1
|
Mahajani S, Salahi A, Gonzalez B, Nelson C, Hsiung F. Decoding complexity: the need to enhance precision and streamline spatial understanding in neuroscience. Neural Regen Res 2025; 20:801-802. [PMID: 38886946 PMCID: PMC11433921 DOI: 10.4103/nrr.nrr-d-23-02067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/21/2024] [Indexed: 06/20/2024] Open
|
2
|
Hong I, Kim J, Hainmueller T, Kim DW, Keijser J, Johnson RC, Park SH, Limjunyawong N, Yang Z, Cheon D, Hwang T, Agarwal A, Cholvin T, Krienen FM, McCarroll SA, Dong X, Leopold DA, Blackshaw S, Sprekeler H, Bergles DE, Bartos M, Brown SP, Huganir RL. Calcium-permeable AMPA receptors govern PV neuron feature selectivity. Nature 2024:10.1038/s41586-024-08027-2. [PMID: 39358515 DOI: 10.1038/s41586-024-08027-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/05/2024] [Indexed: 10/04/2024]
Abstract
The brain helps us survive by forming internal representations of the external world1,2. Excitatory cortical neurons are often precisely tuned to specific external stimuli3,4. However, inhibitory neurons, such as parvalbumin-positive (PV) interneurons, are generally less selective5. PV interneurons differ from excitatory neurons in their neurotransmitter receptor subtypes, including AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) receptors (AMPARs)6,7. Excitatory neurons express calcium-impermeable AMPARs that contain the GluA2 subunit (encoded by GRIA2), whereas PV interneurons express receptors that lack the GluA2 subunit and are calcium-permeable (CP-AMPARs). Here we demonstrate a causal relationship between CP-AMPAR expression and the low feature selectivity of PV interneurons. We find low expression stoichiometry of GRIA2 mRNA relative to other subunits in PV interneurons that is conserved across ferrets, rodents, marmosets and humans, and causes abundant CP-AMPAR expression. Replacing CP-AMPARs in PV interneurons with calcium-impermeable AMPARs increased their orientation selectivity in the visual cortex. Manipulations to induce sparse CP-AMPAR expression demonstrated that this increase was cell-autonomous and could occur with changes beyond development. Notably, excitatory-PV interneuron connectivity rates and unitary synaptic strength were unaltered by CP-AMPAR removal, which suggested that the selectivity of PV interneurons can be altered without markedly changing connectivity. In Gria2-knockout mice, in which all AMPARs are calcium-permeable, excitatory neurons showed significantly degraded orientation selectivity, which suggested that CP-AMPARs are sufficient to drive lower selectivity regardless of cell type. Moreover, hippocampal PV interneurons, which usually exhibit low spatial tuning, became more spatially selective after removing CP-AMPARs, which indicated that CP-AMPARs suppress the feature selectivity of PV interneurons independent of modality. These results reveal a new role of CP-AMPARs in maintaining low-selectivity sensory representation in PV interneurons and implicate a conserved molecular mechanism that distinguishes this cell type in the neocortex.
Collapse
Affiliation(s)
- Ingie Hong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA.
| | - Juhyun Kim
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Emotion, Cognition and Behavior Research Group, Korea Brain Research Institute (KBRI), Daegu, Republic of Korea
| | - Thomas Hainmueller
- Institute for Physiology I, University of Freiburg, Medical Faculty, Freiburg, Germany
- Department of Psychiatry, New York University Langone Medical Center, New York, NY, USA
| | - Dong Won Kim
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Joram Keijser
- Modelling of Cognitive Processes, Technical University of Berlin, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Einstein Center for Neurosciences Berlin, Berlin, Germany
| | - Richard C Johnson
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Soo Hyun Park
- Section on Cognitive Neurophysiology and Imaging, National Institute of Mental Health, Bethesda, MD, USA
- Department of Brain and Cognitive Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Nathachit Limjunyawong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center of Research Excellence in Allergy and Immunology, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Zhuonan Yang
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA
| | - David Cheon
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Taeyoung Hwang
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amit Agarwal
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Chica and Heinz Schaller Research Group, Institute for Anatomy and Cell Biology, Heidelberg, Germany
- Interdisciplinary Center for Neurosciences, University of Heidelberg, Heidelberg, Germany
| | - Thibault Cholvin
- Institute for Physiology I, University of Freiburg, Medical Faculty, Freiburg, Germany
| | - Fenna M Krienen
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | | | - Xinzhong Dong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David A Leopold
- Section on Cognitive Neurophysiology and Imaging, National Institute of Mental Health, Bethesda, MD, USA
| | - Seth Blackshaw
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Henning Sprekeler
- Modelling of Cognitive Processes, Technical University of Berlin, Berlin, Germany
- Bernstein Center for Computational Neuroscience Berlin, Berlin, Germany
- Science of Intelligence, Research Cluster of Excellence, Berlin, Germany
| | - Dwight E Bergles
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Marlene Bartos
- Institute for Physiology I, University of Freiburg, Medical Faculty, Freiburg, Germany
| | - Solange P Brown
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Richard L Huganir
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
3
|
Qin S, Wei T, Mo J, Lu L, Chai X, Huang Q, Qi S, Tan G. Research on the shared function of central neurons and breast cancer based on gene expression profile data mining: The role of EMID1 protein antibody expression. Int J Biol Macromol 2024; 277:134393. [PMID: 39094856 DOI: 10.1016/j.ijbiomac.2024.134393] [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: 06/20/2024] [Revised: 07/24/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
In recent years, the incidence of breast cancer has gradually increased, and the research on it has become a hot spot in the scientific community. Central neurons play an important role in breast cancer. This study aims to explore the application of gene expression profile data mining in the study of shared function between central neurons and breast cancer, and focuses on the expression of EMID1 protein antibody. The study collected biomedical images and gene expression profile data of breast cancer patients. Then, we use image processing and analysis technology to extract and analyze features of biomedical images to obtain quantitative features of breast cancer. Gene expression profile data were preprocessed and analyzed to obtain information about breast cancer related genes. Integrating and fusing biomedical images and gene expression profile data, and exploring the sharing function between central neurons and breast cancer through data mining algorithms and statistical analysis methods. The results showed that the expression of EMID1 protein was high in breast cancer tissues, and the expression pattern was similar to that of central neurons. Further functional studies have shown that EMID1 protein is involved in the regulation of proliferation and invasion of breast cancer cells. By regulating the expression level of EMID1 protein, we observed that the proliferation and invasion ability of breast cancer cells were significantly affected. The research results show that through the comprehensive analysis of biomedical images and gene expression profile data, we found the sharing function between central neurons and breast cancer. The central neuronal cell marker genes EMID1 and GREB1L may be used as key biomarkers to regulate the pathogenesis of breast cancer and affect the occurrence and development of breast cancer.
Collapse
Affiliation(s)
- Shuting Qin
- Department of Breast and Thyroid Surgery, Liuzhou People's Hospital, Liuzhou 545005, China
| | - Teng Wei
- Department of Breast and Thyroid Surgery, Liuzhou People's Hospital, Liuzhou 545005, China
| | - Junyang Mo
- Department of Breast and Thyroid Surgery, Liuzhou People's Hospital, Liuzhou 545005, China
| | - Linjie Lu
- Department of Breast and Thyroid Surgery, Liuzhou People's Hospital, Liuzhou 545005, China
| | - Xiao Chai
- Department of Breast and Thyroid Surgery, Liuzhou People's Hospital, Liuzhou 545005, China
| | - Qingyun Huang
- Institute of Neuroscience and Guangxi Key Laboratory of Brain Science, Department of Human Anatomy, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, China; Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Health Commission Key Laboratory of Basic Research on Brain Function and Disease, Nanning 530012, China; China-ASEAN Research Center for Innovation and Development in Brain Science, Nanning 530020, China
| | - Shuya Qi
- Institute of Neuroscience and Guangxi Key Laboratory of Brain Science, Department of Human Anatomy, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, China; Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Health Commission Key Laboratory of Basic Research on Brain Function and Disease, Nanning 530012, China; China-ASEAN Research Center for Innovation and Development in Brain Science, Nanning 530020, China
| | - Guohe Tan
- Institute of Neuroscience and Guangxi Key Laboratory of Brain Science, Department of Human Anatomy, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, China; Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Health Commission Key Laboratory of Basic Research on Brain Function and Disease, Nanning 530012, China; China-ASEAN Research Center for Innovation and Development in Brain Science, Nanning 530020, China; Guangxi Key Laboratory of Regenerative Medicine, Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Nanning 5300212, China.
| |
Collapse
|
4
|
Song J, Zhang C, Fu S, Xu X. Visualized lateral flow assay for logic determination of co-existing viral RNA fragments. Biosens Bioelectron 2024; 261:116519. [PMID: 38917515 DOI: 10.1016/j.bios.2024.116519] [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: 04/16/2024] [Revised: 06/16/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024]
Abstract
Different types of pathogenic viruses that have common transmission path can be co-infected, inducing distinct disease procession in comparison to that infection of one. Also, in the post COVID-19 time, more types of respiratory infectious virus are becoming prevalent and are concurrent. Those bring an urgent need for detection of co-existing viruses. Here, we propose a visualized lateral flow assay for logic determination of co-existing viral RNA fragments. In the presence of specific viral RNA inputs, DNAzyme is de-blocked according to defined logic, and catalyzes the hydrolysis of hairpin-structural substrate. One of cleaved substrates contains DNAzyme domain to realize dual signal amplification, which obtains copious of the other cleaved substrates. The cleaved substrates act as linking strands for bridging DNA-modified gold nanoparticles onto lateral flow strip to induce coloration on test line. "AND", "OR" and "INHIBIT" controlled lateral flow assays are respectively demonstrated for co-existing viral RNA detection, and the visual results can be obtained by the same kind of prepared strip, without need of re-fabricating strips according to logic systems. The work provides a flexible, convenient, visual and logic-processing strategy for simultaneous analysis of co-existing viruses.
Collapse
Affiliation(s)
- Juanjuan Song
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, China
| | - Chuhao Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, China
| | - Siting Fu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, China
| | - Xiaowen Xu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, China.
| |
Collapse
|
5
|
Lotter LD, Saberi A, Hansen JY, Misic B, Paquola C, Barker GJ, Bokde ALW, Desrivières S, Flor H, Grigis A, Garavan H, Gowland P, Heinz A, Brühl R, Martinot JL, Paillère ML, Artiges E, Papadopoulos Orfanos D, Paus T, Poustka L, Hohmann S, Fröhner JH, Smolka MN, Vaidya N, Walter H, Whelan R, Schumann G, Nees F, Banaschewski T, Eickhoff SB, Dukart J. Regional patterns of human cortex development correlate with underlying neurobiology. Nat Commun 2024; 15:7987. [PMID: 39284858 PMCID: PMC11405413 DOI: 10.1038/s41467-024-52366-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 08/29/2024] [Indexed: 09/22/2024] Open
Abstract
Human brain morphology undergoes complex changes over the lifespan. Despite recent progress in tracking brain development via normative models, current knowledge of underlying biological mechanisms is highly limited. We demonstrate that human cortical thickness development and aging trajectories unfold along patterns of molecular and cellular brain organization, traceable from population-level to individual developmental trajectories. During childhood and adolescence, cortex-wide spatial distributions of dopaminergic receptors, inhibitory neurons, glial cell populations, and brain-metabolic features explain up to 50% of the variance associated with a lifespan model of regional cortical thickness trajectories. In contrast, modeled cortical thickness change patterns during adulthood are best explained by cholinergic and glutamatergic neurotransmitter receptor and transporter distributions. These relationships are supported by developmental gene expression trajectories and translate to individual longitudinal data from over 8000 adolescents, explaining up to 59% of developmental change at cohort- and 18% at single-subject level. Integrating neurobiological brain atlases with normative modeling and population neuroimaging provides a biologically meaningful path to understand brain development and aging in living humans.
Collapse
Affiliation(s)
- Leon D Lotter
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich, Germany.
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany.
- Max Planck School of Cognition; Stephanstrasse 1A, Leipzig, Germany.
| | - Amin Saberi
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich, Germany
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Otto Hahn Research Group for Cognitive Neurogenetics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Justine Y Hansen
- McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Bratislav Misic
- McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Casey Paquola
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich, Germany
| | - Gareth J Barker
- Department of Neuroimaging, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Arun L W Bokde
- Discipline of Psychiatry, School of Medicine and Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Sylvane Desrivières
- Centre for Population Neuroscience and Precision Medicine (PONS), Institute of Psychiatry, Psychology & Neuroscience, SGDP Centre, King's College London, London, UK
| | - Herta Flor
- Institute of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Psychology, School of Social Sciences, University of Mannheim, Mannheim, Germany
| | - Antoine Grigis
- NeuroSpin, CEA, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Hugh Garavan
- Departments of Psychiatry and Psychology, University of Vermont, Burlington, VT, USA
| | - Penny Gowland
- Sir Peter Mansfield Imaging Centre School of Physics and Astronomy, University of Nottingham; University Park, Nottingham, UK
| | - Andreas Heinz
- Department of Psychiatry and Psychotherapy CCM, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Rüdiger Brühl
- Physikalisch-Technische Bundesanstalt (PTB); Braunschweig and Berlin, Berlin, Germany
| | - Jean-Luc Martinot
- Ecole Normale Supérieure Paris-Saclay, Université Paris-Saclay, Université paris Cité, INSERM U1299 "Trajectoires Développementales & Psychiatrie"; Centre Borelli, Gif-sur-Yvette, France
| | - Marie-Laure Paillère
- Ecole Normale Supérieure Paris-Saclay, Université Paris-Saclay, Université paris Cité, INSERM U1299 "Trajectoires Développementales & Psychiatrie"; Centre Borelli, Gif-sur-Yvette, France
- AP-HP Sorbonne Université, Department of Child and Adolescent Psychiatry, Pitié-Salpêtrière Hospital, Paris, France
| | - Eric Artiges
- Ecole Normale Supérieure Paris-Saclay, Université Paris-Saclay, Université paris Cité, INSERM U1299 "Trajectoires Développementales & Psychiatrie"; Centre Borelli, Gif-sur-Yvette, France
- Department of Psychiatry, EPS Barthélémy Durand, Etampes, France
| | | | - Tomáš Paus
- Departments of Psychiatry and Neuroscience, Faculty of Medicine and Centre Hospitalier Universitaire Sainte-Justine, University of Montreal, Montréal, QC, Canada
- Department of Psychiatry, McGill University, Montréal, QC, Canada
| | - Luise Poustka
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Medical Centre Göttingen, Göttingen, Germany
| | - Sarah Hohmann
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Juliane H Fröhner
- Department of Psychiatry and Psychotherapy, Technische Universität Dresden, Dresden, Germany
| | - Michael N Smolka
- Department of Psychiatry and Psychotherapy, Technische Universität Dresden, Dresden, Germany
| | - Nilakshi Vaidya
- Centre for Population Neuroscience and Stratified Medicine (PONS), Department of Psychiatry and Neuroscience, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Henrik Walter
- Department of Psychiatry and Psychotherapy CCM, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Robert Whelan
- School of Psychology and Global Brain Health Institute, Trinity College Dublin, Dublin, Ireland
| | - Gunter Schumann
- Centre for Population Neuroscience and Stratified Medicine (PONS), Department of Psychiatry and Neuroscience, Charité Universitätsmedizin Berlin, Berlin, Germany
- Centre for Population Neuroscience and Precision Medicine (PONS), Institute for Science and Technology of Brain-inspired Intelligence (ISTBI), Fudan University, Shanghai, China
| | - Frauke Nees
- Institute of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Institute of Medical Psychology and Medical Sociology, University Medical Center Schleswig-Holstein, Kiel University, Kiel, Germany
| | - Tobias Banaschewski
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- German Center for Mental Health (DZPG), partner site Mannheim-Heidelberg-Ulm, Heidelberg, Germany
| | - Simon B Eickhoff
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich, Germany
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Juergen Dukart
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich, Germany.
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany.
| |
Collapse
|
6
|
Lawler NB, Bhatt U, Agarwal V, Evans CW, Kaluskar P, Amos SE, Chen K, Yao Y, Jiang H, Choi YS, Zheng M, Spagnoli D, Suarez-Martinez I, Zetterlund PB, Wallace VP, Harvey AR, Hodgetts SI, Iyer KS. Transcriptomic Analysis Reveals the Heterogeneous Role of Conducting Films Upon Electrical Stimulation. Adv Healthc Mater 2024:e2400364. [PMID: 39221662 DOI: 10.1002/adhm.202400364] [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: 02/20/2024] [Revised: 07/17/2024] [Indexed: 09/04/2024]
Abstract
Central nervous system (CNS) injuries and neurodegenerative diseases have markedly poor prognoses and can result in permanent dysfunction due to the general inability of CNS neurons to regenerate. Differentiation of transplanted stem cells has emerged as a therapeutic avenue to regenerate tissue architecture in damaged areas. Electrical stimulation is a promising approach for directing the differentiation outcomes and pattern of outgrowth of transplanted stem cells, however traditional inorganic bio-electrodes can induce adverse effects such as inflammation. This study demonstrates the implementation of two organic thin films, a polymer/reduced graphene oxide nanocomposite (P(rGO)) and PEDOT:PSS, that have favorable properties for implementation as conductive materials for electrical stimulation, as well as an inorganic indium tin oxide (ITO) conductive film. Transcriptomic analysis reveals that electrical stimulation improves neuronal differentiation of SH-SY5Y cells on all three films, with the greatest effect for P(rGO). Unique material- and electrical stimuli-mediated effects are observed, associated with differentiation, cell-substrate adhesion, and translation. The work demonstrates that P(rGO) and PEDOT:PSS are highly promising organic materials for the development of biocompatible, conductive scaffolds that will enhance electrically-aided stem cell therapeutics for CNS injuries and neurodegenerative diseases.
Collapse
Affiliation(s)
- Nicholas B Lawler
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- School of Physics, Mathematics and Computing, The University of Western Australia, Perth, WA, 6009, Australia
- ARC Training Centre for Next-Gen Technologies in Biomedical Analysis, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Uditi Bhatt
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- ARC Training Centre for Next-Gen Technologies in Biomedical Analysis, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Vipul Agarwal
- Cluster for Advanced Macromolecular Design (CAMD), School of Chemical Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- ARC Training Centre for Next-Gen Technologies in Biomedical Analysis, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Priya Kaluskar
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- ARC Training Centre for Next-Gen Technologies in Biomedical Analysis, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, 6009, Australia
- Centre for Orthopaedic Research, The UWA Medical School, The University of Western Australia, Perth, WA, 6009, Australia
- Australian Research Council Centre for Personalised Therapeutics Technologies, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Sebastian E Amos
- School of Human Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Kai Chen
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- ARC Training Centre for Next-Gen Technologies in Biomedical Analysis, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Yin Yao
- Electron Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Haibo Jiang
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- ARC Training Centre for Next-Gen Technologies in Biomedical Analysis, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Yu Suk Choi
- ARC Training Centre for Next-Gen Technologies in Biomedical Analysis, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- School of Human Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Minghao Zheng
- Perron Institute for Neurological and Translational Science, Perth, WA, 6009, Australia
- Centre for Orthopaedic Research, The UWA Medical School, The University of Western Australia, Perth, WA, 6009, Australia
| | - Dino Spagnoli
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | | | - Per B Zetterlund
- Cluster for Advanced Macromolecular Design (CAMD), School of Chemical Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Vincent P Wallace
- School of Physics, Mathematics and Computing, The University of Western Australia, Perth, WA, 6009, Australia
| | - Alan R Harvey
- Perron Institute for Neurological and Translational Science, Perth, WA, 6009, Australia
- School of Human Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Stuart I Hodgetts
- Perron Institute for Neurological and Translational Science, Perth, WA, 6009, Australia
- School of Human Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - K Swaminathan Iyer
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- ARC Training Centre for Next-Gen Technologies in Biomedical Analysis, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| |
Collapse
|
7
|
Kim CY, Park Y, Namgung JY, Park Y, Park BY. The macroscale routing mechanism of structural brain connectivity related to body mass index. Hum Brain Mapp 2024; 45:e70019. [PMID: 39230183 PMCID: PMC11372826 DOI: 10.1002/hbm.70019] [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: 10/20/2023] [Revised: 08/05/2024] [Accepted: 08/20/2024] [Indexed: 09/05/2024] Open
Abstract
Understanding the brain's mechanisms in individuals with obesity is important for managing body weight. Prior neuroimaging studies extensively investigated alterations in brain structure and function related to body mass index (BMI). However, how the network communication among the large-scale brain networks differs across BMI is underinvestigated. This study used diffusion magnetic resonance imaging of 290 young adults to identify links between BMI and brain network mechanisms. Navigation efficiency, a measure of network routing, was calculated from the structural connectivity computed using diffusion tractography. The sensory and frontoparietal networks indicated positive associations between navigation efficiency and BMI. The neurotransmitter association analysis identified that serotonergic and dopaminergic receptors, as well as opioid and norepinephrine systems, were related to BMI-related alterations in navigation efficiency. The transcriptomic analysis found that genes associated with network routing across BMI overlapped with genes enriched in excitatory and inhibitory neurons, specifically, gene enrichments related to synaptic transmission and neuron projection. Our findings suggest a valuable insight into understanding BMI-related alterations in brain network routing mechanisms and the potential underlying cellular biology, which might be used as a foundation for BMI-based weight management.
Collapse
Affiliation(s)
- Chae Yeon Kim
- Department of Data Science, Inha University, Incheon, South Korea
| | - Yunseo Park
- Department of Data Science, Inha University, Incheon, South Korea
| | | | - Yeongjun Park
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon, South Korea
| | - Bo-Yong Park
- Department of Brain and Cognitive Engineering, Korea University, Seoul, South Korea
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, South Korea
- Research Center for Small Businesses Ecosystem, Inha University, Incheon, South Korea
| |
Collapse
|
8
|
He D, Li L, Zhang H, Liu F, Li S, Xiu X, Fan C, Qi M, Meng M, Ye J, Mort M, Stenson PD, Cooper DN, Zhao H. Accurate identification of genes associated with brain disorders by integrating heterogeneous genomic data into a Bayesian framework. EBioMedicine 2024; 107:105286. [PMID: 39168091 PMCID: PMC11382033 DOI: 10.1016/j.ebiom.2024.105286] [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: 04/30/2023] [Revised: 07/29/2024] [Accepted: 08/01/2024] [Indexed: 08/23/2024] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have revealed many brain disorder-associated SNPs residing in the noncoding genome, rendering it a challenge to decipher the underlying pathogenic mechanisms. METHODS Here, we present an unsupervised Bayesian framework to identify disease-associated genes by integrating risk SNPs with long-range chromatin interactions (iGOAT), including SNP-SNP interactions extracted from ∼500,000 patients and controls from the UK Biobank, and enhancer-promoter interactions derived from multiple brain cell types at different developmental stages. FINDINGS The application of iGOAT to three psychiatric disorders and three neurodegenerative/neurological diseases predicted sets of high-risk (HRGs) and low-risk (LRGs) genes for each disorder. The HRGs were enriched in drug targets, and exhibited higher expression during prenatal brain developmental stages than postnatal stages, indicating their potential to affect brain development at an early stage. The HRGs associated with Alzheimer's disease were found to share genetic architecture with schizophrenia, bipolar disorder and major depressive disorder according to gene co-expression module analysis and rare variants analysis. Comparisons of this method to the eQTL-based method, the TWAS-based method, and the gene-level GWAS method indicated that the genes identified by our method are more enriched in known brain disorder-related genes, and exhibited higher precision. Finally, the method predicted 205 risk genes not previously reported to be associated with any brain disorder, of which one top-risk gene, MLH1, was experimentally validated as being schizophrenia-associated. INTERPRETATION iGOAT can successfully leverage epigenomic data, phenotype-genotype associations, and protein-protein interactions to advance our understanding of brain disorders, thereby facilitating the development of new therapeutic approaches. FUNDING The work was funded by the National Key Research and Development Program of China (2024YFF1204902), the Natural Science Foundation of China (82371482), Guangzhou Science and Technology Research Plan (2023A03J0659) and Natural Science Foundation of Guangdong (2024A1515011363).
Collapse
Affiliation(s)
- Dan He
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Ling Li
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Huasong Zhang
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Feiyi Liu
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Shaoying Li
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Xuehao Xiu
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Cong Fan
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Mengling Qi
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Meng Meng
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Junping Ye
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, 510006, China.
| |
Collapse
|
9
|
Warden AS, Salem NA, Brenner E, Sutherland GT, Stevens J, Kapoor M, Goate AM, Mayfield RD. Integrative genomics approach identifies glial transcriptomic dysregulation and risk in the cortex of individuals with Alcohol Use Disorder. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.16.607185. [PMID: 39211266 PMCID: PMC11360965 DOI: 10.1101/2024.08.16.607185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Alcohol use disorder (AUD) is a prevalent neuropsychiatric disorder that is a major global health concern, affecting millions of people worldwide. Past molecular studies of AUD used underpowered single cell analysis or bulk homogenates of postmortem brain tissue, which obscures gene expression changes in specific cell types. Here we performed single nuclei RNA-sequencing analysis of 73 post-mortem samples from individuals with AUD (N=36, N nuclei = 248,873) and neurotypical controls (N=37, N nuclei = 210,573) in both sexes across two institutional sites. We identified 32 clusters and found widespread cell type-specific transcriptomic changes across the cortex in AUD, particularly affecting glia. We found the greatest dysregulation in novel microglial and astrocytic subtypes that accounted for the majority of differential gene expression and co-expression modules linked to AUD. Analysis for cell type-specific enrichment of aggregate genetic risk for AUD identified subtypes of microglia and astrocytes as potential key players not only affected by but causally linked to the progression of AUD. These results highlight the importance of cell-type specific molecular changes in AUD and offer opportunities to identify novel targets for treatment.
Collapse
|
10
|
Lotter LD, Saberi A, Hansen JY, Misic B, Paquola C, Barker GJ, Bokde ALW, Desrivières S, Flor H, Grigis A, Garavan H, Gowland P, Heinz A, Brühl R, Martinot JL, Paillère ML, Artiges E, Orfanos DP, Paus T, Poustka L, Hohmann S, Fröhner JH, Smolka MN, Vaidya N, Walter H, Whelan R, Schumann G, Nees F, Banaschewski T, Eickhoff SB, Dukart J. Regional patterns of human cortex development correlate with underlying neurobiology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.05.539537. [PMID: 37205539 PMCID: PMC10187287 DOI: 10.1101/2023.05.05.539537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Human brain morphology undergoes complex changes over the lifespan. Despite recent progress in tracking brain development via normative models, current knowledge of underlying biological mechanisms is highly limited. We demonstrate that human cortical thickness development and aging trajectories unfold along patterns of molecular and cellular brain organization, traceable from population-level to individual developmental trajectories. During childhood and adolescence, cortex-wide spatial distributions of dopaminergic receptors, inhibitory neurons, glial cell populations, and brain-metabolic features explain up to 50% of variance associated with a lifespan model of regional cortical thickness trajectories. In contrast, modeled cortical thickness change patterns during adulthood are best explained by cholinergic and glutamatergic neurotransmitter receptor and transporter distributions. These relationships are supported by developmental gene expression trajectories and translate to individual longitudinal data from over 8,000 adolescents, explaining up to 59% of developmental change at cohort- and 18% at single-subject level. Integrating neurobiological brain atlases with normative modeling and population neuroimaging provides a biologically meaningful path to understand brain development and aging in living humans.
Collapse
Affiliation(s)
- Leon D Lotter
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich; Jülich, Germany
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University; Düsseldorf, Germany
- Max Planck School of Cognition; Stephanstrasse 1A, 04103 Leipzig, Germany
| | - Amin Saberi
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich; Jülich, Germany
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University; Düsseldorf, Germany
- Otto Hahn Research Group for Cognitive Neurogenetics, Max Planck Institute for Human Cognitive and Brain Sciences; Leipzig, Germany
| | - Justine Y Hansen
- McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University; Montréal, QC, Canada
| | - Bratislav Misic
- McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University; Montréal, QC, Canada
| | - Casey Paquola
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich; Jülich, Germany
| | - Gareth J Barker
- Department of Neuroimaging, Institute of Psychiatry, Psychology & Neuroscience, King's College London; London, United Kingdom
| | - Arun L W Bokde
- Discipline of Psychiatry, School of Medicine and Trinity College Institute of Neuroscience, Trinity College Dublin; Dublin, Ireland
| | - Sylvane Desrivières
- Centre for Population Neuroscience and Precision Medicine (PONS), Institute of Psychiatry, Psychology & Neuroscience, SGDP Centre, King's College London; London, United Kingdom
| | - Herta Flor
- Institute of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University; Square J5, Mannheim, Germany
- Department of Psychology, School of Social Sciences, University of Mannheim; 68131 Mannheim, Germany
| | - Antoine Grigis
- NeuroSpin, CEA, Université Paris-Saclay; F-91191 Gif-sur-Yvette, France
| | - Hugh Garavan
- Departments of Psychiatry and Psychology, University of Vermont; 05405 Burlington, Vermont, USA
| | - Penny Gowland
- Sir Peter Mansfield Imaging Centre School of Physics and Astronomy, University of Nottingham; University Park, Nottingham, United Kingdom
| | - Andreas Heinz
- Department of Psychiatry and Psychotherapy CCM, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health; Berlin, Germany
| | - Rüdiger Brühl
- Physikalisch-Technische Bundesanstalt (PTB); Braunschweig and Berlin, Germany
| | - Jean-Luc Martinot
- Ecole Normale Supérieure Paris-Saclay, Université Paris-Saclay, Université paris Cité, INSERM U1299 "Trajectoires Développementales & Psychiatrie"; Centre Borelli CNRS UMR9010, Gif-sur-Yvette, France
| | - Marie-Laure Paillère
- Ecole Normale Supérieure Paris-Saclay, Université Paris-Saclay, Université paris Cité, INSERM U1299 "Trajectoires Développementales & Psychiatrie"; Centre Borelli CNRS UMR9010, Gif-sur-Yvette, France
- AP-HP Sorbonne Université, Department of Child and Adolescent Psychiatry, Pitié-Salpêtrière Hospital; Paris, France
| | - Eric Artiges
- Ecole Normale Supérieure Paris-Saclay, Université Paris-Saclay, Université paris Cité, INSERM U1299 "Trajectoires Développementales & Psychiatrie"; Centre Borelli CNRS UMR9010, Gif-sur-Yvette, France
- Department of Psychiatry, EPS Barthélémy Durand; Etampes, France
| | | | - Tomáš Paus
- Departments of Psychiatry and Neuroscience, Faculty of Medicine and Centre Hospitalier Universitaire Sainte-Justine, University of Montreal; Montréal, Quebec, Canada
- Department of Psychiatry, McGill University; Montreal, Quebec, Canada
| | - Luise Poustka
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Medical Centre Göttingen; von-Siebold-Str. 5, 37075, Göttingen, Germany
| | - Sarah Hohmann
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University; Square J5, 68159 Mannheim, Germany
| | - Juliane H Fröhner
- Department of Psychiatry and Psychotherapy, Technische Universität Dresden; Dresden, Germany
| | - Michael N Smolka
- Department of Psychiatry and Psychotherapy, Technische Universität Dresden; Dresden, Germany
| | - Nilakshi Vaidya
- Centre for Population Neuroscience and Stratified Medicine (PONS), Department of Psychiatry and Neuroscience, Charité Universitätsmedizin Berlin; Berlin, Germany
| | - Henrik Walter
- Department of Psychiatry and Psychotherapy CCM, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health; Berlin, Germany
| | - Robert Whelan
- School of Psychology and Global Brain Health Institute, Trinity College Dublin; Dublin, Ireland
| | - Gunter Schumann
- Centre for Population Neuroscience and Stratified Medicine (PONS), Department of Psychiatry and Neuroscience, Charité Universitätsmedizin Berlin; Berlin, Germany
- Centre for Population Neuroscience and Precision Medicine (PONS), Institute for Science and Technology of Brain-inspired Intelligence (ISTBI), Fudan University; Shanghai, China
| | - Frauke Nees
- Institute of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University; Square J5, Mannheim, Germany
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University; Square J5, 68159 Mannheim, Germany
- Institute of Medical Psychology and Medical Sociology, University Medical Center Schleswig-Holstein, Kiel University; Kiel, Germany
| | - Tobias Banaschewski
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University; Square J5, 68159 Mannheim, Germany
- German Center for Mental Health (DZPG), partner site Mannheim-Heidelberg-Ulm; Heidelberg, Germany
| | - Simon B Eickhoff
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich; Jülich, Germany
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University; Düsseldorf, Germany
| | - Juergen Dukart
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich; Jülich, Germany
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University; Düsseldorf, Germany
| |
Collapse
|
11
|
Feierman ER, Louzon S, Prescott NA, Biaco T, Gao Q, Qiu Q, Choi K, Palozola KC, Voss AJ, Mehta SD, Quaye CN, Lynch KT, Fuccillo MV, Wu H, David Y, Korb E. Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory. Mol Cell 2024; 84:2822-2837.e11. [PMID: 39025074 PMCID: PMC11316635 DOI: 10.1016/j.molcel.2024.06.025] [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: 12/20/2023] [Revised: 05/02/2024] [Accepted: 06/24/2024] [Indexed: 07/20/2024]
Abstract
Histone proteins affect gene expression through multiple mechanisms, including through exchange with histone variants. Recent findings link histone variants to neurological disorders, yet few are well studied in the brain. Most notably, widely expressed variants of H2B remain elusive. We applied recently developed antibodies, biochemical assays, and sequencing approaches to reveal broad expression of the H2B variant H2BE and defined its role in regulating chromatin structure, neuronal transcription, and mouse behavior. We find that H2BE is enriched at promoters, and a single unique amino acid allows it to dramatically enhance chromatin accessibility. Further, we show that H2BE is critical for synaptic gene expression and long-term memory. Together, these data reveal a mechanism linking histone variants to chromatin accessibility, transcriptional regulation, neuronal function, and memory. This work further identifies a widely expressed H2B variant and uncovers a single histone amino acid with profound effects on genomic structure.
Collapse
Affiliation(s)
- Emily R Feierman
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sean Louzon
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nicholas A Prescott
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Tracy Biaco
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Qingzeng Gao
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kyuhyun Choi
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Katherine C Palozola
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Anna J Voss
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shreya D Mehta
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Camille N Quaye
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Katherine T Lynch
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Marc V Fuccillo
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Erica Korb
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
12
|
Rastogi M, Bartolucci M, Nanni M, Aloisio M, Vozzi D, Petretto A, Contestabile A, Cancedda L. Integrative multi-omic analysis reveals conserved cell-projection deficits in human Down syndrome brains. Neuron 2024; 112:2503-2523.e10. [PMID: 38810652 DOI: 10.1016/j.neuron.2024.05.002] [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: 01/02/2023] [Revised: 03/17/2024] [Accepted: 05/01/2024] [Indexed: 05/31/2024]
Abstract
Down syndrome (DS) is the most common genetic cause of cognitive disability. However, it is largely unclear how triplication of a small gene subset may impinge on diverse aspects of DS brain physiopathology. Here, we took a multi-omic approach and simultaneously analyzed by RNA-seq and proteomics the expression signatures of two diverse regions of human postmortem DS brains. We found that the overexpression of triplicated genes triggered global expression dysregulation, differentially affecting transcripts, miRNAs, and proteins involved in both known and novel biological candidate pathways. Among the latter, we observed an alteration in RNA splicing, specifically modulating the expression of genes involved in cytoskeleton and axonal dynamics in DS brains. Accordingly, we found an alteration in axonal polarization in neurons from DS human iPSCs and mice. Thus, our study provides an integrated multilayer expression database capable of identifying new potential targets to aid in designing future clinical interventions for DS.
Collapse
Affiliation(s)
- Mohit Rastogi
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - Martina Bartolucci
- Core Facilities - Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, Genova 16147, Italy
| | - Marina Nanni
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy
| | | | - Diego Vozzi
- Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova 16152, Italy
| | - Andrea Petretto
- Core Facilities - Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, Genova 16147, Italy
| | - Andrea Contestabile
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy.
| | - Laura Cancedda
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy; Dulbecco Telethon Institute, Rome 00185, Italy.
| |
Collapse
|
13
|
Schwalbe DC, Stornetta DS, Abraham-Fan RJ, Souza GMPR, Jalil M, Crook ME, Campbell JN, Abbott SBG. Molecular Organization of Autonomic, Respiratory, and Spinally-Projecting Neurons in the Mouse Ventrolateral Medulla. J Neurosci 2024; 44:e2211232024. [PMID: 38918066 PMCID: PMC11293450 DOI: 10.1523/jneurosci.2211-23.2024] [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: 11/28/2023] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/27/2024] Open
Abstract
The ventrolateral medulla (VLM) is a crucial region in the brain for visceral and somatic control, serving as a significant source of synaptic input to the spinal cord. Experimental studies have shown that gene expression in individual VLM neurons is predictive of their function. However, the molecular and cellular organization of the VLM has remained uncertain. This study aimed to create a comprehensive dataset of VLM cells using single-cell RNA sequencing in male and female mice. The dataset was enriched with targeted sequencing of spinally-projecting and adrenergic/noradrenergic VLM neurons. Based on differentially expressed genes, the resulting dataset of 114,805 VLM cells identifies 23 subtypes of neurons, excluding those in the inferior olive, and five subtypes of astrocytes. Spinally-projecting neurons were found to be abundant in seven subtypes of neurons, which were validated through in situ hybridization. These subtypes included adrenergic/noradrenergic neurons, serotonergic neurons, and neurons expressing gene markers associated with premotor neurons in the ventromedial medulla. Further analysis of adrenergic/noradrenergic neurons and serotonergic neurons identified nine and six subtypes, respectively, within each class of monoaminergic neurons. Marker genes that identify the neural network responsible for breathing were concentrated in two subtypes of neurons, delineated from each other by markers for excitatory and inhibitory neurons. These datasets are available for public download and for analysis with a user-friendly interface. Collectively, this study provides a fine-scale molecular identification of cells in the VLM, forming the foundation for a better understanding of the VLM's role in vital functions and motor control.
Collapse
Affiliation(s)
- Dana C Schwalbe
- Departments of Biology, University of Virginia, Charlottesville, Virginia 22904
| | | | | | | | - Maira Jalil
- Departments of Biology, University of Virginia, Charlottesville, Virginia 22904
| | - Maisie E Crook
- Departments of Biology, University of Virginia, Charlottesville, Virginia 22904
| | - John N Campbell
- Departments of Biology, University of Virginia, Charlottesville, Virginia 22904
| | | |
Collapse
|
14
|
Cote AC, Young HE, Huckins LM. Critical reasoning on the co-expression module QTL in the dorsolateral prefrontal cortex. HGG ADVANCES 2024; 5:100311. [PMID: 38773772 PMCID: PMC11214266 DOI: 10.1016/j.xhgg.2024.100311] [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: 10/23/2023] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 05/24/2024] Open
Abstract
Expression quantitative trait locus (eQTL) analysis is a popular method of gaining insight into the function of regulatory variation. While cis-eQTL resources have been instrumental in linking genome-wide association study variants to gene function, complex trait heritability may be additionally mediated by other forms of gene regulation. Toward this end, novel eQTL methods leverage gene co-expression (module-QTL) to investigate joint regulation of gene modules by single genetic variants. Here we broadly define a "module-QTL" as the association of a genetic variant with a summary measure of gene co-expression. This approach aims to reduce the multiple testing burden of a trans-eQTL search through the consolidation of gene-based testing and provide biological context to eQTLs shared between genes. In this article we provide an in-depth examination of the co-expression module eQTL (module-QTL) through literature review, theoretical investigation, and real-data application of the module-QTL to three large prefrontal cortex genotype-RNA sequencing datasets. We find module-QTLs in our study that are disease associated and reproducible are not additionally informative beyond cis- or trans-eQTLs for module genes. Through comparison to prior studies, we highlight promises and limitations of the module-QTL across study designs and provide recommendations for further investigation of the module-QTL framework.
Collapse
Affiliation(s)
- Alanna C Cote
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Hannah E Young
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura M Huckins
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06511, USA.
| |
Collapse
|
15
|
Kuo A, Hansen KD, Hicks SC. Quantification and statistical modeling of droplet-based single-nucleus RNA-sequencing data. Biostatistics 2024; 25:801-817. [PMID: 37257175 PMCID: PMC11247185 DOI: 10.1093/biostatistics/kxad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 03/22/2023] [Accepted: 04/19/2023] [Indexed: 06/02/2023] Open
Abstract
In complex tissues containing cells that are difficult to dissociate, single-nucleus RNA-sequencing (snRNA-seq) has become the preferred experimental technology over single-cell RNA-sequencing (scRNA-seq) to measure gene expression. To accurately model these data in downstream analyses, previous work has shown that droplet-based scRNA-seq data are not zero-inflated, but whether droplet-based snRNA-seq data follow the same probability distributions has not been systematically evaluated. Using pseudonegative control data from nuclei in mouse cortex sequenced with the 10x Genomics Chromium system and mouse kidney sequenced with the DropSeq system, we found that droplet-based snRNA-seq data follow a negative binomial distribution, suggesting that parametric statistical models applied to scRNA-seq are transferable to snRNA-seq. Furthermore, we found that the quantification choices in adapting quantification mapping strategies from scRNA-seq to snRNA-seq can play a significant role in downstream analyses and biological interpretation. In particular, reference transcriptomes that do not include intronic regions result in significantly smaller library sizes and incongruous cell type classifications. We also confirmed the presence of a gene length bias in snRNA-seq data, which we show is present in both exonic and intronic reads, and investigate potential causes for the bias.
Collapse
Affiliation(s)
- Albert Kuo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205, USA
| | - Kasper D Hansen
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205, USA
- Department of Genetic Medicine, Johns Hopkins School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA
| | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205, USA
| |
Collapse
|
16
|
De Jonghe J, Opzoomer JW, Vilas-Zornoza A, Crane P, Nilges BS, Vicari M, Lee H, Lara-Astiaso D, Gross T, Morf J, Schneider K, Cudini J, Ramos-Mucci L, Mooijman D, Tiklová K, Salas SM, Langseth CM, Kashikar ND, Roberts CES, Lundeberg J, Nilsson M, Shalek AK, Cribbs AP, Taylor-King JP. A community effort to track commercial single-cell and spatial 'omic technologies and business trends. Nat Biotechnol 2024; 42:1017-1023. [PMID: 39020213 DOI: 10.1038/s41587-024-02305-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Affiliation(s)
| | - James W Opzoomer
- Cell Communication Lab, Department of Oncology, University College London Cancer Institute, London, UK
- Relation Therapeutics, London, UK
| | | | | | | | - Marco Vicari
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Hower Lee
- spatialist AB, Stockholm, Sweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - David Lara-Astiaso
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Hematology, University of Cambridge, Cambridge, UK
| | | | - Jörg Morf
- Skyhawk Therapeutics, Basel, Switzerland
| | | | | | | | | | - Katarína Tiklová
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Sergio Marco Salas
- spatialist AB, Stockholm, Sweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Christoffer Mattsson Langseth
- spatialist AB, Stockholm, Sweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | | | - Charles E S Roberts
- Relation Therapeutics, London, UK
- ARK Investment Management, St. Petersburg, FL, USA
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Alex K Shalek
- Relation Therapeutics, London, UK
- Institute for Medical Engineering and Science, Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Adam P Cribbs
- Caeruleus Genomics, Oxford, UK
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK
- Oxford Centre for Translational Myeloma Research University of Oxford, Oxford, UK
| | | |
Collapse
|
17
|
Bielefeld P, Martirosyan A, Martín-Suárez S, Apresyan A, Meerhoff GF, Pestana F, Poovathingal S, Reijner N, Koning W, Clement RA, Van der Veen I, Toledo EM, Polzer O, Durá I, Hovhannisyan S, Nilges BS, Bogdoll A, Kashikar ND, Lucassen PJ, Belgard TG, Encinas JM, Holt MG, Fitzsimons CP. Traumatic brain injury promotes neurogenesis at the cost of astrogliogenesis in the adult hippocampus of male mice. Nat Commun 2024; 15:5222. [PMID: 38890340 PMCID: PMC11189490 DOI: 10.1038/s41467-024-49299-6] [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: 04/21/2023] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Traumatic brain injury (TBI) can result in long-lasting changes in hippocampal function. The changes induced by TBI on the hippocampus contribute to cognitive deficits. The adult hippocampus harbors neural stem cells (NSCs) that generate neurons (neurogenesis), and astrocytes (astrogliogenesis). While deregulation of hippocampal NSCs and neurogenesis have been observed after TBI, it is not known how TBI may affect hippocampal astrogliogenesis. Using a controlled cortical impact model of TBI in male mice, single cell RNA sequencing and spatial transcriptomics, we assessed how TBI affected hippocampal NSCs and the neuronal and astroglial lineages derived from them. We observe an increase in NSC-derived neuronal cells and a concomitant decrease in NSC-derived astrocytic cells, together with changes in gene expression and cell dysplasia within the dentate gyrus. Here, we show that TBI modifies NSC fate to promote neurogenesis at the cost of astrogliogenesis and identify specific cell populations as possible targets to counteract TBI-induced cellular changes in the adult hippocampus.
Collapse
Affiliation(s)
- P Bielefeld
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - A Martirosyan
- VIB Center for Brain and Disease Research, Leuven, Belgium
- KU Leuven-Department of Neurosciences, Leuven, Belgium
| | - S Martín-Suárez
- Achucarro Basque Center for Neuroscience, Sede Bldg, Campus, UPV/EHU, Barrio Sarriena S/N, Leioa, Spain
| | - A Apresyan
- Armenian Bioinformatics Institute, Yerevan, Armenia
| | - G F Meerhoff
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - F Pestana
- VIB Center for Brain and Disease Research, Leuven, Belgium
- KU Leuven-Department of Neurosciences, Leuven, Belgium
| | - S Poovathingal
- VIB Center for Brain and Disease Research, Leuven, Belgium
- KU Leuven-Department of Neurosciences, Leuven, Belgium
| | - N Reijner
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - W Koning
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - R A Clement
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - I Van der Veen
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - E M Toledo
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - O Polzer
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - I Durá
- Achucarro Basque Center for Neuroscience, Sede Bldg, Campus, UPV/EHU, Barrio Sarriena S/N, Leioa, Spain
| | - S Hovhannisyan
- Department of Mathematics and Mechanics, Yerevan State University, Yerevan, Armenia
| | - B S Nilges
- Resolve Biosciences GmbH, Monheim am Rhein, Germany
- OMAPiX GmbH, Langenfeld (Rheinland), Langenfeld, Germany
| | - A Bogdoll
- Resolve Biosciences GmbH, Monheim am Rhein, Germany
| | - N D Kashikar
- Resolve Biosciences GmbH, Monheim am Rhein, Germany
- OMAPiX GmbH, Langenfeld (Rheinland), Langenfeld, Germany
| | - P J Lucassen
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | | | - J M Encinas
- Achucarro Basque Center for Neuroscience, Sede Bldg, Campus, UPV/EHU, Barrio Sarriena S/N, Leioa, Spain
- Department of Neuroscience, University of the Basque Country (UPV/EHU), Campus, UPV/EHU, Barrio Sarriena S/N, Leioa, Spain
- IKERBASQUE, The Basque Foundation for Science, Plaza Euskadi 5, Bilbao, Spain
| | - M G Holt
- VIB Center for Brain and Disease Research, Leuven, Belgium.
- KU Leuven-Department of Neurosciences, Leuven, Belgium.
- Instituto de Investigaçāo e Inovaçāo em Saúde (i3S), University of Porto, Porto, Portugal.
| | - C P Fitzsimons
- Brain Plasticity Department, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
18
|
Ament SA, Campbell RR, Lobo MK, Receveur JP, Agrawal K, Borjabad A, Byrareddy SN, Chang L, Clarke D, Emani P, Gabuzda D, Gaulton KJ, Giglio M, Giorgi FM, Gok B, Guda C, Hadas E, Herb BR, Hu W, Huttner A, Ishmam MR, Jacobs MM, Kelschenbach J, Kim DW, Lee C, Liu S, Liu X, Madras BK, Mahurkar AA, Mash DC, Mukamel EA, Niu M, O'Connor RM, Pagan CM, Pang APS, Pillai P, Repunte-Canonigo V, Ruzicka WB, Stanley J, Tickle T, Tsai SYA, Wang A, Wills L, Wilson AM, Wright SN, Xu S, Yang J, Zand M, Zhang L, Zhang J, Akbarian S, Buch S, Cheng CS, Corley MJ, Fox HS, Gerstein M, Gummuluru S, Heiman M, Ho YC, Kellis M, Kenny PJ, Kluger Y, Milner TA, Moore DJ, Morgello S, Ndhlovu LC, Rana TM, Sanna PP, Satterlee JS, Sestan N, Spector SA, Spudich S, Tilgner HU, Volsky DJ, White OR, Williams DW, Zeng H. The single-cell opioid responses in the context of HIV (SCORCH) consortium. Mol Psychiatry 2024:10.1038/s41380-024-02620-7. [PMID: 38879719 DOI: 10.1038/s41380-024-02620-7] [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: 11/05/2023] [Revised: 05/12/2024] [Accepted: 05/17/2024] [Indexed: 06/19/2024]
Abstract
Substance use disorders (SUD) and drug addiction are major threats to public health, impacting not only the millions of individuals struggling with SUD, but also surrounding families and communities. One of the seminal challenges in treating and studying addiction in human populations is the high prevalence of co-morbid conditions, including an increased risk of contracting a human immunodeficiency virus (HIV) infection. Of the ~15 million people who inject drugs globally, 17% are persons with HIV. Conversely, HIV is a risk factor for SUD because chronic pain syndromes, often encountered in persons with HIV, can lead to an increased use of opioid pain medications that in turn can increase the risk for opioid addiction. We hypothesize that SUD and HIV exert shared effects on brain cell types, including adaptations related to neuroplasticity, neurodegeneration, and neuroinflammation. Basic research is needed to refine our understanding of these affected cell types and adaptations. Studying the effects of SUD in the context of HIV at the single-cell level represents a compelling strategy to understand the reciprocal interactions among both conditions, made feasible by the availability of large, extensively-phenotyped human brain tissue collections that have been amassed by the Neuro-HIV research community. In addition, sophisticated animal models that have been developed for both conditions provide a means to precisely evaluate specific exposures and stages of disease. We propose that single-cell genomics is a uniquely powerful technology to characterize the effects of SUD and HIV in the brain, integrating data from human cohorts and animal models. We have formed the Single-Cell Opioid Responses in the Context of HIV (SCORCH) consortium to carry out this strategy.
Collapse
Affiliation(s)
- Seth A Ament
- University of Maryland School of Medicine, Baltimore, MD, USA.
| | | | - Mary Kay Lobo
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | | | | | - Linda Chang
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | - Dana Gabuzda
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Michelle Giglio
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | | | - Eran Hadas
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian R Herb
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Wen Hu
- Weill Cornell Medicine, New York, NY, USA
| | | | | | | | | | | | - Cheyu Lee
- University of California Irvine, Irvine, CA, USA
| | - Shuhui Liu
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xiaokun Liu
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Anup A Mahurkar
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | - Meng Niu
- University of Nebraska Medical Center, Omaha, NE, USA
| | | | | | | | - Piya Pillai
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - W Brad Ruzicka
- McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | | | | | | | - Allen Wang
- University of California San Diego, La Jolla, CA, USA
| | - Lauren Wills
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Siwei Xu
- University of California Irvine, Irvine, CA, USA
| | | | - Maryam Zand
- University of California San Diego, La Jolla, CA, USA
| | - Le Zhang
- Yale School of Medicine, New Haven, CT, USA
| | - Jing Zhang
- University of California Irvine, Irvine, CA, USA
| | | | - Shilpa Buch
- University of Nebraska Medical Center, Omaha, NE, USA
| | | | | | - Howard S Fox
- University of Nebraska Medical Center, Omaha, NE, USA
| | | | | | - Myriam Heiman
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ya-Chi Ho
- Yale School of Medicine, New Haven, CT, USA
| | - Manolis Kellis
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paul J Kenny
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - David J Moore
- University of California San Diego, La Jolla, CA, USA
| | - Susan Morgello
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Tariq M Rana
- University of California San Diego, La Jolla, CA, USA
| | | | | | | | | | | | | | - David J Volsky
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Owen R White
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| |
Collapse
|
19
|
Wang HLV, Xiang JF, Yuan C, Veire AM, Gendron TF, Murray ME, Tansey MG, Hu J, Gearing M, Glass JD, Jin P, Corces VG, McEachin ZT. pTDP-43 levels correlate with cell type specific molecular alterations in the prefrontal cortex of C9orf72 ALS/FTD patients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.12.523820. [PMID: 36711601 PMCID: PMC9882184 DOI: 10.1101/2023.01.12.523820] [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: 01/15/2023]
Abstract
Repeat expansions in the C9orf72 gene are the most common genetic cause of amyotrophic lateral sclerosis and familial frontotemporal dementia (ALS/FTD). To identify molecular defects that take place in the dorsolateral frontal cortex of patients with C9orf72 ALS/FTD, we compared healthy controls with C9orf72 ALS/FTD donor samples staged based on the levels of cortical phosphorylated TAR DNA binding protein (pTDP-43), a neuropathological hallmark of disease progression. We identified distinct molecular changes in different cell types that take place during FTD development. Loss of neurosurveillance microglia and activation of the complement cascade take place early, when pTDP-43 aggregates are absent or very low, and become more pronounced in late stages, suggesting an initial involvement of microglia in disease progression. Reduction of layer 2-3 cortical projection neurons with high expression of CUX2/LAMP5 also occurs early, and the reduction becomes more pronounced as pTDP-43 accumulates. Several unique features were observed only in samples with high levels of pTDP-43, including global alteration of chromatin accessibility in oligodendrocytes, microglia, and astrocytes; higher ratios of premature oligodendrocytes; increased levels of the noncoding RNA NEAT1 in astrocytes and neurons, and higher amount of phosphorylated ribosomal protein S6. Our findings reveal previously unknown progressive functional changes in major cell types found in the frontal cortex of C9orf72 ALS/FTD patients that shed light on the mechanisms underlying the pathology of this disease.
Collapse
Affiliation(s)
- Hsiao-Lin V. Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Emory Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322
| | - Jian-Feng Xiang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Chenyang Yuan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Austin M. Veire
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224
| | | | | | - Malú G. Tansey
- Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL 32607
- Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32607
| | - Jian Hu
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Marla Gearing
- Emory Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322
| | - Jonathan D. Glass
- Emory Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Emory Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322
| | - Victor G. Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Emory Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322
| | - Zachary T. McEachin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Emory Center for Neurodegenerative Diseases, Emory University School of Medicine, Atlanta, GA 30322
| |
Collapse
|
20
|
Cai X, Zhang W, Zheng X, Xu Y, Li Y. scEM: A New Ensemble Framework for Predicting Cell Type Composition Based on scRNA-Seq Data. Interdiscip Sci 2024; 16:304-317. [PMID: 38368575 DOI: 10.1007/s12539-023-00601-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/22/2023] [Accepted: 12/24/2023] [Indexed: 02/19/2024]
Abstract
With the advent of single-cell RNA sequencing (scRNA-seq) technology, many scRNA-seq data have become available, providing an unprecedented opportunity to explore cellular composition and heterogeneity. Recently, many computational algorithms for predicting cell type composition have been developed, and these methods are typically evaluated on different datasets and performance metrics using diverse techniques. Consequently, the lack of comprehensive and standardized comparative analysis makes it difficult to gain a clear understanding of the strengths and weaknesses of these methods. To address this gap, we reviewed 20 cutting-edge unsupervised cell type identification methods and evaluated these methods comprehensively using 24 real scRNA-seq datasets of varying scales. In addition, we proposed a new ensemble cell-type identification method, named scEM, which learns the consensus similarity matrix by applying the entropy weight method to the four representative methods are selected. The Louvain algorithm is adopted to obtain the final classification of individual cells based on the consensus matrix. Extensive evaluation and comparison with 11 other similarity-based methods under real scRNA-seq datasets demonstrate that the newly developed ensemble algorithm scEM is effective in predicting cellular type composition.
Collapse
Affiliation(s)
- Xianxian Cai
- School of Sciences, East China Jiaotong University, Nanchang, 330013, China
| | - Wei Zhang
- School of Sciences, East China Jiaotong University, Nanchang, 330013, China.
| | - Xiaoying Zheng
- Operations research and planning department, Naval University of Engineering, Wuhan, 430033, China
| | - Yaxin Xu
- School of Sciences, East China Jiaotong University, Nanchang, 330013, China
| | - Yuanyuan Li
- School of Mathematics and Physics, Wuhan Institute of Technology, Wuhan, China
| |
Collapse
|
21
|
Ji J, Chao H, Chen H, Liao J, Shi W, Ye Y, Wang T, You Y, Liu N, Ji J, Petretto E. Decoding frontotemporal and cell-type-specific vulnerabilities to neuropsychiatric disorders and psychoactive drugs. Open Biol 2024; 14:240063. [PMID: 38864245 DOI: 10.1098/rsob.240063] [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: 03/13/2024] [Accepted: 04/29/2024] [Indexed: 06/13/2024] Open
Abstract
Frontotemporal lobe abnormalities are linked to neuropsychiatric disorders and cognition, but the role of cellular heterogeneity between temporal lobe (TL) and frontal lobe (FL) in the vulnerability to genetic risk factors remains to be elucidated. We integrated single-nucleus transcriptome analysis in 'fresh' human FL and TL with genetic susceptibility, gene dysregulation in neuropsychiatric disease and psychoactive drug response data. We show how intrinsic differences between TL and FL contribute to the vulnerability of specific cell types to both genetic risk factors and psychoactive drugs. Neuronal populations, specifically PVALB neurons, were most highly vulnerable to genetic risk factors for psychiatric disease. These psychiatric disease-associated genes were mostly upregulated in the TL, and dysregulated in the brain of patients with obsessive-compulsive disorder, bipolar disorder and schizophrenia. Among these genes, GRIN2A and SLC12A5, implicated in schizophrenia and bipolar disorder, were significantly upregulated in TL PVALB neurons and in psychiatric disease patients' brain. PVALB neurons from the TL were twofold more vulnerable to psychoactive drugs than to genetic risk factors, showing the influence and specificity of frontotemporal lobe differences on cell vulnerabilities. These studies provide a cell type resolved map of the impact of brain regional differences on cell type vulnerabilities in neuropsychiatric disorders.
Collapse
Affiliation(s)
- Jiatong Ji
- Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University (CPU), Nanjing, Jiangsu 211198, People's Republic of China
| | - Honglu Chao
- Department of Neurosurgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, People's Republic of China
| | - Huimei Chen
- Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University (CPU), Nanjing, Jiangsu 211198, People's Republic of China
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Jun Liao
- High Performance Computing Center, School of Science, China Pharmaceutical University (CPU), Nanjing, Jiangsu 211198, People's Republic of China
| | - Wenqian Shi
- Department of Neurosurgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, People's Republic of China
| | - Yangfan Ye
- Department of Neurosurgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, People's Republic of China
| | - Tian Wang
- Department of Neurosurgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, People's Republic of China
| | - Yongping You
- Department of Neurosurgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, People's Republic of China
| | - Ning Liu
- Department of Neurosurgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, People's Republic of China
| | - Jing Ji
- Department of Neurosurgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, People's Republic of China
- Department of Neurosurgery, The Affiliated Kizilsu Kirghiz Autonomous Prefecture People's Hospital of Nanjing Medical University, Xinjiang, Artux 845350, People's Republic of China
- Gusu School, Nanjing Medical University, Suzhou, Jiangsu 215006, People's Republic of China
| | - Enrico Petretto
- Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University (CPU), Nanjing, Jiangsu 211198, People's Republic of China
- Duke-NUS Medical School, Singapore 169857, Singapore
| |
Collapse
|
22
|
Osetrova M, Tkachev A, Mair W, Guijarro Larraz P, Efimova O, Kurochkin I, Stekolshchikova E, Anikanov N, Foo JC, Cazenave-Gassiot A, Mitina A, Ogurtsova P, Guo S, Potashnikova DM, Gulin AA, Vasin AA, Sarycheva A, Vladimirov G, Fedorova M, Kostyukevich Y, Nikolaev E, Wenk MR, Khrameeva EE, Khaitovich P. Lipidome atlas of the adult human brain. Nat Commun 2024; 15:4455. [PMID: 38796479 PMCID: PMC11127996 DOI: 10.1038/s41467-024-48734-y] [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: 12/15/2022] [Accepted: 05/07/2024] [Indexed: 05/28/2024] Open
Abstract
Lipids are the most abundant but poorly explored components of the human brain. Here, we present a lipidome map of the human brain comprising 75 regions, including 52 neocortical ones. The lipidome composition varies greatly among the brain regions, affecting 93% of the 419 analyzed lipids. These differences reflect the brain's structural characteristics, such as myelin content (345 lipids) and cell type composition (353 lipids), but also functional traits: functional connectivity (76 lipids) and information processing hierarchy (60 lipids). Combining lipid composition and mRNA expression data further enhances functional connectivity association. Biochemically, lipids linked with structural and functional brain features display distinct lipid class distribution, unsaturation extent, and prevalence of omega-3 and omega-6 fatty acid residues. We verified our conclusions by parallel analysis of three adult macaque brains, targeted analysis of 216 lipids, mass spectrometry imaging, and lipidome assessment of sorted murine neurons.
Collapse
Affiliation(s)
- Maria Osetrova
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Anna Tkachev
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Waltraud Mair
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Olga Efimova
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Ilia Kurochkin
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | | | - Juat Chin Foo
- Singapore Lipidomics Incubator, Life Sciences Institute and Precision Medicine Translational Research Program, Department of Biochemistry, Yong Loo Lin School of Medicine; National University of Singapore, Singapore, Singapore
| | - Amaury Cazenave-Gassiot
- Singapore Lipidomics Incubator, Life Sciences Institute and Precision Medicine Translational Research Program, Department of Biochemistry, Yong Loo Lin School of Medicine; National University of Singapore, Singapore, Singapore
| | | | | | - Song Guo
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Daria M Potashnikova
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander A Gulin
- N. N. Semenov Federal Research Center for Chemical Physics Russian Academy of Sciences, Moscow, Russia
| | - Alexander A Vasin
- N. N. Semenov Federal Research Center for Chemical Physics Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | | | - Gleb Vladimirov
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | | | - Evgeny Nikolaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Markus R Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute and Precision Medicine Translational Research Program, Department of Biochemistry, Yong Loo Lin School of Medicine; National University of Singapore, Singapore, Singapore.
| | | | | |
Collapse
|
23
|
Kumari P, Kaur M, Dindhoria K, Ashford B, Amarasinghe SL, Thind AS. Advances in long-read single-cell transcriptomics. Hum Genet 2024:10.1007/s00439-024-02678-x. [PMID: 38787419 DOI: 10.1007/s00439-024-02678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/07/2024] [Indexed: 05/25/2024]
Abstract
Long-read single-cell transcriptomics (scRNA-Seq) is revolutionizing the way we profile heterogeneity in disease. Traditional short-read scRNA-Seq methods are limited in their ability to provide complete transcript coverage, resolve isoforms, and identify novel transcripts. The scRNA-Seq protocols developed for long-read sequencing platforms overcome these limitations by enabling the characterization of full-length transcripts. Long-read scRNA-Seq techniques initially suffered from comparatively poor accuracy compared to short read scRNA-Seq. However, with improvements in accuracy, accessibility, and cost efficiency, long-reads are gaining popularity in the field of scRNA-Seq. This review details the advances in long-read scRNA-Seq, with an emphasis on library preparation protocols and downstream bioinformatics analysis tools.
Collapse
Affiliation(s)
- Pallawi Kumari
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Manmeet Kaur
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Kiran Dindhoria
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Bruce Ashford
- Illawarra Shoalhaven Local Health District (ISLHD), NSW Health, Wollongong, NSW, Australia
| | - Shanika L Amarasinghe
- Monash Biomedical Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Walter and Eliza Hall Institute of Medical Research, 1G, Royal Parade, Parkville, VIC, 3025, Australia
| | - Amarinder Singh Thind
- Illawarra Shoalhaven Local Health District (ISLHD), NSW Health, Wollongong, NSW, Australia.
- The School of Chemistry and Molecular Bioscience (SCMB), University of Wollongong, Loftus St, Wollongong, NSW, 2500, Australia.
| |
Collapse
|
24
|
Tang C, Sun Q, Zeng X, Yang X, Liu F, Zhao J, Shen Y, Liu B, Wen J, Li Y. Cell-type specific inference from bulk RNA-sequencing data by integrating single cell reference profiles via EPIC-unmix. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595514. [PMID: 38826297 PMCID: PMC11142188 DOI: 10.1101/2024.05.23.595514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Cell type specific (CTS) analysis is essential to reveal biological insights obscured in bulk tissue data. However, single-cell (sc) or single-nuclei (sn) resolution data are still cost-prohibitive for large-scale samples. Thus, computational methods to perform deconvolution from bulk tissue data are highly valuable. We here present EPIC-unmix, a novel two-step empirical Bayesian method integrating reference sc/sn RNA-seq data and bulk RNA-seq data from target samples to enhance the accuracy of CTS inference. We demonstrate through comprehensive simulations across three tissues that EPIC-unmix achieved 4.6% - 109.8% higher accuracy compared to alternative methods. By applying EPIC-unmix to human bulk brain RNA-seq data from the ROSMAP and MSBB cohorts, we identified multiple genes differentially expressed between Alzheimer's disease (AD) cases versus controls in a CTS manner, including 57.4% novel genes not identified using similar sample size sc/snRNA-seq data, indicating the power of our in-silico approach. Among the 6-69% overlapping, 83%-100% are in consistent direction with those from sc/snRNA-seq data, supporting the reliability of our findings. EPIC-unmix inferred CTS expression profiles similarly empowers CTS eQTL analysis. Among the novel eQTLs, we highlight a microglia eQTL for AD risk gene AP3B2, obscured in bulk and missed by sc/snRNA-seq based eQTL analysis. The variant resides in a microglia-specific cCRE, forming chromatin loop with AP3B2 promoter region in microglia. Taken together, we believe EPIC-unmix will be a valuable tool to enable more powerful CTS analysis.
Collapse
Affiliation(s)
- Chenwei Tang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xinyue Zeng
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xiaoyu Yang
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Fei Liu
- Department of Pharmacy and Pharmaceutical Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Jinying Zhao
- Department of Epidemiology, College of Public Health & Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA; Center for Genetic Epidemiology and Bioinformatics, University of Florida, Gainesville, FL, USA
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Bixiang Liu
- Department of Pharmacy and Pharmaceutical Sciences, Faculty of Science, National University of Singapore, Singapore
- Department of Biomedical Informatics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jia Wen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| |
Collapse
|
25
|
Wamsley B, Bicks L, Cheng Y, Kawaguchi R, Quintero D, Margolis M, Grundman J, Liu J, Xiao S, Hawken N, Mazariegos S, Geschwind DH. Molecular cascades and cell type-specific signatures in ASD revealed by single-cell genomics. Science 2024; 384:eadh2602. [PMID: 38781372 DOI: 10.1126/science.adh2602] [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: 02/21/2023] [Accepted: 02/28/2024] [Indexed: 05/25/2024]
Abstract
Genomic profiling in postmortem brain from autistic individuals has consistently revealed convergent molecular changes. What drives these changes and how they relate to genetic susceptibility in this complex condition are not well understood. We performed deep single-nucleus RNA sequencing (snRNA-seq) to examine cell composition and transcriptomics, identifying dysregulation of cell type-specific gene regulatory networks (GRNs) in autism spectrum disorder (ASD), which we corroborated using single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) and spatial transcriptomics. Transcriptomic changes were primarily cell type specific, involving multiple cell types, most prominently interhemispheric and callosal-projecting neurons, interneurons within superficial laminae, and distinct glial reactive states involving oligodendrocytes, microglia, and astrocytes. Autism-associated GRN drivers and their targets were enriched in rare and common genetic risk variants, connecting autism genetic susceptibility and cellular and circuit alterations in the human brain.
Collapse
Affiliation(s)
- Brie Wamsley
- Program in Neurobehavioral Genetics and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lucy Bicks
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yuyan Cheng
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Riki Kawaguchi
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Diana Quintero
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael Margolis
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jennifer Grundman
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jianyin Liu
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shaohua Xiao
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Natalie Hawken
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Samantha Mazariegos
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel H Geschwind
- Program in Neurobehavioral Genetics and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
26
|
Collier L, Seah C, Hicks EM, Holtzheimer PE, Krystal JH, Girgenti MJ, Huckins LM, Johnston KJA. The impact of chronic pain on brain gene expression. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.20.24307630. [PMID: 38826319 PMCID: PMC11142271 DOI: 10.1101/2024.05.20.24307630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Background Chronic pain affects one fifth of American adults, contributing significant public health burden. Chronic pain mechanisms can be further understood through investigating brain gene expression. Methods We tested differentially expressed genes (DEGs) in chronic pain, migraine, lifetime fentanyl and oxymorphone use, and with chronic pain genetic risk in four brain regions (dACC, DLPFC, MeA, BLA) and imputed cell type expression data from 304 postmortem donors. We compared findings across traits and with independent transcriptomics resources, and performed gene-set enrichment. Results We identified two chronic pain DEGs: B4GALT and VEGFB in bulk dACC. We found over 2000 (primarily BLA microglia) chronic pain cell type DEGs. Findings were enriched for mouse microglia pain genes, and for hypoxia and immune response. Cross-trait DEG overlap was minimal. Conclusions Chronic pain-associated gene expression is heterogeneous across cell type, largely distinct from that in pain-related traits, and shows BLA microglia are a key cell type.
Collapse
Affiliation(s)
- Lily Collier
- Department of Biological Sciences, Columbia University, New York City, NY
- Department of Psychiatry, Division of Molecular Psychiatry, Yale University, New Haven, CT
| | - Carina Seah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Emily M Hicks
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Paul E Holtzheimer
- National Center for PTSD, U.S. Department of Veterans Affairs
- Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - John H Krystal
- Department of Psychiatry, Division of Molecular Psychiatry, Yale University, New Haven, CT
- Clinical Neuroscience Division, National Center for PTSD, VA Connecticut Healthcare System, West Haven, CT
| | - Matthew J Girgenti
- Department of Psychiatry, Division of Molecular Psychiatry, Yale University, New Haven, CT
- Clinical Neuroscience Division, National Center for PTSD, VA Connecticut Healthcare System, West Haven, CT
| | - Laura M Huckins
- Department of Psychiatry, Division of Molecular Psychiatry, Yale University, New Haven, CT
| | - Keira J A Johnston
- Department of Psychiatry, Division of Molecular Psychiatry, Yale University, New Haven, CT
| |
Collapse
|
27
|
Huang S, Shi W, Li S, Fan Q, Yang C, Cao J, Wu L. Advanced sequencing-based high-throughput and long-read single-cell transcriptome analysis. LAB ON A CHIP 2024; 24:2601-2621. [PMID: 38669201 DOI: 10.1039/d4lc00105b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Cells are the fundamental building blocks of living systems, exhibiting significant heterogeneity. The transcriptome connects the cellular genotype and phenotype, and profiling single-cell transcriptomes is critical for uncovering distinct cell types, states, and the interplay between cells in development, health, and disease. Nevertheless, single-cell transcriptome analysis faces daunting challenges due to the low abundance and diverse nature of RNAs in individual cells, as well as their heterogeneous expression. The advent and continuous advancements of next-generation sequencing (NGS) and third-generation sequencing (TGS) technologies have solved these problems and facilitated the high-throughput, sensitive, full-length, and rapid profiling of single-cell RNAs. In this review, we provide a broad introduction to current methodologies for single-cell transcriptome sequencing. First, state-of-the-art advancements in high-throughput and full-length single-cell RNA sequencing (scRNA-seq) platforms using NGS are reviewed. Next, TGS-based long-read scRNA-seq methods are summarized. Finally, a brief conclusion and perspectives for comprehensive single-cell transcriptome analysis are discussed.
Collapse
Affiliation(s)
- Shanqing Huang
- Discipline of Intelligent Instrument and Equipment, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Weixiong Shi
- Discipline of Intelligent Instrument and Equipment, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shiyu Li
- Discipline of Intelligent Instrument and Equipment, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Qian Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Chaoyong Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
- Discipline of Intelligent Instrument and Equipment, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jiao Cao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Lingling Wu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| |
Collapse
|
28
|
Lee CY, Riffle D, Xiong Y, Momtaz N, Lei Y, Pariser JM, Sikdar D, Hwang A, Duan Z, Zhang J. Characterizing dysregulations via cell-cell communications in Alzheimer's brains using single-cell transcriptomes. BMC Neurosci 2024; 25:24. [PMID: 38741048 PMCID: PMC11089696 DOI: 10.1186/s12868-024-00867-y] [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: 12/15/2023] [Accepted: 04/01/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a devastating neurodegenerative disorder affecting 44 million people worldwide, leading to cognitive decline, memory loss, and significant impairment in daily functioning. The recent single-cell sequencing technology has revolutionized genetic and genomic resolution by enabling scientists to explore the diversity of gene expression patterns at the finest resolution. Most existing studies have solely focused on molecular perturbations within each cell, but cells live in microenvironments rather than in isolated entities. Here, we leveraged the large-scale and publicly available single-nucleus RNA sequencing in the human prefrontal cortex to investigate cell-to-cell communication in healthy brains and their perturbations in AD. We uniformly processed the snRNA-seq with strict QCs and labeled canonical cell types consistent with the definitions from the BRAIN Initiative Cell Census Network. From ligand and receptor gene expression, we built a high-confidence cell-to-cell communication network to investigate signaling differences between AD and healthy brains. RESULTS Specifically, we first performed broad communication pattern analyses to highlight that biologically related cell types in normal brains rely on largely overlapping signaling networks and that the AD brain exhibits the irregular inter-mixing of cell types and signaling pathways. Secondly, we performed a more focused cell-type-centric analysis and found that excitatory neurons in AD have significantly increased their communications to inhibitory neurons, while inhibitory neurons and other non-neuronal cells globally decreased theirs to all cells. Then, we delved deeper with a signaling-centric view, showing that canonical signaling pathways CSF, TGFβ, and CX3C are significantly dysregulated in their signaling to the cell type microglia/PVM and from endothelial to neuronal cells for the WNT pathway. Finally, after extracting 23 known AD risk genes, our intracellular communication analysis revealed a strong connection of extracellular ligand genes APP, APOE, and PSEN1 to intracellular AD risk genes TREM2, ABCA1, and APP in the communication from astrocytes and microglia to neurons. CONCLUSIONS In summary, with the novel advances in single-cell sequencing technologies, we show that cellular signaling is regulated in a cell-type-specific manner and that improper regulation of extracellular signaling genes is linked to intracellular risk genes, giving the mechanistic intra- and inter-cellular picture of AD.
Collapse
Affiliation(s)
- Che Yu Lee
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Dylan Riffle
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Yifeng Xiong
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Nadia Momtaz
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Yutong Lei
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Joseph M Pariser
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Diptanshu Sikdar
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Ahyeon Hwang
- Department of Computer Science, University of California, Irvine, CA, USA
- Mathematical, Computational and Systems Biology, University of California, Irvine, CA, USA
| | - Ziheng Duan
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, CA, USA.
| |
Collapse
|
29
|
Vornholt E, Liharska LE, Cheng E, Hashemi A, Park YJ, Ziafat K, Wilkins L, Silk H, Linares LM, Thompson RC, Sullivan B, Moya E, Nadkarni GN, Sebra R, Schadt EE, Kopell BH, Charney AW, Beckmann ND. Characterizing cell type specific transcriptional differences between the living and postmortem human brain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.01.24306590. [PMID: 38746297 PMCID: PMC11092720 DOI: 10.1101/2024.05.01.24306590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Single-nucleus RNA sequencing (snRNA-seq) is often used to define gene expression patterns characteristic of brain cell types as well as to identify cell type specific gene expression signatures of neurological and mental illnesses in postmortem human brains. As methods to obtain brain tissue from living individuals emerge, it is essential to characterize gene expression differences associated with tissue originating from either living or postmortem subjects using snRNA-seq, and to assess whether and how such differences may impact snRNA-seq studies of brain tissue. To address this, human prefrontal cortex single nuclei gene expression was generated and compared between 31 samples from living individuals and 21 postmortem samples. The same cell types were consistently identified in living and postmortem nuclei, though for each cell type, a large proportion of genes were differentially expressed between samples from postmortem and living individuals. Notably, estimation of cell type proportions by cell type deconvolution of pseudo-bulk data was found to be more accurate in samples from living individuals. To allow for future integration of living and postmortem brain gene expression, a model was developed that quantifies from gene expression data the probability a human brain tissue sample was obtained postmortem. These probabilities are established as a means to statistically account for the gene expression differences between samples from living and postmortem individuals. Together, the results presented here provide a deep characterization of both differences between snRNA-seq derived from samples from living and postmortem individuals, as well as qualify and account for their effect on common analyses performed on this type of data.
Collapse
|
30
|
Kampmann M. Molecular and cellular mechanisms of selective vulnerability in neurodegenerative diseases. Nat Rev Neurosci 2024; 25:351-371. [PMID: 38575768 DOI: 10.1038/s41583-024-00806-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2024] [Indexed: 04/06/2024]
Abstract
The selective vulnerability of specific neuronal subtypes is a hallmark of neurodegenerative diseases. In this Review, I summarize our current understanding of the brain regions and cell types that are selectively vulnerable in different neurodegenerative diseases and describe the proposed underlying cell-autonomous and non-cell-autonomous mechanisms. I highlight how recent methodological innovations - including single-cell transcriptomics, CRISPR-based screens and human cell-based models of disease - are enabling new breakthroughs in our understanding of selective vulnerability. An understanding of the molecular mechanisms that determine selective vulnerability and resilience would shed light on the key processes that drive neurodegeneration and point to potential therapeutic strategies to protect vulnerable cell populations.
Collapse
Affiliation(s)
- Martin Kampmann
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
31
|
Xie G, Toledo MP, Hu X, Yong HJ, Sanchez PS, Liu C, Naji A, Irianto J, Wang YJ. NKX2-2 based nuclei sorting on frozen human archival pancreas enables the enrichment of islet endocrine populations for single-nucleus RNA sequencing. BMC Genomics 2024; 25:427. [PMID: 38689254 PMCID: PMC11059690 DOI: 10.1186/s12864-024-10335-w] [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: 01/03/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Current approaches to profile the single-cell transcriptomics of human pancreatic endocrine cells almost exclusively rely on freshly isolated islets. However, human islets are limited in availability. Furthermore, the extensive processing steps during islet isolation and subsequent single cell dissolution might alter gene expressions. In this work, we report the development of a single-nucleus RNA sequencing (snRNA-seq) approach with targeted islet cell enrichment for endocrine-population focused transcriptomic profiling using frozen archival pancreatic tissues without islet isolation. RESULTS We cross-compared five nuclei isolation protocols and selected the citric acid method as the best strategy to isolate nuclei with high RNA integrity and low cytoplasmic contamination from frozen archival human pancreata. We innovated fluorescence-activated nuclei sorting based on the positive signal of NKX2-2 antibody to enrich nuclei of the endocrine population from the entire nuclei pool of the pancreas. Our sample preparation procedure generated high-quality single-nucleus gene-expression libraries while preserving the endocrine population diversity. In comparison with single-cell RNA sequencing (scRNA-seq) library generated with live cells from freshly isolated human islets, the snRNA-seq library displayed comparable endocrine cellular composition and cell type signature gene expression. However, between these two types of libraries, differential enrichments of transcripts belonging to different functional classes could be observed. CONCLUSIONS Our work fills a technological gap and helps to unleash frozen archival pancreatic tissues for molecular profiling targeting the endocrine population. This study opens doors to retrospective mappings of endocrine cell dynamics in pancreatic tissues of complex histopathology. We expect that our protocol is applicable to enrich nuclei for transcriptomics studies from various populations in different types of frozen archival tissues.
Collapse
Affiliation(s)
- Gengqiang Xie
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Maria Pilar Toledo
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Xue Hu
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Hyo Jeong Yong
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Pamela Sandoval Sanchez
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Chengyang Liu
- Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Ali Naji
- Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Jerome Irianto
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Yue J Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA.
| |
Collapse
|
32
|
Flønes IH, Toker L, Sandnes DA, Castelli M, Mostafavi S, Lura N, Shadad O, Fernandez-Vizarra E, Painous C, Pérez-Soriano A, Compta Y, Molina-Porcel L, Alves G, Tysnes OB, Dölle C, Nido GS, Tzoulis C. Mitochondrial complex I deficiency stratifies idiopathic Parkinson's disease. Nat Commun 2024; 15:3631. [PMID: 38684731 PMCID: PMC11059185 DOI: 10.1038/s41467-024-47867-4] [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: 08/02/2022] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Idiopathic Parkinson's disease (iPD) is believed to have a heterogeneous pathophysiology, but molecular disease subtypes have not been identified. Here, we show that iPD can be stratified according to the severity of neuronal respiratory complex I (CI) deficiency, and identify two emerging disease subtypes with distinct molecular and clinical profiles. The CI deficient (CI-PD) subtype accounts for approximately a fourth of all cases, and is characterized by anatomically widespread neuronal CI deficiency, a distinct cell type-specific gene expression profile, increased load of neuronal mtDNA deletions, and a predilection for non-tremor dominant motor phenotypes. In contrast, the non-CI deficient (nCI-PD) subtype exhibits no evidence of mitochondrial impairment outside the dopaminergic substantia nigra and has a predilection for a tremor dominant phenotype. These findings constitute a step towards resolving the biological heterogeneity of iPD with implications for both mechanistic understanding and treatment strategies.
Collapse
Affiliation(s)
- Irene H Flønes
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5021, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway
- K.G. Jebsen Center for Translational Research in Parkinson's disease, University of Bergen, Pb 7804, 5020, Bergen, Norway
| | - Lilah Toker
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5021, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway
- K.G. Jebsen Center for Translational Research in Parkinson's disease, University of Bergen, Pb 7804, 5020, Bergen, Norway
| | - Dagny Ann Sandnes
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5021, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway
| | - Martina Castelli
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5021, Bergen, Norway
| | - Sepideh Mostafavi
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5021, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway
| | - Njål Lura
- Mohn Medical Imaging and Visualization Centre, Department of Radiology, Haukeland University Hospital, Bergen, Norway
- Section for Radiology, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Omnia Shadad
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5021, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway
| | - Erika Fernandez-Vizarra
- MRC-Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
- Veneto Institute of Molecular Medicine, 35131, Padova, Italy
| | - Cèlia Painous
- Parkinson's disease & Movement Disorders Unit, Neurology Service, Hospital Clínic I Universitari de Barcelona; IDIBAPS, CIBERNED (CB06/05/0018-ISCIII), ERN-RND, Institut Clínic de Neurociències (Maria de Maeztu excellence centre), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Alexandra Pérez-Soriano
- Parkinson's disease & Movement Disorders Unit, Neurology Service, Hospital Clínic I Universitari de Barcelona; IDIBAPS, CIBERNED (CB06/05/0018-ISCIII), ERN-RND, Institut Clínic de Neurociències (Maria de Maeztu excellence centre), Universitat de Barcelona, Barcelona, Catalonia, Spain
- UParkinson - Sinapsi Neurología, Centre Mèdic Teknon Grup Hospitalari Quirón Salud, Barcelona, Spain
| | - Yaroslau Compta
- Parkinson's disease & Movement Disorders Unit, Neurology Service, Hospital Clínic I Universitari de Barcelona; IDIBAPS, CIBERNED (CB06/05/0018-ISCIII), ERN-RND, Institut Clínic de Neurociències (Maria de Maeztu excellence centre), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Laura Molina-Porcel
- Alzheimer's disease and other cognitive disorders unit. Neurology Service, Hospital Clínic, Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Neurological Tissue Bank, Biobanc-Hospital Clínic-IDIBAPS, Barcelona, Spain
| | - Guido Alves
- The Norwegian Centre for Movement Disorders and Department of Neurology, Stavanger University Hospital, Pb 8100, 4068, Stavanger, Norway
- Department of Mathematics and Natural Sciences, University of Stavanger, 4062, Stavanger, Norway
| | - Ole-Bjørn Tysnes
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5021, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway
| | - Christian Dölle
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5021, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway
- K.G. Jebsen Center for Translational Research in Parkinson's disease, University of Bergen, Pb 7804, 5020, Bergen, Norway
| | - Gonzalo S Nido
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5021, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway
- K.G. Jebsen Center for Translational Research in Parkinson's disease, University of Bergen, Pb 7804, 5020, Bergen, Norway
| | - Charalampos Tzoulis
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5021, Bergen, Norway.
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway.
- K.G. Jebsen Center for Translational Research in Parkinson's disease, University of Bergen, Pb 7804, 5020, Bergen, Norway.
| |
Collapse
|
33
|
Zhu B, Ainsworth RI, Wang Z, Liu Z, Sierra S, Deng C, Callado LF, Meana JJ, Wang W, Lu C, González-Maeso J. Antipsychotic-induced epigenomic reorganization in frontal cortex of individuals with schizophrenia. eLife 2024; 12:RP92393. [PMID: 38648100 PMCID: PMC11034945 DOI: 10.7554/elife.92393] [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] [Indexed: 04/25/2024] Open
Abstract
Genome-wide association studies have revealed >270 loci associated with schizophrenia risk, yet these genetic factors do not seem to be sufficient to fully explain the molecular determinants behind this psychiatric condition. Epigenetic marks such as post-translational histone modifications remain largely plastic during development and adulthood, allowing a dynamic impact of environmental factors, including antipsychotic medications, on access to genes and regulatory elements. However, few studies so far have profiled cell-specific genome-wide histone modifications in postmortem brain samples from schizophrenia subjects, or the effect of antipsychotic treatment on such epigenetic marks. Here, we conducted ChIP-seq analyses focusing on histone marks indicative of active enhancers (H3K27ac) and active promoters (H3K4me3), alongside RNA-seq, using frontal cortex samples from antipsychotic-free (AF) and antipsychotic-treated (AT) individuals with schizophrenia, as well as individually matched controls (n=58). Schizophrenia subjects exhibited thousands of neuronal and non-neuronal epigenetic differences at regions that included several susceptibility genetic loci, such as NRG1, DISC1, and DRD3. By analyzing the AF and AT cohorts separately, we identified schizophrenia-associated alterations in specific transcription factors, their regulatees, and epigenomic and transcriptomic features that were reversed by antipsychotic treatment; as well as those that represented a consequence of antipsychotic medication rather than a hallmark of schizophrenia in postmortem human brain samples. Notably, we also found that the effect of age on epigenomic landscapes was more pronounced in frontal cortex of AT-schizophrenics, as compared to AF-schizophrenics and controls. Together, these data provide important evidence of epigenetic alterations in the frontal cortex of individuals with schizophrenia, and remark for the first time on the impact of age and antipsychotic treatment on chromatin organization.
Collapse
Affiliation(s)
- Bohan Zhu
- Department of Chemical Engineering, Virginia TechBlacksburgUnited States
| | - Richard I Ainsworth
- Department of Chemistry and Biochemistry, University of California, San DiegoLa JollaUnited States
| | - Zengmiao Wang
- Department of Chemistry and Biochemistry, University of California, San DiegoLa JollaUnited States
| | - Zhengzhi Liu
- Department of Biomedical Engineering and Mechanics, Virginia TechBlacksburgUnited States
| | - Salvador Sierra
- Department of Physiology and Biophysics, Virginia Commonwealth University School of MedicineRichmondUnited States
| | - Chengyu Deng
- Department of Chemical Engineering, Virginia TechBlacksburgUnited States
| | - Luis F Callado
- Department of Pharmacology, University of the Basque Country UPV/EHU, CIBERSAM, Biocruces Health Research InstituteBizkaiaSpain
| | - J Javier Meana
- Department of Pharmacology, University of the Basque Country UPV/EHU, CIBERSAM, Biocruces Health Research InstituteBizkaiaSpain
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San DiegoLa JollaUnited States
- Department of Cellular and Molecular Medicine, University of California, San DiegoLa JollaUnited States
| | - Chang Lu
- Department of Chemical Engineering, Virginia TechBlacksburgUnited States
| | - Javier González-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University School of MedicineRichmondUnited States
| |
Collapse
|
34
|
Mitic N, Neuschulz A, Spanjaard B, Schneider J, Fresmann N, Novoselc KT, Strunk T, Münster L, Olivares-Chauvet P, Ninkovic J, Junker JP. Dissecting the spatiotemporal diversity of adult neural stem cells. Mol Syst Biol 2024; 20:321-337. [PMID: 38365956 PMCID: PMC10987636 DOI: 10.1038/s44320-024-00022-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: 05/04/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
Adult stem cells are important for tissue turnover and regeneration. However, in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here, we dissected the diversity of neural stem cells in the adult zebrafish brain, an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single-cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze the regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells, with some subtypes being restricted to a single brain region, while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation, with different states being involved in proliferative and non-proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for the functional manipulation of neural stem cell subtypes.
Collapse
Affiliation(s)
- Nina Mitic
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Anika Neuschulz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Humboldt Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Bastiaan Spanjaard
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Julia Schneider
- Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Stem Cell Research, Munich, Germany
- Biomedical Center Munich (BMC), Department of Cell Biology and Anatomy, Medical Faculty, LMU, Munich, Germany
- Graduate School of Systemic Neurosciences, LMU, Munich, Germany
| | - Nora Fresmann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Klara Tereza Novoselc
- Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Stem Cell Research, Munich, Germany
- Biomedical Center Munich (BMC), Department of Cell Biology and Anatomy, Medical Faculty, LMU, Munich, Germany
- Graduate School of Systemic Neurosciences, LMU, Munich, Germany
| | - Taraneh Strunk
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Lisa Münster
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Pedro Olivares-Chauvet
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Jovica Ninkovic
- Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Stem Cell Research, Munich, Germany
- Biomedical Center Munich (BMC), Department of Cell Biology and Anatomy, Medical Faculty, LMU, Munich, Germany
| | - Jan Philipp Junker
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Berlin, Germany.
| |
Collapse
|
35
|
Petersen M, Hoffstaedter F, Nägele FL, Mayer C, Schell M, Rimmele DL, Zyriax BC, Zeller T, Kühn S, Gallinat J, Fiehler J, Twerenbold R, Omidvarnia A, Patil KR, Eickhoff SB, Thomalla G, Cheng B. A latent clinical-anatomical dimension relating metabolic syndrome to brain structure and cognition. eLife 2024; 12:RP93246. [PMID: 38512127 PMCID: PMC10957178 DOI: 10.7554/elife.93246] [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] [Indexed: 03/22/2024] Open
Abstract
The link between metabolic syndrome (MetS) and neurodegenerative as well as cerebrovascular conditions holds substantial implications for brain health in at-risk populations. This study elucidates the complex relationship between MetS and brain health by conducting a comprehensive examination of cardiometabolic risk factors, brain morphology, and cognitive function in 40,087 individuals. Multivariate, data-driven statistics identified a latent dimension linking more severe MetS to widespread brain morphological abnormalities, accounting for up to 71% of shared variance in the data. This dimension was replicable across sub-samples. In a mediation analysis, we could demonstrate that MetS-related brain morphological abnormalities mediated the link between MetS severity and cognitive performance in multiple domains. Employing imaging transcriptomics and connectomics, our results also suggest that MetS-related morphological abnormalities are linked to the regional cellular composition and macroscopic brain network organization. By leveraging extensive, multi-domain data combined with a dimensional stratification approach, our analysis provides profound insights into the association of MetS and brain health. These findings can inform effective therapeutic and risk mitigation strategies aimed at maintaining brain integrity.
Collapse
Affiliation(s)
- Marvin Petersen
- Department of Neurology, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Felix Hoffstaedter
- Institute for Systems Neuroscience, Medical Faculty, Heinrich-Heine University DüsseldorfDüsseldorfGermany
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM-7), Research Center JülichJülichGermany
| | - Felix L Nägele
- Department of Neurology, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Carola Mayer
- Department of Neurology, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Maximilian Schell
- Department of Neurology, University Medical Center Hamburg-EppendorfHamburgGermany
| | - D Leander Rimmele
- Department of Neurology, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Birgit-Christiane Zyriax
- Midwifery Science-Health Services Research and Prevention, Institute for Health Services Research in Dermatology and Nursing (IVDP), University Medical Center Hamburg-EppendorfHamburgGermany
| | - Tanja Zeller
- Department of Cardiology, University Heart and Vascular CenterHamburgGermany
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/LuebeckHamburgGermany
- University Center of Cardiovascular Science, University Heart and Vascular CenterHamburgGermany
| | - Simone Kühn
- Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Jürgen Gallinat
- Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Jens Fiehler
- Department of Diagnostic and Interventional Neuroradiology, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Raphael Twerenbold
- Department of Cardiology, University Heart and Vascular CenterHamburgGermany
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/LuebeckHamburgGermany
- University Center of Cardiovascular Science, University Heart and Vascular CenterHamburgGermany
- Epidemiological Study Center, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Amir Omidvarnia
- Institute for Systems Neuroscience, Medical Faculty, Heinrich-Heine University DüsseldorfDüsseldorfGermany
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM-7), Research Center JülichJülichGermany
| | - Kaustubh R Patil
- Institute for Systems Neuroscience, Medical Faculty, Heinrich-Heine University DüsseldorfDüsseldorfGermany
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM-7), Research Center JülichJülichGermany
| | - Simon B Eickhoff
- Institute for Systems Neuroscience, Medical Faculty, Heinrich-Heine University DüsseldorfDüsseldorfGermany
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM-7), Research Center JülichJülichGermany
| | - Goetz Thomalla
- Department of Neurology, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Bastian Cheng
- Department of Neurology, University Medical Center Hamburg-EppendorfHamburgGermany
| |
Collapse
|
36
|
Lin S, Feng D, Han X, Li L, Lin Y, Gao H. Microfluidic platform for omics analysis on single cells with diverse morphology and size: A review. Anal Chim Acta 2024; 1294:342217. [PMID: 38336406 DOI: 10.1016/j.aca.2024.342217] [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: 08/29/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Microfluidic techniques have emerged as powerful tools in single-cell research, facilitating the exploration of omics information from individual cells. Cell morphology is crucial for gene expression and physiological processes. However, there is currently a lack of integrated analysis of morphology and single-cell omics information. A critical challenge remains: what platform technologies are the best option to decode omics data of cells that are complex in morphology and size? RESULTS This review highlights achievements in microfluidic-based single-cell omics and isolation of cells based on morphology, along with other cell sorting methods based on physical characteristics. Various microfluidic platforms for single-cell isolation are systematically presented, showcasing their diversity and adaptability. The discussion focuses on microfluidic devices tailored to the distinct single-cell isolation requirements in plants and animals, emphasizing the significance of considering cell morphology and cell size in optimizing single-cell omics strategies. Simultaneously, it explores the application of microfluidic single-cell sorting technologies to single-cell sequencing, aiming to effectively integrate information about cell shape and size. SIGNIFICANCE AND NOVELTY The novelty lies in presenting a comprehensive overview of recent accomplishments in microfluidic-based single-cell omics, emphasizing the integration of different microfluidic platforms and their implications for cell morphology-based isolation. By underscoring the pivotal role of the specialized morphology of different cells in single-cell research, this review provides robust support for delving deeper into the exploration of single-cell omics data.
Collapse
Affiliation(s)
- Shujin Lin
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China; Central Laboratory at the Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, China
| | - Dan Feng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China.
| | - Ling Li
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China; The First Clinical Medical College of Fujian Medical University, Fuzhou, 350004, China; Hepatopancreatobiliary Surgery Department, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350004, China.
| | - Yao Lin
- Central Laboratory at the Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, China; Collaborative Innovation Center for Rehabilitation Technology, Fujian University of Traditional Chinese Medicine, China.
| | - Haibing Gao
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, China.
| |
Collapse
|
37
|
Wagstyl K, Adler S, Seidlitz J, Vandekar S, Mallard TT, Dear R, DeCasien AR, Satterthwaite TD, Liu S, Vértes PE, Shinohara RT, Alexander-Bloch A, Geschwind DH, Raznahan A. Transcriptional cartography integrates multiscale biology of the human cortex. eLife 2024; 12:RP86933. [PMID: 38324465 PMCID: PMC10945526 DOI: 10.7554/elife.86933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024] Open
Abstract
The cerebral cortex underlies many of our unique strengths and vulnerabilities, but efforts to understand human cortical organization are challenged by reliance on incompatible measurement methods at different spatial scales. Macroscale features such as cortical folding and functional activation are accessed through spatially dense neuroimaging maps, whereas microscale cellular and molecular features are typically measured with sparse postmortem sampling. Here, we integrate these distinct windows on brain organization by building upon existing postmortem data to impute, validate, and analyze a library of spatially dense neuroimaging-like maps of human cortical gene expression. These maps allow spatially unbiased discovery of cortical zones with extreme transcriptional profiles or unusually rapid transcriptional change which index distinct microstructure and predict neuroimaging measures of cortical folding and functional activation. Modules of spatially coexpressed genes define a family of canonical expression maps that integrate diverse spatial scales and temporal epochs of human brain organization - ranging from protein-protein interactions to large-scale systems for cognitive processing. These module maps also parse neuropsychiatric risk genes into subsets which tag distinct cyto-laminar features and differentially predict the location of altered cortical anatomy and gene expression in patients. Taken together, the methods, resources, and findings described here advance our understanding of human cortical organization and offer flexible bridges to connect scientific fields operating at different spatial scales of human brain research.
Collapse
Affiliation(s)
- Konrad Wagstyl
- Wellcome Centre for Human Neuroimaging, University College LondonLondonUnited Kingdom
| | - Sophie Adler
- UCL Great Ormond Street Institute for Child HealthHolbornUnited Kingdom
| | - Jakob Seidlitz
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Simon Vandekar
- Department of Biostatistics, Vanderbilt UniversityNashvilleUnited States
| | - Travis T Mallard
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Psychiatry, Harvard Medical SchoolBostonUnited States
| | - Richard Dear
- Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
| | - Alex R DeCasien
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
| | - Theodore D Satterthwaite
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Lifespan Informatics and Neuroimaging Center, University of Pennsylvania School of MedicinePhiladelphiaUnited States
| | - Siyuan Liu
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
| | - Petra E Vértes
- Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Aaron Alexander-Bloch
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Daniel H Geschwind
- Center for Autism Research and Treatment, Semel Institute, Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Armin Raznahan
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
| |
Collapse
|
38
|
Chai YC, To SK, Simorgh S, Zaunz S, Zhu Y, Ahuja K, Lemaitre A, Ramezankhani R, van der Veer BK, Wierda K, Verhulst S, van Grunsven LA, Pasque V, Verfaillie C. Spatially Self-Organized Three-Dimensional Neural Concentroid as a Novel Reductionist Humanized Model to Study Neurovascular Development. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304421. [PMID: 38037510 PMCID: PMC10837345 DOI: 10.1002/advs.202304421] [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: 07/02/2023] [Revised: 10/15/2023] [Indexed: 12/02/2023]
Abstract
Although human pluripotent stem cell (PSC)-derived brain organoids have enabled researchers to gain insight into human brain development and disease, these organoids contain solely ectodermal cells and are not vascularized as occurs during brain development. Here it is created less complex and more homogenous large neural constructs starting from PSC-derived neuroprogenitor cells (NPC), by fusing small NPC spheroids into so-called concentroids. Such concentroids consisted of a pro-angiogenic core, containing neuronal and outer radial glia cells, surrounded by an astroglia-dense outer layer. Incorporating PSC-derived endothelial cells (EC) around and/or in the concentroids promoted vascularization, accompanied by differential outgrowth and differentiation of neuronal and astroglia cells, as well as the development of ectodermal-derived pericyte-like mural cells co-localizing with EC networks. Single nucleus transcriptomic analysis revealed an enhanced neural cell subtype maturation and diversity in EC-containing concentroids, which better resemble the fetal human brain compared to classical organoids or NPC-only concentroids. This PSC-derived "vascularized" concentroid brain model will facilitate the study of neurovascular/blood-brain barrier development, neural cell migration, and the development of effective in vitro vascularization strategies of brain mimics.
Collapse
Affiliation(s)
- Yoke Chin Chai
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - San Kit To
- Stem Cell Institute LeuvenDepartment of Development and RegenerationLeuven Institute for Single Cell Omics (LISCO)KU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Susan Simorgh
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Samantha Zaunz
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - YingLi Zhu
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Karan Ahuja
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Alix Lemaitre
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Roya Ramezankhani
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Bernard K. van der Veer
- Laboratory for Stem Cell and Developmental EpigeneticsDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Keimpe Wierda
- Electrophysiology Expert UnitVIB‐KU Leuven Center for Brain & Disease ResearchLeuven3000Belgium
| | - Stefaan Verhulst
- Liver Cell Biology Research GroupVrije Universiteit Brussel (VUB)Brussels1090Belgium
| | - Leo A. van Grunsven
- Liver Cell Biology Research GroupVrije Universiteit Brussel (VUB)Brussels1090Belgium
| | - Vincent Pasque
- Stem Cell Institute LeuvenDepartment of Development and RegenerationLeuven Institute for Single Cell Omics (LISCO)KU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Catherine Verfaillie
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| |
Collapse
|
39
|
Zhang D, Chen Y, Wei Y, Chen H, Wu Y, Wu L, Li J, Ren Q, Miao C, Zhu T, Liu J, Ke B, Zhou C. Spatial transcriptomics and single-nucleus RNA sequencing reveal a transcriptomic atlas of adult human spinal cord. eLife 2024; 12:RP92046. [PMID: 38289829 PMCID: PMC10945563 DOI: 10.7554/elife.92046] [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] [Indexed: 02/01/2024] Open
Abstract
Despite the recognized importance of the spinal cord in sensory processing, motor behaviors, and neural diseases, the underlying organization of neuronal clusters and their spatial location remain elusive. Recently, several studies have attempted to define the neuronal types and functional heterogeneity in the spinal cord using single-cell or single-nucleus RNA sequencing in animal models or developing humans. However, molecular evidence of cellular heterogeneity in the adult human spinal cord is limited. Here, we classified spinal cord neurons into 21 subclusters and determined their distribution from nine human donors using single-nucleus RNA sequencing and spatial transcriptomics. Moreover, we compared the human findings with previously published single-nucleus data of the adult mouse spinal cord, which revealed an overall similarity in the neuronal composition of the spinal cord between the two species while simultaneously highlighting some degree of heterogeneity. Additionally, we examined the sex differences in the spinal neuronal subclusters. Several genes, such as SCN10A and HCN1, showed sex differences in motor neurons. Finally, we classified human dorsal root ganglia (DRG) neurons using spatial transcriptomics and explored the putative interactions between DRG and spinal cord neuronal subclusters. In summary, these results illustrate the complexity and diversity of spinal neurons in humans and provide an important resource for future research to explore the molecular mechanisms underlying spinal cord physiology and diseases.
Collapse
Affiliation(s)
- Donghang Zhang
- Department of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
| | - Yali Chen
- Department of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
| | - Yiyong Wei
- Department of Anesthesiology, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College)ShenhenChina
| | - Hongjun Chen
- Department of Intensive Care Unit, Affiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Yujie Wu
- Department of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
| | - Lin Wu
- Department of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
| | - Jin Li
- Department of Orthopedic Surgery, Affiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Qiyang Ren
- Department of Anesthesiology, Affiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Changhong Miao
- Department of Anesthesiology, Zhongshan Hospital, Fudan UniversityShanghaiChina
| | - Tao Zhu
- Department of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
| | - Jin Liu
- Department of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
| | - Bowen Ke
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
| | - Cheng Zhou
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan UniversityChengduChina
| |
Collapse
|
40
|
Xie Y, Chen L, Wang L, Liu T, Zheng Y, Si L, Ge H, Xu H, Xiao L, Wang G. Single-nucleus transcriptomic analysis reveals the relationship between gene expression in oligodendrocyte lineage and major depressive disorder. J Transl Med 2024; 22:109. [PMID: 38281050 PMCID: PMC10822185 DOI: 10.1186/s12967-023-04727-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 11/13/2023] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND Major depressive disorder (MDD) is a common mental illness that affects millions of people worldwide and imposes a heavy burden on individuals, families and society. Previous studies on MDD predominantly focused on neurons and employed bulk homogenates of brain tissues. This paper aims to decipher the relationship between oligodendrocyte lineage (OL) development and MDD at the single-cell resolution level. METHODS Here, we present the use of a guided regularized random forest (GRRF) algorithm to explore single-nucleus RNA sequencing profiles (GSE144136) of the OL at four developmental stages, which contains dorsolateral prefrontal cortex of 17 healthy controls (HC) and 17 MDD cases, generated by Nagy C et al. We prioritized and ordered differentially expressed genes (DEGs) based on Nagy et al., which could predominantly discriminate cells in the four developmental stages and two adjacent developmental stages of the OL. We further screened top-ranked genes that distinguished between HC and MDD in four developmental stages. Moreover, we estimated the performance of the GRRF model via the area under the curve value. Additionally, we validated the pivotal candidate gene Malat1 in animal models. RESULTS We found that, among the four developmental stages, the onset development of OL (OPC2) possesses the best predictive power for distinguishing HC and MDD, and long noncoding RNA MALAT1 has top-ranked importance value in candidate genes of four developmental stages. In addition, results of fluorescence in situ hybridization assay showed that Malat1 plays a critical role in the occurrence of depression. CONCLUSIONS Our work elucidates the mechanism of MDD from the perspective of OL development at the single-cell resolution level and provides novel insight into the occurrence of depression.
Collapse
Affiliation(s)
- Yinping Xie
- Institute of Neuropsychiatry, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lijuan Chen
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Leimin Wang
- School of Automation, China University of Geosciences, Wuhan, China
| | - Tongou Liu
- The First Clinical College of Hubei University of Chinese Medicine, Wuhan, China
| | - Yage Zheng
- Judicial Appraisal Institute, Renmin Hospital of Hubei Province, Wuhan, China
| | - Lujia Si
- Department of Psychiatry, Renmin Hospital of Wuhan University, Wuhan, China
| | - Hailong Ge
- Department of Psychiatry, Renmin Hospital of Wuhan University, Wuhan, China
| | - Hong Xu
- Department of Psychiatry, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ling Xiao
- Institute of Neuropsychiatry, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Gaohua Wang
- Institute of Neuropsychiatry, Renmin Hospital of Wuhan University, Wuhan, China.
| |
Collapse
|
41
|
Hannon E, Dempster EL, Davies JP, Chioza B, Blake GET, Burrage J, Policicchio S, Franklin A, Walker EM, Bamford RA, Schalkwyk LC, Mill J. Quantifying the proportion of different cell types in the human cortex using DNA methylation profiles. BMC Biol 2024; 22:17. [PMID: 38273288 PMCID: PMC10809680 DOI: 10.1186/s12915-024-01827-y] [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: 07/05/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Due to interindividual variation in the cellular composition of the human cortex, it is essential that covariates that capture these differences are included in epigenome-wide association studies using bulk tissue. As experimentally derived cell counts are often unavailable, computational solutions have been adopted to estimate the proportion of different cell types using DNA methylation data. Here, we validate and profile the use of an expanded reference DNA methylation dataset incorporating two neuronal and three glial cell subtypes for quantifying the cellular composition of the human cortex. RESULTS We tested eight reference panels containing different combinations of neuronal- and glial cell types and characterised their performance in deconvoluting cell proportions from computationally reconstructed or empirically derived human cortex DNA methylation data. Our analyses demonstrate that while these novel brain deconvolution models produce accurate estimates of cellular proportions from profiles generated on postnatal human cortex samples, they are not appropriate for the use in prenatal cortex or cerebellum tissue samples. Applying our models to an extensive collection of empirical datasets, we show that glial cells are twice as abundant as neuronal cells in the human cortex and identify significant associations between increased Alzheimer's disease neuropathology and the proportion of specific cell types including a decrease in NeuNNeg/SOX10Neg nuclei and an increase of NeuNNeg/SOX10Pos nuclei. CONCLUSIONS Our novel deconvolution models produce accurate estimates for cell proportions in the human cortex. These models are available as a resource to the community enabling the control of cellular heterogeneity in epigenetic studies of brain disorders performed on bulk cortex tissue.
Collapse
Affiliation(s)
- Eilis Hannon
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK.
| | - Emma L Dempster
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Jonathan P Davies
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Barry Chioza
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Georgina E T Blake
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Joe Burrage
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Stefania Policicchio
- Italian Institute of Technology, Center for Human Technologies (CHT), Genova, Italy
| | - Alice Franklin
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Emma M Walker
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Rosemary A Bamford
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Leonard C Schalkwyk
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| |
Collapse
|
42
|
Hu B, Zhuang XL, Zhou L, Zhang G, Cooper DN, Wu DD. Deciphering the Role of Rapidly Evolving Conserved Elements in Primate Brain Development and Exploring Their Potential Involvement in Alzheimer's Disease. Mol Biol Evol 2024; 41:msae001. [PMID: 38175672 PMCID: PMC10798191 DOI: 10.1093/molbev/msae001] [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: 08/30/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/05/2024] Open
Abstract
Although previous studies have identified human-specific accelerated regions as playing a key role in the recent evolution of the human brain, the characteristics and cellular functions of rapidly evolving conserved elements (RECEs) in ancestral primate lineages remain largely unexplored. Here, based on large-scale primate genome assemblies, we identify 888 RECEs that have been highly conserved in primates that exhibit significantly accelerated substitution rates in the ancestor of the Simiiformes. This primate lineage exhibits remarkable morphological innovations, including an expanded brain mass. Integrative multiomic analyses reveal that RECEs harbor sequences with potential cis-regulatory functions that are activated in the adult human brain. Importantly, genes linked to RECEs exhibit pronounced expression trajectories in the adult brain relative to the fetal stage. Furthermore, we observed an increase in the chromatin accessibility of RECEs in oligodendrocytes from individuals with Alzheimer's disease (AD) compared to that of a control group, indicating that these RECEs may contribute to brain aging and AD. Our findings serve to expand our knowledge of the genetic underpinnings of brain function during primate evolution.
Collapse
Affiliation(s)
- Benxia Hu
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiao-Lin Zhuang
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Long Zhou
- Center of Evolutionary and Organismal Biology, and Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Guangdong, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Guangdong, China
| | - Guojie Zhang
- Center of Evolutionary and Organismal Biology, and Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Guangdong, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Guangdong, China
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Dong-Dong Wu
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| |
Collapse
|
43
|
Zhou DY, Su X, Wu Y, Yang Y, Zhang L, Cheng S, Shao M, Li W, Zhang Z, Wang L, Lv L, Li M, Song M. Decreased CNNM2 expression in prefrontal cortex affects sensorimotor gating function, cognition, dendritic spine morphogenesis and risk of schizophrenia. Neuropsychopharmacology 2024; 49:433-442. [PMID: 37715107 PMCID: PMC10724213 DOI: 10.1038/s41386-023-01732-y] [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: 11/16/2022] [Revised: 08/15/2023] [Accepted: 08/31/2023] [Indexed: 09/17/2023]
Abstract
Genome-wide association studies (GWASs) have reported multiple single nucleotide polymorphisms (SNPs) associated with schizophrenia, yet the underlying molecular mechanisms are largely unknown. In this study, we aimed to identify schizophrenia relevant genes showing alterations in mRNA and protein expression associated with risk SNPs at the 10q24.32-33 GWAS locus. We carried out the quantitative trait loci (QTL) and summary data-based Mendelian randomization (SMR) analyses, using the PsychENCODE dorsolateral prefrontal cortex (DLPFC) expression QTL (eQTL) database, as well as the ROSMAP and Banner DLPFC protein QTL (pQTL) datasets. The gene CNNM2 (encoding a magnesium transporter) at 10q24.32-33 was identified to be a robust schizophrenia risk gene, and was highly expressed in human neurons according to single cell RNA-seq (scRNA-seq) data. We further revealed that reduced Cnnm2 in the mPFC of mice led to impaired cognition and compromised sensorimotor gating function, and decreased Cnnm2 in primary cortical neurons altered dendritic spine morphogenesis, confirming the link between CNNM2 and endophenotypes of schizophrenia. Proteomics analyses showed that reduced Cnnm2 level changed expression of proteins associated with neuronal structure and function. Together, these results identify a robust gene in the pathogenesis of schizophrenia.
Collapse
Affiliation(s)
- Dan-Yang Zhou
- Yunnan Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xi Su
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yong Wu
- Research Center for Mental Health and Neuroscience, Wuhan Mental Health Center, Wuhan, Hubei, China
- Affiliated Wuhan Mental Health Center, Jianghan University, Wuhan, Hubei, China
| | - Yongfeng Yang
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Luwen Zhang
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Shumin Cheng
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Minglong Shao
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Wenqiang Li
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Zhaohui Zhang
- Department of Psychiatry, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Lu Wang
- Yunnan Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Luxian Lv
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
- Henan Province People's Hospital, Zhengzhou, Henan, China
| | - Ming Li
- Yunnan Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China.
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Meng Song
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China.
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China.
| |
Collapse
|
44
|
Xu X, Chen G, Zhou H, Liu Y, Ding H, Wang Z, Shen H, Li X, Li H. Downregulation of Nrp1 transcription promotes blood-brain barrier disruption following experimental cerebral ischemia-reperfusion. Neurosci Lett 2024; 818:137553. [PMID: 37949291 DOI: 10.1016/j.neulet.2023.137553] [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: 07/27/2023] [Revised: 11/02/2023] [Accepted: 11/05/2023] [Indexed: 11/12/2023]
Abstract
Disruption of the blood-brain barrier (BBB) following cerebral ischemia-reperfusion injury (CIRI) is a major factor in the pathophysiology of stroke. Endothelial cell-cell communication is essential for maintaining BBB integrity. By analyzing GSE227651 data, we found that a decrease in endothelial cell-cell communication mediated by Sema3/Nrp1 may be due to the downregulation of Nrp1 transcription, which could contribute to BBB breakdown after CIRI. We confirmed this hypothesis by using western blot analysis to show a reduction in Nrp1 protein levels in penumbra endothelial cells after CIRI in mice. We then overexpressed Nrp1 specifically in brain endothelial cells using adeno-associated virus in mice. Furthermore, Nrp1 overexpression had a protective effect on BBB integrity, as evidenced by a decrease in IgG and albumin leakage caused by CIRI in mice. Finally, we found that Nrp1 overexpression also reduced brain cell death and neurological deficits induced by cerebral ischemia-reperfusion in mice. Our findings suggest that Nrp1 downregulation may be a key factor in the breakdown of endothelial cell-cell communication and subsequent BBB disruption following CIRI. Targeting Nrp1-mediated pathways may be a promising approach for mitigating BBB damage and alleviating neurological consequences in stroke patients.
Collapse
Affiliation(s)
- Xiang Xu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, Jiangsu Province, 215006, China
| | - Gang Chen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, Jiangsu Province, 215006, China
| | - Hai Zhou
- Department of Neurosurgery, Binhai County People's Hospital, Binhai, Jiangsu, 224500, China
| | - Yangyang Liu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, Jiangsu Province, 215006, China
| | - Haojie Ding
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, Jiangsu Province, 215006, China
| | - Zongqi Wang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, Jiangsu Province, 215006, China
| | - Haitao Shen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, Jiangsu Province, 215006, China
| | - Xiang Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, Jiangsu Province, 215006, China
| | - Haiying Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, Jiangsu Province, 215006, China.
| |
Collapse
|
45
|
Wang T. Human stem cells hold the key to the study of human neural infectious disorders. Exp Neurol 2024; 371:114575. [PMID: 37914567 DOI: 10.1016/j.expneurol.2023.114575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Affiliation(s)
- Tongguang Wang
- Translational Neuroscience Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
46
|
Martini L, Amprimo G, Di Carlo S, Olmo G, Ferraris C, Savino A, Bardini R. Neuronal Spike Shapes (NSS): A straightforward approach to investigate heterogeneity in neuronal excitability states. Comput Biol Med 2024; 168:107783. [PMID: 38056213 DOI: 10.1016/j.compbiomed.2023.107783] [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: 06/26/2023] [Revised: 10/23/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
The mammalian brain exhibits a remarkable diversity of neurons, contributing to its intricate architecture and functional complexity. The analysis of multimodal single-cell datasets enables the investigation of cell types and states heterogeneity. In this study, we introduce the Neuronal Spike Shapes (NSS), a straightforward approach for the exploration of excitability states of neurons based on their Action Potential (AP) waveforms. The NSS method describes the AP waveform based on a triangular representation complemented by a set of derived electrophysiological (EP) features. To support this hypothesis, we validate the proposed approach on two datasets of murine cortical neurons, focusing it on GABAergic neurons. The validation process involves a combination of NSS-based clustering analysis, features exploration, Differential Expression (DE), and Gene Ontology (GO) enrichment analysis. Results show that the NSS-based analysis captures neuronal excitability states that possess biological relevance independently of cell subtype. In particular, Neuronal Spike Shapes (NSS) captures, among others, a well-characterized fast-spiking excitability state, supported by both electrophysiological and transcriptomic validation. Gene Ontology Enrichment Analysis reveals voltage-gated potassium (K+) channels as specific markers of the identified NSS partitions. This finding strongly corroborates the biological relevance of NSS partitions as excitability states, as the expression of voltage-gated K+ channels regulates the hyperpolarization phase of the AP, being directly implicated in the regulation of neuronal excitability.
Collapse
Affiliation(s)
- Lorenzo Martini
- Politecnico di Torino - Control and Computer Engineering Department, Corso Duca degli Abruzzi, 24, Turin, 10129, Italy.
| | - Gianluca Amprimo
- Politecnico di Torino - Control and Computer Engineering Department, Corso Duca degli Abruzzi, 24, Turin, 10129, Italy; Institute of Electronics, Information Engineering and Telecommunications, National Research Council, Corso Duca degli Abruzzi, 24, Turin, 10029, Italy.
| | - Stefano Di Carlo
- Politecnico di Torino - Control and Computer Engineering Department, Corso Duca degli Abruzzi, 24, Turin, 10129, Italy. https://www.smilies.polito.it
| | - Gabriella Olmo
- Politecnico di Torino - Control and Computer Engineering Department, Corso Duca degli Abruzzi, 24, Turin, 10129, Italy. https://www.sysbio.polito.it/analytics-technologies-health/
| | - Claudia Ferraris
- Institute of Electronics, Information Engineering and Telecommunications, National Research Council, Corso Duca degli Abruzzi, 24, Turin, 10029, Italy. https://www.ieiit.cnr.it/people/Ferraris-Claudia
| | - Alessandro Savino
- Politecnico di Torino - Control and Computer Engineering Department, Corso Duca degli Abruzzi, 24, Turin, 10129, Italy. https://www.smilies.polito.it
| | - Roberta Bardini
- Politecnico di Torino - Control and Computer Engineering Department, Corso Duca degli Abruzzi, 24, Turin, 10129, Italy.
| |
Collapse
|
47
|
Swaminath S, Russell AB. The use of single-cell RNA-seq to study heterogeneity at varying levels of virus-host interactions. PLoS Pathog 2024; 20:e1011898. [PMID: 38236826 PMCID: PMC10796064 DOI: 10.1371/journal.ppat.1011898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024] Open
Abstract
The outcome of viral infection depends on the diversity of the infecting viral population and the heterogeneity of the cell population that is infected. Until almost a decade ago, the study of these dynamic processes during viral infection was challenging and limited to certain targeted measurements. Presently, with the use of single-cell sequencing technology, the complex interface defined by the interactions of cells with infecting virus can now be studied across the breadth of the transcriptome in thousands of individual cells simultaneously. In this review, we will describe the use of single-cell RNA sequencing (scRNA-seq) to study the heterogeneity of viral infections, ranging from individual virions to the immune response between infected individuals. In addition, we highlight certain key experimental limitations and methodological decisions that are critical to analyzing scRNA-seq data at each scale.
Collapse
Affiliation(s)
- Sharmada Swaminath
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alistair B. Russell
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| |
Collapse
|
48
|
Seah C, Signer R, Deans M, Bader H, Rusielewicz T, Hicks EM, Young H, Cote A, Townsley K, Xu C, Hunter CJ, McCarthy B, Goldberg J, Dobariya S, Holtzherimer PE, Young KA, Noggle SA, Krystal JH, Paull D, Girgenti MJ, Yehuda R, Brennand KJ, Huckins LM. Common genetic variation impacts stress response in the brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.27.573459. [PMID: 38234801 PMCID: PMC10793429 DOI: 10.1101/2023.12.27.573459] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
To explain why individuals exposed to identical stressors experience divergent clinical outcomes, we determine how molecular encoding of stress modifies genetic risk for brain disorders. Analysis of post-mortem brain (n=304) revealed 8557 stress-interactive expression quantitative trait loci (eQTLs) that dysregulate expression of 915 eGenes in response to stress, and lie in stress-related transcription factor binding sites. Response to stress is robust across experimental paradigms: up to 50% of stress-interactive eGenes validate in glucocorticoid treated hiPSC-derived neurons (n=39 donors). Stress-interactive eGenes show brain region- and cell type-specificity, and, in post-mortem brain, implicate glial and endothelial mechanisms. Stress dysregulates long-term expression of disorder risk genes in a genotype-dependent manner; stress-interactive transcriptomic imputation uncovered 139 novel genes conferring brain disorder risk only in the context of traumatic stress. Molecular stress-encoding explains individualized responses to traumatic stress; incorporating trauma into genomic studies of brain disorders is likely to improve diagnosis, prognosis, and drug discovery.
Collapse
|
49
|
Jonnalagadda D, Kihara Y, Groves A, Ray M, Saha A, Ellington C, Lee-Okada HC, Furihata T, Yokomizo T, Quadros EV, Rivera R, Chun J. FTY720 requires vitamin B 12-TCN2-CD320 signaling in astrocytes to reduce disease in an animal model of multiple sclerosis. Cell Rep 2023; 42:113545. [PMID: 38064339 PMCID: PMC11066976 DOI: 10.1016/j.celrep.2023.113545] [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: 10/04/2021] [Revised: 10/24/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023] Open
Abstract
Vitamin B12 (B12) deficiency causes neurological manifestations resembling multiple sclerosis (MS); however, a molecular explanation for the similarity is unknown. FTY720 (fingolimod) is a sphingosine 1-phosphate (S1P) receptor modulator and sphingosine analog approved for MS therapy that can functionally antagonize S1P1. Here, we report that FTY720 suppresses neuroinflammation by functionally and physically regulating the B12 pathways. Genetic and pharmacological S1P1 inhibition upregulates a transcobalamin 2 (TCN2)-B12 receptor, CD320, in immediate-early astrocytes (ieAstrocytes; a c-Fos-activated astrocyte subset that tracks with experimental autoimmune encephalomyelitis [EAE] severity). CD320 is also reduced in MS plaques. Deficiency of CD320 or dietary B12 restriction worsens EAE and eliminates FTY720's efficacy while concomitantly downregulating type I interferon signaling. TCN2 functions as a chaperone for FTY720 and sphingosine, whose complex induces astrocytic CD320 internalization, suggesting a delivery mechanism of FTY720/sphingosine via the TCN2-CD320 pathway. Taken together, the B12-TCN2-CD320 pathway is essential for the mechanism of action of FTY720.
Collapse
Affiliation(s)
- Deepa Jonnalagadda
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yasuyuki Kihara
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Aran Groves
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA; Neuroscience Graduate Program, School of Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Manisha Ray
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Arjun Saha
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Clayton Ellington
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hyeon-Cheol Lee-Okada
- Department of Biochemistry, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Tomomi Furihata
- Laboratory of Clinical Pharmacy and Experimental Therapeutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Takehiko Yokomizo
- Department of Biochemistry, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Edward V Quadros
- Department of Medicine, SUNY-Downstate Medical Center, 450 Clarkson Avenue, Brooklyn, NY 11203, USA
| | - Richard Rivera
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
50
|
Petersen M, Hoffstaedter F, Nägele FL, Mayer C, Schell M, Rimmele DL, Zyriax BC, Zeller T, Kühn S, Gallinat J, Fiehler J, Twerenbold R, Omidvarnia A, Patil KR, Eickhoff SB, Thomalla G, Cheng B. A latent clinical-anatomical dimension relating metabolic syndrome to brain structure and cognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529531. [PMID: 36865285 PMCID: PMC9980040 DOI: 10.1101/2023.02.22.529531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The link between metabolic syndrome (MetS) and neurodegenerative as well cerebrovascular conditions holds substantial implications for brain health in at-risk populations. This study elucidates the complex relationship between MetS and brain health by conducting a comprehensive examination of cardiometabolic risk factors, cortical morphology, and cognitive function in 40,087 individuals. Multivariate, data-driven statistics identified a latent dimension linking more severe MetS to widespread brain morphological abnormalities, accounting for up to 71% of shared variance in the data. This dimension was replicable across sub-samples. In a mediation analysis we could demonstrate that MetS-related brain morphological abnormalities mediated the link between MetS severity and cognitive performance in multiple domains. Employing imaging transcriptomics and connectomics, our results also suggest that MetS-related morphological abnormalities are linked to the regional cellular composition and macroscopic brain network organization. By leveraging extensive, multi-domain data combined with a dimensional stratification approach, our analysis provides profound insights into the association of MetS and brain health. These findings can inform effective therapeutic and risk mitigation strategies aimed at maintaining brain integrity.
Collapse
Affiliation(s)
- Marvin Petersen
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Felix Hoffstaedter
- Institute for Systems Neuroscience, Medical Faculty, Heinrich-Heine University Düsseldorf, Moorenstraße 5, 40225 Düsseldorf, Germany
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM-7), Research Center Ju lich, Wilhelm-Johnen-Straße, 52425 Ju lich, Germany
| | - Felix L. Nägele
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Carola Mayer
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Maximilian Schell
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - D. Leander Rimmele
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Birgit-Christiane Zyriax
- Midwifery Science-Health Services Research and Prevention, Institute for Health Services Research in Dermatology and Nursing (IVDP), University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Tanja Zeller
- Department of Cardiology, University Heart and Vascular Center, Martinistraße 52, 20251 Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Luebeck, Martinistraße 52, 20251 Hamburg, Germany
- University Center of Cardiovascular Science, University Heart and Vascular Center, Martinistraße 52, 20251 Hamburg, Germany
| | - Simone Kühn
- Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Jürgen Gallinat
- Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Jens Fiehler
- Department of Diagnostic and Interventional Neuroradiology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Raphael Twerenbold
- Department of Cardiology, University Heart and Vascular Center, Martinistraße 52, 20251 Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Luebeck, Martinistraße 52, 20251 Hamburg, Germany
- University Center of Cardiovascular Science, University Heart and Vascular Center, Martinistraße 52, 20251 Hamburg, Germany
- Epidemiological Study Center, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Amir Omidvarnia
- Institute for Systems Neuroscience, Medical Faculty, Heinrich-Heine University Düsseldorf, Moorenstraße 5, 40225 Düsseldorf, Germany
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM-7), Research Center Ju lich, Wilhelm-Johnen-Straße, 52425 Ju lich, Germany
| | - Kaustubh R. Patil
- Institute for Systems Neuroscience, Medical Faculty, Heinrich-Heine University Düsseldorf, Moorenstraße 5, 40225 Düsseldorf, Germany
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM-7), Research Center Ju lich, Wilhelm-Johnen-Straße, 52425 Ju lich, Germany
| | - Simon B. Eickhoff
- Institute for Systems Neuroscience, Medical Faculty, Heinrich-Heine University Düsseldorf, Moorenstraße 5, 40225 Düsseldorf, Germany
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM-7), Research Center Ju lich, Wilhelm-Johnen-Straße, 52425 Ju lich, Germany
| | - Götz Thomalla
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Bastian Cheng
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| |
Collapse
|