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      Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry

      research-article
      1 , 2 , 3 , 4 , 5 , 5 , 1 , 2 , 3 , 4 , 5 , 1 , 2 , 3 , 4 , 5 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 5 , 5 , 9 , 9 , 12 , 5 , 4 , 4 , 13 , 14 , 15 , 8 , 16 , 11 , 17 , 18 , 13 , 4 , 4 , 19 , 14 , 20 , 21 , 22 , 23 , 7 , 8 , 8 , 12 , 9 , 24 , 5 , 1 , 2 , 3 , 4 , 5 , 25 , Accelerating Medicines Partnership Rheumatoid Arthritis and Lupus (AMP RA/SLE) 26 9 , 10 , 21 , 27 , 19 , 28 , 1 , 2 , 3 , 4 , 5 , 8 , 29 , 30 , 27 , 28 , 19 , 14 , 18 , 7 , 8 , 1 , 2 , 3 , 4 , 5 , 5 , 31 , 19 , 4 , 7 , 32 , 33 , 34 , 9 , 33 , 34 , 19 , 4 , 23 , 21 , 33 , 34
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          Abstract

          To define the cell populations that drive joint inflammation in rheumatoid arthritis (RA), we applied single-cell RNA sequencing (scRNA-seq), mass cytometry, bulk RNA-seq and flow cytometry to T cells, B cells, monocytes and fibroblasts from 51 samples of synovial tissue from patients with RA or osteoarthritis. Utilizing an integrated strategy based on canonical correlation analysis of 5,265 scRNA-seq profiles, we identified 18 unique cell populations. Combining mass cytometry and transcriptomics together revealed cell states expanded in RA synovia: THY1(CD90) + HLA-DRA hi sublining fibroblasts, IL1B + pro-inflammatory monocytes, ITGAX + TBX21 + autoimmune-associated B cells and PDCD1 + T peripheral helper (Tph) and T follicular helper (Tfh). We defined distinct subsets of CD8 + T cells characterized by a GZMK +, GZMB + and GNLY + phenotype. We mapped inflammatory mediators to their source cell populations; for example, we attributed IL6 expression to THY1 + HLA-DRA hi fibroblasts, and IL1B production to pro-inflammatory monocytes. These populations are potentially key mediators of RA pathogenesis.

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          Most cited references35

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          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Single-cell RNA sequencing to explore immune cell heterogeneity

            New technologies that enable the profiling of single cells using next-generation sequencing offer an unbiased approach for studying immune cell diversity.
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              A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis.

              We present a penalized matrix decomposition (PMD), a new framework for computing a rank-K approximation for a matrix. We approximate the matrix X as circumflexX = sigma(k=1)(K) d(k)u(k)v(k)(T), where d(k), u(k), and v(k) minimize the squared Frobenius norm of X - circumflexX, subject to penalties on u(k) and v(k). This results in a regularized version of the singular value decomposition. Of particular interest is the use of L(1)-penalties on u(k) and v(k), which yields a decomposition of X using sparse vectors. We show that when the PMD is applied using an L(1)-penalty on v(k) but not on u(k), a method for sparse principal components results. In fact, this yields an efficient algorithm for the "SCoTLASS" proposal (Jolliffe and others 2003) for obtaining sparse principal components. This method is demonstrated on a publicly available gene expression data set. We also establish connections between the SCoTLASS method for sparse principal component analysis and the method of Zou and others (2006). In addition, we show that when the PMD is applied to a cross-products matrix, it results in a method for penalized canonical correlation analysis (CCA). We apply this penalized CCA method to simulated data and to a genomic data set consisting of gene expression and DNA copy number measurements on the same set of samples.
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                Author and article information

                Journal
                100941354
                21750
                Nat Immunol
                Nat. Immunol.
                Nature immunology
                1529-2908
                1529-2916
                19 March 2019
                06 May 2019
                July 2019
                06 November 2019
                : 20
                : 7
                : 928-942
                Affiliations
                [1 ]Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA 02115, USA
                [2 ]Division of Rheumatology and Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
                [3 ]Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115 USA
                [4 ]Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
                [5 ]Division of Rheumatology, Immunology, Allergy, Brigham and Women’s Hospital and Harvard Medical School, MA 02115, USA
                [6 ]Department of Rheumatology, Barts Health NHS Trust, London, E1 1BB, UK
                [7 ]Division of Rheumatology, Hospital for Special Surgery, New York, NY 10021, USA
                [8 ]Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
                [9 ]Division of Allergy, Immunology and Rheumatology, Department of Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
                [10 ]Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294-2182, USA
                [11 ]Division of Rheumatology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
                [12 ]Arthritis and Tissue Degeneration, Hospital for Special Surgery, New York, NY 10021, USA
                [13 ]Department of Medicine, Division of Rheumatology, Allergy and Immunology, University of California, San Diego, La Jolla, CA 92093 USA
                [14 ]Division of Rheumatology, Department of Medicine, Northwestern University Feinberg School of Medicine. Chicago, IL 60611, USA
                [15 ]Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
                [16 ]Department of Pathology and Laboratory Medicine, Hospital for Special Surgery, New York, NY 10021, USA
                [17 ]Feinstein Institute for Medical Research, Northwell Health, Manhasset, New York, NY 11030, USA
                [18 ]Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261 USA
                [19 ]Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, MA 02115, USA
                [20 ]Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Queen Mary University of London, E1 4NS, UK
                [21 ]NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, B15 2WB, UK
                [22 ]University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2TH, UK
                [23 ]Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO 80220, USA
                [24 ]Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY 14642, USA
                [25 ]Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
                [26 ]A list of members and affiliations appears at the end of the paper
                [27 ]Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
                [28 ]Department of Arthritis & Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
                [29 ]Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
                [30 ]David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021, USA
                [31 ]Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
                [32 ]The Rockefeller University, New York, NY 10065, USA
                [33 ]Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA 94305, USA
                [34 ]The Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, CA 94305, USA
                Author notes

                AUTHOR CONTRIBUTIONS

                S.K., S.M.G., D.T., L.B.H., K.S.-E., A.M.M., D.L.B., J.H.A., V.P.B., V.M.H., A.F., C.P., H.P., G.S.F., L.M., P.K.G., W.A. and L.T.D. recruited patients and obtained synovial tissues. B.F.B., E.D. and E.M.G. performed histological assessment of tissues. K.W., D.A.R., G.F.M.W., and M.B.B. designed and implemented tissue processing and cell sorting pipeline. J.A.L. obtained mass cytometry data from samples. N.H., C.N., and T.M.E. obtained single cell RNA-seq data from samples. F.Z., K.S., C.Y.F., D.J.L. and S.R. conducted computational and statistical analysis. A.H.J., J.R.-M., N.M.P., and C.R., designed and performed validation experiments. K.S., F.Z., and J.R.M. implemented the website. J.A., S.L.B., C.D.B., J.H.B., J.D., J.M.G., M.G., L.B.I., E.A.J., J.A.J., J.K., Y.C.L., M.J.M., M.M., F.M., J.N., A.N., D.E.O., M.P., C.R., W.H.R., A.S., D.S., J.S., J.D.T., and P.J.U. contributed to the procurement and processing of samples, design of the AMP study. S.R., M.B.B., J.H.A., and L.T.D. supervised the research. F.Z., K.W., K.S, and S.R. generated figures and wrote the initial draft. K.S, C.Y.F. D.A.R, L.T.D., J.H.A, M.B.B. edited the draft, and all the authors participated in writing the final manuscript.

                [^]

                Co-first authors

                [*]

                Co-senior authors

                Correspondence and requests for materials should be addressed to Soumya Raychaudhuri, 77 Avenue Louis Pasteur, Harvard New Research Building, Suite 250D, Boston, MA 02446, USA. soumya@ 123456broadinstitute.org ; 617-525-4484 (tel); 617-525-4488 (fax)
                Article
                NIHMS1524330
                10.1038/s41590-019-0378-1
                6602051
                31061532
                86faa119-455d-4f8f-8965-5a1bb9626611

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                Immunology

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