251
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Ding L, Balsamo G, Diamantaki M, Preston-Ferrer P, Burgalossi A. Opto-juxtacellular interrogation of neural circuits in freely moving mice. Nat Protoc 2023; 18:2415-2440. [PMID: 37420087 DOI: 10.1038/s41596-023-00842-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/11/2023] [Indexed: 07/09/2023]
Abstract
Neural circuits are assembled from an enormous variety of neuronal cell types. Although significant advances have been made in classifying neurons on the basis of morphological, molecular and electrophysiological properties, understanding how this diversity contributes to brain function during behavior has remained a major experimental challenge. Here, we present an extension to our previous protocol, in which we describe the technical procedures for performing juxtacellular opto-tagging of single neurons in freely moving mice by using Channelrhodopsin-2-expressing viral vectors. This method allows one to selectively target molecularly defined cell classes for in vivo single-cell recordings. The targeted cells can be labeled via juxtacellular procedures and further characterized via post-hoc morphological and molecular analysis. In its current form, the protocol allows multiple recording and labeling attempts to be performed within individual animals, by means of a mechanical pipette micropositioning system. We provide proof-of-principle validation of this technique by recording from Calbindin-positive pyramidal neurons in the mouse hippocampus during spatial exploration; however, this approach can easily be extended to other behaviors and cortical or subcortical areas. The procedures described here, from the viral injection to the histological processing of brain sections, can be completed in ~4-5 weeks.This protocol is an extension to: Nat. Protoc. 9, 2369-2381 (2014): https://doi.org/10.1038/nprot.2014.161.
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Affiliation(s)
- Lingjun Ding
- Institute of Neurobiology, Eberhard Karls University of Tübingen, Tübingen, Germany
- Werner-Reichardt Centre for Integrative Neuroscience, Tübingen, Germany
- Graduate Training Centre of Neuroscience-International Max-Planck Research School (IMPRS), Tübingen, Germany
| | - Giuseppe Balsamo
- Institute of Neurobiology, Eberhard Karls University of Tübingen, Tübingen, Germany
- Werner-Reichardt Centre for Integrative Neuroscience, Tübingen, Germany
- Graduate Training Centre of Neuroscience-International Max-Planck Research School (IMPRS), Tübingen, Germany
| | - Maria Diamantaki
- Institute of Neurobiology, Eberhard Karls University of Tübingen, Tübingen, Germany
- Werner-Reichardt Centre for Integrative Neuroscience, Tübingen, Germany
- Graduate Training Centre of Neuroscience-International Max-Planck Research School (IMPRS), Tübingen, Germany
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, Heraklion, Greece
| | - Patricia Preston-Ferrer
- Institute of Neurobiology, Eberhard Karls University of Tübingen, Tübingen, Germany.
- Werner-Reichardt Centre for Integrative Neuroscience, Tübingen, Germany.
| | - Andrea Burgalossi
- Institute of Neurobiology, Eberhard Karls University of Tübingen, Tübingen, Germany.
- Werner-Reichardt Centre for Integrative Neuroscience, Tübingen, Germany.
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252
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Jin K, Yao Z, van Velthoven CTJ, Kaplan ES, Glattfelder K, Barlow ST, Boyer G, Carey D, Casper T, Chakka AB, Chakrabarty R, Clark M, Departee M, Desierto M, Gary A, Gloe J, Goldy J, Guilford N, Guzman J, Hirschstein D, Lee C, Liang E, Pham T, Reding M, Ronellenfitch K, Ruiz A, Sevigny J, Shapovalova N, Shulga L, Sulc J, Torkelson A, Tung H, Levi B, Sunkin SM, Dee N, Esposito L, Smith K, Tasic B, Zeng H. Cell-type specific molecular signatures of aging revealed in a brain-wide transcriptomic cell-type atlas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550355. [PMID: 38168182 PMCID: PMC10760145 DOI: 10.1101/2023.07.26.550355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Biological aging can be defined as a gradual loss of homeostasis across various aspects of molecular and cellular function. Aging is a complex and dynamic process which influences distinct cell types in a myriad of ways. The cellular architecture of the mammalian brain is heterogeneous and diverse, making it challenging to identify precise areas and cell types of the brain that are more susceptible to aging than others. Here, we present a high-resolution single-cell RNA sequencing dataset containing ~1.2 million high-quality single-cell transcriptomic profiles of brain cells from young adult and aged mice across both sexes, including areas spanning the forebrain, midbrain, and hindbrain. We find age-associated gene expression signatures across nearly all 130+ neuronal and non-neuronal cell subclasses we identified. We detect the greatest gene expression changes in non-neuronal cell types, suggesting that different cell types in the brain vary in their susceptibility to aging. We identify specific, age-enriched clusters within specific glial, vascular, and immune cell types from both cortical and subcortical regions of the brain, and specific gene expression changes associated with cell senescence, inflammation, decrease in new myelination, and decreased vasculature integrity. We also identify genes with expression changes across multiple cell subclasses, pointing to certain mechanisms of aging that may occur across wide regions or broad cell types of the brain. Finally, we discover the greatest gene expression changes in cell types localized to the third ventricle of the hypothalamus, including tanycytes, ependymal cells, and Tbx3+ neurons found in the arcuate nucleus that are part of the neuronal circuits regulating food intake and energy homeostasis. These findings suggest that the area surrounding the third ventricle in the hypothalamus may be a hub for aging in the mouse brain. Overall, we reveal a dynamic landscape of cell-type-specific transcriptomic changes in the brain associated with normal aging that will serve as a foundation for the investigation of functional changes in the aging process and the interaction of aging and diseases.
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Affiliation(s)
- Kelly Jin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Daniel Carey
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Max Departee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jessica Gloe
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Josh Sevigny
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Boaz Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
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253
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Miyoshi E, Morabito S, Henningfield CM, Rahimzadeh N, Kiani Shabestari S, Das S, Michael N, Reese F, Shi Z, Cao Z, Scarfone V, Arreola MA, Lu J, Wright S, Silva J, Leavy K, Lott IT, Doran E, Yong WH, Shahin S, Perez-Rosendahl M, Head E, Green KN, Swarup V. Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.24.550282. [PMID: 37546983 PMCID: PMC10402031 DOI: 10.1101/2023.07.24.550282] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The pathogenesis of Alzheimer's disease (AD) depends on environmental and heritable factors, with remarkable differences evident between individuals at the molecular level. Here we present a transcriptomic survey of AD using spatial transcriptomics (ST) and single-nucleus RNA-seq in cortical samples from early-stage AD, late-stage AD, and AD in Down Syndrome (AD in DS) donors. Studying AD in DS provides an opportunity to enhance our understanding of the AD transcriptome, potentially bridging the gap between genetic mouse models and sporadic AD. Our analysis revealed spatial and cell-type specific changes in disease, with broad similarities in these changes between sAD and AD in DS. We performed additional ST experiments in a disease timecourse of 5xFAD and wildtype mice to facilitate cross-species comparisons. Finally, amyloid plaque and fibril imaging in the same tissue samples used for ST enabled us to directly link changes in gene expression with accumulation and spread of pathology.
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Affiliation(s)
- Emily Miyoshi
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Samuel Morabito
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
- Mathematical, Computational, and Systems Biology (MCSB) Program, University of California Irvine, Irvine, CA, USA
- Center for Complex Biological Systems (CCBS), University of California Irvine, Irvine, CA, USA
| | - Caden M Henningfield
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Negin Rahimzadeh
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
- Mathematical, Computational, and Systems Biology (MCSB) Program, University of California Irvine, Irvine, CA, USA
- Center for Complex Biological Systems (CCBS), University of California Irvine, Irvine, CA, USA
| | - Sepideh Kiani Shabestari
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA, USA
| | - Sudeshna Das
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Neethu Michael
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Fairlie Reese
- Center for Complex Biological Systems (CCBS), University of California Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Zechuan Shi
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Zhenkun Cao
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
| | - Vanessa Scarfone
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA, USA
| | - Miguel A Arreola
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Jackie Lu
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
| | - Sierra Wright
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Justine Silva
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Kelsey Leavy
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Ira T Lott
- Department of Pediatrics, University of California Irvine School of Medicine, Orange, CA, USA
| | - Eric Doran
- Department of Pediatrics, University of California Irvine School of Medicine, Orange, CA, USA
| | - William H Yong
- Department of Pathology and Laboratory Medicine, University of California Irvine , Irvine, CA, USA
| | - Saba Shahin
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Mari Perez-Rosendahl
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
- Department of Pathology and Laboratory Medicine, University of California Irvine , Irvine, CA, USA
| | - Elizabeth Head
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
- Department of Pathology and Laboratory Medicine, University of California Irvine , Irvine, CA, USA
| | - Kim N Green
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
- Center for Complex Biological Systems (CCBS), University of California Irvine, Irvine, CA, USA
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254
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Liu Y, Jiang S, Li Y, Zhao S, Yun Z, Zhao ZH, Zhang L, Wang G, Chen X, Manubens-Gil L, Hang Y, Garcia-Forn M, Wang W, Rubeis SD, Wu Z, Osten P, Gong H, Hawrylycz M, Mitra P, Dong H, Luo Q, Ascoli GA, Zeng H, Liu L, Peng H. Full-Spectrum Neuronal Diversity and Stereotypy through Whole Brain Morphometry. RESEARCH SQUARE 2023:rs.3.rs-3146034. [PMID: 37546984 PMCID: PMC10402258 DOI: 10.21203/rs.3.rs-3146034/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
We conducted a large-scale study of whole-brain morphometry, analyzing 3.7 peta-voxels of mouse brain images at the single-cell resolution, producing one of the largest multi-morphometry databases of mammalian brains to date. We spatially registered 205 mouse brains and associated data from six Brain Initiative Cell Census Network (BICCN) data sources covering three major imaging modalities from five collaborative projects to the Allen Common Coordinate Framework (CCF) atlas, annotated 3D locations of cell bodies of 227,581 neurons, modeled 15,441 dendritic microenvironments, characterized the full morphology of 1,891 neurons along with their axonal motifs, and detected 2.58 million putative synaptic boutons. Our analysis covers six levels of information related to neuronal populations, dendritic microenvironments, single-cell full morphology, sub-neuronal dendritic and axonal arborization, axonal boutons, and structural motifs, along with a quantitative characterization of the diversity and stereotypy of patterns at each level. We identified 16 modules consisting of highly intercorrelated brain regions in 13 functional brain areas corresponding to 314 anatomical regions in CCF. Our analysis revealed the dendritic microenvironment as a powerful method for delineating brain regions of cell types and potential subtypes. We also found that full neuronal morphologies can be categorized into four distinct classes based on spatially tuned morphological features, with substantial cross-areal diversity in apical dendrites, basal dendrites, and axonal arbors, along with quantified stereotypy within cortical, thalamic and striatal regions. The lamination of somas was found to be more effective in differentiating neuron arbors within the cortex. Further analysis of diverging and converging projections of individual neurons in 25 regions throughout the brain reveals branching preferences in the brain-wide and local distributions of axonal boutons. Overall, our study provides a comprehensive description of key anatomical structures of neurons and their types, covering a wide range of scales and features, and contributes to our understanding of neuronal diversity and its function in the mammalian brain.
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Affiliation(s)
- Yufeng Liu
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Shengdian Jiang
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Yingxin Li
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Sujun Zhao
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Zhixi Yun
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Zuo-Han Zhao
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Lingli Zhang
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Gaoyu Wang
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Xin Chen
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Linus Manubens-Gil
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Yuning Hang
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Marta Garcia-Forn
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wei Wang
- Appel Alzheimer’s Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Cell, Developmental & Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhuhao Wu
- Appel Alzheimer’s Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Cell, Developmental & Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pavel Osten
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Hui Gong
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
| | | | - Partha Mitra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Hongwei Dong
- Center for Integrative Connectomics, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Qingming Luo
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Haikou, China
| | - Giorgio A. Ascoli
- Volgenau School of Engineering, George Mason University, Fairfax, VA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lijuan Liu
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Hanchuan Peng
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
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255
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Huang TH, Lin YS, Hsiao CW, Wang LY, Ajibola MI, Abdulmajeed WI, Lin YL, Li YJ, Chen CY, Lien CC, Chiu CD, Cheng IHJ. Differential expression of GABA A receptor subunits δ and α6 mediates tonic inhibition in parvalbumin and somatostatin interneurons in the mouse hippocampus. Front Cell Neurosci 2023; 17:1146278. [PMID: 37545878 PMCID: PMC10397515 DOI: 10.3389/fncel.2023.1146278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/14/2023] [Indexed: 08/08/2023] Open
Abstract
Inhibitory γ-aminobutyric acid (GABA)-ergic interneurons mediate inhibition in neuronal circuitry and support normal brain function. Consequently, dysregulation of inhibition is implicated in various brain disorders. Parvalbumin (PV) and somatostatin (SST) interneurons, the two major types of GABAergic inhibitory interneurons in the hippocampus, exhibit distinct morpho-physiological properties and coordinate information processing and memory formation. However, the molecular mechanisms underlying the specialized properties of PV and SST interneurons remain unclear. This study aimed to compare the transcriptomic differences between these two classes of interneurons in the hippocampus using the ribosome tagging approach. The results revealed distinct expressions of genes such as voltage-gated ion channels and GABAA receptor subunits between PV and SST interneurons. Gabrd and Gabra6 were identified as contributors to the contrasting tonic GABAergic inhibition observed in PV and SST interneurons. Moreover, some of the differentially expressed genes were associated with schizophrenia and epilepsy. In conclusion, our results provide molecular insights into the distinct roles of PV and SST interneurons in health and disease.
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Affiliation(s)
- Tzu-Hsuan Huang
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Sian Lin
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX, United States
| | - Chiao-Wan Hsiao
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Liang-Yun Wang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Musa Iyiola Ajibola
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, College of Life Sciences, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Wahab Imam Abdulmajeed
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, College of Life Sciences, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | - Yu-Ling Lin
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yu-Jui Li
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Cho-Yi Chen
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Cheng-Chang Lien
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, College of Life Sciences, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Cheng-Di Chiu
- Department of Neurosurgery, China Medical University Hospital, Taichung, Taiwan
- Spine Center, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Biomedical Science, China Medical University, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Irene Han-Juo Cheng
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
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256
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Xie F, Armand EJ, Yao Z, Liu H, Bartlett A, Behrens MM, Li YE, Lucero JD, Luo C, Nery JR, Pinto-Duarte A, Poirion OB, Preissl S, Rivkin AC, Tasic B, Zeng H, Ren B, Ecker JR, Mukamel EA. Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes. CELL GENOMICS 2023; 3:100342. [PMID: 37492103 PMCID: PMC10363915 DOI: 10.1016/j.xgen.2023.100342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 03/09/2023] [Accepted: 05/17/2023] [Indexed: 07/27/2023]
Abstract
Single-cell sequencing could help to solve the fundamental challenge of linking millions of cell-type-specific enhancers with their target genes. However, this task is confounded by patterns of gene co-expression in much the same way that genetic correlation due to linkage disequilibrium confounds fine-mapping in genome-wide association studies (GWAS). We developed a non-parametric permutation-based procedure to establish stringent statistical criteria to control the risk of false-positive associations in enhancer-gene association studies (EGAS). We applied our procedure to large-scale transcriptome and epigenome data from multiple tissues and species, including the mouse and human brain, to predict enhancer-gene associations genome wide. We tested the functional validity of our predictions by comparing them with chromatin conformation data and causal enhancer perturbation experiments. Our study shows how controlling for gene co-expression enables robust enhancer-gene linkage using single-cell sequencing data.
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Affiliation(s)
- Fangming Xie
- Department of Physics, University of California San Diego, La Jolla, CA 92037, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ethan J. Armand
- Department of Cognitive Science, University of California San Diego, La Jolla, CA 92037, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - M. Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Yang Eric Li
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Jacinta D. Lucero
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Chongyuan Luo
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Joseph R. Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Antonio Pinto-Duarte
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Olivier B. Poirion
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA
- The Jackson Laboratory, Farmington, CT, USA
| | - Sebastian Preissl
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Angeline C. Rivkin
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Joseph R. Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Eran A. Mukamel
- Department of Cognitive Science, University of California San Diego, La Jolla, CA 92037, USA
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257
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de Vries SEJ, Siegle JH, Koch C. Sharing neurophysiology data from the Allen Brain Observatory. eLife 2023; 12:e85550. [PMID: 37432073 PMCID: PMC10335829 DOI: 10.7554/elife.85550] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/27/2023] [Indexed: 07/12/2023] Open
Abstract
Nullius in verba ('trust no one'), chosen as the motto of the Royal Society in 1660, implies that independently verifiable observations-rather than authoritative claims-are a defining feature of empirical science. As the complexity of modern scientific instrumentation has made exact replications prohibitive, sharing data is now essential for ensuring the trustworthiness of one's findings. While embraced in spirit by many, in practice open data sharing remains the exception in contemporary systems neuroscience. Here, we take stock of the Allen Brain Observatory, an effort to share data and metadata associated with surveys of neuronal activity in the visual system of laboratory mice. Data from these surveys have been used to produce new discoveries, to validate computational algorithms, and as a benchmark for comparison with other data, resulting in over 100 publications and preprints to date. We distill some of the lessons learned about open surveys and data reuse, including remaining barriers to data sharing and what might be done to address these.
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258
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Shi Y, Cui H, Li X, Chen L, Zhang C, Zhao X, Li X, Shao Q, Sun Q, Yan K, Wang G. Laminar and dorsoventral organization of layer 1 interneuronal microcircuitry in superficial layers of the medial entorhinal cortex. Cell Rep 2023; 42:112782. [PMID: 37436894 DOI: 10.1016/j.celrep.2023.112782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 04/03/2023] [Accepted: 06/24/2023] [Indexed: 07/14/2023] Open
Abstract
Layer 1 (L1) interneurons (INs) participate in various brain functions by gating information flow in the neocortex, but their role in the medial entorhinal cortex (MEC) is still unknown, largely due to scant knowledge of MEC L1 microcircuitry. Using simultaneous triple-octuple whole-cell recordings and morphological reconstructions, we comprehensively depict L1IN networks in the MEC. We identify three morphologically distinct types of L1INs with characteristic electrophysiological properties. We dissect intra- and inter-laminar cell-type-specific microcircuits of L1INs, showing connectivity patterns different from those in the neocortex. Remarkably, motif analysis reveals transitive and clustered features of L1 networks, as well as over-represented trans-laminar motifs. Finally, we demonstrate the dorsoventral gradient of L1IN microcircuits, with dorsal L1 neurogliaform cells receiving fewer intra-laminar inputs but exerting more inhibition on L2 principal neurons. These results thus present a more comprehensive picture of L1IN microcircuitry, which is indispensable for deciphering the function of L1INs in the MEC.
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Affiliation(s)
- Yuying Shi
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Hui Cui
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Xiaoyue Li
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Ligu Chen
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Chen Zhang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Xinran Zhao
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Xiaowan Li
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Qiming Shao
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Qiang Sun
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Kaiyue Yan
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Guangfu Wang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China.
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259
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Zhang Q, Jiang S, Schroeder A, Hu J, Li K, Zhang B, Dai D, Lee EB, Xiao R, Li M. Leveraging spatial transcriptomics data to recover cell locations in single-cell RNA-seq with CeLEry. Nat Commun 2023; 14:4050. [PMID: 37422469 PMCID: PMC10329686 DOI: 10.1038/s41467-023-39895-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/03/2023] [Indexed: 07/10/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity in health and disease. However, the lack of physical relationships among dissociated cells has limited its applications. To address this issue, we present CeLEry (Cell Location recovEry), a supervised deep learning algorithm that leverages gene expression and spatial location relationships learned from spatial transcriptomics to recover the spatial origins of cells in scRNA-seq. CeLEry has an optional data augmentation procedure via a variational autoencoder, which improves the method's robustness and allows it to overcome noise in scRNA-seq data. We show that CeLEry can infer the spatial origins of cells in scRNA-seq at multiple levels, including 2D location and spatial domain of a cell, while also providing uncertainty estimates for the recovered locations. Our comprehensive benchmarking evaluations on multiple datasets generated from brain and cancer tissues using Visium, MERSCOPE, MERFISH, and Xenium demonstrate that CeLEry can reliably recover the spatial location information for cells using scRNA-seq data.
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Affiliation(s)
- Qihuang Zhang
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, McGill University, Montreal, QC, Canada.
| | - Shunzhou Jiang
- Statistical Center for Single-Cell and Spatial Genomics, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Amelia Schroeder
- Statistical Center for Single-Cell and Spatial Genomics, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jian Hu
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Kejie Li
- Research Department, Biogen, Inc., 225 Binney St., Cambridge, MA, 02142, USA
| | - Baohong Zhang
- Research Department, Biogen, Inc., 225 Binney St., Cambridge, MA, 02142, USA
| | - David Dai
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rui Xiao
- Statistical Center for Single-Cell and Spatial Genomics, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mingyao Li
- Statistical Center for Single-Cell and Spatial Genomics, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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260
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Nir Y, de Lecea L. Sleep and vigilance states: Embracing spatiotemporal dynamics. Neuron 2023; 111:1998-2011. [PMID: 37148873 DOI: 10.1016/j.neuron.2023.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/08/2023] [Accepted: 04/12/2023] [Indexed: 05/08/2023]
Abstract
The classic view of sleep and vigilance states is a global stationary perspective driven by the interaction between neuromodulators and thalamocortical systems. However, recent data are challenging this view by demonstrating that vigilance states are highly dynamic and regionally complex. Spatially, sleep- and wake-like states often co-occur across distinct brain regions, as in unihemispheric sleep, local sleep in wakefulness, and during development. Temporally, dynamic switching prevails around state transitions, during extended wakefulness, and in fragmented sleep. This knowledge, together with methods monitoring brain activity across multiple regions simultaneously at millisecond resolution with cell-type specificity, is rapidly shifting how we consider vigilance states. A new perspective incorporating multiple spatial and temporal scales may have important implications for considering the governing neuromodulatory mechanisms, the functional roles of vigilance states, and their behavioral manifestations. A modular and dynamic view highlights novel avenues for finer spatiotemporal interventions to improve sleep function.
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Affiliation(s)
- Yuval Nir
- Department of Physiology and Pharmacology, Faculty of Medicine, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel; Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel; The Sieratzki-Sagol Center for Sleep Medicine, Tel-Aviv Sourasky Medical Center, Tel-Aviv 64239, Israel.
| | - Luis de Lecea
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA.
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261
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Harvey RE, Robinson HL, Liu C, Oliva A, Fernandez-Ruiz A. Hippocampo-cortical circuits for selective memory encoding, routing, and replay. Neuron 2023; 111:2076-2090.e9. [PMID: 37196658 PMCID: PMC11146684 DOI: 10.1016/j.neuron.2023.04.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/15/2023] [Accepted: 04/12/2023] [Indexed: 05/19/2023]
Abstract
Traditionally considered a homogeneous cell type, hippocampal pyramidal cells have been recently shown to be highly diverse. However, how this cellular diversity relates to the different hippocampal network computations that support memory-guided behavior is not yet known. We show that the anatomical identity of pyramidal cells is a major organizing principle of CA1 assembly dynamics, the emergence of memory replay, and cortical projection patterns in rats. Segregated pyramidal cell subpopulations encoded trajectory and choice-specific information or tracked changes in reward configuration respectively, and their activity was selectively read out by different cortical targets. Furthermore, distinct hippocampo-cortical assemblies coordinated the reactivation of complementary memory representations. These findings reveal the existence of specialized hippocampo-cortical subcircuits and provide a cellular mechanism that supports the computational flexibility and memory capacities of these structures.
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Affiliation(s)
- Ryan E Harvey
- Department of Neurobiology & Behavior, Cornell University, Ithaca, NY, USA
| | - Heath L Robinson
- Department of Neurobiology & Behavior, Cornell University, Ithaca, NY, USA
| | - Can Liu
- Department of Neurobiology & Behavior, Cornell University, Ithaca, NY, USA
| | - Azahara Oliva
- Department of Neurobiology & Behavior, Cornell University, Ithaca, NY, USA.
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262
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Tzou FY, Hornemann T, Yeh JY, Huang SY. The pathophysiological role of dihydroceramide desaturase in the nervous system. Prog Lipid Res 2023; 91:101236. [PMID: 37187315 DOI: 10.1016/j.plipres.2023.101236] [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: 11/13/2022] [Revised: 04/18/2023] [Accepted: 05/12/2023] [Indexed: 05/17/2023]
Abstract
Dihydroceramide desaturase 1 (DEGS1) converts dihydroceramide (dhCer) to ceramide (Cer) by inserting a C4-C5 trans (∆4E) double bond into the sphingoid backbone. Low DEGS activity causes accumulation of dhCer and other dihydrosphingolipid species. Although dhCer and Cer are structurally very similar, their imbalances can have major consequences both in vitro and in vivo. Mutations in the human DEGS1 gene are known to cause severe neurological defects, such as hypomyelinating leukodystrophy. Likewise, inhibition of DEGS1 activity in fly and zebrafish models causes dhCer accumulation and subsequent neuronal dysfunction, suggesting that DEGS1 activity plays a conserved and critical role in the nervous system. Dihydrosphingolipids and their desaturated counterparts are known to control various essential processes, including autophagy, exosome biogenesis, ER stress, cell proliferation, and cell death. Furthermore, model membranes with either dihydrosphingolipids or sphingolipids exhibit different biophysical properties, including membrane permeability and packing, thermal stability, and lipid diffusion. However, the links between molecular properties, in vivo functional data, and clinical manifestations that underlie impaired DEGS1 function remain largely unresolved. In this review, we summarize the known biological and pathophysiological roles of dhCer and its derivative dihydrosphingolipid species in the nervous system, and we highlight several possible disease mechanisms that warrant further investigation.
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Affiliation(s)
- Fei-Yang Tzou
- Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Thorsten Hornemann
- Institute for Clinical Chemistry, University Hospital and University Zurich, 8091 Zürich, Switzerland
| | - Jui-Yu Yeh
- Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shu-Yi Huang
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan.
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263
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Cao JW, Mao XY, Zhu L, Zhou ZS, Jiang SN, Liu LY, Zhang SQ, Fu Y, Xu WD, Yu YC. Correlation Analysis of Molecularly-Defined Cortical Interneuron Populations with Morpho-Electric Properties in Layer V of Mouse Neocortex. Neurosci Bull 2023; 39:1069-1086. [PMID: 36422797 PMCID: PMC10313633 DOI: 10.1007/s12264-022-00983-x] [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: 06/16/2022] [Accepted: 08/16/2022] [Indexed: 11/25/2022] Open
Abstract
Cortical interneurons can be categorized into distinct populations based on multiple modalities, including molecular signatures and morpho-electrical (M/E) properties. Recently, many transcriptomic signatures based on single-cell RNA-seq have been identified in cortical interneurons. However, whether different interneuron populations defined by transcriptomic signature expressions correspond to distinct M/E subtypes is still unknown. Here, we applied the Patch-PCR approach to simultaneously obtain the M/E properties and messenger RNA (mRNA) expression of >600 interneurons in layer V of the mouse somatosensory cortex (S1). Subsequently, we identified 11 M/E subtypes, 9 neurochemical cell populations (NCs), and 20 transcriptomic cell populations (TCs) in this cortical lamina. Further analysis revealed that cells in many NCs and TCs comprised several M/E types and were difficult to clearly distinguish morpho-electrically. A similar analysis of layer V interneurons of mouse primary visual cortex (V1) and motor cortex (M1) gave results largely comparable to S1. Comparison between S1, V1, and M1 suggested that, compared to V1, S1 interneurons were morpho-electrically more similar to M1. Our study reveals the presence of substantial M/E variations in cortical interneuron populations defined by molecular expression.
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Affiliation(s)
- Jun-Wei Cao
- Jing'an District Central Hospital of Shanghai, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China
| | - Xiao-Yi Mao
- School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Liang Zhu
- Department of Vascular Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, China
| | - Zhi-Shuo Zhou
- School of Data Science, Fudan University, Shanghai, 200433, China
| | - Shao-Na Jiang
- Jing'an District Central Hospital of Shanghai, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China
| | - Lin-Yun Liu
- Jing'an District Central Hospital of Shanghai, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China
| | - Shu-Qing Zhang
- Jing'an District Central Hospital of Shanghai, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China
| | - Yinghui Fu
- Jing'an District Central Hospital of Shanghai, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China
| | - Wen-Dong Xu
- The National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200032, China.
| | - Yong-Chun Yu
- Jing'an District Central Hospital of Shanghai, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China.
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264
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Zeng H, Huang J, Ren J, Wang CK, Tang Z, Zhou H, Zhou Y, Shi H, Aditham A, Sui X, Chen H, Lo JA, Wang X. Spatially resolved single-cell translatomics at molecular resolution. Science 2023; 380:eadd3067. [PMID: 37384709 PMCID: PMC11146668 DOI: 10.1126/science.add3067] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 05/07/2023] [Indexed: 07/01/2023]
Abstract
The precise control of messenger RNA (mRNA) translation is a crucial step in posttranscriptional gene regulation of cellular physiology. However, it remains a challenge to systematically study mRNA translation at the transcriptomic scale with spatial and single-cell resolution. Here, we report the development of ribosome-bound mRNA mapping (RIBOmap), a highly multiplexed three-dimensional in situ profiling method to detect cellular translatome. RIBOmap profiling of 981 genes in HeLa cells revealed cell cycle-dependent translational control and colocalized translation of functional gene modules. We mapped 5413 genes in mouse brain tissues, yielding spatially resolved single-cell translatomic profiles for 119,173 cells and revealing cell type-specific and brain region-specific translational regulation, including translation remodeling during oligodendrocyte maturation. Our method detected widespread patterns of localized translation in neuronal and glial cells in intact brain tissue networks.
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Affiliation(s)
- Hu Zeng
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jiahao Huang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jingyi Ren
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Zefang Tang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Haowen Zhou
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yiming Zhou
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hailing Shi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Abhishek Aditham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xin Sui
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hongyu Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jennifer A. Lo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xiao Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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265
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Quigley LD, Pendry R, Mendoza ML, Pfeiffer BE, Volk LJ. Experience alters hippocampal and cortical network communication via a KIBRA-dependent mechanism. Cell Rep 2023; 42:112662. [PMID: 37347662 PMCID: PMC10592482 DOI: 10.1016/j.celrep.2023.112662] [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: 06/02/2022] [Revised: 04/11/2023] [Accepted: 06/01/2023] [Indexed: 06/24/2023] Open
Abstract
Synaptic plasticity is hypothesized to underlie "replay" of salient experience during hippocampal sharp-wave/ripple (SWR)-based ensemble activity and to facilitate systems-level memory consolidation coordinated by SWRs and cortical sleep spindles. It remains unclear how molecular changes at synapses contribute to experience-induced modification of network function. The synaptic protein KIBRA regulates plasticity and memory. To determine the impact of KIBRA-regulated plasticity on circuit dynamics, we recorded in vivo neural activity from wild-type (WT) mice and littermates lacking KIBRA and examined circuit function before, during, and after novel experience. In WT mice, experience altered population activity and oscillatory dynamics in a manner consistent with incorporation of new information content in replay and enhanced hippocampal-cortical communication. While baseline SWR features were normal in KIBRA conditional knockout (cKO) mice, experience-dependent alterations in SWRs were absent. Furthermore, intra-hippocampal and hippocampal-cortical communication during SWRs was disrupted following KIBRA deletion. These results indicate molecular mechanisms that underlie network-level adaptations to experience.
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Affiliation(s)
- Lilyana D Quigley
- Neuroscience Graduate Program, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Robert Pendry
- Neuroscience Graduate Program, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Matthew L Mendoza
- Neuroscience Graduate Program, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brad E Pfeiffer
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA; Peter O' Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lenora J Volk
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Psychiatry, UT Southwestern Medical Center, Dallas, TX 75390, USA; Peter O' Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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266
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Goff KM, Liebergall SR, Jiang E, Somarowthu A, Goldberg EM. VIP interneuron impairment promotes in vivo circuit dysfunction and autism-related behaviors in Dravet syndrome. Cell Rep 2023; 42:112628. [PMID: 37310860 PMCID: PMC10592464 DOI: 10.1016/j.celrep.2023.112628] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 04/01/2023] [Accepted: 05/24/2023] [Indexed: 06/15/2023] Open
Abstract
Dravet syndrome (DS) is a severe neurodevelopmental disorder caused by loss-of-function variants in SCN1A, which encodes the voltage-gated sodium channel subunit Nav1.1. We recently showed that neocortical vasoactive intestinal peptide interneurons (VIP-INs) express Nav1.1 and are hypoexcitable in DS (Scn1a+/-) mice. Here, we investigate VIP-IN function at the circuit and behavioral level by performing in vivo 2-photon calcium imaging in awake wild-type (WT) and Scn1a+/- mice. VIP-IN and pyramidal neuron activation during behavioral transition from quiet wakefulness to active running is diminished in Scn1a+/- mice, and optogenetic activation of VIP-INs restores pyramidal neuron activity to WT levels during locomotion. VIP-IN selective Scn1a deletion reproduces core autism-spectrum-disorder-related behaviors in addition to cellular- and circuit-level deficits in VIP-IN function, but without epilepsy, sudden death, or avoidance behaviors seen in the global model. Hence, VIP-INs are impaired in vivo, which may underlie non-seizure cognitive and behavioral comorbidities in DS.
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Affiliation(s)
- Kevin M Goff
- Medical Scientist Training Program (MSTP), The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Neuroscience Graduate Group, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Neuroscience, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sophie R Liebergall
- Medical Scientist Training Program (MSTP), The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Neuroscience Graduate Group, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Neuroscience, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Evan Jiang
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ala Somarowthu
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ethan M Goldberg
- Neuroscience Graduate Group, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Neurology, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Neuroscience, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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267
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Levy-Myers R, Daudelin D, Na CH, Sockanathan S. An independent regulator of global release pathways in astrocytes generates a subtype of extracellular vesicles required for postsynaptic function. SCIENCE ADVANCES 2023; 9:eadg2067. [PMID: 37352348 PMCID: PMC10289663 DOI: 10.1126/sciadv.adg2067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/18/2023] [Indexed: 06/25/2023]
Abstract
Extracellular vesicles (EVs) are heterogeneous in size, composition, and function. We show that the six-transmembrane protein glycerophosphodiester phosphodiesterase 3 (GDE3) regulates actin remodeling, a global EV biogenic pathway, to release an EV subtype with distinct functions. GDE3 is necessary and sufficient for releasing EVs containing annexin A1 and GDE3 from the plasma membrane via Wiskott-Aldrich syndrome protein family member 3 (WAVE3), a major regulator of actin dynamics. GDE3 is expressed in astrocytes but not neurons, yet mice lacking GDE3 [Gde3 knockout (KO)] have decreased miniature excitatory postsynaptic current (mEPSC) amplitudes in hippocampal CA1 neurons. EVs from cultured wild-type astrocytes restore mEPSC amplitudes in Gde3 KOs, while EVs from Gde3 KO astrocytes or astrocytes inhibited for WAVE3 actin branching activity do not. Thus, GDE3-WAVE3 is a nonredundant astrocytic pathway that remodels actin to release a functionally distinct EV subtype, supporting the concept that independent regulation of global EV release pathways differentially regulates EV signaling within the cellular EV landscape.
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Affiliation(s)
- Reuben Levy-Myers
- The Solomon Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, PCTB1004, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Daniel Daudelin
- The Solomon Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, PCTB1004, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Chan Hyun Na
- Department of Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, MRB 706, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Shanthini Sockanathan
- The Solomon Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, PCTB1004, 725 N. Wolfe Street, Baltimore, MD 21205, USA
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268
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Liu L, Yun Z, Manubens-Gil L, Chen H, Xiong F, Dong H, Zeng H, Hawrylycz M, Ascoli GA, Peng H. Neuronal Connectivity as a Determinant of Cell Types and Subtypes. RESEARCH SQUARE 2023:rs.3.rs-2960606. [PMID: 37398060 PMCID: PMC10312949 DOI: 10.21203/rs.3.rs-2960606/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Classifications of single neurons at brain-wide scale is a powerful way to characterize the structural and functional organization of a brain. We acquired and standardized a large morphology database of 20,158 mouse neurons, and generated a whole-brain scale potential connectivity map of single neurons based on their dendritic and axonal arbors. With such an anatomy-morphology-connectivity mapping, we defined neuron connectivity types and subtypes (both called "c-types" for simplicity) for neurons in 31 brain regions. We found that neuronal subtypes defined by connectivity in the same regions may share statistically higher correlation in their dendritic and axonal features than neurons having contrary connectivity patterns. Subtypes defined by connectivity show distinct separation with each other, which cannot be recapitulated by morphology features, population projections, transcriptomic, and electrophysiological data produced to date. Within this paradigm, we were able to characterize the diversity in secondary motor cortical neurons, and subtype connectivity patterns in thalamocortical pathways. Our finding underscores the importance of connectivity in characterizing the modularity of brain anatomy, as well as the cell types and their subtypes. These results highlight that c-types supplement conventionally recognized transcriptional cell types (t-types), electrophysiological cell types (e-types), and morphological cell types (m-types) as an important determinant of cell classes and their identities.
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Affiliation(s)
- Lijuan Liu
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
| | - Zhixi Yun
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
| | - Linus Manubens-Gil
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
| | | | - Feng Xiong
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
| | - Hongwei Dong
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Giorgio A. Ascoli
- Center for Neural Informatics, Bioengineering Department, and Neuroscience Program, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA
| | - Hanchuan Peng
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
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269
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Straiker A, Dvorakova M, Bosquez-Berger T, Blahos J, Mackie K. A collection of cannabinoid-related negative findings from autaptic hippocampal neurons. Sci Rep 2023; 13:9610. [PMID: 37311900 PMCID: PMC10264370 DOI: 10.1038/s41598-023-36710-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 06/08/2023] [Indexed: 06/15/2023] Open
Abstract
Autaptic hippocampal neurons are an architecturally simple model of neurotransmission that express several forms of cannabinoid signaling. Over the past twenty years this model has proven valuable for studies ranging from enzymatic control of endocannabinoid production and breakdown, to CB1 receptor structure/function, to CB2 signaling, understanding 'spice' (synthetic cannabinoid) pharmacology, and more. However, while studying cannabinoid signaling in these neurons, we have occasionally encountered what one might call 'interesting negatives', valid and informative findings in the context of our experimental design that, given the nature of scientific publishing, may not otherwise find their way into the scientific literature. In autaptic hippocampal neurons we have found that: (1) The fatty acid binding protein (FABP) blocker SBFI-26 does not alter CB1-mediated neuroplasticity. (2) 1-AG signals poorly relative to 2-AG in autaptic neurons. (3) Indomethacin is not a CB1 PAM in autaptic neurons. (4) The CB1-associated protein SGIP1a is not necessary for CB1 desensitization. We are presenting these negative or perplexing findings in the hope that they will prove beneficial to other laboratories and elicit fruitful discussions regarding their relevance and significance.
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Affiliation(s)
- Alex Straiker
- Department of Psychological and Brain Sciences, Gill Center for Biomolecular Science, Program in Neuroscience, Indiana University, Bloomington, IN, 47405, USA.
| | - Michaela Dvorakova
- Department of Psychological and Brain Sciences, Gill Center for Biomolecular Science, Program in Neuroscience, Indiana University, Bloomington, IN, 47405, USA
| | - Taryn Bosquez-Berger
- Department of Psychological and Brain Sciences, Gill Center for Biomolecular Science, Program in Neuroscience, Indiana University, Bloomington, IN, 47405, USA
| | - Jaroslav Blahos
- Department of Molecular Pharmacology, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague 4, Czech Republic
| | - Ken Mackie
- Department of Psychological and Brain Sciences, Gill Center for Biomolecular Science, Program in Neuroscience, Indiana University, Bloomington, IN, 47405, USA
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270
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Kouvaros S, Bizup B, Solis O, Kumar M, Ventriglia E, Curry FP, Michaelides M, Tzounopoulos T. A CRE/DRE dual recombinase transgenic mouse reveals synaptic zinc-mediated thalamocortical neuromodulation. SCIENCE ADVANCES 2023; 9:eadf3525. [PMID: 37294760 PMCID: PMC10256168 DOI: 10.1126/sciadv.adf3525] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 05/05/2023] [Indexed: 06/11/2023]
Abstract
Synaptic zinc is a neuromodulator that shapes synaptic transmission and sensory processing. The maintenance of synaptic zinc is dependent on the vesicular zinc transporter, ZnT3. Hence, the ZnT3 knockout mouse has been a key tool for studying the mechanisms and functions of synaptic zinc. However, the use of this constitutive knockout mouse has notable limitations, including developmental, compensatory, and brain and cell type specificity issues. To overcome these limitations, we developed and characterized a dual recombinase transgenic mouse, which combines the Cre and Dre recombinase systems. This mouse allows for tamoxifen-inducible Cre-dependent expression of exogenous genes or knockout of floxed genes in ZnT3-expressing neurons and DreO-dependent region and cell type-specific conditional ZnT3 knockout in adult mice. Using this system, we reveal a neuromodulatory mechanism whereby zinc release from thalamic neurons modulates N-methyl-d-aspartate receptor activity in layer 5 pyramidal tract neurons, unmasking previously unknown features of cortical neuromodulation.
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Affiliation(s)
- Stylianos Kouvaros
- Pittsburgh Hearing Research Center, Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Brandon Bizup
- Pittsburgh Hearing Research Center, Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Oscar Solis
- Biobehavioral Imaging and Molecular Neuropsychopharmacology Unit, National Institute on Drug Abuse Intramural Research Program, Baltimore, MD 21224, USA
| | - Manoj Kumar
- Pittsburgh Hearing Research Center, Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Emilya Ventriglia
- Biobehavioral Imaging and Molecular Neuropsychopharmacology Unit, National Institute on Drug Abuse Intramural Research Program, Baltimore, MD 21224, USA
| | - Fallon P. Curry
- Biobehavioral Imaging and Molecular Neuropsychopharmacology Unit, National Institute on Drug Abuse Intramural Research Program, Baltimore, MD 21224, USA
| | - Michael Michaelides
- Biobehavioral Imaging and Molecular Neuropsychopharmacology Unit, National Institute on Drug Abuse Intramural Research Program, Baltimore, MD 21224, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thanos Tzounopoulos
- Pittsburgh Hearing Research Center, Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA 15261, USA
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271
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Hawrylycz M, Martone ME, Ascoli GA, Bjaalie JG, Dong HW, Ghosh SS, Gillis J, Hertzano R, Haynor DR, Hof PR, Kim Y, Lein E, Liu Y, Miller JA, Mitra PP, Mukamel E, Ng L, Osumi-Sutherland D, Peng H, Ray PL, Sanchez R, Regev A, Ropelewski A, Scheuermann RH, Tan SZK, Thompson CL, Tickle T, Tilgner H, Varghese M, Wester B, White O, Zeng H, Aevermann B, Allemang D, Ament S, Athey TL, Baker C, Baker KS, Baker PM, Bandrowski A, Banerjee S, Bishwakarma P, Carr A, Chen M, Choudhury R, Cool J, Creasy H, D’Orazi F, Degatano K, Dichter B, Ding SL, Dolbeare T, Ecker JR, Fang R, Fillion-Robin JC, Fliss TP, Gee J, Gillespie T, Gouwens N, Zhang GQ, Halchenko YO, Harris NL, Herb BR, Hintiryan H, Hood G, Horvath S, Huo B, Jarecka D, Jiang S, Khajouei F, Kiernan EA, Kir H, Kruse L, Lee C, Lelieveldt B, Li Y, Liu H, Liu L, Markuhar A, Mathews J, Mathews KL, Mezias C, Miller MI, Mollenkopf T, Mufti S, Mungall CJ, Orvis J, Puchades MA, Qu L, Receveur JP, Ren B, Sjoquist N, Staats B, Tward D, van Velthoven CTJ, Wang Q, Xie F, Xu H, Yao Z, Yun Z, Zhang YR, Zheng WJ, Zingg B. A guide to the BRAIN Initiative Cell Census Network data ecosystem. PLoS Biol 2023; 21:e3002133. [PMID: 37390046 PMCID: PMC10313015 DOI: 10.1371/journal.pbio.3002133] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023] Open
Abstract
Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.
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Affiliation(s)
- Michael Hawrylycz
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Maryann E. Martone
- Department of Neuroscience, University of California San Diego, San Diego, California, United States of America
- San Francisco Veterans Affairs Medical Center, San Francisco, California, United States of America
| | - Giorgio A. Ascoli
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, Volgenau School of Engineering, George Mason University, Fairfax, Virginia, United States of America
| | - Jan G. Bjaalie
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Hong-Wei Dong
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America
| | - Satrajit S. Ghosh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jesse Gillis
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Ronna Hertzano
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - David R. Haynor
- Department of Radiology, University of Washington, Seattle, Washington, United States of America
| | - Patrick R. Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Yongsoo Kim
- Department of Neural and Behavioral Sciences, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania, United States of America
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Yufeng Liu
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Jeremy A. Miller
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Partha P. Mitra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Eran Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, California, United States of America
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - David Osumi-Sutherland
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Hanchuan Peng
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Patrick L. Ray
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Raymond Sanchez
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Aviv Regev
- Genentech, South San Francisco, California, United States of America
| | - Alex Ropelewski
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | | | - Shawn Zheng Kai Tan
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Carol L. Thompson
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Timothy Tickle
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Hagen Tilgner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, United States of America
| | - Merina Varghese
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Brock Wester
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, United States of America
| | - Owen White
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Brian Aevermann
- Chan Zuckerberg Initiative, Redwood City, California, United States of America
| | - David Allemang
- Kitware Inc., Albany, New York, United States of America
| | - Seth Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Thomas L. Athey
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Cody Baker
- CatalystNeuro, Benicia, California, United States of America
| | - Katherine S. Baker
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Pamela M. Baker
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Anita Bandrowski
- Department of Neuroscience, University of California San Diego, San Diego, California, United States of America
| | - Samik Banerjee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Prajal Bishwakarma
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Ambrose Carr
- Chan Zuckerberg Initiative, Redwood City, California, United States of America
| | - Min Chen
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Roni Choudhury
- Kitware Inc., Albany, New York, United States of America
| | - Jonah Cool
- Chan Zuckerberg Initiative, Redwood City, California, United States of America
| | - Heather Creasy
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Florence D’Orazi
- Chan Zuckerberg Initiative, Redwood City, California, United States of America
| | - Kylee Degatano
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Song-Lin Ding
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Joseph R. Ecker
- Genomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies La Jolla, California, United States of America
| | - Rongxin Fang
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
| | | | - Timothy P. Fliss
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - James Gee
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tom Gillespie
- Department of Neuroscience, University of California San Diego, San Diego, California, United States of America
| | - Nathan Gouwens
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Guo-Qiang Zhang
- Texas Institute for Restorative Neurotechnologies, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Yaroslav O. Halchenko
- Department of Psychological and Brain Sciences, Dartmouth College, Hannover, New Hampshire, United States of America
| | - Nomi L. Harris
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Brian R. Herb
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Houri Hintiryan
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America
| | - Gregory Hood
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Sam Horvath
- Kitware Inc., Albany, New York, United States of America
| | - Bingxing Huo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Dorota Jarecka
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Shengdian Jiang
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Farzaneh Khajouei
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Elizabeth A. Kiernan
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Huseyin Kir
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Boudewijn Lelieveldt
- Department of Intelligent Systems, Delft University of Technology, Delft, the Netherlands
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Yang Li
- Center for Epigenomics, Department of Cellular and Molecular Medicine, UC San Diego School of Medicine, La Jolla, California, United States of America
| | - Hanqing Liu
- Genomic Analysis Laboratory, Howard Hughes Medical Institute, The Salk Institute for Biological Studies La Jolla, California, United States of America
| | - Lijuan Liu
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Anup Markuhar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - James Mathews
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Kaylee L. Mathews
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Chris Mezias
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Michael I. Miller
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tyler Mollenkopf
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Shoaib Mufti
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Christopher J. Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Joshua Orvis
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Maja A. Puchades
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Lei Qu
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Joseph P. Receveur
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Bing Ren
- Center for Epigenomics, Department of Cellular and Molecular Medicine, UC San Diego School of Medicine, La Jolla, California, United States of America
- Ludwig Institute for Cancer Research, La Jolla, California, United States of America
| | - Nathan Sjoquist
- Microsoft Corporation, Seattle, Washington, United States of America
| | - Brian Staats
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Daniel Tward
- UCLA Brain Mapping Center, University of California, Los Angeles, California, United States of America
| | | | - Quanxin Wang
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Fangming Xie
- Department of Chemistry and Biochemistry, University of California Los Angeles, California, United States of America
| | - Hua Xu
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Zhixi Yun
- SEU-Allen Institute Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu Province, China
| | - Yun Renee Zhang
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - W. Jim Zheng
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Brian Zingg
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at University of California, Los Angeles, California, United States of America
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272
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Piwecka M, Rajewsky N, Rybak-Wolf A. Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease. Nat Rev Neurol 2023; 19:346-362. [PMID: 37198436 PMCID: PMC10191412 DOI: 10.1038/s41582-023-00809-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2023] [Indexed: 05/19/2023]
Abstract
In the past decade, single-cell technologies have proliferated and improved from their technically challenging beginnings to become common laboratory methods capable of determining the expression of thousands of genes in thousands of cells simultaneously. The field has progressed by taking the CNS as a primary research subject - the cellular complexity and multiplicity of neuronal cell types provide fertile ground for the increasing power of single-cell methods. Current single-cell RNA sequencing methods can quantify gene expression with sufficient accuracy to finely resolve even subtle differences between cell types and states, thus providing a great tool for studying the molecular and cellular repertoire of the CNS and its disorders. However, single-cell RNA sequencing requires the dissociation of tissue samples, which means that the interrelationships between cells are lost. Spatial transcriptomic methods bypass tissue dissociation and retain this spatial information, thereby allowing gene expression to be assessed across thousands of cells within the context of tissue structural organization. Here, we discuss how single-cell and spatially resolved transcriptomics have been contributing to unravelling the pathomechanisms underlying brain disorders. We focus on three areas where we feel these new technologies have provided particularly useful insights: selective neuronal vulnerability, neuroimmune dysfunction and cell-type-specific treatment response. We also discuss the limitations and future directions of single-cell and spatial RNA sequencing technologies.
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Affiliation(s)
- Monika Piwecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Agnieszka Rybak-Wolf
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Center for Molecular Medicine, Berlin, Germany.
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273
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Lawrence JA, Aguilar-Calvo P, Ojeda-Juárez D, Khuu H, Soldau K, Pizzo DP, Wang J, Malik A, Shay TF, Sullivan EE, Aulston B, Song SM, Callender JA, Sanchez H, Geschwind MD, Roy S, Rissman RA, Trejo J, Tanaka N, Wu C, Chen X, Patrick GN, Sigurdson CJ. Diminished Neuronal ESCRT-0 Function Exacerbates AMPA Receptor Derangement and Accelerates Prion-Induced Neurodegeneration. J Neurosci 2023; 43:3970-3984. [PMID: 37019623 PMCID: PMC10219035 DOI: 10.1523/jneurosci.1878-22.2023] [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: 10/02/2022] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/07/2023] Open
Abstract
Endolysosomal defects in neurons are central to the pathogenesis of prion and other neurodegenerative disorders. In prion disease, prion oligomers traffic through the multivesicular body (MVB) and are routed for degradation in lysosomes or for release in exosomes, yet how prions impact proteostatic pathways is unclear. We found that prion-affected human and mouse brain showed a marked reduction in Hrs and STAM1 (ESCRT-0), which route ubiquitinated membrane proteins from early endosomes into MVBs. To determine how the reduction in ESCRT-0 impacts prion conversion and cellular toxicity in vivo, we prion-challenged conditional knockout mice (male and female) having Hrs deleted from neurons, astrocytes, or microglia. The neuronal, but not astrocytic or microglial, Hrs-depleted mice showed a shortened survival and an acceleration in synaptic derangements, including an accumulation of ubiquitinated proteins, deregulation of phosphorylated AMPA and metabotropic glutamate receptors, and profoundly altered synaptic structure, all of which occurred later in the prion-infected control mice. Finally, we found that neuronal Hrs (nHrs) depletion increased surface levels of the cellular prion protein, PrPC, which may contribute to the rapidly advancing disease through neurotoxic signaling. Taken together, the reduced Hrs in the prion-affected brain hampers ubiquitinated protein clearance at the synapse, exacerbates postsynaptic glutamate receptor deregulation, and accelerates neurodegeneration.SIGNIFICANCE STATEMENT Prion diseases are rapidly progressive neurodegenerative disorders characterized by prion aggregate spread through the central nervous system. Early disease features include ubiquitinated protein accumulation and synapse loss. Here, we investigate how prion aggregates alter ubiquitinated protein clearance pathways (ESCRT) in mouse and human prion-infected brain, discovering a marked reduction in Hrs. Using a prion-infection mouse model with neuronal Hrs (nHrs) depleted, we show that low neuronal Hrs is detrimental and markedly shortens survival time while accelerating synaptic derangements, including ubiquitinated protein accumulation, indicating that Hrs loss exacerbates prion disease progression. Additionally, Hrs depletion increases the surface distribution of prion protein (PrPC), linked to aggregate-induced neurotoxic signaling, suggesting that Hrs loss in prion disease accelerates disease through enhancing PrPC-mediated neurotoxic signaling.
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Affiliation(s)
- Jessica A Lawrence
- Department of Pathology, University of California, San Diego, La, Jolla, California, 92093
| | - Patricia Aguilar-Calvo
- Department of Pathology, University of California, San Diego, La, Jolla, California, 92093
| | - Daniel Ojeda-Juárez
- Department of Pathology, University of California, San Diego, La, Jolla, California, 92093
| | - Helen Khuu
- Department of Pathology, University of California, San Diego, La, Jolla, California, 92093
| | - Katrin Soldau
- Department of Pathology, University of California, San Diego, La, Jolla, California, 92093
| | - Donald P Pizzo
- Department of Pathology, University of California, San Diego, La, Jolla, California, 92093
| | - Jin Wang
- Department of Pathology, University of California, San Diego, La, Jolla, California, 92093
| | - Adela Malik
- Department of Pathology, University of California, San Diego, La, Jolla, California, 92093
| | - Timothy F Shay
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Erin E Sullivan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Brent Aulston
- Department of Neurosciences, University of California, San Diego, La Jolla, California 92093
| | - Seung Min Song
- Department of Pathology, University of California, San Diego, La, Jolla, California, 92093
| | - Julia A Callender
- Department of Pathology, University of California, San Diego, La, Jolla, California, 92093
| | - Henry Sanchez
- Department of Pathology, University of California, San Francisco, San Francisco, California 94143
| | - Michael D Geschwind
- Department of Neurology, Memory and Aging Center, University of California, San Francisco (UCSF), San Francisco, California 94143
| | - Subhojit Roy
- Department of Pathology, University of California, San Diego, La, Jolla, California, 92093
- Department of Neurosciences, University of California, San Diego, La Jolla, California 92093
| | - Robert A Rissman
- Department of Neurosciences, University of California, San Diego, La Jolla, California 92093
| | - JoAnn Trejo
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093
| | - Nobuyuki Tanaka
- Division of Tumor Immunobiology, Miyagi Cancer Center Research Institute, Natori 981-1293, Japan
- Division of Tumor Immunobiology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Chengbiao Wu
- Department of Neurosciences, University of California, San Diego, La Jolla, California 92093
| | - Xu Chen
- Department of Neurosciences, University of California, San Diego, La Jolla, California 92093
| | - Gentry N Patrick
- Department of Biology, University of California, San Diego, La Jolla, California 92093
| | - Christina J Sigurdson
- Department of Pathology, University of California, San Diego, La, Jolla, California, 92093
- Department of Pathology, Microbiology, and Immunology, University of California, Davis, Davis, California 95616
- Department of Medicine, University of California, San Diego, La Jolla, California 92093
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274
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Koch NA, Sonnenberg L, Hedrich UBS, Lauxmann S, Benda J. Loss or gain of function? Effects of ion channel mutations on neuronal firing depend on the neuron type. Front Neurol 2023; 14:1194811. [PMID: 37292138 PMCID: PMC10244640 DOI: 10.3389/fneur.2023.1194811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/03/2023] [Indexed: 06/10/2023] Open
Abstract
Introduction Clinically relevant mutations to voltage-gated ion channels, called channelopathies, alter ion channel function, properties of ionic currents, and neuronal firing. The effects of ion channel mutations are routinely assessed and characterized as loss of function (LOF) or gain of function (GOF) at the level of ionic currents. However, emerging personalized medicine approaches based on LOF/GOF characterization have limited therapeutic success. Potential reasons are among others that the translation from this binary characterization to neuronal firing is currently not well-understood-especially when considering different neuronal cell types. In this study, we investigate the impact of neuronal cell type on the firing outcome of ion channel mutations. Methods To this end, we simulated a diverse collection of single-compartment, conductance-based neuron models that differed in their composition of ionic currents. We systematically analyzed the effects of changes in ion current properties on firing in different neuronal types. Additionally, we simulated the effects of known mutations in KCNA1 gene encoding the KV1.1 potassium channel subtype associated with episodic ataxia type 1 (EA1). Results These simulations revealed that the outcome of a given change in ion channel properties on neuronal excitability depends on neuron type, i.e., the properties and expression levels of the unaffected ionic currents. Discussion Consequently, neuron-type specific effects are vital to a full understanding of the effects of channelopathies on neuronal excitability and are an important step toward improving the efficacy and precision of personalized medicine approaches.
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Affiliation(s)
- Nils A. Koch
- Institute of Neurobiology, Faculty of Mathematics and Natural Sciences, University of Tübingen, Tübingen, Germany
- Bernstein Center for Computational Neuroscience Tübingen, Tübingen, Germany
| | - Lukas Sonnenberg
- Institute of Neurobiology, Faculty of Mathematics and Natural Sciences, University of Tübingen, Tübingen, Germany
- Bernstein Center for Computational Neuroscience Tübingen, Tübingen, Germany
| | - Ulrike B. S. Hedrich
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Stephan Lauxmann
- Institute of Neurobiology, Faculty of Mathematics and Natural Sciences, University of Tübingen, Tübingen, Germany
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Jan Benda
- Institute of Neurobiology, Faculty of Mathematics and Natural Sciences, University of Tübingen, Tübingen, Germany
- Bernstein Center for Computational Neuroscience Tübingen, Tübingen, Germany
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275
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Luo J, Wu X, Cheng Y, Chen G, Wang J, Song X. Expression quantitative trait locus studies in the era of single-cell omics. Front Genet 2023; 14:1182579. [PMID: 37284065 PMCID: PMC10239882 DOI: 10.3389/fgene.2023.1182579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/26/2023] [Indexed: 06/08/2023] Open
Abstract
Genome-wide association studies have revealed that the regulation of gene expression bridges genetic variants and complex phenotypes. Profiling of the bulk transcriptome coupled with linkage analysis (expression quantitative trait locus (eQTL) mapping) has advanced our understanding of the relationship between genetic variants and gene regulation in the context of complex phenotypes. However, bulk transcriptomics has inherited limitations as the regulation of gene expression tends to be cell-type-specific. The advent of single-cell RNA-seq technology now enables the identification of the cell-type-specific regulation of gene expression through a single-cell eQTL (sc-eQTL). In this review, we first provide an overview of sc-eQTL studies, including data processing and the mapping procedure of the sc-eQTL. We then discuss the benefits and limitations of sc-eQTL analyses. Finally, we present an overview of the current and future applications of sc-eQTL discoveries.
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Affiliation(s)
- Jie Luo
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro‐products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuan Cheng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guang Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro‐products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jian Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro‐products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xijiao Song
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro‐products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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276
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Gao L, Liu S, Wang Y, Wu Q, Gou L, Yan J. Single-neuron analysis of dendrites and axons reveals the network organization in mouse prefrontal cortex. Nat Neurosci 2023:10.1038/s41593-023-01339-y. [PMID: 37217724 DOI: 10.1038/s41593-023-01339-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 04/18/2023] [Indexed: 05/24/2023]
Abstract
The structures of dendrites and axons form the basis for the connectivity of neural network, but their precise relationship at single-neuron level remains unclear. Here we report the complete dendrite and axon morphology of nearly 2,000 neurons in mouse prefrontal cortex (PFC). We identified morphological variations of somata, dendrites and axons across laminar layers and PFC subregions and the general rules of somatodendritic scaling with cytoarchitecture. We uncovered 24 morphologically distinguishable dendrite subtypes in 1,515 pyramidal projection neurons and 405 atypical pyramidal projection neurons and spiny stellate neurons with unique axon projection patterns. Furthermore, correspondence analysis among dendrites, local axons and long-range axons revealed coherent morphological changes associated with electrophysiological phenotypes. Finally, integrative dendrite-axon analysis uncovered the organization of potential intra-column, inter-hemispheric and inter-column connectivity among projection neuron types in PFC. Together, our study provides a comprehensive structural repertoire for the reconstruction and analysis of PFC neural network.
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Affiliation(s)
- Le Gao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Sang Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Yanzhi Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Qiwen Wu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Lingfeng Gou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Jun Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China.
- Shanghai Research Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China.
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277
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Ho NJ, Chen X, Lei Y, Gu S. Decoding hereditary spastic paraplegia pathogenicity through transcriptomic profiling. Zool Res 2023; 44:650-662. [PMID: 37161652 PMCID: PMC10236304 DOI: 10.24272/j.issn.2095-8137.2022.281] [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: 12/30/2022] [Accepted: 05/10/2023] [Indexed: 05/11/2023] Open
Abstract
Hereditary spastic paraplegia (HSP) is a group of genetic motor neuron diseases resulting from length-dependent axonal degeneration of the corticospinal upper motor neurons. Due to the advancement of next-generation sequencing, more than 70 novel HSP disease-causing genes have been identified in the past decade. Despite this, our understanding of HSP physiopathology and the development of efficient management and treatment strategies remain poor. One major challenge in studying HSP pathogenicity is selective neuronal vulnerability, characterized by the manifestation of clinical symptoms that are restricted to specific neuronal populations, despite the presence of germline disease-causing variants in every cell of the patient. Furthermore, disease genes may exhibit ubiquitous expression patterns and involve a myriad of different pathways to cause motor neuron degeneration. In the current review, we explore the correlation between transcriptomic data and clinical manifestations, as well as the importance of interspecies models by comparing tissue-specific transcriptomic profiles of humans and mice, expression patterns of different genes in the brain during development, and single-cell transcriptomic data from related tissues. Furthermore, we discuss the potential of emerging single-cell RNA sequencing technologies to resolve unanswered questions related to HSP pathogenicity.
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Affiliation(s)
- Nicolas James Ho
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiao Chen
- Dr. Li Dak Sum-Yip Yio Chin Center for Stem Cells and Regenerative Medicine and Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang University-University of Edinburgh Institute & School of Basic Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, Zhejiang, 310058 China
| | - Yong Lei
- School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong 518172, China
- The Chinese University of Hong Kong (Shenzhen), Shenzhen Futian Biomedical Innovation R&D Center, Shenzhen, Guangdong 518172, China. E-mail:
| | - Shen Gu
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Kunming Institute of Zoology Chinese Academy of Sciences, The Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Hong Kong SAR, China
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, China. E-mail:
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278
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Goralski T, Meyerdirk L, Breton L, Brasseur L, Kurgat K, DeWeerd D, Turner L, Becker K, Adams M, Newhouse D, Henderson MX. Spatial transcriptomics reveals molecular dysfunction associated with Lewy pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.541144. [PMID: 37292685 PMCID: PMC10245657 DOI: 10.1101/2023.05.17.541144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lewy pathology composed of α-synuclein is the key pathological hallmark of Parkinson's disease (PD), found both in dopaminergic neurons that control motor function, and throughout cortical regions that control cognitive function. Recent work has investigated which dopaminergic neurons are most susceptible to death, but little is known about which neurons are vulnerable to developing Lewy pathology and what molecular changes an aggregate induces. In the current study, we use spatial transcriptomics to selectively capture whole transcriptome signatures from cortical neurons with Lewy pathology compared to those without pathology in the same brains. We find, both in PD and in a mouse model of PD, that there are specific classes of excitatory neurons that are vulnerable to developing Lewy pathology in the cortex. Further, we identify conserved gene expression changes in aggregate-bearing neurons that we designate the Lewy-associated molecular dysfunction from aggregates (LAMDA) signature. This gene signature indicates that neurons with aggregates downregulate synaptic, mitochondrial, ubiquitin-proteasome, endo-lysosomal, and cytoskeletal genes and upregulate DNA repair and complement/cytokine genes. However, beyond DNA repair gene upregulation, we find that neurons also activate apoptotic pathways, suggesting that if DNA repair fails, neurons undergo programmed cell death. Our results identify neurons vulnerable to Lewy pathology in the PD cortex and identify a conserved signature of molecular dysfunction in both mice and humans.
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Affiliation(s)
- Thomas Goralski
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Lindsay Meyerdirk
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Libby Breton
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Laura Brasseur
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
| | - Kevin Kurgat
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Daniella DeWeerd
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | | | | | | | | | - Michael X. Henderson
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
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279
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Kumar P, Goettemoeller AM, Espinosa-Garcia C, Tobin BR, Tfaily A, Nelson RS, Natu A, Dammer EB, Santiago JV, Malepati S, Cheng L, Xiao H, Duong D, Seyfried NT, Wood LB, Rowan MJ, Rangaraju S. Native-state proteomics of Parvalbumin interneurons identifies novel molecular signatures and metabolic vulnerabilities to early Alzheimer's disease pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.541038. [PMID: 37292756 PMCID: PMC10245729 DOI: 10.1101/2023.05.17.541038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
One of the earliest pathophysiological perturbations in Alzheimer's Disease (AD) may arise from dysfunction of fast-spiking parvalbumin (PV) interneurons (PV-INs). Defining early protein-level (proteomic) alterations in PV-INs can provide key biological and translationally relevant insights. Here, we use cell-type-specific in vivo biotinylation of proteins (CIBOP) coupled with mass spectrometry to obtain native-state proteomes of PV interneurons. PV-INs exhibited proteomic signatures of high metabolic, mitochondrial, and translational activity, with over-representation of causally linked AD genetic risk factors. Analyses of bulk brain proteomes indicated strong correlations between PV-IN proteins with cognitive decline in humans, and with progressive neuropathology in humans and mouse models of Aβ pathology. Furthermore, PV-IN-specific proteomes revealed unique signatures of increased mitochondrial and metabolic proteins, but decreased synaptic and mTOR signaling proteins in response to early Aβ pathology. PV-specific changes were not apparent in whole-brain proteomes. These findings showcase the first native state PV-IN proteomes in mammalian brain, revealing a molecular basis for their unique vulnerabilities in AD.
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280
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Schwabenland M, Mossad O, Sievert A, Peres AG, Ringel E, Baasch S, Kolter J, Cascone G, Dokalis N, Vlachos A, Ruzsics Z, Henneke P, Prinz M, Blank T. Neonatal immune challenge poses a sex-specific risk for epigenetic microglial reprogramming and behavioral impairment. Nat Commun 2023; 14:2721. [PMID: 37169749 PMCID: PMC10175500 DOI: 10.1038/s41467-023-38373-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
While the precise processes underlying a sex bias in the development of central nervous system (CNS) disorders are unknown, there is growing evidence that an early life immune activation can contribute to the disease pathogenesis. When we mimicked an early systemic viral infection or applied murine cytomegalovirus (MCMV) systemically in neonatal female and male mice, only male adolescent mice presented behavioral deficits, including reduced social behavior and cognition. This was paralleled by an increased amount of infiltrating T cells in the brain parenchyma, enhanced interferon-γ (IFNγ) signaling, and epigenetic reprogramming of microglial cells. These microglial cells showed increased phagocytic activity, which resulted in abnormal loss of excitatory synapses within the hippocampal brain region. None of these alterations were seen in female adolescent mice. Our findings underscore the early postnatal period's susceptibility to cause sex-dependent long-term CNS deficiencies following infections.
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Affiliation(s)
- Marius Schwabenland
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Omar Mossad
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Annika Sievert
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Adam G Peres
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Elena Ringel
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian Baasch
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julia Kolter
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Giulia Cascone
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nikolaos Dokalis
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Andreas Vlachos
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Basics in Neuromodulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Zsolt Ruzsics
- Institute for Virology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Philipp Henneke
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Basics in Neuromodulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Thomas Blank
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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281
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Chamberland S, Grant G, Machold R, Nebet ER, Tian G, Hanani M, Kullander K, Tsien RW. Functional specialization of hippocampal somatostatin-expressing interneurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.27.538511. [PMID: 37162922 PMCID: PMC10168348 DOI: 10.1101/2023.04.27.538511] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Hippocampal somatostatin-expressing (Sst) GABAergic interneurons (INs) exhibit considerable anatomical and functional heterogeneity. Recent single cell transcriptome analyses have provided a comprehensive Sst-IN subtype census, a plausible molecular ground truth of neuronal identity whose links to specific functionality remain incomplete. Here, we designed an approach to identify and access subpopulations of Sst-INs based on transcriptomic features. Four mouse models based on single or combinatorial Cre- and Flp- expression differentiated functionally distinct subpopulations of CA1 hippocampal Sst-INs that largely tiled the morpho-functional parameter space of the Sst-INs superfamily. Notably, the Sst;;Tac1 intersection revealed a population of bistratified INs that preferentially synapsed onto fast-spiking interneurons (FS-INs) and were both necessary and sufficient to interrupt their firing. In contrast, the Ndnf;;Nkx2-1 intersection identified a population of oriens lacunosum-moleculare (OLM) INs that predominantly targeted CA1 pyramidal neurons, avoiding FS-INs. Overall, our results provide a framework to translate neuronal transcriptomic identity into discrete functional subtypes that capture the diverse specializations of hippocampal Sst-INs.
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Affiliation(s)
- Simon Chamberland
- NYU Neuroscience Institute and Department of Neuroscience and Physiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Gariel Grant
- NYU Neuroscience Institute and Department of Neuroscience and Physiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Robert Machold
- NYU Neuroscience Institute and Department of Neuroscience and Physiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Erica R. Nebet
- NYU Neuroscience Institute and Department of Neuroscience and Physiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Guoling Tian
- NYU Neuroscience Institute and Department of Neuroscience and Physiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Monica Hanani
- NYU Neuroscience Institute and Department of Neuroscience and Physiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Klas Kullander
- Developmental Genetics, Department of Neuroscience, Uppsala University, Uppsala 752 37, Uppsala län, Sweden
| | - Richard W. Tsien
- NYU Neuroscience Institute and Department of Neuroscience and Physiology, NYU Langone Medical Center, New York, NY 10016, USA
- Center for Neural Science, New York University, New York, NY, 10003, USA
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282
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Canales A, Scheuer KS, Zhao X, Jackson MB. Unitary synaptic responses of parvalbumin interneurons evoked by excitatory neurons in the mouse barrel cortex. Cereb Cortex 2023; 33:5108-5121. [PMID: 36227216 PMCID: PMC10151880 DOI: 10.1093/cercor/bhac403] [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: 04/20/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
The mammalian cortex integrates and processes information to transform sensory inputs into perceptions and motor outputs. These operations are performed by networks of excitatory and inhibitory neurons distributed through the cortical layers. Parvalbumin interneurons (PVIs) are the most abundant type of inhibitory cortical neuron. With axons projecting within and between layers, PVIs supply feedforward and feedback inhibition to control and modulate circuit function. Distinct populations of excitatory neurons recruit different PVI populations, but the specializations of these synapses are poorly understood. Here, we targeted a genetically encoded hybrid voltage sensor to PVIs and used fluorescence imaging in mouse somatosensory cortex slices to record their voltage changes. Stimulating a single visually identified excitatory neuron with small-tipped theta-glass electrodes depolarized multiple PVIs, and a common threshold suggested that stimulation elicited unitary synaptic potentials in response to a single excitatory neuron. Excitatory neurons depolarized PVIs in multiple layers, with the most residing in the layer of the stimulated neuron. Spiny stellate cells depolarized PVIs more strongly than pyramidal cells by up to 77%, suggesting a greater role for stellate cells in recruiting PVI inhibition and controlling cortical computations. Response half-width also varied between different excitatory inputs. These results demonstrate functional differences between excitatory synapses on PVIs.
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Affiliation(s)
- Alejandra Canales
- Department of Neuroscience, University of Wisconsin, Madison, WI 53705, United States
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, United States
| | - Katherine S Scheuer
- Department of Neuroscience, University of Wisconsin, Madison, WI 53705, United States
| | - Xinyu Zhao
- Department of Neuroscience, University of Wisconsin, Madison, WI 53705, United States
| | - Meyer B Jackson
- Department of Neuroscience, University of Wisconsin, Madison, WI 53705, United States
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283
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Chan YC, Kienle E, Oti M, Di Liddo A, Mendez-Lago M, Aschauer DF, Peter M, Pagani M, Arnold C, Vonderheit A, Schön C, Kreuz S, Stark A, Rumpel S. An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo. Sci Rep 2023; 13:6745. [PMID: 37185990 PMCID: PMC10130037 DOI: 10.1038/s41598-023-33448-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
Enhancers are important cis-regulatory elements controlling cell-type specific expression patterns of genes. Furthermore, combinations of enhancers and minimal promoters are utilized to construct small, artificial promoters for gene delivery vectors. Large-scale functional screening methodology to construct genomic maps of enhancer activities has been successfully established in cultured cell lines, however, not yet applied to terminally differentiated cells and tissues in a living animal. Here, we transposed the Self-Transcribing Active Regulatory Region Sequencing (STARR-seq) technique to the mouse brain using adeno-associated-viruses (AAV) for the delivery of a highly complex screening library tiling entire genomic regions and covering in total 3 Mb of the mouse genome. We identified 483 sequences with enhancer activity, including sequences that were not predicted by DNA accessibility or histone marks. Characterizing the expression patterns of fluorescent reporters controlled by nine candidate sequences, we observed differential expression patterns also in sparse cell types. Together, our study provides an entry point for the unbiased study of enhancer activities in organisms during health and disease.
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Affiliation(s)
- Ya-Chien Chan
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Eike Kienle
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Martin Oti
- Institute of Molecular Biology GmbH (IMB), Mainz, Germany
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an Der Riß, Germany
| | | | | | - Dominik F Aschauer
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Manuel Peter
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Michaela Pagani
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Cosmas Arnold
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | | | - Christian Schön
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an Der Riß, Germany
| | - Sebastian Kreuz
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an Der Riß, Germany
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Simon Rumpel
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany.
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284
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Wei Y, Nandi A, Jia X, Siegle JH, Denman D, Lee SY, Buchin A, Van Geit W, Mosher CP, Olsen S, Anastassiou CA. Associations between in vitro, in vivo and in silico cell classes in mouse primary visual cortex. Nat Commun 2023; 14:2344. [PMID: 37095130 PMCID: PMC10126114 DOI: 10.1038/s41467-023-37844-8] [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: 04/07/2021] [Accepted: 03/31/2023] [Indexed: 04/26/2023] Open
Abstract
The brain consists of many cell classes yet in vivo electrophysiology recordings are typically unable to identify and monitor their activity in the behaving animal. Here, we employed a systematic approach to link cellular, multi-modal in vitro properties from experiments with in vivo recorded units via computational modeling and optotagging experiments. We found two one-channel and six multi-channel clusters in mouse visual cortex with distinct in vivo properties in terms of activity, cortical depth, and behavior. We used biophysical models to map the two one- and the six multi-channel clusters to specific in vitro classes with unique morphology, excitability and conductance properties that explain their distinct extracellular signatures and functional characteristics. These concepts were tested in ground-truth optotagging experiments with two inhibitory classes unveiling distinct in vivo properties. This multi-modal approach presents a powerful way to separate in vivo clusters and infer their cellular properties from first principles.
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Affiliation(s)
- Yina Wei
- Zhejiang Lab, Hangzhou, 311100, China.
- Allen Institute for Brain Science, Seattle, WA, 98109, USA.
| | - Anirban Nandi
- Allen Institute for Brain Science, Seattle, WA, 98109, USA
| | - Xiaoxuan Jia
- Allen Institute for Brain Science, Seattle, WA, 98109, USA
- School of Life Sciences/McGovern Institute for Brain Research, Tsinghua University, 100084, Beijing, China
| | | | | | - Soo Yeun Lee
- Allen Institute for Brain Science, Seattle, WA, 98109, USA
| | - Anatoly Buchin
- Allen Institute for Brain Science, Seattle, WA, 98109, USA
- Cajal Neuroscience Inc, Seattle, WA, 98102, USA
| | - Werner Van Geit
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL) Campus Biotech, Geneva, 1202, Switzerland
| | - Clayton P Mosher
- Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Shawn Olsen
- Allen Institute for Brain Science, Seattle, WA, 98109, USA
| | - Costas A Anastassiou
- Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
- Center for Neural Science and Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
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285
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Neel DV, Basu H, Gunner G, Bergstresser MD, Giadone RM, Chung H, Miao R, Chou V, Brody E, Jiang X, Lee E, Watts ME, Marques C, Held A, Wainger B, Lagier-Tourenne C, Zhang YJ, Petrucelli L, Young-Pearse TL, Chen-Plotkin AS, Rubin LL, Lieberman J, Chiu IM. Gasdermin-E mediates mitochondrial damage in axons and neurodegeneration. Neuron 2023; 111:1222-1240.e9. [PMID: 36917977 PMCID: PMC10121894 DOI: 10.1016/j.neuron.2023.02.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 10/27/2022] [Accepted: 02/10/2023] [Indexed: 03/14/2023]
Abstract
Mitochondrial dysfunction and axon loss are hallmarks of neurologic diseases. Gasdermin (GSDM) proteins are executioner pore-forming molecules that mediate cell death, yet their roles in the central nervous system (CNS) are not well understood. Here, we find that one GSDM family member, GSDME, is expressed by both mouse and human neurons. GSDME plays a role in mitochondrial damage and axon loss. Mitochondrial neurotoxins induced caspase-dependent GSDME cleavage and rapid localization to mitochondria in axons, where GSDME promoted mitochondrial depolarization, trafficking defects, and neurite retraction. Frontotemporal dementia (FTD)/amyotrophic lateral sclerosis (ALS)-associated proteins TDP-43 and PR-50 induced GSDME-mediated damage to mitochondria and neurite loss. GSDME knockdown protected against neurite loss in ALS patient iPSC-derived motor neurons. Knockout of GSDME in SOD1G93A ALS mice prolonged survival, ameliorated motor dysfunction, rescued motor neuron loss, and reduced neuroinflammation. We identify GSDME as an executioner of neuronal mitochondrial dysfunction that may contribute to neurodegeneration.
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Affiliation(s)
- Dylan V Neel
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Himanish Basu
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Georgia Gunner
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Richard M Giadone
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Haeji Chung
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Rui Miao
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Vicky Chou
- Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Eliza Brody
- Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xin Jiang
- Department of Neurology, Mass General Institute for Neurodegenerative Disease (MIND), Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Edward Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michelle E Watts
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Christine Marques
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Aaron Held
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Brian Wainger
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Clotilde Lagier-Tourenne
- Department of Neurology, Mass General Institute for Neurodegenerative Disease (MIND), Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA
| | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Alice S Chen-Plotkin
- Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lee L Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
| | - Isaac M Chiu
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA.
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286
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Liu H, Zeng Q, Zhou J, Bartlett A, Wang BA, Berube P, Tian W, Kenworthy M, Altshul J, Nery JR, Chen H, Castanon RG, Zu S, Li YE, Lucero J, Osteen JK, Pinto-Duarte A, Lee J, Rink J, Cho S, Emerson N, Nunn M, O'Connor C, Yao Z, Smith KA, Tasic B, Zeng H, Luo C, Dixon JR, Ren B, Behrens MM, Ecker JR. Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.16.536509. [PMID: 37131654 PMCID: PMC10153407 DOI: 10.1101/2023.04.16.536509] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Cytosine DNA methylation is essential in brain development and has been implicated in various neurological disorders. A comprehensive understanding of DNA methylation diversity across the entire brain in the context of the brain's 3D spatial organization is essential for building a complete molecular atlas of brain cell types and understanding their gene regulatory landscapes. To this end, we employed optimized single-nucleus methylome (snmC-seq3) and multi-omic (snm3C-seq1) sequencing technologies to generate 301,626 methylomes and 176,003 chromatin conformation/methylome joint profiles from 117 dissected regions throughout the adult mouse brain. Using iterative clustering and integrating with companion whole-brain transcriptome and chromatin accessibility datasets, we constructed a methylation-based cell type taxonomy that contains 4,673 cell groups and 261 cross-modality-annotated subclasses. We identified millions of differentially methylated regions (DMRs) across the genome, representing potential gene regulation elements. Notably, we observed spatial cytosine methylation patterns on both genes and regulatory elements in cell types within and across brain regions. Brain-wide multiplexed error-robust fluorescence in situ hybridization (MERFISH2) data validated the association of this spatial epigenetic diversity with transcription and allowed the mapping of the DNA methylation and topology information into anatomical structures more precisely than our dissections. Furthermore, multi-scale chromatin conformation diversities occur in important neuronal genes, highly associated with DNA methylation and transcription changes. Brain-wide cell type comparison allowed us to build a regulatory model for each gene, linking transcription factors, DMRs, chromatin contacts, and downstream genes to establish regulatory networks. Finally, intragenic DNA methylation and chromatin conformation patterns predicted alternative gene isoform expression observed in a companion whole-brain SMART-seq3 dataset. Our study establishes the first brain-wide, single-cell resolution DNA methylome and 3D multi-omic atlas, providing an unparalleled resource for comprehending the mouse brain's cellular-spatial and regulatory genome diversity.
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Affiliation(s)
- Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Qiurui Zeng
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Jingtian Zhou
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bang-An Wang
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Peter Berube
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Wei Tian
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mia Kenworthy
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jordan Altshul
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Huaming Chen
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rosa G Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Songpeng Zu
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Yang Eric Li
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Jacinta Lucero
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Julia K Osteen
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Antonio Pinto-Duarte
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jasper Lee
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jon Rink
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Silvia Cho
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nora Emerson
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Michael Nunn
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Carolyn O'Connor
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Chongyuan Luo
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Jesse R Dixon
- Peptide Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Institute of Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - M Margarita Behrens
- Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
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287
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Wei Y, Nandi A, Jia X, Siegle JH, Denman D, Lee SY, Buchin A, Geit WV, Mosher CP, Olsen S, Anastassiou CA. Associations between in vitro , in vivo and in silico cell classes in mouse primary visual cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.532851. [PMID: 37131710 PMCID: PMC10153154 DOI: 10.1101/2023.04.17.532851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The brain consists of many cell classes yet in vivo electrophysiology recordings are typically unable to identify and monitor their activity in the behaving animal. Here, we employed a systematic approach to link cellular, multi-modal in vitro properties from experiments with in vivo recorded units via computational modeling and optotagging experiments. We found two one-channel and six multi-channel clusters in mouse visual cortex with distinct in vivo properties in terms of activity, cortical depth, and behavior. We used biophysical models to map the two one- and the six multi-channel clusters to specific in vitro classes with unique morphology, excitability and conductance properties that explain their distinct extracellular signatures and functional characteristics. These concepts were tested in ground-truth optotagging experiments with two inhibitory classes unveiling distinct in vivo properties. This multi-modal approach presents a powerful way to separate in vivo clusters and infer their cellular properties from first principles.
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Affiliation(s)
- Yina Wei
- Zhejiang Lab, Hangzhou 311100, China
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Anirban Nandi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Xiaoxuan Jia
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- School of Life Sciences, Tsinghua University, Beijing, 100084, China, IDG/McGovern Institute for Brain Research at Tsinghua University, Beijing, 100084, China
| | | | | | - Soo Yeun Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Anatoly Buchin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Cajal Neuroscience Inc, Seattle, WA 98102, USA
| | - Werner Van Geit
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL) Campus Biotech, Geneva 1202, Switzerland
| | - Clayton P. Mosher
- Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Shawn Olsen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Costas A. Anastassiou
- Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Center for Neural Science and Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Lead contact
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288
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Hostetler RE, Hu H, Agmon A. Genetically Defined Subtypes of Somatostatin-Containing Cortical Interneurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526850. [PMID: 36778499 PMCID: PMC9915678 DOI: 10.1101/2023.02.02.526850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Inhibitory interneurons play a crucial role in proper development and function of the mammalian cerebral cortex. Of the different inhibitory subclasses, dendritic-targeting, somatostatin-containing (SOM) interneurons may be the most diverse. Earlier studies used transgenic mouse lines to identify and characterize subtypes of SOM interneurons by morphological, electrophysiological and neurochemical properties. More recently, large-scale studies classified SOM interneurons into 13 morpho-electro-transcriptomic (MET) types. It remains unclear, however, how these various classification schemes relate to each other, and experimental access to MET types has been limited by the scarcity of type-specific mouse driver lines. To begin to address these issues we crossed Flp and Cre driver mouse lines and a dual-color combinatorial reporter, allowing experimental access to genetically defined SOM subsets. Brains from adult mice of both sexes were retrogradely dye-labeled from the pial surface to identify layer 1-projecting neurons, and immunostained against several marker proteins, allowing correlation of genetic label, axonal target and marker protein expression in the same neurons. Using whole-cell recordings ex-vivo, we compared electrophysiological properties between intersectional and transgenic SOM subsets. We identified two layer 1-targeting intersectional subsets with non-overlapping marker protein expression and electrophysiological properties which, together with a previously characterized layer 4-targeting subtype, account for about half of all layer 5 SOM cells and >40% of all SOM cells, and appear to map onto 5 of the 13 MET types. Genetic access to these subtypes will allow researchers to determine their synaptic inputs and outputs and uncover their roles in cortical computations and animal behavior. SIGNIFICANCE STATEMENT Inhibitory neurons are critically important for proper development and function of the cerebral cortex. Although a minority population, they are highly diverse, which poses a major challenge to investigating their contributions to cortical computations and animal and human behavior. As a step towards understanding this diversity we crossed genetically modified mouse lines to allow detailed examination of genetically-defined groups of the most diverse inhibitory subtype, somatostatin-containing interneurons. We identified and characterized three somatostatin subtypes in the deep cortical layers with distinct combinations of anatomical, neurochemical and electrophysiological properties. Future studies could now use these genetic tools to examine how these different subtypes are integrated into the cortical circuit and what roles they play during sensory, cognitive or motor behavior.
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Affiliation(s)
- Rachel E Hostetler
- Dept. of Neuroscience, West Virginia University School of Medicine, WV Rockefeller Neuroscience Institute, Morgantown, WV 26506, USA
| | - Hang Hu
- Dept. of Neuroscience, West Virginia University School of Medicine, WV Rockefeller Neuroscience Institute, Morgantown, WV 26506, USA
| | - Ariel Agmon
- Dept. of Neuroscience, West Virginia University School of Medicine, WV Rockefeller Neuroscience Institute, Morgantown, WV 26506, USA
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289
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Coleman K, Hu J, Schroeder A, Lee EB, Li M. SpaDecon: cell-type deconvolution in spatial transcriptomics with semi-supervised learning. Commun Biol 2023; 6:378. [PMID: 37029267 PMCID: PMC10082183 DOI: 10.1038/s42003-023-04761-x] [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: 05/03/2022] [Accepted: 03/24/2023] [Indexed: 04/09/2023] Open
Abstract
Spatially resolved transcriptomics (SRT) has advanced our understanding of the spatial patterns of gene expression, but the lack of single-cell resolution in spatial barcoding-based SRT hinders the inference of specific locations of individual cells. To determine the spatial distribution of cell types in SRT, we present SpaDecon, a semi-supervised learning approach that incorporates gene expression, spatial location, and histology information for cell-type deconvolution. SpaDecon was evaluated through analyses of four real SRT datasets using knowledge of the expected distributions of cell types. Quantitative evaluations were performed for four pseudo-SRT datasets constructed according to benchmark proportions. Using mean squared error and Jensen-Shannon divergence with the benchmark proportions as evaluation criteria, we show that SpaDecon performance surpasses that of published cell-type deconvolution methods. Given the accuracy and computational speed of SpaDecon, we anticipate it will be valuable for SRT data analysis and will facilitate the integration of genomics and digital pathology.
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Affiliation(s)
- Kyle Coleman
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Jian Hu
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Amelia Schroeder
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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290
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Joglekar A, Hu W, Zhang B, Narykov O, Diekhans M, Balacco J, Ndhlovu LC, Milner TA, Fedrigo O, Jarvis ED, Sheynkman G, Korkin D, Ross ME, Tilgner HU. Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.02.535281. [PMID: 37066387 PMCID: PMC10103983 DOI: 10.1101/2023.04.02.535281] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
RNA isoforms influence cell identity and function. Until recently, technological limitations prevented a genome-wide appraisal of isoform influence on cell identity in various parts of the brain. Using enhanced long-read single-cell isoform sequencing, we comprehensively analyze RNA isoforms in multiple mouse brain regions, cell subtypes, and developmental timepoints from postnatal day 14 (P14) to adult (P56). For 75% of genes, full-length isoform expression varies along one or more axes of phenotypic origin, underscoring the pervasiveness of isoform regulation across multiple scales. As expected, splicing varies strongly between cell types. However, certain gene classes including neurotransmitter release and reuptake as well as synapse turnover, harbor significant variability in the same cell type across anatomical regions, suggesting differences in network activity may influence cell-type identity. Glial brain-region specificity in isoform expression includes strong poly(A)-site regulation, whereas neurons have stronger TSS regulation. Furthermore, developmental patterns of cell-type specific splicing are especially pronounced in the murine adolescent transition from P21 to P28. The same cell type traced across development shows more isoform variability than across adult anatomical regions, indicating a coordinated modulation of functional programs dictating neural development. As most cell-type specific exons in P56 mouse hippocampus behave similarly in newly generated data from human hippocampi, these principles may be extrapolated to human brain. However, human brains have evolved additional cell-type specificity in splicing, suggesting gain-of-function isoforms. Taken together, we present a detailed single-cell atlas of full-length brain isoform regulation across development and anatomical regions, providing a previously unappreciated degree of isoform variability across multiple scales of the brain.
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Affiliation(s)
- Anoushka Joglekar
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Wen Hu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | | | - Oleksandr Narykov
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA, USA
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Lishomwa C Ndhlovu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Teresa A Milner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, the Rockefeller University, New York, NY
| | - Erich D Jarvis
- Vertebrate Genome Lab, the Rockefeller University, New York, NY
- Laboratory of Neurogenetics of Language, the Rockefeller University, New York, NY
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Gloria Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, Virginia, USA
| | - Dmitry Korkin
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA, USA
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA, USA
| | - M Elizabeth Ross
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Hagen U Tilgner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
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291
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Zeighami Y, Bakken TE, Nickl-Jockschat T, Peterson Z, Jegga AG, Miller JA, Schulkin J, Evans AC, Lein ES, Hawrylycz M. A comparison of anatomic and cellular transcriptome structures across 40 human brain diseases. PLoS Biol 2023; 21:e3002058. [PMID: 37079537 PMCID: PMC10118126 DOI: 10.1371/journal.pbio.3002058] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 03/02/2023] [Indexed: 04/21/2023] Open
Abstract
Genes associated with risk for brain disease exhibit characteristic expression patterns that reflect both anatomical and cell type relationships. Brain-wide transcriptomic patterns of disease risk genes provide a molecular-based signature, based on differential co-expression, that is often unique to that disease. Brain diseases can be compared and aggregated based on the similarity of their signatures which often associates diseases from diverse phenotypic classes. Analysis of 40 common human brain diseases identifies 5 major transcriptional patterns, representing tumor-related, neurodegenerative, psychiatric and substance abuse, and 2 mixed groups of diseases affecting basal ganglia and hypothalamus. Further, for diseases with enriched expression in cortex, single-nucleus data in the middle temporal gyrus (MTG) exhibits a cell type expression gradient separating neurodegenerative, psychiatric, and substance abuse diseases, with unique excitatory cell type expression differentiating psychiatric diseases. Through mapping of homologous cell types between mouse and human, most disease risk genes are found to act in common cell types, while having species-specific expression in those types and preserving similar phenotypic classification within species. These results describe structural and cellular transcriptomic relationships of disease risk genes in the adult brain and provide a molecular-based strategy for classifying and comparing diseases, potentially identifying novel disease relationships.
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Affiliation(s)
- Yashar Zeighami
- Douglas Research Centre, Department of Psychiatry, McGill University, Montreal, Canada
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Trygve E. Bakken
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Thomas Nickl-Jockschat
- Department of Psychiatry, Neuroscience and Pharmacology, Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, United States of America
| | - Zeru Peterson
- Department of Psychiatry, Neuroscience and Pharmacology, Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa, United States of America
| | - Anil G. Jegga
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Jeremy A. Miller
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Jay Schulkin
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Alan C. Evans
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Ed S. Lein
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Michael Hawrylycz
- Allen Institute for Brain Science, Seattle, Washington, United States of America
- University of Washington, Department of Genome Sciences, Seattle, Washington, United States of America
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292
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Zhao L, Mühleisen TW, Pelzer DI, Burger B, Beins EC, Forstner AJ, Herms S, Hoffmann P, Amunts K, Palomero-Gallagher N, Cichon S. Relationships between neurotransmitter receptor densities and expression levels of their corresponding genes in the human hippocampus. Neuroimage 2023; 273:120095. [PMID: 37030412 PMCID: PMC10167541 DOI: 10.1016/j.neuroimage.2023.120095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/02/2023] [Accepted: 04/05/2023] [Indexed: 04/08/2023] Open
Abstract
Neurotransmitter receptors are key molecules in signal transmission, their alterations are associated with brain dysfunction. Relationships between receptors and their corresponding genes are poorly understood, especially in humans. We combined in vitro receptor autoradiography and RNA sequencing to quantify, in the same tissue samples (7 subjects), the densities of 14 receptors and expression levels of their corresponding 43 genes in the Cornu Ammonis (CA) and dentate gyrus (DG) of human hippocampus. Significant differences in receptor densities between both structures were found only for metabotropic receptors, whereas significant differences in RNA expression levels mostly pertained ionotropic receptors. Receptor fingerprints of CA and DG differ in shapes but have similar sizes; the opposite holds true for their "RNA fingerprints", which represent the expression levels of multiple genes in a single area. In addition, the correlation coefficients between receptor densities and corresponding gene expression levels vary widely and the mean correlation strength was weak-to-moderate. Our results suggest that receptor densities are not only controlled by corresponding RNA expression levels, but also by multiple regionally specific post-translational factors.
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293
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Chang C, Zuo H, Li Y. Recent advances in deciphering hippocampus complexity using single-cell transcriptomics. Neurobiol Dis 2023; 179:106062. [PMID: 36878328 DOI: 10.1016/j.nbd.2023.106062] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023] Open
Abstract
Single-cell and single-nucleus RNA sequencing (scRNA-seq and snRNA-seq) technologies have emerged as revolutionary and powerful tools, which have helped in achieving significant progress in biomedical research over the last decade. scRNA-seq and snRNA-seq resolve heterogeneous cell populations from different tissues and help reveal the function and dynamics at the single-cell level. The hippocampus is an essential component for cognitive functions, including learning, memory, and emotion regulation. However, the molecular mechanisms underlying the activity of hippocampus have not been fully elucidated. The development of scRNA-seq and snRNA-seq technologies provides strong support for attaining an in-depth understanding of hippocampal cell types and gene expression regulation from the single-cell transcriptome profiling perspective. This review summarizes the applications of scRNA-seq and snRNA-seq in the hippocampus to further expand our knowledge of the molecular mechanisms related to hippocampal development, health, and diseases.
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Affiliation(s)
- Chenxu Chang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hongyan Zuo
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Yang Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
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294
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Yao S, Levi BP. Linking connectome with transcriptome using a self-inactivating rabies virus. Nat Methods 2023; 20:493-494. [PMID: 36864201 DOI: 10.1038/s41592-023-01803-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Affiliation(s)
- Shenqin Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA.
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295
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Gamlin CR, Schneider-Mizell CM, Mallory M, Elabbady L, Gouwens N, Williams G, Mukora A, Dalley R, Bodor A, Brittain D, Buchanan J, Bumbarger D, Kapner D, Kinn S, Mahalingam G, Seshamani S, Takeno M, Torres R, Yin W, Nicovich PR, Bae JA, Castro MA, Dorkenwald S, Halageri A, Jia Z, Jordan C, Kemnitz N, Lee K, Li K, Lu R, Macrina T, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Silversmith W, Turner NL, Wong W, Wu J, Yu S, Berg J, Jarsky T, Lee B, Seung HS, Zeng H, Reid RC, Collman F, da Costa NM, Sorensen SA. Integrating EM and Patch-seq data: Synaptic connectivity and target specificity of predicted Sst transcriptomic types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.22.533857. [PMID: 36993629 PMCID: PMC10055412 DOI: 10.1101/2023.03.22.533857] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Neural circuit function is shaped both by the cell types that comprise the circuit and the connections between those cell types 1 . Neural cell types have previously been defined by morphology 2, 3 , electrophysiology 4, 5 , transcriptomic expression 6-8 , connectivity 9-13 , or even a combination of such modalities 14-16 . More recently, the Patch-seq technique has enabled the characterization of morphology (M), electrophysiology (E), and transcriptomic (T) properties from individual cells 17-20 . Using this technique, these properties were integrated to define 28, inhibitory multimodal, MET-types in mouse primary visual cortex 21 . It is unknown how these MET-types connect within the broader cortical circuitry however. Here we show that we can predict the MET-type identity of inhibitory cells within a large-scale electron microscopy (EM) dataset and these MET-types have distinct ultrastructural features and synapse connectivity patterns. We found that EM Martinotti cells, a well defined morphological cell type 22, 23 known to be Somatostatin positive (Sst+) 24, 25 , were successfully predicted to belong to Sst+ MET-types. Each identified MET-type had distinct axon myelination patterns and synapsed onto specific excitatory targets. Our results demonstrate that morphological features can be used to link cell type identities across imaging modalities, which enables further comparison of connectivity in relation to transcriptomic or electrophysiological properties. Furthermore, our results show that MET-types have distinct connectivity patterns, supporting the use of MET-types and connectivity to meaningfully define cell types.
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296
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Shrestha P, Jaganathan A, Huilgol D, Ballon C, Hwangbo Y, Mills AA. Chd5 Regulates the Transcription Factor Six3 to Promote Neuronal Differentiation. Stem Cells 2023; 41:242-251. [PMID: 36636025 PMCID: PMC10020979 DOI: 10.1093/stmcls/sxad002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 12/16/2022] [Indexed: 01/14/2023]
Abstract
Chromodomain helicase DNA-binding protein 5 (Chd5) is an ATP-dependent chromatin remodeler that promotes neuronal differentiation. However, the mechanism behind the action of Chd5 during neurogenesis is not clearly understood. Here we use transcriptional profiling of cells obtained from Chd5 deficient mice at early and late stages of neuronal differentiation to show that Chd5 regulates neurogenesis by directing stepwise transcriptional changes. During early stages of neurogenesis, Chd5 promotes expression of the proneural transcription factor Six3 to repress Wnt5a, a non-canonical Wnt ligand essential for the maturation of neurons. This previously unappreciated ability of Chd5 to transcriptionally repress neuronal maturation factors is critical for both lineage specification and maturation. Thus, Chd5 facilitates early transcriptional changes in neural stem cells, thereby initiating transcriptional programs essential for neuronal fate specification.
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Affiliation(s)
- Padmina Shrestha
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Molecular and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | | | - Dhananjay Huilgol
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Carlos Ballon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yon Hwangbo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Alea A Mills
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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297
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Barron JJ, Mroz NM, Taloma SE, Dahlgren MW, Ortiz-Carpena J, Dorman LC, Vainchtein ID, Escoubas CC, Molofsky AB, Molofsky AV. Group 2 innate lymphoid cells promote inhibitory synapse development and social behavior. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.532850. [PMID: 36993292 PMCID: PMC10055027 DOI: 10.1101/2023.03.16.532850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The innate immune system plays essential roles in brain synaptic development, and immune dysregulation is implicated in neurodevelopmental diseases. Here we show that a subset of innate lymphocytes (group 2 innate lymphoid cells, ILC2s) is required for cortical inhibitory synapse maturation and adult social behavior. ILC2s expanded in the developing meninges and produced a surge of their canonical cytokine Interleukin-13 (IL-13) between postnatal days 5-15. Loss of ILC2s decreased cortical inhibitory synapse numbers in the postnatal period where as ILC2 transplant was sufficient to increase inhibitory synapse numbers. Deletion of the IL-4/IL-13 receptor (Il4ra) from inhibitory neurons phenocopied the reduction inhibitory synapses. Both ILC2 deficient and neuronal Il4ra deficient animals had similar and selective impairments in adult social behavior. These data define a type 2 immune circuit in early life that shapes adult brain function.
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Affiliation(s)
- Jerika J. Barron
- Departments of Psychiatry/Weill Institute for Neurosciences
- Biomedical Sciences Graduate Program
| | - Nicholas M. Mroz
- Biomedical Sciences Graduate Program
- Department of Laboratory Medicine. University of California, San Francisco, San Francisco, CA
| | - Sunrae E. Taloma
- Departments of Psychiatry/Weill Institute for Neurosciences
- Neuroscience Graduate Program
| | - Madelene W. Dahlgren
- Department of Laboratory Medicine. University of California, San Francisco, San Francisco, CA
| | - Jorge Ortiz-Carpena
- Department of Laboratory Medicine. University of California, San Francisco, San Francisco, CA
| | - Leah C. Dorman
- Departments of Psychiatry/Weill Institute for Neurosciences
- Neuroscience Graduate Program
| | | | | | - Ari B. Molofsky
- Department of Laboratory Medicine. University of California, San Francisco, San Francisco, CA
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298
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Lee DR, Zhang Y, Rhodes CT, Petros TJ. Generation of single-cell and single-nuclei suspensions from embryonic and adult mouse brains. STAR Protoc 2023; 4:101944. [PMID: 36520627 PMCID: PMC9791422 DOI: 10.1016/j.xpro.2022.101944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/09/2022] [Accepted: 11/23/2022] [Indexed: 12/16/2022] Open
Abstract
Efficient protocols to generate single-cell and single-nuclei suspensions are critical for the burgeoning field of single-cell/single-nuclei sequencing. Here we describe procedures to generate single-cell and single-nuclei suspensions from embryonic and adult mouse brains. This protocol can be modified for any brain region and/or neural cell type. For complete details on the use and execution of this protocol, please refer to Lee et al. (2022),1 Rhodes et al. (2022),2 Mahadevan et al. (2021),3 Ekins et al. (2020),4 and Wester et al. (2019).5.
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Affiliation(s)
- Dongjin R Lee
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute for Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Yajun Zhang
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute for Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Christopher T Rhodes
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute for Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Timothy J Petros
- Unit on Cellular and Molecular Neurodevelopment, Eunice Kennedy Shriver National Institute for Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA.
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299
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Cortical interneuron specification and diversification in the era of big data. Curr Opin Neurobiol 2023; 80:102703. [PMID: 36933450 DOI: 10.1016/j.conb.2023.102703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 02/02/2023] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Inhibition in the mammalian cerebral cortex is mediated by a small population of highly diverse GABAergic interneurons. These largely local neurons are interspersed among excitatory projection neurons and exert pivotal regulation on the formation and function of cortical circuits. We are beginning to understand the extent of GABAergic neuron diversity and how this is generated and shaped during brain development in mice and humans. In this review, we summarise recent findings and discuss how new technologies are being used to further advance our knowledge. Understanding how inhibitory neurons are generated in the embryo is an essential pre-requisite of stem cell therapy, an evolving area of research, aimed at correcting human disorders that result in inhibitory dysfunction.
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300
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Khazaei S, Chen CCL, Andrade AF, Kabir N, Azarafshar P, Morcos SM, França JA, Lopes M, Lund PJ, Danieau G, Worme S, Adnani L, Nzirorera N, Chen X, Yogarajah G, Russo C, Zeinieh M, Wong CJ, Bryant L, Hébert S, Tong B, Sihota TS, Faury D, Puligandla E, Jawhar W, Sandy V, Cowan M, Nakada EM, Jerome-Majewska LA, Ellezam B, Gomes CC, Denecke J, Lessel D, McDonald MT, Pizoli CE, Taylor K, Cocanougher BT, Bhoj EJ, Gingras AC, Garcia BA, Lu C, Campos EI, Kleinman CL, Garzia L, Jabado N. Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration. Cell 2023; 186:1162-1178.e20. [PMID: 36931244 PMCID: PMC10112048 DOI: 10.1016/j.cell.2023.02.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 11/04/2022] [Accepted: 02/16/2023] [Indexed: 03/18/2023]
Abstract
Germline histone H3.3 amino acid substitutions, including H3.3G34R/V, cause severe neurodevelopmental syndromes. To understand how these mutations impact brain development, we generated H3.3G34R/V/W knock-in mice and identified strikingly distinct developmental defects for each mutation. H3.3G34R-mutants exhibited progressive microcephaly and neurodegeneration, with abnormal accumulation of disease-associated microglia and concurrent neuronal depletion. G34R severely decreased H3K36me2 on the mutant H3.3 tail, impairing recruitment of DNA methyltransferase DNMT3A and its redistribution on chromatin. These changes were concurrent with sustained expression of complement and other innate immune genes possibly through loss of non-CG (CH) methylation and silencing of neuronal gene promoters through aberrant CG methylation. Complement expression in G34R brains may lead to neuroinflammation possibly accounting for progressive neurodegeneration. Our study reveals that H3.3G34-substitutions have differential impact on the epigenome, which underlie the diverse phenotypes observed, and uncovers potential roles for H3K36me2 and DNMT3A-dependent CH-methylation in modulating synaptic pruning and neuroinflammation in post-natal brains.
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Affiliation(s)
- Sima Khazaei
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Carol C L Chen
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | | | - Nisha Kabir
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Pariya Azarafshar
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Shahir M Morcos
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Josiane Alves França
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mariana Lopes
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Peder J Lund
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Geoffroy Danieau
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Orthopedic Surgery, Faculty of Surgery, McGill University, Montreal, QC H3G 1A4, Canada
| | - Samantha Worme
- Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Lata Adnani
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Nadine Nzirorera
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA; Marine College, Shandong University, Weihai 264209, China
| | - Gayathri Yogarajah
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Department of Biochemistry and Molecular Medicine, Université de Montreal, Research Center of the CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada
| | - Caterina Russo
- Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Michele Zeinieh
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Cassandra J Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Laura Bryant
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Steven Hébert
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Bethany Tong
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Tianna S Sihota
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Damien Faury
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Evan Puligandla
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Wajih Jawhar
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Child Health and Human Development, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
| | - Veronica Sandy
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Mitra Cowan
- McGill Integrated Core for Animal Modeling (MICAM), McGill University, Montreal, QC, Canada
| | - Emily M Nakada
- Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Loydie A Jerome-Majewska
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Benjamin Ellezam
- Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Carolina Cavalieri Gomes
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Eppendorf, Hamburg, Germany
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Institute of Human Genetics, University Hospital of the Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Marie T McDonald
- Division of Medical Genetics, Duke University Hospital, Durham, NC, USA
| | - Carolyn E Pizoli
- Division of Pediatric Neurology, Duke University Hospital, Durham, NC, USA
| | - Kathryn Taylor
- Division of Medical Genetics, Duke University Hospital, Durham, NC, USA
| | | | | | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Eric I Campos
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Livia Garzia
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Orthopedic Surgery, Faculty of Surgery, McGill University, Montreal, QC H3G 1A4, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada.
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