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Dura-Bernal S, Herrera B, Lupascu C, Marsh BM, Gandolfi D, Marasco A, Neymotin S, Romani A, Solinas S, Bazhenov M, Hay E, Migliore M, Reinmann M, Arkhipov A. Large-Scale Mechanistic Models of Brain Circuits with Biophysically and Morphologically Detailed Neurons. J Neurosci 2024; 44:e1236242024. [PMID: 39358017 PMCID: PMC11450527 DOI: 10.1523/jneurosci.1236-24.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/09/2024] [Accepted: 07/31/2024] [Indexed: 10/04/2024] Open
Abstract
Understanding the brain requires studying its multiscale interactions from molecules to networks. The increasing availability of large-scale datasets detailing brain circuit composition, connectivity, and activity is transforming neuroscience. However, integrating and interpreting this data remains challenging. Concurrently, advances in supercomputing and sophisticated modeling tools now enable the development of highly detailed, large-scale biophysical circuit models. These mechanistic multiscale models offer a method to systematically integrate experimental data, facilitating investigations into brain structure, function, and disease. This review, based on a Society for Neuroscience 2024 MiniSymposium, aims to disseminate recent advances in large-scale mechanistic modeling to the broader community. It highlights (1) examples of current models for various brain regions developed through experimental data integration; (2) their predictive capabilities regarding cellular and circuit mechanisms underlying experimental recordings (e.g., membrane voltage, spikes, local-field potential, electroencephalography/magnetoencephalography) and brain function; and (3) their use in simulating biomarkers for brain diseases like epilepsy, depression, schizophrenia, and Parkinson's, aiding in understanding their biophysical underpinnings and developing novel treatments. The review showcases state-of-the-art models covering hippocampus, somatosensory, visual, motor, auditory cortical, and thalamic circuits across species. These models predict neural activity at multiple scales and provide insights into the biophysical mechanisms underlying sensation, motor behavior, brain signals, neural coding, disease, pharmacological interventions, and neural stimulation. Collaboration with experimental neuroscientists and clinicians is essential for the development and validation of these models, particularly as datasets grow. Hence, this review aims to foster interest in detailed brain circuit models, leading to cross-disciplinary collaborations that accelerate brain research.
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Affiliation(s)
- Salvador Dura-Bernal
- State University of New York (SUNY) Downstate Health Sciences University, Brooklyn, New York 11203
- Nathan S. Kline Institute for Psychiatric Research, Orangeburg, New York 10962
| | | | - Carmen Lupascu
- Institute of Biophysics, National Research Council/Human Brain Project, Palermo 90146, Italy
| | - Brianna M Marsh
- University of California San Diego, La Jolla, California 92093
| | - Daniela Gandolfi
- Department of Engineering "Enzo Ferrari", University of Modena and Reggio Emilia, Modena 41125, Italy
| | | | - Samuel Neymotin
- Nathan S. Kline Institute for Psychiatric Research, Orangeburg, New York 10962
- School of Medicine, New York University, New York 10012
| | - Armando Romani
- Swiss Federal Institute of Technology Lausanne (EPFL)/Blue Brain Project, Lausanne 1015, Switzerland
| | | | - Maxim Bazhenov
- University of California San Diego, La Jolla, California 92093
| | - Etay Hay
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, Ontario M5T 1R8, Canada
- University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Michele Migliore
- Institute of Biophysics, National Research Council/Human Brain Project, Palermo 90146, Italy
| | - Michael Reinmann
- Swiss Federal Institute of Technology Lausanne (EPFL)/Blue Brain Project, Lausanne 1015, Switzerland
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Mackey CA, Duecker K, Neymotin S, Dura-Bernal S, Haegens S, Barczak A, O'Connell MN, Jones SR, Ding M, Ghuman AS, Schroeder CE. Is there a ubiquitous spectrolaminar motif of local field potential power across primate neocortex? BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.18.613490. [PMID: 39345528 PMCID: PMC11429918 DOI: 10.1101/2024.09.18.613490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Mendoza-Halliday, Major et al., 2024 ("The Paper")1 advocates a local field potential (LFP)-based approach to functional identification of cortical layers during "laminar" (simultaneous recordings from all cortical layers) multielectrode recordings in nonhuman primates (NHPs). The Paper describes a "ubiquitous spectrolaminar motif" in the primate neocortex: 1) 75-150 Hz power peaks in the supragranular layers, 2) 10-19 Hz power peaks in the infragranular layers and 3) the crossing point of their laminar power gradients identifies Layer 4 (L4). Identification of L4 is critical in general, but especially for The Paper as the "motif" discovery is couched within a framework whose central hypothesis is that gamma activity originates in the supragranular layers and reflects feedforward activity, while alpha-beta activity originates in the infragranular layers and reflects feedback activity. In an impressive scientific effort, The Paper analyzed laminar data from 14 cortical areas in 2 prior macaque studies and compared them to marmoset, mouse, and human data to further bolster the canonical nature of the motif. Identification of such canonical principles of brain operation is clearly a topic of broad scientific interest. Similarly, a reliable online method for L4 identification would be of broad scientific value for the rapidly increasing use of laminar recordings using numerous evolving technologies. Despite The Paper's strengths, and its potential for scientific impact, a series of concerns that are fundamental to the analysis and interpretation of laminar activity profile data in general, and local field potential (LFP) signals in particular, led us to question its conclusions. We thus evaluated the generality of The Paper's methods and findings using new sets of data comprised of stimulus-evoked laminar response profiles from primary and higher-order auditory cortices (A1 and belt cortex), and primary visual cortex (V1). The rationale for using these areas as a test bed for new methods is that their laminar anatomy and physiology have already been extensively characterized by prior studies, and there is general agreement across laboratories on key matters like L4 identification. Our analyses indicate that The Paper's findings do not generalize well to any of these cortical areas. In particular, we find The Paper's methods for L4 identification to be unreliable. Moreover, both methodological and statistical concerns, outlined below and in the supplement, question the stated prevalence of the motif in The Paper's published dataset. After summarizing our findings and related broader concerns, we briefly critique the evidence from biophysical modeling studies cited to support The Paper's conclusions. While our findings are at odds with the proposition of a ubiquitous spectrolaminar motif in the primate neocortex, The Paper already has, and will continue to spark debate and further experimentation. Hopefully this countervailing presentation will lead to robust collegial efforts to define optimal strategies for applying laminar recording methods in future studies.
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Affiliation(s)
- C A Mackey
- Center for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA
| | - K Duecker
- Department of Neuroscience, Brown University, Providence, Rhode Island 02912
| | - S Neymotin
- Center for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA
- Department Psychiatry, NYU Grossman School of Medicine, New York, NY, USA
| | - S Dura-Bernal
- Center for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA
- Department of Physiology and Pharmacology, State University of New York (SUNY) Downstate Health Sciences University, Brooklyn, NY, USA
| | - S Haegens
- Department of Psychiatry, Columbia University, New York, USA
- Division of Systems Neuroscience, New York State Psychiatric Institute, New York, USA
| | - A Barczak
- Center for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA
| | - M N O'Connell
- Center for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA
- Department of Psychiatry, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - S R Jones
- Department of Neuroscience, Brown University, Providence, Rhode Island 02912
- Center for Neurorestoration and Neurotechnology, Providence VA Medical Center, Providence, Rhode Island 02908
| | - M Ding
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL
| | - A S Ghuman
- Center for Neuroscience at the University of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
- Center for the Neural Basis of Cognition, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - C E Schroeder
- Center for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA
- Departments of Psychiatry and Neurology, Columbia University, New York, USA
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Goldfarb M. Fibroblast growth factor homologous factors: canonical and non-canonical mechanisms of action. J Physiol 2024; 602:4097-4110. [PMID: 39083261 DOI: 10.1113/jp286313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 07/16/2024] [Indexed: 09/01/2024] Open
Abstract
Since their discovery nearly 30 years ago, fibroblast growth factor homologous factors (FHFs) are now known to control the functionality of excitable tissues through a range of mechanisms. Nervous and cardiac system dysfunctions are caused by loss- or gain-of-function mutations in FHF genes. The best understood 'canonical' targets for FHF action are voltage-gated sodium channels, and recent studies have expanded the repertoire of ways that FHFs modulate sodium channel gating. Additional 'non-canonical' functions of FHFs in excitable and non-excitable cells, including cancer cells, have been reported over the past dozen years. This review summarizes and evaluates reported canonical and non-canonical FHF functions.
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Affiliation(s)
- Mitchell Goldfarb
- Department of Biological Sciences, Hunter College of City University, New York, New York, USA
- Biology Program, The Graduate Center City University, New York, New York, USA
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Griffith EY, ElSayed M, Dura-Bernal S, Neymotin SA, Uhlrich DJ, Lytton WW, Zhu JJ. Mechanism of an Intrinsic Oscillation in Rat Geniculate Interneurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597830. [PMID: 38895250 PMCID: PMC11185623 DOI: 10.1101/2024.06.06.597830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Depolarizing current injections produced a rhythmic bursting of action potentials - a bursting oscillation - in a set of local interneurons in the lateral geniculate nucleus (LGN) of rats. The current dynamics underlying this firing pattern have not been determined, though this cell type constitutes an important cellular component of thalamocortical circuitry, and contributes to both pathologic and non-pathologic brain states. We thus investigated the source of the bursting oscillation using pharmacological manipulations in LGN slices in vitro and in silico. 1. Selective blockade of calcium channel subtypes revealed that high-threshold calcium currentsI L andI P contributed strongly to the oscillation. 2. Increased extracellular K+ concentration (decreased K+currents) eliminated the oscillation. 3. Selective blockade of K+ channel subtypes demonstrated that the calcium-sensitive potassium current (I A H P ) was of primary importance. A morphologically simplified, multicompartment model of the thalamic interneuron characterized the oscillation as follows: 1. The low-threshold calcium currentI T provided the strong initial burst characteristic of the oscillation. 2. Alternating fluxes through high-threshold calcium channels andI A H P then provided the continuing oscillation's burst and interburst periods respectively. This interplay betweenI L andI A H P contrasts with the current dynamics underlying oscillations in thalamocortical and reticularis neurons, which primarily involveI T andI H , orI T andI A H P respectively. These findings thus point to a novel electrophysiological mechanism for generating intrinsic oscillations in a major thalamic cell type. Because local interneurons can sculpt the behavior of thalamocortical circuits, these results suggest new targets for the manipulation of ascending thalamocortical network activity.
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Affiliation(s)
- Erica Y Griffith
- Department of Neural and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY
- Center for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY
| | - Mohamed ElSayed
- Department of Psychiatry, Geisel School of Medicine at Dartmouth, Hanover, NH
- Department of Biomedical Engineering, SUNY Downstate School of Graduate Studies, Brooklyn, NY
- Department of Psychiatry, New Hampshire Hospital, Concord, NH
| | - Salvador Dura-Bernal
- Center for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY
- Department of Physiology and Pharmacology, SUNY Downstate Health Sciences University, Brooklyn, NY
| | - Samuel A Neymotin
- Center for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY
- Department of Psychiatry, New York University School of Medicine, New York, NY
| | - Daniel J Uhlrich
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - William W Lytton
- Department of Physiology and Pharmacology, SUNY Downstate Health Sciences University, Brooklyn, NY
- Department of Neurology, Kings County Hospital, Brooklyn, NY
| | - J Julius Zhu
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA
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Guet-McCreight A, Chameh HM, Mazza F, Prevot TD, Valiante TA, Sibille E, Hay E. In-silico testing of new pharmacology for restoring inhibition and human cortical function in depression. Commun Biol 2024; 7:225. [PMID: 38396202 PMCID: PMC10891083 DOI: 10.1038/s42003-024-05907-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Reduced inhibition by somatostatin-expressing interneurons is associated with depression. Administration of positive allosteric modulators of α5 subunit-containing GABAA receptor (α5-PAM) that selectively target this lost inhibition exhibit antidepressant and pro-cognitive effects in rodent models of chronic stress. However, the functional effects of α5-PAM on the human brain in vivo are unknown, and currently cannot be assessed experimentally. We modeled the effects of α5-PAM on tonic inhibition as measured in human neurons, and tested in silico α5-PAM effects on detailed models of human cortical microcircuits in health and depression. We found that α5-PAM effectively recovered impaired cortical processing as quantified by stimulus detection metrics, and also recovered the power spectral density profile of the microcircuit EEG signals. We performed an α5-PAM dose-response and identified simulated EEG biomarker candidates. Our results serve to de-risk and facilitate α5-PAM translation and provide biomarkers in non-invasive brain signals for monitoring target engagement and drug efficacy.
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Affiliation(s)
- Alexandre Guet-McCreight
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada.
| | | | - Frank Mazza
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Thomas D Prevot
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Taufik A Valiante
- Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
- Department of Surgery, University of Toronto, Toronto, ON, Canada
- Center for Advancing Neurotechnological Innovation to Application, Toronto, ON, Canada
- Max Planck-University of Toronto Center for Neural Science and Technology, Toronto, ON, Canada
| | - Etienne Sibille
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Etay Hay
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada.
- Department of Physiology, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
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Neymotin SA, Tal I, Barczak A, O'Connell MN, McGinnis T, Markowitz N, Espinal E, Griffith E, Anwar H, Dura-Bernal S, Schroeder CE, Lytton WW, Jones SR, Bickel S, Lakatos P. Detecting Spontaneous Neural Oscillation Events in Primate Auditory Cortex. eNeuro 2022; 9:ENEURO.0281-21.2022. [PMID: 35906065 PMCID: PMC9395248 DOI: 10.1523/eneuro.0281-21.2022] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 05/20/2022] [Accepted: 06/20/2022] [Indexed: 11/21/2022] Open
Abstract
Electrophysiological oscillations in the brain have been shown to occur as multicycle events, with onset and offset dependent on behavioral and cognitive state. To provide a baseline for state-related and task-related events, we quantified oscillation features in resting-state recordings. We developed an open-source wavelet-based tool to detect and characterize such oscillation events (OEvents) and exemplify the use of this tool in both simulations and two invasively-recorded electrophysiology datasets: one from human, and one from nonhuman primate (NHP) auditory system. After removing incidentally occurring event-related potentials (ERPs), we used OEvents to quantify oscillation features. We identified ∼2 million oscillation events, classified within traditional frequency bands: δ, θ, α, β, low γ, γ, and high γ. Oscillation events of 1-44 cycles could be identified in at least one frequency band 90% of the time in human and NHP recordings. Individual oscillation events were characterized by nonconstant frequency and amplitude. This result necessarily contrasts with prior studies which assumed frequency constancy, but is consistent with evidence from event-associated oscillations. We measured oscillation event duration, frequency span, and waveform shape. Oscillations tended to exhibit multiple cycles per event, verifiable by comparing filtered to unfiltered waveforms. In addition to the clear intraevent rhythmicity, there was also evidence of interevent rhythmicity within bands, demonstrated by finding that coefficient of variation of interval distributions and Fano factor (FF) measures differed significantly from a Poisson distribution assumption. Overall, our study provides an easy-to-use tool to study oscillation events at the single-trial level or in ongoing recordings, and demonstrates that rhythmic, multicycle oscillation events dominate auditory cortical dynamics.
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Affiliation(s)
- Samuel A Neymotin
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962
- Department Psychiatry, New York University Grossman School of Medicine, New York, NY 10016
| | - Idan Tal
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962
- Departments of Neurosurgery and Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY 10032
| | - Annamaria Barczak
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962
| | - Monica N O'Connell
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962
| | - Tammy McGinnis
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962
| | - Noah Markowitz
- Department Neurology and Neurosurgery, The Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY 11030
| | - Elizabeth Espinal
- Department Neurology and Neurosurgery, The Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY 11030
| | - Erica Griffith
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962
- Department Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, NY 11203
| | - Haroon Anwar
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962
| | - Salvador Dura-Bernal
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962
- Department Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, NY 11203
| | - Charles E Schroeder
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962
- Departments of Neurosurgery and Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY 10032
| | - William W Lytton
- Department Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, NY 11203
- Department Neurology, Kings County Hospital Center, Brooklyn, NY 11203
| | - Stephanie R Jones
- Department Neuroscience and Carney Institute for Brain Science, Brown University, Providence, RI 02906
| | - Stephan Bickel
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962
- Department Neurology and Neurosurgery, The Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY 11030
| | - Peter Lakatos
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962
- Department Psychiatry, New York University Grossman School of Medicine, New York, NY 10016
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