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1
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Perez RK, Gordon MG, Subramaniam M, Kim MC, Hartoularos GC, Targ S, Sun Y, Ogorodnikov A, Bueno R, Lu A, Thompson M, Rappoport N, Dahl A, Lanata CM, Matloubian M, Maliskova L, Kwek SS, Li T, Slyper M, Waldman J, Dionne D, Rozenblatt-Rosen O, Fong L, Dall’Era M, Balliu B, Regev A, Yazdany J, Criswell LA, Zaitlen N, Ye CJ. Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus. Science 2022; 376:eabf1970. [PMID: 35389781 PMCID: PMC9297655 DOI: 10.1126/science.abf1970] [Citation(s) in RCA: 112] [Impact Index Per Article: 56.0] [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
Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. Knowledge of circulating immune cell types and states associated with SLE remains incomplete. We profiled more than 1.2 million peripheral blood mononuclear cells (162 cases, 99 controls) with multiplexed single-cell RNA sequencing (mux-seq). Cases exhibited elevated expression of type 1 interferon-stimulated genes (ISGs) in monocytes, reduction of naïve CD4+ T cells that correlated with monocyte ISG expression, and expansion of repertoire-restricted cytotoxic GZMH+ CD8+ T cells. Cell type-specific expression features predicted case-control status and stratified patients into two molecular subtypes. We integrated dense genotyping data to map cell type-specific cis-expression quantitative trait loci and to link SLE-associated variants to cell type-specific expression. These results demonstrate mux-seq as a systematic approach to characterize cellular composition, identify transcriptional signatures, and annotate genetic variants associated with SLE.
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Affiliation(s)
- Richard K. Perez
- School of Medicine, University of California, San Francisco, CA, USA
| | - M. Grace Gordon
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Meena Subramaniam
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Min Cheol Kim
- School of Medicine, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, CA, USA
- UC Berkeley–UCSF Graduate Program in Bioengineering, San Francisco, CA, USA
| | - George C. Hartoularos
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Sasha Targ
- School of Medicine, University of California, San Francisco, CA, USA
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, CA, USA
| | - Yang Sun
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Anton Ogorodnikov
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Raymund Bueno
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Andrew Lu
- UCLA-Caltech Medical Scientist Training Program, Los Angeles, CA, USA
| | - Mike Thompson
- Department of Computer Science, University of California, Los Angeles, CA, USA
| | - Nadav Rappoport
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Andrew Dahl
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Cristina M. Lanata
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, CA, USA
| | - Mehrdad Matloubian
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, CA, USA
| | - Lenka Maliskova
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Serena S. Kwek
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Tony Li
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | | | - Lawrence Fong
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Maria Dall’Era
- School of Medicine, University of California, San Francisco, CA, USA
| | - Brunilda Balliu
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jinoos Yazdany
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Lindsey A. Criswell
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, CA, USA
| | - Noah Zaitlen
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
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2
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Yang Z, Wu CAM, Targ S, Allen CDC. IL-21 is a broad negative regulator of IgE class switch recombination in mouse and human B cells. J Exp Med 2020; 217:133860. [PMID: 32130409 PMCID: PMC7201927 DOI: 10.1084/jem.20190472] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 11/24/2019] [Accepted: 01/24/2020] [Indexed: 12/12/2022] Open
Abstract
IgE antibodies may elicit potent allergic reactions, and their production is tightly controlled. The tendency to generate IgE has been thought to reflect the balance between type 1 and type 2 cytokines, with the latter promoting IgE. Here, we reevaluated this paradigm by a direct cellular analysis, demonstrating that IgE production was not limited to type 2 immune responses yet was generally constrained in vivo. IL-21 was a critical negative regulator of IgE responses, whereas IFN-γ, IL-6, and IL-10 were dispensable. Follicular helper T cells were the primary source of IL-21 that inhibited IgE responses by directly engaging the IL-21 receptor on B cells and triggering STAT3-dependent signaling. We reconciled previous discordant results between mouse and human B cells and revealed that the inhibition of IgE class switch recombination by IL-21 was attenuated by CD40 signaling, whereas IgG1 class switch recombination was potentiated by IL-21 in the context of limited IL-4. These findings establish key features of the extrinsic regulation of IgE production by cytokines.
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Affiliation(s)
- Zhiyong Yang
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA.,Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA
| | - Chung-An M Wu
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA.,Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA
| | - Sasha Targ
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA.,Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA
| | - Christopher D C Allen
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA.,Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA.,Department of Anatomy, University of California, San Francisco, San Francisco, CA
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3
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Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, Ye CJ. Author Correction: Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat Biotechnol 2020; 38:1356. [PMID: 33057163 DOI: 10.1038/s41587-020-0715-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA.
| | - Meena Subramaniam
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA.,Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA.,Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sasha Targ
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA.,Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA.,Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.,Medical Scientist Training Program (MSTP), University of California, San Francisco, San Francisco, California, USA
| | - Michelle Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA.,Diabetes Center, University of California, San Francisco, San Francisco, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Lenka Maliskova
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA.,Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Elizabeth McCarthy
- Medical Scientist Training Program (MSTP), University of California, San Francisco, San Francisco, California, USA
| | - Eunice Wan
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
| | - Simon Wong
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
| | - Lauren Byrnes
- Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Cristina M Lanata
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA.,Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Rachel E Gate
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA.,Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA.,Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sara Mostafavi
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA.,Diabetes Center, University of California, San Francisco, San Francisco, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA.,Department of Medicine, University of California, San Francisco, San Francisco, California, USA.,UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Noah Zaitlen
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA.,Department of Medicine, University of California, San Francisco, San Francisco, California, USA.,Lung Biology Center, University of California, San Francisco, San Francisco, California, USA
| | - Lindsey A Criswell
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA.,Department of Medicine, University of California, San Francisco, San Francisco, California, USA.,Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, California, USA.,Department of Orofacial Sciences, University of California, San Francisco, San Francisco, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA. .,Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA. .,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA. .,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.
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4
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Furman D, Campisi J, Verdin E, Carrera-Bastos P, Targ S, Franceschi C, Ferrucci L, Gilroy DW, Fasano A, Miller GW, Miller AH, Mantovani A, Weyand CM, Barzilai N, Goronzy JJ, Rando TA, Effros RB, Lucia A, Kleinstreuer N, Slavich GM. Chronic inflammation in the etiology of disease across the life span. Nat Med 2019; 25:1822-1832. [PMID: 31806905 DOI: 10.1038/s41591-019-0675-0] [Citation(s) in RCA: 1910] [Impact Index Per Article: 382.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 10/31/2019] [Indexed: 02/06/2023]
Abstract
Although intermittent increases in inflammation are critical for survival during physical injury and infection, recent research has revealed that certain social, environmental and lifestyle factors can promote systemic chronic inflammation (SCI) that can, in turn, lead to several diseases that collectively represent the leading causes of disability and mortality worldwide, such as cardiovascular disease, cancer, diabetes mellitus, chronic kidney disease, non-alcoholic fatty liver disease and autoimmune and neurodegenerative disorders. In the present Perspective we describe the multi-level mechanisms underlying SCI and several risk factors that promote this health-damaging phenotype, including infections, physical inactivity, poor diet, environmental and industrial toxicants and psychological stress. Furthermore, we suggest potential strategies for advancing the early diagnosis, prevention and treatment of SCI.
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Affiliation(s)
- David Furman
- Buck Institute for Research on Aging, Novato, CA, USA. .,Stanford 1000 Immunomes Project, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA. .,Institute for Research in Translational Medicine, Universidad Austral, CONICET, Pilar, Buenos Aires, Argentina. .,Iuve Inc., San Mateo, CA, USA.
| | - Judith Campisi
- Buck Institute for Research on Aging, Novato, CA, USA.,Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Pedro Carrera-Bastos
- Center for Primary Health Care Research, Lund University/Region Skåne, Skåne University Hospital, Malmö, Sweden
| | - Sasha Targ
- Iuve Inc., San Mateo, CA, USA.,Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
| | - Claudio Franceschi
- IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy.,Department of Applied Mathematics and Laboratory of Systems Biology of Aging, Lobachevsky University, Nizhny Novgorod, Russia
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Derek W Gilroy
- Centre for Clinical Pharmacology and Therapeutics, Division of Medicine, University College London, London, UK
| | - Alessio Fasano
- MassGeneral Hospital for Children, Harvard Medical School, Boston, MA, USA
| | - Gary W Miller
- Department of Environmental Health Sciences, School of Public Health, Columbia University Medical Center, New York, NY, USA
| | - Andrew H Miller
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Alberto Mantovani
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy.,William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University, London, UK
| | - Cornelia M Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Nir Barzilai
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Jorg J Goronzy
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas A Rando
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.,Center for Tissue Regeneration, Repair and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Rita B Effros
- Department of Pathology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alejandro Lucia
- Faculty of Sport Sciences, Universidad Europea de Madrid, Madrid, Spain.,Research Institute of the Hospital 12 de Octubre (i+12), Madrid, Spain
| | - Nicole Kleinstreuer
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA.,NTP Interagency Center for the Evaluation of Alternative Toxicological Methods, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - George M Slavich
- Cousins Center for Psychoneuroimmunology and Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, USA
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5
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Allen CDC, Yang Z, Wu CAM, Targ S. IL-21 is a major suppressor of IgE production in mice and humans. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.123.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Antibodies of the IgE isotype may elicit potent allergic reactions and their production is tightly controlled. The tendency to develop allergic responses has been historically thought to depend on the balance between T helper type 1 (Th1) responses that suppress IgE, versus T helper type 2 (Th2) responses that promote IgE production, based on the activities of the prototypical cytokines interferon gamma (IFN-γ) and interleukin (IL)-4, respectively. Here we reevaluated this paradigm by a direct cellular analysis, demonstrating that IgE production was not limited to type 2 immune responses, yet was generally constrained in vivo. We determined that the cytokine IL-21 was a critical negative regulator of IgE responses, whereas IFN-γ was dispensable. IL-21 inhibited IgE responses by directly engaging the IL-21 receptor on B cells and triggering STAT3-dependent signaling. We reconcile previous discordant results between mouse and human B cells and reveal that the inhibition of IgE responses by IL-21 is modulated by CD40 signaling. The suppression of IgE responses by IL-21 correlated with reduced IgE germline transcription, but was independent of apoptosis, indicating that IL-21 inhibits IgE class switch recombination. These findings establish key features of the extrinsic regulation of IgE production by cytokines.
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Affiliation(s)
| | | | | | - Sasha Targ
- 1University of California, San Francisco
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6
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Oh DY, Kwek SS, Mangul S, Raju SS, Targ S, Burra A, Chow E, Aran D, Porten S, Meng MV, Friedlander TW, Ye CJ, Fong L. Abstract 4688: Single-cell discrimination of altered human T cell states in the bladder tumor microenvironment. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Bladder cancer can be responsive to immunotherapies such as anti-PD-1 and anti-PD-L1 checkpoint inhibitors, but overall response rates are low. Tumor-resident T cells demonstrate considerable heterogeneity as far as antigenic repertoire and phenotype. Whether the bladder tumor environment is enriched for specific types of T cells with a particular functional profile and antigenic specificity, and whether these tumor-specific populations are associated with treatment or response to immunotherapy, remains unclear. We performed single-cell RNA sequencing of CD4+ and CD8+ T cells from localized human bladder tumors and paired adjacent non-malignant bladder. We also assessed resected bladder tumors treated with neoadjuvant chemotherapy or atezolizumab (anti-PD-L1) as part of an ongoing phase II trial. We find both known and unexpected CD4+ T cell functional populations that are specific to the tumor microenvironment, including regulatory T cells and a novel population of cytotoxic CD4+ T cells. Furthermore, by combining whole-transcriptome data with paired T cell receptor identification on single cells, we find that tumor-specific CD4+ populations are clonally expanded and utilize an antigenic repertoire which is distinct from uninvolved bladder. These findings provide evidence for specialization of both phenotype and antigenic specificity of CD4+ T cells in the bladder tumor environment, and indicate that a limited number of tumor-specific antigens may drive in situ expansion and differentiation of specialized CD4+ subsets whose function may be critical to tumor control.
Citation Format: David Yoonsuk Oh, Serena S. Kwek, Serghei Mangul, Siddharth S. Raju, Sasha Targ, Arun Burra, Eric Chow, Dvir Aran, Sima Porten, Maxwell V. Meng, Terence W. Friedlander, Chun Jimmie Ye, Lawrence Fong. Single-cell discrimination of altered human T cell states in the bladder tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4688.
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Affiliation(s)
| | - Serena S. Kwek
- 1University of California, San Francisco, San Francisco, CA
| | | | | | - Sasha Targ
- 1University of California, San Francisco, San Francisco, CA
| | - Arun Burra
- 1University of California, San Francisco, San Francisco, CA
| | - Eric Chow
- 1University of California, San Francisco, San Francisco, CA
| | - Dvir Aran
- 1University of California, San Francisco, San Francisco, CA
| | - Sima Porten
- 1University of California, San Francisco, San Francisco, CA
| | | | | | - Chun Jimmie Ye
- 1University of California, San Francisco, San Francisco, CA
| | - Lawrence Fong
- 1University of California, San Francisco, San Francisco, CA
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7
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Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, Ye CJ. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat Biotechnol 2018; 36:89-94. [PMID: 29227470 PMCID: PMC5784859 DOI: 10.1038/nbt.4042] [Citation(s) in RCA: 483] [Impact Index Per Article: 80.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 11/16/2017] [Indexed: 12/25/2022]
Abstract
Droplet single-cell RNA-sequencing (dscRNA-seq) has enabled rapid, massively parallel profiling of transcriptomes. However, assessing differential expression across multiple individuals has been hampered by inefficient sample processing and technical batch effects. Here we describe a computational tool, demuxlet, that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). These capabilities enable multiplexed dscRNA-seq experiments in which cells from unrelated individuals are pooled and captured at higher throughput than in standard workflows. Using simulated data, we show that 50 single-nucleotide polymorphisms (SNPs) per cell are sufficient to assign 97% of singlets and identify 92% of doublets in pools of up to 64 individuals. Given genotyping data for each of eight pooled samples, demuxlet correctly recovers the sample identity of >99% of singlets and identifies doublets at rates consistent with previous estimates. We apply demuxlet to assess cell-type-specific changes in gene expression in 8 pooled lupus patient samples treated with interferon (IFN)-β and perform eQTL analysis on 23 pooled samples.
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Affiliation(s)
- Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Meena Subramaniam
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sasha Targ
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- Medical Scientist Training Program (MSTP), University of California, San Francisco, San Francisco, California, USA
| | - Michelle Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
- Diabetes Center, University of California, San Francisco, San Francisco, California, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Lenka Maliskova
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Elizabeth McCarthy
- Medical Scientist Training Program (MSTP), University of California, San Francisco, San Francisco, California, USA
| | - Eunice Wan
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
| | - Simon Wong
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
| | - Lauren Byrnes
- Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Cristina M Lanata
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Rachel E Gate
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sara Mostafavi
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
- Diabetes Center, University of California, San Francisco, San Francisco, California, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Noah Zaitlen
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Lung Biology Center, University of California, San Francisco, San Francisco, California, USA
| | - Lindsey A Criswell
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, California, USA
- Department of Orofacial Sciences, University of California, San Francisco, San Francisco, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
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8
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Tas JMJ, Mesin L, Pasqual G, Targ S, Jacobsen JT, Mano YM, Chen CS, Weill JC, Reynaud CA, Browne EP, Meyer-Hermann M, Victora GD. Visualizing antibody affinity maturation in germinal centers. Science 2016; 351:1048-54. [PMID: 26912368 DOI: 10.1126/science.aad3439] [Citation(s) in RCA: 296] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 02/02/2016] [Indexed: 12/17/2022]
Abstract
Antibodies somatically mutate to attain high affinity in germinal centers (GCs). There, competition between B cell clones and among somatic mutants of each clone drives an increase in average affinity across the population. The extent to which higher-affinity cells eliminating competitors restricts clonal diversity is unknown. By combining multiphoton microscopy and sequencing, we show that tens to hundreds of distinct B cell clones seed each GC and that GCs lose clonal diversity at widely disparate rates. Furthermore, efficient affinity maturation can occur in the absence of homogenizing selection, ensuring that many clones can mature in parallel within the same GC. Our findings have implications for development of vaccines in which antibodies with nonimmunodominant specificities must be elicited, as is the case for HIV-1 and influenza.
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Affiliation(s)
- Jeroen M J Tas
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Luka Mesin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Giulia Pasqual
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sasha Targ
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Johanne T Jacobsen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Yasuko M Mano
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Casie S Chen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Jean-Claude Weill
- Institut Necker-Enfants Malades, INSERM U1151-CNRS UMR 8253, Sorbonne Paris Cité, Université Paris Descartes, Faculté de Médecine-Site Broussais, 75014 Paris, France
| | - Claude-Agnès Reynaud
- Institut Necker-Enfants Malades, INSERM U1151-CNRS UMR 8253, Sorbonne Paris Cité, Université Paris Descartes, Faculté de Médecine-Site Broussais, 75014 Paris, France
| | - Edward P Browne
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Inhoffenstraβe7, 38124 Braunschweig, Germany.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Gabriel D Victora
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
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9
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Shulman Z, Gitlin AD, Targ S, Jankovic M, Pasqual G, Nussenzweig MC, Victora GD. T follicular helper cell dynamics in germinal centers. Science 2013; 341:673-7. [PMID: 23887872 DOI: 10.1126/science.1241680] [Citation(s) in RCA: 261] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
T follicular helper (T(FH)) cells are a specialized subset of effector T cells that provide help to and thereby select high-affinity B cells in germinal centers (GCs). To examine the dynamic behavior of T(FH) cells in GCs in mice, we used two-photon microscopy in combination with a photoactivatable fluorescent reporter. Unlike GC B cells, which are clonally restricted, T(FH) cells distributed among all GCs in lymph nodes and continually emigrated into the follicle and neighboring GCs. Moreover, newly activated T(FH) cells invaded preexisting GCs, where they contributed to B cell selection and plasmablast differentiation. Our data suggest that the dynamic exchange of T(FH) cells between GCs ensures maximal diversification of T cell help and that their ability to enter ongoing GCs accommodates antigenic variation during the immune response.
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Affiliation(s)
- Ziv Shulman
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10021, USA
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