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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. | Roos, Matthew J; Luna, Diego; Din, Dowlette-Mary Alam El; Hartung, Thomas; Smirnova, Lena; Proescher, Alex; Johnson, Erik C: Modeling Organoid Population Electrophysiology Dynamics. In: bioRxiv, 2025. (Type: Journal Article | Abstract | Links | BibTeX) @article{Roos2025, title = {Modeling Organoid Population Electrophysiology Dynamics}, author = {Matthew J. Roos and Diego Luna and Dowlette-Mary Alam El Din and Thomas Hartung and Lena Smirnova and Alex Proescher and Erik C. Johnson}, url = {https://www.biorxiv.org/content/10.1101/2025.03.02.641081v1}, doi = {10.1101/2025.03.02.641081}, year = {2025}, date = {2025-03-02}, journal = {bioRxiv}, abstract = {Improving models to investigate neurodegenerative disease, neurodevelopmental disease, neuro-toxicology and neuropharmacology is critical to improve our basic understanding of the human nervous system, as well as to accelerate discovery of interventions and drugs. Improved models of the human central nervous system could enable critical discoveries related to functional changes induced by sensory stimulation or toxic exposures. Neural organoids, complex three-dimensional cell cultures derived from adult human stem cells, have been grown with complex connectivity and neuroanatomy. Moreover, these cultures have been interfaced with bi-directional electrical stimulation and recording, as well as chemical stimulation. This effort sought to develop new computational techniques which could be applied to comparative studies using neural organoids. In particular, we adapted CEBRA, a state of the art model from the in vivo modeling literature, to generate 2D and 3D embeddings (projections into structured low-dimensional spaces) of high dimensional neural organoid electrophysiology data. This can be done in an unsupervised or semi-supervised manner. Results indicate these embeddings can be quickly and reliably generated and serve as a low-dimensional, interpretable embeddings for characterizing changes in neural organoid activity over time, as well as clustering results around known bursting phenomena. Moreover, we demonstrate that mixtures of von Mises-Fisher distributions can be used as a parametric model for these embedding spaces to enable statistics hypothesis testing. This technique may enable new types of comparative studies using neural organoids, and may be critical for creating a representation for quantitative comparison and validation of neural organoid models against human and animal data. Looking ahead, this work could allow the formulation of a new class of experiments investigating the functional impact of toxins, genetic manipulations, or pharmacological interventions on human neurons.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Improving models to investigate neurodegenerative disease, neurodevelopmental disease, neuro-toxicology and neuropharmacology is critical to improve our basic understanding of the human nervous system, as well as to accelerate discovery of interventions and drugs. Improved models of the human central nervous system could enable critical discoveries related to functional changes induced by sensory stimulation or toxic exposures. Neural organoids, complex three-dimensional cell cultures derived from adult human stem cells, have been grown with complex connectivity and neuroanatomy. Moreover, these cultures have been interfaced with bi-directional electrical stimulation and recording, as well as chemical stimulation. This effort sought to develop new computational techniques which could be applied to comparative studies using neural organoids. In particular, we adapted CEBRA, a state of the art model from the in vivo modeling literature, to generate 2D and 3D embeddings (projections into structured low-dimensional spaces) of high dimensional neural organoid electrophysiology data. This can be done in an unsupervised or semi-supervised manner. Results indicate these embeddings can be quickly and reliably generated and serve as a low-dimensional, interpretable embeddings for characterizing changes in neural organoid activity over time, as well as clustering results around known bursting phenomena. Moreover, we demonstrate that mixtures of von Mises-Fisher distributions can be used as a parametric model for these embedding spaces to enable statistics hypothesis testing. This technique may enable new types of comparative studies using neural organoids, and may be critical for creating a representation for quantitative comparison and validation of neural organoid models against human and animal data. Looking ahead, this work could allow the formulation of a new class of experiments investigating the functional impact of toxins, genetic manipulations, or pharmacological interventions on human neurons. |
| 2. | Ishimoto, Taiga; Abe, Takashi; Nakamura, Yuko; Tsuyama, Tomonori; Kondoh, Kunio; Naoto, ; Kajitani, ; Yoshida, Kaede; Takeuchi, Yuichi; Kato, Kan X; Xu, Shucheng; Koduki, Maru; Ichimura, Momoka; Itoi, Takito; Shimba, Kenta; Yamaguchi, Yoshifumi; Minami, Masabumi; Koike, Shinsuke; Kasai, Kiyoto; Ye, Jessica J; Takebayashi, Minoru; Yamagata, Kazuya; Toda, Chitoku: Chronic social defeat causes dysregulation of systemic glucose metabolism via the cerebellar fastigial nucleus. In: bioRxiv, 2025. (Type: Journal Article | Abstract | Links | BibTeX) @article{Ishimoto2025, title = {Chronic social defeat causes dysregulation of systemic glucose metabolism via the cerebellar fastigial nucleus}, author = {Taiga Ishimoto and Takashi Abe and Yuko Nakamura and Tomonori Tsuyama and Kunio Kondoh and Naoto and Kajitani and Kaede Yoshida and Yuichi Takeuchi and Kan X. Kato and Shucheng Xu and Maru Koduki and Momoka Ichimura and Takito Itoi and Kenta Shimba and Yoshifumi Yamaguchi and Masabumi Minami and Shinsuke Koike and Kiyoto Kasai and Jessica J Ye and Minoru Takebayashi and Kazuya Yamagata and Chitoku Toda}, url = {https://www.biorxiv.org/content/10.1101/2025.02.18.638938v1}, doi = {10.1101/2025.02.18.638938}, year = {2025}, date = {2025-02-19}, journal = {bioRxiv}, abstract = {Chronic psychological stress leads to hyperglycemia through the endocrine and sympathetic nervous systems, which contributes to the development of type II diabetes mellitus (T2DM). Higher plasma corticosteroids after stress is one well-established driver of insulin resistance in peripheral tissues. However, previous studies have indicated that only a fraction of patients with depression and post-traumatic disorder (PTSD) who develop T2DM exhibit hypocortisolism, so corticosteroids do not fully explain psychological stress-induced T2DM. Here, we find that chronic social defeat stress (CSDS) in mice enhances gluconeogenesis, which is accompanied by a decrease in plasma insulin, an increase in plasma catecholamines, and a drop in plasma corticosterone levels. We further reveal that these metabolic and endocrinological changes are mediated by the activation of neurons projecting from the cerebellar fastigial nucleus (FN) to the medullary parasolitary nucleus (PSol). These neurons are crucial in shifting the body’s primary energy source from glucose to lipids. Additionally, data from patients with depression reveal correlations between the presence of cerebellar abnormalities and both worsening depressive symptoms and elevated HbA1c levels. These findings highlight a previously unappreciated role of the cerebellum in metabolic regulation and its importance as a potential therapeutic target in depression, PTSD, and similar psychological disorders.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Chronic psychological stress leads to hyperglycemia through the endocrine and sympathetic nervous systems, which contributes to the development of type II diabetes mellitus (T2DM). Higher plasma corticosteroids after stress is one well-established driver of insulin resistance in peripheral tissues. However, previous studies have indicated that only a fraction of patients with depression and post-traumatic disorder (PTSD) who develop T2DM exhibit hypocortisolism, so corticosteroids do not fully explain psychological stress-induced T2DM. Here, we find that chronic social defeat stress (CSDS) in mice enhances gluconeogenesis, which is accompanied by a decrease in plasma insulin, an increase in plasma catecholamines, and a drop in plasma corticosterone levels. We further reveal that these metabolic and endocrinological changes are mediated by the activation of neurons projecting from the cerebellar fastigial nucleus (FN) to the medullary parasolitary nucleus (PSol). These neurons are crucial in shifting the body’s primary energy source from glucose to lipids. Additionally, data from patients with depression reveal correlations between the presence of cerebellar abnormalities and both worsening depressive symptoms and elevated HbA1c levels. These findings highlight a previously unappreciated role of the cerebellum in metabolic regulation and its importance as a potential therapeutic target in depression, PTSD, and similar psychological disorders. |
| 3. | Zhao, Jianyi; Wu, Linshi; Cai, Gang; Ou, Dan; Liao, Keman; Yang, Jian; Zhou, Li; Huang, Renhua; Lin, Shukai; Huang, Xi; Lv, Qi; Chen, Juxiang; Cao, Lu; Chen, Jiayi; Lin, Yingying: Targeting PGE2 mediated senescent neuron improves tumour therapy. In: Neuro-Oncology, 2025. (Type: Journal Article | Abstract | Links | BibTeX) @article{Zhao2025, title = {Targeting PGE2 mediated senescent neuron improves tumour therapy}, author = {Jianyi Zhao and Linshi Wu and Gang Cai and Dan Ou and Keman Liao and Jian Yang and Li Zhou and Renhua Huang and Shukai Lin and Xi Huang and Qi Lv and Juxiang Chen and Lu Cao and Jiayi Chen and Yingying Lin}, url = {https://doi.org/10.1093/neuonc/noaf045}, doi = {10.1093/neuonc/noaf045}, year = {2025}, date = {2025-02-18}, journal = {Neuro-Oncology}, abstract = {Recent studies have highlighted bidirectional signalling between tumours and neurons; however, the interactions between tumours and neurons in response to radio-/chemotherapy remain obscure, which hampers the tumour treatment.Glioblastoma organoids (GBOs) and primary neuron coculture, targeted metabonomics, RNA pulldown, mass spectrum, co-immunoprecipitation, RNA-sequencing, transcript/protein validations and multi-electrode arrays were performed to analyse neuron-tumour interaction in response to therapy. In vivo validations were conducted in orthotopic mouse models. Diagnostic and prognostic values were evaluated in serum, tissue-microarray as well as TCGA.GBOs recruited and induced pro-tumour-survival senescent neurons upon radiation/chemotherapeutic treatment. Targeted metabonomics revealed that significantly increased tumour-derived prostaglandin E2 (PGE2) induced neuronal senescence phenotype. Screening of enzymes involved in PGE2 synthesis identified prostaglandin E synthase 3 (PTGES3) as the key enzyme responsible for PGE2 upregulation. Biochemical studies revealed that irradiation or chemotherapeutic drug-triggered asparagine endopeptidase (AEP) specifically cleaved eIF4A1 to produce teIF4A1-C, which dissociated from DDX6 and recruited eIF4A3 and PABPN1 to promote the mRNA stability of PTGES3. Elevated PGE2 reciprocally enhanced AEP expression. Inhibiting PGE2 or AEP reduced neuronal senescence and delayed tumour progression. Strikingly, single-cell analysis further showed that expressions of AEP/PTGES3/EIF4A1 in tumour cells were consistent with senescent neuronal CDKN1A in high-neuronal-connectivity glioblastoma. The serum PGE2 concentration was elevated after radiation and higher in resistant glioblastoma patients. High expression of PTGES3 was associated with a poor prognosis.Our study revealed that the AEP/PGE2 feedback loop modulates tumour-induced neuronal senescence upon radio-/chemotherapy and highlight the therapeutic value to improve tumour therapy.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recent studies have highlighted bidirectional signalling between tumours and neurons; however, the interactions between tumours and neurons in response to radio-/chemotherapy remain obscure, which hampers the tumour treatment.Glioblastoma organoids (GBOs) and primary neuron coculture, targeted metabonomics, RNA pulldown, mass spectrum, co-immunoprecipitation, RNA-sequencing, transcript/protein validations and multi-electrode arrays were performed to analyse neuron-tumour interaction in response to therapy. In vivo validations were conducted in orthotopic mouse models. Diagnostic and prognostic values were evaluated in serum, tissue-microarray as well as TCGA.GBOs recruited and induced pro-tumour-survival senescent neurons upon radiation/chemotherapeutic treatment. Targeted metabonomics revealed that significantly increased tumour-derived prostaglandin E2 (PGE2) induced neuronal senescence phenotype. Screening of enzymes involved in PGE2 synthesis identified prostaglandin E synthase 3 (PTGES3) as the key enzyme responsible for PGE2 upregulation. Biochemical studies revealed that irradiation or chemotherapeutic drug-triggered asparagine endopeptidase (AEP) specifically cleaved eIF4A1 to produce teIF4A1-C, which dissociated from DDX6 and recruited eIF4A3 and PABPN1 to promote the mRNA stability of PTGES3. Elevated PGE2 reciprocally enhanced AEP expression. Inhibiting PGE2 or AEP reduced neuronal senescence and delayed tumour progression. Strikingly, single-cell analysis further showed that expressions of AEP/PTGES3/EIF4A1 in tumour cells were consistent with senescent neuronal CDKN1A in high-neuronal-connectivity glioblastoma. The serum PGE2 concentration was elevated after radiation and higher in resistant glioblastoma patients. High expression of PTGES3 was associated with a poor prognosis.Our study revealed that the AEP/PGE2 feedback loop modulates tumour-induced neuronal senescence upon radio-/chemotherapy and highlight the therapeutic value to improve tumour therapy. |
| 4. | Ikeda, Narumitsu; Akita, Dai; Takahashi, Hirokazu: Emergent functions of noise-driven spontaneous activity: Homeostatic maintenance of criticality and memory consolidation. In: arXiv, 2025. (Type: Journal Article | Abstract | Links | BibTeX) @article{Ikeda2025, title = {Emergent functions of noise-driven spontaneous activity: Homeostatic maintenance of criticality and memory consolidation}, author = {Narumitsu Ikeda and Dai Akita and Hirokazu Takahashi}, url = {http://arxiv.org/abs/2502.10946}, doi = {10.48550/arXiv.2502.10946}, year = {2025}, date = {2025-02-16}, journal = {arXiv}, abstract = {Unlike digital computers, the brain exhibits spontaneous activity even during complete rest, despite the evolutionary pressure for energy efficiency. Inspired by the critical brain hypothesis, which proposes that the brain operates optimally near a critical point of phase transition in the dynamics of neural networks to improve computational efficiency, we postulate that spontaneous activity plays a homeostatic role in the development and maintenance of criticality. Criticality in the brain is associated with the balance between excitatory and inhibitory synaptic inputs (EI balance), which is essential for maintaining neural computation performance. Here, we hypothesize that both criticality and EI balance are stabilized by appropriate noise levels and spike-timing-dependent plasticity (STDP) windows. Using spiking neural network (SNN) simulations and in vitro experiments with dissociated neuronal cultures, we demonstrated that while repetitive stimuli transiently disrupt both criticality and EI balance, spontaneous activity can develop and maintain these properties and prolong the fading memory of past stimuli. Our findings suggest that the brain may achieve self-optimization and memory consolidation as emergent functions of noise-driven spontaneous activity. This noise-harnessing mechanism provides insights for designing energy-efficient neural networks, and may explain the critical function of sleep in maintaining homeostasis and consolidating memory.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Unlike digital computers, the brain exhibits spontaneous activity even during complete rest, despite the evolutionary pressure for energy efficiency. Inspired by the critical brain hypothesis, which proposes that the brain operates optimally near a critical point of phase transition in the dynamics of neural networks to improve computational efficiency, we postulate that spontaneous activity plays a homeostatic role in the development and maintenance of criticality. Criticality in the brain is associated with the balance between excitatory and inhibitory synaptic inputs (EI balance), which is essential for maintaining neural computation performance. Here, we hypothesize that both criticality and EI balance are stabilized by appropriate noise levels and spike-timing-dependent plasticity (STDP) windows. Using spiking neural network (SNN) simulations and in vitro experiments with dissociated neuronal cultures, we demonstrated that while repetitive stimuli transiently disrupt both criticality and EI balance, spontaneous activity can develop and maintain these properties and prolong the fading memory of past stimuli. Our findings suggest that the brain may achieve self-optimization and memory consolidation as emergent functions of noise-driven spontaneous activity. This noise-harnessing mechanism provides insights for designing energy-efficient neural networks, and may explain the critical function of sleep in maintaining homeostasis and consolidating memory. |
| 5. | Sifringer, Léo; Fratzl, Alex; Clément, Blandine F; Chansoria, Parth; Mönkemöller, Leah S; Duru, Jens; Ihle, Stephan J; Steffens, Simon; Beltraminelli, Anna; Ceylan, Eylul; Hengsteler, Julian; Maurer, Benedikt; Weaver, Sean M; Tringides, Christina M; Vulić, Katarina; Madduri, Srinivas; Zenobi-Wong, Marcy; Roska, Botond; Vörös, János; Ruff, Tobias: An Implantable Biohybrid Neural Interface Toward Synaptic Deep Brain Stimulation. In: Advanced Functional Materials, 2025. (Type: Journal Article | Abstract | Links | BibTeX) @article{Sifringer2025, title = {An Implantable Biohybrid Neural Interface Toward Synaptic Deep Brain Stimulation}, author = {Léo Sifringer and Alex Fratzl and Blandine F. Clément and Parth Chansoria and Leah S. Mönkemöller and Jens Duru and Stephan J. Ihle and Simon Steffens and Anna Beltraminelli and Eylul Ceylan and Julian Hengsteler and Benedikt Maurer and Sean M. Weaver and Christina M. Tringides and Katarina Vulić and Srinivas Madduri and Marcy Zenobi-Wong and Botond Roska and János Vörös and Tobias Ruff}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adfm.202416557}, doi = {10.1002/adfm.202416557}, year = {2025}, date = {2025-02-09}, journal = {Advanced Functional Materials}, abstract = {In patients with sensory nerve loss, such as those experiencing optic nerve damage that leads to vision loss, the thalamus no longer receives the corresponding sensory input. To restore functional sensory input, it is necessary to bypass the damaged circuits, which can be achieved by directly stimulating the appropriate sensory thalamic nuclei. However, available deep brain stimulation electrodes do not provide the resolution required for effective sensory restoration. Therefore, this work develops an implantable biohybrid neural interface aimed at innervating and synaptically stimulating deep brain targets. The interface combines a stretchable stimulation array with an aligned microfluidic axon guidance system seeded with neural spheroids to facilitate the development of a 3 mm long nerve-like structure. A bioresorbable hydrogel nerve conduit is used as a bridge between the tissue and the biohybrid implant. Stimulation of the spheroids within the biohybrid structure in vitro and use of high-density CMOS microelectrode arrays show faithful activity conduction across the device. Although functional in vivo innervation and synapse formation has not yet been achieved in this study, implantation of the biohybrid nerve onto the mouse cortex shows that neural spheroids grow axons in vivo and remain functionally active for more than 22 days post-implantation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In patients with sensory nerve loss, such as those experiencing optic nerve damage that leads to vision loss, the thalamus no longer receives the corresponding sensory input. To restore functional sensory input, it is necessary to bypass the damaged circuits, which can be achieved by directly stimulating the appropriate sensory thalamic nuclei. However, available deep brain stimulation electrodes do not provide the resolution required for effective sensory restoration. Therefore, this work develops an implantable biohybrid neural interface aimed at innervating and synaptically stimulating deep brain targets. The interface combines a stretchable stimulation array with an aligned microfluidic axon guidance system seeded with neural spheroids to facilitate the development of a 3 mm long nerve-like structure. A bioresorbable hydrogel nerve conduit is used as a bridge between the tissue and the biohybrid implant. Stimulation of the spheroids within the biohybrid structure in vitro and use of high-density CMOS microelectrode arrays show faithful activity conduction across the device. Although functional in vivo innervation and synapse formation has not yet been achieved in this study, implantation of the biohybrid nerve onto the mouse cortex shows that neural spheroids grow axons in vivo and remain functionally active for more than 22 days post-implantation. |
| 6. | Lee, Jaeyong; Liu, Jia: Flexible and stretchable bioelectronics for organoids. In: Springer Nature Link, 2025. (Type: Journal Article | Abstract | Links | BibTeX) @article{Lee2025, title = {Flexible and stretchable bioelectronics for organoids}, author = {Jaeyong Lee and Jia Liu}, url = {https://doi.org/10.1007/s44258-024-00046-y}, doi = {10.1007/s44258-024-00046-y}, year = {2025}, date = {2025-02-01}, journal = {Springer Nature Link}, abstract = {Organoids have gained significant interest due to their ability to recapitulate the structural, molecular, and functional complexity of corresponding organs. While methods have been developed to characterize and benchmark organoid structural and molecular properties, capturing the functional development and maturation of organoids remains challenging. To address this, the development of multifunctional bioelectronics for interfacing with organoids has been actively pursued. However, conventional electronics face limitations in achieving multifunctional recording and control across the entire three-dimensional (3D) volume of organoids in a long-term stable manner due to the large morphological and cellular composition changes during development. In this review, we first discuss the application of conventional electronics for organoid interfacing. We then focus on the development of flexible and stretchable electronics designed to create organoid/electronics hybrids for chronically stable interfaces. We also review recent advancements in flexible multifunctional electronics for charting multimodal cell activities throughout development. Furthermore, we explore the integration of flexible bioelectronics with other characterization modalities for comprehensive multimodal charting of cells within 3D tissues. Finally, we discuss the potential of integrating artificial intelligence into the organoid system through embedded electronics, harnessing organoid intelligence for biosymbiotic computational systems. These advancements could provide valuable tools for characterizing organoid functional development and maturation, establishing patient-specific models, developing therapeutic opportunities, and exploring novel computational strategies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Organoids have gained significant interest due to their ability to recapitulate the structural, molecular, and functional complexity of corresponding organs. While methods have been developed to characterize and benchmark organoid structural and molecular properties, capturing the functional development and maturation of organoids remains challenging. To address this, the development of multifunctional bioelectronics for interfacing with organoids has been actively pursued. However, conventional electronics face limitations in achieving multifunctional recording and control across the entire three-dimensional (3D) volume of organoids in a long-term stable manner due to the large morphological and cellular composition changes during development. In this review, we first discuss the application of conventional electronics for organoid interfacing. We then focus on the development of flexible and stretchable electronics designed to create organoid/electronics hybrids for chronically stable interfaces. We also review recent advancements in flexible multifunctional electronics for charting multimodal cell activities throughout development. Furthermore, we explore the integration of flexible bioelectronics with other characterization modalities for comprehensive multimodal charting of cells within 3D tissues. Finally, we discuss the potential of integrating artificial intelligence into the organoid system through embedded electronics, harnessing organoid intelligence for biosymbiotic computational systems. These advancements could provide valuable tools for characterizing organoid functional development and maturation, establishing patient-specific models, developing therapeutic opportunities, and exploring novel computational strategies. |
| 7. | Nakamuta, Asahi; Akita, Dai; Zhang, He; Kawahara, Yuta; Takahashi, Hirokazu; Teramae, Jun-nosuke: Self-organization of high-dimensional geometry of neural activity in culture. In: bioRxiv, 2025. (Type: Journal Article | Abstract | Links | BibTeX) @article{Nakamuta2025, title = {Self-organization of high-dimensional geometry of neural activity in culture}, author = {Asahi Nakamuta and Dai Akita and He Zhang and Yuta Kawahara and Hirokazu Takahashi and Jun-nosuke Teramae}, url = {https://www.biorxiv.org/content/10.1101/2025.01.14.630383v1}, doi = {10.1101/2025.01.14.630383}, year = {2025}, date = {2025-01-16}, journal = {bioRxiv}, abstract = {A vast number of neurons exhibit high-dimensional coordination for brain computation, both in processing sensory input and in generating spontaneous activity without external stimuli. Recent advancements in large-scale recordings have revealed that this high-dimensional population activity exhibits a scale-free structure, characterized by power law and distinct spatial patterns in principal components (PCs). However, the mechanisms underlying the formation of this high-dimensional neural coordination remain poorly understood. Specifically, it is unclear whether the characteristic high-dimensional structure of population activity emerges through self-organization or is shaped by the learning of sensory stimuli in animals. To address this question and clearly differentiate between these two possibilities, we investigated large-scale neural activity in dissociated neuronal culture using high-density multi-electrode arrays. Our findings demonstrate that the high-dimensional structure of neural activity self-organizes during network development in the absence of explicit sensory stimuli provided to animals. As the cultures mature, the PC variance exhibits a power-law decay, and the spatial structures of PCs transition from global to localized patterns, driven by the temporal correlations of neural activity. Furthermore, we observed an unexpected co-occurrence between the power-law decay in PCA and neuronal avalanches, suggesting a link between self-organized criticality and high-dimensional activity. Using a recurrent neural network model, we show that both phenomena can arise from biologically plausible heavy-tailed synaptic connectivity. By highlighting a developmental origin of the high-dimensional structure of neural activity, these findings deepen our understanding of how coordinated neural computations are achieved in the brain.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A vast number of neurons exhibit high-dimensional coordination for brain computation, both in processing sensory input and in generating spontaneous activity without external stimuli. Recent advancements in large-scale recordings have revealed that this high-dimensional population activity exhibits a scale-free structure, characterized by power law and distinct spatial patterns in principal components (PCs). However, the mechanisms underlying the formation of this high-dimensional neural coordination remain poorly understood. Specifically, it is unclear whether the characteristic high-dimensional structure of population activity emerges through self-organization or is shaped by the learning of sensory stimuli in animals. To address this question and clearly differentiate between these two possibilities, we investigated large-scale neural activity in dissociated neuronal culture using high-density multi-electrode arrays. Our findings demonstrate that the high-dimensional structure of neural activity self-organizes during network development in the absence of explicit sensory stimuli provided to animals. As the cultures mature, the PC variance exhibits a power-law decay, and the spatial structures of PCs transition from global to localized patterns, driven by the temporal correlations of neural activity. Furthermore, we observed an unexpected co-occurrence between the power-law decay in PCA and neuronal avalanches, suggesting a link between self-organized criticality and high-dimensional activity. Using a recurrent neural network model, we show that both phenomena can arise from biologically plausible heavy-tailed synaptic connectivity. By highlighting a developmental origin of the high-dimensional structure of neural activity, these findings deepen our understanding of how coordinated neural computations are achieved in the brain. |
| 8. | Chow, Siu Yu A; Hu, Huaruo; Duenki, Tomoya; Asakura, Takuya; Sugimura, Sota; Ikeuchi, Yoshiho: Repetitive Stimulation Modifies Network Characteristics of Neural Organoid Circuits. In: bioRxiv, 2025. (Type: Journal Article | Abstract | Links | BibTeX) @article{Chow2025, title = {Repetitive Stimulation Modifies Network Characteristics of Neural Organoid Circuits}, author = {Siu Yu A. Chow and Huaruo Hu and Tomoya Duenki and Takuya Asakura and Sota Sugimura and Yoshiho Ikeuchi}, url = {https://www.biorxiv.org/content/10.1101/2025.01.16.633310v1}, doi = {https://doi.org/10.1101/2025.01.16.633310}, year = {2025}, date = {2025-01-16}, journal = {bioRxiv}, abstract = {Neural organoids form complex networks but lack external stimuli and hierarchical structures crucial for refining functional microcircuits. In this study, we modeled the hierarchical and modular network organization by connecting multiple organoids and tested if the connection enhances the external stimuli-induced network refinement. We cultured networks of one, two, or three organoids on high-density microelectrode arrays, applied repetitive stimulation at two input locations from the microelectrodes, and monitored emergence of output signals that can decode the stimulus locations with machine learning algorithms. After two weeks of daily stimulation, networks of three organoids showed significantly higher stimulus decoding capability compared to the simpler one- or two-organoid networks. Long-term stimulation induced pronounced changes in the three-organoid network’s response patterns, spontaneous activity, and inter- and intra-organoid functional connectivity. These findings underscore the importance of hierarchical network organization, e.g. creating distinct subnetworks with specialized roles, for stimuli-induced formation of circuits with robust input-output functionality.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Neural organoids form complex networks but lack external stimuli and hierarchical structures crucial for refining functional microcircuits. In this study, we modeled the hierarchical and modular network organization by connecting multiple organoids and tested if the connection enhances the external stimuli-induced network refinement. We cultured networks of one, two, or three organoids on high-density microelectrode arrays, applied repetitive stimulation at two input locations from the microelectrodes, and monitored emergence of output signals that can decode the stimulus locations with machine learning algorithms. After two weeks of daily stimulation, networks of three organoids showed significantly higher stimulus decoding capability compared to the simpler one- or two-organoid networks. Long-term stimulation induced pronounced changes in the three-organoid network’s response patterns, spontaneous activity, and inter- and intra-organoid functional connectivity. These findings underscore the importance of hierarchical network organization, e.g. creating distinct subnetworks with specialized roles, for stimuli-induced formation of circuits with robust input-output functionality. |
| 9. | Küchler, Joël; Vulíc, Katarina; Yao, Haotian; Valmaggia, Christian; Ihle, Stephan J; Weaver, Sean; Vörös, János: Engineered Biological Neural Networks as Basic Logic Operators. In: bioRxiv, 2025. (Type: Journal Article | Abstract | Links | BibTeX) @article{Küchler2025, title = {Engineered Biological Neural Networks as Basic Logic Operators}, author = {Joël Küchler and Katarina Vulíc and Haotian Yao and Christian Valmaggia and Stephan J. Ihle and Sean Weaver and János Vörös }, url = {https://www.biorxiv.org/content/10.1101/2024.12.23.630065v2}, doi = {https://doi.org/10.1101/2024.12.23.630065}, year = {2025}, date = {2025-01-15}, journal = {bioRxiv}, abstract = {We present an in vitro neuronal network with controlled topology capable of performing basic Boolean computations, such as NAND and OR. Neurons cultured within polydimethylsiloxane (PDMS) microstructures on high-density microelectrode arrays (HD-MEAs) enable precise interaction through extracellular voltage stimulation and spiking activity recording. The architecture of our system allows for creating non-linear functions with two inputs and one output. Additionally, we analyze various encoding schemes, comparing the limitations of rate coding with the potential advantages of spike-timing-based coding strategies. This work contributes to the advancement of hybrid intelligence and biocomputing by offering insights into neural information encoding and decoding with the potential to create fully biological computational systems. }, keywords = {}, pubstate = {published}, tppubtype = {article} } We present an in vitro neuronal network with controlled topology capable of performing basic Boolean computations, such as NAND and OR. Neurons cultured within polydimethylsiloxane (PDMS) microstructures on high-density microelectrode arrays (HD-MEAs) enable precise interaction through extracellular voltage stimulation and spiking activity recording. The architecture of our system allows for creating non-linear functions with two inputs and one output. Additionally, we analyze various encoding schemes, comparing the limitations of rate coding with the potential advantages of spike-timing-based coding strategies. This work contributes to the advancement of hybrid intelligence and biocomputing by offering insights into neural information encoding and decoding with the potential to create fully biological computational systems. |
| 10. | Setsu, Selena; Morimoto, Satoru; Nakamura, Shiho; Ozawa, Fumiko; Utami, Kagistia Hana; Nishiyama, Ayumi; Suzuki, Naoki; Aoki, Masashi; Takeshita, Yukio; Tomari, Yukihide; Okano, Hideyuki: Swift induction of human spinal lower motor neurons and robust ALS cell screening via single-cell imaging. In: Stem Cell Reports, 2025. (Type: Journal Article | Abstract | Links | BibTeX) @article{Setsu2025, title = {Swift induction of human spinal lower motor neurons and robust ALS cell screening via single-cell imaging}, author = {Selena Setsu and Satoru Morimoto and Shiho Nakamura and Fumiko Ozawa and Kagistia Hana Utami and Ayumi Nishiyama and Naoki Suzuki and Masashi Aoki and Yukio Takeshita and Yukihide Tomari and Hideyuki Okano}, url = {https://www.cell.com/stem-cell-reports/abstract/S2213-6711(24)00321-7}, doi = {10.1016/j.stemcr.2024.11.007}, year = {2025}, date = {2025-01-14}, journal = {Stem Cell Reports}, abstract = {This study introduces a novel method for rapidly and efficiently inducing human spinal lower motor neurons (LMNs) from induced pluripotent stem cells (iPSCs) to eventually elucidate the pathomechanisms of amyotrophic lateral sclerosis (ALS) and facilitate drug screening. Previous methods were limited by low induction efficiency, poor LMN purity, or labor-intensive induction and evaluation processes. Our protocol overcomes these challenges, achieving around 80% induction efficiency within just two weeks by combining a small molecule-based approach with transcription factor transduction. Moreover, to exclude non-LMN cells from the analysis, we utilized timelapse microscopy and machine learning to analyze the morphology and viability of iPSC-derived LMNs on a single-cell basis, establishing an effective pathophysiological evaluation system. This rapid, efficient, and streamlined protocol, along with our single-cell-based evaluation method, enables large-scale analysis and drug screening using iPSC-derived motor neurons.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This study introduces a novel method for rapidly and efficiently inducing human spinal lower motor neurons (LMNs) from induced pluripotent stem cells (iPSCs) to eventually elucidate the pathomechanisms of amyotrophic lateral sclerosis (ALS) and facilitate drug screening. Previous methods were limited by low induction efficiency, poor LMN purity, or labor-intensive induction and evaluation processes. Our protocol overcomes these challenges, achieving around 80% induction efficiency within just two weeks by combining a small molecule-based approach with transcription factor transduction. Moreover, to exclude non-LMN cells from the analysis, we utilized timelapse microscopy and machine learning to analyze the morphology and viability of iPSC-derived LMNs on a single-cell basis, establishing an effective pathophysiological evaluation system. This rapid, efficient, and streamlined protocol, along with our single-cell-based evaluation method, enables large-scale analysis and drug screening using iPSC-derived motor neurons. |
| 11. | Vinci, Ersilia; Beretta, Stefania; Colombo, Veronica; Zippo, Antonio; Catanese, Alberto; Wiegreffe, Christoph; Britsch, Stefan; Boeckers, Tobias; Verpelli, Chiara; Sala, Carlo: Regulation of Dendrite and Dendritic Spine Formation by TCF20. In: Journal of Neurochemistry, 2025. (Type: Journal Article | Abstract | Links | BibTeX) @article{Vinci2025, title = {Regulation of Dendrite and Dendritic Spine Formation by TCF20}, author = {Ersilia Vinci and Stefania Beretta and Veronica Colombo and Antonio Zippo and Alberto Catanese and Christoph Wiegreffe and Stefan Britsch and Tobias Boeckers and Chiara Verpelli and Carlo Sala}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jnc.16297}, doi = {10.1111/jnc.16297}, year = {2025}, date = {2025-01-13}, journal = {Journal of Neurochemistry}, abstract = {Mutations in the Transcription Factor 20 (TCF20) have been identified in patients with autism spectrum disorders (ASDs), intellectual disabilities (IDs), and other neurological issues. Recently, a new syndrome called TCF20-associated neurodevelopmental disorders (TAND) has been described, with specific clinical features. While TCF20's role in the neurogenesis of mouse embryos has been reported, little is known about its molecular function in neurons. In this study, we demonstrate that TCF20 is expressed in all analyzed brain regions in mice, and its expression increases during brain development but decreases in muscle tissue. Our findings suggest that TCF20 plays a central role in dendritic arborization and dendritic spine formation processes. RNA sequencing analysis revealed a downregulation of pre- and postsynaptic pathways in TCF20 knockdown neurons. We also found decreased levels of GABRA1, BDNF, PSD-95, and c-Fos in total homogenates and in synaptosomal preparations of knockdown TCF20 rat cortical cultures. Furthermore, synaptosomal preparations of knockdown TCF20 rat cortical cultures showed significant downregulation of GluN2B and GABRA5, while GluA2 was significantly upregulated. Overall, our data suggest that TCF20 plays an essential role in neuronal development and function by modulating the expression of proteins involved in dendrite and synapse formation and function.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Mutations in the Transcription Factor 20 (TCF20) have been identified in patients with autism spectrum disorders (ASDs), intellectual disabilities (IDs), and other neurological issues. Recently, a new syndrome called TCF20-associated neurodevelopmental disorders (TAND) has been described, with specific clinical features. While TCF20's role in the neurogenesis of mouse embryos has been reported, little is known about its molecular function in neurons. In this study, we demonstrate that TCF20 is expressed in all analyzed brain regions in mice, and its expression increases during brain development but decreases in muscle tissue. Our findings suggest that TCF20 plays a central role in dendritic arborization and dendritic spine formation processes. RNA sequencing analysis revealed a downregulation of pre- and postsynaptic pathways in TCF20 knockdown neurons. We also found decreased levels of GABRA1, BDNF, PSD-95, and c-Fos in total homogenates and in synaptosomal preparations of knockdown TCF20 rat cortical cultures. Furthermore, synaptosomal preparations of knockdown TCF20 rat cortical cultures showed significant downregulation of GluN2B and GABRA5, while GluA2 was significantly upregulated. Overall, our data suggest that TCF20 plays an essential role in neuronal development and function by modulating the expression of proteins involved in dendrite and synapse formation and function. |
| 12. | Branco, Mariana A; Nunes, Mafalda Marques; Rayagra, Ana Luísa; Tenreiro, Miguel F; Cabral, Joaquim M S; Diogo, Maria Margarida: Recreating Coronary Vascularization and Sympathetic Innervation of Myocardium on a Human Pluripotent Stem Cell-derived Heart Organoid. In: bioRxiv, 2025. (Type: Journal Article | Abstract | Links | BibTeX) @article{Branco2025, title = {Recreating Coronary Vascularization and Sympathetic Innervation of Myocardium on a Human Pluripotent Stem Cell-derived Heart Organoid}, author = {Mariana A. Branco and Mafalda Marques Nunes and Ana Luísa Rayagra and Miguel F. Tenreiro and Joaquim M.S. Cabral and Maria Margarida Diogo}, url = {http://biorxiv.org/lookup/doi/10.1101/2025.01.10.632325}, doi = {10.1101/2025.01.10.632325}, year = {2025}, date = {2025-01-10}, journal = {bioRxiv}, abstract = {Coronary vascularization and sympathetic innervation of the myocardium is a concomitant event during embryonic heart development and both systems are crucial to ensure normal adult heart function. Here we describe a self-organized hiPSC-derived heart organoid that recreates both the coronary vascular plexus and the sympathetic neuronal network of the ventricle myocardium, with a physiologically relevant in-vivo-like structural organization and function. Through modulation of PDGF-β and VEGF signalling pathways, we attained a heart organoid that incorporates 1) an external epicardial layer (mesothelium) of DACH1, NR2F2 and WT1 positive cells, 2) a sub-epicardial space from where a functional primary coronary vascular plexus of CD31+/DACH1+ cells emerge, 3) a compact myocardial region adjacent to the epicardium, enriched in proliferative cardiomyocytes and ECM deposition, and 4) a sympathetic neuronal network that controls heart organoid contraction. Therefore, the human heart organoid described herein, is a unique model to study new regenerative medicine-based approaches to restore innervation and promote re-vascularization in adult heart after ischemic events and to perform adult and developmental cardiotoxicity studies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Coronary vascularization and sympathetic innervation of the myocardium is a concomitant event during embryonic heart development and both systems are crucial to ensure normal adult heart function. Here we describe a self-organized hiPSC-derived heart organoid that recreates both the coronary vascular plexus and the sympathetic neuronal network of the ventricle myocardium, with a physiologically relevant in-vivo-like structural organization and function. Through modulation of PDGF-β and VEGF signalling pathways, we attained a heart organoid that incorporates 1) an external epicardial layer (mesothelium) of DACH1, NR2F2 and WT1 positive cells, 2) a sub-epicardial space from where a functional primary coronary vascular plexus of CD31+/DACH1+ cells emerge, 3) a compact myocardial region adjacent to the epicardium, enriched in proliferative cardiomyocytes and ECM deposition, and 4) a sympathetic neuronal network that controls heart organoid contraction. Therefore, the human heart organoid described herein, is a unique model to study new regenerative medicine-based approaches to restore innervation and promote re-vascularization in adult heart after ischemic events and to perform adult and developmental cardiotoxicity studies. |
| 13. | Clément, Blandine F; Petrella, Lorenzo; Wallimann, Lea; Duru, Jens; Tringides, Christina M; Vörös, János; Ruff, Tobias: An In Vitro Platform for Characterizing Axonal Electrophysiology of Individual Human iPSC-derived Nociceptors. In: bioRxiv, 2025. (Type: Journal Article | Abstract | Links | BibTeX) @article{Clement2025, title = {An In Vitro Platform for Characterizing Axonal Electrophysiology of Individual Human iPSC-derived Nociceptors}, author = {Blandine F. Clément and Lorenzo Petrella and Lea Wallimann and Jens Duru and Christina M. Tringides and János Vörös and Tobias Ruff}, url = {http://biorxiv.org/lookup/doi/10.1101/2025.01.08.631429}, doi = {10.1101/2025.01.08.631429}, year = {2025}, date = {2025-01-10}, journal = {bioRxiv}, abstract = {Current treatments against severe forms of neuropathic pain demonstrate insufficient efficacy or lead to unwanted side effects as they fail to specifically target the affected nociceptors - a specialized subclass of sensory neurons conveying potentially damaging stimuli information to the central nervous system. Neuropathic pain may involve different nociceptor subtypes in different patients. Tools that can distinguish nociceptive axons would enable a more targeted compound screening. Therefore, we developed an in vitro platform combining a CMOS-based high-density microelectrode array with a polydimethylsiloxane (PDMS) guiding microstructure that captures the electrophysiological responses of nociceptors. Human induced pluripotent stem cell-derived (iPSC) nociceptors were cultured at low density with axons distributed through parallel 4 × 10 µm microchannels exiting the seeding well before converging to a bigger axon-collecting channel. This configuration allowed the measurement of stimulation-induced responses of individual axons. Nociceptors were found to exhibit a great diversity of electrophysiological response profiles that can be classified into different functional archetypes. Moreover, we show that some responses are affected by applying the TRPV1 agonist capsaicin. Overall, results using our platform demonstrate that we were able to distinguish nociceptive axons from different subtypes. The platform provides a promising tool for screening potential candidates for nociceptor-specific drugs.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Current treatments against severe forms of neuropathic pain demonstrate insufficient efficacy or lead to unwanted side effects as they fail to specifically target the affected nociceptors - a specialized subclass of sensory neurons conveying potentially damaging stimuli information to the central nervous system. Neuropathic pain may involve different nociceptor subtypes in different patients. Tools that can distinguish nociceptive axons would enable a more targeted compound screening. Therefore, we developed an in vitro platform combining a CMOS-based high-density microelectrode array with a polydimethylsiloxane (PDMS) guiding microstructure that captures the electrophysiological responses of nociceptors. Human induced pluripotent stem cell-derived (iPSC) nociceptors were cultured at low density with axons distributed through parallel 4 × 10 µm microchannels exiting the seeding well before converging to a bigger axon-collecting channel. This configuration allowed the measurement of stimulation-induced responses of individual axons. Nociceptors were found to exhibit a great diversity of electrophysiological response profiles that can be classified into different functional archetypes. Moreover, we show that some responses are affected by applying the TRPV1 agonist capsaicin. Overall, results using our platform demonstrate that we were able to distinguish nociceptive axons from different subtypes. The platform provides a promising tool for screening potential candidates for nociceptor-specific drugs. |
| 14. | Yang, Ziqin; Teaney, Nicole A; Buttermore, Elizabeth D; Sahin, Mustafa; Afshar-Saber, Wardiya: Harnessing the potential of human induced pluripotent stem cells, functional assays and machine learning for neurodevelopmental disorders. In: Frontiers in Neuroscience, 2025. (Type: Journal Article | Abstract | Links | BibTeX) @article{Yang2025, title = {Harnessing the potential of human induced pluripotent stem cells, functional assays and machine learning for neurodevelopmental disorders}, author = {Ziqin Yang and Nicole A. Teaney and Elizabeth D. Buttermore and Mustafa Sahin and Wardiya Afshar-Saber}, url = {https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2024.1524577/full}, doi = {10.3389/fnins.2024.1524577}, year = {2025}, date = {2025-01-08}, journal = {Frontiers in Neuroscience}, abstract = {Neurodevelopmental disorders (NDDs) affect 4.7% of the global population and are associated with delays in brain development and a spectrum of impairments that can lead to lifelong disability and even mortality. Identification of biomarkers for accurate diagnosis and medications for effective treatment are lacking, in part due to the historical use of preclinical model systems that do not translate well to the clinic for neurological disorders, such as rodents and heterologous cell lines. Human-induced pluripotent stem cells (hiPSCs) are a promising in vitro system for modeling NDDs, providing opportunities to understand mechanisms driving NDDs in human neurons. Functional assays, including patch clamping, multielectrode array, and imaging-based assays, are popular tools employed with hiPSC disease models for disease investigation. Recent progress in machine learning (ML) algorithms also presents unprecedented opportunities to advance the NDD research process. In this review, we compare two-dimensional and three-dimensional hiPSC formats for disease modeling, discuss the applications of functional assays, and offer insights on incorporating ML into hiPSC-based NDD research and drug screening.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Neurodevelopmental disorders (NDDs) affect 4.7% of the global population and are associated with delays in brain development and a spectrum of impairments that can lead to lifelong disability and even mortality. Identification of biomarkers for accurate diagnosis and medications for effective treatment are lacking, in part due to the historical use of preclinical model systems that do not translate well to the clinic for neurological disorders, such as rodents and heterologous cell lines. Human-induced pluripotent stem cells (hiPSCs) are a promising in vitro system for modeling NDDs, providing opportunities to understand mechanisms driving NDDs in human neurons. Functional assays, including patch clamping, multielectrode array, and imaging-based assays, are popular tools employed with hiPSC disease models for disease investigation. Recent progress in machine learning (ML) algorithms also presents unprecedented opportunities to advance the NDD research process. In this review, we compare two-dimensional and three-dimensional hiPSC formats for disease modeling, discuss the applications of functional assays, and offer insights on incorporating ML into hiPSC-based NDD research and drug screening. |
| 15. | Duenki, Tomoya; Ikeuchi, Yoshiho: Insulative Compression of Neuronal Tissues on Microelectrode Arrays by Perfluorodecalin Enhances Electrophysiological Measurements. In: Advanced Healthcare Materials , 2025. (Type: Journal Article | Abstract | Links | BibTeX) @article{Duenki2025, title = {Insulative Compression of Neuronal Tissues on Microelectrode Arrays by Perfluorodecalin Enhances Electrophysiological Measurements}, author = {Tomoya Duenki and Yoshiho Ikeuchi}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adhm.202403771}, doi = {10.1002/adhm.202403771}, year = {2025}, date = {2025-01-05}, journal = {Advanced Healthcare Materials }, abstract = {Microelectrode array (MEA) techniques provide a powerful method for exploration of neural network dynamics. A critical challenge is to interface 3D neural tissues including neural organoids with the flat MEAs surface, as it is essential to place neurons near to the electrodes for recording weak extracellular signals of neurons. To enhance performance of MEAs, most research have focused on improving their surface treatment, while little attention has been given to improve the tissue-MEA interactions from the medium side. Here, a strategy is introduced to augment MEA measurements by overlaying perfluorodecalin (PFD), a biocompatible fluorinated solvent, over neural tissues. Laying PFD over cerebral organoids insulates and compresses the tissues on MEA, which significantly enhances electrophysiological recordings. Even subtle signals such as the propagation of action potentials in bundled axons of motor nerve organoids can be detected with the technique. Moreover, PFD stabilizes tissues in acute recordings and its transparency allows optogenetic manipulations. This research highlights the potential of PFD as a tool for refining electrophysiological measurements of in vitro neuronal cultures. This can open new avenues to leverage precision of neuroscientific investigations and expanding the toolkit for in vitro studies of neural function and connectivity.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Microelectrode array (MEA) techniques provide a powerful method for exploration of neural network dynamics. A critical challenge is to interface 3D neural tissues including neural organoids with the flat MEAs surface, as it is essential to place neurons near to the electrodes for recording weak extracellular signals of neurons. To enhance performance of MEAs, most research have focused on improving their surface treatment, while little attention has been given to improve the tissue-MEA interactions from the medium side. Here, a strategy is introduced to augment MEA measurements by overlaying perfluorodecalin (PFD), a biocompatible fluorinated solvent, over neural tissues. Laying PFD over cerebral organoids insulates and compresses the tissues on MEA, which significantly enhances electrophysiological recordings. Even subtle signals such as the propagation of action potentials in bundled axons of motor nerve organoids can be detected with the technique. Moreover, PFD stabilizes tissues in acute recordings and its transparency allows optogenetic manipulations. This research highlights the potential of PFD as a tool for refining electrophysiological measurements of in vitro neuronal cultures. This can open new avenues to leverage precision of neuroscientific investigations and expanding the toolkit for in vitro studies of neural function and connectivity. |
| 16. | Tanveer, Md Sayed; Patel, Dhruvik; Schweiger, Hunter E; Abu-Bonsrah, Kwaku Dad; Watmuff, Brad; Azadi, Azin; Pryshchep, Sergey; Narayanan, Karthikeyan; Puleo, Christopher; Natarajan, Kannathal; Mostajo-Radji, Mohammed A; Kagan, Brett J; Wang, Ge: Starting a Synthetic Biological Intelligence Lab from Scratch. In: arXiv, 2024. (Type: Journal Article | Abstract | Links | BibTeX) @article{Tanveer2024, title = {Starting a Synthetic Biological Intelligence Lab from Scratch}, author = {Md Sayed Tanveer and Dhruvik Patel and Hunter E. Schweiger and Kwaku Dad Abu-Bonsrah and Brad Watmuff and Azin Azadi and Sergey Pryshchep and Karthikeyan Narayanan and Christopher Puleo and Kannathal Natarajan and Mohammed A. Mostajo-Radji and Brett J. Kagan and Ge Wang}, url = {http://arxiv.org/abs/2412.14112}, doi = {10.48550/arXiv.2412.14112}, year = {2024}, date = {2024-12-18}, journal = {arXiv}, abstract = {With the recent advancements in artificial intelligence, researchers and industries are deploying gigantic models trained on billions of samples. While training these models consumes a huge amount of energy, human brains produce similar outputs (along with other capabilities) with massively lower data and energy requirements. For this reason, more researchers are increasingly considering alternatives. One of these alternatives is known as synthetic biological intelligence, which involves training in vitro neurons for goal-directed tasks. This multidisciplinary field requires knowledge of tissue engineering, bio-materials, digital signal processing, computer programming, neuroscience, and even artificial intelligence. The multidisciplinary requirements make starting synthetic biological intelligence research highly non-trivial and time-consuming. Generally, most labs either specialize in the biological aspects or the computational ones. Here, we propose how a lab focusing on computational aspects, including machine learning and device interfacing, can start working on synthetic biological intelligence, including organoid intelligence. We will also discuss computational aspects, which can be helpful for labs that focus on biological research. To facilitate synthetic biological intelligence research, we will describe such a general process step by step, including risks and precautions that could lead to substantial delay or additional cost.}, keywords = {}, pubstate = {published}, tppubtype = {article} } With the recent advancements in artificial intelligence, researchers and industries are deploying gigantic models trained on billions of samples. While training these models consumes a huge amount of energy, human brains produce similar outputs (along with other capabilities) with massively lower data and energy requirements. For this reason, more researchers are increasingly considering alternatives. One of these alternatives is known as synthetic biological intelligence, which involves training in vitro neurons for goal-directed tasks. This multidisciplinary field requires knowledge of tissue engineering, bio-materials, digital signal processing, computer programming, neuroscience, and even artificial intelligence. The multidisciplinary requirements make starting synthetic biological intelligence research highly non-trivial and time-consuming. Generally, most labs either specialize in the biological aspects or the computational ones. Here, we propose how a lab focusing on computational aspects, including machine learning and device interfacing, can start working on synthetic biological intelligence, including organoid intelligence. We will also discuss computational aspects, which can be helpful for labs that focus on biological research. To facilitate synthetic biological intelligence research, we will describe such a general process step by step, including risks and precautions that could lead to substantial delay or additional cost. |
| 17. | Robbins, Ash; Schweiger, Hunter E; Hernandez, Sebastian; Spaeth, Alex; Voitiuk, Kateryna; Parks, David F; van der Molen, Tjitse; Geng, Jinghui; Sharf, Tal; Mostajo-Radji, Mohammed A; Haussler, David; Teodorescu, Mircea: Goal-Directed Learning in Cortical Organoids. In: bioRxiv, 2024. (Type: Journal Article | Abstract | Links | BibTeX) @article{Robbins2024, title = {Goal-Directed Learning in Cortical Organoids}, author = {Ash Robbins and Hunter E. Schweiger and Sebastian Hernandez and Alex Spaeth and Kateryna Voitiuk and David F. Parks and Tjitse van der Molen and Jinghui Geng and Tal Sharf and Mohammed A. Mostajo-Radji and David Haussler and Mircea Teodorescu}, url = {https://www.biorxiv.org/content/10.1101/2024.12.07.627350v1}, doi = {10.1101/2024.12.07.627350}, year = {2024}, date = {2024-12-12}, journal = {bioRxiv}, abstract = {Experimental neuroscience techniques are advancing rapidly, with major recent developments in high-density electrophysiology and targeted electrical stimulation. In combination with these techniques, cortical organoids derived from pluripotent stem cells show great promise as in vitro models of brain development and function. Although sensory input is vital to neurodevelopment in vivo, few studies have explored the effect of meaningful input to in vitro neural cultures over time. In this work, we demonstrate the first example of goal-directed learning in brain organoids. We developed a closed-loop electrophysiology framework to embody mouse cortical organoids into a simulated dynamical task (the inverted pendulum problem known as ‘Cartpole’) and evaluate learning through high-frequency training signals. Longitudinal experiments enabled by this framework illuminate how different methods of selecting training signals enable improvement on the tasks. We found that for most organoids, training signals chosen by artificial reinforcement learning yield better performance on the task than randomly chosen training signals or the absence of a training signal. This systematic approach to studying learning mechanisms in vitro opens new possibilities for therapeutic interventions and biological computation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Experimental neuroscience techniques are advancing rapidly, with major recent developments in high-density electrophysiology and targeted electrical stimulation. In combination with these techniques, cortical organoids derived from pluripotent stem cells show great promise as in vitro models of brain development and function. Although sensory input is vital to neurodevelopment in vivo, few studies have explored the effect of meaningful input to in vitro neural cultures over time. In this work, we demonstrate the first example of goal-directed learning in brain organoids. We developed a closed-loop electrophysiology framework to embody mouse cortical organoids into a simulated dynamical task (the inverted pendulum problem known as ‘Cartpole’) and evaluate learning through high-frequency training signals. Longitudinal experiments enabled by this framework illuminate how different methods of selecting training signals enable improvement on the tasks. We found that for most organoids, training signals chosen by artificial reinforcement learning yield better performance on the task than randomly chosen training signals or the absence of a training signal. This systematic approach to studying learning mechanisms in vitro opens new possibilities for therapeutic interventions and biological computation. |
| 18. | Voitiuk, Kateryna; Seiler, Spencer T; de Melo, Mirella Pessoa; Geng, Jinghui; van der Molen, Tjitse; Hernandez, Sebastian; Schweiger, Hunter E; Sevetson, Jess L; Parks, David F; Robbins, Ash; Torres-Montoya, Sebastian; Ehrlich, Drew; Elliott, Matthew A T; Sharf, Tal; Haussler, David; Mostajo-Radji, Mohammed A; Salama, Sofie R; Teodorescu, Mircea: A feedback-driven brain organoid platform enables automated maintenance and high-resolution neural activity monitoring. In: bioRxiv, 2024. (Type: Journal Article | Abstract | Links | BibTeX) @article{Voitiuk2024b, title = {A feedback-driven brain organoid platform enables automated maintenance and high-resolution neural activity monitoring}, author = {Kateryna Voitiuk and Spencer T. Seiler and Mirella Pessoa de Melo and Jinghui Geng and Tjitse van der Molen and Sebastian Hernandez and Hunter E. Schweiger and Jess L. Sevetson and David F. Parks and Ash Robbins and Sebastian Torres-Montoya and Drew Ehrlich and Matthew A. T. Elliott and Tal Sharf and David Haussler and Mohammed A. Mostajo-Radji and Sofie R. Salama and Mircea Teodorescu}, url = {https://www.biorxiv.org/content/10.1101/2024.03.15.585237v5}, doi = {10.1101/2024.03.15.585237}, year = {2024}, date = {2024-12-07}, journal = {bioRxiv}, abstract = {The analysis of tissue cultures, particularly brain organoids, requires a sophisticated integration and coordination of multiple technologies for monitoring and measuring. We have developed an automated research platform enabling independent devices to achieve collaborative objectives for feedback-driven cell culture studies. Our approach enables continuous, communicative, non-invasive interactions within an Internet of Things (IoT) architecture among various sensing and actuation devices, achieving precisely timed control of in vitro biological experiments. The framework integrates microfluidics, electrophysiology, and imaging devices to maintain cerebral cortex organoids while measuring their neuronal activity. The organoids are cultured in custom, 3D-printed chambers affixed to commercial microelectrode arrays. Periodic feeding is achieved using programmable microfluidic pumps. We developed a computer vision fluid volume estimator used as feedback to rectify deviations in microfluidic perfusion during media feeding/aspiration cycles. We validated the system with a set of 7-day studies of mouse cerebral cortex organoids, comparing manual and automated protocols. The automated protocols were validated in maintaining robust neural activity throughout the experiment. The automated system enabled hourly electrophysiology recordings for the 7-day studies. Median neural unit firing rates increased for every sample and dynamic patterns of organoid firing rates were revealed by high-frequency recordings. Surprisingly, feeding did not affect firing rate. Furthermore, performing media exchange during a recording showed no acute effects on firing rate, enabling the use of this automated platform for reagent screening studies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The analysis of tissue cultures, particularly brain organoids, requires a sophisticated integration and coordination of multiple technologies for monitoring and measuring. We have developed an automated research platform enabling independent devices to achieve collaborative objectives for feedback-driven cell culture studies. Our approach enables continuous, communicative, non-invasive interactions within an Internet of Things (IoT) architecture among various sensing and actuation devices, achieving precisely timed control of in vitro biological experiments. The framework integrates microfluidics, electrophysiology, and imaging devices to maintain cerebral cortex organoids while measuring their neuronal activity. The organoids are cultured in custom, 3D-printed chambers affixed to commercial microelectrode arrays. Periodic feeding is achieved using programmable microfluidic pumps. We developed a computer vision fluid volume estimator used as feedback to rectify deviations in microfluidic perfusion during media feeding/aspiration cycles. We validated the system with a set of 7-day studies of mouse cerebral cortex organoids, comparing manual and automated protocols. The automated protocols were validated in maintaining robust neural activity throughout the experiment. The automated system enabled hourly electrophysiology recordings for the 7-day studies. Median neural unit firing rates increased for every sample and dynamic patterns of organoid firing rates were revealed by high-frequency recordings. Surprisingly, feeding did not affect firing rate. Furthermore, performing media exchange during a recording showed no acute effects on firing rate, enabling the use of this automated platform for reagent screening studies. |
| 19. | Vacca, F; Galluzzi, F; Blanco-Formoso, M; Gianiorio, T; Fazioa, De A F; Tantussi, F; Stürmer, S; Haq, W; Zrenner, E; Chaffio, A; lC. Joffrois,; Picaud, S; Benfenati, F; Angelis, De F; Colombo, E: Solid-State Nanopores for Spatially Resolved Chemical Neuromodulation. In: Nano Letters , 2024. (Type: Journal Article | Abstract | Links | BibTeX) @article{Vacca2024, title = {Solid-State Nanopores for Spatially Resolved Chemical Neuromodulation}, author = {F. Vacca and F. Galluzzi and M. Blanco-Formoso and T. Gianiorio and A.F. De Fazioa and F. Tantussi and S. Stürmer and W. Haq and E. Zrenner and A. Chaffio and lC. Joffrois and S. Picaud and F. Benfenati and F. De Angelis and E. Colombo}, url = {https://pubs.acs.org/doi/10.1021/acs.nanolett.4c02604}, doi = {10.1021/acs.nanolett.4c02604}, year = {2024}, date = {2024-11-19}, journal = {Nano Letters }, abstract = {Most neural prosthetic devices are based on electrical stimulation, although the modulation of neuronal activity by a localized chemical delivery would better mimic physiological synaptic machinery. In the past decade, various drug delivery approaches attempted to emulate synaptic transmission, although they were hampered by poor retention of their cargo while reaching the target destination, low spatial resolution, and poor biocompatibility and stability of the materials involved. Here, we propose a planar solid-state device for multisite neurotransmitter translocation at the nanoscale consisting of a nanopatterned ceramic membrane connected to a reservoir designed to store neurotransmitters. We achieved diffusion-mediated glutamate stimulation of primary neurons, while we showed the feasibility to translocate other molecules through the pores by either pressure or diffusion, proving the versatility of the proposed technology. Finally, the system proved to be a promising neuronal stimulation interface in mice and nonhuman primates ex vivo, paving the way toward a biomimetic chemical stimulation in neural prosthetics and brain machine interfaces.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Most neural prosthetic devices are based on electrical stimulation, although the modulation of neuronal activity by a localized chemical delivery would better mimic physiological synaptic machinery. In the past decade, various drug delivery approaches attempted to emulate synaptic transmission, although they were hampered by poor retention of their cargo while reaching the target destination, low spatial resolution, and poor biocompatibility and stability of the materials involved. Here, we propose a planar solid-state device for multisite neurotransmitter translocation at the nanoscale consisting of a nanopatterned ceramic membrane connected to a reservoir designed to store neurotransmitters. We achieved diffusion-mediated glutamate stimulation of primary neurons, while we showed the feasibility to translocate other molecules through the pores by either pressure or diffusion, proving the versatility of the proposed technology. Finally, the system proved to be a promising neuronal stimulation interface in mice and nonhuman primates ex vivo, paving the way toward a biomimetic chemical stimulation in neural prosthetics and brain machine interfaces. |
| 20. | Andrews, John P; Geng, Jinghui; Voitiuk, Kateryna; Elliott, Matthew A T; Shin, David; Robbins, Ash; Spaeth, Alex; Wang, Albert; Li, Lin; Solis, Daniel; Keefe, Matthew G; Sevetson, Jessica L; de Jesús, Julio Rivera A; Donohue, Kevin C; Larson, Hanh H; Ehrlich, Drew; Auguste, Kurtis I; Salama, Sofie; Sohal, Vikaas; Sharf, Tal; Haussler, David; Cadwell, Cathryn R; Schaffer, David V; Chang, Edward F; Teodorescu, Mircea; Nowakowski, Tomasz Jan: Multimodal Evaluation of Network Activity and Optogenetic Interventions in Human Hippocampal Slices. In: Nature Neuroscience , 2024. (Type: Journal Article | Abstract | Links | BibTeX) @article{Andrews2024, title = {Multimodal Evaluation of Network Activity and Optogenetic Interventions in Human Hippocampal Slices}, author = {John P. Andrews and Jinghui Geng and Kateryna Voitiuk and Matthew A. T. Elliott and David Shin and Ash Robbins and Alex Spaeth and Albert Wang and Lin Li and Daniel Solis and Matthew G. Keefe and Jessica L. Sevetson and Julio A. Rivera de Jesús and Kevin C. Donohue and H. Hanh Larson and Drew Ehrlich and Kurtis I. Auguste and Sofie Salama and Vikaas Sohal and Tal Sharf and David Haussler and Cathryn R. Cadwell and David V. Schaffer and Edward F. Chang and Mircea Teodorescu and Tomasz Jan Nowakowski}, url = {https://www.nature.com/articles/s41593-024-01782-5}, doi = {10.1038/s41593-024-01782-5}, year = {2024}, date = {2024-11-15}, journal = {Nature Neuroscience }, abstract = {Seizures are made up of the coordinated activity of networks of neurons, suggesting that control of neurons in the pathologic circuits of epilepsy could allow for control of the disease. Optogenetics has been effective at stopping seizure-like activity in non-human disease models by increasing inhibitory tone or decreasing excitation, although this effect has not been shown in human brain tissue. Many of the genetic means for achieving c hannelrhodopsin expression in non-human models are not possible in humans, and vector-mediated methods are susceptible to species-specific tropism that may affect translational potential. Here we demonstrate adeno-associated virus–mediated, optogenetic reductions in network firing rates of human hippocampal slices recorded on high-density microelectrode arrays under several hyperactivity-provoking conditions. This platform can serve to bridge the gap between human and animal studies by exploring genetic interventions on network activity in human brain tissue.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Seizures are made up of the coordinated activity of networks of neurons, suggesting that control of neurons in the pathologic circuits of epilepsy could allow for control of the disease. Optogenetics has been effective at stopping seizure-like activity in non-human disease models by increasing inhibitory tone or decreasing excitation, although this effect has not been shown in human brain tissue. Many of the genetic means for achieving c hannelrhodopsin expression in non-human models are not possible in humans, and vector-mediated methods are susceptible to species-specific tropism that may affect translational potential. Here we demonstrate adeno-associated virus–mediated, optogenetic reductions in network firing rates of human hippocampal slices recorded on high-density microelectrode arrays under several hyperactivity-provoking conditions. This platform can serve to bridge the gap between human and animal studies by exploring genetic interventions on network activity in human brain tissue. |
Roos, Matthew J; Luna, Diego; Din, Dowlette-Mary Alam El; Hartung, Thomas; Smirnova, Lena; Proescher, Alex; Johnson, Erik C Modeling Organoid Population Electrophysiology Dynamics Journal Article bioRxiv, 2025. Abstract | Links | BibTeX | タグ: 3D Culture, MaxTwo, Organoids Ishimoto, Taiga; Abe, Takashi; Nakamura, Yuko; Tsuyama, Tomonori; Kondoh, Kunio; Naoto, ; Kajitani, ; Yoshida, Kaede; Takeuchi, Yuichi; Kato, Kan X; Xu, Shucheng; Koduki, Maru; Ichimura, Momoka; Itoi, Takito; Shimba, Kenta; Yamaguchi, Yoshifumi; Minami, Masabumi; Koike, Shinsuke; Kasai, Kiyoto; Ye, Jessica J; Takebayashi, Minoru; Yamagata, Kazuya; Toda, Chitoku Chronic social defeat causes dysregulation of systemic glucose metabolism via the cerebellar fastigial nucleus Journal Article bioRxiv, 2025. Abstract | Links | BibTeX | タグ: 3D Culture, HD-MEA, MaxOne, Slices Zhao, Jianyi; Wu, Linshi; Cai, Gang; Ou, Dan; Liao, Keman; Yang, Jian; Zhou, Li; Huang, Renhua; Lin, Shukai; Huang, Xi; Lv, Qi; Chen, Juxiang; Cao, Lu; Chen, Jiayi; Lin, Yingying Targeting PGE2 mediated senescent neuron improves tumour therapy Journal Article Neuro-Oncology, 2025. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, HD-MEA, MaxOne Ikeda, Narumitsu; Akita, Dai; Takahashi, Hirokazu Emergent functions of noise-driven spontaneous activity: Homeostatic maintenance of criticality and memory consolidation Journal Article arXiv, 2025. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, HD-MEA, MaxOne Sifringer, Léo; Fratzl, Alex; Clément, Blandine F; Chansoria, Parth; Mönkemöller, Leah S; Duru, Jens; Ihle, Stephan J; Steffens, Simon; Beltraminelli, Anna; Ceylan, Eylul; Hengsteler, Julian; Maurer, Benedikt; Weaver, Sean M; Tringides, Christina M; Vulić, Katarina; Madduri, Srinivas; Zenobi-Wong, Marcy; Roska, Botond; Vörös, János; Ruff, Tobias An Implantable Biohybrid Neural Interface Toward Synaptic Deep Brain Stimulation Journal Article Advanced Functional Materials, 2025. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, 3D Culture, HD-MEA, MaxOne, Organoids Lee, Jaeyong; Liu, Jia Flexible and stretchable bioelectronics for organoids Journal Article Springer Nature Link, 2025. Abstract | Links | BibTeX | タグ: HD-MEA, Organoids Chow, Siu Yu A; Hu, Huaruo; Duenki, Tomoya; Asakura, Takuya; Sugimura, Sota; Ikeuchi, Yoshiho Repetitive Stimulation Modifies Network Characteristics of Neural Organoid Circuits Journal Article bioRxiv, 2025. Abstract | Links | BibTeX | タグ: 3D Culture, HD-MEA, MaxOne, Organoids, Stimulation Nakamuta, Asahi; Akita, Dai; Zhang, He; Kawahara, Yuta; Takahashi, Hirokazu; Teramae, Jun-nosuke Self-organization of high-dimensional geometry of neural activity in culture Journal Article bioRxiv, 2025. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, HD-MEA, MaxOne, MEA Metrics Küchler, Joël; Vulíc, Katarina; Yao, Haotian; Valmaggia, Christian; Ihle, Stephan J; Weaver, Sean; Vörös, János Engineered Biological Neural Networks as Basic Logic Operators Journal Article bioRxiv, 2025. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, HD-MEA, MaxOne, Neuronal Networks Setsu, Selena; Morimoto, Satoru; Nakamura, Shiho; Ozawa, Fumiko; Utami, Kagistia Hana; Nishiyama, Ayumi; Suzuki, Naoki; Aoki, Masashi; Takeshita, Yukio; Tomari, Yukihide; Okano, Hideyuki Swift induction of human spinal lower motor neurons and robust ALS cell screening via single-cell imaging Journal Article Stem Cell Reports, 2025. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, HD-MEA, IPSC, MaxOne Vinci, Ersilia; Beretta, Stefania; Colombo, Veronica; Zippo, Antonio; Catanese, Alberto; Wiegreffe, Christoph; Britsch, Stefan; Boeckers, Tobias; Verpelli, Chiara; Sala, Carlo Regulation of Dendrite and Dendritic Spine Formation by TCF20 Journal Article Journal of Neurochemistry, 2025. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, MaxTwo Clément, Blandine F; Petrella, Lorenzo; Wallimann, Lea; Duru, Jens; Tringides, Christina M; Vörös, János; Ruff, Tobias An In Vitro Platform for Characterizing Axonal Electrophysiology of Individual Human iPSC-derived Nociceptors Journal Article bioRxiv, 2025. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, HD-MEA, IPSC, MaxOne, Neuronal Networks Branco, Mariana A; Nunes, Mafalda Marques; Rayagra, Ana Luísa; Tenreiro, Miguel F; Cabral, Joaquim M S; Diogo, Maria Margarida Recreating Coronary Vascularization and Sympathetic Innervation of Myocardium on a Human Pluripotent Stem Cell-derived Heart Organoid Journal Article bioRxiv, 2025. Abstract | Links | BibTeX | タグ: 3D Culture, Axon Tracking Assay, Cardiomyocytes, Data Analysis, HD-MEA, IPSC, Organoids Yang, Ziqin; Teaney, Nicole A; Buttermore, Elizabeth D; Sahin, Mustafa; Afshar-Saber, Wardiya Harnessing the potential of human induced pluripotent stem cells, functional assays and machine learning for neurodevelopmental disorders Journal Article Frontiers in Neuroscience, 2025. Abstract | Links | BibTeX | タグ: HD-MEA, IPSC, MaxOne Duenki, Tomoya; Ikeuchi, Yoshiho Insulative Compression of Neuronal Tissues on Microelectrode Arrays by Perfluorodecalin Enhances Electrophysiological Measurements Journal Article Advanced Healthcare Materials , 2025. Abstract | Links | BibTeX | タグ: 3D Culture, Axon Tracking Assay, MEA Technology, Neuronal Networks Tanveer, Md Sayed; Patel, Dhruvik; Schweiger, Hunter E; Abu-Bonsrah, Kwaku Dad; Watmuff, Brad; Azadi, Azin; Pryshchep, Sergey; Narayanan, Karthikeyan; Puleo, Christopher; Natarajan, Kannathal; Mostajo-Radji, Mohammed A; Kagan, Brett J; Wang, Ge Starting a Synthetic Biological Intelligence Lab from Scratch Journal Article arXiv, 2024. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, 3D Culture, Activity Scan Assay, Data Analysis, MaxOne, Network Assay, Primary Neuronal Cell Culture Robbins, Ash; Schweiger, Hunter E; Hernandez, Sebastian; Spaeth, Alex; Voitiuk, Kateryna; Parks, David F; van der Molen, Tjitse; Geng, Jinghui; Sharf, Tal; Mostajo-Radji, Mohammed A; Haussler, David; Teodorescu, Mircea Goal-Directed Learning in Cortical Organoids Journal Article bioRxiv, 2024. Abstract | Links | BibTeX | タグ: 3D Culture, HD-MEA, MaxOne, Organoids Voitiuk, Kateryna; Seiler, Spencer T; de Melo, Mirella Pessoa; Geng, Jinghui; van der Molen, Tjitse; Hernandez, Sebastian; Schweiger, Hunter E; Sevetson, Jess L; Parks, David F; Robbins, Ash; Torres-Montoya, Sebastian; Ehrlich, Drew; Elliott, Matthew A T; Sharf, Tal; Haussler, David; Mostajo-Radji, Mohammed A; Salama, Sofie R; Teodorescu, Mircea A feedback-driven brain organoid platform enables automated maintenance and high-resolution neural activity monitoring Journal Article bioRxiv, 2024. Abstract | Links | BibTeX | タグ: 3D Culture, HD-MEA, MaxOne, Organoids Vacca, F; Galluzzi, F; Blanco-Formoso, M; Gianiorio, T; Fazioa, De A F; Tantussi, F; Stürmer, S; Haq, W; Zrenner, E; Chaffio, A; lC. Joffrois,; Picaud, S; Benfenati, F; Angelis, De F; Colombo, E Solid-State Nanopores for Spatially Resolved Chemical Neuromodulation Journal Article Nano Letters , 2024. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, MaxOne, Primary Neuronal Cell Culture, Retina, Stimulation Andrews, John P; Geng, Jinghui; Voitiuk, Kateryna; Elliott, Matthew A T; Shin, David; Robbins, Ash; Spaeth, Alex; Wang, Albert; Li, Lin; Solis, Daniel; Keefe, Matthew G; Sevetson, Jessica L; de Jesús, Julio Rivera A; Donohue, Kevin C; Larson, Hanh H; Ehrlich, Drew; Auguste, Kurtis I; Salama, Sofie; Sohal, Vikaas; Sharf, Tal; Haussler, David; Cadwell, Cathryn R; Schaffer, David V; Chang, Edward F; Teodorescu, Mircea; Nowakowski, Tomasz Jan Multimodal Evaluation of Network Activity and Optogenetic Interventions in Human Hippocampal Slices Journal Article Nature Neuroscience , 2024. Abstract | Links | BibTeX | タグ: Brain Slice, HD-MEA, MaxOne, MEA Metrics, MEA Technology Elliott, Matthew A T; Andrews, John P; van der Molen, Tjitse; Geng, Jinghui; Spaeth, Alex; Voituik, Kateryna; Core, Cordero; Gillespie, Thomas; Sinervo, Ari; Parks, David F; Robbins, Ash; Solís, Daniel; Chang, Edward F; Nowakowski, Tomasz Jan; Teodorescu, Mircea; Haussler, David; Sharf, Tal Pathological Microcircuits Initiate Epileptiform Events in Patient Hippocampal Slices Journal Article bioRxiv, 2024. Abstract | Links | BibTeX | タグ: Brain Slice, HD-MEA, MaxOne, MEA Technology, Neuronal Networks Geng, Jinghui; Voitiuk, Kateryna; Parks, David F; Robbins, Ash; Alex
Spaeth, ; Sevetson, Jessica L; Hernandez, Sebastian; Schweiger, Hunter E; Andrews, John P; Seiler, Spencer T; Elliott, Matthew A T; Chang, Edward F; Nowakowski, Tomasz J; Currie, Rob; Mostajo-Radji, Mohammed A; Haussler, David; Sharf, Tal; Salama, Sofie R; Teodorescu, Mircea Multiscale Cloud-based Pipeline for Neuronal Electrophysiology Analysis and Visualization Journal Article bioRxiv, 2024. Abstract | Links | BibTeX | タグ: 3D Culture, Brain Slice, HD-MEA, MaxOne, MEA Technology, Organoids Kobayashi, Toki; Shimba, Kenta; Narumi, Taiyo; Asahina, Takahiro; Kotani, Kiyoshi; Jimbo, Yasuhiko Revealing Single-Neuron and Network-Activity Interaction by Combining High-Density Microelectrode Array and Optogenetics Journal Article Nature Communications , 2024. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, MaxOne, Neuronal Networks, Primary Neuronal Cell Culture, Stimulation Hoang, Huu; Matsumoto, Nobuyoshi; Miyano, Miyuki; Ikegaya, Yuji; Cortese, Aurelio Dopamine-induced Relaxation of Spike Synchrony Diversifies Burst Patterns in Cultured Hippocampal Networks Journal Article Neural Networks , 2024. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, HD-MEA, MaxOne, Neuronal Networks, Primary Neuronal Cell Culture Bertacchi, Michele; Maharaux, Gwendoline; Loubat, Agnès; Jung, Matthieu; Studer, Michèle FGF8-Mediated Gene Regulation Affects Regional Identity in Human Cerebral Organoids Journal Article eLife , 2024. Abstract | Links | BibTeX | タグ: 3D Culture, Activity Scan Assay, Axon Tracking Assay, HD-MEA, MaxOne, MEA Metrics, Network Assay, Neuronal Networks, Organoids Fenton, Timothy A; Haouchine, Olivia Y; Hallam, Elizabeth B; Smith, Emily M; Jackson, Kiya C; Rahbarian, Darlene; Canales, Cesar P; Adhikari, Anna; Nord, Alex S; Ben-Shalom, Roy; Silverman, Jill L Hyperexcitability and Translational Phenotypes in a Preclinical Mouse Model of SYNGAP1-related Intellectual Disability Journal Article Translational Psychiatry , 2024. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, HD-MEA, MEA Technology, Neuronal Networks, Primary Neuronal Cell Culture Sawada, Takeshi; Iino, Yusuke; Yoshida, Kensuke; Okazaki, Hitoshi; Nomura, Shinnosuke; Shimizu, Chika; Arima, Tomoki; Juichi, Motoki; Zhou, Siqi; Kurabayashi, Nobuhiro; Sakurai, Takeshi; Yagishita, Sho; Yanagisawa, Masashi; Toyoizumi, Taro; Kasai, Haruo; Shi, Shoi Prefrontal Synaptic Regulation of Homeostatic Sleep Pressure Revealed Through Synaptic Chemogenetics Journal Article Science , 2024. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, HD-MEA, MaxOne, MEA Technology, Primary Neuronal Cell Culture, Spike Sorting Din, Dowlette-Mary Alam El; Moenkemoeller, Leah; Loeffler, Alon; Habibollahi, Forough; Schenkman, Jack; Mitra, Amitav; van der Molen, Tjitse; Ding, Lixuan; Laird, Jason; Maren, ; Schenke, ; Johnson, Erik C; Kagan, Brett J; Hartung, Thomas; Smirnova, Lena Human Neural Organoid Microphysiological Systems Show the Building Blocks Necessary for Basic Learning and Memory Journal Article bioRxiv, 2024. Abstract | Links | BibTeX | タグ: 3D Culture, Activity Scan Assay, Axon Tracking Assay, HD-MEA, IPSC, MaxTwo, MEA Technology, Network Assay, Organoids, Spike Sorting, Stimulation Zhang, Xinyu; Burattini, Margherita; Duru, Jens; Chala, Nafsika; Wyssen, Nino; Cofiño-Fabres, Carla; Rivera-Arbeláez, José Manuel; Passier, Robert; Poulikakos, Dimos; Aldo Ferrari, Christina Tringides ; Vörös, János; Luciani, Giovanni Battista; Miragoli, Michele; Zambelli, Tomaso Multimodal Mapping of Electrical and Mechanical Latency of Human-Induced Pluripotent Stem Cell-Derived Cardiomyocyte Layers Journal Article ACS Nano, 2024, ISSN: 1936-0851. Abstract | Links | BibTeX | タグ: Cardiomyocytes, HD-MEA, IPSC, MaxOne, MEA Technology Cartiglia, Matteo; Costa, Filippo; Narayanan, Shyam; Bui, Cat-Vu H; Ulusan, Hasan; Risia, Nicoletta; Haessig, Germain; Hierlemann, Andreas; Cardes, Fernando; Indiveri, Giacomo A 4096 Channel Event-based Multielectrode Array with Asynchronous Outputs Compatible with Neuromorphic Processors Journal Article Nature Communications, 2024. Abstract | Links | BibTeX | タグ: ETH-CMOS-MEA, MEA Technology Lee, Jihyun; Duperrex, Eliane; El-Battrawy, Ibrahim; Hohn, Alyssa; M., Ardan; Saguner, ; Duru, Firat; Emmenegger, Vishalini; Cyganek, Lukas; Hierlemann, Andreas; Ulusan, Hasan CardioMEA: Comprehensive Data Analysis Platform for Studying Cardiac Diseases and Drug Responses Journal Article bioRxiv, 2024. Abstract | Links | BibTeX | タグ: Cardiomyocytes, IPSC, MEA Technology Hoang, Huu; Matsumoto, Nobuyoshi; Miyano, Miyuki; Ikegaya, Yuji; Cortese, Aurelio Dopamine-induced Relaxation of Connectivity Diversifies Burst Patterns in Cultured Hippocampal Networks Journal Article bioRxiv, 2024. Abstract | Links | BibTeX | タグ: Activity Scan Assay, HD-MEA, MaxOne, MEA Technology, Network Assay, Neuronal Networks, Primary Neuronal Cell Culture Beaubois, Romain; Cheslet, Jérémy; Duenki, Tomoya; Venuto, Giuseppe De; Carè, Marta; Khoyratee, Farad; Chiappalone, Michela; Branchereau, Pascal; Ikeuchi, Yoshiho; Levi, Timothée BiœmuS: A new tool for neurological disorders studies through real-time emulation and hybridization using biomimetic Spiking Neural Network Journal Article Nature Communications, 2024. Abstract | Links | BibTeX | タグ: Activity Scan Assay, closed loop stimulation, HD-MEA, IPSC, MaxOne, MEA Technology, Modeling, Organoids, Stimulation Buccino, Alessio Paolo; Damart, Tanguy; Bartram, Julian; Mandge, Darshan; Xue, Xiaohan; Zbili, Mickael; Gänswein, Tobias; Jaquier, Aurélien; Emmenegger, Vishalini; Markram, Henry; Hierlemann, Andreas; Geit, Werner Van A Multimodal Fitting Approach to Construct Single-Neuron Models with Patch Clamp and High-Density Microelectrode Arrays Journal Article Neural Computation (MIT Press), 2024. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, ETH-CMOS-MEA, HD-MEA, MEA Metrics, MEA Technology Servais, Bram; Mahmoudi, Negar; Gautam, Vini; Tong, Wei; Ibbotson, Michael R; Nisbet, David R; Collins, David Engineering Brain-on-a-Chip Platforms Journal Article Nature Reviews Bioengineering, 2024. Abstract | Links | BibTeX | タグ: 3D Culture, MEA Technology Sifringer, Léo; Fratzl, Alex; Clément, Blandine F; Chansoria, Parth; Mönkemöller, Leah S; Duru, Jens; Ihle, Stephan J; Steffens, Simon; Beltraminelli, Anna; Ceylan, Eylul; Hengsteler, Julian; Maurer, Benedikt; Weaver, Sean M; Tringides, Christina M; Vulić, Katarina; Madduri, Srinivas; Zenobi-Wong, Marcy; Roska, Botond; Vörös, János; Ruff, Tobias An implantable biohybrid nerve model towards synaptic deep brain stimulation Journal Article bioRxiv, 2024. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, 3D Culture, CMOS, HD-MEA, MaxOne, MEA Technology, Primary Neuronal Cell Culture, Retina Khajehnejad, Moein; Habibollahi, Forough; Paul, Aswin; Razi, Adeel; Kagan, Brett J Biological Neurons Compete with Deep Reinforcement Learning in Sample Efficiency in a Simulated Gameworld Journal Article arXiv , 2024. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, closed loop stimulation, HD-MEA, IPSC, Machine Learning, MaxOne, Modeling, Primary Neuronal Cell Culture Bucci, Annalisa; Büttner, Marc; Domdei, Niklas; Rosselli, Federica Bianca; Znidaric, Matej; Diggelmann, Roland; Gennaro, Martina De; Cowan, Cameron S; Harmening, Wolf; Hierlemann, Andreas; Roska, Botond; Franke, Felix Action potential propagation speed compensates for traveling distance in the human retina Journal Article bioRxiv , 2024. Abstract | Links | BibTeX | タグ: Activity Assay, Activity Scan Assay, Axon Tracking Assay, HD-MEA, MaxOne, MEA Metrics, MEA Technology, Microfluidics, Modeling, Retina, Slices, Spike Sorting Donner, Christian; Bartram, Julian; Hornauer, Philipp; Kim, Taehoon; Roqueiro, Damian; Hierlemann, Andreas; Obozinski, Guillaume; Schröter, Manuel Ensemble learning and ground-truth validation of synaptic connectivity inferred from spike trains Journal Article PLOS Computational Biology, 2024. Abstract | Links | BibTeX | タグ: ETH-CMOS-MEA, HD-MEA, MaxTwo, MEA Metrics, MEA Technology, Modeling, Primary Neuronal Cell Culture, Spike Sorting, Synapses Kesdoğan, Aylin B; Neureiter, Anika; Gaebler, Arnim J; Kalia, Anil K; Körner, Jannis; Lampert, Angelika Analgesic Effect of Botulinum Toxin in Neuropathic Pain is Sodium Channel Independent Journal Article Neuropharmacology, 2024. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, Activity Scan Assay, HD-MEA, IPSC, MaxTwo, MEA Metrics, MEA Technology van der Molen, Tjitse; Lim, Max; Bartram, Julian; Cheng, Zhuowei; Robbins, Ash; Parks, David F; Petzold, Linda R; Hierlemann, Andreas; Haussler, David; Hansma, Paul K; Tovar, Kenneth R; Kosik, Kenneth S RT-Sort: an action potential propagation-based algorithm for real time spike detection and sorting with millisecond latencies Journal Article bioRxiv, 2024. Abstract | Links | BibTeX | タグ: 3D Culture, Action Potential, closed loop stimulation, HD-MEA, MEA Metrics, MEA Technology, Organoids, Spike Sorting, Stimulation Tetzlaff, Svenja K; Reyhan, Ekin; Bengtson, Peter C; Schroers, Julian; Wagner, Julia; Schubert, Marc C; Layer, Nikolas; Puschhof, Maria C; Faymonville, Anton J; Drewa, Nina; Pramatarov, Rangel L; Wissmann, Niklas; Alhalabi, Obada; Heuer, Alina; Sivapalan, Nirosan; Campos, Joaquín; Boztepe, Berin; Scheck, Jonas G; Villa, Giulia; Schröter, Manuel; Sahm, Felix; Forsberg-Nilsson, Karin; Breckwoldt, Michael O; Acuna, Claudio; Suchorska, Bogdana; Heiland, Dieter Henrik; Saez-Rodriguez, Julio; Venkataramani, Varun Characterizing and targeting glioblastoma neuron-tumor networks with retrograde tracing Journal Article bioRxiv, 2024. Abstract | Links | BibTeX | タグ: 3D Culture, HD-MEA, MaxTwo, MEA Metrics, MEA Technology, Organoids, Primary Neuronal Cell Culture Fenton, Timothy A; Haouchine, Olivia Y; Hallam, Elizabeth L; Smith, Emily M; Jackson, Kiya C; Rahbarian, Darlene; Canales, Cesar; Adhikari, Anna; Nord, Alexander S; Ben-Shalom, Roy; Silverman, Jill L Hyperexcitability and translational phenotypes in a preclinical mouse model of SYNGAP1-Related Intellectual Disability Journal Article Research Square, 2024. Abstract | Links | BibTeX | タグ: Activity Scan Assay, HD-MEA, MaxOne, MEA Metrics, MEA Technology, Network Assay, Primary Neuronal Cell Culture, Spike Sorting Voitiuk, Kateryna; Seiler, Spencer T; de Melo, Mirella Pessoa; Geng, Jinghui; Hernandez, Sebastian; Schweiger, Hunter E; Sevetson, Jess L; Parks, David F; Robbins, Ash; Torres-Montoya, Sebastian; Ehrlich, Drew; Elliott, Matthew A T; Sharf, Tal; Haussler, David; Mostajo-Radji, Mohammed A; Salama, Sofie R; Teodorescu, Mircea A feedback-driven IoT microfluidic, electrophysiology, and imaging platform for brain organoid studies Journal Article bioRxiv, 2024. Abstract | Links | BibTeX | タグ: Activity Scan Assay, HD-MEA, MaxOne, MEA Metrics, MEA Technology, Microfluidics, Organoids 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 Wang, Guodong; Zhang, Dandan; Qin, Liangshan; Liu, Quanhui; Tang, Wenkui; Liu, Mingxing; Xu, Fan; Tang, Fen; Cheng, Leping; Mo, Huiming; Yuan, Xiang; Wang, Zhiqiang; Huang, Ben Forskolin-driven conversion of human somatic cells into induced neurons through regulation of the cAMP-CREB1-JNK signaling Journal Article Theranostics , 2024. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, HD-MEA, MaxOne, MEA Technology 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 van der Molen, Tjitse; Spaeth, Alex; Chini, Mattia; Bartram, Julian; Dendukuri, Aditya; Zhang, Zongren; Bhaskaran-Nair, Kiran; Blauvelt, Lon J; Petzold, Linda R; Hansma, Paul K; Teodorescu, Mircea; Hierlemann, Andreas; Hengen, Keith B; Hanganu-Opatz, Ileana L; Kosik, Kenneth S; Sharf, Tal Protosequences in human cortical organoids model intrinsic states in the developing cortex Journal Article bioRxiv, 2023. Abstract | Links | BibTeX | タグ: MaxOne, Organoids Lin, Hsiu-Chuan; Janssens, Jasper; Kroell, Ann-Sophie; Hornauer, Philipp; Santel, Malgorzata; Okamoto, Ryoko; Karava, Kyriaki; Priouret, Marthe; Garcia, Maria Pascual; Schroeter, Manuel; Camp, Gray J; Treutlein, Barbara Human neuron subtype programming through combinatorial patterning with scRNA-seq readouts Journal Article bioRxiv, 2023. Abstract | Links | BibTeX | タグ: 2D Neuronal Culture, Activity Scan Assay, Axon Tracking Assay, HD-MEA, MaxTwo, Network Assay
2025
title = {Modeling Organoid Population Electrophysiology Dynamics},
author = {Matthew J. Roos and Diego Luna and Dowlette-Mary Alam El Din and Thomas Hartung and Lena Smirnova and Alex Proescher and Erik C. Johnson},
url = {https://www.biorxiv.org/content/10.1101/2025.03.02.641081v1},
doi = {10.1101/2025.03.02.641081},
year = {2025},
date = {2025-03-02},
journal = {bioRxiv},
abstract = {Improving models to investigate neurodegenerative disease, neurodevelopmental disease, neuro-toxicology and neuropharmacology is critical to improve our basic understanding of the human nervous system, as well as to accelerate discovery of interventions and drugs. Improved models of the human central nervous system could enable critical discoveries related to functional changes induced by sensory stimulation or toxic exposures. Neural organoids, complex three-dimensional cell cultures derived from adult human stem cells, have been grown with complex connectivity and neuroanatomy. Moreover, these cultures have been interfaced with bi-directional electrical stimulation and recording, as well as chemical stimulation. This effort sought to develop new computational techniques which could be applied to comparative studies using neural organoids. In particular, we adapted CEBRA, a state of the art model from the in vivo modeling literature, to generate 2D and 3D embeddings (projections into structured low-dimensional spaces) of high dimensional neural organoid electrophysiology data. This can be done in an unsupervised or semi-supervised manner. Results indicate these embeddings can be quickly and reliably generated and serve as a low-dimensional, interpretable embeddings for characterizing changes in neural organoid activity over time, as well as clustering results around known bursting phenomena. Moreover, we demonstrate that mixtures of von Mises-Fisher distributions can be used as a parametric model for these embedding spaces to enable statistics hypothesis testing. This technique may enable new types of comparative studies using neural organoids, and may be critical for creating a representation for quantitative comparison and validation of neural organoid models against human and animal data. Looking ahead, this work could allow the formulation of a new class of experiments investigating the functional impact of toxins, genetic manipulations, or pharmacological interventions on human neurons.},
keywords = {3D Culture, MaxTwo, Organoids},
pubstate = {published},
tppubtype = {article}
}
title = {Chronic social defeat causes dysregulation of systemic glucose metabolism via the cerebellar fastigial nucleus},
author = {Taiga Ishimoto and Takashi Abe and Yuko Nakamura and Tomonori Tsuyama and Kunio Kondoh and Naoto and Kajitani and Kaede Yoshida and Yuichi Takeuchi and Kan X. Kato and Shucheng Xu and Maru Koduki and Momoka Ichimura and Takito Itoi and Kenta Shimba and Yoshifumi Yamaguchi and Masabumi Minami and Shinsuke Koike and Kiyoto Kasai and Jessica J Ye and Minoru Takebayashi and Kazuya Yamagata and Chitoku Toda},
url = {https://www.biorxiv.org/content/10.1101/2025.02.18.638938v1},
doi = {10.1101/2025.02.18.638938},
year = {2025},
date = {2025-02-19},
journal = {bioRxiv},
abstract = {Chronic psychological stress leads to hyperglycemia through the endocrine and sympathetic nervous systems, which contributes to the development of type II diabetes mellitus (T2DM). Higher plasma corticosteroids after stress is one well-established driver of insulin resistance in peripheral tissues. However, previous studies have indicated that only a fraction of patients with depression and post-traumatic disorder (PTSD) who develop T2DM exhibit hypocortisolism, so corticosteroids do not fully explain psychological stress-induced T2DM. Here, we find that chronic social defeat stress (CSDS) in mice enhances gluconeogenesis, which is accompanied by a decrease in plasma insulin, an increase in plasma catecholamines, and a drop in plasma corticosterone levels. We further reveal that these metabolic and endocrinological changes are mediated by the activation of neurons projecting from the cerebellar fastigial nucleus (FN) to the medullary parasolitary nucleus (PSol). These neurons are crucial in shifting the body’s primary energy source from glucose to lipids. Additionally, data from patients with depression reveal correlations between the presence of cerebellar abnormalities and both worsening depressive symptoms and elevated HbA1c levels. These findings highlight a previously unappreciated role of the cerebellum in metabolic regulation and its importance as a potential therapeutic target in depression, PTSD, and similar psychological disorders.},
keywords = {3D Culture, HD-MEA, MaxOne, Slices},
pubstate = {published},
tppubtype = {article}
}
title = {Targeting PGE2 mediated senescent neuron improves tumour therapy},
author = {Jianyi Zhao and Linshi Wu and Gang Cai and Dan Ou and Keman Liao and Jian Yang and Li Zhou and Renhua Huang and Shukai Lin and Xi Huang and Qi Lv and Juxiang Chen and Lu Cao and Jiayi Chen and Yingying Lin},
url = {https://doi.org/10.1093/neuonc/noaf045},
doi = {10.1093/neuonc/noaf045},
year = {2025},
date = {2025-02-18},
journal = {Neuro-Oncology},
abstract = {Recent studies have highlighted bidirectional signalling between tumours and neurons; however, the interactions between tumours and neurons in response to radio-/chemotherapy remain obscure, which hampers the tumour treatment.Glioblastoma organoids (GBOs) and primary neuron coculture, targeted metabonomics, RNA pulldown, mass spectrum, co-immunoprecipitation, RNA-sequencing, transcript/protein validations and multi-electrode arrays were performed to analyse neuron-tumour interaction in response to therapy. In vivo validations were conducted in orthotopic mouse models. Diagnostic and prognostic values were evaluated in serum, tissue-microarray as well as TCGA.GBOs recruited and induced pro-tumour-survival senescent neurons upon radiation/chemotherapeutic treatment. Targeted metabonomics revealed that significantly increased tumour-derived prostaglandin E2 (PGE2) induced neuronal senescence phenotype. Screening of enzymes involved in PGE2 synthesis identified prostaglandin E synthase 3 (PTGES3) as the key enzyme responsible for PGE2 upregulation. Biochemical studies revealed that irradiation or chemotherapeutic drug-triggered asparagine endopeptidase (AEP) specifically cleaved eIF4A1 to produce teIF4A1-C, which dissociated from DDX6 and recruited eIF4A3 and PABPN1 to promote the mRNA stability of PTGES3. Elevated PGE2 reciprocally enhanced AEP expression. Inhibiting PGE2 or AEP reduced neuronal senescence and delayed tumour progression. Strikingly, single-cell analysis further showed that expressions of AEP/PTGES3/EIF4A1 in tumour cells were consistent with senescent neuronal CDKN1A in high-neuronal-connectivity glioblastoma. The serum PGE2 concentration was elevated after radiation and higher in resistant glioblastoma patients. High expression of PTGES3 was associated with a poor prognosis.Our study revealed that the AEP/PGE2 feedback loop modulates tumour-induced neuronal senescence upon radio-/chemotherapy and highlight the therapeutic value to improve tumour therapy.},
keywords = {2D Neuronal Culture, HD-MEA, MaxOne},
pubstate = {published},
tppubtype = {article}
}
title = {Emergent functions of noise-driven spontaneous activity: Homeostatic maintenance of criticality and memory consolidation},
author = {Narumitsu Ikeda and Dai Akita and Hirokazu Takahashi},
url = {http://arxiv.org/abs/2502.10946},
doi = {10.48550/arXiv.2502.10946},
year = {2025},
date = {2025-02-16},
journal = {arXiv},
abstract = {Unlike digital computers, the brain exhibits spontaneous activity even during complete rest, despite the evolutionary pressure for energy efficiency. Inspired by the critical brain hypothesis, which proposes that the brain operates optimally near a critical point of phase transition in the dynamics of neural networks to improve computational efficiency, we postulate that spontaneous activity plays a homeostatic role in the development and maintenance of criticality. Criticality in the brain is associated with the balance between excitatory and inhibitory synaptic inputs (EI balance), which is essential for maintaining neural computation performance. Here, we hypothesize that both criticality and EI balance are stabilized by appropriate noise levels and spike-timing-dependent plasticity (STDP) windows. Using spiking neural network (SNN) simulations and in vitro experiments with dissociated neuronal cultures, we demonstrated that while repetitive stimuli transiently disrupt both criticality and EI balance, spontaneous activity can develop and maintain these properties and prolong the fading memory of past stimuli. Our findings suggest that the brain may achieve self-optimization and memory consolidation as emergent functions of noise-driven spontaneous activity. This noise-harnessing mechanism provides insights for designing energy-efficient neural networks, and may explain the critical function of sleep in maintaining homeostasis and consolidating memory.},
keywords = {2D Neuronal Culture, HD-MEA, MaxOne},
pubstate = {published},
tppubtype = {article}
}
title = {An Implantable Biohybrid Neural Interface Toward Synaptic Deep Brain Stimulation},
author = {Léo Sifringer and Alex Fratzl and Blandine F. Clément and Parth Chansoria and Leah S. Mönkemöller and Jens Duru and Stephan J. Ihle and Simon Steffens and Anna Beltraminelli and Eylul Ceylan and Julian Hengsteler and Benedikt Maurer and Sean M. Weaver and Christina M. Tringides and Katarina Vulić and Srinivas Madduri and Marcy Zenobi-Wong and Botond Roska and János Vörös and Tobias Ruff},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adfm.202416557},
doi = {10.1002/adfm.202416557},
year = {2025},
date = {2025-02-09},
journal = {Advanced Functional Materials},
abstract = {In patients with sensory nerve loss, such as those experiencing optic nerve damage that leads to vision loss, the thalamus no longer receives the corresponding sensory input. To restore functional sensory input, it is necessary to bypass the damaged circuits, which can be achieved by directly stimulating the appropriate sensory thalamic nuclei. However, available deep brain stimulation electrodes do not provide the resolution required for effective sensory restoration. Therefore, this work develops an implantable biohybrid neural interface aimed at innervating and synaptically stimulating deep brain targets. The interface combines a stretchable stimulation array with an aligned microfluidic axon guidance system seeded with neural spheroids to facilitate the development of a 3 mm long nerve-like structure. A bioresorbable hydrogel nerve conduit is used as a bridge between the tissue and the biohybrid implant. Stimulation of the spheroids within the biohybrid structure in vitro and use of high-density CMOS microelectrode arrays show faithful activity conduction across the device. Although functional in vivo innervation and synapse formation has not yet been achieved in this study, implantation of the biohybrid nerve onto the mouse cortex shows that neural spheroids grow axons in vivo and remain functionally active for more than 22 days post-implantation.},
keywords = {2D Neuronal Culture, 3D Culture, HD-MEA, MaxOne, Organoids},
pubstate = {published},
tppubtype = {article}
}
title = {Flexible and stretchable bioelectronics for organoids},
author = {Jaeyong Lee and Jia Liu},
url = {https://doi.org/10.1007/s44258-024-00046-y},
doi = {10.1007/s44258-024-00046-y},
year = {2025},
date = {2025-02-01},
journal = {Springer Nature Link},
abstract = {Organoids have gained significant interest due to their ability to recapitulate the structural, molecular, and functional complexity of corresponding organs. While methods have been developed to characterize and benchmark organoid structural and molecular properties, capturing the functional development and maturation of organoids remains challenging. To address this, the development of multifunctional bioelectronics for interfacing with organoids has been actively pursued. However, conventional electronics face limitations in achieving multifunctional recording and control across the entire three-dimensional (3D) volume of organoids in a long-term stable manner due to the large morphological and cellular composition changes during development. In this review, we first discuss the application of conventional electronics for organoid interfacing. We then focus on the development of flexible and stretchable electronics designed to create organoid/electronics hybrids for chronically stable interfaces. We also review recent advancements in flexible multifunctional electronics for charting multimodal cell activities throughout development. Furthermore, we explore the integration of flexible bioelectronics with other characterization modalities for comprehensive multimodal charting of cells within 3D tissues. Finally, we discuss the potential of integrating artificial intelligence into the organoid system through embedded electronics, harnessing organoid intelligence for biosymbiotic computational systems. These advancements could provide valuable tools for characterizing organoid functional development and maturation, establishing patient-specific models, developing therapeutic opportunities, and exploring novel computational strategies.},
keywords = {HD-MEA, Organoids},
pubstate = {published},
tppubtype = {article}
}
title = {Repetitive Stimulation Modifies Network Characteristics of Neural Organoid Circuits},
author = {Siu Yu A. Chow and Huaruo Hu and Tomoya Duenki and Takuya Asakura and Sota Sugimura and Yoshiho Ikeuchi},
url = {https://www.biorxiv.org/content/10.1101/2025.01.16.633310v1},
doi = {https://doi.org/10.1101/2025.01.16.633310},
year = {2025},
date = {2025-01-16},
journal = {bioRxiv},
abstract = {Neural organoids form complex networks but lack external stimuli and hierarchical structures crucial for refining functional microcircuits. In this study, we modeled the hierarchical and modular network organization by connecting multiple organoids and tested if the connection enhances the external stimuli-induced network refinement. We cultured networks of one, two, or three organoids on high-density microelectrode arrays, applied repetitive stimulation at two input locations from the microelectrodes, and monitored emergence of output signals that can decode the stimulus locations with machine learning algorithms. After two weeks of daily stimulation, networks of three organoids showed significantly higher stimulus decoding capability compared to the simpler one- or two-organoid networks. Long-term stimulation induced pronounced changes in the three-organoid network’s response patterns, spontaneous activity, and inter- and intra-organoid functional connectivity. These findings underscore the importance of hierarchical network organization, e.g. creating distinct subnetworks with specialized roles, for stimuli-induced formation of circuits with robust input-output functionality.},
keywords = {3D Culture, HD-MEA, MaxOne, Organoids, Stimulation},
pubstate = {published},
tppubtype = {article}
}
title = {Self-organization of high-dimensional geometry of neural activity in culture},
author = {Asahi Nakamuta and Dai Akita and He Zhang and Yuta Kawahara and Hirokazu Takahashi and Jun-nosuke Teramae},
url = {https://www.biorxiv.org/content/10.1101/2025.01.14.630383v1},
doi = {10.1101/2025.01.14.630383},
year = {2025},
date = {2025-01-16},
journal = {bioRxiv},
abstract = {A vast number of neurons exhibit high-dimensional coordination for brain computation, both in processing sensory input and in generating spontaneous activity without external stimuli. Recent advancements in large-scale recordings have revealed that this high-dimensional population activity exhibits a scale-free structure, characterized by power law and distinct spatial patterns in principal components (PCs). However, the mechanisms underlying the formation of this high-dimensional neural coordination remain poorly understood. Specifically, it is unclear whether the characteristic high-dimensional structure of population activity emerges through self-organization or is shaped by the learning of sensory stimuli in animals. To address this question and clearly differentiate between these two possibilities, we investigated large-scale neural activity in dissociated neuronal culture using high-density multi-electrode arrays. Our findings demonstrate that the high-dimensional structure of neural activity self-organizes during network development in the absence of explicit sensory stimuli provided to animals. As the cultures mature, the PC variance exhibits a power-law decay, and the spatial structures of PCs transition from global to localized patterns, driven by the temporal correlations of neural activity. Furthermore, we observed an unexpected co-occurrence between the power-law decay in PCA and neuronal avalanches, suggesting a link between self-organized criticality and high-dimensional activity. Using a recurrent neural network model, we show that both phenomena can arise from biologically plausible heavy-tailed synaptic connectivity. By highlighting a developmental origin of the high-dimensional structure of neural activity, these findings deepen our understanding of how coordinated neural computations are achieved in the brain.},
keywords = {2D Neuronal Culture, HD-MEA, MaxOne, MEA Metrics},
pubstate = {published},
tppubtype = {article}
}
title = {Engineered Biological Neural Networks as Basic Logic Operators},
author = {Joël Küchler and Katarina Vulíc and Haotian Yao and Christian Valmaggia and Stephan J. Ihle and Sean Weaver and János Vörös },
url = {https://www.biorxiv.org/content/10.1101/2024.12.23.630065v2},
doi = {https://doi.org/10.1101/2024.12.23.630065},
year = {2025},
date = {2025-01-15},
journal = {bioRxiv},
abstract = {We present an in vitro neuronal network with controlled topology capable of performing basic Boolean computations, such as NAND and OR. Neurons cultured within polydimethylsiloxane (PDMS) microstructures on high-density microelectrode arrays (HD-MEAs) enable precise interaction through extracellular voltage stimulation and spiking activity recording. The architecture of our system allows for creating non-linear functions with two inputs and one output. Additionally, we analyze various encoding schemes, comparing the limitations of rate coding with the potential advantages of spike-timing-based coding strategies. This work contributes to the advancement of hybrid intelligence and biocomputing by offering insights into neural information encoding and decoding with the potential to create fully biological computational systems.
},
keywords = {2D Neuronal Culture, HD-MEA, MaxOne, Neuronal Networks},
pubstate = {published},
tppubtype = {article}
}
title = {Swift induction of human spinal lower motor neurons and robust ALS cell screening via single-cell imaging},
author = {Selena Setsu and Satoru Morimoto and Shiho Nakamura and Fumiko Ozawa and Kagistia Hana Utami and Ayumi Nishiyama and Naoki Suzuki and Masashi Aoki and Yukio Takeshita and Yukihide Tomari and Hideyuki Okano},
url = {https://www.cell.com/stem-cell-reports/abstract/S2213-6711(24)00321-7},
doi = {10.1016/j.stemcr.2024.11.007},
year = {2025},
date = {2025-01-14},
journal = {Stem Cell Reports},
abstract = {This study introduces a novel method for rapidly and efficiently inducing human spinal lower motor neurons (LMNs) from induced pluripotent stem cells (iPSCs) to eventually elucidate the pathomechanisms of amyotrophic lateral sclerosis (ALS) and facilitate drug screening. Previous methods were limited by low induction efficiency, poor LMN purity, or labor-intensive induction and evaluation processes. Our protocol overcomes these challenges, achieving around 80% induction efficiency within just two weeks by combining a small molecule-based approach with transcription factor transduction. Moreover, to exclude non-LMN cells from the analysis, we utilized timelapse microscopy and machine learning to analyze the morphology and viability of iPSC-derived LMNs on a single-cell basis, establishing an effective pathophysiological evaluation system. This rapid, efficient, and streamlined protocol, along with our single-cell-based evaluation method, enables large-scale analysis and drug screening using iPSC-derived motor neurons.},
keywords = {2D Neuronal Culture, HD-MEA, IPSC, MaxOne},
pubstate = {published},
tppubtype = {article}
}
title = {Regulation of Dendrite and Dendritic Spine Formation by TCF20},
author = {Ersilia Vinci and Stefania Beretta and Veronica Colombo and Antonio Zippo and Alberto Catanese and Christoph Wiegreffe and Stefan Britsch and Tobias Boeckers and Chiara Verpelli and Carlo Sala},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jnc.16297},
doi = {10.1111/jnc.16297},
year = {2025},
date = {2025-01-13},
journal = {Journal of Neurochemistry},
abstract = {Mutations in the Transcription Factor 20 (TCF20) have been identified in patients with autism spectrum disorders (ASDs), intellectual disabilities (IDs), and other neurological issues. Recently, a new syndrome called TCF20-associated neurodevelopmental disorders (TAND) has been described, with specific clinical features. While TCF20's role in the neurogenesis of mouse embryos has been reported, little is known about its molecular function in neurons. In this study, we demonstrate that TCF20 is expressed in all analyzed brain regions in mice, and its expression increases during brain development but decreases in muscle tissue. Our findings suggest that TCF20 plays a central role in dendritic arborization and dendritic spine formation processes. RNA sequencing analysis revealed a downregulation of pre- and postsynaptic pathways in TCF20 knockdown neurons. We also found decreased levels of GABRA1, BDNF, PSD-95, and c-Fos in total homogenates and in synaptosomal preparations of knockdown TCF20 rat cortical cultures. Furthermore, synaptosomal preparations of knockdown TCF20 rat cortical cultures showed significant downregulation of GluN2B and GABRA5, while GluA2 was significantly upregulated. Overall, our data suggest that TCF20 plays an essential role in neuronal development and function by modulating the expression of proteins involved in dendrite and synapse formation and function.},
keywords = {2D Neuronal Culture, MaxTwo},
pubstate = {published},
tppubtype = {article}
}
title = {An In Vitro Platform for Characterizing Axonal Electrophysiology of Individual Human iPSC-derived Nociceptors},
author = {Blandine F. Clément and Lorenzo Petrella and Lea Wallimann and Jens Duru and Christina M. Tringides and János Vörös and Tobias Ruff},
url = {http://biorxiv.org/lookup/doi/10.1101/2025.01.08.631429},
doi = {10.1101/2025.01.08.631429},
year = {2025},
date = {2025-01-10},
journal = {bioRxiv},
abstract = {Current treatments against severe forms of neuropathic pain demonstrate insufficient efficacy or lead to unwanted side effects as they fail to specifically target the affected nociceptors - a specialized subclass of sensory neurons conveying potentially damaging stimuli information to the central nervous system. Neuropathic pain may involve different nociceptor subtypes in different patients. Tools that can distinguish nociceptive axons would enable a more targeted compound screening. Therefore, we developed an in vitro platform combining a CMOS-based high-density microelectrode array with a polydimethylsiloxane (PDMS) guiding microstructure that captures the electrophysiological responses of nociceptors. Human induced pluripotent stem cell-derived (iPSC) nociceptors were cultured at low density with axons distributed through parallel 4 × 10 µm microchannels exiting the seeding well before converging to a bigger axon-collecting channel. This configuration allowed the measurement of stimulation-induced responses of individual axons. Nociceptors were found to exhibit a great diversity of electrophysiological response profiles that can be classified into different functional archetypes. Moreover, we show that some responses are affected by applying the TRPV1 agonist capsaicin. Overall, results using our platform demonstrate that we were able to distinguish nociceptive axons from different subtypes. The platform provides a promising tool for screening potential candidates for nociceptor-specific drugs.},
keywords = {2D Neuronal Culture, HD-MEA, IPSC, MaxOne, Neuronal Networks},
pubstate = {published},
tppubtype = {article}
}
title = {Recreating Coronary Vascularization and Sympathetic Innervation of Myocardium on a Human Pluripotent Stem Cell-derived Heart Organoid},
author = {Mariana A. Branco and Mafalda Marques Nunes and Ana Luísa Rayagra and Miguel F. Tenreiro and Joaquim M.S. Cabral and Maria Margarida Diogo},
url = {http://biorxiv.org/lookup/doi/10.1101/2025.01.10.632325},
doi = {10.1101/2025.01.10.632325},
year = {2025},
date = {2025-01-10},
journal = {bioRxiv},
abstract = {Coronary vascularization and sympathetic innervation of the myocardium is a concomitant event during embryonic heart development and both systems are crucial to ensure normal adult heart function. Here we describe a self-organized hiPSC-derived heart organoid that recreates both the coronary vascular plexus and the sympathetic neuronal network of the ventricle myocardium, with a physiologically relevant in-vivo-like structural organization and function. Through modulation of PDGF-β and VEGF signalling pathways, we attained a heart organoid that incorporates 1) an external epicardial layer (mesothelium) of DACH1, NR2F2 and WT1 positive cells, 2) a sub-epicardial space from where a functional primary coronary vascular plexus of CD31+/DACH1+ cells emerge, 3) a compact myocardial region adjacent to the epicardium, enriched in proliferative cardiomyocytes and ECM deposition, and 4) a sympathetic neuronal network that controls heart organoid contraction. Therefore, the human heart organoid described herein, is a unique model to study new regenerative medicine-based approaches to restore innervation and promote re-vascularization in adult heart after ischemic events and to perform adult and developmental cardiotoxicity studies.},
keywords = {3D Culture, Axon Tracking Assay, Cardiomyocytes, Data Analysis, HD-MEA, IPSC, Organoids},
pubstate = {published},
tppubtype = {article}
}
title = {Harnessing the potential of human induced pluripotent stem cells, functional assays and machine learning for neurodevelopmental disorders},
author = {Ziqin Yang and Nicole A. Teaney and Elizabeth D. Buttermore and Mustafa Sahin and Wardiya Afshar-Saber},
url = {https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2024.1524577/full},
doi = {10.3389/fnins.2024.1524577},
year = {2025},
date = {2025-01-08},
journal = {Frontiers in Neuroscience},
abstract = {Neurodevelopmental disorders (NDDs) affect 4.7% of the global population and are associated with delays in brain development and a spectrum of impairments that can lead to lifelong disability and even mortality. Identification of biomarkers for accurate diagnosis and medications for effective treatment are lacking, in part due to the historical use of preclinical model systems that do not translate well to the clinic for neurological disorders, such as rodents and heterologous cell lines. Human-induced pluripotent stem cells (hiPSCs) are a promising in vitro system for modeling NDDs, providing opportunities to understand mechanisms driving NDDs in human neurons. Functional assays, including patch clamping, multielectrode array, and imaging-based assays, are popular tools employed with hiPSC disease models for disease investigation. Recent progress in machine learning (ML) algorithms also presents unprecedented opportunities to advance the NDD research process. In this review, we compare two-dimensional and three-dimensional hiPSC formats for disease modeling, discuss the applications of functional assays, and offer insights on incorporating ML into hiPSC-based NDD research and drug screening.},
keywords = {HD-MEA, IPSC, MaxOne},
pubstate = {published},
tppubtype = {article}
}
title = {Insulative Compression of Neuronal Tissues on Microelectrode Arrays by Perfluorodecalin Enhances Electrophysiological Measurements},
author = {Tomoya Duenki and Yoshiho Ikeuchi},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adhm.202403771},
doi = {10.1002/adhm.202403771},
year = {2025},
date = {2025-01-05},
journal = {Advanced Healthcare Materials },
abstract = {Microelectrode array (MEA) techniques provide a powerful method for exploration of neural network dynamics. A critical challenge is to interface 3D neural tissues including neural organoids with the flat MEAs surface, as it is essential to place neurons near to the electrodes for recording weak extracellular signals of neurons. To enhance performance of MEAs, most research have focused on improving their surface treatment, while little attention has been given to improve the tissue-MEA interactions from the medium side. Here, a strategy is introduced to augment MEA measurements by overlaying perfluorodecalin (PFD), a biocompatible fluorinated solvent, over neural tissues. Laying PFD over cerebral organoids insulates and compresses the tissues on MEA, which significantly enhances electrophysiological recordings. Even subtle signals such as the propagation of action potentials in bundled axons of motor nerve organoids can be detected with the technique. Moreover, PFD stabilizes tissues in acute recordings and its transparency allows optogenetic manipulations. This research highlights the potential of PFD as a tool for refining electrophysiological measurements of in vitro neuronal cultures. This can open new avenues to leverage precision of neuroscientific investigations and expanding the toolkit for in vitro studies of neural function and connectivity.},
keywords = {3D Culture, Axon Tracking Assay, MEA Technology, Neuronal Networks},
pubstate = {published},
tppubtype = {article}
}
2024
title = {Starting a Synthetic Biological Intelligence Lab from Scratch},
author = {Md Sayed Tanveer and Dhruvik Patel and Hunter E. Schweiger and Kwaku Dad Abu-Bonsrah and Brad Watmuff and Azin Azadi and Sergey Pryshchep and Karthikeyan Narayanan and Christopher Puleo and Kannathal Natarajan and Mohammed A. Mostajo-Radji and Brett J. Kagan and Ge Wang},
url = {http://arxiv.org/abs/2412.14112},
doi = {10.48550/arXiv.2412.14112},
year = {2024},
date = {2024-12-18},
journal = {arXiv},
abstract = {With the recent advancements in artificial intelligence, researchers and industries are deploying gigantic models trained on billions of samples. While training these models consumes a huge amount of energy, human brains produce similar outputs (along with other capabilities) with massively lower data and energy requirements. For this reason, more researchers are increasingly considering alternatives. One of these alternatives is known as synthetic biological intelligence, which involves training in vitro neurons for goal-directed tasks. This multidisciplinary field requires knowledge of tissue engineering, bio-materials, digital signal processing, computer programming, neuroscience, and even artificial intelligence. The multidisciplinary requirements make starting synthetic biological intelligence research highly non-trivial and time-consuming. Generally, most labs either specialize in the biological aspects or the computational ones. Here, we propose how a lab focusing on computational aspects, including machine learning and device interfacing, can start working on synthetic biological intelligence, including organoid intelligence. We will also discuss computational aspects, which can be helpful for labs that focus on biological research. To facilitate synthetic biological intelligence research, we will describe such a general process step by step, including risks and precautions that could lead to substantial delay or additional cost.},
keywords = {2D Neuronal Culture, 3D Culture, Activity Scan Assay, Data Analysis, MaxOne, Network Assay, Primary Neuronal Cell Culture},
pubstate = {published},
tppubtype = {article}
}
title = {Goal-Directed Learning in Cortical Organoids},
author = {Ash Robbins and Hunter E. Schweiger and Sebastian Hernandez and Alex Spaeth and Kateryna Voitiuk and David F. Parks and Tjitse van der Molen and Jinghui Geng and Tal Sharf and Mohammed A. Mostajo-Radji and David Haussler and Mircea Teodorescu},
url = {https://www.biorxiv.org/content/10.1101/2024.12.07.627350v1},
doi = {10.1101/2024.12.07.627350},
year = {2024},
date = {2024-12-12},
journal = {bioRxiv},
abstract = {Experimental neuroscience techniques are advancing rapidly, with major recent developments in high-density electrophysiology and targeted electrical stimulation. In combination with these techniques, cortical organoids derived from pluripotent stem cells show great promise as in vitro models of brain development and function. Although sensory input is vital to neurodevelopment in vivo, few studies have explored the effect of meaningful input to in vitro neural cultures over time. In this work, we demonstrate the first example of goal-directed learning in brain organoids. We developed a closed-loop electrophysiology framework to embody mouse cortical organoids into a simulated dynamical task (the inverted pendulum problem known as ‘Cartpole’) and evaluate learning through high-frequency training signals. Longitudinal experiments enabled by this framework illuminate how different methods of selecting training signals enable improvement on the tasks. We found that for most organoids, training signals chosen by artificial reinforcement learning yield better performance on the task than randomly chosen training signals or the absence of a training signal. This systematic approach to studying learning mechanisms in vitro opens new possibilities for therapeutic interventions and biological computation.},
keywords = {3D Culture, HD-MEA, MaxOne, Organoids},
pubstate = {published},
tppubtype = {article}
}
title = {A feedback-driven brain organoid platform enables automated maintenance and high-resolution neural activity monitoring},
author = {Kateryna Voitiuk and Spencer T. Seiler and Mirella Pessoa de Melo and Jinghui Geng and Tjitse van der Molen and Sebastian Hernandez and Hunter E. Schweiger and Jess L. Sevetson and David F. Parks and Ash Robbins and Sebastian Torres-Montoya and Drew Ehrlich and Matthew A. T. Elliott and Tal Sharf and David Haussler and Mohammed A. Mostajo-Radji and Sofie R. Salama and Mircea Teodorescu},
url = {https://www.biorxiv.org/content/10.1101/2024.03.15.585237v5},
doi = {10.1101/2024.03.15.585237},
year = {2024},
date = {2024-12-07},
journal = {bioRxiv},
abstract = {The analysis of tissue cultures, particularly brain organoids, requires a sophisticated integration and coordination of multiple technologies for monitoring and measuring. We have developed an automated research platform enabling independent devices to achieve collaborative objectives for feedback-driven cell culture studies. Our approach enables continuous, communicative, non-invasive interactions within an Internet of Things (IoT) architecture among various sensing and actuation devices, achieving precisely timed control of in vitro biological experiments. The framework integrates microfluidics, electrophysiology, and imaging devices to maintain cerebral cortex organoids while measuring their neuronal activity. The organoids are cultured in custom, 3D-printed chambers affixed to commercial microelectrode arrays. Periodic feeding is achieved using programmable microfluidic pumps. We developed a computer vision fluid volume estimator used as feedback to rectify deviations in microfluidic perfusion during media feeding/aspiration cycles. We validated the system with a set of 7-day studies of mouse cerebral cortex organoids, comparing manual and automated protocols. The automated protocols were validated in maintaining robust neural activity throughout the experiment. The automated system enabled hourly electrophysiology recordings for the 7-day studies. Median neural unit firing rates increased for every sample and dynamic patterns of organoid firing rates were revealed by high-frequency recordings. Surprisingly, feeding did not affect firing rate. Furthermore, performing media exchange during a recording showed no acute effects on firing rate, enabling the use of this automated platform for reagent screening studies.},
keywords = {3D Culture, HD-MEA, MaxOne, Organoids},
pubstate = {published},
tppubtype = {article}
}
title = {Solid-State Nanopores for Spatially Resolved Chemical Neuromodulation},
author = {F. Vacca and F. Galluzzi and M. Blanco-Formoso and T. Gianiorio and A.F. De Fazioa and F. Tantussi and S. Stürmer and W. Haq and E. Zrenner and A. Chaffio and lC. Joffrois and S. Picaud and F. Benfenati and F. De Angelis and E. Colombo},
url = {https://pubs.acs.org/doi/10.1021/acs.nanolett.4c02604},
doi = {10.1021/acs.nanolett.4c02604},
year = {2024},
date = {2024-11-19},
journal = {Nano Letters },
abstract = {Most neural prosthetic devices are based on electrical stimulation, although the modulation of neuronal activity by a localized chemical delivery would better mimic physiological synaptic machinery. In the past decade, various drug delivery approaches attempted to emulate synaptic transmission, although they were hampered by poor retention of their cargo while reaching the target destination, low spatial resolution, and poor biocompatibility and stability of the materials involved. Here, we propose a planar solid-state device for multisite neurotransmitter translocation at the nanoscale consisting of a nanopatterned ceramic membrane connected to a reservoir designed to store neurotransmitters. We achieved diffusion-mediated glutamate stimulation of primary neurons, while we showed the feasibility to translocate other molecules through the pores by either pressure or diffusion, proving the versatility of the proposed technology. Finally, the system proved to be a promising neuronal stimulation interface in mice and nonhuman primates ex vivo, paving the way toward a biomimetic chemical stimulation in neural prosthetics and brain machine interfaces.},
keywords = {2D Neuronal Culture, MaxOne, Primary Neuronal Cell Culture, Retina, Stimulation},
pubstate = {published},
tppubtype = {article}
}
title = {Multimodal Evaluation of Network Activity and Optogenetic Interventions in Human Hippocampal Slices},
author = {John P. Andrews and Jinghui Geng and Kateryna Voitiuk and Matthew A. T. Elliott and David Shin and Ash Robbins and Alex Spaeth and Albert Wang and Lin Li and Daniel Solis and Matthew G. Keefe and Jessica L. Sevetson and Julio A. Rivera de Jesús and Kevin C. Donohue and H. Hanh Larson and Drew Ehrlich and Kurtis I. Auguste and Sofie Salama and Vikaas Sohal and Tal Sharf and David Haussler and Cathryn R. Cadwell and David V. Schaffer and Edward F. Chang and Mircea Teodorescu and Tomasz Jan Nowakowski},
url = {https://www.nature.com/articles/s41593-024-01782-5},
doi = {10.1038/s41593-024-01782-5},
year = {2024},
date = {2024-11-15},
journal = {Nature Neuroscience },
abstract = {Seizures are made up of the coordinated activity of networks of neurons, suggesting that control of neurons in the pathologic circuits of epilepsy could allow for control of the disease. Optogenetics has been effective at stopping seizure-like activity in non-human disease models by increasing inhibitory tone or decreasing excitation, although this effect has not been shown in human brain tissue. Many of the genetic means for achieving c hannelrhodopsin expression in non-human models are not possible in humans, and vector-mediated methods are susceptible to species-specific tropism that may affect translational potential. Here we demonstrate adeno-associated virus–mediated, optogenetic reductions in network firing rates of human hippocampal slices recorded on high-density microelectrode arrays under several hyperactivity-provoking conditions. This platform can serve to bridge the gap between human and animal studies by exploring genetic interventions on network activity in human brain tissue.},
keywords = {Brain Slice, HD-MEA, MaxOne, MEA Metrics, MEA Technology},
pubstate = {published},
tppubtype = {article}
}
title = {Pathological Microcircuits Initiate Epileptiform Events in Patient Hippocampal Slices},
author = {Matthew A.T. Elliott and John P. Andrews and Tjitse van der Molen and Jinghui Geng and Alex Spaeth and Kateryna Voituik and Cordero Core and Thomas Gillespie and Ari Sinervo and David F. Parks and Ash Robbins and Daniel Solís and Edward F. Chang and Tomasz Jan Nowakowski and Mircea Teodorescu and David Haussler and Tal Sharf},
url = {https://www.biorxiv.org/content/10.1101/2024.11.13.623525v1},
doi = {https://doi.org/10.1101/2024.11.13.623525},
year = {2024},
date = {2024-11-14},
journal = {bioRxiv},
abstract = {How seizures begin at the level of microscopic neural circuits remains unknown. High-density CMOS microelectrode arrays provide a new avenue for investigating neuronal network activity, with unprecedented spatial and temporal resolution. We use high-density CMOS-based microelectrode arrays to probe the network activity of human hippocampal brain slices from six patients with mesial temporal lobe epilepsy in the presence of hyperactivity promoting media. Two slices from the dentate gyrus exhibited epileptiform activity in the presence of low magnesium media with kainic acid. Both slices displayed an electrophysiological phenotype consistent with a reciprocally connected circuit, suggesting a recurrent feedback loop is a key driver of epileptiform onset. Larger prospective studies are needed, but these findings have the potential to elucidate the network signals underlying the initiation of seizure behavior.},
keywords = {Brain Slice, HD-MEA, MaxOne, MEA Technology, Neuronal Networks},
pubstate = {published},
tppubtype = {article}
}
title = {Multiscale Cloud-based Pipeline for Neuronal Electrophysiology Analysis and Visualization},
author = {Jinghui Geng and Kateryna Voitiuk and David F. Parks and Ash Robbins and Alex
Spaeth and Jessica L. Sevetson and Sebastian Hernandez and Hunter E. Schweiger
and John P. Andrews and Spencer T. Seiler and Matthew A.T. Elliott and Edward F. Chang and Tomasz J. Nowakowski and Rob Currie and Mohammed A. Mostajo-Radji and David Haussler and Tal Sharf and Sofie R. Salama and Mircea Teodorescu},
url = {https://www.biorxiv.org/content/10.1101/2024.11.14.623530v1},
doi = {https://doi.org/10.1101/2024.11.14.623530},
year = {2024},
date = {2024-11-14},
journal = {bioRxiv},
abstract = {Electrophysiology offers a high-resolution method for real-time measurement of neural activity. The vast amount of data generated requires efficient storage and sophisticated processing to extract neural function and network dynamics. However, analysis is often challenging due to the need for multiple software tools with different runtime dependencies. Longitudinal recordings from high-density microelectrode arrays (HD-MEAs) can be of considerable size for local storage, complicating data management, sharing, and backup. To address these challenges, we developed an open-source cloud-based pipeline to store, analyze, and visualize neuronal electrophysiology recordings from HD-MEAs. This pipeline is dependency agnostic by utilizing cloud storage, cloud computing resources, and an Internet of Things messaging protocol. We containerized the analysis algorithms to serve as scalable and flexible building blocks within the pipeline. We designed graphical user interfaces and command line tools to remove the requirement of programming skills. The interactive visualizations provide multi-modality information on various neuronal features. This cloud-based pipeline is an efficient solution for electrophysiology data processing, the limitations of local software tools, and storage constraints. It simplifies the electrophysiology data analysis process and facilitates understanding neuronal activity. In this paper, we applied this pipeline on two types of cultures, cortical organoids and ex vivo brain slice recordings.},
keywords = {3D Culture, Brain Slice, HD-MEA, MaxOne, MEA Technology, Organoids},
pubstate = {published},
tppubtype = {article}
}
title = {Revealing Single-Neuron and Network-Activity Interaction by Combining High-Density Microelectrode Array and Optogenetics},
author = {Toki Kobayashi and Kenta Shimba and Taiyo Narumi and Takahiro Asahina and Kiyoshi Kotani and Yasuhiko Jimbo },
url = {https://www.nature.com/articles/s41467-024-53505-w},
doi = {10.1038/s41467-024-53505-w},
year = {2024},
date = {2024-11-11},
journal = {Nature Communications },
abstract = {The synchronous activity of neuronal networksisconsideredcrucialforbrain function. However, the interaction between single-neuron activity and network-wide activity remains poorly understood. This study explored this interaction within cultured networks of rat cortical neurons. Employing a combination of high-density microelectrode array recording and optogenetic stimulation, we established an experimental setup enabling simultaneous recording and stimulation at a precise single-neuron level that can be scaled to the level of the whole network. Leveraging our system, we identified a network burst-dependent response change in single neurons, providing a possible mechanism for the network-burst-dependent loss of information within the network and consequent cognitive impairment during epileptic seizures. Additionally, we directly recorded a leader neuron initiating a spontaneous network burst and characterized its firing properties, indicating that the bursting activity of hub neurons in the brain can initiate network-wide activity. Our study offers valuable insights into brain networks characterized by a combination of bottom-up self-organization and top-down regulation.},
keywords = {2D Neuronal Culture, MaxOne, Neuronal Networks, Primary Neuronal Cell Culture, Stimulation},
pubstate = {published},
tppubtype = {article}
}
title = {Dopamine-induced Relaxation of Spike Synchrony Diversifies Burst Patterns in Cultured Hippocampal Networks},
author = {Huu Hoang and Nobuyoshi Matsumoto and Miyuki Miyano and Yuji Ikegaya and Aurelio Cortese },
url = {https://linkinghub.elsevier.com/retrieve/pii/S0893608024008177},
doi = {10.1016/j.neunet.2024.106888},
year = {2024},
date = {2024-11-07},
journal = {Neural Networks },
abstract = {The intricate interplay of neurotransmitters orchestrates a symphony of neural activity in the hippocampus, with dopamine emerging as a key conductor in this complex ensemble. Despite numerous studies uncovering the cellular mechanisms of dopamine, its influence on hippocampal neural networks remains elusive. Combining in vitro electrophysiological recordings of rat embryonic hippocampal neurons, pharmacological interventions, and computational analyses of spike trains, we found that dopamine induces a relaxation in network synchrony. This relaxation expands the repertoire of burst dynamics within these hippocampal networks, a phenomenon notably absent under the administration of dopamine antagonists. Our study provides a thorough understanding of how dopamine signaling influences the formation of functional networks among hippocampal neurons.},
keywords = {2D Neuronal Culture, HD-MEA, MaxOne, Neuronal Networks, Primary Neuronal Cell Culture},
pubstate = {published},
tppubtype = {article}
}
title = {FGF8-Mediated Gene Regulation Affects Regional Identity in Human Cerebral Organoids},
author = {Michele Bertacchi and Gwendoline Maharaux and Agnès Loubat and Matthieu Jung and Michèle Studer},
url = {https://elifesciences.org/articles/98096#content},
doi = {https://doi.org/10.7554/eLife.98096},
year = {2024},
date = {2024-11-01},
journal = {eLife },
abstract = {The morphogen FGF8 establishes graded positional cues imparting regional cellular responses via modulation of early target genes. The roles of FGF signaling and its effector genes remain poorly characterized in human experimental models mimicking early fetal telencephalic development. We used hiPSC-derived cerebral organoids as an in vitro platform to investigate the effect of FGF8 signaling on neural identity and differentiation. We found that FGF8 treatment increases cellular heterogeneity, leading to distinct telencephalic and mesencephalic-like domains that co-develop in multi-regional organoids. Within telencephalic regions, FGF8 affects the anteroposterior and dorsoventral identity of neural progenitors and the balance between GABAergic and glutamatergic neurons, thus impacting spontaneous neuronal network activity. Moreover, FGF8 efficiently modulates key regulators responsible for several human neurodevelopmental disorders. Overall, our results show that FGF8 signaling is directly involved in both regional patterning and cellular diversity in human cerebral organoids and in modulating genes associated with normal and pathological neural development.},
keywords = {3D Culture, Activity Scan Assay, Axon Tracking Assay, HD-MEA, MaxOne, MEA Metrics, Network Assay, Neuronal Networks, Organoids},
pubstate = {published},
tppubtype = {article}
}
title = {Hyperexcitability and Translational Phenotypes in a Preclinical Mouse Model of SYNGAP1-related Intellectual Disability},
author = {Timothy A. Fenton and Olivia Y. Haouchine and Elizabeth B. Hallam and Emily M. Smith and Kiya C. Jackson and Darlene Rahbarian and Cesar P. Canales and Anna Adhikari and Alex S. Nord and Roy Ben-Shalom and Jill L. Silverman},
url = {https://www.nature.com/articles/s41398-024-03077-6},
doi = {https://doi.org/10.1038/s41398-024-03077-6},
year = {2024},
date = {2024-10-02},
journal = {Translational Psychiatry },
abstract = {Disruption of SYNGAP1 directly causes a genetically identifiable neurodevelopmental disorder (NDD) called SYNGAP1-related intellectual disability (SRID). Without functional SynGAP1 protein, individuals are developmentally delayed and have prominent features of intellectual disability (ID), motor impairments, and epilepsy. Over the past two decades, there have been numerous discoveries indicating the critical role of Syngap1. Several rodent models with a loss of Syngap1 have been engineered, identifying precise roles in neuronal structure and function, as well as key biochemical pathways key for synapse integrity. Homozygous loss of SYNGAP1/Syngap1 is lethal. Heterozygous mutations of Syngap1 result in a broad range of behavioral phenotypes. Our in vivo functional data, using the original mouse model from the Huganir laboratory, corroborated behaviors including robust hyperactivity and deficits in learning and memory in young adults. Furthermore, we described impairments in the domain of sleep, characterized using neurophysiological data that was collected with wireless, telemetric electroencephalography (EEG). Syngap1+/− mice exhibited elevated spiking events and spike trains, in addition to elevated power, most notably in the delta power frequency. For the first time, we illustrated that primary neurons from Syngap1+/− mice displayed: 1) increased network firing activity, 2) greater bursts, 3) and shorter inter-burst intervals between peaks, by utilizing high density microelectrode arrays (HD-MEA). Our work bridges in vitro electrophysiological neuronal activity and function with in vivo neurophysiological brain activity and function. These data elucidate quantitative, translational biomarkers in vivo and in vitro that can be utilized for the development and efficacy assessment of targeted treatments for SRID.},
keywords = {2D Neuronal Culture, HD-MEA, MEA Technology, Neuronal Networks, Primary Neuronal Cell Culture},
pubstate = {published},
tppubtype = {article}
}
title = {Prefrontal Synaptic Regulation of Homeostatic Sleep Pressure Revealed Through Synaptic Chemogenetics},
author = {Takeshi Sawada and Yusuke Iino and Kensuke Yoshida and Hitoshi Okazaki and Shinnosuke Nomura and Chika Shimizu and Tomoki Arima and Motoki Juichi and Siqi Zhou and Nobuhiro Kurabayashi and Takeshi Sakurai and Sho Yagishita and Masashi Yanagisawa and Taro Toyoizumi and Haruo Kasai and Shoi Shi},
url = {https://www.science.org/doi/10.1126/science.adl3043},
doi = {10.1126/science.adl3043},
year = {2024},
date = {2024-09-27},
journal = {Science },
abstract = {Sleep is regulated by homeostatic processes, yet the biological basis of sleep pressure that accumulates during wakefulness, triggers sleep, and dissipates during sleep remains elusive. We explored a causal relationship between cellular synaptic strength and electroencephalography delta power indicating macro-level sleep pressure by developing a theoretical framework and a molecular tool to manipulate synaptic strength. The mathematical model predicted that increased synaptic strength promotes the neuronal “down state” and raises the delta power. Our molecular tool (synapse-targeted chemically induced translocation of Kalirin-7, SYNCit-K), which induces dendritic spine enlargement and synaptic potentiation through chemically induced translocation of protein Kalirin-7, demonstrated that synaptic potentiation of excitatory neurons in the prefrontal cortex (PFC) increases nonrapid eye movement sleep amounts and delta power. Thus, synaptic strength of PFC excitatory neurons dictates sleep pressure in mammals.},
keywords = {2D Neuronal Culture, HD-MEA, MaxOne, MEA Technology, Primary Neuronal Cell Culture, Spike Sorting},
pubstate = {published},
tppubtype = {article}
}
title = {Human Neural Organoid Microphysiological Systems Show the Building Blocks Necessary for Basic Learning and Memory},
author = {Dowlette-Mary Alam El Din and Leah Moenkemoeller and Alon Loeffler and Forough Habibollahi and Jack Schenkman and Amitav Mitra and Tjitse van der Molen and Lixuan Ding and Jason Laird and Maren and Schenke and Erik C. Johnson and Brett J. Kagan and Thomas Hartung and Lena Smirnova},
url = {http://biorxiv.org/lookup/doi/10.1101/2024.09.17.613333},
doi = {10.1101/2024.09.17.613333},
year = {2024},
date = {2024-09-19},
journal = {bioRxiv},
abstract = {Brain Microphysiological Systems including neural organoids derived from human induced pluripotent stem cells offer a unique lens to study the intricate workings of the human brain. This paper investigates the foundational elements of learning and memory in neural organoids, also known as Organoid Intelligence by quantifying immediate early gene expression, synaptic plasticity, neuronal network dynamics, and criticality to demonstrate the utility of these organoids in basic science research. Neural organoids showed synapse formation, glutamatergic and GABAergic receptor expression, immediate early gene expression basally and evoked, functional connectivity, criticality, and synaptic plasticity in response to theta-burst stimulation. In addition, pharmacological interventions on GABAergic and glutamatergic receptors, and input specific theta-burst stimulation further shed light on the capacity of neural organoids to mirror synaptic modulation and short-term potentiation, demonstrating their potential as tools for studying neurophysiological and neurological processes and informing therapeutic strategies for diseases.},
keywords = {3D Culture, Activity Scan Assay, Axon Tracking Assay, HD-MEA, IPSC, MaxTwo, MEA Technology, Network Assay, Organoids, Spike Sorting, Stimulation},
pubstate = {published},
tppubtype = {article}
}
title = {Multimodal Mapping of Electrical and Mechanical Latency of Human-Induced Pluripotent Stem Cell-Derived Cardiomyocyte Layers},
author = {Xinyu Zhang and Margherita Burattini and Jens Duru and Nafsika Chala and Nino Wyssen and Carla Cofiño-Fabres and José Manuel Rivera-Arbeláez and Robert Passier and Dimos Poulikakos and Aldo Ferrari, Christina Tringides and János Vörös and Giovanni Battista Luciani and Michele Miragoli and Tomaso Zambelli},
url = {https://doi.org/10.1021/acsnano.4c03896},
doi = {10.1021/acsnano.4c03896},
issn = {1936-0851},
year = {2024},
date = {2024-08-22},
journal = {ACS Nano},
abstract = {The synchronization of the electrical and mechanical coupling assures the physiological pump function of the heart, but life-threatening pathologies may jeopardize this equilibrium. Recently, human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have emerged as a model for personalized investigation because they can recapitulate human diseased traits, such as compromised electrical capacity or mechanical circuit disruption. This research avails the model of hiPSC-CMs and showcases innovative techniques to study the electrical and mechanical properties as well as their modulation due to inherited cardiomyopathies. In this work, hiPSC-CMs carrying either Brugada syndrome (BRU) or dilated cardiomyopathy (DCM), were organized in a bilayer configuration to first validate the experimental methods and second mimic the physiological environment. High-density CMOS-based microelectrode arrays (HD-MEA) have been employed to study the electrical activity. Furthermore, mechanical function was investigated via quantitative video-based evaluation, upon stimulation with a β-adrenergic agonist. This study introduces two experimental methods. First, high-throughput mechanical measurements in the hiPSC-CM layers (xy-inspection) are obtained using both a recently developed optical tracker (OPT) and confocal reference-free traction force microscopy (cTFM) aimed to quantify cardiac kinematics. Second, atomic force microscopy (AFM) with FluidFM probes, combined with the xy-inspection methods, supplemented a three-dimensional understanding of cell−cell mechanical coupling (xyz-inspection). This particular combination represents amulti-technique approach to detecting electrical and mechanical latency among the cell layers, examining differences and possible implications following inherited cardiomyopathies. It can not only detect disease characteristics in the proposed in vitro model but also quantitatively assess its response to drugs, thereby demonstrating its feasibility as ascalable tool for clinical and pharmacological studies.},
keywords = {Cardiomyocytes, HD-MEA, IPSC, MaxOne, MEA Technology},
pubstate = {published},
tppubtype = {article}
}
title = {A 4096 Channel Event-based Multielectrode Array with Asynchronous Outputs Compatible with Neuromorphic Processors},
author = {Matteo Cartiglia and Filippo Costa and Shyam Narayanan and Cat-Vu H. Bui and Hasan Ulusan and Nicoletta Risia and Germain Haessig and Andreas Hierlemann and Fernando Cardes and Giacomo Indiveri},
url = {https://www.nature.com/articles/s41467-024-50783-2},
doi = {10.1038/s41467-024-50783-2},
year = {2024},
date = {2024-08-21},
journal = {Nature Communications},
abstract = {io-signal sensing is pivotal in medical bioelectronics. Traditional methods focus on high sampling rates, leading to large amounts of irrelevant data and high energy consumption. We introduce a self-clocked microelectrode array (MEA) that digitizes bio-signals at the pixel level by encoding changes as asynchronous digital address-events only when they exceed a threshold, significantly reducing off-chip data transmission. This novel MEA comprises a 64 × 64 electrode array, an asynchronous 2D-arbiter, and an Address-Event Representation (AER) communication block. Each pixel operates autonomously, monitoring voltage fluctuations from cellular activity and producing digital pulses for significant changes. Positive and negative signal changes are encoded as “up” and “down” events and are routed off-chip via the asynchronous arbiter. We present results from chip characterization and experimental measurements using electrogenic cells. Additionally, we interface the MEA to a mixed-signal neuromorphic processor, demonstrating a prototype for end-to-end event-based bio-signal sensing and processing.},
keywords = {ETH-CMOS-MEA, MEA Technology},
pubstate = {published},
tppubtype = {article}
}
title = {CardioMEA: Comprehensive Data Analysis Platform for Studying Cardiac Diseases and Drug Responses},
author = {Jihyun Lee and Eliane Duperrex and Ibrahim El-Battrawy and Alyssa Hohn and Ardan M. and Saguner and Firat Duru and Vishalini Emmenegger and Lukas Cyganek and Andreas Hierlemann and Hasan Ulusan},
url = {https://www.biorxiv.org/content/10.1101/2024.07.28.605490v1},
doi = {10.1101/2024.07.28.605490},
year = {2024},
date = {2024-07-29},
journal = {bioRxiv},
abstract = {In recent years, high-density microelectrode arrays (HD-MEAs) have emerged as a 25 valuable tool in preclinical research for characterizing the electrophysiology of human 26 induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). HD-MEAs enable the 27 capturing of both extracellular and intracellular signals on a large scale, while minimizing 28 potential damage to the cell. However, a gap exists between technological advancements 29 of HD-MEAs and the availability of effective data-analysis platforms. To address this 30 need, we introduce CardioMEA, a comprehensive data-analysis platform designed 31 specifically for HD-MEA data that have been obtained from iPSC-CMs. CardioMEA 32 features scalable data processing pipelines and an interactive web-based dashboard for 33 advanced visualization and analysis. In addition to its core functionalities, CardioMEA incorporates modules designed to discern crucial electrophysiological features between diseased and healthy iPSC-CMs. Notably, CardioMEA has the unique capability to analyze both extracellular and intracellular signals, thereby facilitating customized analyses for specific research tasks. We demonstrate the practical application of CardioMEA by analyzing electrophysiological signals from iPSC-CM cultures exposed to seven antiarrhythmic drugs. CardioMEA holds great potential as an intuitive, user-friendly platform for studying cardiac diseases and assessing drug effects.},
keywords = {Cardiomyocytes, IPSC, MEA Technology},
pubstate = {published},
tppubtype = {article}
}
title = {Dopamine-induced Relaxation of Connectivity Diversifies Burst Patterns in Cultured Hippocampal Networks},
author = {Huu Hoang and Nobuyoshi Matsumoto and Miyuki Miyano and Yuji Ikegaya and Aurelio Cortese},
url = {https://www.biorxiv.org/content/10.1101/2024.06.26.600923v1},
doi = {10.1101/2024.06.26.600923},
year = {2024},
date = {2024-06-30},
journal = {bioRxiv},
abstract = {The intricate interplay of neurotransmitters orchestrates a symphony of neural activity in the hippocampus, with dopamine emerging as a key conductor in this complex ensemble. Despite numerous studies uncovering the cellular mechanisms of dopamine, its influence on hippocampal neural networks remains elusive. Combining in vitro electrophysiological recordings of rat embryonic hippocampal neurons, pharmacological interventions, and computational analyses of spike trains, we found that dopamine induces a relaxation in network connectivity, characterised by a reduction in spike coherence. This relaxation expands the repertoire of burst dynamics within these hippocampal networks, a phenomenon notably absent under the administration of dopamine antagonists. Our study provides a thorough understanding of the roles of dopamine signalling in shaping functional networks of hippocampal neurons.},
keywords = {Activity Scan Assay, HD-MEA, MaxOne, MEA Technology, Network Assay, Neuronal Networks, Primary Neuronal Cell Culture},
pubstate = {published},
tppubtype = {article}
}
title = {BiœmuS: A new tool for neurological disorders studies through real-time emulation and hybridization using biomimetic Spiking Neural Network},
author = {Romain Beaubois and Jérémy Cheslet and Tomoya Duenki and Giuseppe De Venuto and Marta Carè and Farad Khoyratee and Michela Chiappalone and Pascal Branchereau and Yoshiho Ikeuchi and Timothée Levi },
url = {https://www.nature.com/articles/s41467-024-48905-x},
doi = {10.1038/s41467-024-48905-x},
year = {2024},
date = {2024-06-20},
journal = {Nature Communications},
abstract = {Characterization and modeling of biological neural networks has emerged as a field driving significant advancements in our understanding of brain function and related pathologies. As of today, pharmacological treatments for neurological disorders remain limited, pushing the exploration of promising alternative approaches such as electroceutics. Recent research in bioelectronics and neuromorphic engineering have fostered the development of the new generation of neuroprostheses for brain repair. However, achieving their full potential necessitates a deeper understanding of biohybrid interaction. In this study, we present a novel real-time, biomimetic, cost-effective and user-friendly neural network capable of real-time emulation for biohybrid experiments. Our system facilitates the investigation and replication of biophysically detailed neural network dynamics while prioritizing cost-efficiency, flexibility and ease of use. We showcase the feasibility of conducting biohybrid experiments using standard biophysical interfaces and a variety of biological cells as well as real-time emulation of diverse network configurations. We envision our system as a crucial step towards the development of neuromorphic-based neuroprostheses for bioelectrical therapeutics, enabling seamless communication with biological networks on a comparable timescale. Its embedded real-time functionality enhances practicality and accessibility, amplifying its potential for real-world applications in biohybrid experiments.},
keywords = {Activity Scan Assay, closed loop stimulation, HD-MEA, IPSC, MaxOne, MEA Technology, Modeling, Organoids, Stimulation},
pubstate = {published},
tppubtype = {article}
}
title = {A Multimodal Fitting Approach to Construct Single-Neuron Models with Patch Clamp and High-Density Microelectrode Arrays},
author = {Alessio Paolo Buccino and Tanguy Damart and Julian Bartram and Darshan Mandge and Xiaohan Xue and Mickael Zbili and Tobias Gänswein and Aurélien Jaquier and Vishalini Emmenegger and Henry Markram and Andreas Hierlemann and Werner Van Geit},
url = {https://direct.mit.edu/neco/article/doi/10.1162/neco_a_01672/121124/A-Multimodal-Fitting-Approach-to-Construct-Single},
doi = {10.1162/neco_a_01672},
year = {2024},
date = {2024-06-07},
journal = {Neural Computation (MIT Press)},
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 nonsomatic 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 microelectrode arrays (HD-MEAs). HD-MEAs enable the observation of extracellular potentials and neural activity of neuronal compartments at subcellular 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 multimodal fitting procedure has the potential to augment the modeling efforts of the computational neuroscience community and provide the field with neuronal models that are more realistic and can be better validated.},
keywords = {2D Neuronal Culture, ETH-CMOS-MEA, HD-MEA, MEA Metrics, MEA Technology},
pubstate = {published},
tppubtype = {article}
}
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 multimodal fitting procedure has the potential to augment the modeling efforts of the computational neuroscience community and provide the field with neuronal models that are more realistic and can be better validated.
title = {Engineering Brain-on-a-Chip Platforms},
author = {Bram Servais and Negar Mahmoudi and Vini Gautam and Wei Tong and Michael R. Ibbotson and David R. Nisbet and David Collins},
url = {https://www.nature.com/articles/s44222-024-00184-3},
doi = {10.1038/s44222-024-00184-3},
year = {2024},
date = {2024-06-05},
journal = {Nature Reviews Bioengineering},
abstract = {The increasing prevalence of neurological and psychiatric diseases, such as Alzheimer disease and schizophrenia, necessitates the development of new research tools to investigate these diseases and develop effective treatments. Thus, in vitro brain models, such as brain-on-a-chip devices, have been developed to mimic in vivo biochemical and mechanobiological interactions and to monitor their electrochemical activity. In this Review, we discuss the technologies to build complex brain models. We discuss progress in microfluidic and semiconductor-based technologies that facilitate in vitro modelling of the blood–brain barrier and neuronal circuits to study pathophysiological processes. We further discuss advances in 3D tissue engineering, electrode strategies and materials that, when combined, could allow simulation of the native complexity of brain regions and the interrogation of their activity at cellular length scales. Furthermore, we explore the engineering challenges and opportunities for complex physiologically relevant brain-on-a-chip devices and their future progress.},
keywords = {3D Culture, MEA Technology},
pubstate = {published},
tppubtype = {article}
}
title = {An implantable biohybrid nerve model towards synaptic deep brain stimulation},
author = {Léo Sifringer and Alex Fratzl and Blandine F. Clément and Parth Chansoria and Leah S. Mönkemöller and Jens Duru and Stephan J. Ihle and Simon Steffens and Anna Beltraminelli and Eylul Ceylan and Julian Hengsteler and Benedikt Maurer and Sean M. Weaver and Christina M. Tringides and Katarina Vulić and Srinivas Madduri and Marcy Zenobi-Wong and Botond Roska and János Vörös and Tobias Ruff},
url = {http://biorxiv.org/lookup/doi/10.1101/2024.05.31.596665},
doi = {10.1101/2024.05.31.596665},
year = {2024},
date = {2024-06-03},
journal = {bioRxiv},
abstract = {Restoring functional vision in blind patients lacking a healthy optic nerve requires bypassing retinal circuits, ideally, by directly stimulating the visual thalamus. However, available deep brain stimulation electrodes do not provide the resolution required for vision restoration. We developed an implantable biohybrid nerve model designed for synaptic stimulation of deep brain targets. The interface combines a stretchable stimulation array with an aligned microfluidic axon guidance system seeded with neural spheroids to facilitate the development of a 3 mm long nerve-like structure. A bioresorbable hydrogel nerve conduit was used as a bridge between the tissue and the biohybrid implant. We demonstrated stimulation of spheroids within the biohybrid structure in vitro and used high-density CMOS microelectrode arrays to show faithful activity conduction across the device. Finally, implantation of the biohybrid nerve onto the mouse cortex showed that neural spheroids grow axons in vivo and remain functionally active for more than 22 days post-implantation.},
keywords = {2D Neuronal Culture, 3D Culture, CMOS, HD-MEA, MaxOne, MEA Technology, Primary Neuronal Cell Culture, Retina},
pubstate = {published},
tppubtype = {article}
}
title = {Biological Neurons Compete with Deep Reinforcement Learning in Sample Efficiency in a Simulated Gameworld},
author = {Moein Khajehnejad and Forough Habibollahi and Aswin Paul and Adeel Razi and Brett J. Kagan},
url = {http://arxiv.org/abs/2405.16946},
doi = { https://doi.org/10.48550/arXiv.2405.16946},
year = {2024},
date = {2024-05-27},
journal = {arXiv },
abstract = {How do biological systems and machine learning algorithms compare in the number of samples required to show significant improvements in completing a task? We compared the learning efficiency of in vitro biological neural networks to the state-of-the-art deep reinforcement learning (RL) algorithms in a simplified simulation of the game `Pong'. Using DishBrain, a system that embodies in vitro neural networks with in silico computation using a high-density multi-electrode array, we contrasted the learning rate and the performance of these biological systems against time-matched learning from three state-of-the-art deep RL algorithms (i.e., DQN, A2C, and PPO) in the same game environment. This allowed a meaningful comparison between biological neural systems and deep RL. We find that when samples are limited to a real-world time course, even these very simple biological cultures outperformed deep RL algorithms across various game performance characteristics, implying a higher sample efficiency. Ultimately, even when tested across multiple types of information input to assess the impact of higher dimensional data input, biological neurons showcased faster learning than all deep reinforcement learning agents.},
keywords = {2D Neuronal Culture, closed loop stimulation, HD-MEA, IPSC, Machine Learning, MaxOne, Modeling, Primary Neuronal Cell Culture},
pubstate = {published},
tppubtype = {article}
}
title = {Action potential propagation speed compensates for traveling distance in the human retina},
author = {Annalisa Bucci and Marc Büttner and Niklas Domdei and Federica Bianca Rosselli and Matej Znidaric and Roland Diggelmann and Martina De Gennaro and Cameron S. Cowan and Wolf Harmening and Andreas Hierlemann and Botond Roska and Felix Franke },
url = {http://biorxiv.org/lookup/doi/10.1101/2024.04.30.591867},
doi = {10.1101/2024.04.30.591867},
year = {2024},
date = {2024-05-01},
journal = {bioRxiv },
abstract = {Neural information processing requires accurately timed action potentials arriving from presynaptic neurons at the postsynaptic neuron. However, axons of ganglion cells in the human retina feature low axonal conduction speeds and vastly different lengths, which poses a challenge to the brain for constructing a temporally coherent image over the visual field. Combining results from microelectrode array recordings, human behavioral measurements, transmission electron microscopy, and mathematical modelling of the retinal nerve fiber layer, we demonstrate that axonal propagation speeds compensate for variations in axonal length across the human retina including the fovea. The human brain synchronizes the arrival times of action potentials at the optic disc by increasing the diameters of longer axons, which increases their propagation speeds.},
keywords = {Activity Assay, Activity Scan Assay, Axon Tracking Assay, HD-MEA, MaxOne, MEA Metrics, MEA Technology, Microfluidics, Modeling, Retina, Slices, Spike Sorting},
pubstate = {published},
tppubtype = {article}
}
title = {Ensemble learning and ground-truth validation of synaptic connectivity inferred from spike trains},
author = {Christian Donner and Julian Bartram and Philipp Hornauer and Taehoon Kim and Damian Roqueiro and Andreas Hierlemann and Guillaume Obozinski and Manuel Schröter },
url = {https://dx.plos.org/10.1371/journal.pcbi.1011964},
doi = {10.1371/journal.pcbi.1011964},
year = {2024},
date = {2024-04-29},
journal = {PLOS Computational Biology},
abstract = {Probing the architecture of neuronal circuits and the principles that underlie their functional organization remains an important challenge of modern neurosciences. This holds true, in particular, for the inference of neuronal connectivity from large-scale extracellular recordings. Despite the popularity of this approach and a number of elaborate methods to reconstruct networks, the degree to which synaptic connections can be reconstructed from spike-train recordings alone remains controversial. Here, we provide a framework to probe and compare connectivity inference algorithms, using a combination of synthetic ground-truth and in vitro data sets, where the connectivity labels were obtained from simultaneous high-density microelectrode array (HD-MEA) and patch-clamp recordings. We find that reconstruction performance critically depends on the regularity of the recorded spontaneous activity, i.e., their dynamical regime, the type of connectivity, and the amount of available spike-train data. We therefore introduce an ensemble artificial neural network (eANN) to improve connectivity inference. We train the eANN on the validated outputs of six established inference algorithms and show how it improves network reconstruction accuracy and robustness. Overall, the eANN demonstrated strong performance across different dynamical regimes, worked well on smaller datasets, and improved the detection of synaptic connectivity, especially inhibitory connections. Results indicated that the eANN also improved the topological characterization of neuronal networks. The presented methodology contributes to advancing the performance of inference algorithms and facilitates our understanding of how neuronal activity relates to synaptic connectivity.
Author summary
This study introduces an ensemble artificial neural network (eANN) to infer neuronal connectivity from spike times. We benchmark the eANN against existing connectivity inference algorithms and validate it using in silico simulations and in vitro data obtained from parallel high-density microelectrode array (HD-MEA) and patch-clamp recordings. Results demonstrate that the eANN outperforms all other algorithms across different dynamical regimes and provides a more accurate description of the underlying topological organization of the studied networks. Further examinations of the eANN’s output are conducted to identify which input features are most instrumental in achieving this enhanced performance. In sum, the eANN is a promising approach to improve connectivity inference from spike-train data.},
keywords = {ETH-CMOS-MEA, HD-MEA, MaxTwo, MEA Metrics, MEA Technology, Modeling, Primary Neuronal Cell Culture, Spike Sorting, Synapses},
pubstate = {published},
tppubtype = {article}
}
Author summary
This study introduces an ensemble artificial neural network (eANN) to infer neuronal connectivity from spike times. We benchmark the eANN against existing connectivity inference algorithms and validate it using in silico simulations and in vitro data obtained from parallel high-density microelectrode array (HD-MEA) and patch-clamp recordings. Results demonstrate that the eANN outperforms all other algorithms across different dynamical regimes and provides a more accurate description of the underlying topological organization of the studied networks. Further examinations of the eANN’s output are conducted to identify which input features are most instrumental in achieving this enhanced performance. In sum, the eANN is a promising approach to improve connectivity inference from spike-train data.
title = {Analgesic Effect of Botulinum Toxin in Neuropathic Pain is Sodium Channel Independent},
author = {Aylin B. Kesdoğan and Anika Neureiter and Arnim J. Gaebler and Anil K. Kalia and Jannis Körner and Angelika Lampert },
url = {https://www.sciencedirect.com/science/article/pii/S0028390824001369?via%3Dihub},
doi = {10.1016/j.neuropharm.2024.109967},
year = {2024},
date = {2024-04-23},
journal = {Neuropharmacology},
abstract = {Botulinum neurotoxin type A BoNT/A is used off-label as a third line therapy for neuropathic pain. However, the mechanism of action remains unclear. In recent years, the role of voltage-gated sodium channels (Nav) in neuropathic pain became evident and it was suggested that block of sodium channels by BoNT/A would contribute to its analgesic effect.
We assessed sodium channel function in the presence of BoNT/A in heterologously expressed Nav1.7, Nav1.3, and the neuronal cell line ND7/23 by high throughput automated and manual patch-clamp. We used both the full protein and the isolated catalytic light chain LC/A for acute or long-term extracellular or intracellular exposure. To assess the toxin's effect in a human cellular system, we differentiated induced pluripotent stem cells (iPSC) into sensory neurons from a healthy control and a patient suffering from a hereditary neuropathic pain syndrome (inherited erythromelalgia) carrying the Nav1.7/p.Q875E-mutation and carried out multielectrode-array measurements.
Both BoNT/A and the isolated catalytic light chain LC/A showed limited effects in heterologous expression systems and the neuronal cell line ND7/23. Spontaneous activity in iPSC derived sensory neurons remained unaltered upon BoNT/A exposure both in neurons from the healthy control and the mutation carrying patient.
BoNT/A may not specifically be beneficial in pain syndromes linked to sodium channel variants. The favorable effects of BoNT/A in neuropathic pain are likely based on mechanisms other than sodium channel blockage and new approaches to understand BoNT/A's therapeutic effects are necessary.},
keywords = {2D Neuronal Culture, Activity Scan Assay, HD-MEA, IPSC, MaxTwo, MEA Metrics, MEA Technology},
pubstate = {published},
tppubtype = {article}
}
We assessed sodium channel function in the presence of BoNT/A in heterologously expressed Nav1.7, Nav1.3, and the neuronal cell line ND7/23 by high throughput automated and manual patch-clamp. We used both the full protein and the isolated catalytic light chain LC/A for acute or long-term extracellular or intracellular exposure. To assess the toxin's effect in a human cellular system, we differentiated induced pluripotent stem cells (iPSC) into sensory neurons from a healthy control and a patient suffering from a hereditary neuropathic pain syndrome (inherited erythromelalgia) carrying the Nav1.7/p.Q875E-mutation and carried out multielectrode-array measurements.
Both BoNT/A and the isolated catalytic light chain LC/A showed limited effects in heterologous expression systems and the neuronal cell line ND7/23. Spontaneous activity in iPSC derived sensory neurons remained unaltered upon BoNT/A exposure both in neurons from the healthy control and the mutation carrying patient.
BoNT/A may not specifically be beneficial in pain syndromes linked to sodium channel variants. The favorable effects of BoNT/A in neuropathic pain are likely based on mechanisms other than sodium channel blockage and new approaches to understand BoNT/A's therapeutic effects are necessary.
title = {RT-Sort: an action potential propagation-based algorithm for real time spike detection and sorting with millisecond latencies},
author = {Tjitse van der Molen and Max Lim and Julian Bartram and Zhuowei Cheng and Ash Robbins and David F. Parks and Linda R. Petzold and Andreas Hierlemann and David Haussler and Paul K. Hansma and Kenneth R. Tovar and Kenneth S. Kosik},
url = {http://biorxiv.org/lookup/doi/10.1101/2024.04.08.588620},
doi = {10.1101/2024.04.08.588620},
year = {2024},
date = {2024-04-12},
journal = {bioRxiv},
abstract = {With the use of high density multi electrode recording devices, electrophysiological signals resulting from action potentials of individual neurons can now be reliably detected on multiple adjacent recording electrodes both in vivo and in vitro. Spike sorting assigns these signals to putative neural sources. However, until now, spike sorting can only be performed after completion of the recording, preventing true real time usage of spike sorting algorithms. Utilizing the unique propagation patterns of action potentials along axons detected as high fidelity sequential activations on adjacent electrodes, together with a convolutional neural network based spike detection algorithm, we introduce RT-Sort (Real Time Sorting), a spike sorting algorithm that enables the sorted detection of action potentials within 7.5ms±1.5ms (mean±STD) after the waveform trough while the recording remains ongoing. RT-Sort’s true real-time spike sorting capabilities enable closed loop experiments with latencies comparable to synaptic delay times. We show RT-Sort’s performance on both Multi-Electrode Arrays as well as Neuropixels probes to exemplify RT-Sort’s functionality on different types of recording hardware and electrode configurations.},
keywords = {3D Culture, Action Potential, closed loop stimulation, HD-MEA, MEA Metrics, MEA Technology, Organoids, Spike Sorting, Stimulation},
pubstate = {published},
tppubtype = {article}
}
title = {Characterizing and targeting glioblastoma neuron-tumor networks with retrograde tracing},
author = {Svenja K. Tetzlaff and Ekin Reyhan and C. Peter Bengtson and Julian Schroers and Julia Wagner and Marc C. Schubert and Nikolas Layer and Maria C. Puschhof and Anton J. Faymonville and Nina Drewa and Rangel L. Pramatarov and Niklas Wissmann and Obada Alhalabi and Alina Heuer and Nirosan Sivapalan and Joaquín Campos and Berin Boztepe and Jonas G. Scheck and Giulia Villa and Manuel Schröter and Felix Sahm and Karin Forsberg-Nilsson and Michael O. Breckwoldt and Claudio Acuna and Bogdana Suchorska and Dieter Henrik Heiland and Julio Saez-Rodriguez and Varun Venkataramani},
url = {http://biorxiv.org/lookup/doi/10.1101/2024.03.18.585565},
doi = {10.1101/2024.03.18.585565},
year = {2024},
date = {2024-03-22},
journal = {bioRxiv},
abstract = {Glioblastomas are invasive brain tumors with high therapeutic resistance. Neuron-to-glioma synapses have been shown to promote glioblastoma progression. However, a characterization of tumor-connected neurons has been hampered by a lack of technologies. Here, we adapted retrograde tracing using rabies viruses to investigate and manipulate neuron-tumor networks. Glioblastoma rapidly integrated into neural circuits across the brain engaging in widespread functional communication, with acetylcholinergic neurons driving glioblastoma invasion. We uncovered patient-specific and tumor cell state-dependent differences in synaptogenic gene expression associated with neuron-tumor connectivity and subsequent invasivity. Importantly, radiotherapy enhanced neuron-tumor connectivity by increased neuronal activity. In turn, simultaneous neuronal activity inhibition and radiotherapy showed increased therapeutic effects, indicative of a role for neuron-to-glioma synapses in contributing to therapeutic resistance. Lastly, rabies-mediated genetic ablation of tumor-connected neurons halted glioblastoma progression, offering a viral strategy to tackle glioblastoma. Together, this study provides a framework to comprehensively characterize neuron-tumor networks and target glioblastoma.},
keywords = {3D Culture, HD-MEA, MaxTwo, MEA Metrics, MEA Technology, Organoids, Primary Neuronal Cell Culture},
pubstate = {published},
tppubtype = {article}
}
title = {Hyperexcitability and translational phenotypes in a preclinical mouse model of SYNGAP1-Related Intellectual Disability},
author = {Timothy A Fenton and Olivia Y Haouchine and Elizabeth L Hallam and Emily M Smith and Kiya C Jackson and Darlene Rahbarian and Cesar Canales and Anna Adhikari and Alexander S Nord and Roy Ben-Shalom and Jill L Silverman},
url = {https://www.researchsquare.com/article/rs-4067746/v1},
doi = {10.21203/rs.3.rs-4067746/v1},
year = {2024},
date = {2024-03-19},
journal = {Research Square},
abstract = {Disruption of SYNGAP1 directly causes a genetically identifiable neurodevelopmental disorder (NDD) called SYNGAP1-related intellectual disability (SRID). Without functional SynGAP1 protein, individuals are developmentally delayed and have prominent features of intellectual disability, motor impairments, and epilepsy. Over the past two decades, there have been numerous discoveries indicting the critical role of Syngap1. Several rodent models with a loss of Syngap1 have been engineered identifying precise roles in neuronal structure and function, as well as key biochemical pathways key for synapse integrity. Homozygous loss of Syngap1 is lethal. Heterozygous mutations of Syngap1 result in a broad range of behavioral phenotypes. Our in vivo functional data, using the mouse model from the Huganir laboratory, corroborated earlier reported behaviors including robust hyperactivity and deficits in learning and memory in young adults. In extension, we report impairments in slow wave sleep, a critical component of the domain of sleep. We characterized Syngap1+/- mice by using neurophysiology collected with wireless, telemetric electroencephalography (EEG). Syngap1+/- mice also exhibited elevated spiking events and spike trains, in addition to elevated power, most notably in the delta frequency band. For the first time, we illustrated how primary neurons from Syngap1+/- mice function and display increased network firing activity, greater bursts, and shorter inter-burst intervals between peaks by employing high density microelectrode arrays (HD-MEA). Our reported data bridge in-vitro electrophysiological neuronal activity and function with in vivo neurophysiological brain activity and function. These data elucidate quantitative, translational biomarkers in vivo and in vitro that can be utilized for the development of and efficacy assessment of targeted treatments for SRID.},
keywords = {Activity Scan Assay, HD-MEA, MaxOne, MEA Metrics, MEA Technology, Network Assay, Primary Neuronal Cell Culture, Spike Sorting},
pubstate = {published},
tppubtype = {article}
}
title = {A feedback-driven IoT microfluidic, electrophysiology, and imaging platform for brain organoid studies},
author = {Kateryna Voitiuk and Spencer T. Seiler and Mirella Pessoa de Melo and Jinghui Geng and Sebastian Hernandez and Hunter E. Schweiger and Jess L. Sevetson and David F. Parks and Ash Robbins and Sebastian Torres-Montoya and Drew Ehrlich and Matthew A.T. Elliott and Tal Sharf and David Haussler and Mohammed A. Mostajo-Radji and Sofie R. Salama and Mircea Teodorescu},
url = {http://biorxiv.org/lookup/doi/10.1101/2024.03.15.585237},
doi = {10.1101/2024.03.15.585237},
year = {2024},
date = {2024-03-17},
journal = {bioRxiv},
abstract = {The analysis of tissue cultures, particularly brain organoids, takes a high degree of coordination, measurement, and monitoring. We have developed an automated research platform enabling independent devices to achieve collaborative objectives for feedback-driven cell culture studies. Unified by an Internet of Things (IoT) architecture, our approach enables continuous, communicative interactions among various sensing and actuation devices, achieving precisely timed control of in vitro biological experiments. The framework integrates microfluidics, electrophysiology, and imaging devices to maintain cerebral cortex organoids and monitor their neuronal activity. The organoids are cultured in custom, 3D-printed chambers attached to commercial microelectrode arrays for electrophysiology monitoring. Periodic feeding is achieved using programmable microfluidic pumps. We developed computer vision fluid volume estimations of aspirated media, achieving high accuracy, and used feedback to rectify deviations in microfluidic perfusion during media feeding/aspiration cycles. We validated the system with a 7-day study of mouse cerebral cortex organoids, comparing manual and automated protocols. The automated experimental samples maintained robust neural activity throughout the experiment, comparable with the control samples. The automated system enabled hourly electrophysiology recordings that revealed dramatic temporal changes in neuron firing rates not observed in once-a-day recordings.
One-Sentence Summary:
An IoT laboratory robotics system that enables touch-free feeding, imaging, and electrophysiology of brain organoids.},
keywords = {Activity Scan Assay, HD-MEA, MaxOne, MEA Metrics, MEA Technology, Microfluidics, Organoids},
pubstate = {published},
tppubtype = {article}
}
One-Sentence Summary:
An IoT laboratory robotics system that enables touch-free feeding, imaging, and electrophysiology of brain organoids.
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 = {Forskolin-driven conversion of human somatic cells into induced neurons through regulation of the cAMP-CREB1-JNK signaling},
author = {Guodong Wang and Dandan Zhang and Liangshan Qin and Quanhui Liu and Wenkui Tang and Mingxing Liu and Fan Xu and Fen Tang and Leping Cheng and Huiming Mo and Xiang Yuan and Zhiqiang Wang and Ben Huang},
url = {https://www.thno.org/v14p1701.htm},
doi = {10.7150/thno.92700},
year = {2024},
date = {2024-02-11},
journal = {Theranostics },
abstract = {Human somatic cells can be reprogrammed into neuron cell fate through regulation of a single transcription factor or application of small molecule cocktails.
Methods: Here, we report that forskolin efficiently induces the conversion of human somatic cells into induced neurons (FiNs).
Results: A large population of neuron-like phenotype cells was observed as early as 24-36 h post-induction. There were >90% TUJ1-, >80% MAP2-, and >80% NEUN-positive neurons at 5 days post-induction. Multiple subtypes of neurons were present among TUJ1-positive cells, including >60% cholinergic, >20% glutamatergic, >10% GABAergic, and >5% dopaminergic neurons. FiNs exhibited typical neural electrophysiological activity in vitro and the ability to survive in vitro and in vivo more than 2 months. Mechanistically, forskolin functions in FiN reprogramming by regulating the cAMP-CREB1-JNK signals, which upregulates cAMP-CREB1 expression and downregulates JNK expression.
Conclusion: Overall, our studies identify a safer and efficient single-small-molecule-driven reprogramming approach for induced neuron generation and reveal a novel regulatory mechanism of neuronal cell fate acquisition.},
keywords = {2D Neuronal Culture, HD-MEA, MaxOne, MEA Technology},
pubstate = {published},
tppubtype = {article}
}
Methods: Here, we report that forskolin efficiently induces the conversion of human somatic cells into induced neurons (FiNs).
Results: A large population of neuron-like phenotype cells was observed as early as 24-36 h post-induction. There were >90% TUJ1-, >80% MAP2-, and >80% NEUN-positive neurons at 5 days post-induction. Multiple subtypes of neurons were present among TUJ1-positive cells, including >60% cholinergic, >20% glutamatergic, >10% GABAergic, and >5% dopaminergic neurons. FiNs exhibited typical neural electrophysiological activity in vitro and the ability to survive in vitro and in vivo more than 2 months. Mechanistically, forskolin functions in FiN reprogramming by regulating the cAMP-CREB1-JNK signals, which upregulates cAMP-CREB1 expression and downregulates JNK expression.
Conclusion: Overall, our studies identify a safer and efficient single-small-molecule-driven reprogramming approach for induced neuron generation and reveal a novel regulatory mechanism of neuronal cell fate acquisition.
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 = {Protosequences in human cortical organoids model intrinsic states in the developing cortex},
author = {Tjitse van der Molen and Alex Spaeth and Mattia Chini and Julian Bartram and Aditya Dendukuri and Zongren Zhang and Kiran Bhaskaran-Nair and Lon J. Blauvelt and Linda R. Petzold and Paul K. Hansma and Mircea Teodorescu and Andreas Hierlemann and Keith B. Hengen and Ileana L. Hanganu-Opatz and Kenneth S. Kosik and Tal Sharf},
url = {https://www.biorxiv.org/content/10.1101/2023.12.29.573646v1},
doi = {10.1101/2023.12.29.573646},
year = {2023},
date = {2023-12-30},
journal = {bioRxiv},
abstract = {Neuronal firing sequences are thought to be the basic building blocks of neural coding and information broadcasting within the brain. However, when sequences emerge during neurodevelopment remains unknown. We demonstrate that structured firing sequences are present in spontaneous activity of human brain organoids and ex vivo neonatal brain slices from the murine somatosensory cortex. We observed a balance between temporally rigid and flexible firing patterns that are emergent phenomena in human brain organoids and early postnatal murine somatosensory cortex, but not in primary dissociated cortical cultures. Our findings suggest that temporal sequences do not arise in an experience-dependent manner, but are rather constrained by an innate preconfigured architecture established during neurogenesis. These findings highlight the potential for brain organoids to further explore how exogenous inputs can be used to refine neuronal circuits and enable new studies into the genetic mechanisms that govern assembly of functional circuitry during early human brain development.},
keywords = {MaxOne, Organoids},
pubstate = {published},
tppubtype = {article}
}
title = {Human neuron subtype programming through combinatorial patterning with scRNA-seq readouts},
author = {Hsiu-Chuan Lin and Jasper Janssens and Ann-Sophie Kroell and Philipp Hornauer and Malgorzata Santel and Ryoko Okamoto and Kyriaki Karava and Marthe Priouret and Maria Pascual Garcia and Manuel Schroeter and J. Gray Camp and Barbara Treutlein},
url = {https://www.biorxiv.org/content/10.1101/2023.12.12.571318v2},
doi = {10.1101/2023.12.12.571318},
year = {2023},
date = {2023-12-20},
journal = {bioRxiv},
abstract = {Human neurons programmed through transcription factor (TF) overexpression model neuronal differentiation and neurological diseases. However, programming specific neuron types remains challenging. Here, we modulate developmental signaling pathways combined with TF overexpression to explore the spectrum of neuron subtypes generated from pluripotent stem cells. We screened 480 morphogen signaling modulations coupled with NGN2 or ASCL1/DLX2 induction using a multiplexed single-cell transcriptomic readout. Analysis of 700,000 cells identified diverse excitatory and inhibitory neurons patterned along the anteriorposterior and dorsal-ventral axes of neural tube development. We inferred signaling and TF interaction networks guiding differentiation of forebrain, midbrain, hindbrain, spinal cord, peripheral sympathetic and sensory neurons. Our approach provides a strategy for cell subtype programming and to investigate how cooperative signaling drives neuronal fate.},
keywords = {2D Neuronal Culture, Activity Scan Assay, Axon Tracking Assay, HD-MEA, MaxTwo, Network Assay},
pubstate = {published},
tppubtype = {article}
}