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Reiner BC, Chehimi SN, Merkel R, Toikumo S, Berrettini WH, Kranzler HR, Sanchez-Roige S, Kember RL, Schmidt HD, Crist RC. A single-nucleus transcriptomic atlas of medium spiny neurons in the rat nucleus accumbens. Sci Rep 2024; 14:18258. [PMID: 39107568 PMCID: PMC11303397 DOI: 10.1038/s41598-024-69255-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024] Open
Abstract
Neural processing of rewarding stimuli involves several distinct regions, including the nucleus accumbens (NAc). The majority of NAc neurons are GABAergic projection neurons known as medium spiny neurons (MSNs). MSNs are broadly defined by dopamine receptor expression, but evidence suggests that a wider array of subtypes exist. To study MSN heterogeneity, we analyzed single-nucleus RNA sequencing data from the largest available rat NAc dataset. Analysis of 48,040 NAc MSN nuclei identified major populations belonging to the striosome and matrix compartments. Integration with mouse and human data indicated consistency across species and disease-relevance scoring using genome-wide association study results revealed potentially differential roles for MSN populations in substance use disorders. Additional high-resolution clustering identified 34 transcriptomically distinct subtypes of MSNs definable by a limited number of marker genes. Together, these data demonstrate the diversity of MSNs in the NAc and provide a basis for more targeted genetic manipulation of specific populations.
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Affiliation(s)
- Benjamin C Reiner
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Samar N Chehimi
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Riley Merkel
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biobehavioral Health Sciences, School of Nursing, University of Pennsylvania, Philadelphia, PA, USA
| | - Sylvanus Toikumo
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wade H Berrettini
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Henry R Kranzler
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA, USA
| | - Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Institute for Genomic Medicine, University of California San Diego, San Diego, CA, USA
| | - Rachel L Kember
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA, USA
| | - Heath D Schmidt
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biobehavioral Health Sciences, School of Nursing, University of Pennsylvania, Philadelphia, PA, USA
| | - Richard C Crist
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, 125 South 31st Street, Room 2207, Philadelphia, PA, 19104, USA.
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2
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Johnston KG, Berackey BT, Tran KM, Gelber A, Yu Z, MacGregor GR, Mukamel EA, Tan Z, Green KN, Xu X. Single-cell spatial transcriptomics reveals distinct patterns of dysregulation in non-neuronal and neuronal cells induced by the Trem2 R47H Alzheimer's risk gene mutation. Mol Psychiatry 2024:10.1038/s41380-024-02651-0. [PMID: 39103533 DOI: 10.1038/s41380-024-02651-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 08/07/2024]
Abstract
The R47H missense mutation of the TREM2 gene is a known risk factor for development of Alzheimer's Disease. In this study, we analyze the impact of the Trem2R47H mutation on specific cell types in multiple cortical and subcortical brain regions in the context of wild-type and 5xFAD mouse background. We profile 19 mouse brain sections consisting of wild-type, Trem2R47H, 5xFAD and Trem2R47H; 5xFAD genotypes using MERFISH spatial transcriptomics, a technique that enables subcellular profiling of spatial gene expression. Spatial transcriptomics and neuropathology data are analyzed using our custom pipeline to identify plaque and Trem2R47H-induced transcriptomic dysregulation. We initially analyze cell type-specific transcriptomic alterations induced by plaque proximity. Next, we analyze spatial distributions of disease associated microglia and astrocytes, and how they vary between 5xFAD and Trem2R47H; 5xFAD mouse models. Finally, we analyze the impact of the Trem2R47H mutation on neuronal transcriptomes. The Trem2R47H mutation induces consistent upregulation of Bdnf and Ntrk2 across many cortical excitatory neuron types, independent of amyloid pathology. Spatial investigation of genotype enriched subclusters identified spatially localized neuronal subpopulations reduced in 5xFAD and Trem2R47H; 5xFAD mice. Overall, our MERFISH spatial transcriptomics analysis identifies glial and neuronal transcriptomic alterations induced independently by 5xFAD and Trem2R47H mutations, impacting inflammatory responses in microglia and astrocytes, and activity and BDNF signaling in neurons.
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Affiliation(s)
- Kevin G Johnston
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Bereket T Berackey
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, CA, 92697, USA
| | - Kristine M Tran
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA, 92697, USA
| | - Alon Gelber
- Department of Cognitive Science, University of California, San Diego, CA, 92037, USA
| | - Zhaoxia Yu
- Department of Statistics, School of Computer and Information Science, University of California, Irvine, CA, 92697, USA
- Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA
| | - Grant R MacGregor
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), Irvine, USA
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, CA, 92037, USA
| | - Zhiqun Tan
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
- Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), Irvine, USA
- Department of Molecular Biology and Biochemistry School of Biological Sciences, University of California, Irvine, CA, 92697, USA
| | - Kim N Green
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA, 92697, USA
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), Irvine, USA
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA.
- Department of Biomedical Engineering, University of California, Irvine, CA, 92697, USA.
- Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA.
- Institute for Memory Impairments and Neurological Disorders (UCI MIND), Irvine, USA.
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3
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Wang H, Torous W, Gong B, Purdom E. Visualizing scRNA-Seq Data at Population Scale with GloScope. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.29.542786. [PMID: 37398321 PMCID: PMC10312527 DOI: 10.1101/2023.05.29.542786] [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
Increasingly, scRNA-Seq studies explore cell populations across different samples and the effect of sample heterogeneity on organism's phenotype. However, relatively few bioinformatic methods have been developed which adequately address the variation between samples for such population-level analyses. We propose a framework for representing the entire single-cell profile of a sample, which we call a GloScope representation. We implement GloScope on scRNA-Seq datasets from study designs ranging from 12 to over 300 samples and demonstrate how GloScope allows researchers to perform essential bioinformatic tasks at the sample-level, in particular visualization and quality control assessment.
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4
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Levites Y, Dammer EB, Ran Y, Tsering W, Duong D, Abreha M, Gadhavi J, Lolo K, Trejo-Lopez J, Phillips J, Iturbe A, Erquizi A, Moore BD, Ryu D, Natu A, Dillon K, Torrellas J, Moran C, Ladd T, Afroz F, Islam T, Jagirdar J, Funk CC, Robinson M, Rangaraju S, Borchelt DR, Ertekin-Taner N, Kelly JW, Heppner FL, Johnson ECB, McFarland K, Levey AI, Prokop S, Seyfried NT, Golde TE. Integrative proteomics identifies a conserved Aβ amyloid responsome, novel plaque proteins, and pathology modifiers in Alzheimer's disease. Cell Rep Med 2024:101669. [PMID: 39127040 DOI: 10.1016/j.xcrm.2024.101669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 04/15/2024] [Accepted: 07/10/2024] [Indexed: 08/12/2024]
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disorder that develops over decades. AD brain proteomics reveals vast alterations in protein levels and numerous altered biologic pathways. Here, we compare AD brain proteome and network changes with the brain proteomes of amyloid β (Aβ)-depositing mice to identify conserved and divergent protein networks with the conserved networks identifying an Aβ amyloid responsome. Proteins in the most conserved network (M42) accumulate in plaques, cerebrovascular amyloid (CAA), and/or dystrophic neuronal processes, and overexpression of two M42 proteins, midkine (Mdk) and pleiotrophin (PTN), increases the accumulation of Aβ in plaques and CAA. M42 proteins bind amyloid fibrils in vitro, and MDK and PTN co-accumulate with cardiac transthyretin amyloid. M42 proteins appear intimately linked to amyloid deposition and can regulate amyloid deposition, suggesting that they are pathology modifiers and thus putative therapeutic targets. We posit that amyloid-scaffolded accumulation of numerous M42+ proteins is a central mechanism mediating downstream pathophysiology in AD.
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Affiliation(s)
- Yona Levites
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B Dammer
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Yong Ran
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Wangchen Tsering
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA; Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA
| | - Duc Duong
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Measho Abreha
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Joshna Gadhavi
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Kiara Lolo
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA; Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA
| | - Jorge Trejo-Lopez
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA; Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA
| | - Jennifer Phillips
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA; Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA
| | - Andrea Iturbe
- Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Aya Erquizi
- Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Brenda D Moore
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Danny Ryu
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Aditya Natu
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Kristy Dillon
- Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Jose Torrellas
- Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Corey Moran
- Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Thomas Ladd
- Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA
| | - Farhana Afroz
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Tariful Islam
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Jaishree Jagirdar
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
| | - Cory C Funk
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | - David R Borchelt
- Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Nilüfer Ertekin-Taner
- Mayo Clinic, Department of Neuroscience, Jacksonville, FL, USA; Mayo Clinic, Department of Neurology, Jacksonville, FL, USA
| | - Jeffrey W Kelly
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Frank L Heppner
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 110117 Berlin, Germany; German Center for Neurodegenerative Diseases (DZNE) Berlin, 110117 Berlin, Germany; Cluster of Excellence, NeuroCure, Charitéplatz, 110117 Berlin, Germany
| | - Erik C B Johnson
- Department of Neurology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Karen McFarland
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Allan I Levey
- Department of Neurology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Stefan Prokop
- Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA; Evelyn F. and William L. McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, USA; Department of Neurology, College of Medicine, University of Florida, Gainesville, FL, USA.
| | - Nicholas T Seyfried
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA.
| | - Todd E Golde
- Department of Pharmacology and Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Department of Neurology, School of Medicine, Emory University, Atlanta, GA, USA; Goizueta Brain Health Institute and Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA; Center for Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, USA.
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5
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Alves M, Gil B, Villegas-Salmerón J, Salari V, Martins-Ferreira R, Arribas Blázquez M, Menéndez Méndez A, Da Rosa Gerbatin R, Smith J, de Diego-Garcia L, Conte G, Sierra-Marquez J, Merino Serrais P, Mitra M, Fernandez Martin A, Wang Y, Kesavan J, Melia C, Parras A, Beamer E, Zimmer B, Heiland M, Cavanagh B, Parcianello Cipolat R, Morgan J, Teng X, Prehn JHM, Fabene PF, Bertini G, Artalejo AR, Ballestar E, Nicke A, Olivos-Oré LA, Connolly NMC, Henshall DC, Engel T. Opposing effects of the purinergic P2X7 receptor on seizures in neurons and microglia in male mice. Brain Behav Immun 2024; 120:121-140. [PMID: 38777288 DOI: 10.1016/j.bbi.2024.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 04/28/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND The purinergic ATP-gated P2X7 receptor (P2X7R) is increasingly recognized to contribute to pathological neuroinflammation and brain hyperexcitability. P2X7R expression has been shown to be increased in the brain, including both microglia and neurons, in experimental models of epilepsy and patients. To date, the cell type-specific downstream effects of P2X7Rs during seizures remain, however, incompletely understood. METHODS Effects of P2X7R signaling on seizures and epilepsy were analyzed in induced seizure models using male mice including the kainic acid model of status epilepticus and pentylenetetrazole model and in male and female mice in a genetic model of Dravet syndrome. RNA sequencing was used to analyze P2X7R downstream signaling during seizures. To investigate the cell type-specific role of the P2X7R during seizures and epilepsy, we generated mice lacking exon 2 of the P2rx7 gene in either microglia (P2rx7:Cx3cr1-Cre) or neurons (P2rx7:Thy-1-Cre). To investigate the protective potential of overexpressing P2X7R in GABAergic interneurons, P2X7Rs were overexpressed using adeno-associated virus transduction under the mDlx promoter. RESULTS RNA sequencing of hippocampal tissue from wild-type and P2X7R knock-out mice identified both glial and neuronal genes, in particular genes involved in GABAergic signaling, under the control of the P2X7R following seizures. Mice with deleted P2rx7 in microglia displayed less severe acute seizures and developed a milder form of epilepsy, and microglia displayed an anti-inflammatory molecular profile. In contrast, mice lacking P2rx7 in neurons showed a more severe seizure phenotype when compared to epileptic wild-type mice. Analysis of single-cell expression data revealed that human P2RX7 expression is elevated in the hippocampus of patients with temporal lobe epilepsy in excitatory and inhibitory neurons. Functional studies determined that GABAergic interneurons display increased responses to P2X7R activation in experimental epilepsy. Finally, we show that viral transduction of P2X7R in GABAergic interneurons protects against evoked and spontaneous seizures in experimental temporal lobe epilepsy and in mice lacking Scn1a, a model of Dravet syndrome. CONCLUSIONS Our results suggest a dual and opposing action of P2X7R in epilepsy and suggest P2X7R overexpression in GABAergic interneurons as a novel therapeutic strategy for acquired and, possibly, genetic forms of epilepsy.
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Affiliation(s)
- Mariana Alves
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland
| | - Beatriz Gil
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland
| | - Javier Villegas-Salmerón
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland; The SFI Centre for Research Training in Genomics Data Science, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland
| | - Valentina Salari
- Department of Neurosciences, Biomedicine and Movement Sciences, School of Medicine, University of Verona, 37134 Verona, Italy
| | - Ricardo Martins-Ferreira
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain; Immunogenetics Laboratory, Molecular Pathology and Immunology, Instituto de Ciências Biomédicas Abel Salazar - Universidade do Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; Autoimmunity and Neuroscience Group, UMIB - Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - Marina Arribas Blázquez
- Department of Pharmacology and Toxicology, Veterinary Faculty, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, 28040 Madrid, Spain
| | - Aida Menéndez Méndez
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; Department of Medicine, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, 28670, Villaviciosa de Odon, Spain
| | - Rogerio Da Rosa Gerbatin
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Jonathon Smith
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Laura de Diego-Garcia
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; Ocupharm Research Group, Faculty of Optics and Optometry, Complutense University of Madrid, Avda. Arcos de Jalon, 118 (28037), Madrid, Spain
| | - Giorgia Conte
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland
| | - Juan Sierra-Marquez
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany; Laboratorio Cajal de Circuitos Corticales (CTB), Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Campus Montegancedo S/N, Pozuelo de Alarcon, 28223 Madrid, Spain; Instituto Cajal, Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28002, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Paula Merino Serrais
- Laboratorio Cajal de Circuitos Corticales (CTB), Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Campus Montegancedo S/N, Pozuelo de Alarcon, 28223 Madrid, Spain
| | - Meghma Mitra
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland
| | - Ana Fernandez Martin
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland
| | - Yitao Wang
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Jaideep Kesavan
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Ciara Melia
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; VivoArchitect, Route de la Corniche 5, 1066 Epalinges, Vaud, Switzerland
| | - Alberto Parras
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland
| | - Edward Beamer
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Béla Zimmer
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Mona Heiland
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Brenton Cavanagh
- Cellular and Molecular Imaging Core, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland
| | - Rafael Parcianello Cipolat
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - James Morgan
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9PL, UK
| | - Xinchen Teng
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Jochen H M Prehn
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Paolo F Fabene
- Department of Neurosciences, Biomedicine and Movement Sciences, School of Medicine, University of Verona, 37134 Verona, Italy; Section of Anatomy and Histology, Department of Neurosciences, Biomedicine, and Movement Science, Faculty of Medicine, University of Verona, Verona, Italy; Section of Innovation Biomedicine, Department of Engineering for Innovation Medicine, Faculty of Medicine, University of Verona, Verona, Italy
| | - Giuseppe Bertini
- Department of Neurosciences, Biomedicine and Movement Sciences, School of Medicine, University of Verona, 37134 Verona, Italy
| | - Antonio R Artalejo
- Department of Pharmacology and Toxicology, Veterinary Faculty, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, 28040 Madrid, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain; Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai 200241, China
| | - Annette Nicke
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Luis A Olivos-Oré
- Department of Pharmacology and Toxicology, Veterinary Faculty, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, 28040 Madrid, Spain
| | - Niamh M C Connolly
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - David C Henshall
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland
| | - Tobias Engel
- Department of Physiology & Medical Physics, RCSI University of Medicine & Health Sciences, Dublin D02 YN77, Ireland; FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin D02 YN77, Ireland.
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6
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Guo J, You L, Zhou Y, Hu J, Li J, Yang W, Tang X, Sun Y, Gu Y, Dong Y, Chen X, Sato C, Zinman L, Rogaeva E, Wang J, Chen Y, Zhang M. Spatial enrichment and genomic analyses reveal the link of NOMO1 with amyotrophic lateral sclerosis. Brain 2024; 147:2826-2841. [PMID: 38643019 DOI: 10.1093/brain/awae123] [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: 10/21/2023] [Revised: 03/07/2024] [Accepted: 03/24/2024] [Indexed: 04/22/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a severe motor neuron disease with uncertain genetic predisposition in most sporadic cases. The spatial architecture of cell types and gene expression are the basis of cell-cell interactions, biological function and disease pathology, but are not well investigated in the human motor cortex, a key ALS-relevant brain region. Recent studies indicated single nucleus transcriptomic features of motor neuron vulnerability in ALS motor cortex. However, the brain regional vulnerability of ALS-associated genes and the genetic link between region-specific genes and ALS risk remain largely unclear. Here, we developed an entropy-weighted differential gene expression matrix-based tool (SpatialE) to identify the spatial enrichment of gene sets in spatial transcriptomics. We benchmarked SpatialE against another enrichment tool (multimodal intersection analysis) using spatial transcriptomics data from both human and mouse brain tissues. To investigate regional vulnerability, we analysed three human motor cortex and two dorsolateral prefrontal cortex tissues for spatial enrichment of ALS-associated genes. We also used Cell2location to estimate the abundance of cell types in ALS-related cortex layers. To dissect the link of regionally expressed genes and ALS risk, we performed burden analyses of rare loss-of-function variants detected by whole-genome sequencing in ALS patients and controls, then analysed differential gene expression in the TargetALS RNA-sequencing dataset. SpatialE showed more accurate and specific spatial enrichment of regional cell type markers than multimodal intersection analysis in both mouse brain and human dorsolateral prefrontal cortex. Spatial transcriptomic analyses of human motor cortex showed heterogeneous cell types and spatial gene expression profiles. We found that 260 manually curated ALS-associated genes are significantly enriched in layer 5 of the motor cortex, with abundant expression of upper motor neurons and layer 5 excitatory neurons. Burden analyses of rare loss-of-function variants in Layer 5-associated genes nominated NOMO1 as a novel ALS-associated gene in a combined sample set of 6814 ALS patients and 3324 controls (P = 0.029). Gene expression analyses in CNS tissues revealed downregulation of NOMO1 in ALS, which is consistent with a loss-of-function disease mechanism. In conclusion, our integrated spatial transcriptomics and genomic analyses identified regional brain vulnerability in ALS and the association of a layer 5 gene (NOMO1) with ALS risk.
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Affiliation(s)
- Jingyan Guo
- The First Rehabilitation Hospital of Shanghai, Department of Medical Genetics, School of Medicine, Tongji University, 200090, Shanghai, China
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, 200120, Shanghai, China
| | - Linya You
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China
- Key Laboratory of Medical Computing and Computer Assisted Intervention of Shanghai, 200032, Shanghai, China
| | - Yu Zhou
- The First Rehabilitation Hospital of Shanghai, Department of Medical Genetics, School of Medicine, Tongji University, 200090, Shanghai, China
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, 200120, Shanghai, China
| | - Jiali Hu
- The First Rehabilitation Hospital of Shanghai, Department of Medical Genetics, School of Medicine, Tongji University, 200090, Shanghai, China
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, 200120, Shanghai, China
| | - Jiahao Li
- The First Rehabilitation Hospital of Shanghai, Department of Medical Genetics, School of Medicine, Tongji University, 200090, Shanghai, China
| | - Wanli Yang
- The First Rehabilitation Hospital of Shanghai, Department of Medical Genetics, School of Medicine, Tongji University, 200090, Shanghai, China
| | - Xuelin Tang
- The First Rehabilitation Hospital of Shanghai, Department of Medical Genetics, School of Medicine, Tongji University, 200090, Shanghai, China
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, 200120, Shanghai, China
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 0S8, Canada
| | - Yimin Sun
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Yuqi Gu
- The First Rehabilitation Hospital of Shanghai, Department of Medical Genetics, School of Medicine, Tongji University, 200090, Shanghai, China
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, 200120, Shanghai, China
| | - Yi Dong
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Xi Chen
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Christine Sato
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 0S8, Canada
| | - Lorne Zinman
- Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Division of Neurology, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5T 0S8, Canada
- Division of Neurology, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Jian Wang
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Yan Chen
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, Fudan University, 200040, Shanghai, China
| | - Ming Zhang
- The First Rehabilitation Hospital of Shanghai, Department of Medical Genetics, School of Medicine, Tongji University, 200090, Shanghai, China
- State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, 200120, Shanghai, China
- Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, 200331, Shanghai, China
- Institute for Advanced Study, Tongji University, 200092, Shanghai, China
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7
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Murphy KR, Farrell JS, Bendig J, Mitra A, Luff C, Stelzer IA, Yamaguchi H, Angelakos CC, Choi M, Bian W, DiIanni T, Pujol EM, Matosevich N, Airan R, Gaudillière B, Konofagou EE, Butts-Pauly K, Soltesz I, de Lecea L. Optimized ultrasound neuromodulation for non-invasive control of behavior and physiology. Neuron 2024:S0896-6273(24)00493-8. [PMID: 39079529 DOI: 10.1016/j.neuron.2024.07.002] [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: 11/27/2023] [Revised: 05/09/2024] [Accepted: 07/02/2024] [Indexed: 08/09/2024]
Abstract
Focused ultrasound can non-invasively modulate neural activity, but whether effective stimulation parameters generalize across brain regions and cell types remains unknown. We used focused ultrasound coupled with fiber photometry to identify optimal neuromodulation parameters for four different arousal centers of the brain in an effort to yield overt changes in behavior. Applying coordinate descent, we found that optimal parameters for excitation or inhibition are highly distinct, the effects of which are generally conserved across brain regions and cell types. Optimized stimulations induced clear, target-specific behavioral effects, whereas non-optimized protocols of equivalent energy resulted in substantially less or no change in behavior. These outcomes were independent of auditory confounds and, contrary to expectation, accompanied by a cyclooxygenase-dependent and prolonged reduction in local blood flow and temperature with brain-region-specific scaling. These findings demonstrate that carefully tuned and targeted ultrasound can exhibit powerful effects on complex behavior and physiology.
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Affiliation(s)
- Keith R Murphy
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Jordan S Farrell
- Department of Neurosurgery, Stanford University, Stanford, CA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, USA; F.M. Kirby Neurobiology Center, Harvard Medical School, Boston, MA, USA
| | - Jonas Bendig
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Anish Mitra
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Charlotte Luff
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Ina A Stelzer
- Department of Anesthesia, Stanford University, Stanford, CA, USA
| | - Hiroshi Yamaguchi
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA; Department of Neuroscience, Nagoya University, Nagoya, Japan
| | | | - Mihyun Choi
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Wenjie Bian
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Tommaso DiIanni
- Department of Radiology, Stanford University, Stanford, CA, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Esther Martinez Pujol
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Noa Matosevich
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Raag Airan
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Brice Gaudillière
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Elisa E Konofagou
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Kim Butts-Pauly
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Ivan Soltesz
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Luis de Lecea
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
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8
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Wahl D, Risen SJ, Osburn SC, Emge T, Sharma S, Gilberto VS, Chatterjee A, Nagpal P, Moreno JA, LaRocca TJ. Nanoligomers targeting NF-κB and NLRP3 reduce neuroinflammation and improve cognitive function with aging and tauopathy. J Neuroinflammation 2024; 21:182. [PMID: 39068433 PMCID: PMC11283709 DOI: 10.1186/s12974-024-03182-9] [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: 02/13/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024] Open
Abstract
Neuroinflammation contributes to impaired cognitive function in brain aging and neurodegenerative disorders like Alzheimer's disease, which is characterized by the aggregation of pathological tau. One major driver of both age- and tau-associated neuroinflammation is the NF-κB and NLRP3 signaling axis. However, current treatments targeting NF-κB or NLRP3 may have adverse/systemic effects, and most have not been clinically translatable. In this study, we tested the efficacy of a novel, nucleic acid therapeutic (Nanoligomer) cocktail specifically targeting both NF-κB and NLRP3 in the brain for reducing neuroinflammation and improving cognitive function in old (aged 19 months) wildtype mice, and in rTg4510 tau pathology mice (aged 2 months). We found that 4 weeks of NF-κB/NLRP3-targeting Nanoligomer treatment strongly reduced neuro-inflammatory cytokine profiles in the brain and improved cognitive-behavioral function in both old and rTg4510 mice. These effects of NF-κB/NLRP3-targeting Nanoligomers were also associated with reduced glial cell activation and pathology, favorable changes in transcriptome signatures of glia-associated inflammation (reduced) and neuronal health (increased), and positive systemic effects. Collectively, our results provide a basis for future translational studies targeting both NF-κB and NLRP3 in the brain, perhaps using Nanoligomers, to inhibit neuroinflammation and improve cognitive function with aging and neurodegeneration.
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Affiliation(s)
- Devin Wahl
- Department of Health and Exercise Science, Colorado State University, 1582 Campus Delivery, Fort Collins, CO, 80523, USA
- Columbine Health Systems Center for Healthy Aging, Colorado State University, Fort Collins, CO, USA
| | - Sydney J Risen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
- Brain Research Center, Colorado State University, Fort Collins, CO, USA
| | - Shelby C Osburn
- Department of Health and Exercise Science, Colorado State University, 1582 Campus Delivery, Fort Collins, CO, 80523, USA
- Columbine Health Systems Center for Healthy Aging, Colorado State University, Fort Collins, CO, USA
| | - Tobias Emge
- Department of Health and Exercise Science, Colorado State University, 1582 Campus Delivery, Fort Collins, CO, 80523, USA
- Columbine Health Systems Center for Healthy Aging, Colorado State University, Fort Collins, CO, USA
| | - Sadhana Sharma
- Sachi Bio, Colorado Technology Center, Louisville, CO, USA
| | | | | | | | - Julie A Moreno
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
- Brain Research Center, Colorado State University, Fort Collins, CO, USA
| | - Thomas J LaRocca
- Department of Health and Exercise Science, Colorado State University, 1582 Campus Delivery, Fort Collins, CO, 80523, USA.
- Columbine Health Systems Center for Healthy Aging, Colorado State University, Fort Collins, CO, USA.
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9
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Machold R, Rudy B. Genetic approaches to elucidating cortical and hippocampal GABAergic interneuron diversity. Front Cell Neurosci 2024; 18:1414955. [PMID: 39113758 PMCID: PMC11303334 DOI: 10.3389/fncel.2024.1414955] [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: 04/09/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
GABAergic interneurons (INs) in the mammalian forebrain represent a diverse population of cells that provide specialized forms of local inhibition to regulate neural circuit activity. Over the last few decades, the development of a palette of genetic tools along with the generation of single-cell transcriptomic data has begun to reveal the molecular basis of IN diversity, thereby providing deep insights into how different IN subtypes function in the forebrain. In this review, we outline the emerging picture of cortical and hippocampal IN speciation as defined by transcriptomics and developmental origin and summarize the genetic strategies that have been utilized to target specific IN subtypes, along with the technical considerations inherent to each approach. Collectively, these methods have greatly facilitated our understanding of how IN subtypes regulate forebrain circuitry via cell type and compartment-specific inhibition and thus have illuminated a path toward potential therapeutic interventions for a variety of neurocognitive disorders.
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Affiliation(s)
- Robert Machold
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, United States
| | - Bernardo Rudy
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, United States
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, United States
- Department of Anesthesiology, Perioperative Care and Pain Medicine, New York University Grossman School of Medicine, New York, NY, United States
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10
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Mathys H, Boix CA, Akay LA, Xia Z, Davila-Velderrain J, Ng AP, Jiang X, Abdelhady G, Galani K, Mantero J, Band N, James BT, Babu S, Galiana-Melendez F, Louderback K, Prokopenko D, Tanzi RE, Bennett DA, Tsai LH, Kellis M. Single-cell multiregion dissection of Alzheimer's disease. Nature 2024:10.1038/s41586-024-07606-7. [PMID: 39048816 DOI: 10.1038/s41586-024-07606-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 05/24/2024] [Indexed: 07/27/2024]
Abstract
Alzheimer's disease is the leading cause of dementia worldwide, but the cellular pathways that underlie its pathological progression across brain regions remain poorly understood1-3. Here we report a single-cell transcriptomic atlas of six different brain regions in the aged human brain, covering 1.3 million cells from 283 post-mortem human brain samples across 48 individuals with and without Alzheimer's disease. We identify 76 cell types, including region-specific subtypes of astrocytes and excitatory neurons and an inhibitory interneuron population unique to the thalamus and distinct from canonical inhibitory subclasses. We identify vulnerable populations of excitatory and inhibitory neurons that are depleted in specific brain regions in Alzheimer's disease, and provide evidence that the Reelin signalling pathway is involved in modulating the vulnerability of these neurons. We develop a scalable method for discovering gene modules, which we use to identify cell-type-specific and region-specific modules that are altered in Alzheimer's disease and to annotate transcriptomic differences associated with diverse pathological variables. We identify an astrocyte program that is associated with cognitive resilience to Alzheimer's disease pathology, tying choline metabolism and polyamine biosynthesis in astrocytes to preserved cognitive function late in life. Together, our study develops a regional atlas of the ageing human brain and provides insights into cellular vulnerability, response and resilience to Alzheimer's disease pathology.
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Affiliation(s)
- Hansruedi Mathys
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Carles A Boix
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computational and Systems Biology Program, MIT, Cambridge, MA, USA
| | - Leyla Anne Akay
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Ziting Xia
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Harvard-MIT Health Sciences and Technology Program, MIT, Cambridge, MA, USA
| | | | - Ayesha P Ng
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Xueqiao Jiang
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Ghada Abdelhady
- University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kyriaki Galani
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julio Mantero
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neil Band
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Benjamin T James
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sudhagar Babu
- University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Fabiola Galiana-Melendez
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Kate Louderback
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Dmitry Prokopenko
- Genetics and Aging Research Unit, McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Li-Huei Tsai
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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11
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Lu X, Ni P, Suarez-Meade P, Ma Y, Forrest EN, Wang G, Wang Y, Quiñones-Hinojosa A, Gerstein M, Jiang YH. Transcriptional determinism and stochasticity contribute to the complexity of autism-associated SHANK family genes. Cell Rep 2024; 43:114376. [PMID: 38900637 DOI: 10.1016/j.celrep.2024.114376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/08/2024] [Accepted: 05/31/2024] [Indexed: 06/22/2024] Open
Abstract
Precision of transcription is critical because transcriptional dysregulation is disease causing. Traditional methods of transcriptional profiling are inadequate to elucidate the full spectrum of the transcriptome, particularly for longer and less abundant mRNAs. SHANK3 is one of the most common autism causative genes. Twenty-four Shank3-mutant animal lines have been developed for autism modeling. However, their preclinical validity has been questioned due to incomplete Shank3 transcript structure. We apply an integrative approach combining cDNA-capture and long-read sequencing to profile the SHANK3 transcriptome in humans and mice. We unexpectedly discover an extremely complex SHANK3 transcriptome. Specific SHANK3 transcripts are altered in Shank3-mutant mice and postmortem brain tissues from individuals with autism spectrum disorder. The enhanced SHANK3 transcriptome significantly improves the detection rate for potential deleterious variants from genomics studies of neuropsychiatric disorders. Our findings suggest that both deterministic and stochastic transcription of the genome is associated with SHANK family genes.
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Affiliation(s)
- Xiaona Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Pengyu Ni
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Yu Ma
- Department of Neurology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Emily Niemitz Forrest
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Guilin Wang
- Keck Microarray Shared Resource, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yi Wang
- Department of Neurology, Children's Hospital of Fudan University, Shanghai 201102, China
| | | | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA; Department of Biomedical Informatics & Data Science, Yale University, New Haven, CT 06520, USA
| | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA; Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA.
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12
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Furlanis E, Dai M, Garcia BL, Vergara J, Pereira A, Pelkey K, Tran T, Gorissen BL, Vlachos A, Hairston A, Huang S, Dwivedi D, Du S, Wills S, McMahon J, Lee AT, Chang EF, Razzaq T, Qazi A, Vargish G, Yuan X, Caccavano A, Hunt S, Chittajallu R, McLean N, Hewit L, Paranzino E, Rice H, Cummins AC, Plotnikova A, Mohanty A, Tangen AC, Shin JH, Azadi R, Eldridge MA, Alvarez VA, Averbeck BB, Alyahyay M, Vallejo TR, Soheib M, Vattino LG, MacGregor CP, Banks E, Olah VJ, Naskar S, Hill S, Liebergall S, Badiani R, Hyde L, Xu Q, Allaway KC, Goldberg EM, Nowakowski TJ, Lee S, Takesian AE, Ibrahim LA, Iqbal A, McBain CJ, Dimidschstein J, Fishell G, Wang Y. An enhancer-AAV toolbox to target and manipulate distinct interneuron subtypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603924. [PMID: 39091835 PMCID: PMC11291062 DOI: 10.1101/2024.07.17.603924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
In recent years, we and others have identified a number of enhancers that, when incorporated into rAAV vectors, can restrict the transgene expression to particular neuronal populations. Yet, viral tools to access and manipulate fine neuronal subtypes are still limited. Here, we performed systematic analysis of single cell genomic data to identify enhancer candidates for each of the cortical interneuron subtypes. We established a set of enhancer-AAV tools that are highly specific for distinct cortical interneuron populations and striatal cholinergic neurons. These enhancers, when used in the context of different effectors, can target (fluorescent proteins), observe activity (GCaMP) and manipulate (opto- or chemo-genetics) specific neuronal subtypes. We also validated our enhancer-AAV tools across species. Thus, we provide the field with a powerful set of tools to study neural circuits and functions and to develop precise and targeted therapy.
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Affiliation(s)
- Elisabetta Furlanis
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- These authors contributed equally
| | - Min Dai
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- These authors contributed equally
| | - Brenda Leyva Garcia
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Josselyn Vergara
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ana Pereira
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kenneth Pelkey
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Thien Tran
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bram L. Gorissen
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anna Vlachos
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Ariel Hairston
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
| | - Shuhan Huang
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
| | - Deepanjali Dwivedi
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Du
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sara Wills
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Justin McMahon
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anthony T. Lee
- Department of Neurological Surgery, University of California San Francisco, San Francisco, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, USA
| | - Edward F. Chang
- Department of Neurological Surgery, University of California San Francisco, San Francisco, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, USA
| | | | | | - Geoffrey Vargish
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Xiaoqing Yuan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Adam Caccavano
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Steven Hunt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Ramesh Chittajallu
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Nadiya McLean
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Lauren Hewit
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Emily Paranzino
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Haley Rice
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Alex C. Cummins
- National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892-4415, USA
| | - Anya Plotnikova
- National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892-4415, USA
| | - Arya Mohanty
- National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892-4415, USA
| | - Anne Claire Tangen
- National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892-4415, USA
| | - Jung Hoon Shin
- National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892-4415, USA
| | - Reza Azadi
- National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892-4415, USA
| | - Mark A.G. Eldridge
- National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892-4415, USA
| | - Veronica A. Alvarez
- National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892-4415, USA
| | - Bruno B. Averbeck
- National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892-4415, USA
| | - Mansour Alyahyay
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
| | - Tania Reyes Vallejo
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
| | - Mohammed Soheib
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
| | - Lucas G. Vattino
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary Boston, USA
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School Boston, USA
| | - Cathryn P. MacGregor
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary Boston, USA
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School Boston, USA
| | - Emmie Banks
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Viktor Janos Olah
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Shovan Naskar
- Unit of Functional Neural Circuit, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sophie Hill
- Department of Neuroscience, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sophie Liebergall
- Department of Neuroscience, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Rohan Badiani
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lili Hyde
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Qing Xu
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
- Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Kathryn C. Allaway
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ethan M. Goldberg
- Department of Neuroscience, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Tomasz J. Nowakowski
- Department of Neurological Surgery, University of California San Francisco, San Francisco, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, USA
- Department of Anatomy, University of California, San Francisco (UCSF), San Francisco, CA, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Soohyun Lee
- Unit of Functional Neural Circuit, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anne E. Takesian
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary Boston, USA
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School Boston, USA
| | - Leena A. Ibrahim
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
| | | | - Chris J. McBain
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Jordane Dimidschstein
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gord Fishell
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yating Wang
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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13
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Wu SJ, Dai M, Yang SP, McCann C, Qiu Y, Marrero GJ, Stogsdill JA, Di Bella DJ, Xu Q, Farhi SL, Macosko EZ, Chen F, Fishell G. Pyramidal neurons proportionately alter the identity and survival of specific cortical interneuron subtypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.20.604399. [PMID: 39071350 PMCID: PMC11275907 DOI: 10.1101/2024.07.20.604399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The mammalian cerebral cortex comprises a complex neuronal network that maintains a delicate balance between excitatory neurons and inhibitory interneurons. Previous studies, including our own research, have shown that specific interneuron subtypes are closely associated with particular pyramidal neuron types, forming stereotyped local inhibitory microcircuits. However, the developmental processes that establish these precise networks are not well understood. Here we show that pyramidal neuron types are instrumental in driving the terminal differentiation and maintaining the survival of specific associated interneuron subtypes. In a wild-type cortex, the relative abundance of different interneuron subtypes aligns precisely with the pyramidal neuron types to which they synaptically target. In Fezf2 mutant cortex, characterized by the absence of layer 5 pyramidal tract neurons and an expansion of layer 6 intratelencephalic neurons, we observed a corresponding decrease in associated layer 5b interneurons and an increase in layer 6 subtypes. Interestingly, these shifts in composition are achieved through mechanisms specific to different interneuron types. While SST interneurons adjust their abundance to the change in pyramidal neuron prevalence through the regulation of programmed cell death, parvalbumin interneurons alter their identity. These findings illustrate two key strategies by which the dynamic interplay between pyramidal neurons and interneurons allows local microcircuits to be sculpted precisely. These insights underscore the precise roles of extrinsic signals from pyramidal cells in the establishment of interneuron diversity and their subsequent integration into local cortical microcircuits.
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14
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Walker H, Frost NA. Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction. iScience 2024; 27:110355. [PMID: 39045099 PMCID: PMC11263963 DOI: 10.1016/j.isci.2024.110355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/01/2024] [Accepted: 06/20/2024] [Indexed: 07/25/2024] Open
Abstract
Social interactions are encoded by the coordinated activity of heterogeneous cell types within distributed brain regions including the medial prefrontal cortex (mPFC). However, our understanding of the cell types which comprise the social ensemble has been limited by available mouse lines and reliance on single marker genes. We identified differentially active neuronal populations during social interactions by quantifying immediate-early gene (IEG) expression using snRNA-sequencing. These studies revealed that distinct prefrontal neuron populations composed of heterogeneous cell types are activated by social interaction. Evaluation of IEG expression within these recruited neuronal populations revealed cell-type and region-specific programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal insights into the neuronal populations which compose the social ensemble.
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Affiliation(s)
- Hailee Walker
- University of Utah, Department of Neurology, Salt Lake City, UT 84132, USA
| | - Nicholas A. Frost
- University of Utah, Department of Neurology, Salt Lake City, UT 84132, USA
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15
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Agmon A, Barth AL. A brief history of somatostatin interneuron taxonomy or: how many somatostatin subtypes are there, really? Front Neural Circuits 2024; 18:1436915. [PMID: 39091993 PMCID: PMC11292610 DOI: 10.3389/fncir.2024.1436915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/28/2024] [Indexed: 08/04/2024] Open
Abstract
We provide a brief (and unabashedly biased) overview of the pre-transcriptomic history of somatostatin interneuron taxonomy, followed by a chronological summary of the large-scale, NIH-supported effort over the last ten years to generate a comprehensive, single-cell RNA-seq-based taxonomy of cortical neurons. Focusing on somatostatin interneurons, we present the perspective of experimental neuroscientists trying to incorporate the new classification schemes into their own research while struggling to keep up with the ever-increasing number of proposed cell types, which seems to double every two years. We suggest that for experimental analysis, the most useful taxonomic level is the subdivision of somatostatin interneurons into ten or so "supertypes," which closely agrees with their more traditional classification by morphological, electrophysiological and neurochemical features. We argue that finer subdivisions ("t-types" or "clusters"), based on slight variations in gene expression profiles but lacking clear phenotypic differences, are less useful to researchers and may actually defeat the purpose of classifying neurons to begin with. We end by stressing the need for generating novel tools (mouse lines, viral vectors) for genetically targeting distinct supertypes for expression of fluorescent reporters, calcium sensors and excitatory or inhibitory opsins, allowing neuroscientists to chart the input and output synaptic connections of each proposed subtype, reveal the position they occupy in the cortical network and examine experimentally their roles in sensorimotor behaviors and cognitive brain functions.
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Affiliation(s)
- Ariel Agmon
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, United States
| | - Alison L. Barth
- Department of Biological Sciences, Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA, United States
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16
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Pérez RF, Tezanos P, Peñarroya A, González-Ramón A, Urdinguio RG, Gancedo-Verdejo J, Tejedor JR, Santamarina-Ojeda P, Alba-Linares JJ, Sainz-Ledo L, Roberti A, López V, Mangas C, Moro M, Cintado Reyes E, Muela Martínez P, Rodríguez-Santamaría M, Ortea I, Iglesias-Rey R, Castilla-Silgado J, Tomás-Zapico C, Iglesias-Gutiérrez E, Fernández-García B, Sanchez-Mut JV, Trejo JL, Fernández AF, Fraga MF. A multiomic atlas of the aging hippocampus reveals molecular changes in response to environmental enrichment. Nat Commun 2024; 15:5829. [PMID: 39013876 PMCID: PMC11252340 DOI: 10.1038/s41467-024-49608-z] [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: 09/12/2023] [Accepted: 06/10/2024] [Indexed: 07/18/2024] Open
Abstract
Aging involves the deterioration of organismal function, leading to the emergence of multiple pathologies. Environmental stimuli, including lifestyle, can influence the trajectory of this process and may be used as tools in the pursuit of healthy aging. To evaluate the role of epigenetic mechanisms in this context, we have generated bulk tissue and single cell multi-omic maps of the male mouse dorsal hippocampus in young and old animals exposed to environmental stimulation in the form of enriched environments. We present a molecular atlas of the aging process, highlighting two distinct axes, related to inflammation and to the dysregulation of mRNA metabolism, at the functional RNA and protein level. Additionally, we report the alteration of heterochromatin domains, including the loss of bivalent chromatin and the uncovering of a heterochromatin-switch phenomenon whereby constitutive heterochromatin loss is partially mitigated through gains in facultative heterochromatin. Notably, we observed the multi-omic reversal of a great number of aging-associated alterations in the context of environmental enrichment, which was particularly linked to glial and oligodendrocyte pathways. In conclusion, our work describes the epigenomic landscape of environmental stimulation in the context of aging and reveals how lifestyle intervention can lead to the multi-layered reversal of aging-associated decline.
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Affiliation(s)
- Raúl F Pérez
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Patricia Tezanos
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
- Programa de Doctorado en Neurociencia, Universidad Autónoma de Madrid-Instituto Cajal, 28002, Madrid, Spain
| | - Alfonso Peñarroya
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
| | - Alejandro González-Ramón
- Laboratory of Functional Epi-Genomics of Aging and Alzheimer's disease, Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550, Alicante, Spain
| | - Rocío G Urdinguio
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Javier Gancedo-Verdejo
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Juan Ramón Tejedor
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Pablo Santamarina-Ojeda
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Juan José Alba-Linares
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Lidia Sainz-Ledo
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
| | - Annalisa Roberti
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
| | - Virginia López
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Cristina Mangas
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
| | - María Moro
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
| | - Elisa Cintado Reyes
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
- Programa de Doctorado en Neurociencia, Universidad Autónoma de Madrid-Instituto Cajal, 28002, Madrid, Spain
| | - Pablo Muela Martínez
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
- Programa de Doctorado en Neurociencia, Universidad Autónoma de Madrid-Instituto Cajal, 28002, Madrid, Spain
| | - Mar Rodríguez-Santamaría
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Bioterio y unidad de imagen preclínica, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Ignacio Ortea
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Proteomics Unit, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), 33011, Oviedo, Spain
| | - Ramón Iglesias-Rey
- Neuroimaging and Biotechnology Laboratory (NOBEL), Clinical Neurosciences Research Laboratory (LINC), Health Research Institute of Santiago de Compostela (IDIS), 15706, Santiago de Compostela, Spain
| | - Juan Castilla-Silgado
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Cristina Tomás-Zapico
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Eduardo Iglesias-Gutiérrez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Benjamín Fernández-García
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Jose Vicente Sanchez-Mut
- Laboratory of Functional Epi-Genomics of Aging and Alzheimer's disease, Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550, Alicante, Spain
| | - José Luis Trejo
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
| | - Agustín F Fernández
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain.
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain.
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain.
| | - Mario F Fraga
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain.
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain.
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain.
- Departamento de Biología de Organismos y Sistemas, Área de Fisiología Vegetal, Universidad de Oviedo, 33006, Oviedo, Spain.
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17
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Montani C, Balasco L, Pagani M, Alvino FG, Barsotti N, de Guzman AE, Galbusera A, de Felice A, Nickl-Jockschat TK, Migliarini S, Casarosa S, Lau P, Mattioni L, Pasqualetti M, Provenzano G, Bozzi Y, Lombardo MV, Gozzi A. Sex-biasing influence of autism-associated Ube3a gene overdosage at connectomic, behavioral, and transcriptomic levels. SCIENCE ADVANCES 2024; 10:eadg1421. [PMID: 38996019 PMCID: PMC11244557 DOI: 10.1126/sciadv.adg1421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 06/07/2024] [Indexed: 07/14/2024]
Abstract
Genomic mechanisms enhancing risk in males may contribute to sex bias in autism. The ubiquitin protein ligase E3A gene (Ube3a) affects cellular homeostasis via control of protein turnover and by acting as transcriptional coactivator with steroid hormone receptors. Overdosage of Ube3a via duplication or triplication of chromosomal region 15q11-13 causes 1 to 2% of autistic cases. Here, we test the hypothesis that increased dosage of Ube3a may influence autism-relevant phenotypes in a sex-biased manner. We show that mice with extra copies of Ube3a exhibit sex-biasing effects on brain connectomics and autism-relevant behaviors. These effects are associated with transcriptional dysregulation of autism-associated genes, as well as genes differentially expressed in 15q duplication and in autistic people. Increased Ube3a dosage also affects expression of genes on the X chromosome, genes influenced by sex steroid hormone, and genes sex-differentially regulated by transcription factors. These results suggest that Ube3a overdosage can contribute to sex bias in neurodevelopmental conditions via influence on sex-differential mechanisms.
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Affiliation(s)
- Caterina Montani
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
| | - Luigi Balasco
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Marco Pagani
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
- Autism Center, Child Mind Institute, New York, NY, USA
- IMT School for Advanced Studies, Lucca, Italy
| | - Filomena Grazia Alvino
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
| | - Noemi Barsotti
- Unit of Cell and Developmental Biology, Department of Biology, University of Pisa, Pisa, Italy
| | - A. Elizabeth de Guzman
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
| | - Alberto Galbusera
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
| | - Alessia de Felice
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
| | - Thomas K. Nickl-Jockschat
- Department of Psychiatry and Psychotherapy, Otto-von-Guericke University, Magdeburg, Germany
- German Center for Mental Health (DZPG), partner site Halle-Jena-Magdeburg, Germany
- Center for Intervention and Research on adaptive and maladaptive brain Circuits underlying mental health (C-I-R-C), Halle-Jena-Magdeburg, Germany
| | - Sara Migliarini
- Unit of Cell and Developmental Biology, Department of Biology, University of Pisa, Pisa, Italy
| | - Simona Casarosa
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Centre for Medical Sciences (CISMed), University of Trento, Trento, Italy
| | - Pierre Lau
- Istituto Italiano di Tecnologia, Center for Human Technologies, Genova, Italy
| | - Lorenzo Mattioni
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Massimo Pasqualetti
- Unit of Cell and Developmental Biology, Department of Biology, University of Pisa, Pisa, Italy
| | - Giovanni Provenzano
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Yuri Bozzi
- Center for Mind/Brain Sciences (CIMeC), University of Trento, Rovereto, Italy
- CNR Neuroscience Institute, Pisa, Italy
| | - Michael V. Lombardo
- Laboratory for Autism and Neurodevelopmental Disorders, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
| | - Alessandro Gozzi
- Functional Neuroimaging Laboratory, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, CNCS@UNITN, Rovereto, Italy
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18
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Polyzou A, Fuchs J, Kroon C, Kotoula A, Delis F, Turko P, Antoniou K, Eickholt B, Leondaritis G. Cell type-specific and subcellular expression of phospholipid phosphatase-related proteins to modulate lyso-phosphatidic acid synaptic signaling in the developing and adult CNS. J Neurochem 2024. [PMID: 38994820 DOI: 10.1111/jnc.16169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024]
Abstract
Lysophosphatidic acid (LPA) is a bioactive phospholipid that participates in critical processes in neural development and adult brain function and is implicated in various pathophysiological conditions. Along with its six well-characterized receptors, atypical regulators of LPA signaling have also been suggested, including phospholipid phosphatase-related proteins (PLPPRs). PLPPRs have been mostly studied in the developing brain where they control LPA-dependent axon guidance, cortical network hyperexcitability, and glutamatergic neurotransmission. PLPPR4 and PLPPR3 represent two closely related proteins reported to localize predominantly in dendrites and axons, respectively, and differ in their developmental expression patterns. Herein, we have revised the expression patterns of PLPPRs in the cerebellum, dorsal and ventral hippocampus, prefrontal cortex (PFC), nucleus accumbens, and striatum during development and in the adult using quantitative PCR. Expression patterns of Plppr2,4 and 5 were consistent with previous studies, whereas Plppr3 and Plppr1 exhibited a unique expression profile in nucleus accumbens (NAc) and striatum in later developmental and adult stages, which we verified at the protein level for PLPPR3. To investigate neuron type-specific expression at the single cell level, we developed a bioinformatic tool to analyze recent single-cell RNA-sequencing data in the cerebral cortex and hippocampus of adult mice. Our analysis revealed a widespread but also selective adult neuron-type expression with higher expression levels of Plppr3, Plppr1, and Plppr5 in GABAergic and Plppr4 and Plppr2 in glutamatergic neurons. PLPPR4 has been identified as a post-synaptic modulator of LPA levels in glutamatergic synapses operating via an uptake mechanism, to control LPA-dependent cortical network hyperexcitability. Using subcellular fractionation experiments, we found that both PLPPR4 and PLPPR3 are co-expressed in adult synaptosomal membranes. Furthermore, flow cytometry experiments in HEK293 cells showed comparable LPA uptake by PLPPR4 and PLPPR3, whereas PLPRR3, but not PLPPR4, induced also uptake of monoacylglycerol, the dephosphorylation product of LPA. We propose that synaptic LPA may be subject to both pre-synaptic and post-synaptic mechanisms of regulation by PLPPRs in addition to LPARs in developing and adult synapses.
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Affiliation(s)
- Alexandra Polyzou
- Department of Pharmacology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Joachim Fuchs
- Institute of Molecular Biology and Biochemistry, Charité -Universitätsmedizin-Berlin, Berlin, Germany
| | - Cristina Kroon
- Institute of Molecular Biology and Biochemistry, Charité -Universitätsmedizin-Berlin, Berlin, Germany
| | - Androniki Kotoula
- Department of Pharmacology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Foteini Delis
- Department of Pharmacology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Paul Turko
- Institut für Integrative Neuroanatomie, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Katerina Antoniou
- Department of Pharmacology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
- Institute of Biosciences, University Research Center Ioannina, University of Ioannina, Ioannina, Greece
| | - Britta Eickholt
- Institute of Molecular Biology and Biochemistry, Charité -Universitätsmedizin-Berlin, Berlin, Germany
| | - George Leondaritis
- Department of Pharmacology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
- Institute of Biosciences, University Research Center Ioannina, University of Ioannina, Ioannina, Greece
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19
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Gómez-Pascual A, Glikman DM, Ng HX, Tomkins JE, Lu L, Xu Y, Ashbrook DG, Kaczorowski C, Kempermann G, Killmar J, Mozhui K, Ohlenschläger O, Aebersold R, Ingram DK, Williams EG, Williams RW, Overall RW, Jucker M, de Bakker DEM. The Pgb1 locus controls glycogen aggregation in astrocytes of the aged hippocampus without impacting cognitive function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.22.567373. [PMID: 38045339 PMCID: PMC10690248 DOI: 10.1101/2023.11.22.567373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
In aged humans and mice, aggregates of hypobranched glycogen molecules called polyglucosan bodies (PGBs) accumulate in hippocampal astrocytes. PGBs are known to drive cognitive decline in neurological diseases but remain largely unstudied in the context of typical brain aging. Here, we show that PGBs arise in autophagy-dysregulated astrocytes of the aged C57BL/6J mouse hippocampus. To map the genetic cause of age-related PGB accumulation, we quantified PGB burden in 32 fully sequenced BXD-recombinant inbred mouse strains, which display a 400-fold variation in hippocampal PGB burden at 16-18 months of age. A major modifier locus was mapped to chromosome 1 at 72-75 Mb, which we defined as the Pgb1 locus. To evaluate candidate genes and downstream mechanisms by which Pgb1 controls the aggregation of glycogen, extensive hippocampal transcriptomic and proteomic datasets were produced for aged mice of the BXD family. We utilized these datasets to identify Smarcal1 and Usp37 as potential regulators of PGB accumulation. To assess the effect of PGB burden on age-related cognitive decline, we performed phenome-wide association scans, transcriptomic analyses as well as conditioned fear memory and Y-maze testing. Importantly, we did not find any evidence suggesting a negative impact of PGBs on cognition. Taken together, our study demonstrates that the Pgb1 locus controls glycogen aggregation in astrocytes of the aged hippocampus without affecting age-related cognitive decline.
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Affiliation(s)
- A Gómez-Pascual
- Department of Information and Communications Engineering, University of Murcia, Murcia, Spain
| | | | - H X Ng
- Department of Cognitive Science University of California, San Diego, USA
| | - J E Tomkins
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - L Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Center, Memphis, TN, USA
| | - Y Xu
- Department of Cellular Neurology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - D G Ashbrook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Center, Memphis, TN, USA
| | | | - G Kempermann
- German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany
| | - J Killmar
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Center, Memphis, TN, USA
| | - K Mozhui
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Center, Memphis, TN, USA
- Department of Preventive Medicine, College of Medicine, University of Tennessee Health Center, Memphis, TN, USA
| | - O Ohlenschläger
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - R Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich. Zurich, Switzerland
| | - D K Ingram
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA, USA
| | - E G Williams
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg
| | - R W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Center, Memphis, TN, USA
| | - R W Overall
- Humboldt University of Berlin, Berlin, Germany
| | - M Jucker
- Department of Cellular Neurology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - D E M de Bakker
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
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20
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Zou LS, Cable DM, Barrera-Lopez IA, Zhao T, Murray E, Aryee MJ, Chen F, Irizarry RA. Detection of allele-specific expression in spatial transcriptomics with spASE. Genome Biol 2024; 25:180. [PMID: 38978101 PMCID: PMC11229351 DOI: 10.1186/s13059-024-03317-4] [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: 11/02/2023] [Accepted: 06/20/2024] [Indexed: 07/10/2024] Open
Abstract
Spatial transcriptomics technologies permit the study of the spatial distribution of RNA at near-single-cell resolution genome-wide. However, the feasibility of studying spatial allele-specific expression (ASE) from these data remains uncharacterized. Here, we introduce spASE, a computational framework for detecting and estimating spatial ASE. To tackle the challenges presented by cell type mixtures and a low signal to noise ratio, we implement a hierarchical model involving additive mixtures of spatial smoothing splines. We apply our method to allele-resolved Visium and Slide-seq from the mouse cerebellum and hippocampus and report new insight into the landscape of spatial and cell type-specific ASE therein.
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Affiliation(s)
- Luli S Zou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Dylan M Cable
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, 02139, USA
| | | | - Tongtong Zhao
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Martin J Aryee
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Rafael A Irizarry
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
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21
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Tuñon-Ortiz A, Tränkner D, Raines O, Mahnke A, Brockway S, Grega M, Zelikowsky M, Williams ME. Inhibitory neurons defined by a synaptogenic molecule impair memory discrimination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602304. [PMID: 39005261 PMCID: PMC11245094 DOI: 10.1101/2024.07.05.602304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The CA3 region is central to hippocampal function during learning and memory because of its unique connectivity. CA3 pyramidal neurons are the targets of huge, excitatory mossy fiber synapses from DG axons and have an unusually high degree of excitatory recurrent connectivity. Thus, inhibition likely plays an outsized importance in constraining runaway excitation and shaping CA3 ensembles during learning and memory. Here, we investigate the function of a group of dendrite-targeting, hippocampal GABAergic neurons defined by expression of the synaptogenic adhesion molecule, Kirrel3. We discovered that activating Kirrel3-expressing GABAergic neurons impairs memory discrimination by inhibiting CA3 pyramidal neurons in novel contexts. Kirrel3 is required for DG-to-GABA synapse formation and variants in Kirrel3 are strong risk factors for neurodevelopmental disorders. Thus, our work suggests that Kirrel3-GABA neurons are a critical source of feed-forward inhibition from DG to CA3 during contextual memory whose activity may be specifically disrupted in some brain disorders.
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Affiliation(s)
- Arnulfo Tuñon-Ortiz
- Department of Neurobiology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Dimitri Tränkner
- Department of Neurobiology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Olivia Raines
- Department of Neurobiology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Abbey Mahnke
- Department of Neurobiology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Sarah Brockway
- Department of Neurobiology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Matthew Grega
- Department of Neurobiology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Moriel Zelikowsky
- Department of Neurobiology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Megan E Williams
- Department of Neurobiology, University of Utah School of Medicine, Salt Lake City, UT 84112
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22
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Howe JR, Chan CL, Lee D, Blanquart M, Romero HK, Zadina AN, Lemieux ME, Mills F, Desplats PA, Tye KM, Root CM. Control of innate olfactory valence by segregated cortical amygdala circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600895. [PMID: 38979308 PMCID: PMC11230396 DOI: 10.1101/2024.06.26.600895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Animals perform innate behaviors that are stereotyped responses to specific evolutionarily relevant stimuli in the absence of prior learning or experience. These behaviors can be reduced to an axis of valence, whereby specific odors evoke approach or avoidance. The cortical amygdala (plCoA) mediates innate attraction and aversion to odor. However, little is known about how this brain area gives rise to behaviors of opposing motivational valence. Here, we sought to define the circuit features of plCoA that give rise to innate olfactory behaviors of valence. We characterized the physiology, gene expression, and projections of this structure, identifying a divergent, topographic organization that selectively controls innate attraction and avoidance to odor. First, we examined odor-evoked responses in these areas and found sparse encoding of odor identity, but not valence. We next considered a topographic organization and found that optogenetic stimulation of the anterior and posterior domains of plCoA elicits attraction and avoidance, respectively, suggesting a functional axis for valence. Using single cell and spatial RNA sequencing, we identified the molecular cell types in plCoA, revealing an anteroposterior gradient in cell types, whereby anterior glutamatergic neurons preferentially express Slc17a6 and posterior neurons express Slc17a7. Activation of these respective cell types recapitulates appetitive and aversive valence behaviors, and chemogenetic inhibition reveals partial necessity for valence responses to innate appetitive or aversive odors. Finally, we identified topographically organized circuits defined by projections, whereby anterior neurons preferentially project to medial amygdala, and posterior neurons preferentially project to nucleus accumbens, which are respectively sufficient and necessary for innate negative and positive olfactory valence. Together, these data advance our understanding of how the olfactory system generates stereotypic, hardwired attraction and avoidance, and supports a model whereby distinct, topographically distributed plCoA populations direct innate olfactory valence responses by signaling to divergent valence-specific targets, linking upstream olfactory identity to downstream valence behaviors, through a population code. This represents a novel circuit motif in which valence encoding is represented not by the firing properties of individual neurons, but by population level identity encoding that is routed through divergent targets to mediate distinct valence.
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Affiliation(s)
- James R Howe
- Department of Biological Sciences, Section of Neuroscience, University of California, San Diego, La Jolla, CA 92093, USA
- Neurosciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- These authors contributed equally
| | - Chung-Lung Chan
- Department of Biological Sciences, Section of Neuroscience, University of California, San Diego, La Jolla, CA 92093, USA
- These authors contributed equally
| | - Donghyung Lee
- Department of Biological Sciences, Section of Neuroscience, University of California, San Diego, La Jolla, CA 92093, USA
| | - Marlon Blanquart
- Department of Biological Sciences, Section of Neuroscience, University of California, San Diego, La Jolla, CA 92093, USA
| | - Haylie K Romero
- Neurosciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Abigail N Zadina
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10027, USA
| | | | - Fergil Mills
- Salk Institute for Biological Sciences, La Jolla, CA 92037, USA
| | - Paula A Desplats
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kay M Tye
- Department of Biological Sciences, Section of Neuroscience, University of California, San Diego, La Jolla, CA 92093, USA
- Salk Institute for Biological Sciences, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, La Jolla, CA 92037, USA
| | - Cory M Root
- Department of Biological Sciences, Section of Neuroscience, University of California, San Diego, La Jolla, CA 92093, USA
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23
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Di Bella DJ, Domínguez-Iturza N, Brown JR, Arlotta P. Making Ramón y Cajal proud: Development of cell identity and diversity in the cerebral cortex. Neuron 2024; 112:2091-2111. [PMID: 38754415 DOI: 10.1016/j.neuron.2024.04.021] [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: 12/15/2023] [Revised: 03/28/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024]
Abstract
Since the beautiful images of Santiago Ramón y Cajal provided a first glimpse into the immense diversity and complexity of cell types found in the cerebral cortex, neuroscience has been challenged and inspired to understand how these diverse cells are generated and how they interact with each other to orchestrate the development of this remarkable tissue. Some fundamental questions drive the field's quest to understand cortical development: what are the mechanistic principles that govern the emergence of neuronal diversity? How do extrinsic and intrinsic signals integrate with physical forces and activity to shape cell identity? How do the diverse populations of neurons and glia influence each other during development to guarantee proper integration and function? The advent of powerful new technologies to profile and perturb cortical development at unprecedented resolution and across a variety of modalities has offered a new opportunity to integrate past knowledge with brand new data. Here, we review some of this progress using cortical excitatory projection neurons as a system to draw out general principles of cell diversification and the role of cell-cell interactions during cortical development.
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Affiliation(s)
- Daniela J Di Bella
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Nuria Domínguez-Iturza
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Juliana R Brown
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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24
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Liu M, Wang C, Huo L, Cao J, Mao X, He Z, Hu C, Sun H, Deng W, He W, Chen Y, Gu M, Liao J, Guo N, He X, Wu Q, Chen J, Zhang L, Wang X, Shang C, Dong J. Complexin-1 enhances ultrasound neurotransmission in the mammalian auditory pathway. Nat Genet 2024; 56:1503-1515. [PMID: 38834904 DOI: 10.1038/s41588-024-01781-z] [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: 11/19/2022] [Accepted: 04/25/2024] [Indexed: 06/06/2024]
Abstract
Unlike megabats, which rely on well-developed vision, microbats use ultrasonic echolocation to navigate and locate prey. To study ultrasound perception, here we compared the auditory cortices of microbats and megabats by constructing reference genomes and single-nucleus atlases for four species. We found that parvalbumin (PV)+ neurons exhibited evident cross-species differences and could respond to ultrasound signals, whereas their silencing severely affected ultrasound perception in the mouse auditory cortex. Moreover, megabat PV+ neurons expressed low levels of complexins (CPLX1-CPLX4), which can facilitate neurotransmitter release, while microbat PV+ neurons highly expressed CPLX1, which improves neurotransmission efficiency. Further perturbation of Cplx1 in PV+ neurons impaired ultrasound perception in the mouse auditory cortex. In addition, CPLX1 functioned in other parts of the auditory pathway in microbats but not megabats and exhibited convergent evolution between echolocating microbats and whales. Altogether, we conclude that CPLX1 expression throughout the entire auditory pathway can enhance mammalian ultrasound neurotransmission.
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Affiliation(s)
- Meiling Liu
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Changliang Wang
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Lifang Huo
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Jie Cao
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Ziqing He
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Chuanxia Hu
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Haijian Sun
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Wenjun Deng
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Weiya He
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Yifu Chen
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Meifeng Gu
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Jiayu Liao
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Ning Guo
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Xiangyang He
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China.
| | - Xiaoqun Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China.
| | - Congping Shang
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.
| | - Ji Dong
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.
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25
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Liang B, Deng Y, Zhong Y, Chen X, Huang Y, Li Z, Huang X, Yang X, Du J, Ye R, Xian H, Feng Y, Bai R, Fan B, Yang X, Huang Z. Gastrointestinal Incomplete Degradation Exacerbates Neurotoxic Effects of PLA Microplastics via Oligomer Nanoplastics Formation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401009. [PMID: 38751156 PMCID: PMC11267364 DOI: 10.1002/advs.202401009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/06/2024] [Indexed: 07/25/2024]
Abstract
Biodegradable plastics, hailed for their environmental friendliness, may pose unforeseen risks as they undergo gastrointestinal degradation, forming oligomer nanoplastics. Despite this, the influence of gastrointestinal degradation on the potential human toxicity of biodegradable plastics remains poorly understood. To this end, the impact of the murine in vivo digestive system is investigated on the biotransformation, biodistribution, and toxicity of PLA polymer and PLA oligomer MPs. Through a 28-day repeated oral gavage study in mice, it is revealed that PLA polymer and oligomer microplastics undergo incomplete and complete degradation, respectively, in the gastrointestinal tract. Incompletely degraded PLA polymer microplastics transform into oligomer nanoplastics, heightening bioavailability and toxicity, thereby exacerbating overall toxic effects. Conversely, complete degradation of PLA oligomer microplastics reduces bioavailability and mitigates toxicity, offering a potential avenue for toxicity reduction. Additionally, the study illuminates shared targets and toxicity mechanisms in Parkinson's disease-like neurotoxicity induced by both PLA polymer and PLA oligomer microplastics. This involves the upregulation of MICU3 in midbrains, leading to neuronal mitochondrial calcium overload. Notably, neurotoxicity is mitigated by inhibiting mitochondrial calcium influx with MCU-i4 or facilitating mitochondrial calcium efflux with DBcAMP in mice. These findings enhance the understanding of the toxicological implications of biodegradable microplastics on human health.
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Affiliation(s)
- Boxuan Liang
- The Tenth Affiliated Hospital, Southern Medical University (Dongguan People's Hospital)Southern Medical UniversityDongguan523059China
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Yanhong Deng
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Yizhou Zhong
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Xiaoqing Chen
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Yuji Huang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Zhiming Li
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Xiyun Huang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Xiaohong Yang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Jiaxin Du
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Rongyi Ye
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Hongyi Xian
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Yu Feng
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Ruobing Bai
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Bingchi Fan
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Xingfen Yang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchResearch Center for Food safety and HealthSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Zhenlie Huang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
- Department of Cardiovascular SurgeryZhujiang Hospital, Southern Medical UniversityGuangzhou510280China
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26
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Sun ED, Ma R, Zou J. SPRITE: improving spatial gene expression imputation with gene and cell networks. Bioinformatics 2024; 40:i521-i528. [PMID: 38940132 PMCID: PMC11211834 DOI: 10.1093/bioinformatics/btae253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION Spatially resolved single-cell transcriptomics have provided unprecedented insights into gene expression in situ, particularly in the context of cell interactions or organization of tissues. However, current technologies for profiling spatial gene expression at single-cell resolution are generally limited to the measurement of a small number of genes. To address this limitation, several algorithms have been developed to impute or predict the expression of additional genes that were not present in the measured gene panel. Current algorithms do not leverage the rich spatial and gene relational information in spatial transcriptomics. To improve spatial gene expression predictions, we introduce Spatial Propagation and Reinforcement of Imputed Transcript Expression (SPRITE) as a meta-algorithm that processes predictions obtained from existing methods by propagating information across gene correlation networks and spatial neighborhood graphs. RESULTS SPRITE improves spatial gene expression predictions across multiple spatial transcriptomics datasets. Furthermore, SPRITE predicted spatial gene expression leads to improved clustering, visualization, and classification of cells. SPRITE can be used in spatial transcriptomics data analysis to improve inferences based on predicted gene expression. AVAILABILITY AND IMPLEMENTATION The SPRITE software package is available at https://github.com/sunericd/SPRITE. Code for generating experiments and analyses in the manuscript is available at https://github.com/sunericd/sprite-figures-and-analyses.
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Affiliation(s)
- Eric D Sun
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, United States
| | - Rong Ma
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, United States
| | - James Zou
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, United States
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27
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Castro-Mendoza PB, Weaver CM, Chang W, Medalla M, Rockland KS, Lowery L, McDonough E, Varghese M, Hof PR, Meyer DE, Luebke JI. Proteomic features of gray matter layers and superficial white matter of the rhesus monkey neocortex: comparison of prefrontal area 46 and occipital area 17. Brain Struct Funct 2024:10.1007/s00429-024-02819-y. [PMID: 38943018 DOI: 10.1007/s00429-024-02819-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/08/2024] [Indexed: 06/30/2024]
Abstract
In this novel large-scale multiplexed immunofluorescence study we comprehensively characterized and compared layer-specific proteomic features within regions of interest of the widely divergent dorsolateral prefrontal cortex (A46) and primary visual cortex (A17) of adult rhesus monkeys. Twenty-eight markers were imaged in rounds of sequential staining, and their spatial distribution precisely quantified within gray matter layers and superficial white matter. Cells were classified as neurons, astrocytes, oligodendrocytes, microglia, or endothelial cells. The distribution of fibers and blood vessels were assessed by quantification of staining intensity across regions of interest. This method revealed multivariate similarities and differences between layers and areas. Protein expression in neurons was the strongest determinant of both laminar and regional differences, whereas protein expression in glia was more important for intra-areal laminar distinctions. Among specific results, we observed a lower glia-to-neuron ratio in A17 than in A46 and the pan-neuronal markers HuD and NeuN were differentially distributed in both brain areas with a lower intensity of NeuN in layers 4 and 5 of A17 compared to A46 and other A17 layers. Astrocytes and oligodendrocytes exhibited distinct marker-specific laminar distributions that differed between regions; notably, there was a high proportion of ALDH1L1-expressing astrocytes and of oligodendrocyte markers in layer 4 of A17. The many nuanced differences in protein expression between layers and regions observed here highlight the need for direct assessment of proteins, in addition to RNA expression, and set the stage for future protein-focused studies of these and other brain regions in normal and pathological conditions.
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Affiliation(s)
- Paola B Castro-Mendoza
- Department of Anatomy and Neurobiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA
- Center for Systems Neuroscience, Boston University, Boston, MA, 02215, USA
| | - Christina M Weaver
- Department of Mathematics, Franklin and Marshall College, Lancaster, PA, 17604, USA
| | - Wayne Chang
- Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA
| | - Maria Medalla
- Department of Anatomy and Neurobiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA
- Center for Systems Neuroscience, Boston University, Boston, MA, 02215, USA
| | - Kathleen S Rockland
- Department of Anatomy and Neurobiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Lisa Lowery
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA
| | | | - Merina Varghese
- Nash Family Department of Neuroscience, Friedman Brain Institute, and Center for Discovery and Innovation, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
| | - Patrick R Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, and Center for Discovery and Innovation, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
| | - Dan E Meyer
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA
| | - Jennifer I Luebke
- Department of Anatomy and Neurobiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA.
- Center for Systems Neuroscience, Boston University, Boston, MA, 02215, USA.
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28
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Barik S, Riddell T. The Brain-Heart Network of Syncope. Int J Mol Sci 2024; 25:6959. [PMID: 39000068 PMCID: PMC11241714 DOI: 10.3390/ijms25136959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/23/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Observed and recorded in various forms since ancient times, 'syncope' is often popularly called 'fainting', such that the two terms are used synonymously. Syncope/fainting can be caused by a variety of conditions, including but not limited to head injuries, vertigo, and oxygen deficiency. Here, we draw on a large body of literature on syncope, including the role of a recently discovered set of specialized mammalian neurons. Although the etiology of syncope still remains a mystery, we have attempted to provide a comprehensive account of what is known and what still needs to be performed. Much of our understanding of syncope is owing to studies in the laboratory mouse, whereas evidence from human patients remains scarce. Interestingly, the cardioinhibitory Bezold-Jarisch reflex, recognized in the early 1900s, has an intriguing similarity to-and forms the basis of-syncope. In this review, we have integrated this minimal model into the modern view of the brain-neuron-heart signaling loop of syncope, to which several signaling events contribute. Molecular signaling is our major focus here, presented in terms of a normal heart, and thus, syncope due to abnormal or weak heart activity is not discussed in detail. In addition, we have offered possible directions for clinical intervention based on this model. Overall, this article is expected to generate interest in chronic vertigo and syncope/fainting, an enigmatic condition that affects most humans at some point in life; it is also hoped that this may lead to a mechanism-based clinical intervention in the future.
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Affiliation(s)
- Sailen Barik
- Independent Researcher, EonBio, 3780 Pelham Drive, Mobile, AL 36619, USA
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29
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Xavier AM, Lin Q, Kang CJ, Cheadle L. A single-cell transcriptomic atlas of sensory-dependent gene expression in developing mouse visual cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600673. [PMID: 38979325 PMCID: PMC11230371 DOI: 10.1101/2024.06.25.600673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Sensory experience drives the refinement and maturation of neural circuits during postnatal brain development through molecular mechanisms that remain to be fully elucidated. One likely mechanism involves the sensory-dependent expression of genes that encode direct mediators of circuit remodeling within developing cells. However, while studies in adult systems have begun to uncover crucial roles for sensory-induced genes in modifying circuit connectivity, the gene programs induced by brain cells in response to sensory experience during development remain to be fully characterized. Here, we present a single-nucleus RNA-sequencing dataset describing the transcriptional responses of cells in mouse visual cortex to sensory deprivation or sensory stimulation during a developmental window when visual input is necessary for circuit refinement. We sequenced 118,529 individual nuclei across sixteen neuronal and non-neuronal cortical cell types isolated from control, sensory deprived, and sensory stimulated mice, identifying 1,268 unique sensory-induced genes within the developing brain. To demonstrate the utility of this resource, we compared the architecture and ontology of sensory-induced gene programs between cell types, annotated transcriptional induction and repression events based upon RNA velocity, and discovered Neurexin and Neuregulin signaling networks that underlie cell-cell interactions via CellChat . We find that excitatory neurons, especially layer 2/3 pyramidal neurons, are highly sensitive to sensory stimulation, and that the sensory-induced genes in these cells are poised to strengthen synapse-to-nucleus crosstalk by heightening protein serine/threonine kinase activity. Altogether, we expect this dataset to significantly broaden our understanding of the molecular mechanisms through which sensory experience shapes neural circuit wiring in the developing brain.
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30
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Mallach A, Zielonka M, van Lieshout V, An Y, Khoo JH, Vanheusden M, Chen WT, Moechars D, Arancibia-Carcamo IL, Fiers M, De Strooper B. Microglia-astrocyte crosstalk in the amyloid plaque niche of an Alzheimer's disease mouse model, as revealed by spatial transcriptomics. Cell Rep 2024; 43:114216. [PMID: 38819990 DOI: 10.1016/j.celrep.2024.114216] [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: 06/20/2023] [Revised: 02/02/2024] [Accepted: 04/25/2024] [Indexed: 06/02/2024] Open
Abstract
The amyloid plaque niche is a pivotal hallmark of Alzheimer's disease (AD). Here, we employ two high-resolution spatial transcriptomics (ST) platforms, CosMx and Spatial Enhanced Resolution Omics-sequencing (Stereo-seq), to characterize the transcriptomic alterations, cellular compositions, and signaling perturbations in the amyloid plaque niche in an AD mouse model. We discover heterogeneity in the cellular composition of plaque niches, marked by an increase in microglial accumulation. We profile the transcriptomic alterations of glial cells in the vicinity of plaques and conclude that the microglial response to plaques is consistent across different brain regions, while the astrocytic response is more heterogeneous. Meanwhile, as the microglial density of plaque niches increases, astrocytes acquire a more neurotoxic phenotype and play a key role in inducing GABAergic signaling and decreasing glutamatergic signaling in hippocampal neurons. We thus show that the accumulation of microglia around hippocampal plaques disrupts astrocytic signaling, in turn inducing an imbalance in neuronal synaptic signaling.
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Affiliation(s)
- Anna Mallach
- UK Dementia Research Institute at UCL, University College London, London WC1E 6BT, UK; The Francis Crick Institute, London NW1 1AT, UK; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Magdalena Zielonka
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium
| | - Veerle van Lieshout
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium
| | - Yanru An
- BGI Research, 49276 Riga, Latvia
| | | | - Marisa Vanheusden
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium; Discovery Biology, Muna Therapeutics, Leuven, Belgium
| | - Wei-Ting Chen
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium; Discovery Biology, Muna Therapeutics, Leuven, Belgium
| | - Daan Moechars
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium
| | - I Lorena Arancibia-Carcamo
- UK Dementia Research Institute at UCL, University College London, London WC1E 6BT, UK; The Francis Crick Institute, London NW1 1AT, UK
| | - Mark Fiers
- UK Dementia Research Institute at UCL, University College London, London WC1E 6BT, UK; The Francis Crick Institute, London NW1 1AT, UK; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Bart De Strooper
- UK Dementia Research Institute at UCL, University College London, London WC1E 6BT, UK; The Francis Crick Institute, London NW1 1AT, UK; Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium; Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain & Disease Research, VIB, Leuven, Belgium.
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31
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Zhang N, Westerhaus A, Wilson M, Wang E, Goff L, Sockanathan S. Physiological regulation of neuronal Wnt activity is essential for TDP-43 localization and function. EMBO J 2024:10.1038/s44318-024-00156-8. [PMID: 38918634 DOI: 10.1038/s44318-024-00156-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/31/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024] Open
Abstract
Nuclear exclusion of the RNA- and DNA-binding protein TDP-43 can induce neurodegeneration in different diseases. Diverse processes have been implicated to influence TDP-43 mislocalization, including disrupted nucleocytoplasmic transport (NCT); however, the physiological pathways that normally ensure TDP-43 nuclear localization are unclear. The six-transmembrane enzyme glycerophosphodiester phosphodiesterase 2 (GDE2 or GDPD5) cleaves the glycosylphosphatidylinositol (GPI) anchor that tethers some proteins to the membrane. Here we show that GDE2 maintains TDP-43 nuclear localization by regulating the dynamics of canonical Wnt signaling. Ablation of GDE2 causes aberrantly sustained Wnt activation in adult neurons, which is sufficient to cause NCT deficits, nuclear pore abnormalities, and TDP-43 nuclear exclusion. Disruption of GDE2 coincides with TDP-43 abnormalities in postmortem tissue from patients with amyotrophic lateral sclerosis (ALS). Further, GDE2 deficits are evident in human neural cell models of ALS, which display erroneous Wnt activation that, when inhibited, increases mRNA levels of genes regulated by TDP-43. Our study identifies GDE2 as a critical physiological regulator of Wnt signaling in adult neurons and highlights Wnt pathway activation as an unappreciated mechanism contributing to nucleocytoplasmic transport and TDP-43 abnormalities in disease.
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Affiliation(s)
- Nan Zhang
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
| | - Anna Westerhaus
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
| | - Macey Wilson
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
- Department of Cellular Biology, University of Georgia, Biological Sciences 302, 120 Cedar St., Athens, GA, 30602, USA
| | - Ethan Wang
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
| | - Loyal Goff
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
- McKusick-Nathans Department of Genetic Medicine, Kavli Neurodiscovery Institute, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA
| | - Shanthini Sockanathan
- The Solomon Snyder Department of Neuroscience, The Johns Hopkins School of Medicine, 725 N Wolfe Street, Baltimore, MD, 21205, USA.
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32
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Martinez JD, Wilson LG, Brancaleone WP, Peterson KG, Popke DS, Garzon VC, Perez Tremble RE, Donnelly MJ, Mendez Ortega SL, Torres D, Shaver JJ, Jiang S, Yang Z, Aton SJ. Hypnotic treatment improves sleep architecture and EEG disruptions and rescues memory deficits in a mouse model of fragile X syndrome. Cell Rep 2024; 43:114266. [PMID: 38787724 DOI: 10.1016/j.celrep.2024.114266] [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: 07/07/2023] [Revised: 12/20/2023] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Fragile X syndrome (FXS) is associated with disrupted cognition and sleep abnormalities. Sleep loss negatively impacts cognitive function, and one untested possibility is that disrupted cognition in FXS is exacerbated by abnormal sleep. We tested whether ML297, a hypnotic acting on G-protein-activated inward-rectifying potassium (GIRK) channels, could reverse sleep phenotypes and disrupted memory in Fmr1-/y mice. Fmr1-/y mice exhibit reduced non-rapid eye movement (NREM) sleep and fragmented NREM architecture, altered sleep electroencephalogram (EEG) oscillations, and reduced EEG coherence between cortical areas; these are partially reversed following ML297 administration. Treatment following contextual fear or spatial learning restores disrupted memory consolidation in Fmr1-/y mice. During memory recall, Fmr1-/y mice show an altered balance of activity among hippocampal principal neurons vs. parvalbumin-expressing interneurons; this is partially reversed by ML297. Because sleep disruption could impact neurophysiological phenotypes in FXS, augmenting sleep may improve disrupted cognition in this disorder.
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Affiliation(s)
- Jessy D Martinez
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lydia G Wilson
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - William P Brancaleone
- Undergraduate Program in Neuroscience, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kathryn G Peterson
- Undergraduate Program in Neuroscience, University of Michigan, Ann Arbor, MI 48109, USA
| | - Donald S Popke
- Undergraduate Program in Neuroscience, University of Michigan, Ann Arbor, MI 48109, USA
| | - Valentina Caicedo Garzon
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Roxanne E Perez Tremble
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcus J Donnelly
- Undergraduate Program in Neuroscience, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Daniel Torres
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - James J Shaver
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sha Jiang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhongying Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sara J Aton
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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33
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Ratliff JM, Terral G, Lutzu S, Heiss J, Mota J, Stith B, Lechuga AV, Ramakrishnan C, Fenno LE, Daigle T, Deisseroth K, Zeng H, Ngai J, Tasic B, Sjulson L, Rudolph S, Kilduff TS, Batista-Brito R. Neocortical long-range inhibition promotes cortical synchrony and sleep. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599756. [PMID: 38948753 PMCID: PMC11213009 DOI: 10.1101/2024.06.20.599756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Behavioral states such as sleep and wake are highly correlated with specific patterns of rhythmic activity in the cortex. During low arousal states such as slow wave sleep, the cortex is synchronized and dominated by low frequency rhythms coordinated across multiple regions. Although recent evidence suggests that GABAergic inhibitory neurons are key players in cortical state modulation, the in vivo circuit mechanisms coordinating synchronized activity among local and distant neocortical networks are not well understood. Here, we show that somatostatin and chondrolectin co-expressing cells (Sst-Chodl cells), a sparse and unique class of neocortical inhibitory neurons, are selectively active during low arousal states and are largely silent during periods of high arousal. In contrast to other neocortical inhibitory neurons, we show these neurons have long-range axons that project across neocortical areas. Activation of Sst-Chodl cells is sufficient to promote synchronized cortical states characteristic of low arousal, with increased spike co-firing and low frequency brain rhythms, and to alter behavioral states by promoting sleep. Contrary to the prevailing belief that sleep is exclusively driven by subcortical mechanisms, our findings reveal that these long-range inhibitory neurons not only track changes in behavioral state but are sufficient to induce both sleep-like cortical states and sleep behavior, establishing a crucial circuit component in regulating behavioral states.
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Affiliation(s)
- Jacob M Ratliff
- Albert Einstein College of Medicine, New York City, NY, United States
| | - Geoffrey Terral
- Albert Einstein College of Medicine, New York City, NY, United States
| | - Stefano Lutzu
- Albert Einstein College of Medicine, New York City, NY, United States
| | - Jaime Heiss
- Biosciences Division, SRI International, Menlo Park, CA 94025, United States
| | - Julie Mota
- Albert Einstein College of Medicine, New York City, NY, United States
| | - Bianca Stith
- Albert Einstein College of Medicine, New York City, NY, United States
| | | | | | - Lief E Fenno
- The University of Texas at Austin, Austin, TX, United States
| | - Tanya Daigle
- Allen Institute for Brain Science, Seattle, WA, United States
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, United States
| | - John Ngai
- National Institute of Neurological Disease and Stroke, Bethesda, MD, United States
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA, United States
| | - Lucas Sjulson
- Albert Einstein College of Medicine, New York City, NY, United States
| | - Stephanie Rudolph
- Albert Einstein College of Medicine, New York City, NY, United States
| | - Thomas S. Kilduff
- Biosciences Division, SRI International, Menlo Park, CA 94025, United States
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Dalton GD, Siecinski SK, Nikolova VD, Cofer GP, Hornburg KJ, Qi Y, Johnson GA, Jiang YH, Moy SS, Gregory SG. Transcriptome analysis identifies an ASD-Like phenotype in oligodendrocytes and microglia from C58/J amygdala that is dependent on sex and sociability. BEHAVIORAL AND BRAIN FUNCTIONS : BBF 2024; 20:14. [PMID: 38898502 PMCID: PMC11188533 DOI: 10.1186/s12993-024-00240-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Autism Spectrum Disorder (ASD) is a group of neurodevelopmental disorders with higher incidence in males and is characterized by atypical verbal/nonverbal communication, restricted interests that can be accompanied by repetitive behavior, and disturbances in social behavior. This study investigated brain mechanisms that contribute to sociability deficits and sex differences in an ASD animal model. METHODS Sociability was measured in C58/J and C57BL/6J mice using the 3-chamber social choice test. Bulk RNA-Seq and snRNA-Seq identified transcriptional changes in C58/J and C57BL/6J amygdala within which DMRseq was used to measure differentially methylated regions in amygdala. RESULTS C58/J mice displayed divergent social strata in the 3-chamber test. Transcriptional and pathway signatures revealed immune-related biological processes differ between C58/J and C57BL/6J amygdala. Hypermethylated and hypomethylated genes were identified in C58/J versus C57BL/6J amygdala. snRNA-Seq data in C58/J amygdala identified differential transcriptional signatures within oligodendrocytes and microglia characterized by increased ASD risk gene expression and predicted impaired myelination that was dependent on sex and sociability. RNA velocity, gene regulatory network, and cell communication analysis showed diminished oligodendrocyte/microglia differentiation. Findings were verified using Bulk RNA-Seq and demonstrated oxytocin's beneficial effects on myelin gene expression. LIMITATIONS Our findings are significant. However, limitations can be noted. The cellular mechanisms linking reduced oligodendrocyte differentiation and reduced myelination to an ASD phenotype in C58/J mice need further investigation. Additional snRNA-Seq and spatial studies would determine if effects in oligodendrocytes/microglia are unique to amygdala or if this occurs in other brain regions. Oxytocin's effects need further examination to understand its' potential as an ASD therapeutic. CONCLUSIONS Our work demonstrates the C58/J mouse model's utility in evaluating the influence of sex and sociability on the transcriptome in concomitant brain regions involved in ASD. Our single-nucleus transcriptome analysis elucidates potential pathological roles of oligodendrocytes and microglia in ASD. This investigation provides details regarding regulatory features disrupted in these cell types, including transcriptional gene dysregulation, aberrant cell differentiation, altered gene regulatory networks, and changes to key pathways that promote microglia/oligodendrocyte differentiation. Our studies provide insight into interactions between genetic risk and epigenetic processes associated with divergent affiliative behavior and lack of positive sociability.
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Affiliation(s)
- George D Dalton
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, 27701, USA
| | - Stephen K Siecinski
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, 27701, USA
| | - Viktoriya D Nikolova
- Department of Psychiatry, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27516, USA
| | - Gary P Cofer
- Center for In Vivo Microscopy, Duke University, Durham, NC, 27710, USA
| | | | - Yi Qi
- Center for In Vivo Microscopy, Duke University, Durham, NC, 27710, USA
| | - G Allan Johnson
- Center for In Vivo Microscopy, Duke University, Durham, NC, 27710, USA
| | - Yong-Hui Jiang
- Department of Genetics, Neuroscience, and Pediatrics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Sheryl S Moy
- Department of Psychiatry, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27516, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, 27701, USA.
- Department of Neurology, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Neurology, Molecular Genetics and Microbiology Duke Molecular Physiology Institute, 300 N. Duke Street, DUMC 104775, Durham, NC, 27701, USA.
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van Velthoven CTJ, Gao Y, Kunst M, Lee C, McMillen D, Chakka AB, Casper T, Clark M, Chakrabarty R, Daniel S, Dolbeare T, Ferrer R, Gloe J, Goldy J, Guzman J, Halterman C, Ho W, Huang M, James K, Nguy B, Pham T, Ronellenfitch K, Thomas ED, Torkelson A, Pagan CM, Kruse L, Dee N, Ng L, Waters J, Smith KA, Tasic B, Yao Z, Zeng H. The transcriptomic and spatial organization of telencephalic GABAergic neuronal types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599583. [PMID: 38948843 PMCID: PMC11212977 DOI: 10.1101/2024.06.18.599583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The telencephalon of the mammalian brain comprises multiple regions and circuit pathways that play adaptive and integrative roles in a variety of brain functions. There is a wide array of GABAergic neurons in the telencephalon; they play a multitude of circuit functions, and dysfunction of these neurons has been implicated in diverse brain disorders. In this study, we conducted a systematic and in-depth analysis of the transcriptomic and spatial organization of GABAergic neuronal types in all regions of the mouse telencephalon and their developmental origins. This was accomplished by utilizing 611,423 single-cell transcriptomes from the comprehensive and high-resolution transcriptomic and spatial cell type atlas for the adult whole mouse brain we have generated, supplemented with an additional single-cell RNA-sequencing dataset containing 99,438 high-quality single-cell transcriptomes collected from the pre- and postnatal developing mouse brain. We present a hierarchically organized adult telencephalic GABAergic neuronal cell type taxonomy of 7 classes, 52 subclasses, 284 supertypes, and 1,051 clusters, as well as a corresponding developmental taxonomy of 450 clusters across different ages. Detailed charting efforts reveal extraordinary complexity where relationships among cell types reflect both spatial locations and developmental origins. Transcriptomically and developmentally related cell types can often be found in distant and diverse brain regions indicating that long-distance migration and dispersion is a common characteristic of nearly all classes of telencephalic GABAergic neurons. Additionally, we find various spatial dimensions of both discrete and continuous variations among related cell types that are correlated with gene expression gradients. Lastly, we find that cortical, striatal and some pallidal GABAergic neurons undergo extensive postnatal diversification, whereas septal and most pallidal GABAergic neuronal types emerge simultaneously during the embryonic stage with limited postnatal diversification. Overall, the telencephalic GABAergic cell type taxonomy can serve as a foundational reference for molecular, structural and functional studies of cell types and circuits by the entire community.
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Affiliation(s)
| | - Yuan Gao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Scott Daniel
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Dolbeare
- 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
| | | | | | - Windy Ho
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Mike Huang
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Beagan Nguy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
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Csikós V, Dóra F, Láng T, Darai L, Szendi V, Tóth A, Cservenák M, Dobolyi A. Social Isolation Induces Changes in the Monoaminergic Signalling in the Rat Medial Prefrontal Cortex. Cells 2024; 13:1043. [PMID: 38920671 PMCID: PMC11201939 DOI: 10.3390/cells13121043] [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: 04/21/2024] [Revised: 06/02/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
(1) Background: The effects of short-term social isolation during adulthood have not yet been fully established in rats behaviourally, and not at all transcriptomically in the medial prefrontal cortex (mPFC). (2) Methods: We measured the behavioural effects of housing adult male rats in pairs or alone for 10 days. We also used RNA sequencing to measure the accompanying gene expression alterations in the mPFC of male rats. (3) Results: The isolated animals exhibited reduced sociability and social novelty preference, but increased social interaction. There was no change in their aggression, anxiety, or depression-like activity. Transcriptomic analysis revealed a differential expression of 46 genes between the groups. The KEGG pathway analysis showed that differentially expressed genes are involved in neuroactive ligand-receptor interactions, particularly in the dopaminergic and peptidergic systems, and addiction. Subsequent validation confirmed the decreased level of three altered genes: regulator of G protein signalling 9 (Rgs9), serotonin receptor 2c (Htr2c), and Prodynorphin (Pdyn), which are involved in dopaminergic, serotonergic, and peptidergic function, respectively. Antagonizing Htr2c confirmed its role in social novelty discrimination. (4) Conclusions: Social homeostatic regulations include monoaminergic and peptidergic systems of the mPFC.
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Affiliation(s)
- Vivien Csikós
- Laboratory of Molecular and Systems Neurobiology, Department of Physiology and Neurobiology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Fanni Dóra
- Laboratory of Neuromorphology, Department of Anatomy, Histology and Embryology, Semmelweis University, 1094 Budapest, Hungary
| | - Tamás Láng
- Laboratory of Neuromorphology, Department of Anatomy, Histology and Embryology, Semmelweis University, 1094 Budapest, Hungary
| | - Luca Darai
- Laboratory of Molecular and Systems Neurobiology, Department of Physiology and Neurobiology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Vivien Szendi
- Laboratory of Molecular and Systems Neurobiology, Department of Physiology and Neurobiology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Attila Tóth
- In Vivo Electrophysiology Research Group, Department of Physiology and Neurobiology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Melinda Cservenák
- Laboratory of Molecular and Systems Neurobiology, Department of Physiology and Neurobiology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Arpád Dobolyi
- Laboratory of Molecular and Systems Neurobiology, Department of Physiology and Neurobiology, Eötvös Loránd University, 1117 Budapest, Hungary
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Rebboah E, Rezaie N, Williams BA, Weimer AK, Shi M, Yang X, Liang HY, Dionne LA, Reese F, Trout D, Jou J, Youngworth I, Reinholdt L, Morabito S, Snyder MP, Wold BJ, Mortazavi A. The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598567. [PMID: 38915583 PMCID: PMC11195270 DOI: 10.1101/2024.06.12.598567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Postnatal genomic regulation significantly influences tissue and organ maturation but is under-studied relative to existing genomic catalogs of adult tissues or prenatal development in mouse. The ENCODE4 consortium generated the first comprehensive single-nucleus resource of postnatal regulatory events across a diverse set of mouse tissues. The collection spans seven postnatal time points, mirroring human development from childhood to adulthood, and encompasses five core tissues. We identified 30 cell types, further subdivided into 69 subtypes and cell states across adrenal gland, left cerebral cortex, hippocampus, heart, and gastrocnemius muscle. Our annotations cover both known and novel cell differentiation dynamics ranging from early hippocampal neurogenesis to a new sex-specific adrenal gland population during puberty. We used an ensemble Latent Dirichlet Allocation strategy with a curated vocabulary of 2,701 regulatory genes to identify regulatory "topics," each of which is a gene vector, linked to cell type differentiation, subtype specialization, and transitions between cell states. We find recurrent regulatory topics in tissue-resident macrophages, neural cell types, endothelial cells across multiple tissues, and cycling cells of the adrenal gland and heart. Cell-type-specific topics are enriched in transcription factors and microRNA host genes, while chromatin regulators dominate mitosis topics. Corresponding chromatin accessibility data reveal dynamic and sex-specific regulatory elements, with enriched motifs matching transcription factors in regulatory topics. Together, these analyses identify both tissue-specific and common regulatory programs in postnatal development across multiple tissues through the lens of the factors regulating transcription.
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Affiliation(s)
- Elisabeth Rebboah
- Developmental and Cell Biology, University of California Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, USA
| | - Narges Rezaie
- Developmental and Cell Biology, University of California Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, USA
| | - Brian A. Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Annika K. Weimer
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Minyi Shi
- Department of Next Generation Sequencing and Microchemistry, Proteomics and Lipidomics, Genentech, San Francisco, USA
| | - Xinqiong Yang
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Heidi Yahan Liang
- Developmental and Cell Biology, University of California Irvine, Irvine, USA
| | | | - Fairlie Reese
- Developmental and Cell Biology, University of California Irvine, Irvine, USA
| | - Diane Trout
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Jennifer Jou
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Ingrid Youngworth
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | | | - Samuel Morabito
- Developmental and Cell Biology, University of California Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, USA
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Barbara J. Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Ali Mortazavi
- Developmental and Cell Biology, University of California Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, USA
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Gonzalez-Ferrer J, Lehrer J, O'Farrell A, Paten B, Teodorescu M, Haussler D, Jonsson VD, Mostajo-Radji MA. SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis. CELL GENOMICS 2024; 4:100581. [PMID: 38823397 PMCID: PMC11228957 DOI: 10.1016/j.xgen.2024.100581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Cell atlases serve as vital references for automating cell labeling in new samples, yet existing classification algorithms struggle with accuracy. Here we introduce SIMS (scalable, interpretable machine learning for single cell), a low-code data-efficient pipeline for single-cell RNA classification. We benchmark SIMS against datasets from different tissues and species. We demonstrate SIMS's efficacy in classifying cells in the brain, achieving high accuracy even with small training sets (<3,500 cells) and across different samples. SIMS accurately predicts neuronal subtypes in the developing brain, shedding light on genetic changes during neuronal differentiation and postmitotic fate refinement. Finally, we apply SIMS to single-cell RNA datasets of cortical organoids to predict cell identities and uncover genetic variations between cell lines. SIMS identifies cell-line differences and misannotated cell lineages in human cortical organoids derived from different pluripotent stem cell lines. Altogether, we show that SIMS is a versatile and robust tool for cell-type classification from single-cell datasets.
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Affiliation(s)
- Jesus Gonzalez-Ferrer
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Julian Lehrer
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Applied Mathematics, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Ash O'Farrell
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Benedict Paten
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Mircea Teodorescu
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - David Haussler
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Vanessa D Jonsson
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Applied Mathematics, University of California, Santa Cruz, Santa Cruz, CA 95060, USA.
| | - Mohammed A Mostajo-Radji
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA.
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39
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Rahimi A, Vale-Silva LA, Fälth Savitski M, Tanevski J, Saez-Rodriguez J. DOT: a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics. Nat Commun 2024; 15:4994. [PMID: 38862466 PMCID: PMC11167014 DOI: 10.1038/s41467-024-48868-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 05/14/2024] [Indexed: 06/13/2024] Open
Abstract
Single-cell transcriptomics and spatially-resolved imaging/sequencing technologies have revolutionized biomedical research. However, they suffer from lack of spatial information and a trade-off of resolution and gene coverage, respectively. We propose DOT, a multi-objective optimization framework for transferring cellular features across these data modalities, thus integrating their complementary information. DOT uses genes beyond those common to the data modalities, exploits the local spatial context, transfers spatial features beyond cell-type information, and infers absolute/relative abundance of cell populations at tissue locations. Thus, DOT bridges single-cell transcriptomics data with both high- and low-resolution spatially-resolved data. Moreover, DOT combines practical aspects related to cell composition, heterogeneity, technical effects, and integration of prior knowledge. Our fast implementation based on the Frank-Wolfe algorithm achieves state-of-the-art or improved performance in localizing cell features in high- and low-resolution spatial data and estimating the expression of unmeasured genes in low-coverage spatial data.
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Affiliation(s)
- Arezou Rahimi
- Institute for Computational Biomedicine, Heidelberg University & Heidelberg University Hospital, Heidelberg, Germany
- Cellzome GmbH, GlaxoSmithKline, Heidelberg, Germany
| | | | | | - Jovan Tanevski
- Institute for Computational Biomedicine, Heidelberg University & Heidelberg University Hospital, Heidelberg, Germany.
- Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia.
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Heidelberg University & Heidelberg University Hospital, Heidelberg, Germany.
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40
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Ben-Simon Y, Hooper M, Narayan S, Daigle T, Dwivedi D, Way SW, Oster A, Stafford DA, Mich JK, Taormina MJ, Martinez RA, Opitz-Araya X, Roth JR, Allen S, Ayala A, Bakken TE, Barcelli T, Barta S, Bendrick J, Bertagnolli D, Bowlus J, Boyer G, Brouner K, Casian B, Casper T, Chakka AB, Chakrabarty R, Chance RK, Chavan S, Departee M, Donadio N, Dotson N, Egdorf T, Gabitto M, Gary A, Gasperini M, Goldy J, Gore BB, Graybuck L, Greisman N, Haeseleer F, Halterman C, Helback O, Hockemeyer D, Huang C, Huff S, Hunker A, Johansen N, Juneau Z, Kalmbach B, Khem S, Kutsal R, Larsen R, Lee C, Lee AY, Leibly M, Lenz GH, Liang E, Lusk N, Malone J, Mollenkopf T, Morin E, Newman D, Ng L, Ngo K, Omstead V, Oyama A, Pham T, Pom CA, Potekhina L, Ransford S, Rette D, Rimorin C, Rocha D, Ruiz A, Sanchez RE, Sedeno-Cortes A, Sevigny JP, Shapovalova N, Shulga L, Sigler AR, Siverts LA, Somasundaram S, Stewart K, Tieu M, Trader C, van Velthoven CT, Walker M, Weed N, Wirthlin M, Wood T, Wynalda B, Yao Z, Zhou T, Ariza J, Dee N, Reding M, Ronellenfitch K, Mufti S, Sunkin SM, Smith KA, Esposito L, Waters J, Thyagarajan B, Yao S, Lein ES, Zeng H, Levi BP, Ngai J, Ting J, Tasic B. A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.597244. [PMID: 38915722 PMCID: PMC11195086 DOI: 10.1101/2024.06.10.597244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The mammalian cortex is comprised of cells with different morphological, physiological, and molecular properties that can be classified according to shared properties into cell types. Defining the contribution of each cell type to the computational and cognitive processes that are guided by the cortex is essential for understanding its function in health and disease. We use transcriptomic and epigenomic cortical cell type taxonomies from mice and humans to define marker genes and enhancers, and to build genetic tools for cortical cell types. Here, we present a large toolkit for selective targeting of cortical populations, including mouse transgenic lines and recombinant adeno-associated virus (AAV) vectors containing genomic enhancers. We report evaluation of fifteen new transgenic driver lines and over 680 different enhancer AAVs covering all major subclasses of cortical cells, with many achieving a high degree of specificity, comparable with existing transgenic lines. We find that the transgenic lines based on marker genes can provide exceptional specificity and completeness of cell type labeling, but frequently require generation of a triple-transgenic cross for best usability/specificity. On the other hand, enhancer AAVs are easy to screen and use, and can be easily modified to express diverse cargo, such as recombinases. However, their use depends on many factors, such as viral titer and route of administration. The tools reported here as well as the scaled process of tool creation provide an unprecedented resource that should enable diverse experimental strategies towards understanding mammalian cortex and brain function.
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Affiliation(s)
- Yoav Ben-Simon
- Allen Institute for Brain Science, Seattle, WA 98109
- equivalent contribution
| | - Marcus Hooper
- Allen Institute for Brain Science, Seattle, WA 98109
- equivalent contribution
| | - Sujatha Narayan
- Allen Institute for Brain Science, Seattle, WA 98109
- equivalent contribution
| | - Tanya Daigle
- Allen Institute for Brain Science, Seattle, WA 98109
- equivalent contribution
| | | | - Sharon W. Way
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Aaron Oster
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - John K. Mich
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Jada R. Roth
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Shona Allen
- University of California, Berkeley, Berkeley, CA 94720
| | - Angela Ayala
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Stuard Barta
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | | | | | | | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Sakshi Chavan
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Bryan B. Gore
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Noah Greisman
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | | | - Cindy Huang
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Sydney Huff
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Avery Hunker
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Zoe Juneau
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Shannon Khem
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Rana Kutsal
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Angus Y. Lee
- University of California, Berkeley, Berkeley, CA 94720
| | | | | | | | - Nicholas Lusk
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Elyse Morin
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Dakota Newman
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Alana Oyama
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Shea Ransford
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Dean Rette
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Dana Rocha
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Augustin Ruiz
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | | | | | - Ana R. Sigler
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Kaiya Stewart
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Natalie Weed
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Toren Wood
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Thomas Zhou
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Shoaib Mufti
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Luke Esposito
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Shenqin Yao
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Ed S. Lein
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Boaz P. Levi
- Allen Institute for Brain Science, Seattle, WA 98109
| | - John Ngai
- University of California, Berkeley, Berkeley, CA 94720
- Present affiliation: National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
| | - Jonathan Ting
- Allen Institute for Brain Science, Seattle, WA 98109
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Qiao M. Deciphering the genetic code of neuronal type connectivity through bilinear modeling. eLife 2024; 12:RP91532. [PMID: 38857169 PMCID: PMC11164534 DOI: 10.7554/elife.91532] [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] [Indexed: 06/12/2024] Open
Abstract
Understanding how different neuronal types connect and communicate is critical to interpreting brain function and behavior. However, it has remained a formidable challenge to decipher the genetic underpinnings that dictate the specific connections formed between neuronal types. To address this, we propose a novel bilinear modeling approach that leverages the architecture similar to that of recommendation systems. Our model transforms the gene expressions of presynaptic and postsynaptic neuronal types, obtained from single-cell transcriptomics, into a covariance matrix. The objective is to construct this covariance matrix that closely mirrors a connectivity matrix, derived from connectomic data, reflecting the known anatomical connections between these neuronal types. When tested on a dataset of Caenorhabditis elegans, our model achieved a performance comparable to, if slightly better than, the previously proposed spatial connectome model (SCM) in reconstructing electrical synaptic connectivity based on gene expressions. Through a comparative analysis, our model not only captured all genetic interactions identified by the SCM but also inferred additional ones. Applied to a mouse retinal neuronal dataset, the bilinear model successfully recapitulated recognized connectivity motifs between bipolar cells and retinal ganglion cells, and provided interpretable insights into genetic interactions shaping the connectivity. Specifically, it identified unique genetic signatures associated with different connectivity motifs, including genes important to cell-cell adhesion and synapse formation, highlighting their role in orchestrating specific synaptic connections between these neurons. Our work establishes an innovative computational strategy for decoding the genetic programming of neuronal type connectivity. It not only sets a new benchmark for single-cell transcriptomic analysis of synaptic connections but also paves the way for mechanistic studies of neural circuit assembly and genetic manipulation of circuit wiring.
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Affiliation(s)
- Mu Qiao
- LinkedInMountain ViewUnited States
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42
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Jedrasiak-Cape I, Rybicki-Kler C, Brooks I, Ghosh M, Brennan EK, Kailasa S, Ekins TG, Rupp A, Ahmed OJ. Cell-type-specific cholinergic control of granular retrosplenial cortex with implications for angular velocity coding across brain states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597341. [PMID: 38895393 PMCID: PMC11185600 DOI: 10.1101/2024.06.04.597341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Cholinergic receptor activation enables the persistent firing of cortical pyramidal neurons, providing a key cellular basis for theories of spatial navigation involving working memory, path integration, and head direction encoding. The granular retrosplenial cortex (RSG) is important for spatially-guided behaviors, but how acetylcholine impacts RSG neurons is unknown. Here, we show that a transcriptomically, morphologically, and biophysically distinct RSG cell-type - the low-rheobase (LR) neuron - has a very distinct expression profile of cholinergic muscarinic receptors compared to all other neighboring excitatory neuronal subtypes. LR neurons do not fire persistently in response to cholinergic agonists, in stark contrast to all other principal neuronal subtypes examined within the RSG and across midline cortex. This lack of persistence allows LR neuron models to rapidly compute angular head velocity (AHV), independent of cholinergic changes seen during navigation. Thus, LR neurons can consistently compute AHV across brain states, highlighting the specialized RSG neural codes supporting navigation.
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Affiliation(s)
| | - Chloe Rybicki-Kler
- Dept. of Psychology, University of Michigan, Ann Arbor, MI 48109
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109
| | - Isla Brooks
- Dept. of Psychology, University of Michigan, Ann Arbor, MI 48109
| | - Megha Ghosh
- Dept. of Psychology, University of Michigan, Ann Arbor, MI 48109
| | - Ellen K.W. Brennan
- Dept. of Psychology, University of Michigan, Ann Arbor, MI 48109
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109
| | - Sameer Kailasa
- Dept. of Mathematics, University of Michigan, Ann Arbor, MI 48109
| | - Tyler G. Ekins
- Dept. of Psychology, University of Michigan, Ann Arbor, MI 48109
| | - Alan Rupp
- Dept. of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Omar J. Ahmed
- Dept. of Psychology, University of Michigan, Ann Arbor, MI 48109
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109
- Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI 48109
- Dept. of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
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43
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Silva DB, Trinidad M, Ljungdahl A, Revalde JL, Berguig GY, Wallace W, Patrick CS, Bomba L, Arkin M, Dong S, Estrada K, Hutchinson K, LeBowitz JH, Schlessinger A, Johannesen KM, Møller RS, Giacomini KM, Froelich S, Sanders SJ, Wuster A. Haploinsufficiency underlies the neurodevelopmental consequences of SLC6A1 variants. Am J Hum Genet 2024; 111:1222-1238. [PMID: 38781976 PMCID: PMC11179425 DOI: 10.1016/j.ajhg.2024.04.021] [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: 09/19/2023] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Heterozygous variants in SLC6A1, encoding the GAT-1 GABA transporter, are associated with seizures, developmental delay, and autism. The majority of affected individuals carry missense variants, many of which are recurrent germline de novo mutations, raising the possibility of gain-of-function or dominant-negative effects. To understand the functional consequences, we performed an in vitro GABA uptake assay for 213 unique variants, including 24 control variants. De novo variants consistently resulted in a decrease in GABA uptake, in keeping with haploinsufficiency underlying all neurodevelopmental phenotypes. Where present, ClinVar pathogenicity reports correlated well with GABA uptake data; the functional data can inform future reports for the remaining 72% of unscored variants. Surface localization was assessed for 86 variants; two-thirds of loss-of-function missense variants prevented GAT-1 from being present on the membrane while GAT-1 was on the surface but with reduced activity for the remaining third. Surprisingly, recurrent de novo missense variants showed moderate loss-of-function effects that reduced GABA uptake with no evidence for dominant-negative or gain-of-function effects. Using linear regression across multiple missense severity scores to extrapolate the functional data to all potential SLC6A1 missense variants, we observe an abundance of GAT-1 residues that are sensitive to substitution. The extent of this missense vulnerability accounts for the clinically observed missense enrichment; overlap with hypermutable CpG sites accounts for the recurrent missense variants. Strategies to increase the expression of the wild-type SLC6A1 allele are likely to be beneficial across neurodevelopmental disorders, though the developmental stage and extent of required rescue remain unknown.
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Affiliation(s)
- Dina Buitrago Silva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Marena Trinidad
- BioMarin Pharmaceutical Inc., Novato, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alicia Ljungdahl
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford OX3 7TY, UK
| | - Jezrael L Revalde
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Cory S Patrick
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | | | - Michelle Arkin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | | | - Keino Hutchinson
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Katrine M Johannesen
- Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Rikke S Møller
- Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark; Department of Epilepsy Genetics and Personalized Medicine, Member of ERN Epicare, Danish Epilepsy Centre, Dianalund, Denmark
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | | | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford OX3 7TY, UK.
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44
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Zheng Y, Cong X, Liu H, Storey KB, Chen M. Neuronal cell populations in circumoral nerve ring of sea cucumber Apostichopus japonicus: Ultrastructure and transcriptional profile. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101263. [PMID: 38850626 DOI: 10.1016/j.cbd.2024.101263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/24/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
The echinoderm nervous system has been studied as a model for understanding the evolution of the chordate nervous system. Neuronal cells are essential groups that release a 'cocktail' of messenger molecules providing a spectrum of biological actions in the nervous system. Among echinoderms, most evidence on neuronal cell types has been obtained from starfish and sea urchin. In sea cucumbers, most research has focused on the location of neuronal cells, whereas their transcriptional features have rarely been investigated. Here, we observed the ultrastructure of neuronal cells in the sea cucumber, Apostichopus japonicus. The transcriptional profile of neuronal cells from the circumoral nerve ring (CNR) was investigated using single-cell RNA sequencing (scRNA-seq), and a total of six neuronal cell types were identified. 26 neuropeptide precursor genes (NPPs) and 28 G-protein-coupled receptors (GPCR) were expressed in the six neuronal cell types, comprising five NPP/NP-GPCR pairs. Unsupervised pseudotime analysis of neuronal cells showed their different differentiation status. We also located the neuronal cells in the CNR by immunofluorescence (IF) and identified the potential hub genes of key cell populations. This broad resource serves as a valuable support in the development of cell-specific markers for accurate cell-type identification in sea cucumbers. It also contributes to facilitating comparison across species, providing a deeper understanding of the evolutionary processes of neuronal cells.
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Affiliation(s)
- Yingqiu Zheng
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China. https://twitter.com/Yingqiu_Zheng
| | - Xiao Cong
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China
| | - Huachen Liu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China
| | - Kenneth B Storey
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Muyan Chen
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, PR China.
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45
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Wan T, Fu C, Peng J, Lu J, Li P, Zhuo J. Repairing the in situ hybridization missing data in the hippocampus region by using a 3D residual U-Net model. BIOMEDICAL OPTICS EXPRESS 2024; 15:3541-3554. [PMID: 38867784 PMCID: PMC11166418 DOI: 10.1364/boe.522078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/31/2024] [Accepted: 04/22/2024] [Indexed: 06/14/2024]
Abstract
The hippocampus is a critical brain region. Transcriptome data provides valuable insights into the structure and function of the hippocampus at the gene level. However, transcriptome data is often incomplete. To address this issue, we use the convolutional neural network model to repair the missing voxels in the hippocampus region, based on Allen institute coronal slices in situ hybridization (ISH) dataset. Moreover, we analyze the gene expression correlation between coronal and sagittal dataset in the hippocampus region. The results demonstrated that the trend of gene expression correlation between the coronal and sagittal datasets remained consistent following the repair of missing data in the coronal ISH dataset. In the last, we use repaired ISH dataset to identify novel genes specific to hippocampal subregions. Our findings demonstrate the accuracy and effectiveness of using deep learning method to repair ISH missing data. After being repaired, ISH has the potential to improve our comprehension of the hippocampus's structure and function.
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Affiliation(s)
- Tong Wan
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572025, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572025, China
| | - Changping Fu
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572025, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572025, China
| | - Jiinbo Peng
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572025, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572025, China
| | - Jinling Lu
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572025, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572025, China
- Britton Chance Center for Biomedical Photonics and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Science, HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou 215100, China
| | - Pengcheng Li
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572025, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572025, China
- Britton Chance Center for Biomedical Photonics and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Science, HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou 215100, China
| | - JunJie Zhuo
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Sanya 572025, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Sanya 572025, China
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46
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Sampson MM, Morgan RK, Sloan SA, Bakulski KM. Single-cell investigation of lead toxicity from neurodevelopment to neurodegeneration: Current review and future opportunities. CURRENT OPINION IN TOXICOLOGY 2024; 38:100464. [PMID: 39086983 PMCID: PMC11290315 DOI: 10.1016/j.cotox.2024.100464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Human exposure to the metal lead (Pb) is prevalent and associated with adverse neurodevelopmental and neurodegenerative outcomes. Pb disrupts normal brain function by inducing oxidative stress and neuroinflammation, altering cellular metabolism, and displacing essential metals. Prior studies on the molecular impacts of Pb have examined bulk tissues, which collapse information across all cell types, or in targeted cells, which are limited to cell autonomous effects. These approaches are unable to represent the complete biological implications of Pb exposure because the brain is a cooperative network of highly heterogeneous cells, with cellular diversity and proportions shifting throughout development, by brain region, and with disease. New technologies are necessary to investigate whether Pb and other environmental exposures alter cell composition in the brain and whether they cause molecular changes in a cell-type-specific manner. Cutting-edge, single-cell approaches now enable research resolving cell-type-specific effects from bulk tissues. This article reviews existing Pb neurotoxicology studies with genome-wide molecular signatures and provides a path forward for the field to implement single-cell approaches with practical recommendations.
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Affiliation(s)
- Maureen M Sampson
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Rachel K Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Steven A Sloan
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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47
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Ahmed NI, Khandelwal N, Anderson AG, Oh E, Vollmer RM, Kulkarni A, Gibson JR, Konopka G. Compensation between FOXP transcription factors maintains proper striatal function. Cell Rep 2024; 43:114257. [PMID: 38761373 PMCID: PMC11234887 DOI: 10.1016/j.celrep.2024.114257] [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: 07/25/2023] [Revised: 02/05/2024] [Accepted: 05/05/2024] [Indexed: 05/20/2024] Open
Abstract
Spiny projection neurons (SPNs) of the striatum are critical in integrating neurochemical information to coordinate motor and reward-based behavior. Mutations in the regulatory transcription factors expressed in SPNs can result in neurodevelopmental disorders (NDDs). Paralogous transcription factors Foxp1 and Foxp2, which are both expressed in the dopamine receptor 1 (D1) expressing SPNs, are known to have variants implicated in NDDs. Utilizing mice with a D1-SPN-specific loss of Foxp1, Foxp2, or both and a combination of behavior, electrophysiology, and cell-type-specific genomic analysis, loss of both genes results in impaired motor and social behavior as well as increased firing of the D1-SPNs. Differential gene expression analysis implicates genes involved in autism risk, electrophysiological properties, and neuronal development and function. Viral-mediated re-expression of Foxp1 into the double knockouts is sufficient to restore electrophysiological and behavioral deficits. These data indicate complementary roles between Foxp1 and Foxp2 in the D1-SPNs.
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Affiliation(s)
- Newaz I Ahmed
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Nitin Khandelwal
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Ashley G Anderson
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Emily Oh
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Rachael M Vollmer
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Ashwinikumar Kulkarni
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Jay R Gibson
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA.
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48
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Cornejo MP, Fernandez G, Cabral A, Barrile F, Heredia F, García Romero G, Zubimendi Sampieri JP, Quelas JI, Cantel S, Fehrentz JA, Alonso A, Pla R, Ferran JL, Andreoli MF, De Francesco PN, Perelló M. GHSR in a Subset of GABA Neurons Controls Food Deprivation-Induced Hyperphagia in Male Mice. Endocrinology 2024; 165:bqae061. [PMID: 38815068 DOI: 10.1210/endocr/bqae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
The growth hormone secretagogue receptor (GHSR), primarily known as the receptor for the hunger hormone ghrelin, potently controls food intake, yet the specific Ghsr-expressing cells mediating the orexigenic effects of this receptor remain incompletely characterized. Since Ghsr is expressed in gamma-aminobutyric acid (GABA)-producing neurons, we sought to investigate whether the selective expression of Ghsr in a subset of GABA neurons is sufficient to mediate GHSR's effects on feeding. First, we crossed mice that express a tamoxifen-dependent Cre recombinase in the subset of GABA neurons that express glutamic acid decarboxylase 2 (Gad2) enzyme (Gad2-CreER mice) with reporter mice, and found that ghrelin mainly targets a subset of Gad2-expressing neurons located in the hypothalamic arcuate nucleus (ARH) and that is predominantly segregated from Agouti-related protein (AgRP)-expressing neurons. Analysis of various single-cell RNA-sequencing datasets further corroborated that the primary subset of cells coexpressing Gad2 and Ghsr in the mouse brain are non-AgRP ARH neurons. Next, we crossed Gad2-CreER mice with reactivable GHSR-deficient mice to generate mice expressing Ghsr only in Gad2-expressing neurons (Gad2-GHSR mice). We found that ghrelin treatment induced the expression of the marker of transcriptional activation c-Fos in the ARH of Gad2-GHSR mice, yet failed to induce food intake. In contrast, food deprivation-induced refeeding was higher in Gad2-GHSR mice than in GHSR-deficient mice and similar to wild-type mice, suggesting that ghrelin-independent roles of GHSR in a subset of GABA neurons is sufficient for eliciting full compensatory hyperphagia in mice.
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Affiliation(s)
- María Paula Cornejo
- Grupo de Neurofisiología, Instituto Multidisciplinario de Biología Celular (IMBICE), Universidad Nacional la Plata (UNLP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA), La Plata 1900, Buenos Aires, Argentina
| | - Gimena Fernandez
- Grupo de Neurofisiología, Instituto Multidisciplinario de Biología Celular (IMBICE), Universidad Nacional la Plata (UNLP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA), La Plata 1900, Buenos Aires, Argentina
| | - Agustina Cabral
- Grupo de Neurofisiología, Instituto Multidisciplinario de Biología Celular (IMBICE), Universidad Nacional la Plata (UNLP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA), La Plata 1900, Buenos Aires, Argentina
| | - Franco Barrile
- Grupo de Neurofisiología, Instituto Multidisciplinario de Biología Celular (IMBICE), Universidad Nacional la Plata (UNLP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA), La Plata 1900, Buenos Aires, Argentina
| | - Florencia Heredia
- Grupo de Neurofisiología, Instituto Multidisciplinario de Biología Celular (IMBICE), Universidad Nacional la Plata (UNLP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA), La Plata 1900, Buenos Aires, Argentina
| | - Guadalupe García Romero
- Grupo de Neurofisiología, Instituto Multidisciplinario de Biología Celular (IMBICE), Universidad Nacional la Plata (UNLP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA), La Plata 1900, Buenos Aires, Argentina
| | | | | | - Sonia Cantel
- Institut des Biomolécules Max Mousseron, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Jean-Alain Fehrentz
- Institut des Biomolécules Max Mousseron, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Antonia Alonso
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, University of Murcia, Murcia 30100, Spain
- Institute of Biomedical Research of Murcia-IMIB, Virgen de la Arrixaca University Hospital, Murcia 30100, Spain
| | - Ramon Pla
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, University of Murcia, Murcia 30100, Spain
- Institute of Biomedical Research of Murcia-IMIB, Virgen de la Arrixaca University Hospital, Murcia 30100, Spain
| | - José Luis Ferran
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, University of Murcia, Murcia 30100, Spain
- Institute of Biomedical Research of Murcia-IMIB, Virgen de la Arrixaca University Hospital, Murcia 30100, Spain
| | - María Florencia Andreoli
- Instituto de Desarrollo e Investigaciones Pediátricas (IDIP), HIAEP Sor María Ludovica de La Plata, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA), La Plata 1900, Buenos Aires, Argentina
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala 751 24, Sweden
| | - Pablo Nicolas De Francesco
- Grupo de Neurofisiología, Instituto Multidisciplinario de Biología Celular (IMBICE), Universidad Nacional la Plata (UNLP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA), La Plata 1900, Buenos Aires, Argentina
| | - Mario Perelló
- Grupo de Neurofisiología, Instituto Multidisciplinario de Biología Celular (IMBICE), Universidad Nacional la Plata (UNLP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA), La Plata 1900, Buenos Aires, Argentina
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala 751 24, Sweden
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49
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Liu Y, Zhang J, Jiang Z, Qin M, Xu M, Zhang S, Ma G. Organization of corticocortical and thalamocortical top-down inputs in the primary visual cortex. Nat Commun 2024; 15:4495. [PMID: 38802410 PMCID: PMC11130321 DOI: 10.1038/s41467-024-48924-8] [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: 10/16/2023] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
Unified visual perception requires integration of bottom-up and top-down inputs in the primary visual cortex (V1), yet the organization of top-down inputs in V1 remains unclear. Here, we used optogenetics-assisted circuit mapping to identify how multiple top-down inputs from higher-order cortical and thalamic areas engage V1 excitatory and inhibitory neurons. Top-down inputs overlap in superficial layers yet segregate in deep layers. Inputs from the medial secondary visual cortex (V2M) and anterior cingulate cortex (ACA) converge on L6 Pyrs, whereas ventrolateral orbitofrontal cortex (ORBvl) and lateral posterior thalamic nucleus (LP) inputs are processed in parallel in Pyr-type-specific subnetworks (Pyr←ORBvl and Pyr←LP) and drive mutual inhibition between them via local interneurons. Our study deepens understanding of the top-down modulation mechanisms of visual processing and establishes that V2M and ACA inputs in L6 employ integrated processing distinct from the parallel processing of LP and ORBvl inputs in L5.
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Affiliation(s)
- Yanmei Liu
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jiahe Zhang
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhishan Jiang
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Meiling Qin
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Min Xu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Siyu Zhang
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China.
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Guofen Ma
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China.
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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50
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Reiner BC, Chehimi SN, Merkel R, Toikumo S, Berrettini WH, Kranzler HR, Sanchez-Roige S, Kember RL, Schmidt HD, Crist RC. A single-nucleus transcriptomic atlas of medium spiny neurons in the rat nucleus accumbens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.26.595949. [PMID: 38826289 PMCID: PMC11142250 DOI: 10.1101/2024.05.26.595949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Neural processing of rewarding stimuli involves several distinct regions, including the nucleus accumbens (NAc). The majority of NAc neurons are GABAergic projection neurons known as medium spiny neurons (MSNs). MSNs are broadly defined by dopamine receptor expression, but evidence suggests that a wider array of subtypes exist. To study MSN heterogeneity, we analyzed single-nucleus RNA sequencing data from the largest available rat NAc dataset. Analysis of 48,040 NAc MSN nuclei identified major populations belonging to the striosome and matrix compartments. Integration with mouse and human data indicated consistency across species and disease-relevance scoring using genome-wide association study results revealed potentially differential roles for MSN populations in substance use disorders. Additional high-resolution clustering identified 34 transcriptomically distinct subtypes of MSNs definable by a limited number of marker genes. Together, these data demonstrate the diversity of MSNs in the NAc and provide a basis for more targeted genetic manipulation of specific populations.
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