = {published},
tppubtype = {article}
}
title = {A CMOS-based highly scalable flexible neural electrode interface},
author = {Eric T. Zhao and Jacob M. Hull and Nofar Mintz Hemed and Hasan Ulusan and Julian Bartram and Anqi Zhang and Pingyu Wang and Albert Pham and Silvia Ronchi, John R. Huguenard and Andreas Hierlemann and Nicholas A. Melosh},
url = {https://www.science.org/doi/10.1126/sciadv.adf9524},
doi = {DOI: 10.1126/sciadv.adf9524},
year = {2023},
date = {2023-06-07},
journal = {Science Advances},
abstract = {Perception, thoughts, and actions are encoded by the coordinated activity of large neuronal populations spread over large areas. However, existing electrophysiological devices are limited by their scalability in capturing this cortex-wide activity. Here, we developed an electrode connector based on an ultra-conformable thin-film electrode array that self-assembles onto silicon microelectrode arrays enabling multithousand channel counts at a millimeter scale. The interconnects are formed using microfabricated electrode pads suspended by thin support arms, termed Flex2Chip. Capillary-assisted assembly drives the pads to deform toward the chip surface, and van der Waals forces maintain this deformation, establishing Ohmic contact. Flex2Chip arrays successfully measured extracellular action potentials ex vivo and resolved micrometer scale seizure propagation trajectories in epileptic mice. We find that seizure dynamics in absence epilepsy in the Scn8a+/− model do not have constant propagation trajectories.},
keywords = {3D Culture, HD-MEA, MaxOne, Other Tissues, Slices},
pubstate = {published},
tppubtype = {article}
}
title = {Cultured Vagal Afferent Neurons as Sensors for Intestinal Effector Molecules},
author = {Gregory Girardi and Danielle Zumpano and Noah Goshi and Helen Raybould and Erkin Seker},
url = {https://www.mdpi.com/2079-6374/13/6/601},
doi = {10.3390/bios13060601},
year = {2023},
date = {2023-05-31},
journal = {biosensors},
abstract = {The gut–brain axis embodies the bi-directional communication between the gastrointestinal tract and the central nervous system (CNS), where vagal afferent neurons (VANs) serve as sensors for a variety of gut-derived signals. The gut is colonized by a large and diverse population of microorganisms that communicate via small (effector) molecules, which also act on the VAN terminals situated in the gut viscera and consequently influence many CNS processes. However, the convoluted in vivo environment makes it difficult to study the causative impact of the effector molecules on VAN activation or desensitization. Here, we report on a VAN culture and its proof-of-principle demonstration as a cell-based sensor to monitor the influence of gastrointestinal effector molecules on neuronal behavior. We initially compared the effect of surface coatings (poly-L-lysine vs. Matrigel) and culture media composition (serum vs. growth factor supplement) on neurite growth as a surrogate of VAN regeneration following tissue harvesting, where the Matrigel coating, but not the media composition, played a significant role in the increased neurite growth. We then used both live-cell calcium imaging and extracellular electrophysiological recordings to show that the VANs responded to classical effector molecules of endogenous and exogenous origin (cholecystokinin serotonin and capsaicin) in a complex fashion. We expect this study to enable platforms for screening various effector molecules and their influence on VAN activity, assessed by their information-rich electrophysiological fingerprints.},
keywords = {2D Neuronal Culture, HD-MEA, MaxOne, MEA Technology, Primary Neuronal Cell Culture},
pubstate = {published},
tppubtype = {article}
}
title = {Parallel reconstruction of the excitatory and inhibitory inputs received by single neurons reveals the synaptic basis of recurrent spiking},
author = {Julian Bartram and Felix Franke and Sreedhar Saseendran Kumar and Alessio Paolo Buccino and Xiaohan Xue and Tobias Gänswein and Manuel Schröter and Taehoon Kim and Krishna Chaitanya Kasuba and Andreas Hierlemann},
url = {https://elifesciences.org/reviewed-preprints/86820},
doi = {10.7554/eLife.86820},
year = {2023},
date = {2023-05-17},
journal = {eLife},
abstract = {Self-sustained recurrent activity in cortical networks is thought to be important for multiple crucial processes, including circuit development and homeostasis. Yet, the precise relationship between the synaptic input patterns and the spiking output of individual neurons remains largely unresolved. Here, we developed, validated and applied a novel in vitro experimental platform and analytical procedures that provide – for individual neurons – simultaneous excitatory and inhibitory synaptic activity estimates during recurrent network activity. Our approach combines whole-network high-density microelectrode array (HD-MEA) recordings from rat neuronal cultures with patch clamping and enables a comprehensive mapping and characterization of active incoming connections to single postsynaptic neurons. We found that, during network states with excitation(E)-inhibition(I) balance, postsynaptic spiking coincided precisely with the maxima of fast fluctuations in the input E/I ratio. These spike-associated E/I ratio escalations were largely due to a rapid bidirectional change in synaptic inhibition that was modulated by the network-activity level. Our approach also uncovered the underlying circuit architecture and we show that individual neurons received a few key inhibitory connections – often from special hub neurons – that were instrumental in controlling postsynaptic spiking. Balanced network theory predicts dynamical regimes governed by small and rapid input fluctuation and featuring a fast neuronal responsiveness. Our findings – obtained in self-organized neuronal cultures – suggest that the emergence of these favorable regimes and associated network architectures is an inherent property of cortical networks in general.},
keywords = {HD-MEA, MaxOne, MEA Metrics, MEA Technology, Modeling, Primary Neuronal Cell Culture, Spike Sorting},
pubstate = {published},
tppubtype = {article}
}
title = {Investigation of the input-output relationship of engineered neural networks using high-density microelectrode arrays},
author = {Jens Duru and Benedikt Maurer and Ciara Giles Doran and Robert Jelitto and Joël Küchler and Stephan J. Ihle and Tobias Ruff and Robert John and Barbara Genocchi and János Vörös},
url = {https://www.ssrn.com/abstract=4427959},
doi = {DOI: 10.2139/ssrn.4427959},
year = {2023},
date = {2023-04-24},
journal = {SSRN},
abstract = {Bottom-up neuroscience utilizes small, engineered biological neural networks to study neuronal activity in systems of reduced complexity. We present a platform that establishes up to six independent networks formed by primary rat neurons on planar complementary metal–oxide–semiconductor (CMOS) microelectrode arrays (MEAs). We introduce an approach that allows repetitive stimulation and recording of network activity at any of the over 700 electrodes underlying a network. We demonstrate that the continuous application of a repetitive super-threshold stimulus yields a reproducible network answer within a 15 ms post-stimulus window. This response can be tracked with high spatiotemporal resolution across the whole extent of the network. Moreover, we show that the location of the stimulation plays a significant role in the networks’ early response to the stimulus. By applying a stimulation pattern to all network-underlying electrodes in sequence, the sensitivity of the whole network to the stimulus can be visualized. We demonstrate that microchannels reduce the voltage stimulation threshold and induce the strongest network response. By varying the stimulation amplitude and frequency we reveal discrete network transition points. Finally, we introduce vector fields to follow stimulation-induced spike propagation pathways within the network. Overall we show that our defined neural networks on CMOS MEAs enable us to elicit highly reproducible activity patterns that can be precisely modulated by stimulation amplitude, stimulation frequency and the site of stimulation.},
keywords = {HD-MEA, MaxOne, MEA Technology, Primary Neuronal Cell Culture, Spike Sorting, Stimulation},
pubstate = {published},
tppubtype = {article}
}
title = {Generation of functional posterior spinal motor neurons from hPSCs-derived human spinal cord neural progenitor cells},
author = {He Jax Xu and Yao Yao and Fenyong Yao and Jiehui Chen and Meishi Li and Xianfa Yang and Sheng Li and Fangru Lu and Ping Hu and Shuijin He and Guangdun Peng and Naihe Jing},
url = {https://cellregeneration.springeropen.com/articles/10.1186/s13619-023-00159-6},
doi = {10.1186/s13619-023-00159-6},
year = {2023},
date = {2023-03-23},
journal = {Cell Regeneration},
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 inappropriate regional identity and functional immaturity for the study and treatment of posterior spinal cord related injuries. 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, Activity Scan Assay, Axon Tracking Assay, HD-MEA, IPSC, MaxOne, MEA Technology, Network Assay, Organoids},
pubstate = {published},
tppubtype = {article}
}
title = {Brain Organoid Computing for Artificial Intelligence},
author = {Hongwei Cai and Zheng Ao and Chunhui Tian and Zhuhao Wu and Hongcheng Liu and Jason Tchieu and Mingxia Gu and Ken Mackie and and Feng Guo},
url = {https://www.biorxiv.org/content/10.1101/2023.02.28.530502v1},
doi = {10.1101/2023.02.28.530502},
year = {2023},
date = {2023-03-01},
journal = {bioRxiv},
abstract = {Brain-inspired hardware emulates the structure and working principles of a biological brain and may address the hardware bottleneck for fast-growing artificial intelligence (AI). Current brain-inspired silicon chips are promising but still limit their power to fully mimic brain function for AI computing. Here, we develop Brainoware, living AI hardware that harnesses the computation power of 3D biological neural networks in a brain organoid. Brain-like 3D in vitro cultures compute by receiving and sending information via a multielectrode array. Applying spatiotemporal electrical stimulation, this approach not only exhibits nonlinear dynamics and fading memory properties but also learns from training data. Further experiments demonstrate real-world applications in solving non-linear equations. This approach may provide new insights into AI hardware.
},
keywords = {HD-MEA, Machine Learning, MaxOne, MEA Technology, Modeling, Organoids, Stimulation},
pubstate = {published},
tppubtype = {article}
}
title = {Multiplex epigenome editing of MECP2 to rescue Rett syndrome neurons},
author = {Junming Qian and Xiaonan Guan and Bing Xie and Chuanyun Xu and Jacqueline Niu and Xin Tang and Charles H. Li and Henry M. Colecraft and Rudolf Jaenisch and X. Shawn Liu},
url = {https://www.science.org/doi/10.1126/scitranslmed.add4666},
doi = {10.1126/scitranslmed.add4666},
year = {2023},
date = {2023-01-18},
journal = {Science Translational Medicine},
abstract = {Rettsyndrome(RTT)isanX-linkedneurodevelopmental disorder caused byloss-of-function heterozygous mutationsofmethyl CpG-binding protein2(MECP2) ontheXchromosome inyoungfemales. Reactivationofthe silent wild-type MECP2 allelefromtheinactiveXchromosome (Xi)represents apromising therapeutic opportunity forfemale patients withRTT.Here,weapplied amultiple xepigenome editing approachtoreactivate MECP2 fromXiinRTThuman embryonicstemcells(hESCs) andderivedneurons.Demethyla tionofthe MECP2 promoter bydCas9-T et1withtarget single-guide RNAreactivatedMECP2 fromXiinRTThESCs without detectable off-target effects atthetranscriptional level.Neuronsderivedfrommethyla tion-edited RTThESCs maintained MECP2 reactivationandreversedthesmaller somasizeandelectrophysiological abnormalities, twohallmarks ofRTT.InRTTneurons,insulationofthemethyla tion-edited MECP2 locusbydCpf1-CT CF (acatalytically deadCpf1fusedwithCCCTC-binding factor)withtarget CRISPR RNAenhanced MECP2 reactivationandrescued RTT-relatedneuronaldefects, providing aproof-of-concept studyforepigenome editing to treatRTTandpotentially otherdominant X-linkeddiseases.},
keywords = {2D Neuronal Culture, HD-MEA, IPSC, MaxTwo, MEA Technology},
pubstate = {published},
tppubtype = {article}
}
title = {Parallel reconstruction of the excitatory and inhibitory inputs received by single neurons reveals the synaptic basis of recurrent spiking},
author = {Julian Bartram and Felix Franke and Sreedhar Saseendran Kumar and Alessio Paolo Buccino and Xiaohan Xue and Tobias Gänswein and Manuel Schröter and Taehoon Kim and Krishna Chaitanya Kasuba and Andreas Hierlemann},
url = {https://www.biorxiv.org/content/10.1101/2023.01.06.523018v2},
doi = {https://doi.org/10.1101/2023.01.06.523018},
year = {2023},
date = {2023-01-08},
journal = {bioRxiv},
abstract = {Self-sustained recurrent activity in cortical networks is thought to be important for multiple crucial processes, including circuit development and homeostasis. However, the precise relationship between synaptic input patterns and spiking output of individual neurons remains unresolved during spontaneous network activity. Here, using whole-network high-density microelectrode array (HD-MEA) recordings and patch clamping, we developed a novel experimental approach and analytical tools that provide a comprehensive long-term input-output characterization of individual neurons in cortical cell cultures. We found that, during in vivo-like network activity with excitation(E)-inhibition(I) balance, postsynaptic spiking coincided with the maxima of rapid, network state-dependent fluctuations in the input E/I ratio. Our approach also uncovered the underlying circuit architecture and we identified a few key inhibitory inputs – often from special hub neurons – that were instrumental in mediating these E/I ratio changes. Balanced network theory predicts dynamical regimes governed by input fluctuation and featuring a fast neuronal responsiveness. Our findings – obtained in self-organized neuronal cultures – suggest that the emergence of these favorable regimes and associated network architectures is an inherent property of all cortical networks.},
keywords = {CMOS, HD-MEA, Modeling, Primary Neuronal Cell Culture, Spike Sorting},
pubstate = {published},
tppubtype = {article}
}
2022
title = {A functional neuron maturation device provides convenient application on microelectrode array for neural network measurement},
author = {Xiaobo Han and Naoki Matsuda and Yuto Ishibashi and Aoi Odawara and Sayuri Takahashi and Norie Tooi and Koshi Kinoshita and Ikuro Suzuki },
url = {https://biomaterialsres.biomedcentral.com/articles/10.1186/s40824-022-00324-z},
doi = {https://doi.org/10.1186/s40824-022-00324-z},
year = {2022},
date = {2022-12-20},
journal = {Biomaterials Research},
abstract = {Background
Microelectrode array (MEA) systems are valuable for in vitro assessment of neurotoxicity and drug efficiency. However, several difficulties such as protracted functional maturation and high experimental costs hinder the use of MEA analysis requiring human induced pluripotent stem cells (hiPSCs). Neural network functional parameters are also needed for in vitro to in vivo extrapolation.
Methods
In the present study, we produced a cost effective nanofiber culture platform, the SCAD device, for long-term culture of hiPSC-derived neurons and primary peripheral neurons. The notable advantage of SCAD device is convenient application on multiple MEA systems for neuron functional analysis.
Results
We showed that the SCAD device could promote functional maturation of cultured hiPSC-derived neurons, and neurons responded appropriately to convulsant agents. Furthermore, we successfully analyzed parameters for in vitro to in vivo extrapolation, i.e., low-frequency components and synaptic propagation velocity of the signal, potentially reflecting neural network functions from neurons cultured on SCAD device. Finally, we measured the axonal conduction velocity of peripheral neurons. Conclusions: Neurons cultured on SCAD devices might constitute a reliable in vitro platform to investigate neuron functions, drug efficacy and toxicity, and neuropathological mechanisms by MEA.},
keywords = {HD-MEA, IPSC, MaxOne, Neuronal cell culture, Organoids, Primary Neuronal Cell Culture},
pubstate = {published},
tppubtype = {article}
}
Microelectrode array (MEA) systems are valuable for in vitro assessment of neurotoxicity and drug efficiency. However, several difficulties such as protracted functional maturation and high experimental costs hinder the use of MEA analysis requiring human induced pluripotent stem cells (hiPSCs). Neural network functional parameters are also needed for in vitro to in vivo extrapolation.
Methods
In the present study, we produced a cost effective nanofiber culture platform, the SCAD device, for long-term culture of hiPSC-derived neurons and primary peripheral neurons. The notable advantage of SCAD device is convenient application on multiple MEA systems for neuron functional analysis.
Results
We showed that the SCAD device could promote functional maturation of cultured hiPSC-derived neurons, and neurons responded appropriately to convulsant agents. Furthermore, we successfully analyzed parameters for in vitro to in vivo extrapolation, i.e., low-frequency components and synaptic propagation velocity of the signal, potentially reflecting neural network functions from neurons cultured on SCAD device. Finally, we measured the axonal conduction velocity of peripheral neurons. Conclusions: Neurons cultured on SCAD devices might constitute a reliable in vitro platform to investigate neuron functions, drug efficacy and toxicity, and neuropathological mechanisms by MEA.
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}
}
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#articleInformation},
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 = {CMOS, HD-MEA, IPSC, MaxOne, Primary Neuronal Cell Culture},
pubstate = {published},
tppubtype = {article}
}
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}
}
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}
}
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}
}
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}
}
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.
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}
}
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.
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}
}
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}
}
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}
}
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}
}
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}
}
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}
}
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}
}
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}
}
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}
}
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}
}
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}
}
2021
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}
}
2020
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}
}
2019
title = {Evaluation of Conduction Properties of Sensory Axons with High-Density Microelectrode Array},
author = {Kenta Shimba and Takahiro Asahina and Koji Sakai and Yasuhiko JImbo and Kiyoshi Kotani},
url = {https://ieeexplore.ieee.org/abstract/document/8990233},
doi = {10.1109/BMEiCON47515.2019.8990233},
year = {2019},
date = {2019-11-20},
abstract = {In vitro modeling of neurodegenerative disorder is a promising method for developing new treatment. However, little is known about myelination and subsequent increase of conduction velocity in vitro. Here, we aim to develop a new method for evaluating salutatory conduction from myelinated sensory axons. First, sensory neurons and Schwann cells were cultured on high-density microelectrode array chips. Myelin sheath formation was confirmed with immunocytochemistry. Axonal signal was detected, and instantaneous conduction velocity was evaluated. As a result, we observed that relatively fast conduction sites between slow conduction sites. Our method is suitable for evaluating conduction properties of sensory axons.},
keywords = {HD-MEA},
pubstate = {published},
tppubtype = {conference}
}
title = {Large-Scale Mapping of Axonal Arbors Using High-Density Microelectrode Arrays},
author = {Bullmann, Torsten; Radivojevic, Milos; Huber, Stefan T: Deligkaris, Kosmas; Hierlemann, Andreas; Frey, Urs},
url = {https://www.frontiersin.org/articles/10.3389/fncel.2019.00404/full},
doi = {10.3389/fncel.2019.00404},
issn = {1662-5102},
year = {2019},
date = {2019-09-06},
journal = {Frontiers in Cellular Neuroscience },
volume = {13},
abstract = {Understanding the role of axons in neuronal information processing is a fundamental task in neuroscience. Over the last years, sophisticated patch-clamp investigations have provided unexpected and exciting data on axonal phenomena and functioning, but there is still a need for methods to investigate full axonal arbors at sufficient throughput. Here, we present a new method for the simultaneous mapping of the axonal arbors of a large number of individual neurons, which relies on their extracellular signals that have been recorded with high-density microelectrode arrays (HD-MEAs). The segmentation of axons was performed based on the local correlation of extracellular signals. Comparison of the results with both, ground truth and receiver operator characteristics, shows that the new segmentation method outperforms previously used methods. Using a standard HD-MEA, we mapped the axonal arbors of 68 neurons in <6 h. The fully automated method can be extended to new generations of HD-MEAs with larger data output and is estimated to provide data of axonal arbors of thousands of neurons within recording sessions of a few hours.},
keywords = {Axonal Arbors, HD-MEA},
pubstate = {published},
tppubtype = {article}
}
title = {Classification of Inhibitory and Excitatory Neurons of Dissociated Cultures Based on Action Potential Waveforms on High-density CMOS Microelectrode Arrays},
author = {Takeshi Mita and Douglas J. Bakkum and Urs Frey and Andreas Hierlemann and Ryohei Kanzaki and Hirokazu Takahashi },
url = {https://www.jstage.jst.go.jp/article/ieejeiss/139/5/139_615/_article/-char/en},
doi = {10.1541/ieejeiss.139.615},
issn = {1348-8155},
year = {2019},
date = {2019-05-01},
journal = {IEEJ Transactions on Electronics, Information and Systems},
volume = {139},
number = {5},
pages = {615-624},
abstract = {Electrophysiological data from in vivo and slice preparations show that inhibitory neurons had shorter duration action potentials (AP) than excitatory neurons. However, this criterion has not yet been established in dissociated cultured neurons. In the present study, we used a high-density CMOS microelectrode array to extracellularly investigate neural signals in primary dissociated cultures of rat neocortex, and we characterized AP waveforms to discriminate excitatory and inhibitory neurons. The CMOS array offers the possibility to acquire comprehensive spatio-temporal neural activity patterns with 11,011 electrodes in about 2×1.75 mm2 area at 20-kHz sampling rate. The waveforms of APs were investigated around cell bodies of neurons, which were classified into either excitatory neurons or inhibitory neurons on the basis of MAP2 and GABA immunostaining images. Consistent with previous in vivo and slice studies, we demonstrated that AP waveforms of inhibitory neurons had shorter durations and recovery time than those of excitatory neurons. The discrimination accuracy was around 0.9 in the receiver-operating characteristics (ROC) analyses. Additionally, taking advantage of non-invasive CMOS recording, we investigated AP waveforms throughout development of cultures. We confirmed that APs were classified into two classes, i.e., putative excitatory and inhibitory neurons, regardless of developmental stages, and found that the duration and recovery time of AP shortened in matured cultures. Thus, AP waveforms have rich information about cell types and developmental stages, which are of worth to elucidate underlying mechanisms of neuronal dynamics in spatio-temporal patterns.},
keywords = {Action Potential, HD-MEA},
pubstate = {published},
tppubtype = {article}
}
title = {Technologies to Study Action Potential Propagation With a Focus on HD-MEAs},
author = {Vishalini Emmenegger and Marie Engelene J. Obien and Felix Franke and Andreas Hierlemann},
url = {https://www.frontiersin.org/articles/10.3389/fncel.2019.00159/full},
doi = {10.3389/fncel.2019.00159 },
issn = {1662-5102 },
year = {2019},
date = {2019-04-26},
journal = {Frontiers in Cellular Neuroscience},
volume = {13},
pages = {1-11},
abstract = {Axons convey information in neuronal circuits via reliable conduction of action potentials from the axon initial segment to the presynaptic terminals. Recent experimental findings increasingly evidence that the axonal function is not limited to the simple transmission of action potentials. Advances in subcellular-resolution recording techniques have shown that axons display activity-dependent modulation in spike shape and conduction velocity, which influence synaptic strength and latency. We briefly review, here, how recent methodological developments facilitate the understanding of the axon physiology. We included the three most common methods, i.e. genetically encoded voltage imaging, subcellular patch-clamp and high-density microelectrode arrays (HD-MEAs). We then describe the potential of using HD-MEAs in studying axonal physiology in more detail. Due to their robustness, amenability to high-throughput and high spatiotemporal resolution, HD-MEAs can provide a direct functional electrical readout of single cells and cellular ensembles at subcellular resolution. HD-MEAs can, therefore, be employed in investigating axonal pathologies, the effects of large-scale genomic interventions (e.g., with RNAi or CRISPR) or in compound screenings. A combination of extracellular microelectrode arrays, intracellular microelectrodes and optical imaging may potentially reveal yet unexplored repertoires of axonal functions.},
keywords = {Action Potential, HD-MEA},
pubstate = {published},
tppubtype = {article}
}
2018
title = {Impedance Spectroscopy and Electrophysiological Imaging of Cells With a High-Density CMOS Microelectrode Array System},
author = {Vijay Viswam and Raziyeh Bounik and Amir Shadmani and Jelena Dragas and Cedar Urwyler and Julia Alicia Boos and Marie Engelene J. Obien and Jan Muller and Yihui Chen and Andreas Hierlemann},
url = {https://ieeexplore.ieee.org/document/8532304},
doi = {10.1109/TBCAS.2018.2881044},
issn = {1932-4545},
year = {2018},
date = {2018-11-12},
journal = {IEEE Transactions on Biomedical Circuits and Systems},
volume = {12},
number = {6},
pages = {1356-1368},
abstract = {A monolithic multi-functional CMOS microelectrode array system was developed that enables label-free electrochemical impedance spectroscopy of cells in vitro at high spatiotemporal resolution. The electrode array includes 59,760 platinum microelectrodes, densely packed within a 4.5 mm × 2.5 mm sensing region at a pitch of 13.5 μm. A total of 32 on-chip lock-in amplifiers can be used to measure the impedance of any arbitrarily chosen subset of electrodes in the array. A sinusoidal voltage, generated by an on-chip waveform generator with a frequency range from 1 Hz to 1 MHz, was applied to the reference electrode. The sensing currents through the selected recording electrodes were amplified, demodulated, filtered, and digitized to obtain the magnitude and phase information of the respective impedances. The circuitry consumes only 412 μW at 3.3 V supply voltage and occupies only 0.1 mm 2 , for each channel. The system also included 2048 extracellular action-potential recording channels on the same chip. Proof of concept measurements of electrical impedance imaging and electrophysiology recording of cardiac cells and brain slices are demonstrated in this paper. Optical and impedance images showed a strong correlation.},
keywords = {HD-MEA},
pubstate = {published},
tppubtype = {article}
}