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Callegari F, Brofiga M, Massobrio P. Modeling the three-dimensional connectivity of in vitro cortical ensembles coupled to Micro-Electrode Arrays. PLoS Comput Biol 2023; 19:e1010825. [PMID: 36780570 PMCID: PMC9956882 DOI: 10.1371/journal.pcbi.1010825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 02/24/2023] [Accepted: 12/17/2022] [Indexed: 02/15/2023] Open
Abstract
Nowadays, in vitro three-dimensional (3D) neuronal networks are becoming a consolidated experimental model to overcome most of the intrinsic limitations of bi-dimensional (2D) assemblies. In the 3D environment, experimental evidence revealed a wider repertoire of activity patterns, characterized by a modulation of the bursting features, than the one observed in 2D cultures. However, it is not totally clear and understood what pushes the neuronal networks towards different dynamical regimes. One possible explanation could be the underlying connectivity, which could involve a larger number of neurons in a 3D rather than a 2D space and could organize following well-defined topological schemes. Driven by experimental findings, achieved by recording 3D cortical networks organized in multi-layered structures coupled to Micro-Electrode Arrays (MEAs), in the present work we developed a large-scale computational network model made up of leaky integrate-and-fire (LIF) neurons to investigate possible structural configurations able to sustain the emerging patterns of electrophysiological activity. In particular, we investigated the role of the number of layers defining a 3D assembly and the spatial distribution of the connections within and among the layers. These configurations give rise to different patterns of activity that could be compared to the ones emerging from real in vitro 3D neuronal populations. Our results suggest that the introduction of three-dimensionality induced a global reduction in both firing and bursting rates with respect to 2D models. In addition, we found that there is a minimum number of layers necessary to obtain a change in the dynamics of the network. However, the effects produced by a 3D organization of the cells is somewhat mitigated if a scale-free connectivity is implemented in either one or all the layers of the network. Finally, the best matching of the experimental data is achieved supposing a 3D connectivity organized in structured bundles of links located in different areas of the 2D network.
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Affiliation(s)
- Francesca Callegari
- Department of Informatics, Bioengineering, Robotics and Systems Engineering (DIBRIS), University of Genova, Genova, Italy
| | - Martina Brofiga
- Department of Informatics, Bioengineering, Robotics and Systems Engineering (DIBRIS), University of Genova, Genova, Italy
- ScreenNeuroPharm, Sanremo, Italy
| | - Paolo Massobrio
- Department of Informatics, Bioengineering, Robotics and Systems Engineering (DIBRIS), University of Genova, Genova, Italy
- National Institute for Nuclear Physics (INFN), Genova, Italy
- * E-mail:
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Duru J, Küchler J, Ihle SJ, Forró C, Bernardi A, Girardin S, Hengsteler J, Wheeler S, Vörös J, Ruff T. Engineered Biological Neural Networks on High Density CMOS Microelectrode Arrays. Front Neurosci 2022; 16:829884. [PMID: 35264928 PMCID: PMC8900719 DOI: 10.3389/fnins.2022.829884] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/27/2022] [Indexed: 12/18/2022] Open
Abstract
In bottom-up neuroscience, questions on neural information processing are addressed by engineering small but reproducible biological neural networks of defined network topology in vitro. The network topology can be controlled by culturing neurons within polydimethylsiloxane (PDMS) microstructures that are combined with microelectrode arrays (MEAs) for electric access to the network. However, currently used glass MEAs are limited to 256 electrodes and pose a limitation to the spatial resolution as well as the design of more complex microstructures. The use of high density complementary metal-oxide-semiconductor (CMOS) MEAs greatly increases the spatial resolution, enabling sub-cellular readout and stimulation of neurons in defined neural networks. Unfortunately, the non-planar surface of CMOS MEAs complicates the attachment of PDMS microstructures. To overcome the problem of axons escaping the microstructures through the ridges of the CMOS MEA, we stamp-transferred a thin film of hexane-diluted PDMS onto the array such that the PDMS filled the ridges at the contact surface of the microstructures without clogging the axon guidance channels. This method resulted in 23 % of structurally fully connected but sealed networks on the CMOS MEA of which about 45 % showed spiking activity in all channels. Moreover, we provide an impedance-based method to visualize the exact location of the microstructures on the MEA and show that our method can confine axonal growth within the PDMS microstructures. Finally, the high spatial resolution of the CMOS MEA enabled us to show that action potentials follow the unidirectional topology of our circular multi-node microstructure.
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Affiliation(s)
- Jens Duru
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Joël Küchler
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Stephan J. Ihle
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Csaba Forró
- Cui Laboratory, Stanford University, Stanford, CA, United States
| | - Aeneas Bernardi
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Sophie Girardin
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Julian Hengsteler
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Stephen Wheeler
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Tobias Ruff
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
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Brofiga M, Pisano M, Tedesco M, Raiteri R, Massobrio P. Three-dimensionality shapes the dynamics of cortical interconnected to hippocampal networks. J Neural Eng 2020; 17:056044. [DOI: 10.1088/1741-2552/abc023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Forró C, Thompson-Steckel G, Weaver S, Weydert S, Ihle S, Dermutz H, Aebersold MJ, Pilz R, Demkó L, Vörös J. Modular microstructure design to build neuronal networks of defined functional connectivity. Biosens Bioelectron 2018; 122:75-87. [DOI: 10.1016/j.bios.2018.08.075] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/27/2018] [Accepted: 08/30/2018] [Indexed: 02/01/2023]
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Orenstein O, Keren H. Development of Cortical Networks under Continuous Stimulation. Front Mol Neurosci 2017; 10:18. [PMID: 28197075 PMCID: PMC5281561 DOI: 10.3389/fnmol.2017.00018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/13/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ophir Orenstein
- Network Biology Research Laboratory, Electrical Engineering, Technion - Israel Institute of TechnologyHaifa, Israel; Department of Physiology, Biophysics and Systems Biology, Technion - Israel Institute of TechnologyHaifa, Israel
| | - Hanna Keren
- Network Biology Research Laboratory, Electrical Engineering, Technion - Israel Institute of TechnologyHaifa, Israel; Department of Physiology, Biophysics and Systems Biology, Technion - Israel Institute of TechnologyHaifa, Israel
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Abstract
The difficulty to understand, diagnose, and treat neurological disorders stems from the great complexity of the central nervous system on different levels of physiological granularity. The individual components, their interactions, and dynamics involved in brain development and function can be represented as molecular, cellular, or functional networks, where diseases are perturbations of networks. These networks can become a useful research tool in investigating neurological disorders if they are properly tailored to reflect corresponding mechanisms. Here, we review approaches to construct networks specific for neurological disorders describing disease-related pathology on different scales: the molecular, cellular, and brain level. We also briefly discuss cross-scale network analysis as a necessary integrator of these scales.
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Poli D, Pastore VP, Massobrio P. Functional connectivity in in vitro neuronal assemblies. Front Neural Circuits 2015; 9:57. [PMID: 26500505 PMCID: PMC4595785 DOI: 10.3389/fncir.2015.00057] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/22/2015] [Indexed: 01/21/2023] Open
Abstract
Complex network topologies represent the necessary substrate to support complex brain functions. In this work, we reviewed in vitro neuronal networks coupled to Micro-Electrode Arrays (MEAs) as biological substrate. Networks of dissociated neurons developing in vitro and coupled to MEAs, represent a valid experimental model for studying the mechanisms governing the formation, organization and conservation of neuronal cell assemblies. In this review, we present some examples of the use of statistical Cluster Coefficients and Small World indices to infer topological rules underlying the dynamics exhibited by homogeneous and engineered neuronal networks.
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Affiliation(s)
- Daniele Poli
- Department of Informatics, Bioengineering, Robotics and System Engineering, University of Genova Genova, Italy
| | - Vito P Pastore
- Department of Informatics, Bioengineering, Robotics and System Engineering, University of Genova Genova, Italy
| | - Paolo Massobrio
- Department of Informatics, Bioengineering, Robotics and System Engineering, University of Genova Genova, Italy
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Napoli A, Obeid I. Comparative Analysis of Human and Rodent Brain Primary Neuronal Culture Spontaneous Activity Using Micro-Electrode Array Technology. J Cell Biochem 2015; 117:559-65. [PMID: 26284690 DOI: 10.1002/jcb.25312] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 11/06/2022]
Abstract
Electrical activity in embryonic brain tissue has typically been studied using Micro Electrode Array (MEA) technology to make dozens of simultaneous recordings from dissociated neuronal cultures, brain stem cell progenitors, or brain slices from fetal rodents. Although these rodent neuronal primary culture electrical properties are mostly investigated, it has not been yet established to what extent the electrical characteristics of rodent brain neuronal cultures can be generalized to those of humans. A direct comparison of spontaneous spiking activity between rodent and human primary neurons grown under the same in vitro conditions using MEA technology has never been carried out before and will be described in the present study. Human and rodent dissociated fetal brain neuronal cultures were established in-vitro by culturing on a glass grid of 60 planar microelectrodes neurons under identical conditions. Three different cultures of human neurons were produced from tissue sourced from a single aborted fetus (at 16-18 gestational weeks) and these were compared with seven different cultures of embryonic rat neurons (at 18 gestational days) originally isolated from a single rat. The results show that the human and rodent cultures behaved significantly differently. Whereas the rodent cultures demonstrated robust spontaneous activation and network activity after only 10 days, the human cultures required nearly 40 days to achieve a substantially weaker level of electrical function. These results suggest that rat neuron preparations may yield inferences that do not necessarily transfer to humans.
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Affiliation(s)
- Alessandro Napoli
- Department of Electrical and Computer Engineering, College of Engineering, Temple University, Philadelphia, Pennsylvania.,Department of Neuroscience and Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Iyad Obeid
- Department of Electrical and Computer Engineering, College of Engineering, Temple University, Philadelphia, Pennsylvania
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