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Jonsson AH, Zhang F, Dunlap G, Gomez-Rivas E, Watts GFM, Faust HJ, Rupani KV, Mears JR, Meednu N, Wang R, Keras G, Coblyn JS, Massarotti EM, Todd DJ, Anolik JH, McDavid A, Wei K, Rao DA, Raychaudhuri S, Brenner MB. Granzyme K + CD8 T cells form a core population in inflamed human tissue. Sci Transl Med 2022; 14:eabo0686. [PMID: 35704599 PMCID: PMC9972878 DOI: 10.1126/scitranslmed.abo0686] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [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: 12/17/2022]
Abstract
T cell-derived pro-inflammatory cytokines are a major driver of rheumatoid arthritis (RA) pathogenesis. Although these cytokines have traditionally been attributed to CD4 T cells, we have found that CD8 T cells are notably abundant in synovium and make more interferon (IFN)-γ and nearly as much tumor necrosis factor (TNF) as their CD4 T cell counterparts. Furthermore, using unbiased high-dimensional single-cell RNA-seq and flow cytometric data, we found that the vast majority of synovial tissue and synovial fluid CD8 T cells belong to an effector CD8 T cell population characterized by high expression of granzyme K (GzmK) and low expression of granzyme B (GzmB) and perforin. Functional experiments demonstrate that these GzmK+ GzmB+ CD8 T cells are major cytokine producers with low cytotoxic potential. Using T cell receptor repertoire data, we found that CD8 GzmK+ GzmB+ T cells are clonally expanded in synovial tissues and maintain their granzyme expression and overall cell state in blood, suggesting that they are enriched in tissue but also circulate. Using GzmK and GzmB signatures, we found that GzmK-expressing CD8 T cells were also the major CD8 T cell population in the gut, kidney, and coronavirus disease 2019 (COVID-19) bronchoalveolar lavage fluid, suggesting that they form a core population of tissue-associated T cells across diseases and human tissues. We term this population tissue-enriched expressing GzmK or TteK CD8 cells. Armed to produce cytokines in response to both antigen-dependent and antigen-independent stimuli, CD8 TteK cells have the potential to drive inflammation.
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Affiliation(s)
- A. Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
| | - Fan Zhang
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
- Center for Data Sciences, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Division of Rheumatology and the Center for Health Artificial Intelligence, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Garrett Dunlap
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
| | - Emma Gomez-Rivas
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
| | - Gerald F. M. Watts
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
| | - Heather J. Faust
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
| | - Karishma Vijay Rupani
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
| | - Joseph R. Mears
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
- Center for Data Sciences, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
| | - Nida Meednu
- Division of Rheumatology and the Center for Health Artificial Intelligence, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Runci Wang
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
| | - Gregory Keras
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
| | - Jonathan S. Coblyn
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
| | - Elena M. Massarotti
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
| | - Derrick J. Todd
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
| | - Jennifer H. Anolik
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center; Rochester, NY 14642, USA
| | - Andrew McDavid
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry; Rochester, NY 14642, USA
| | | | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
| | - Deepak A. Rao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
- Center for Data Sciences, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester; Manchester M13 9PT, UK
| | - Michael B. Brenner
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School; Boston, MA 02115, USA
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Zhang F, Mears JR, Shakib L, Beynor JI, Shanaj S, Korsunsky I, Nathan A, Donlin LT, Raychaudhuri S. IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 lungs and inflammatory diseases with tissue inflammation. Genome Med 2021; 13:64. [PMID: 33879239 PMCID: PMC8057009 DOI: 10.1186/s13073-021-00881-3] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 03/29/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Immunosuppressive and anti-cytokine treatment may have a protective effect for patients with COVID-19. Understanding the immune cell states shared between COVID-19 and other inflammatory diseases with established therapies may help nominate immunomodulatory therapies. METHODS To identify cellular phenotypes that may be shared across tissues affected by disparate inflammatory diseases, we developed a meta-analysis and integration pipeline that models and removes the effects of technology, tissue of origin, and donor that confound cell-type identification. Using this approach, we integrated > 300,000 single-cell transcriptomic profiles from COVID-19-affected lungs and tissues from healthy subjects and patients with five inflammatory diseases: rheumatoid arthritis (RA), Crohn's disease (CD), ulcerative colitis (UC), systemic lupus erythematosus (SLE), and interstitial lung disease. We tested the association of shared immune states with severe/inflamed status compared to healthy control using mixed-effects modeling. To define environmental factors within these tissues that shape shared macrophage phenotypes, we stimulated human blood-derived macrophages with defined combinations of inflammatory factors, emphasizing in particular antiviral interferons IFN-beta (IFN-β) and IFN-gamma (IFN-γ), and pro-inflammatory cytokines such as TNF. RESULTS We built an immune cell reference consisting of > 300,000 single-cell profiles from 125 healthy or disease-affected donors from COVID-19 and five inflammatory diseases. We observed a CXCL10+ CCL2+ inflammatory macrophage state that is shared and strikingly abundant in severe COVID-19 bronchoalveolar lavage samples, inflamed RA synovium, inflamed CD ileum, and UC colon. These cells exhibited a distinct arrangement of pro-inflammatory and interferon response genes, including elevated levels of CXCL10, CXCL9, CCL2, CCL3, GBP1, STAT1, and IL1B. Further, we found this macrophage phenotype is induced upon co-stimulation by IFN-γ and TNF-α. CONCLUSIONS Our integrative analysis identified immune cell states shared across inflamed tissues affected by inflammatory diseases and COVID-19. Our study supports a key role for IFN-γ together with TNF-α in driving an abundant inflammatory macrophage phenotype in severe COVID-19-affected lungs, as well as inflamed RA synovium, CD ileum, and UC colon, which may be targeted by existing immunomodulatory therapies.
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Affiliation(s)
- Fan Zhang
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Joseph R Mears
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Lorien Shakib
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA
| | - Jessica I Beynor
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Sara Shanaj
- Arthritis and Tissue Degeneration, Hospital for Special Surgery, New York, NY, USA
| | - Ilya Korsunsky
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Laura T Donlin
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA.
- Arthritis and Tissue Degeneration, Hospital for Special Surgery, New York, NY, USA.
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK.
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Zhang F, Mears JR, Shakib L, Beynor JI, Shanaj S, Korsunsky I, Nathan A, Donlin LT, Raychaudhuri S. IFN- γ and TNF- α drive a CXCL10 + CCL2 + macrophage phenotype expanded in severe COVID-19 and other diseases with tissue inflammation. bioRxiv 2020:2020.08.05.238360. [PMID: 32793902 PMCID: PMC7418716 DOI: 10.1101/2020.08.05.238360] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Immunosuppressive and anti-cytokine treatment may have a protective effect for patients with COVID-19. Understanding the immune cell states shared between COVID-19 and other inflammatory diseases with established therapies may help nominate immunomodulatory therapies. Using an integrative strategy, we built a reference by meta-analyzing > 300,000 immune cells from COVID-19 and 5 inflammatory diseases including rheumatoid arthritis (RA), Crohn's disease (CD), ulcerative colitis (UC), lupus, and interstitial lung disease. Our cross-disease analysis revealed that an FCN1 + inflammatory macrophage state is common to COVID-19 bronchoalveolar lavage samples, RA synovium, CD ileum, and UC colon. We also observed that a CXCL10 + CCL2 + inflammatory macrophage state is abundant in severe COVID-19, inflamed CD and RA, and expresses inflammatory genes such as GBP1, STAT1 , and IL1B . We found that the CXCL10 + CCL2 + macrophages are transcriptionally similar to blood-derived macrophages stimulated with TNF- α and IFN- γ ex vivo . Our findings suggest that IFN- γ , alongside TNF- α , might be a key driver of this abundant inflammatory macrophage phenotype in severe COVID-19 and other inflammatory diseases, which may be targeted by existing immunomodulatory therapies.
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Affiliation(s)
- Fan Zhang
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School, MA 02115, USA
| | - Joseph R. Mears
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School, MA 02115, USA
| | - Lorien Shakib
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Jessica I. Beynor
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School, MA 02115, USA
| | - Sara Shanaj
- Arthritis and Tissue Degeneration, Hospital for Special Surgery, New York, NY, USA
| | - Ilya Korsunsky
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School, MA 02115, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School, MA 02115, USA
| | - Laura T. Donlin
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
- Arthritis and Tissue Degeneration, Hospital for Special Surgery, New York, NY, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School, MA 02115, USA
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
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