1
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Schlachetzki JC, Gianella S, Ouyang Z, Lana AJ, Yang X, O'Brien S, Challacombe JF, Gaskill PJ, Jordan-Sciutto KL, Chaillon A, Moore D, Achim CL, Ellis RJ, Smith DM, Glass CK. Gene expression and chromatin conformation of microglia in virally suppressed people with HIV. Life Sci Alliance 2024; 7:e202402736. [PMID: 39060113 PMCID: PMC11282357 DOI: 10.26508/lsa.202402736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
The presence of HIV in sequestered reservoirs is a central impediment to a functional cure, allowing HIV to persist despite life-long antiretroviral therapy (ART), and driving a variety of comorbid conditions. Our understanding of the latent HIV reservoir in the central nervous system is incomplete, because of difficulties in accessing human central nervous system tissues. Microglia contribute to HIV reservoirs, but the molecular phenotype of HIV-infected microglia is poorly understood. We leveraged the unique "Last Gift" rapid autopsy program, in which people with HIV are closely followed until days or even hours before death. Microglial populations were heterogeneous regarding their gene expression profiles but showed similar chromatin accessibility landscapes. Despite ART, we detected occasional microglia containing cell-associated HIV RNA and HIV DNA integrated into open regions of the host's genome (∼0.005%). Microglia with detectable HIV RNA showed an inflammatory phenotype. These results demonstrate a distinct myeloid cell reservoir in the brains of people with HIV despite suppressive ART. Strategies for curing HIV and neurocognitive impairment will need to consider the myeloid compartment to be successful.
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Affiliation(s)
- Johannes Cm Schlachetzki
- https://ror.org/01vf2g217 Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
- https://ror.org/01vf2g217 Department of Neurosciences, University of California San Diego, San Diego, CA, USA
| | - Sara Gianella
- https://ror.org/01vf2g217 Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, CA, USA
| | - Zhengyu Ouyang
- https://ror.org/01vf2g217 Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Addison J Lana
- https://ror.org/01vf2g217 Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Sydney O'Brien
- https://ror.org/01vf2g217 Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Jean F Challacombe
- https://ror.org/01vf2g217 Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Peter J Gaskill
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Kelly L Jordan-Sciutto
- Department of Oral Medicine, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Antoine Chaillon
- https://ror.org/01vf2g217 Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, CA, USA
| | - David Moore
- https://ror.org/01vf2g217 Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Cristian L Achim
- https://ror.org/01vf2g217 Department of Pathology, University of California San Diego, San Diego, CA, USA
| | - Ronald J Ellis
- https://ror.org/01vf2g217 Department of Neurosciences, University of California San Diego, San Diego, CA, USA
| | - Davey M Smith
- https://ror.org/01vf2g217 Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, CA, USA
| | - Christopher K Glass
- https://ror.org/01vf2g217 Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
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2
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Gulati GS, D'Silva JP, Liu Y, Wang L, Newman AM. Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00768-2. [PMID: 39169166 DOI: 10.1038/s41580-024-00768-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2024] [Indexed: 08/23/2024]
Abstract
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has emerged as a tool to contextualize single cells in multicellular neighbourhoods and to identify spatially recurrent phenotypes, or ecotypes. These technologies have generated vast datasets with targeted-transcriptome and whole-transcriptome profiles of hundreds to millions of cells. Such data have provided new insights into developmental hierarchies, cellular plasticity and diverse tissue microenvironments, and spurred a burst of innovation in computational methods for single-cell analysis. In this Review, we discuss recent advancements, ongoing challenges and prospects in identifying and characterizing cell states and multicellular neighbourhoods. We discuss recent progress in sample processing, data integration, identification of subtle cell states, trajectory modelling, deconvolution and spatial analysis. Furthermore, we discuss the increasing application of deep learning, including foundation models, in analysing single-cell and spatial transcriptomics data. Finally, we discuss recent applications of these tools in the fields of stem cell biology, immunology, and tumour biology, and the future of single-cell and spatial transcriptomics in biological research and its translation to the clinic.
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Affiliation(s)
- Gunsagar S Gulati
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Yunhe Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Aaron M Newman
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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3
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Martins-Ferreira R, Calafell-Segura J, Chaves J, Ciudad L, Martins da Silva A, Pinho e Costa P, Leal B, Ballestar E. Purinergic exposure induces epigenomic and transcriptomic-mediated preconditioning resembling epilepsy-associated microglial states. iScience 2024; 27:110546. [PMID: 39184445 PMCID: PMC11342283 DOI: 10.1016/j.isci.2024.110546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 03/10/2024] [Accepted: 07/16/2024] [Indexed: 08/27/2024] Open
Abstract
Microglia play a crucial role in a range of neuropathologies through exacerbated activation. Microglial inflammatory responses can be influenced by prior exposures to noxious stimuli, like increased levels of extracellular adenosine and ATP. These are characteristic of brain insults like epileptic seizures and could potentially shape subsequent responses through epigenetic regulation. We investigated DNA methylation and expression changes in human microglia-like cells differentiated from monocytes following ATP-mediated preconditioning. We demonstrate that microglia-like cells display homeostatic microglial features, shown by surface markers, transcriptome, and DNA methylome. After exposure to ATP, TLR-mediated activation leads to an exacerbated pro-inflammatory response. These changes are accompanied by methylation and transcriptional reprogramming associated with enhanced immune-related functions. The reprogramming associated with ATP-mediated preconditioning leads to profiles found in microglial subsets linked to epilepsy. Purine-driven microglia immune preconditioning drives epigenetic and transcriptional changes that could contribute to altered functions of microglia during seizure development and progression.
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Affiliation(s)
- Ricardo Martins-Ferreira
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Immunogenetics Laboratory, Molecular Pathology and Immunology Department, Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), 4050-313 Porto, Portugal
- Autoimmunity and Neuroscience Group. Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - Josep Calafell-Segura
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - João Chaves
- Autoimmunity and Neuroscience Group. Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
- Neurology Service, Centro Hospitalar Universitário de Santo António (CHUdSA), 4099-001 Porto, Portugal
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - António Martins da Silva
- Autoimmunity and Neuroscience Group. Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
- Neurophysiology Service, CHUdSA 4099-001 Porto, Portugal
| | - Paulo Pinho e Costa
- Immunogenetics Laboratory, Molecular Pathology and Immunology Department, Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), 4050-313 Porto, Portugal
- Autoimmunity and Neuroscience Group. Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
- Department of Human Genetics, Instituto Nacional de Saúde Dr. Ricardo Jorge 4000-055 Porto, Portugal
| | - Bárbara Leal
- Immunogenetics Laboratory, Molecular Pathology and Immunology Department, Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), 4050-313 Porto, Portugal
- Autoimmunity and Neuroscience Group. Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai 200241, China
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4
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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.
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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.
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5
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Mathys H, Boix CA, Akay LA, Xia Z, Davila-Velderrain J, Ng AP, Jiang X, Abdelhady G, Galani K, Mantero J, Band N, James BT, Babu S, Galiana-Melendez F, Louderback K, Prokopenko D, Tanzi RE, Bennett DA, Tsai LH, Kellis M. Single-cell multiregion dissection of Alzheimer's disease. Nature 2024; 632:858-868. [PMID: 39048816 PMCID: PMC11338834 DOI: 10.1038/s41586-024-07606-7] [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: 06/20/2022] [Accepted: 05/24/2024] [Indexed: 07/27/2024]
Abstract
Alzheimer's disease is the leading cause of dementia worldwide, but the cellular pathways that underlie its pathological progression across brain regions remain poorly understood1-3. Here we report a single-cell transcriptomic atlas of six different brain regions in the aged human brain, covering 1.3 million cells from 283 post-mortem human brain samples across 48 individuals with and without Alzheimer's disease. We identify 76 cell types, including region-specific subtypes of astrocytes and excitatory neurons and an inhibitory interneuron population unique to the thalamus and distinct from canonical inhibitory subclasses. We identify vulnerable populations of excitatory and inhibitory neurons that are depleted in specific brain regions in Alzheimer's disease, and provide evidence that the Reelin signalling pathway is involved in modulating the vulnerability of these neurons. We develop a scalable method for discovering gene modules, which we use to identify cell-type-specific and region-specific modules that are altered in Alzheimer's disease and to annotate transcriptomic differences associated with diverse pathological variables. We identify an astrocyte program that is associated with cognitive resilience to Alzheimer's disease pathology, tying choline metabolism and polyamine biosynthesis in astrocytes to preserved cognitive function late in life. Together, our study develops a regional atlas of the ageing human brain and provides insights into cellular vulnerability, response and resilience to Alzheimer's disease pathology.
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Affiliation(s)
- Hansruedi Mathys
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Carles A Boix
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computational and Systems Biology Program, MIT, Cambridge, MA, USA
| | - Leyla Anne Akay
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Ziting Xia
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Harvard-MIT Health Sciences and Technology Program, MIT, Cambridge, MA, USA
| | | | - Ayesha P Ng
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Xueqiao Jiang
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Ghada Abdelhady
- University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kyriaki Galani
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julio Mantero
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neil Band
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Benjamin T James
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sudhagar Babu
- University of Pittsburgh Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Fabiola Galiana-Melendez
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Kate Louderback
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Dmitry Prokopenko
- Genetics and Aging Research Unit, McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Li-Huei Tsai
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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6
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Wen Y, Yang H, Hong Y. Transcriptomic Approaches to Cardiomyocyte-Biomaterial Interactions: A Review. ACS Biomater Sci Eng 2024; 10:4175-4194. [PMID: 38934720 DOI: 10.1021/acsbiomaterials.4c00303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Biomaterials, essential for supporting, enhancing, and repairing damaged tissues, play a critical role in various medical applications. This Review focuses on the interaction of biomaterials and cardiomyocytes, emphasizing the unique significance of transcriptomic approaches in understanding their interactions, which are pivotal in cardiac bioengineering and regenerative medicine. Transcriptomic approaches serve as powerful tools to investigate how cardiomyocytes respond to biomaterials, shedding light on the gene expression patterns, regulatory pathways, and cellular processes involved in these interactions. Emerging technologies such as bulk RNA-seq, single-cell RNA-seq, single-nucleus RNA-seq, and spatial transcriptomics offer promising avenues for more precise and in-depth investigations. Longitudinal studies, pathway analyses, and machine learning techniques further improve the ability to explore the complex regulatory mechanisms involved. This review also discusses the challenges and opportunities of utilizing transcriptomic techniques in cardiomyocyte-biomaterial research. Although there are ongoing challenges such as costs, cell size limitation, sample differences, and complex analytical process, there exist exciting prospects in comprehensive gene expression analyses, biomaterial design, cardiac disease treatment, and drug testing. These multimodal methodologies have the capacity to deepen our understanding of the intricate interaction network between cardiomyocytes and biomaterials, potentially revolutionizing cardiac research with the aim of promoting heart health, and they are also promising for studying interactions between biomaterials and other cell types.
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Affiliation(s)
- Yufeng Wen
- Department of Bioengineering, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Huaxiao Yang
- Department of Biomedical Engineering, University of North Texas, Denton, Texas 76207, United States
| | - Yi Hong
- Department of Bioengineering, University of Texas at Arlington, Arlington, Texas 76019, United States
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7
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Castro-Mendoza PB, Weaver CM, Chang W, Medalla M, Rockland KS, Lowery L, McDonough E, Varghese M, Hof PR, Meyer DE, Luebke JI. Proteomic features of gray matter layers and superficial white matter of the rhesus monkey neocortex: comparison of prefrontal area 46 and occipital area 17. Brain Struct Funct 2024:10.1007/s00429-024-02819-y. [PMID: 38943018 DOI: 10.1007/s00429-024-02819-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/08/2024] [Indexed: 06/30/2024]
Abstract
In this novel large-scale multiplexed immunofluorescence study we comprehensively characterized and compared layer-specific proteomic features within regions of interest of the widely divergent dorsolateral prefrontal cortex (A46) and primary visual cortex (A17) of adult rhesus monkeys. Twenty-eight markers were imaged in rounds of sequential staining, and their spatial distribution precisely quantified within gray matter layers and superficial white matter. Cells were classified as neurons, astrocytes, oligodendrocytes, microglia, or endothelial cells. The distribution of fibers and blood vessels were assessed by quantification of staining intensity across regions of interest. This method revealed multivariate similarities and differences between layers and areas. Protein expression in neurons was the strongest determinant of both laminar and regional differences, whereas protein expression in glia was more important for intra-areal laminar distinctions. Among specific results, we observed a lower glia-to-neuron ratio in A17 than in A46 and the pan-neuronal markers HuD and NeuN were differentially distributed in both brain areas with a lower intensity of NeuN in layers 4 and 5 of A17 compared to A46 and other A17 layers. Astrocytes and oligodendrocytes exhibited distinct marker-specific laminar distributions that differed between regions; notably, there was a high proportion of ALDH1L1-expressing astrocytes and of oligodendrocyte markers in layer 4 of A17. The many nuanced differences in protein expression between layers and regions observed here highlight the need for direct assessment of proteins, in addition to RNA expression, and set the stage for future protein-focused studies of these and other brain regions in normal and pathological conditions.
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Affiliation(s)
- Paola B Castro-Mendoza
- Department of Anatomy and Neurobiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA
- Center for Systems Neuroscience, Boston University, Boston, MA, 02215, USA
| | - Christina M Weaver
- Department of Mathematics, Franklin and Marshall College, Lancaster, PA, 17604, USA
| | - Wayne Chang
- Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA
| | - Maria Medalla
- Department of Anatomy and Neurobiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA
- Center for Systems Neuroscience, Boston University, Boston, MA, 02215, USA
| | - Kathleen S Rockland
- Department of Anatomy and Neurobiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Lisa Lowery
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA
| | | | - Merina Varghese
- Nash Family Department of Neuroscience, Friedman Brain Institute, and Center for Discovery and Innovation, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
| | - Patrick R Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, and Center for Discovery and Innovation, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
| | - Dan E Meyer
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA
| | - Jennifer I Luebke
- Department of Anatomy and Neurobiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA.
- Center for Systems Neuroscience, Boston University, Boston, MA, 02215, USA.
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8
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Gonzalez-Ferrer J, Lehrer J, O'Farrell A, Paten B, Teodorescu M, Haussler D, Jonsson VD, Mostajo-Radji MA. SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis. CELL GENOMICS 2024; 4:100581. [PMID: 38823397 PMCID: PMC11228957 DOI: 10.1016/j.xgen.2024.100581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Cell atlases serve as vital references for automating cell labeling in new samples, yet existing classification algorithms struggle with accuracy. Here we introduce SIMS (scalable, interpretable machine learning for single cell), a low-code data-efficient pipeline for single-cell RNA classification. We benchmark SIMS against datasets from different tissues and species. We demonstrate SIMS's efficacy in classifying cells in the brain, achieving high accuracy even with small training sets (<3,500 cells) and across different samples. SIMS accurately predicts neuronal subtypes in the developing brain, shedding light on genetic changes during neuronal differentiation and postmitotic fate refinement. Finally, we apply SIMS to single-cell RNA datasets of cortical organoids to predict cell identities and uncover genetic variations between cell lines. SIMS identifies cell-line differences and misannotated cell lineages in human cortical organoids derived from different pluripotent stem cell lines. Altogether, we show that SIMS is a versatile and robust tool for cell-type classification from single-cell datasets.
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Affiliation(s)
- Jesus Gonzalez-Ferrer
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Julian Lehrer
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Applied Mathematics, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Ash O'Farrell
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Benedict Paten
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Mircea Teodorescu
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - David Haussler
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Vanessa D Jonsson
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Applied Mathematics, University of California, Santa Cruz, Santa Cruz, CA 95060, USA.
| | - Mohammed A Mostajo-Radji
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA.
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9
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Wang S, Huang Y, Wang F, Han Q, Ren N, Wang X, Cui Y, Yuan Z, Xia H. A cell atlas of the adult female Aedes aegypti midgut revealed by single-cell RNA sequencing. Sci Data 2024; 11:587. [PMID: 38839790 PMCID: PMC11153528 DOI: 10.1038/s41597-024-03432-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/28/2024] [Indexed: 06/07/2024] Open
Abstract
Aedes aegypti is a primary vector for transmitting various arboviruses, including Yellow fever, dengue and Zika virus. The mosquito midgut is the principal organ for blood meal digestion, nutrient absorption and the initial site of arbovirus infection. Although a previous study delineated midgut's transcriptome of Ae. aegypti at the single-nucleus resolution, there still lacks an established protocol for isolating and RNA sequencing of single cells of Ae. aegypti midgut, which is required for investigating arbovirus-midgut interaction at the single-cell level. Here, we established an atlas of the midgut cells for Ae. aegypti by single-cell RNA sequencing. We annotated the cell clusters including intestinal stem cells/enteroblasts (ISC/EB), cardia cells (Cardia), enterocytes (EC, EC-like), enteroendocrine cells (EE), visceral muscle (VM), fat body cells (FBC) and hemocyte cells (HC). This study will provide a foundation for further studies of arbovirus infection in mosquito midgut at the single-cell level.
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Affiliation(s)
- Shunlong Wang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430200, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Huang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430200, China
| | - Fei Wang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430200, China
| | - Qian Han
- Hainan One Health Key Laboratory, Hainan University, Haikou, 570228, China
| | - Nanjie Ren
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430200, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyu Wang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430200, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingjun Cui
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, 06520, USA.
| | - Zhiming Yuan
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430200, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Han Xia
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430200, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Hubei Jiangxia Laboratory, Wuhan, 430207, China.
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10
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Hatai D, Levenson MT, Rehan VK, Allard P. Inter- and trans-generational impacts of environmental exposures on the germline resolved at the single-cell level. CURRENT OPINION IN TOXICOLOGY 2024; 38:100465. [PMID: 38586548 PMCID: PMC10993723 DOI: 10.1016/j.cotox.2024.100465] [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] [Indexed: 04/09/2024]
Abstract
Reproduction is a remarkably intricate process involving the interaction of multiple cell types and organ systems unfolding over long periods of time and that culminates with the production of gametes. The initiation of germ cell development takes place during embryogenesis but only completes decades later in humans. The complexity inherent to reproduction and its study has long hampered our ability to decipher how environmental agents disrupt this process. Single-cell approaches provide an opportunity for a deeper understanding of the action of toxicants on germline function and analyze how the response to their exposure is differentially distributed across tissues and cell types. In addition to single-cell RNA sequencing, other single-cell or nucleus level approaches such as ATAC-sequencing and multi-omics have expanded the strategies that can be implemented in reproductive toxicological studies to include epigenomic and the nuclear transcriptomic data. Here we will discuss the current state of single-cell technologies and how they can best be utilized to advance reproductive toxicological studies. We will then discuss case studies in two model organisms (Caenorhabditis elegans and mouse) studying different environmental exposures (alcohol and e-cigarettes respectively) to highlight the value of single-cell and single-nucleus approaches for reproductive biology and reproductive toxicology.
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Affiliation(s)
- Dylan Hatai
- UCLA Molecular Toxicology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Max T. Levenson
- UCLA Molecular Toxicology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Virender K. Rehan
- UCLA Molecular Toxicology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
- Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Patrick Allard
- UCLA Molecular Toxicology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
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11
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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.
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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
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12
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Steyn C, Mishi R, Fillmore S, Verhoog MB, More J, Rohlwink UK, Melvill R, Butler J, Enslin JMN, Jacobs M, Sauka-Spengler T, Greco M, Quiñones S, Dulla CG, Raimondo JV, Figaji A, Hockman D. Cell type-specific gene expression dynamics during human brain maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.29.560114. [PMID: 37808657 PMCID: PMC10557738 DOI: 10.1101/2023.09.29.560114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The human brain undergoes protracted post-natal maturation, guided by dynamic changes in gene expression. Most studies exploring these processes have used bulk tissue analyses, which mask cell type-specific gene expression dynamics. Here, using single nucleus (sn)RNA-seq on temporal lobe tissue, including samples of African ancestry, we build a joint paediatric and adult atlas of 75 cell subtypes, which we verify with spatial transcriptomics. We explore the differences between paediatric and adult cell types, revealing the genes and pathways that change during brain maturation. Our results highlight excitatory neuron subtypes, including the LTK and FREM subtypes, that show elevated expression of genes associated with cognition and synaptic plasticity in paediatric tissue. The new resources we present here improve our understanding of the brain during its development and contribute to global efforts to build an inclusive brain cell map.
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Affiliation(s)
- Christina Steyn
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Ruvimbo Mishi
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Stephanie Fillmore
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Matthijs B Verhoog
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Jessica More
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Ursula K Rohlwink
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - Roger Melvill
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - James Butler
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Johannes M N Enslin
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - Muazzam Jacobs
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Immunology, Department of Pathology University of Cape Town
- National Health Laboratory Service, South Africa
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Maria Greco
- Single Cell Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Sadi Quiñones
- Department of Neuroscience, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
- Graduate School of Biomedical Science, Tufts University School of Medicine, Boston, MA, USA
| | - Chris G Dulla
- Department of Neuroscience, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - Joseph V Raimondo
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anthony Figaji
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - Dorit Hockman
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
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13
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Mancuso R, Fattorelli N, Martinez-Muriana A, Davis E, Wolfs L, Van Den Daele J, Geric I, Premereur J, Polanco P, Bijnens B, Preman P, Serneels L, Poovathingal S, Balusu S, Verfaillie C, Fiers M, De Strooper B. Xenografted human microglia display diverse transcriptomic states in response to Alzheimer's disease-related amyloid-β pathology. Nat Neurosci 2024; 27:886-900. [PMID: 38539015 PMCID: PMC11089003 DOI: 10.1038/s41593-024-01600-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/14/2024] [Indexed: 05/14/2024]
Abstract
Microglia are central players in Alzheimer's disease pathology but analyzing microglial states in human brain samples is challenging due to genetic diversity, postmortem delay and admixture of pathologies. To circumvent these issues, here we generated 138,577 single-cell expression profiles of human stem cell-derived microglia xenotransplanted in the brain of the AppNL-G-F model of amyloid pathology and wild-type controls. Xenografted human microglia adopt a disease-associated profile similar to that seen in mouse microglia, but display a more pronounced human leukocyte antigen or HLA state, likely related to antigen presentation in response to amyloid plaques. The human microglial response also involves a pro-inflammatory cytokine/chemokine cytokine response microglia or CRM response to oligomeric Aβ oligomers. Genetic deletion of TREM2 or APOE as well as APOE polymorphisms and TREM2R47H expression in the transplanted microglia modulate these responses differentially. The expression of other Alzheimer's disease risk genes is differentially regulated across the distinct cell states elicited in response to amyloid pathology. Thus, we have identified multiple transcriptomic cell states adopted by human microglia in a multipronged response to Alzheimer's disease-related pathology, which should be taken into account in translational studies.
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Affiliation(s)
- Renzo Mancuso
- Microglia and Inflammation in Neurological Disorders (MIND) Lab, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium.
| | - Nicola Fattorelli
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Anna Martinez-Muriana
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Emma Davis
- UK Dementia Research Institute at UCL, University College London, London, UK
| | - Leen Wolfs
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Johanna Van Den Daele
- Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven Stem Cell Institute, Leuven, Belgium
| | - Ivana Geric
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Jessie Premereur
- Microglia and Inflammation in Neurological Disorders (MIND) Lab, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Paula Polanco
- Microglia and Inflammation in Neurological Disorders (MIND) Lab, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Baukje Bijnens
- Microglia and Inflammation in Neurological Disorders (MIND) Lab, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Pranav Preman
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Lutgarde Serneels
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Suresh Poovathingal
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
| | - Sriram Balusu
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Catherine Verfaillie
- Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven Stem Cell Institute, Leuven, Belgium
| | - Mark Fiers
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
- UK Dementia Research Institute at UCL, University College London, London, UK
| | - Bart De Strooper
- Centre for Brain and Disease Research, Flanders Institute for Biotechnology (VIB), Leuven, Belgium.
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium.
- UK Dementia Research Institute at UCL, University College London, London, UK.
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14
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Scholz R, Brösamle D, Yuan X, Beyer M, Neher JJ. Epigenetic control of microglial immune responses. Immunol Rev 2024; 323:209-226. [PMID: 38491845 DOI: 10.1111/imr.13317] [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: 12/18/2023] [Accepted: 03/02/2024] [Indexed: 03/18/2024]
Abstract
Microglia, the major population of brain-resident macrophages, are now recognized as a heterogeneous population comprising several cell subtypes with different (so far mostly supposed) functions in health and disease. A number of studies have performed molecular characterization of these different microglial activation states over the last years making use of "omics" technologies, that is transcriptomics, proteomics and, less frequently, epigenomics profiling. These approaches offer the possibility to identify disease mechanisms, discover novel diagnostic biomarkers, and develop new therapeutic strategies. Here, we focus on epigenetic profiling as a means to understand microglial immune responses beyond what other omics methods can offer, that is, revealing past and present molecular responses, gene regulatory networks and potential future response trajectories, and defining cell subtype-specific disease relevance through mapping non-coding genetic variants. We review the current knowledge in the field regarding epigenetic regulation of microglial identity and function, provide an exemplary analysis that demonstrates the advantages of performing joint transcriptomic and epigenomic profiling of single microglial cells and discuss how comprehensive epigenetic analyses may enhance our understanding of microglial pathophysiology.
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Affiliation(s)
- Rebekka Scholz
- Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Desirée Brösamle
- Biomedical Center (BMC), Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
- Neuroimmunology and Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Xidi Yuan
- Biomedical Center (BMC), Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
- Neuroimmunology and Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Marc Beyer
- Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and University of Bonn and West German Genome Center, Bonn, Germany
| | - Jonas J Neher
- Biomedical Center (BMC), Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
- Neuroimmunology and Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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15
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Chomyk A, Kucinski R, Kim J, Christie E, Cyncynatus K, Gossman Z, Chen Z, Richardson B, Cameron M, Turner T, Dutta R, Trapp B. Transcript Profiles of Microglia/Macrophage Cells at the Borders of Chronic Active and Subpial Gray Matter Lesions in Multiple Sclerosis. Ann Neurol 2024; 95:907-916. [PMID: 38345145 PMCID: PMC11060930 DOI: 10.1002/ana.26877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/05/2023] [Accepted: 01/03/2024] [Indexed: 05/01/2024]
Abstract
OBJECTIVE Microglia/macrophages line the border of demyelinated lesions in both cerebral white matter and the cortex in the brains of multiple sclerosis patients. Microglia/macrophages associated with chronic white matter lesions are thought to be responsible for slow lesion expansion and disability progression in progressive multiple sclerosis, whereas those lining gray matter lesions are less studied. Profiling these microglia/macrophages could help to focus therapies on genes or pathways specific to lesion expansion and disease progression. METHODS We compared the morphology and transcript profiles of microglia/macrophages associated with borders of white matter (WM line) and subpial gray matter lesions (GM line) using laser capture microscopy. We performed RNA sequencing on isolated cells followed by immunocytochemistry to determine the distribution of translational products of transcripts increased in WM line microglia. RESULTS Cells in the WM line appear activated, with shorter processes and larger cell bodies, whereas those in the GM line appear more homeostatic, with smaller cell bodies and multiple thin processes. Transcript profiling revealed 176 genes in WM lines and 111 genes in GM lines as differentially expressed. Transcripts associated with immune activation and iron homeostasis were increased in WM line microglia, whereas genes belonging to the canonical Wnt signaling pathway were increased in GM line microglia. INTERPRETATION We propose that the mechanisms of demyelination and dynamics of lesion expansion are responsible for differential transcript expression in WM lines and GM lines, and posit that increased expression of the Fc epsilon receptor, spleen tyrosine kinase, and Bruton's tyrosine kinase, play a key role in regulating microglia/macrophage function at the border of chronic active white matter lesions. ANN NEUROL 2024;95:907-916.
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Affiliation(s)
- Anthony Chomyk
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Rikki Kucinski
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jihye Kim
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Emilie Christie
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Kaitlyn Cyncynatus
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Zachary Gossman
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Zhihong Chen
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Brian Richardson
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mark Cameron
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | | | - Ranjan Dutta
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Bruce Trapp
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
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16
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Kim W, Kim M, Kim B. Unraveling the enigma: housekeeping gene Ugt1a7c as a universal biomarker for microglia. Front Psychiatry 2024; 15:1364201. [PMID: 38666091 PMCID: PMC11043603 DOI: 10.3389/fpsyt.2024.1364201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Background Microglia, brain resident macrophages, play multiple roles in maintaining homeostasis, including immunity, surveillance, and protecting the central nervous system through their distinct activation processes. Identifying all types of microglia-driven populations is crucial due to the presence of various phenotypes that differ based on developmental stages or activation states. During embryonic development, the E8.5 yolk sac contains erythromyeloid progenitors that go through different growth phases, eventually resulting in the formation of microglia. In addition, microglia are present in neurological diseases as a diverse population. So far, no individual biomarker for microglia has been discovered that can accurately identify and monitor their development and attributes. Summary Here, we highlight the newly defined biomarker of mouse microglia, UGT1A7C, which exhibits superior stability in expression during microglia development and activation compared to other known microglia biomarkers. The UGT1A7C sensing chemical probe labels all microglia in the 3xTG AD mouse model. The expression of Ugt1a7c is stable during development, with only a 4-fold variation, while other microglia biomarkers, such as Csf1r and Cx3cr1, exhibit at least a 10-fold difference. The UGT1A7C expression remains constant throughout its lifespan. In addition, the expression and activity of UGT1A7C are the same in response to different types of inflammatory activators' treatment in vitro. Conclusion We propose employing UGT1A7C as the representative biomarker for microglia, irrespective of their developmental state, age, or activation status. Using UGT1A7C can reduce the requirement for using multiple biomarkers, enhance the precision of microglia analysis, and even be utilized as a standard for gene/protein expression.
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Affiliation(s)
| | | | - Beomsue Kim
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
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17
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Pineda SS, Lee H, Ulloa-Navas MJ, Linville RM, Garcia FJ, Galani K, Engelberg-Cook E, Castanedes MC, Fitzwalter BE, Pregent LJ, Gardashli ME, DeTure M, Vera-Garcia DV, Hucke ATS, Oskarsson BE, Murray ME, Dickson DW, Heiman M, Belzil VV, Kellis M. Single-cell dissection of the human motor and prefrontal cortices in ALS and FTLD. Cell 2024; 187:1971-1989.e16. [PMID: 38521060 PMCID: PMC11086986 DOI: 10.1016/j.cell.2024.02.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 11/09/2023] [Accepted: 02/23/2024] [Indexed: 03/25/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) share many clinical, pathological, and genetic features, but a detailed understanding of their associated transcriptional alterations across vulnerable cortical cell types is lacking. Here, we report a high-resolution, comparative single-cell molecular atlas of the human primary motor and dorsolateral prefrontal cortices and their transcriptional alterations in sporadic and familial ALS and FTLD. By integrating transcriptional and genetic information, we identify known and previously unidentified vulnerable populations in cortical layer 5 and show that ALS- and FTLD-implicated motor and spindle neurons possess a virtually indistinguishable molecular identity. We implicate potential disease mechanisms affecting these cell types as well as non-neuronal drivers of pathogenesis. Finally, we show that neuron loss in cortical layer 5 tracks more closely with transcriptional identity rather than cellular morphology and extends beyond previously reported vulnerable cell types.
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Affiliation(s)
- S Sebastian Pineda
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Hyeseung Lee
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Raleigh M Linville
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Francisco J Garcia
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kyriakitsa Galani
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | | | | | - Brent E Fitzwalter
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Luc J Pregent
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Michael DeTure
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Andre T S Hucke
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Melissa E Murray
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Myriam Heiman
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | | | - Manolis Kellis
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.
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18
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Wu X, Zhang H. Omics Approaches Unveiling the Biology of Human Atherosclerotic Plaques. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:482-498. [PMID: 38280419 PMCID: PMC10988765 DOI: 10.1016/j.ajpath.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/29/2024]
Abstract
Atherosclerosis is a chronic inflammatory disease of the arterial wall, characterized by the buildup of plaques with the accumulation and transformation of lipids, immune cells, vascular smooth muscle cells, and necrotic cell debris. Plaques with collagen-poor thin fibrous caps infiltrated by macrophages and lymphocytes are considered unstable because they are at the greatest risk of rupture and clinical events. However, the current histologic definition of plaque types may not fully capture the complex molecular nature of atherosclerotic plaque biology and the underlying mechanisms contributing to plaque progression, rupture, and erosion. The advances in omics technologies have changed the understanding of atherosclerosis plaque biology, offering new possibilities to improve risk prediction and discover novel therapeutic targets. Genomic studies have shed light on the genetic predisposition to atherosclerosis, and integrative genomic analyses expedite the translation of genomic discoveries. Transcriptomic, proteomic, metabolomic, and lipidomic studies have refined the understanding of the molecular signature of atherosclerotic plaques, aiding in data-driven hypothesis generation for mechanistic studies and offering new prospects for biomarker discovery. Furthermore, advancements in single-cell technologies and emerging spatial analysis techniques have unveiled the heterogeneity and plasticity of plaque cells. This review discusses key omics-based discoveries that have advanced the understanding of human atherosclerotic plaque biology, focusing on insights derived from omics profiling of human atherosclerotic vascular specimens.
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Affiliation(s)
- Xun Wu
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Hanrui Zhang
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, New York.
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19
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Chamberlin JT, Lee Y, Marth GT, Quinlan AR. Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments. Genome Res 2024; 34:179-188. [PMID: 38355308 PMCID: PMC10984380 DOI: 10.1101/gr.278253.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
A mechanistic understanding of the biological and technical factors that impact transcript measurements is essential to designing and analyzing single-cell and single-nucleus RNA sequencing experiments. Nuclei contain the same pre-mRNA population as cells, but they contain a small subset of the mRNAs. Nonetheless, early studies argued that single-nucleus analysis yielded results comparable to cellular samples if pre-mRNA measurements were included. However, typical workflows do not distinguish between pre-mRNA and mRNA when estimating gene expression, and variation in their relative abundances across cell types has received limited attention. These gaps are especially important given that incorporating pre-mRNA has become commonplace for both assays, despite known gene length bias in pre-mRNA capture. Here, we reanalyze public data sets from mouse and human to describe the mechanisms and contrasting effects of mRNA and pre-mRNA sampling on gene expression and marker gene selection in single-cell and single-nucleus RNA-seq. We show that pre-mRNA levels vary considerably among cell types, which mediates the degree of gene length bias and limits the generalizability of a recently published normalization method intended to correct for this bias. As an alternative, we repurpose an existing post hoc gene length-based correction method from conventional RNA-seq gene set enrichment analysis. Finally, we show that inclusion of pre-mRNA in bioinformatic processing can impart a larger effect than assay choice itself, which is pivotal to the effective reuse of existing data. These analyses advance our understanding of the sources of variation in single-cell and single-nucleus RNA-seq experiments and provide useful guidance for future studies.
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Affiliation(s)
- John T Chamberlin
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah 84108, USA
| | - Younghee Lee
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah 84108, USA
- Seoul National University, College of Veterinary Medicine, Seoul, 08826, South Korea
| | - Gabor T Marth
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, Utah 84112, USA
| | - Aaron R Quinlan
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah 84108, USA;
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, Utah 84112, USA
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20
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Tsartsalis S, Sleven H, Fancy N, Wessely F, Smith AM, Willumsen N, Cheung TKD, Rokicki MJ, Chau V, Ifie E, Khozoie C, Ansorge O, Yang X, Jenkyns MH, Davey K, McGarry A, Muirhead RCJ, Debette S, Jackson JS, Montagne A, Owen DR, Miners JS, Love S, Webber C, Cader MZ, Matthews PM. A single nuclear transcriptomic characterisation of mechanisms responsible for impaired angiogenesis and blood-brain barrier function in Alzheimer's disease. Nat Commun 2024; 15:2243. [PMID: 38472200 PMCID: PMC10933340 DOI: 10.1038/s41467-024-46630-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: 10/18/2021] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Brain perfusion and blood-brain barrier (BBB) integrity are reduced early in Alzheimer's disease (AD). We performed single nucleus RNA sequencing of vascular cells isolated from AD and non-diseased control brains to characterise pathological transcriptional signatures responsible for this. We show that endothelial cells (EC) are enriched for expression of genes associated with susceptibility to AD. Increased β-amyloid is associated with BBB impairment and a dysfunctional angiogenic response related to a failure of increased pro-angiogenic HIF1A to increased VEGFA signalling to EC. This is associated with vascular inflammatory activation, EC senescence and apoptosis. Our genomic dissection of vascular cell risk gene enrichment provides evidence for a role of EC pathology in AD and suggests that reducing vascular inflammatory activation and restoring effective angiogenesis could reduce vascular dysfunction contributing to the genesis or progression of early AD.
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Affiliation(s)
- Stergios Tsartsalis
- Department of Brain Sciences, Imperial College London, London, UK
- Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Hannah Sleven
- Nuffield Department of Clinical Neurosciences, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, Sherrington Road, University of Oxford, Oxford, UK
| | - Nurun Fancy
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Frank Wessely
- UK Dementia Research Institute Centre, Cardiff University, Cardiff, UK
| | - Amy M Smith
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
- Centre for Brain Research and Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
| | - Nanet Willumsen
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - To Ka Dorcas Cheung
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Michal J Rokicki
- UK Dementia Research Institute Centre, Cardiff University, Cardiff, UK
| | - Vicky Chau
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Eseoghene Ifie
- Neuropathology Unit, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Combiz Khozoie
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Olaf Ansorge
- Neuropathology Unit, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Xin Yang
- Department of Brain Sciences, Imperial College London, London, UK
- St Edmund Hall, University of Oxford, Oxford, UK
| | - Marion H Jenkyns
- Department of Brain Sciences, Imperial College London, London, UK
| | - Karen Davey
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Aisling McGarry
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Robert C J Muirhead
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Stephanie Debette
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, Team ELEANOR, UMR 1219, 33000, Bordeaux, France
| | - Johanna S Jackson
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Axel Montagne
- Centre for Clinical Brain Sciences, and UK Dementia Research Institute, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - David R Owen
- Department of Brain Sciences, Imperial College London, London, UK
| | - J Scott Miners
- Dementia Research Group, University of Bristol, Bristol, UK
| | - Seth Love
- Dementia Research Group, University of Bristol, Bristol, UK
| | - Caleb Webber
- UK Dementia Research Institute Centre, Cardiff University, Cardiff, UK
| | - M Zameel Cader
- Nuffield Department of Clinical Neurosciences, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, Sherrington Road, University of Oxford, Oxford, UK
| | - Paul M Matthews
- Department of Brain Sciences, Imperial College London, London, UK.
- UK Dementia Research Institute Centre, Imperial College London, London, UK.
- St Edmund Hall, University of Oxford, Oxford, UK.
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21
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Podleśny-Drabiniok A, Novikova G, Liu Y, Dunst J, Temizer R, Giannarelli C, Marro S, Kreslavsky T, Marcora E, Goate AM. BHLHE40/41 regulate microglia and peripheral macrophage responses associated with Alzheimer's disease and other disorders of lipid-rich tissues. Nat Commun 2024; 15:2058. [PMID: 38448474 PMCID: PMC10917780 DOI: 10.1038/s41467-024-46315-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Genetic and experimental evidence suggests that Alzheimer's disease (AD) risk alleles and genes may influence disease susceptibility by altering the transcriptional and cellular responses of macrophages, including microglia, to damage of lipid-rich tissues like the brain. Recently, sc/nRNA sequencing studies identified similar transcriptional activation states in subpopulations of macrophages in aging and degenerating brains and in other diseased lipid-rich tissues. We collectively refer to these subpopulations of microglia and peripheral macrophages as DLAMs. Using macrophage sc/nRNA-seq data from healthy and diseased human and mouse lipid-rich tissues, we reconstructed gene regulatory networks and identified 11 strong candidate transcriptional regulators of the DLAM response across species. Loss or reduction of two of these transcription factors, BHLHE40/41, in iPSC-derived microglia and human THP-1 macrophages as well as loss of Bhlhe40/41 in mouse microglia, resulted in increased expression of DLAM genes involved in cholesterol clearance and lysosomal processing, increased cholesterol efflux and storage, and increased lysosomal mass and degradative capacity. These findings provide targets for therapeutic modulation of macrophage/microglial function in AD and other disorders affecting lipid-rich tissues.
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Affiliation(s)
- Anna Podleśny-Drabiniok
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gloriia Novikova
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- OMNI Bioinformatics Department, Genentech, Inc., South San Francisco, CA, USA
| | - Yiyuan Liu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Josefine Dunst
- Department of Medicine, Division of Immunology and Allergy, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rose Temizer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chiara Giannarelli
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Samuele Marro
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Taras Kreslavsky
- Department of Medicine, Division of Immunology and Allergy, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Edoardo Marcora
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Alison Mary Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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22
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Andresen AMS, Taylor RS, Grimholt U, Daniels RR, Sun J, Dobie R, Henderson NC, Martin SAM, Macqueen DJ, Fosse JH. Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics. FISH & SHELLFISH IMMUNOLOGY 2024; 146:109357. [PMID: 38181891 DOI: 10.1016/j.fsi.2024.109357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/07/2024]
Abstract
Single-cell transcriptomics is the current gold standard for global gene expression profiling, not only in mammals and model species, but also in non-model fish species. This is a rapidly expanding field, creating a deeper understanding of tissue heterogeneity and the distinct functions of individual cells, making it possible to explore the complexities of immunology and gene expression on a highly resolved level. In this study, we compared two single cell transcriptomic approaches to investigate cellular heterogeneity within the head kidney of healthy farmed Atlantic salmon (Salmo salar). We compared 14,149 cell transcriptomes assayed by single cell RNA-seq (scRNA-seq) with 18,067 nuclei transcriptomes captured by single nucleus RNA-Seq (snRNA-seq). Both approaches detected eight major cell populations in common: granulocytes, heamatopoietic stem cells, erythrocytes, mononuclear phagocytes, thrombocytes, B cells, NK-like cells, and T cells. Four additional cell types, endothelial, epithelial, interrenal, and mesenchymal cells, were detected in the snRNA-seq dataset, but appeared to be lost during preparation of the single cell suspension submitted for scRNA-seq library generation. We identified additional heterogeneity and subpopulations within the B cells, T cells, and endothelial cells, and revealed developmental trajectories of heamatopoietic stem cells into differentiated granulocyte and mononuclear phagocyte populations. Gene expression profiles of B cell subtypes revealed distinct IgM and IgT-skewed resting B cell lineages and provided insights into the regulation of B cell lymphopoiesis. The analysis revealed eleven T cell sub-populations, displaying a level of T cell heterogeneity in salmon head kidney comparable to that observed in mammals, including distinct subsets of cd4/cd8-negative T cells, such as tcrγ positive, progenitor-like, and cytotoxic cells. Although snRNA-seq and scRNA-seq were both useful to resolve cell type-specific expression in the Atlantic salmon head kidney, the snRNA-seq pipeline was overall more robust in identifying several cell types and subpopulations. While scRNA-seq displayed higher levels of ribosomal and mitochondrial genes, snRNA-seq captured more transcription factor genes. However, only scRNA-seq-generated data was useful for cell trajectory inference within the myeloid lineage. In conclusion, this study systematically outlines the relative merits of scRNA-seq and snRNA-seq in Atlantic salmon, enhances understanding of teleost immune cell lineages, and provides a comprehensive list of markers for identifying major cell populations in the head kidney with significant immune relevance.
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Affiliation(s)
| | - Richard S Taylor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Jianxuan Sun
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Ross Dobie
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom
| | - Neil C Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom.
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23
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Lu J, Ren J, Liu J, Lu M, Cui Y, Liao Y, Zhou Y, Gao Y, Tang F, Wang J, Wang S, Wen L, Song L. High-resolution single-cell transcriptomic survey of cardiomyocytes from patients with hypertrophic cardiomyopathy. Cell Prolif 2024; 57:e13557. [PMID: 37766635 PMCID: PMC10905351 DOI: 10.1111/cpr.13557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/28/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a common inherited cardiovascular disease, which can cause heart failure and lead to death. In this study, we performed high-resolution single-cell RNA-sequencing of 2115 individual cardiomyocytes obtained from HCM patients and normal controls. Signature up- and down-regulated genes in HCM were identified by integrative analysis across 37 patients and 41 controls from our data and published human single-cell and single-nucleus RNA-seq datasets, which were further classified into gene modules by single-cell co-expression analysis. Using our high-resolution dataset, we also investigated the heterogeneity among individual cardiomyocytes and revealed five distinct clusters within HCM cardiomyocytes. Interestingly, we showed that some extracellular matrix (ECM) genes were up-regulated in the HCM cardiomyocytes, suggesting that they play a role in cardiac remodelling. Taken together, our study comprehensively profiled the transcriptomic programs of HCM cardiomyocytes and provided insights into molecular mechanisms underlying the pathogenesis of HCM.
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Affiliation(s)
- Jiansen Lu
- College of Life Sciences, Biomedical Pioneering Innovation CenterMinistry of Education Key Laboratory of Cell Proliferation and DifferentiationBeijingChina
- Beijing Advanced Innovation Center for Genomics, College of Life SciencesPeking UniversityBeijingChina
| | - Jie Ren
- College of Life Sciences, Biomedical Pioneering Innovation CenterMinistry of Education Key Laboratory of Cell Proliferation and DifferentiationBeijingChina
- Beijing Advanced Innovation Center for Genomics, College of Life SciencesPeking UniversityBeijingChina
- Peking‐Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina
| | - Jie Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular DiseasesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Minjie Lu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular DiseasesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yueli Cui
- College of Life Sciences, Biomedical Pioneering Innovation CenterMinistry of Education Key Laboratory of Cell Proliferation and DifferentiationBeijingChina
- Beijing Advanced Innovation Center for Genomics, College of Life SciencesPeking UniversityBeijingChina
| | - Yuhan Liao
- College of Life Sciences, Biomedical Pioneering Innovation CenterMinistry of Education Key Laboratory of Cell Proliferation and DifferentiationBeijingChina
- Beijing Advanced Innovation Center for Genomics, College of Life SciencesPeking UniversityBeijingChina
| | - Yuan Zhou
- College of Life Sciences, Biomedical Pioneering Innovation CenterMinistry of Education Key Laboratory of Cell Proliferation and DifferentiationBeijingChina
- Beijing Advanced Innovation Center for Genomics, College of Life SciencesPeking UniversityBeijingChina
| | - Yun Gao
- College of Life Sciences, Biomedical Pioneering Innovation CenterMinistry of Education Key Laboratory of Cell Proliferation and DifferentiationBeijingChina
- Beijing Advanced Innovation Center for Genomics, College of Life SciencesPeking UniversityBeijingChina
| | - Fuchou Tang
- College of Life Sciences, Biomedical Pioneering Innovation CenterMinistry of Education Key Laboratory of Cell Proliferation and DifferentiationBeijingChina
- Beijing Advanced Innovation Center for Genomics, College of Life SciencesPeking UniversityBeijingChina
- Peking‐Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina
| | - Jizheng Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular DiseasesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Shuiyun Wang
- Department of Cardiovascular Surgery, Fuwai Hospital, National Center for Cardiovascular DiseasesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Lu Wen
- College of Life Sciences, Biomedical Pioneering Innovation CenterMinistry of Education Key Laboratory of Cell Proliferation and DifferentiationBeijingChina
- Beijing Advanced Innovation Center for Genomics, College of Life SciencesPeking UniversityBeijingChina
| | - Lei Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular DiseasesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Cardiomyopathy ward, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- National Clinical Research Center for Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular DiseasesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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24
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Takahashi H, Bhagwagar S, Nies SH, Ye H, Han X, Chiasseu MT, Wang G, Mackenzie IR, Strittmatter SM. Reduced progranulin increases tau and α-synuclein inclusions and alters mouse tauopathy phenotypes via glucocerebrosidase. Nat Commun 2024; 15:1434. [PMID: 38365772 PMCID: PMC10873339 DOI: 10.1038/s41467-024-45692-3] [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: 05/16/2022] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
Comorbid proteinopathies are observed in many neurodegenerative disorders including Alzheimer's disease (AD), increase with age, and influence clinical outcomes, yet the mechanisms remain ill-defined. Here, we show that reduction of progranulin (PGRN), a lysosomal protein associated with TDP-43 proteinopathy, also increases tau inclusions, causes concomitant accumulation of α-synuclein and worsens mortality and disinhibited behaviors in tauopathy mice. The increased inclusions paradoxically protect against spatial memory deficit and hippocampal neurodegeneration. PGRN reduction in male tauopathy attenuates activity of β-glucocerebrosidase (GCase), a protein previously associated with synucleinopathy, while increasing glucosylceramide (GlcCer)-positive tau inclusions. In neuronal culture, GCase inhibition enhances tau aggregation induced by AD-tau. Furthermore, purified GlcCer directly promotes tau aggregation in vitro. Neurofibrillary tangles in human tauopathies are also GlcCer-immunoreactive. Thus, in addition to TDP-43, PGRN regulates tau- and synucleinopathies via GCase and GlcCer. A lysosomal PGRN-GCase pathway may be a common therapeutic target for age-related comorbid proteinopathies.
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Affiliation(s)
- Hideyuki Takahashi
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT, 06536, USA
| | - Sanaea Bhagwagar
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT, 06536, USA
- College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah H Nies
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT, 06536, USA
- Graduate School of Cellular and Molecular Neuroscience, University of Tübingen, D-72074, Tübingen, Germany
| | - Hongping Ye
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center At San Antonio, San Antonio, TX, 78229, USA
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center At San Antonio, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center At San Antonio, San Antonio, TX, 78229, USA
| | - Marius T Chiasseu
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT, 06536, USA
| | - Guilin Wang
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, CT, 06520, USA
| | - Ian R Mackenzie
- Department of Pathology, University of British Columbia and Vancouver General Hospital, Vancouver, BC, Canada
| | - Stephen M Strittmatter
- Cellular Neuroscience, Neurodegeneration, Repair, Departments of Neurology and of Neuroscience, Yale University School of Medicine, New Haven, CT, 06536, USA.
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25
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He Z, Chen Q, Wang K, Lin J, Peng Y, Zhang J, Yan X, Jie Y. Single-cell transcriptomics analysis of cellular heterogeneity and immune mechanisms in neurodegenerative diseases. Eur J Neurosci 2024; 59:333-357. [PMID: 38221677 DOI: 10.1111/ejn.16242] [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: 05/17/2023] [Revised: 12/04/2023] [Accepted: 12/12/2023] [Indexed: 01/16/2024]
Abstract
Single-cell transcriptomics analysis is an advanced technology that can describe the intracellular transcriptome in complex tissues. It profiles and analyses datasets by single-cell RNA sequencing. Neurodegenerative diseases are identified by the abnormal apoptosis of neurons in the brain with few or no effective therapy strategies at present, which has been a growing healthcare concern and brought a great burden to society. The transcriptome of individual cells provides deep insights into previously unforeseen cellular heterogeneity and gene expression differences in neurodegenerative disorders. It detects multiple cell subsets and functional changes during pathological progression, which deepens the understanding of the molecular underpinnings and cellular basis of neurodegenerative diseases. Furthermore, the transcriptome analysis of immune cells shows the regulation of immune response. Different subtypes of immune cells and their interaction are found to contribute to disease progression. This finding enables the discovery of novel targets and biomarkers for early diagnosis. In this review, we emphasize the principles of the technology, and its recent progress in the study of cellular heterogeneity and immune mechanisms in neurodegenerative diseases. The application of single-cell transcriptomics analysis in neurodegenerative disorders would help explore the pathogenesis of these diseases and develop novel therapeutic methods.
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Affiliation(s)
- Ziping He
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Qianqian Chen
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Kaiyue Wang
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Jiang Lin
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Yilin Peng
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
| | - Jinlong Zhang
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Department of Forensic Science, School of Basic Medical Science, Xinjiang Medical University, Urumqi, China
| | - Xisheng Yan
- Department of Cardiovascular Medicine, Wuhan Third Hospital & Tongren Hospital of Wuhan University, Wuhan, China
| | - Yan Jie
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, China
- Department of Forensic Science, School of Basic Medical Science, Xinjiang Medical University, Urumqi, China
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26
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Jackson WS, Bauer S, Kaczmarczyk L, Magadi SS. Selective Vulnerability to Neurodegenerative Disease: Insights from Cell Type-Specific Translatome Studies. BIOLOGY 2024; 13:67. [PMID: 38392286 PMCID: PMC10886597 DOI: 10.3390/biology13020067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/24/2024]
Abstract
Neurodegenerative diseases (NDs) manifest a wide variety of clinical symptoms depending on the affected brain regions. Gaining insights into why certain regions are resistant while others are susceptible is vital for advancing therapeutic strategies. While gene expression changes offer clues about disease responses across brain regions, the mixture of cell types therein obscures experimental results. In recent years, methods that analyze the transcriptomes of individual cells (e.g., single-cell RNA sequencing or scRNAseq) have been widely used and have provided invaluable insights into specific cell types. Concurrently, transgene-based techniques that dissect cell type-specific translatomes (CSTs) in model systems, like RiboTag and bacTRAP, offer unique advantages but have received less attention. This review juxtaposes the merits and drawbacks of both methodologies, focusing on the use of CSTs in understanding conditions like amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), Alzheimer's disease (AD), and specific prion diseases like fatal familial insomnia (FFI), genetic Creutzfeldt-Jakob disease (gCJD), and acquired prion disease. We conclude by discussing the emerging trends observed across multiple diseases and emerging methods.
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Affiliation(s)
- Walker S Jackson
- Wallenberg Center for Molecular Medicine, Linköping University, 581 85 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Susanne Bauer
- Wallenberg Center for Molecular Medicine, Linköping University, 581 85 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Lech Kaczmarczyk
- Wallenberg Center for Molecular Medicine, Linköping University, 581 85 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Srivathsa S Magadi
- Wallenberg Center for Molecular Medicine, Linköping University, 581 85 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
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Simon RC, Fleming WT, Senthilkumar P, Briones BA, Ishii KK, Hjort MM, Martin MM, Hashikawa K, Sanders AD, Golden SA, Stuber GD. Opioid-driven disruption of the septal complex reveals a role for neurotensin-expressing neurons in withdrawal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575766. [PMID: 38293241 PMCID: PMC10827099 DOI: 10.1101/2024.01.15.575766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Because opioid withdrawal is an intensely aversive experience, persons with opioid use disorder (OUD) often relapse to avoid it. The lateral septum (LS) is a forebrain structure that is important in aversion processing, and previous studies have linked the lateral septum (LS) to substance use disorders. It is unclear, however, which precise LS cell types might contribute to the maladaptive state of withdrawal. To address this, we used single-nucleus RNA-sequencing to interrogate cell type specific gene expression changes induced by chronic morphine and withdrawal. We discovered that morphine globally disrupted the transcriptional profile of LS cell types, but Neurotensin-expressing neurons (Nts; LS-Nts neurons) were selectively activated by naloxone. Using two-photon calcium imaging and ex vivo electrophysiology, we next demonstrate that LS-Nts neurons receive enhanced glutamatergic drive in morphine-dependent mice and remain hyperactivated during opioid withdrawal. Finally, we showed that activating and silencing LS-Nts neurons during opioid withdrawal regulates pain coping behaviors and sociability. Together, these results suggest that LS-Nts neurons are a key neural substrate involved in opioid withdrawal and establish the LS as a crucial regulator of adaptive behaviors, specifically pertaining to OUD.
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Affiliation(s)
- Rhiana C. Simon
- Center for the Neurobiology of Addiction, Pain, and Emotion (NAPE), University of Washington, Seattle, WA, 98195, USA
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Weston T. Fleming
- Center for the Neurobiology of Addiction, Pain, and Emotion (NAPE), University of Washington, Seattle, WA, 98195, USA
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Pranav Senthilkumar
- Center for the Neurobiology of Addiction, Pain, and Emotion (NAPE), University of Washington, Seattle, WA, 98195, USA
| | - Brandy A. Briones
- Center for the Neurobiology of Addiction, Pain, and Emotion (NAPE), University of Washington, Seattle, WA, 98195, USA
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Kentaro K. Ishii
- Center for the Neurobiology of Addiction, Pain, and Emotion (NAPE), University of Washington, Seattle, WA, 98195, USA
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Madelyn M. Hjort
- Center for the Neurobiology of Addiction, Pain, and Emotion (NAPE), University of Washington, Seattle, WA, 98195, USA
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Madison M. Martin
- Center for the Neurobiology of Addiction, Pain, and Emotion (NAPE), University of Washington, Seattle, WA, 98195, USA
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Koichi Hashikawa
- Center for the Neurobiology of Addiction, Pain, and Emotion (NAPE), University of Washington, Seattle, WA, 98195, USA
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Andrea D. Sanders
- Center for the Neurobiology of Addiction, Pain, and Emotion (NAPE), University of Washington, Seattle, WA, 98195, USA
| | - Sam A. Golden
- Center for the Neurobiology of Addiction, Pain, and Emotion (NAPE), University of Washington, Seattle, WA, 98195, USA
- Department of Biological Structure, University of Washington, Seattle, WA, 98195, USA
| | - Garret D. Stuber
- Center for the Neurobiology of Addiction, Pain, and Emotion (NAPE), University of Washington, Seattle, WA, 98195, USA
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, 98195, USA
- Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA
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28
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Li Y, Girard R, Srinath A, Cruz DV, Ciszewski C, Chen C, Lightle R, Romanos S, Sone JY, Moore T, DeBiasse D, Stadnik A, Lee JJ, Shenkar R, Koskimäki J, Lopez-Ramirez MA, Marchuk DA, Ginsberg MH, Kahn ML, Shi C, Awad IA. Transcriptomic signatures of individual cell types in cerebral cavernous malformation. Cell Commun Signal 2024; 22:23. [PMID: 38195510 PMCID: PMC10775676 DOI: 10.1186/s12964-023-01301-2] [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: 07/19/2023] [Accepted: 08/30/2023] [Indexed: 01/11/2024] Open
Abstract
Cerebral cavernous malformation (CCM) is a hemorrhagic neurovascular disease with no currently available therapeutics. Prior evidence suggests that different cell types may play a role in CCM pathogenesis. The contribution of each cell type to the dysfunctional cellular crosstalk remains unclear. Herein, RNA-seq was performed on fluorescence-activated cell sorted endothelial cells (ECs), pericytes, and neuroglia from CCM lesions and non-lesional brain tissue controls. Differentially Expressed Gene (DEG), pathway and Ligand-Receptor (LR) analyses were performed to characterize the dysfunctional genes of respective cell types within CCMs. Common DEGs among all three cell types were related to inflammation and endothelial-to-mesenchymal transition (EndMT). DEG and pathway analyses supported a role of lesional ECs in dysregulated angiogenesis and increased permeability. VEGFA was particularly upregulated in pericytes. Further pathway and LR analyses identified vascular endothelial growth factor A/ vascular endothelial growth factor receptor 2 signaling in lesional ECs and pericytes that would result in increased angiogenesis. Moreover, lesional pericytes and neuroglia predominantly showed DEGs and pathways mediating the immune response. Further analyses of cell specific gene alterations in CCM endorsed potential contribution to EndMT, coagulation, and a hypoxic microenvironment. Taken together, these findings motivate mechanistic hypotheses regarding non-endothelial contributions to lesion pathobiology and may lead to novel therapeutic targets. Video Abstract.
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Affiliation(s)
- Ying Li
- Department of Neurosurgery, First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- Department of Neurological Surgery, Neurovascular Surgery Program, The University of Chicago, Chicago, IL, USA
| | - Romuald Girard
- Department of Neurological Surgery, Neurovascular Surgery Program, The University of Chicago, Chicago, IL, USA
| | - Abhinav Srinath
- Department of Neurological Surgery, Neurovascular Surgery Program, The University of Chicago, Chicago, IL, USA
| | - Diana Vera Cruz
- Center for Research Informatics, The University of Chicago, Chicago, IL, USA
| | - Cezary Ciszewski
- Human Disease and Immune Discovery Core, The University of Chicago, Chicago, IL, USA
| | - Chang Chen
- Center for Research Informatics, The University of Chicago, Chicago, IL, USA
| | - Rhonda Lightle
- Department of Neurological Surgery, Neurovascular Surgery Program, The University of Chicago, Chicago, IL, USA
| | - Sharbel Romanos
- Department of Neurological Surgery, Neurovascular Surgery Program, The University of Chicago, Chicago, IL, USA
| | - Je Yeong Sone
- Department of Neurological Surgery, Neurovascular Surgery Program, The University of Chicago, Chicago, IL, USA
| | - Thomas Moore
- Department of Neurological Surgery, Neurovascular Surgery Program, The University of Chicago, Chicago, IL, USA
| | - Dorothy DeBiasse
- Department of Neurological Surgery, Neurovascular Surgery Program, The University of Chicago, Chicago, IL, USA
| | - Agnieszka Stadnik
- Department of Neurological Surgery, Neurovascular Surgery Program, The University of Chicago, Chicago, IL, USA
| | - Justine J Lee
- Department of Neurological Surgery, Neurovascular Surgery Program, The University of Chicago, Chicago, IL, USA
| | - Robert Shenkar
- Department of Neurological Surgery, Neurovascular Surgery Program, The University of Chicago, Chicago, IL, USA
| | - Janne Koskimäki
- Department of Neurosurgery, Division of Clinical Neurosciences, Turku University Hospital and University of Turku, Turku, Finland
- Department of Neurosurgery, Oulu University Hospital, Neurocenter, Oulu, Finland
| | - Miguel A Lopez-Ramirez
- Department of Medicine, University of California, La Jolla, San Diego, CA, USA
- Department of Pharmacology, University of California, La Jolla, San Diego, CA, USA
| | - Douglas A Marchuk
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Mark H Ginsberg
- Department of Medicine, University of California, La Jolla, San Diego, CA, USA
| | - Mark L Kahn
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Changbin Shi
- Department of Neurosurgery, First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Issam A Awad
- Department of Neurological Surgery, Neurovascular Surgery Program, The University of Chicago, Chicago, IL, USA.
- Department of Neurological Surgery, University of Chicago Medicine, 5841 S Maryland, MC3026/Neurosurgery J341, Chicago, IL, 60637, USA.
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Han Y, Huang C, Pan Y, Gu X. Single Cell Sequencing Technology and Its Application in Alzheimer's Disease. J Alzheimers Dis 2024; 97:1033-1050. [PMID: 38217599 DOI: 10.3233/jad-230861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
Alzheimer's disease (AD) involves degeneration of cells in the brain. Due to insidious onset and slow progression, AD is often not diagnosed until it gets progressed to a more severe stage. The diagnosis and treatment of AD has been a challenge. In recent years, high-throughput sequencing technologies have exhibited advantages in exploring the pathogenesis of diseases. However, the types of cells of the central nervous system are complex and traditional bulk sequencing cannot reflect their heterogeneity. Single-cell sequencing technology enables study at the individual cell level and has an irreplaceable advantage in the study of complex diseases. In recent years, this field has expanded rapidly and several types of single-cell sequencing technologies have emerged, including transcriptomics, epigenomics, genomics and proteomics. This review article provides an overview of these single-cell sequencing technologies and their application in AD.
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Affiliation(s)
- Yuru Han
- Shanghai Key Laboratory of Molecular Imaging, Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- School of Pharmacy, Shanghai University of Medicine & Health Sciences, Shanghai, China
- School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Congying Huang
- Shanghai Key Laboratory of Molecular Imaging, Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- School of Pharmacy, Shanghai University of Medicine & Health Sciences, Shanghai, China
- School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yuhui Pan
- Center for Disease Control and Prevention of Harbin, Harbin, China
| | - Xuefeng Gu
- Shanghai Key Laboratory of Molecular Imaging, Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- School of Pharmacy, Shanghai University of Medicine & Health Sciences, Shanghai, China
- School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, China
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Lopes KDP, Yu L, Shen X, Qiu Y, Tasaki S, Iatrou A, Beeri MS, Seyfried NT, Menon V, Wang Y, Schneider JA, Cantor H, Bennett DA. Associations of cortical SPP1 and ITGAX with cognition and common neuropathologies in older adults. Alzheimers Dement 2024; 20:525-537. [PMID: 37727065 PMCID: PMC10841499 DOI: 10.1002/alz.13474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/15/2023] [Accepted: 08/21/2023] [Indexed: 09/21/2023]
Abstract
INTRODUCTION The secreted phosphoprotein 1 (SPP1) gene expressed by CD11c+ cells is known to be associated with microglia activation and neuroinflammatory diseases. As most studies rely on mouse models, we investigated these genes and proteins in the cortical brain tissue of older adults and their role in Alzheimer's disease (AD) and related disorders. METHODS We leveraged protein measurements, single-nuclei, and RNASeq data from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP) of over 1200 samples for association analysis. RESULTS Expression of SPP1 and its encoded protein osteopontin were associated with faster cognitive decline and greater odds of common neuropathologies. At single-cell resolution, integrin subunit alpha X (ITGAX) was highly expressed in microglia, where specific subpopulations were associated with AD and cerebral amyloid angiopathy. DISCUSSION The study provides evidence of SPP1 and ITGAX association with cognitive decline and common neuropathologies identifying a microglial subset associated with disease.
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Affiliation(s)
- Katia de Paiva Lopes
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
| | - Lei Yu
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
| | - Xianli Shen
- Department of Cancer Immunology and VirologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of ImmunologyHarvard Medical SchoolBostonMassachusettsUSA
| | - Yiguo Qiu
- Department of Cancer Immunology and VirologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of ImmunologyHarvard Medical SchoolBostonMassachusettsUSA
- Chongqing International Institute for ImmunologyChongqingChina
| | - Shinya Tasaki
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
| | - Artemis Iatrou
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
- Department of Psychiatry, McLean HospitalHarvard Medical SchoolBelmontMassachusettsUSA
| | - Michal Schnaider Beeri
- Joseph Sagol Neuroscience Center, Sheba Medical CenterRamat GanIsrael
- Department of PsychiatryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- The Herbert and Jackeline Krieger Klein Alzheimer's Research CenterRutgers Biomedical and Health Sciences, Rutgers UniversityNew JerseyUSA
| | - Nicholas T. Seyfried
- Goizueta Alzheimer's Disease Research Center, Department of Neurology and Department of BiochemistryEmory University School of MedicineAtlantaGeorgiaUSA
| | - Vilas Menon
- Center for Translational and Computational NeuroimmunologyDepartment of Neurology & Taub Institute for Research on Alzheimer's disease and the Aging BrainColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Yanling Wang
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
| | - Julie A. Schneider
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
- Department of PathologyRush University Medical CenterChicagoIllinoisUSA
| | - Harvey Cantor
- Department of Cancer Immunology and VirologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of ImmunologyHarvard Medical SchoolBostonMassachusettsUSA
| | - David A. Bennett
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
- Department of Neurological SciencesRush University Medical CenterChicagoIllinoisUSA
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Bravo González-Blas C, Matetovici I, Hillen H, Taskiran II, Vandepoel R, Christiaens V, Sansores-García L, Verboven E, Hulselmans G, Poovathingal S, Demeulemeester J, Psatha N, Mauduit D, Halder G, Aerts S. Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation. Nat Cell Biol 2024; 26:153-167. [PMID: 38182825 PMCID: PMC10791584 DOI: 10.1038/s41556-023-01316-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 11/15/2023] [Indexed: 01/07/2024]
Abstract
In the mammalian liver, hepatocytes exhibit diverse metabolic and functional profiles based on their location within the liver lobule. However, it is unclear whether this spatial variation, called zonation, is governed by a well-defined gene regulatory code. Here, using a combination of single-cell multiomics, spatial omics, massively parallel reporter assays and deep learning, we mapped enhancer-gene regulatory networks across mouse liver cell types. We found that zonation affects gene expression and chromatin accessibility in hepatocytes, among other cell types. These states are driven by the repressors TCF7L1 and TBX3, alongside other core hepatocyte transcription factors, such as HNF4A, CEBPA, FOXA1 and ONECUT1. To examine the architecture of the enhancers driving these cell states, we trained a hierarchical deep learning model called DeepLiver. Our study provides a multimodal understanding of the regulatory code underlying hepatocyte identity and their zonation state that can be used to engineer enhancers with specific activity levels and zonation patterns.
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Affiliation(s)
- Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Irina Matetovici
- VIB Center for Brain & Disease Research, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
| | - Hanne Hillen
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Ibrahim Ihsan Taskiran
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Roel Vandepoel
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Leticia Sansores-García
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Elisabeth Verboven
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | | | - Jonas Demeulemeester
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Nikoleta Psatha
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - David Mauduit
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Georg Halder
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium.
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Yu KKH, Basu S, Baquer G, Ahn R, Gantchev J, Jindal S, Regan MS, Abou-Mrad Z, Prabhu MC, Williams MJ, D'Souza AD, Malinowski SW, Hopland K, Elhanati Y, Stopka SA, Stortchevoi A, He Z, Sun J, Chen Y, Espejo AB, Chow KH, Yerrum S, Kao PL, Kerrigan BP, Norberg L, Nielsen D, Puduvalli VK, Huse J, Beroukhim R, Kim YSB, Goswami S, Boire A, Frisken S, Cima MJ, Holdhoff M, Lucas CHG, Bettegowda C, Levine SS, Bale TA, Brennan C, Reardon DA, Lang FF, Antonio Chiocca E, Ligon KL, White FM, Sharma P, Tabar V, Agar NYR. Investigative needle core biopsies for multi-omics in Glioblastoma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.29.23300541. [PMID: 38234840 PMCID: PMC10793534 DOI: 10.1101/2023.12.29.23300541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Glioblastoma (GBM) is a primary brain cancer with an abysmal prognosis and few effective therapies. The ability to investigate the tumor microenvironment before and during treatment would greatly enhance both understanding of disease response and progression, as well as the delivery and impact of therapeutics. Stereotactic biopsies are a routine surgical procedure performed primarily for diagnostic histopathologic purposes. The role of investigative biopsies - tissue sampling for the purpose of understanding tumor microenvironmental responses to treatment using integrated multi-modal molecular analyses ('Multi-omics") has yet to be defined. Secondly, it is unknown whether comparatively small tissue samples from brain biopsies can yield sufficient information with such methods. Here we adapt stereotactic needle core biopsy tissue in two separate patients. In the first patient with recurrent GBM we performed highly resolved multi-omics analysis methods including single cell RNA sequencing, spatial-transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonotype analysis, and MHC Class I immunopeptidomics from biopsy tissue that was obtained from a single procedure. In a second patient we analyzed multi-regional core biopsies to decipher spatial and genomic variance. We also investigated the utility of stereotactic biopsies as a method for generating patient derived xenograft models in a separate patient cohort. Dataset integration across modalities showed good correspondence between spatial modalities, highlighted immune cell associated metabolic pathways and revealed poor correlation between RNA expression and the tumor MHC Class I immunopeptidome. In conclusion, stereotactic needle biopsy cores are of sufficient quality to generate multi-omics data, provide data rich insight into a patient's disease process and tumor immune microenvironment and can be of value in evaluating treatment responses. One sentence summary Integrative multi-omics analysis of stereotactic needle core biopsies in glioblastoma.
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Santiago CP, Gimmen MY, Lu Y, McNally MM, Duncan LH, Creamer TJ, Orzolek LD, Blackshaw S, Singh MS. Comparative Analysis of Single-cell and Single-nucleus RNA-sequencing in a Rabbit Model of Retinal Detachment-related Proliferative Vitreoretinopathy. OPHTHALMOLOGY SCIENCE 2023; 3:100335. [PMID: 37496518 PMCID: PMC10365955 DOI: 10.1016/j.xops.2023.100335] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 07/28/2023]
Abstract
Purpose Proliferative vitreoretinopathy (PVR) is the most common cause of failure of retinal reattachment surgery, and the molecular changes leading to this aberrant wound healing process are currently unknown. Our ultimate goal is to study PVR pathogenesis by employing single-cell transcriptomics to dissect cellular heterogeneity. Design Here we aimed to compare single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA-sequencing (snRNA-seq) of retinal PVR samples in the rabbit model. Participants Unilateral induction of PVR lesions in rabbit eyes with contralateral eyes serving as controls. Methods Proliferative vitreoretinopathy was induced unilaterally in Dutch Belted rabbits. At different timepoints after PVR induction, retinas were dissociated into either cells or nuclei suspension and processed for scRNA-seq or snRNA-seq. Main Outcome Measures Single cell and nuclei transcriptomic profiles of retinas after PVR induction. Results Single-cell RNA sequencing and snRNA-seq were conducted on retinas at 4 hours and 14 days after disease induction. Although the capture rate of unique molecular identifiers and genes were greater in scRNA-seq samples, overall gene expression profiles of individual cell types were highly correlated between scRNA-seq and snRNA-seq. A major disparity between the 2 sequencing modalities was the cell type capture rate, however, with glial cell types overrepresented in scRNA-seq, and inner retinal neurons were enriched by snRNA-seq. Furthermore, fibrotic Müller glia were overrepresented in snRNA-seq samples, whereas reactive Müller glia were overrepresented in scRNA-seq samples. Trajectory analyses were similar between the 2 methods, allowing for the combined analysis of the scRNA-seq and snRNA-seq data sets. Conclusions These findings highlight limitations of both scRNA-seq and snRNA-seq analysis and imply that use of both techniques together can more accurately identify transcriptional networks critical for aberrant fibrogenesis in PVR than using either in isolation. Financial Disclosures Proprietary or commercial disclosure may be found after the references.
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Affiliation(s)
- Clayton P. Santiago
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland
| | - Megan Y. Gimmen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland
| | - Yuchen Lu
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Minda M. McNally
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Leighton H. Duncan
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland
| | - Tyler J. Creamer
- Institute for Basic Biomedical Sciences, Johns Hopkins University, Baltimore, Maryland
| | - Linda D. Orzolek
- Institute for Basic Biomedical Sciences, Johns Hopkins University, Baltimore, Maryland
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, Maryland
| | - Mandeep S. Singh
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Choi H, Lee EJ, Shin JS, Kim H, Bae S, Choi Y, Lee DS. Spatiotemporal characterization of glial cell activation in an Alzheimer's disease model by spatially resolved transcriptomics. Exp Mol Med 2023; 55:2564-2575. [PMID: 38036733 PMCID: PMC10767047 DOI: 10.1038/s12276-023-01123-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 12/02/2023] Open
Abstract
The molecular changes that occur with the progression of Alzheimer's disease (AD) are well known, but an understanding of the spatiotemporal heterogeneity of changes in the brain is lacking. Here, we investigated the spatially resolved transcriptome in a 5XFAD AD model at different ages to understand regional changes at the molecular level. Spatially resolved transcriptomic data were obtained from 5XFAD AD models and age-matched control mice. Differentially expressed genes were identified using spots clustered by anatomical structures. Gene signatures of activation of microglia and astrocytes were calculated and mapped on the spatially resolved transcriptomic data. We identified early alterations in the white matter (WM) of the AD model before the definite accumulation of amyloid plaques in the gray matter (GM). Changes in the early stage of the disease involved primarily glial cell activation in the WM, whereas the changes in the later stage of pathology were prominent in the GM. We confirmed that disease-associated microglia (DAM) and astrocyte (DAA) signatures also showed initial changes in WM and that activation spreads to GM. Trajectory inference using microglial gene sets revealed the subdivision of DAMs with different spatial patterns. Taken together, these results help to understand the spatiotemporal changes associated with reactive glial cells as a major pathophysiological characteristic of AD. The heterogeneous spatial molecular changes apply to identifying diagnostic and therapeutic targets caused by amyloid accumulation in AD.
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Affiliation(s)
- Hongyoon Choi
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Eun Ji Lee
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Jin Seop Shin
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Hyun Kim
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Sungwoo Bae
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Yoori Choi
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea.
| | - Dong Soo Lee
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea.
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Wakid M, Almeida D, Aouabed Z, Rahimian R, Davoli MA, Yerko V, Leonova-Erko E, Richard V, Zahedi R, Borchers C, Turecki G, Mechawar N. Universal method for the isolation of microvessels from frozen brain tissue: A proof-of-concept multiomic investigation of the neurovasculature. Brain Behav Immun Health 2023; 34:100684. [PMID: 37822873 PMCID: PMC10562768 DOI: 10.1016/j.bbih.2023.100684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/29/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023] Open
Abstract
The neurovascular unit, comprised of vascular cell types that collectively regulate cerebral blood flow to meet the needs of coupled neurons, is paramount for the proper function of the central nervous system. The neurovascular unit gatekeeps blood-brain barrier properties, which experiences impairment in several central nervous system diseases associated with neuroinflammation and contributes to pathogenesis. To better understand function and dysfunction at the neurovascular unit and how it may confer inflammatory processes within the brain, isolation and characterization of the neurovascular unit is needed. Here, we describe a singular, standardized protocol to enrich and isolate microvessels from archived snap-frozen human and frozen mouse cerebral cortex using mechanical homogenization and centrifugation-separation that preserves the structural integrity and multicellular composition of microvessel fragments. For the first time, microvessels are isolated from postmortem ventromedial prefrontal cortex tissue and are comprehensively investigated as a structural unit using both RNA sequencing and Liquid Chromatography with tandem mass spectrometry (LC-MS/MS). Both the transcriptome and proteome are obtained and compared, demonstrating that the isolated brain microvessel is a robust model for the NVU and can be used to generate highly informative datasets in both physiological and disease contexts.
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Affiliation(s)
- Marina Wakid
- McGill Group for Suicide Studies, Douglas Research Centre, Montréal, Quebec, Canada
- Integrated Program in Neuroscience, McGill University, Montréal, Quebec, Canada
| | - Daniel Almeida
- McGill Group for Suicide Studies, Douglas Research Centre, Montréal, Quebec, Canada
- Integrated Program in Neuroscience, McGill University, Montréal, Quebec, Canada
| | - Zahia Aouabed
- McGill Group for Suicide Studies, Douglas Research Centre, Montréal, Quebec, Canada
| | - Reza Rahimian
- McGill Group for Suicide Studies, Douglas Research Centre, Montréal, Quebec, Canada
| | | | - Volodymyr Yerko
- McGill Group for Suicide Studies, Douglas Research Centre, Montréal, Quebec, Canada
| | - Elena Leonova-Erko
- McGill Group for Suicide Studies, Douglas Research Centre, Montréal, Quebec, Canada
| | - Vincent Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - René Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Christoph Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Research Centre, Montréal, Quebec, Canada
- Integrated Program in Neuroscience, McGill University, Montréal, Quebec, Canada
- Department of Psychiatry, McGill University, Montréal, Quebec, Canada
| | - Naguib Mechawar
- McGill Group for Suicide Studies, Douglas Research Centre, Montréal, Quebec, Canada
- Integrated Program in Neuroscience, McGill University, Montréal, Quebec, Canada
- Department of Psychiatry, McGill University, Montréal, Quebec, Canada
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36
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Vecchiarelli HA, Tremblay MÈ. Microglial Transcriptional Signatures in the Central Nervous System: Toward A Future of Unraveling Their Function in Health and Disease. Annu Rev Genet 2023; 57:65-86. [PMID: 37384734 DOI: 10.1146/annurev-genet-022223-093643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Microglia, the resident immune cells of the central nervous system (CNS), are primarily derived from the embryonic yolk sac and make their way to the CNS during early development. They play key physiological and immunological roles across the life span, throughout health, injury, and disease. Recent transcriptomic studies have identified gene transcript signatures expressed by microglia that may provide the foundation for unprecedented insights into their functions. Microglial gene expression signatures can help distinguish them from macrophage cell types to a reasonable degree of certainty, depending on the context. Microglial expression patterns further suggest a heterogeneous population comprised of many states that vary according to the spatiotemporal context. Microglial diversity is most pronounced during development, when extensive CNS remodeling takes place, and following disease or injury. A next step of importance for the field will be to identify the functional roles performed by these various microglial states, with the perspective of targeting them therapeutically.
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Affiliation(s)
- Haley A Vecchiarelli
- Division of Medical Sciences, University of Victoria, British Columbia, Canada; ,
| | - Marie-Ève Tremblay
- Division of Medical Sciences, University of Victoria, British Columbia, Canada; ,
- Centre for Advanced Materials and Related Technology and Institute on Aging and Lifelong Health, University of Victoria, British Columbia, Canada
- Département de Médecine Moléculaire and Axe Neurosciences, Centre de Recherche du CHU de Québec, Université Laval, Quebec, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine and Health Sciences, McGill University, Quebec, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, British Columbia, Canada
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Gonzalez-Ferrer J, Lehrer J, O’Farrell A, Paten B, Teodorescu M, Haussler D, Jonsson VD, Mostajo-Radji MA. Unraveling Neuronal Identities Using SIMS: A Deep Learning Label Transfer Tool for Single-Cell RNA Sequencing Analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.529615. [PMID: 36909548 PMCID: PMC10002667 DOI: 10.1101/2023.02.28.529615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Large single-cell RNA datasets have contributed to unprecedented biological insight. Often, these take the form of cell atlases and serve as a reference for automating cell labeling of newly sequenced samples. Yet, classification algorithms have lacked the capacity to accurately annotate cells, particularly in complex datasets. Here we present SIMS (Scalable, Interpretable Machine Learning for Single-Cell), an end-to-end data-efficient machine learning pipeline for discrete classification of single-cell data that can be applied to new datasets with minimal coding. We benchmarked SIMS against common single-cell label transfer tools and demonstrated that it performs as well or better than state of the art algorithms. We then use SIMS to classify cells in one of the most complex tissues: the brain. We show that SIMS classifies cells of the adult cerebral cortex and hippocampus at a remarkably high accuracy. This accuracy is maintained in trans-sample label transfers of the adult human cerebral cortex. We then apply SIMS to classify cells in the developing brain and demonstrate a high level of accuracy at predicting neuronal subtypes, even in periods of fate refinement, shedding light on genetic changes affecting specific cell types across development. Finally, we apply SIMS to single cell datasets of cortical organoids to predict cell identities and unveil genetic variations between cell lines. SIMS identifies cell-line differences and misannotated cell lineages in human cortical organoids derived from different pluripotent stem cell lines. When cell types are obscured by stress signals, label transfer from primary tissue improves the accuracy of cortical organoid annotations, serving as a reliable ground truth. Altogether, we show that SIMS is a versatile and robust tool for cell-type classification from single-cell datasets.
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Affiliation(s)
- Jesus Gonzalez-Ferrer
- These authors contributed equally to this work
- Genomics Institute, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
| | - Julian Lehrer
- These authors contributed equally to this work
- Genomics Institute, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
- Department of Applied Mathematics, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
| | - Ash O’Farrell
- Genomics Institute, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
| | - Benedict Paten
- Genomics Institute, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
| | - Mircea Teodorescu
- Genomics Institute, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
| | - David Haussler
- Genomics Institute, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
| | - Vanessa D. Jonsson
- Department of Applied Mathematics, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
- Co-senior authors
| | - Mohammed A. Mostajo-Radji
- Genomics Institute, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, 95060, CA, USA
- Co-senior authors
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38
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Wang Q, Antone J, Alsop E, Reiman R, Funk C, Bendl J, Dudley JT, Liang WS, Karr TL, Roussos P, Bennett DA, De Jager PL, Serrano GE, Beach TG, Keuren-Jensen KV, Mastroeni D, Reiman EM, Readhead BP. A public resource of single cell transcriptomes and multiscale networks from persons with and without Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563319. [PMID: 37961404 PMCID: PMC10634692 DOI: 10.1101/2023.10.20.563319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The emergence of technologies that can support high-throughput profiling of single cell transcriptomes offers to revolutionize the study of brain tissue from persons with and without Alzheimer's disease (AD). Integration of these data with additional complementary multiomics data such as genetics, proteomics and clinical data provides powerful opportunities to link observed cell subpopulations and molecular network features within a broader disease-relevant context. We report here single nucleus RNA sequencing (snRNA-seq) profiles generated from superior frontal gyrus cortical tissue samples from 101 exceptionally well characterized, aged subjects from the Banner Brain and Body Donation Program in combination with whole genome sequences. We report findings that link common AD risk variants with CR1 expression in oligodendrocytes as well as alterations in peripheral hematological lab parameters, with these observations replicated in an independent, prospective cohort study of ageing and dementia. We also observed an AD-associated CD83(+) microglial subtype with unique molecular networks that encompass many known regulators of AD-relevant microglial biology, and which are associated with immunoglobulin IgG4 production in the transverse colon. These findings illustrate the power of multi-tissue molecular profiling to contextualize snRNA-seq brain transcriptomics and reveal novel disease biology. The transcriptomic, genetic, phenotypic, and network data resources described within this study are available for access and utilization by the scientific community.
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39
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Gorin G, Yoshida S, Pachter L. Assessing Markovian and Delay Models for Single-Nucleus RNA Sequencing. Bull Math Biol 2023; 85:114. [PMID: 37828255 DOI: 10.1007/s11538-023-01213-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 09/11/2023] [Indexed: 10/14/2023]
Abstract
The serial nature of reactions involved in the RNA life-cycle motivates the incorporation of delays in models of transcriptional dynamics. The models couple a transcriptional process to a fairly general set of delayed monomolecular reactions with no feedback. We provide numerical strategies for calculating the RNA copy number distributions induced by these models, and solve several systems with splicing, degradation, and catalysis. An analysis of single-cell and single-nucleus RNA sequencing data using these models reveals that the kinetics of nuclear export do not appear to require invocation of a non-Markovian waiting time.
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Affiliation(s)
- Gennady Gorin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Shawn Yoshida
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, 91125, USA.
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40
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Simorgh S, Mousavi SA, To SK, Pasque V, Wierda K, Vervliet T, Yeganeh M, Pooyan P, Chai YC, Verfaillie C, Baharvand H. A facile method to generate cerebral organoids from human pluripotent stem cells. EXCLI JOURNAL 2023; 22:1055-1076. [PMID: 37927348 PMCID: PMC10620858 DOI: 10.17179/excli2023-6299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023]
Abstract
Human cerebral organoids (COs) are self-organizing three-dimensional (3D) neural structures that provide a human-specific platform to study the cellular and molecular processes that underlie different neurological events. The first step of CO generation from human pluripotent stem cells (hPSCs) is neural induction, which is an in vitro simulation of neural ectoderm development. Several signaling pathways cooperate during neural ectoderm development and in vitro differentiation of hPSCs toward neural cell lineages is also affected by them. In this study, we considered some of the known sources of these variable signaling cues arising from cell culture media components and sought to modulate their effects by applying a comprehensive combination of small molecules and growth factors for CO generation. Histological analysis demonstrated that these COs recapitulate the neural progenitor zone and early cortical layer organization, containing different types of neuronal and glial cells which was in accordance with single-nucleus transcriptome profiling results. Moreover, patch clamp and intracellular Ca2+ dynamic studies demonstrated that the COs behave as a functional neural network. Thus, this method serves as a facile protocol for generating hPSC-derived COs that faithfully mimic the features of their in vivo counterparts in the developing human brain. See also Figure 1(Fig. 1).
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Affiliation(s)
- Susan Simorgh
- Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Seyed Ahmad Mousavi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - San Kit To
- Department of Development and Regeneration, Lab for Epigenetic Reprogramming, Leuven Stem Cell Institute, Leuven Single-Cell Omics Institute and Leuven Cancer Institute, KU Leuven-University of Leuven, Leuven 3000, Belgium
| | - Vincent Pasque
- Department of Development and Regeneration, Lab for Epigenetic Reprogramming, Leuven Stem Cell Institute, Leuven Single-Cell Omics Institute and Leuven Cancer Institute, KU Leuven-University of Leuven, Leuven 3000, Belgium
| | - Keimpe Wierda
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- Electrophysiology Unit, Leuven 3000, Belgium
| | - Tim Vervliet
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Meghdad Yeganeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Paria Pooyan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Yoke Chin Chai
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Catherine Verfaillie
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Hossein Baharvand
- Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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Myers BL, Brayer KJ, Paez-Beltran LE, Keith MS, Suzuki H, Newville J, Anderson RH, Lo Y, Mertz CM, Kollipara R, Borromeo MD, Bachoo RM, Johnson JE, Vue TY. Glioblastoma initiation, migration, and cell types are regulated by core bHLH transcription factors ASCL1 and OLIG2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.30.560206. [PMID: 37873200 PMCID: PMC10592871 DOI: 10.1101/2023.09.30.560206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Glioblastomas (GBMs) are highly aggressive, infiltrative, and heterogeneous brain tumors driven by complex driver mutations and glioma stem cells (GSCs). The neurodevelopmental transcription factors ASCL1 and OLIG2 are co-expressed in GBMs, but their role in regulating the heterogeneity and hierarchy of GBM tumor cells is unclear. Here, we show that oncogenic driver mutations lead to dysregulation of ASCL1 and OLIG2, which function redundantly to initiate brain tumor formation in a mouse model of GBM. Subsequently, the dynamic levels and reciprocal binding of ASCL1 and OLIG2 to each other and to downstream target genes then determine the cell types and degree of migration of tumor cells. Single-cell RNA sequencing (scRNA-seq) reveals that a high level of ASCL1 is key in defining GSCs by upregulating a collection of ribosomal protein, mitochondrial, neural stem cell (NSC), and cancer metastasis genes - all essential for sustaining the high proliferation, migration, and therapeutic resistance of GSCs.
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Liu Z, Yang J, Long Y, Zhang C, Wang D, Zhang X, Dong W, Zhao L, Liu C, Zhai J, Wang E. Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago. NATURE PLANTS 2023; 9:1734-1748. [PMID: 37749242 DOI: 10.1038/s41477-023-01524-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 08/25/2023] [Indexed: 09/27/2023]
Abstract
Establishing legume-rhizobial symbiosis requires precise coordination of complex responses in a time- and cell type-specific manner. Encountering Rhizobium, rapid changes of gene expression levels in host plants occur in the first few hours, which prepare the plants to turn off defence and form a symbiotic relationship with the microbes. Here, we applied single-nucleus RNA sequencing to characterize the roots of Medicago truncatula at 30 min, 6 h and 24 h after nod factor treatment. We found drastic global gene expression reprogramming at 30 min in the epidermis and cortex and most of these changes were restored at 6 h. Moreover, plant defence response genes are activated at 30 min and subsequently suppressed at 6 h in non-meristem cells. Only in the cortical cells but not in other cell types, we found the flavonoid synthase genes required to recruit rhizobia are highly expressed 30 min after inoculation with nod factors. A gene module enriched for symbiotic nitrogen fixation genes showed that MtFER (MtFERONIA) and LYK3 (LysM domain receptor-like kinase 3) share similar responses to symbiotic signals. We further found that MtFER can be phosphorylated by LYK3 and it participates in rhizobial symbiosis. Our results expand our understanding of dynamic spatiotemporal symbiotic responses at the single-cell level.
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Affiliation(s)
- Zhijian Liu
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Jun Yang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yanping Long
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Chi Zhang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Dapeng Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaowei Zhang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wentao Dong
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Li Zhao
- School of Life Sciences, Division of Life Sciences and Medicine, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
| | - Chengwu Liu
- School of Life Sciences, Division of Life Sciences and Medicine, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
| | - Jixian Zhai
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, China.
| | - Ertao Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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Chatzinakos C, Pernia CD, Morrison FG, Iatrou A, McCullough KM, Schuler H, Snijders C, Bajaj T, DiPietro CP, Soliva Estruch M, Gassen NC, Anastasopoulos C, Bharadwaj RA, Bowlby BC, Hartmann J, Maihofer AX, Nievergelt CM, Ressler NM, Wolf EJ, Carlezon WA, Krystal JH, Kleinman JE, Girgenti MJ, Huber BR, Kellis M, Logue MW, Miller MW, Ressler KJ, Daskalakis NP. Single-Nucleus Transcriptome Profiling of Dorsolateral Prefrontal Cortex: Mechanistic Roles for Neuronal Gene Expression, Including the 17q21.31 Locus, in PTSD Stress Response. Am J Psychiatry 2023; 180:739-754. [PMID: 37491937 DOI: 10.1176/appi.ajp.20220478] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
OBJECTIVE Multidisciplinary studies of posttraumatic stress disorder (PTSD) and major depressive disorder (MDD) implicate the dorsolateral prefrontal cortex (DLPFC) in disease risk and pathophysiology. Postmortem brain studies have relied on bulk-tissue RNA sequencing (RNA-seq), but single-cell RNA-seq is needed to dissect cell-type-specific mechanisms. The authors conducted the first single-nucleus RNA-seq postmortem brain study in PTSD to elucidate disease transcriptomic pathology with cell-type-specific resolution. METHOD Profiling of 32 DLPFC samples from 11 individuals with PTSD, 10 with MDD, and 11 control subjects was conducted (∼415K nuclei; >13K cells per sample). A replication sample included 15 DLPFC samples (∼160K nuclei; >11K cells per sample). RESULTS Differential gene expression analyses identified significant single-nucleus RNA-seq differentially expressed genes (snDEGs) in excitatory (EX) and inhibitory (IN) neurons and astrocytes, but not in other cell types or bulk tissue. MDD samples had more false discovery rate-corrected significant snDEGs, and PTSD samples had a greater replication rate. In EX and IN neurons, biological pathways that were differentially enriched in PTSD compared with MDD included glucocorticoid signaling. Furthermore, glucocorticoid signaling in induced pluripotent stem cell (iPSC)-derived cortical neurons demonstrated greater relevance in PTSD and opposite direction of regulation compared with MDD, especially in EX neurons. Many snDEGs were from the 17q21.31 locus and are particularly interesting given causal roles in disease pathogenesis and DLPFC-based neuroimaging (PTSD: ARL17B, LINC02210-CRHR1, and LRRC37A2; MDD: LRRC37A and LRP4), while others were regulated by glucocorticoids in iPSC-derived neurons (PTSD: SLC16A6, TAF1C; MDD: CDH3). CONCLUSIONS The study findings point to cell-type-specific mechanisms of brain stress response in PTSD and MDD, highlighting the importance of examining cell-type-specific gene expression and indicating promising novel biomarkers and therapeutic targets.
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Affiliation(s)
- Chris Chatzinakos
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Cameron D Pernia
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Filomene G Morrison
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Artemis Iatrou
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Kenneth M McCullough
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Heike Schuler
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Clara Snijders
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Thomas Bajaj
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Christopher P DiPietro
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Marina Soliva Estruch
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Nils C Gassen
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Constantin Anastasopoulos
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Rahul A Bharadwaj
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Benjamin C Bowlby
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Jakob Hartmann
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Adam X Maihofer
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Caroline M Nievergelt
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Nicholas M Ressler
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Erika J Wolf
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - William A Carlezon
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - John H Krystal
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Joel E Kleinman
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Matthew J Girgenti
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Bertrand R Huber
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Manolis Kellis
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Mark W Logue
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Mark W Miller
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Kerry J Ressler
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
| | - Nikolaos P Daskalakis
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Mass. (Chatzinakos, Pernia, Iatrou, McCullough, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Hartmann, N.M. Ressler, Carlezon, K.J. Ressler, Daskalakis); Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Mass. (Chatzinakos, Pernia, Iatrou, Schuler, Snijders, DiPietro, Soliva Estruch, Anastasopoulos, Bowlby, Daskalakis); National Center for PTSD, VA Boston Healthcare System, Boston (Morrison, Wolf, Logue, Miller); Department of Psychiatry (Morrison, Wolf, Logue, Miller), Department of Neurology (Huber), and Department of Biomedical Genetics (Logue), Boston University School of Medicine, Boston; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands (Soliva Estruch, Snijders); RG Neurohomeostasis, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Bonn, Bonn, Germany (Bajaj, Gassen); Department of Radiology, University Hospital Basel, University of Basel, Basel, Switzerland (Anastasopoulos); Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore (Bharadwaj, Kleinman); Department of Psychiatry, University of California San Diego, La Jolla (Maihofer, Nievergelt); Center for Excellence in Stress and Mental Health (Maihofer, Nievergelt) and Research Service (Maihofer, Nievergelt), Veterans Affairs San Diego Healthcare System, San Diego; Department of Psychiatry, Yale University School of Medicine, New Haven, Conn. (Krystal, Girgenti); Psychiatry Service, VA Connecticut Healthcare System, West Haven (Krystal, Girgenti); National Center for PTSD, Clinical Neurosciences Division, U.S. Department of Veterans Affairs, West Haven, Conn. (Krystal, Girgenti); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Kleinman); Pathology and Laboratory Medicine, VA Boston Healthcare System, Boston (Huber); Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, and Broad Institute of MIT and Harvard, Cambridge, Mass. (Kellis); Department of Biostatistics, Boston University School of Public Health, Boston (Logue)
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O'Neill NK, Stein TD, Hu J, Rehman H, Campbell JD, Yajima M, Zhang X, Farrer LA. Bulk brain tissue cell-type deconvolution with bias correction for single-nuclei RNA sequencing data using DeTREM. BMC Bioinformatics 2023; 24:349. [PMID: 37726653 PMCID: PMC10507917 DOI: 10.1186/s12859-023-05476-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: 12/06/2022] [Accepted: 09/12/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND Quantifying cell-type abundance in bulk tissue RNA-sequencing enables researchers to better understand complex systems. Newer deconvolution methodologies, such as MuSiC, use cell-type signatures derived from single-cell RNA-sequencing (scRNA-seq) data to make these calculations. Single-nuclei RNA-sequencing (snRNA-seq) reference data can be used instead of scRNA-seq data for tissues such as human brain where single-cell data are difficult to obtain, but accuracy suffers due to sequencing differences between the technologies. RESULTS We propose a modification to MuSiC entitled 'DeTREM' which compensates for sequencing differences between the cell-type signature and bulk RNA-seq datasets in order to better predict cell-type fractions. We show DeTREM to be more accurate than MuSiC in simulated and real human brain bulk RNA-sequencing datasets with various cell-type abundance estimates. We also compare DeTREM to SCDC and CIBERSORTx, two recent deconvolution methods that use scRNA-seq cell-type signatures. We find that they perform well in simulated data but produce less accurate results than DeTREM when used to deconvolute human brain data. CONCLUSION DeTREM improves the deconvolution accuracy of MuSiC and outperforms other deconvolution methods when applied to snRNA-seq data. DeTREM enables accurate cell-type deconvolution in situations where scRNA-seq data are not available. This modification improves characterization cell-type specific effects in brain tissue and identification of cell-type abundance differences under various conditions.
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Affiliation(s)
- Nicholas K O'Neill
- Bioinformatics Program, Boston University, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Thor D Stein
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Veterans Administration Medical Center, Bedford, MA, USA
| | - Junming Hu
- Bioinformatics Program, Boston University, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Habbiburr Rehman
- Department of Medicine (Biomedical Genetics), Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Joshua D Campbell
- Bioinformatics Program, Boston University, Boston, MA, USA
- Department of Medicine (Computational Biomedicine), Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Masanao Yajima
- Department of Mathematics and Statistics, Boston University, Boston, MA, USA
| | - Xiaoling Zhang
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Department of Medicine (Biomedical Genetics), Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, USA.
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
| | - Lindsay A Farrer
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Department of Medicine (Biomedical Genetics), Boston University, Chobanian & Avedisian School of Medicine, Boston, MA, USA.
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
- Department of Ophthalmology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA.
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Tzioras M, Daniels MJD, Davies C, Baxter P, King D, McKay S, Varga B, Popovic K, Hernandez M, Stevenson AJ, Barrington J, Drinkwater E, Borella J, Holloway RK, Tulloch J, Moss J, Latta C, Kandasamy J, Sokol D, Smith C, Miron VE, Káradóttir RT, Hardingham GE, Henstridge CM, Brennan PM, McColl BW, Spires-Jones TL. Human astrocytes and microglia show augmented ingestion of synapses in Alzheimer's disease via MFG-E8. Cell Rep Med 2023; 4:101175. [PMID: 37652017 PMCID: PMC10518633 DOI: 10.1016/j.xcrm.2023.101175] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 01/30/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023]
Abstract
Synapse loss correlates with cognitive decline in Alzheimer's disease (AD). Data from mouse models suggests microglia are important for synapse degeneration, but direct human evidence for any glial involvement in synapse removal in human AD remains to be established. Here we observe astrocytes and microglia from human brains contain greater amounts of synaptic protein in AD compared with non-disease controls, and that proximity to amyloid-β plaques and the APOE4 risk gene exacerbate this effect. In culture, mouse and human astrocytes and primary mouse and human microglia phagocytose AD patient-derived synapses more than synapses from controls. Inhibiting interactions of MFG-E8 rescues the elevated engulfment of AD synapses by astrocytes and microglia without affecting control synapse uptake. Thus, AD promotes increased synapse ingestion by human glial cells at least in part via an MFG-E8 opsonophagocytic mechanism with potential for targeted therapeutic manipulation.
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Affiliation(s)
- Makis Tzioras
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Michael J D Daniels
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Caitlin Davies
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Paul Baxter
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Declan King
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Sean McKay
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Balazs Varga
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Karla Popovic
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Madison Hernandez
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Anna J Stevenson
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Jack Barrington
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Elizabeth Drinkwater
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Julia Borella
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Rebecca K Holloway
- MRC Centre for Reproductive Health, the University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Jane Tulloch
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Jonathan Moss
- MRC Centre for Reproductive Health, the University of Edinburgh, Edinburgh EH16 4TJ, UK; The Roslin Institute, the Royal (Dick) School of Veterinary Studies, the University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Clare Latta
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Jothy Kandasamy
- Department of Clinical Neurosciences, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Drahoslav Sokol
- Department of Clinical Neurosciences, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Colin Smith
- Centre for Clinical Brain Sciences, the University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Veronique E Miron
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; MRC Centre for Reproductive Health, the University of Edinburgh, Edinburgh EH16 4TJ, UK; Barlo Multiple Sclerosis Centre at St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, ON M5B 1T8, Canada
| | | | - Giles E Hardingham
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK
| | | | - Paul M Brennan
- Department of Clinical Neurosciences, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK; Centre for Clinical Brain Sciences, the University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Barry W McColl
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK.
| | - Tara L Spires-Jones
- UK Dementia Research Institute, the University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Discovery Brain Sciences, the University of Edinburgh, Edinburgh EH8 9JZ, UK.
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Feng W, Liu S, Deng Q, Fu S, Yang Y, Dai X, Wang S, Wang Y, Liu Y, Lin X, Pan X, Hao S, Yuan Y, Gu Y, Zhang X, Li H, Liu L, Liu C, Fei JF, Wei X. A scATAC-seq atlas of chromatin accessibility in axolotl brain regions. Sci Data 2023; 10:627. [PMID: 37709774 PMCID: PMC10502032 DOI: 10.1038/s41597-023-02533-0] [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: 05/18/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
Axolotl (Ambystoma mexicanum) is an excellent model for investigating regeneration, the interaction between regenerative and developmental processes, comparative genomics, and evolution. The brain, which serves as the material basis of consciousness, learning, memory, and behavior, is the most complex and advanced organ in axolotl. The modulation of transcription factors is a crucial aspect in determining the function of diverse regions within the brain. There is, however, no comprehensive understanding of the gene regulatory network of axolotl brain regions. Here, we utilized single-cell ATAC sequencing to generate the chromatin accessibility landscapes of 81,199 cells from the olfactory bulb, telencephalon, diencephalon and mesencephalon, hypothalamus and pituitary, and the rhombencephalon. Based on these data, we identified key transcription factors specific to distinct cell types and compared cell type functions across brain regions. Our results provide a foundation for comprehensive analysis of gene regulatory programs, which are valuable for future studies of axolotl brain development, regeneration, and evolution, as well as on the mechanisms underlying cell-type diversity in vertebrate brains.
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Affiliation(s)
- Weimin Feng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Shuai Liu
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Qiuting Deng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Sulei Fu
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, 510631, China
| | - Yunzhi Yang
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Xi Dai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Shuai Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Yijin Wang
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yang Liu
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Xiumei Lin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Xiangyu Pan
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
- Guangdong Cardiovsacular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Shijie Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Yue Yuan
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | - Ying Gu
- BGI-Shenzhen, Shenzhen, 518103, China
| | | | - Hanbo Li
- BGI-Shenzhen, Shenzhen, 518103, China
- BGI-Qingdao, Qingdao, 266555, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
| | - Longqi Liu
- BGI-Hangzhou, Hangzhou, 310012, China
- BGI-Shenzhen, Shenzhen, 518103, China
| | | | - Ji-Feng Fei
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China.
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China.
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China.
| | - Xiaoyu Wei
- BGI-Hangzhou, Hangzhou, 310012, China.
- BGI-Shenzhen, Shenzhen, 518103, China.
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47
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Lemcke R, Egebjerg C, Berendtsen NT, Egerod KL, Thomsen AR, Pers TH, Christensen JP, Kornum BR. Molecular consequences of peripheral Influenza A infection on cell populations in the murine hypothalamus. eLife 2023; 12:RP87515. [PMID: 37698546 PMCID: PMC10497288 DOI: 10.7554/elife.87515] [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: 09/13/2023] Open
Abstract
Infection with Influenza A virus (IAV) causes the well-known symptoms of the flu, including fever, loss of appetite, and excessive sleepiness. These responses, mediated by the brain, will normally disappear once the virus is cleared from the system, but a severe respiratory virus infection may cause long-lasting neurological disturbances. These include encephalitis lethargica and narcolepsy. The mechanisms behind such long lasting changes are unknown. The hypothalamus is a central regulator of the homeostatic response during a viral challenge. To gain insight into the neuronal and non-neuronal molecular changes during an IAV infection, we intranasally infected mice with an H1N1 virus and extracted the brain at different time points. Using single-nucleus RNA sequencing (snRNA-seq) of the hypothalamus, we identify transcriptional effects in all identified cell populations. The snRNA-seq data showed the most pronounced transcriptional response at 3 days past infection, with a strong downregulation of genes across all cell types. General immune processes were mainly impacted in microglia, the brain resident immune cells, where we found increased numbers of cells expressing pro-inflammatory gene networks. In addition, we found that most neuronal cell populations downregulated genes contributing to the energy homeostasis in mitochondria and protein translation in the cytosol, indicating potential reduced cellular and neuronal activity. This might be a preventive mechanism in neuronal cells to avoid intracellular viral replication and attack by phagocytosing cells. The change of microglia gene activity suggest that this is complemented by a shift in microglia activity to provide increased surveillance of their surroundings.
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Affiliation(s)
- René Lemcke
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Christine Egebjerg
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Nicolai T Berendtsen
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Kristoffer L Egerod
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Allan R Thomsen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Tune H Pers
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Jan P Christensen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Birgitte R Kornum
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
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Paryani F, Kwon JS, Ng CW, Madden N, Ofori K, Tang A, Lu H, Li J, Mahajan A, Davidson SM, Basile A, McHugh C, Vonsattel JP, Hickman R, Zody M, Houseman DE, Goldman JE, Yoo AS, Menon V, Al-Dalahmah O. Multi-OMIC analysis of Huntington disease reveals a neuroprotective astrocyte state. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.08.556867. [PMID: 37745577 PMCID: PMC10515780 DOI: 10.1101/2023.09.08.556867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Huntington disease (HD) is an incurable neurodegenerative disease characterized by neuronal loss and astrogliosis. One hallmark of HD is the selective neuronal vulnerability of striatal medium spiny neurons. To date, the underlying mechanisms of this selective vulnerability have not been fully defined. Here, we employed a multi-omic approach including single nucleus RNAseq (snRNAseq), bulk RNAseq, lipidomics, HTT gene CAG repeat length measurements, and multiplexed immunofluorescence on post-mortem brain tissue from multiple brain regions of HD and control donors. We defined a signature of genes that is driven by CAG repeat length and found it enriched in astrocytic and microglial genes. Moreover, weighted gene correlation network analysis showed loss of connectivity of astrocytic and microglial modules in HD and identified modules that correlated with CAG-repeat length which further implicated inflammatory pathways and metabolism. We performed lipidomic analysis of HD and control brains and identified several lipid species that correlate with HD grade, including ceramides and very long chain fatty acids. Integration of lipidomics and bulk transcriptomics identified a consensus gene signature that correlates with HD grade and HD lipidomic abnormalities and implicated the unfolded protein response pathway. Because astrocytes are critical for brain lipid metabolism and play important roles in regulating inflammation, we analyzed our snRNAseq dataset with an emphasis on astrocyte pathology. We found two main astrocyte types that spanned multiple brain regions; these types correspond to protoplasmic astrocytes, and fibrous-like - CD44-positive, astrocytes. HD pathology was differentially associated with these cell types in a region-specific manner. One protoplasmic astrocyte cluster showed high expression of metallothionein genes, the depletion of this cluster positively correlated with the depletion of vulnerable medium spiny neurons in the caudate nucleus. We confirmed that metallothioneins were increased in cingulate HD astrocytes but were unchanged or even decreased in caudate astrocytes. We combined existing genome-wide association studies (GWAS) with a GWA study conducted on HD patients from the original Venezuelan cohort and identified a single-nucleotide polymorphism in the metallothionein gene locus associated with delayed age of onset. Functional studies found that metallothionein overexpressing astrocytes are better able to buffer glutamate and were neuroprotective of patient-derived directly reprogrammed HD MSNs as well as against rotenone-induced neuronal death in vitro. Finally, we found that metallothionein-overexpressing astrocytes increased the phagocytic activity of microglia in vitro and increased the expression of genes involved in fatty acid binding. Together, we identified an astrocytic phenotype that is regionally-enriched in less vulnerable brain regions that can be leveraged to protect neurons in HD.
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Affiliation(s)
- Fahad Paryani
- Department of Neurology, Columbia University Irving Medical Center
| | - Ji-Sun Kwon
- Washington University School of Medicine in St. Louis
| | - Chris W Ng
- Massachusetts Institute of Technology, Department of Biological Engineering
| | - Nacoya Madden
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Kenneth Ofori
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Alice Tang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Hong Lu
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Juncheng Li
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Aayushi Mahajan
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Shawn M. Davidson
- Princeton University, Lewis-Sigler Institute for Integrative Genomics
| | | | | | - Jean Paul Vonsattel
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Richard Hickman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | | | - David E. Houseman
- Massachusetts Institute of Technology, Department of Biological Engineering
| | - James E. Goldman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
| | - Andrew S. Yoo
- Washington University School of Medicine in St. Louis
| | - Vilas Menon
- Department of Neurology, Columbia University Irving Medical Center
| | - Osama Al-Dalahmah
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center
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49
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Daniels RR, Taylor RS, Robledo D, Macqueen DJ. Single cell genomics as a transformative approach for aquaculture research and innovation. REVIEWS IN AQUACULTURE 2023; 15:1618-1637. [PMID: 38505116 PMCID: PMC10946576 DOI: 10.1111/raq.12806] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 03/21/2024]
Abstract
Single cell genomics encompasses a suite of rapidly maturing technologies that measure the molecular profiles of individual cells within target samples. These approaches provide a large up-step in biological information compared to long-established 'bulk' methods that profile the average molecular profiles of all cells in a sample, and have led to transformative advances in understanding of cellular biology, particularly in humans and model organisms. The application of single cell genomics is fast expanding to non-model taxa, including aquaculture species, where numerous research applications are underway with many more envisaged. In this review, we highlight the potential transformative applications of single cell genomics in aquaculture research, considering barriers and potential solutions to the broad uptake of these technologies. Focusing on single cell transcriptomics, we outline considerations for experimental design, including the essential requirement to obtain high quality cells/nuclei for sequencing in ectothermic aquatic species. We further outline data analysis and bioinformatics considerations, tailored to studies with the under-characterized genomes of aquaculture species, where our knowledge of cellular heterogeneity and cell marker genes is immature. Overall, this review offers a useful source of knowledge for researchers aiming to apply single cell genomics to address biological challenges faced by the global aquaculture sector though an improved understanding of cell biology.
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Affiliation(s)
- Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
| | - Richard S. Taylor
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
| | - Daniel J. Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianUK
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50
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Arbabi K, Jiang Y, Howard D, Nigam A, Inoue W, Gonzalez-Burgos G, Felsky D, Tripathy SJ. Investigating microglia-neuron crosstalk by characterizing microglial contamination in human and mouse patch-seq datasets. iScience 2023; 26:107329. [PMID: 37520693 PMCID: PMC10374462 DOI: 10.1016/j.isci.2023.107329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 04/25/2023] [Accepted: 07/06/2023] [Indexed: 08/01/2023] Open
Abstract
Microglia are cells with diverse roles, including the regulation of neuronal excitability. We leveraged Patch-seq to assess the presence and effects of microglia in the local microenvironment of recorded neurons. We first quantified the amounts of microglial transcripts in three Patch-seq datasets of human and mouse neocortical neurons, observing extensive contamination. Variation in microglial contamination was explained foremost by donor identity, particularly in human samples, and additionally by neuronal cell type identity in mice. Gene set enrichment analysis suggests that microglial contamination is reflective of activated microglia, and that these transcriptional signatures are distinct from those captured via single-nucleus RNA-seq. Finally, neurons with greater microglial contamination differed markedly in their electrophysiological characteristics, including lowered input resistances and more depolarized action potential thresholds. Our results generalize beyond Patch-seq to suggest that activated microglia may be widely present across brain slice preparations and contribute to neuron- and donor-related electrophysiological variability in vitro.
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Affiliation(s)
- Keon Arbabi
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Yiyue Jiang
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Derek Howard
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Anukrati Nigam
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Wataru Inoue
- Robarts Research Institute, Western University, London, Canada
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Guillermo Gonzalez-Burgos
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, 3811 O’Hara Street, Pittsburgh, PA 15213, USA
| | - Daniel Felsky
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Shreejoy J. Tripathy
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
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