1
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Clark IC, Mudvari P, Thaploo S, Smith S, Abu-Laban M, Hamouda M, Theberge M, Shah S, Ko SH, Pérez L, Bunis DG, Lee JS, Kilam D, Zakaria S, Choi S, Darko S, Henry AR, Wheeler MA, Hoh R, Butrus S, Deeks SG, Quintana FJ, Douek DC, Abate AR, Boritz EA. HIV silencing and cell survival signatures in infected T cell reservoirs. Nature 2023; 614:318-325. [PMID: 36599978 PMCID: PMC9908556 DOI: 10.1038/s41586-022-05556-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/11/2022] [Indexed: 01/06/2023]
Abstract
Rare CD4 T cells that contain HIV under antiretroviral therapy represent an important barrier to HIV cure1-3, but the infeasibility of isolating and characterizing these cells in their natural state has led to uncertainty about whether they possess distinctive attributes that HIV cure-directed therapies might exploit. Here we address this challenge using a microfluidic technology that isolates the transcriptomes of HIV-infected cells based solely on the detection of HIV DNA. HIV-DNA+ memory CD4 T cells in the blood from people receiving antiretroviral therapy showed inhibition of six transcriptomic pathways, including death receptor signalling, necroptosis signalling and antiproliferative Gα12/13 signalling. Moreover, two groups of genes identified by network co-expression analysis were significantly associated with HIV-DNA+ cells. These genes (n = 145) accounted for just 0.81% of the measured transcriptome and included negative regulators of HIV transcription that were higher in HIV-DNA+ cells, positive regulators of HIV transcription that were lower in HIV-DNA+ cells, and other genes involved in RNA processing, negative regulation of mRNA translation, and regulation of cell state and fate. These findings reveal that HIV-infected memory CD4 T cells under antiretroviral therapy are a distinctive population with host gene expression patterns that favour HIV silencing, cell survival and cell proliferation, with important implications for the development of HIV cure strategies.
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Affiliation(s)
- Iain C Clark
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California, San Francisco, San Francisco, CA, USA
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Bioengineering, California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA, USA
| | - Prakriti Mudvari
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shravan Thaploo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Samuel Smith
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mohammad Abu-Laban
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mehdi Hamouda
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Marc Theberge
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sakshi Shah
- Department of Bioengineering, California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA, USA
| | - Sung Hee Ko
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Liliana Pérez
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel G Bunis
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - James S Lee
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Divya Kilam
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Saami Zakaria
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sally Choi
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Samuel Darko
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amy R Henry
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Salwan Butrus
- Department of Chemical and Biomolecular Engineering, California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California, San Francisco, San Francisco, CA, USA.
| | - Eli A Boritz
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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2
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Clark IC, Wheeler MA, Lee HG, Li Z, Sanmarco LM, Thaploo S, Polonio CM, Shin SW, Scalisi G, Henry AR, Rone JM, Giovannoni F, Charabati M, Akl CF, Aleman DM, Zandee SEJ, Prat A, Douek DC, Boritz EA, Quintana FJ, Abate AR. Identification of astrocyte regulators by nucleic acid cytometry. Nature 2023; 614:326-333. [PMID: 36599367 PMCID: PMC9980163 DOI: 10.1038/s41586-022-05613-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/30/2022] [Indexed: 01/06/2023]
Abstract
Multiple sclerosis is a chronic inflammatory disease of the central nervous system1. Astrocytes are heterogeneous glial cells that are resident in the central nervous system and participate in the pathogenesis of multiple sclerosis and its model experimental autoimmune encephalomyelitis2,3. However, few unique surface markers are available for the isolation of astrocyte subsets, preventing their analysis and the identification of candidate therapeutic targets; these limitations are further amplified by the rarity of pathogenic astrocytes. Here, to address these challenges, we developed focused interrogation of cells by nucleic acid detection and sequencing (FIND-seq), a high-throughput microfluidic cytometry method that combines encapsulation of cells in droplets, PCR-based detection of target nucleic acids and droplet sorting to enable in-depth transcriptomic analyses of cells of interest at single-cell resolution. We applied FIND-seq to study the regulation of astrocytes characterized by the splicing-driven activation of the transcription factor XBP1, which promotes disease pathology in multiple sclerosis and experimental autoimmune encephalomyelitis4. Using FIND-seq in combination with conditional-knockout mice, in vivo CRISPR-Cas9-driven genetic perturbation studies and bulk and single-cell RNA sequencing analyses of samples from mouse experimental autoimmune encephalomyelitis and humans with multiple sclerosis, we identified a new role for the nuclear receptor NR3C2 and its corepressor NCOR2 in limiting XBP1-driven pathogenic astrocyte responses. In summary, we used FIND-seq to identify a therapeutically targetable mechanism that limits XBP1-driven pathogenic astrocyte responses. FIND-seq enables the investigation of previously inaccessible cells, including rare cell subsets defined by unique gene expression signatures or other nucleic acid markers.
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Affiliation(s)
- Iain C Clark
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering, College of Engineering, California Institute for Quantitative Biosciences, QB3, University of California Berkeley, Berkeley, CA, USA
| | - Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hong-Gyun Lee
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhaorong Li
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Liliana M Sanmarco
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shravan Thaploo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Carolina M Polonio
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Seung Won Shin
- Department of Bioengineering, College of Engineering, California Institute for Quantitative Biosciences, QB3, University of California Berkeley, Berkeley, CA, USA
| | - Giulia Scalisi
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joseph M Rone
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Federico Giovannoni
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marc Charabati
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Camilo Faust Akl
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dulce M Aleman
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephanie E J Zandee
- Neuroimmunology Research Lab, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Alexandre Prat
- Neuroimmunology Research Lab, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Eli A Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California San Francisco, San Francisco, CA, USA.
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3
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Clark I, Mudvari P, Thaploo S, Smith S, Abu-Laban M, Deeks S, Quintana F, Douek D, Abate A, Boritz E. OP 1.2 – 00157 HIV Silencing and Cell Survival Signatures of HIV-Infected CD4 T Cell Transcriptomes under Antiretroviral Therapy (ART). J Virus Erad 2022. [DOI: 10.1016/j.jve.2022.100097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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4
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Clark IC, Delley CL, Sun C, Thakur R, Stott SL, Thaploo S, Li Z, Quintana FJ, Abate AR. Targeted Single-Cell RNA and DNA Sequencing With Fluorescence-Activated Droplet Merger. Anal Chem 2020; 92:14616-14623. [PMID: 33049138 PMCID: PMC8182774 DOI: 10.1021/acs.analchem.0c03059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Analyzing every cell in a diverse sample provides insight into population-level heterogeneity, but abundant cell types dominate the analysis and rarer populations are scarcely represented in the data. To focus on specific cell types, the current paradigm is to physically isolate subsets of interest prior to analysis; however, it remains difficult to isolate and then single-cell sequence such populations because of compounding losses. Here, we describe an alternative approach that selectively merges cells with reagents to achieve enzymatic reactions without having to physically isolate cells. We apply this technique to perform single-cell transcriptome and genome sequencing of specific cell subsets. Our method for analyzing heterogeneous populations obviates the need for pre- or post-enrichment and simplifies single-cell workflows, making it useful for other applications in single-cell biology, combinatorial chemical synthesis, and drug screening.
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Affiliation(s)
- Iain C Clark
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Cyrille L Delley
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Chen Sun
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Rohan Thakur
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Shannon L Stott
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Shravan Thaploo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Zhaorong Li
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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5
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Wheeler MA, Clark IC, Tjon EC, Li Z, Zandee SEJ, Couturier CP, Watson BR, Scalisi G, Alkwai S, Rothhammer V, Rotem A, Heyman JA, Thaploo S, Sanmarco LM, Ragoussis J, Weitz DA, Petrecca K, Moffitt JR, Becher B, Antel JP, Prat A, Quintana FJ. MAFG-driven astrocytes promote CNS inflammation. Nature 2020; 578:593-599. [PMID: 32051591 PMCID: PMC8049843 DOI: 10.1038/s41586-020-1999-0] [Citation(s) in RCA: 248] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 12/16/2019] [Indexed: 01/14/2023]
Abstract
Multiple sclerosis is a chronic inflammatory disease of the CNS1. Astrocytes contribute to the pathogenesis of multiple sclerosis2, but little is known about the heterogeneity of astrocytes and its regulation. Here we report the analysis of astrocytes in multiple sclerosis and its preclinical model experimental autoimmune encephalomyelitis (EAE) by single-cell RNA sequencing in combination with cell-specific Ribotag RNA profiling, assay for transposase-accessible chromatin with sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing (ChIP-seq), genome-wide analysis of DNA methylation and in vivo CRISPR-Cas9-based genetic perturbations. We identified astrocytes in EAE and multiple sclerosis that were characterized by decreased expression of NRF2 and increased expression of MAFG, which cooperates with MAT2α to promote DNA methylation and represses antioxidant and anti-inflammatory transcriptional programs. Granulocyte-macrophage colony-stimulating factor (GM-CSF) signalling in astrocytes drives the expression of MAFG and MAT2α and pro-inflammatory transcriptional modules, contributing to CNS pathology in EAE and, potentially, multiple sclerosis. Our results identify candidate therapeutic targets in multiple sclerosis.
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Affiliation(s)
- Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Centre of Excellence for Biomedicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Iain C Clark
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily C Tjon
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhaorong Li
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephanie E J Zandee
- Neuroimmunology Unit, Centre de recherche du CHUM (CRCHUM), Montreal, Quebec, Canada
- Department of Neuroscience, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Charles P Couturier
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Brianna R Watson
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Giulia Scalisi
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sarah Alkwai
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Centre of Excellence for Biomedicine, Brigham and Women's Hospital, Boston, MA, USA
- Centre of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Veit Rothhammer
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Assaf Rotem
- Department of Physics, Harvard University, Cambridge, MA, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - John A Heyman
- Department of Physics, Harvard University, Cambridge, MA, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Shravan Thaploo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Liliana M Sanmarco
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jiannis Ragoussis
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - David A Weitz
- Department of Physics, Harvard University, Cambridge, MA, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Kevin Petrecca
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Jeffrey R Moffitt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Jack P Antel
- Neuroimmunology Unit, Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Alexandre Prat
- Neuroimmunology Unit, Centre de recherche du CHUM (CRCHUM), Montreal, Quebec, Canada
- Department of Neuroscience, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Centre of Excellence for Biomedicine, Brigham and Women's Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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