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Abbaspoor S, Hoffman KL. Circuit dynamics of superficial and deep CA1 pyramidal cells and inhibitory cells in freely moving macaques. Cell Rep 2024; 43:114519. [PMID: 39018243 DOI: 10.1016/j.celrep.2024.114519] [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: 01/21/2024] [Revised: 05/23/2024] [Accepted: 07/02/2024] [Indexed: 07/19/2024] Open
Abstract
Diverse neuron classes in hippocampal CA1 have been identified through the heterogeneity of their cellular/molecular composition. How these classes relate to hippocampal function and the network dynamics that support cognition in primates remains unclear. Here, we report inhibitory functional cell groups in CA1 of freely moving macaques whose diverse response profiles to network states and each other suggest distinct and specific roles in the functional microcircuit of CA1. In addition, pyramidal cells that were grouped by their superficial or deep layer position differed in firing rate, burstiness, and sharp-wave ripple-associated firing. They also showed strata-specific spike-timing interactions with inhibitory cell groups, suggestive of segregated neural populations. Furthermore, ensemble recordings revealed that cell assemblies were preferentially organized according to these strata. These results suggest that hippocampal CA1 in freely moving macaques bears a sublayer-specific circuit organization that may shape its role in cognition.
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Affiliation(s)
- Saman Abbaspoor
- Department of Psychology, Vanderbilt Vision Research Center, Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.
| | - Kari L Hoffman
- Department of Psychology, Vanderbilt Vision Research Center, Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
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Lee AT, Chang EF, Paredes MF, Nowakowski TJ. Large-scale neurophysiology and single-cell profiling in human neuroscience. Nature 2024; 630:587-595. [PMID: 38898291 DOI: 10.1038/s41586-024-07405-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 04/09/2024] [Indexed: 06/21/2024]
Abstract
Advances in large-scale single-unit human neurophysiology, single-cell RNA sequencing, spatial transcriptomics and long-term ex vivo tissue culture of surgically resected human brain tissue have provided an unprecedented opportunity to study human neuroscience. In this Perspective, we describe the development of these paradigms, including Neuropixels and recent brain-cell atlas efforts, and discuss how their convergence will further investigations into the cellular underpinnings of network-level activity in the human brain. Specifically, we introduce a workflow in which functionally mapped samples of human brain tissue resected during awake brain surgery can be cultured ex vivo for multi-modal cellular and functional profiling. We then explore how advances in human neuroscience will affect clinical practice, and conclude by discussing societal and ethical implications to consider. Potential findings from the field of human neuroscience will be vast, ranging from insights into human neurodiversity and evolution to providing cell-type-specific access to study and manipulate diseased circuits in pathology. This Perspective aims to provide a unifying framework for the field of human neuroscience as we welcome an exciting era for understanding the functional cytoarchitecture of the human brain.
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Affiliation(s)
- Anthony T Lee
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Edward F Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mercedes F Paredes
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Tomasz J Nowakowski
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA.
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
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Abbaspoor S, Hoffman KL. Circuit dynamics of superficial and deep CA1 pyramidal cells and inhibitory cells in freely-moving macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.06.570369. [PMID: 38106053 PMCID: PMC10723348 DOI: 10.1101/2023.12.06.570369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Diverse neuron classes in hippocampal CA1 have been identified through the heterogeneity of their cellular/molecular composition. How these classes relate to hippocampal function and the network dynamics that support cognition in primates remains unclear. Here we report inhibitory functional cell groups in CA1 of freely-moving macaques whose diverse response profiles to network states and each other suggest distinct and specific roles in the functional microcircuit of CA1. In addition, pyramidal cells that were segregated into superficial and deep layers differed in firing rate, burstiness, and sharp-wave ripple-associated firing. They also showed strata-specific spike-timing interactions with inhibitory cell groups, suggestive of segregated neural populations. Furthermore, ensemble recordings revealed that cell assemblies were preferentially organized according to these strata. These results suggest sublayer-specific circuit organization in hippocampal CA1 of the freely-moving macaques that may underlie its role in cognition.
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Affiliation(s)
- S Abbaspoor
- Department of Psychology, Vanderbilt Vision Research Center, Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee
| | - K L Hoffman
- Department of Psychology, Vanderbilt Vision Research Center, Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
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Pierré A, Pham T, Pearl J, Datta SR, Ritt JT, Fleischmann A. A perspective on neuroscience data standardization with Neurodata Without Borders. ARXIV 2024:arXiv:2310.04317v2. [PMID: 37873012 PMCID: PMC10593085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Neuroscience research has evolved to generate increasingly large and complex experimental data sets, and advanced data science tools are taking on central roles in neuroscience research. Neurodata Without Borders (NWB), a standard language for neurophysiology data, has recently emerged as a powerful solution for data management, analysis, and sharing. We here discuss our labs' efforts to implement NWB data science pipelines. We describe general principles and specific use cases that illustrate successes, challenges, and non-trivial decisions in software engineering. We hope that our experience can provide guidance for the neuroscience community and help bridge the gap between experimental neuroscience and data science.
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Affiliation(s)
- Andrea Pierré
- Department of Neuroscience, Division of Biology and Medicine, Brown University, Providence, USA
- The Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, USA
| | - Tuan Pham
- Department of Neuroscience, Division of Biology and Medicine, Brown University, Providence, USA
- The Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, USA
| | - Jonah Pearl
- Department of Neurobiology, Harvard Medical School, Boston, USA
| | | | - Jason T. Ritt
- The Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, USA
| | - Alexander Fleischmann
- Department of Neuroscience, Division of Biology and Medicine, Brown University, Providence, USA
- The Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, USA
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Esparza J, Sebastián ER, de la Prida LM. From cell types to population dynamics: Making hippocampal manifolds physiologically interpretable. Curr Opin Neurobiol 2023; 83:102800. [PMID: 37898015 DOI: 10.1016/j.conb.2023.102800] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/30/2023]
Abstract
The study of the hippocampal code is gaining momentum. While the physiological approach targets the contribution of individual cells as determined by genetic, biophysical and circuit factors, the field pushes for a population dynamic approach that considers the representation of behavioural variables by a large number of neurons. In this alternative framework, neuronal activity is projected into low-dimensional manifolds. These manifolds can reveal the structure of population representations, but their physiological interpretation is challenging. Here, we review the recent literature and propose that integrating information regarding behavioral traits, local field potential oscillations and cell-type-specificity into neural manifolds offers strategies to make them interpretable at the physiological level.
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