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Arazi A, Rao DA, Berthier CC, Davidson A, Liu Y, Hoover PJ, Chicoine A, Eisenhaure TM, Jonsson AH, Li S, Lieb DJ, Zhang F, Slowikowski K, Browne EP, Noma A, Sutherby D, Steelman S, Smilek DE, Tosta P, Apruzzese W, Massarotti E, Dall'Era M, Park M, Kamen DL, Furie RA, Payan-Schober F, Pendergraft WF, McInnis EA, Buyon JP, Petri MA, Putterman C, Kalunian KC, Woodle ES, Lederer JA, Hildeman DA, Nusbaum C, Raychaudhuri S, Kretzler M, Anolik JH, Brenner MB, Wofsy D, Hacohen N, Diamond B. The immune cell landscape in kidneys of patients with lupus nephritis. Nat Immunol 2019; 20:902-914. [PMID: 31209404 PMCID: PMC6726437 DOI: 10.1038/s41590-019-0398-x] [Citation(s) in RCA: 415] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 04/05/2019] [Indexed: 02/07/2023]
Abstract
Lupus nephritis is a potentially fatal autoimmune disease for which the
current treatment is ineffective and often toxic. To develop mechanistic
hypotheses of disease, we analyzed kidney samples from patients with lupus
nephritis and from healthy control subjects using single-cell RNA sequencing.
Our analysis revealed 21 subsets of leukocytes active in disease, including
multiple populations of myeloid cells, T cells, natural killer cells and B cells
that demonstrated both pro-inflammatory responses and inflammation-resolving
responses. We found evidence of local activation of B cells correlated with an
age-associated B-cell signature and evidence of progressive stages of monocyte
differentiation within the kidney. A clear interferon response was observed in
most cells. Two chemokine receptors, CXCR4 and
CX3CR1, were broadly expressed, implying a potentially
central role in cell trafficking. Gene expression of immune cells in urine and
kidney was highly correlated, which would suggest that urine might serve as a
surrogate for kidney biopsies.
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Affiliation(s)
- Arnon Arazi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deepak A Rao
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Celine C Berthier
- Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Anne Davidson
- Center for Autoimmune and Musculoskeletal Diseases, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Yanyan Liu
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Paul J Hoover
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam Chicoine
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - A Helena Jonsson
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David J Lieb
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Fan Zhang
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kamil Slowikowski
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edward P Browne
- UNC HIV Cure Center and Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Akiko Noma
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Dawn E Smilek
- Lupus Nephritis Trials Network, University of California San Francisco, San Francisco, CA, USA.,Immune Tolerance Network, University of California San Francisco, San Francisco, CA, USA
| | - Patti Tosta
- Lupus Nephritis Trials Network, University of California San Francisco, San Francisco, CA, USA.,Immune Tolerance Network, University of California San Francisco, San Francisco, CA, USA
| | - William Apruzzese
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Elena Massarotti
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Maria Dall'Era
- Rheumatology Division, University of California San Francisco, San Francisco, CA, USA
| | - Meyeon Park
- Division of Nephrology, University of California San Francisco, San Francisco, CA, USA
| | - Diane L Kamen
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Richard A Furie
- Division of Rheumatology, Northwell Health, Great Neck, NY, USA
| | - Fernanda Payan-Schober
- Department of Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | | | - Elizabeth A McInnis
- University of North Carolina Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, UNC School of Medicine, Chapel Hill, NC, USA
| | - Jill P Buyon
- Department of Medicine, Division of Rheumatology, New York University School of Medicine, New York, NY, USA
| | - Michelle A Petri
- Division of Rheumatology, Johns Hopkins University, Baltimore, MD, USA
| | - Chaim Putterman
- Division of Rheumatology and Department of Microbiology and Immunology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Kenneth C Kalunian
- University of California San Diego School of Medicine, La Jolla, CA, USA
| | - E Steve Woodle
- Division of Transplantation, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - James A Lederer
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David A Hildeman
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | | | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthias Kretzler
- Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer H Anolik
- Department of Medicine, Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Michael B Brenner
- Division of Rheumatology, Immunology, Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David Wofsy
- Rheumatology Division, University of California San Francisco, San Francisco, CA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Betty Diamond
- Center for Autoimmune and Musculoskeletal Diseases, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA.
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Donlin LT, Rao DA, Wei K, Slowikowski K, McGeachy MJ, Turner JD, Meednu N, Mizoguchi F, Gutierrez-Arcelus M, Lieb DJ, Keegan J, Muskat K, Hillman J, Rozo C, Ricker E, Eisenhaure TM, Li S, Browne EP, Chicoine A, Sutherby D, Noma A, Nusbaum C, Kelly S, Pernis AB, Ivashkiv LB, Goodman SM, Robinson WH, Utz PJ, Lederer JA, Gravallese EM, Boyce BF, Hacohen N, Pitzalis C, Gregersen PK, Firestein GS, Raychaudhuri S, Moreland LW, Holers VM, Bykerk VP, Filer A, Boyle DL, Brenner MB, Anolik JH. Methods for high-dimensional analysis of cells dissociated from cryopreserved synovial tissue. Arthritis Res Ther 2018; 20:139. [PMID: 29996944 PMCID: PMC6042350 DOI: 10.1186/s13075-018-1631-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 05/24/2018] [Indexed: 12/29/2022] Open
Abstract
Background Detailed molecular analyses of cells from rheumatoid arthritis (RA) synovium hold promise in identifying cellular phenotypes that drive tissue pathology and joint damage. The Accelerating Medicines Partnership RA/SLE Network aims to deconstruct autoimmune pathology by examining cells within target tissues through multiple high-dimensional assays. Robust standardized protocols need to be developed before cellular phenotypes at a single cell level can be effectively compared across patient samples. Methods Multiple clinical sites collected cryopreserved synovial tissue fragments from arthroplasty and synovial biopsy in a 10% DMSO solution. Mechanical and enzymatic dissociation parameters were optimized for viable cell extraction and surface protein preservation for cell sorting and mass cytometry, as well as for reproducibility in RNA sequencing (RNA-seq). Cryopreserved synovial samples were collectively analyzed at a central processing site by a custom-designed and validated 35-marker mass cytometry panel. In parallel, each sample was flow sorted into fibroblast, T-cell, B-cell, and macrophage suspensions for bulk population RNA-seq and plate-based single-cell CEL-Seq2 RNA-seq. Results Upon dissociation, cryopreserved synovial tissue fragments yielded a high frequency of viable cells, comparable to samples undergoing immediate processing. Optimization of synovial tissue dissociation across six clinical collection sites with ~ 30 arthroplasty and ~ 20 biopsy samples yielded a consensus digestion protocol using 100 μg/ml of Liberase™ TL enzyme preparation. This protocol yielded immune and stromal cell lineages with preserved surface markers and minimized variability across replicate RNA-seq transcriptomes. Mass cytometry analysis of cells from cryopreserved synovium distinguished diverse fibroblast phenotypes, distinct populations of memory B cells and antibody-secreting cells, and multiple CD4+ and CD8+ T-cell activation states. Bulk RNA-seq of sorted cell populations demonstrated robust separation of synovial lymphocytes, fibroblasts, and macrophages. Single-cell RNA-seq produced transcriptomes of over 1000 genes/cell, including transcripts encoding characteristic lineage markers identified. Conclusions We have established a robust protocol to acquire viable cells from cryopreserved synovial tissue with intact transcriptomes and cell surface phenotypes. A centralized pipeline to generate multiple high-dimensional analyses of synovial tissue samples collected across a collaborative network was developed. Integrated analysis of such datasets from large patient cohorts may help define molecular heterogeneity within RA pathology and identify new therapeutic targets and biomarkers. Electronic supplementary material The online version of this article (10.1186/s13075-018-1631-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura T Donlin
- Hospital for Special Surgery, New York, NY, 10021, USA.,Weill Cornell Medical College, New York, NY, 10065, USA
| | - Deepak A Rao
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kevin Wei
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kamil Slowikowski
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - Mandy J McGeachy
- University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Jason D Turner
- University of Birmingham, Queen Elizabeth Hospital, B15 2WB, Birmingham, UK
| | - Nida Meednu
- University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Fumitaka Mizoguchi
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Maria Gutierrez-Arcelus
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - David J Lieb
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - Joshua Keegan
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kaylin Muskat
- University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Joshua Hillman
- University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Cristina Rozo
- Hospital for Special Surgery, New York, NY, 10021, USA
| | - Edd Ricker
- Hospital for Special Surgery, New York, NY, 10021, USA.,Weill Cornell Medical College, New York, NY, 10065, USA
| | | | - Shuqiang Li
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - Edward P Browne
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - Adam Chicoine
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Danielle Sutherby
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - Akiko Noma
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | | | - Chad Nusbaum
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - Stephen Kelly
- Mile End Hospital, Barts Health NHS Trust, E1 1BB, London, UK
| | - Alessandra B Pernis
- Hospital for Special Surgery, New York, NY, 10021, USA.,Weill Cornell Medical College, New York, NY, 10065, USA
| | - Lionel B Ivashkiv
- Hospital for Special Surgery, New York, NY, 10021, USA.,Weill Cornell Medical College, New York, NY, 10065, USA
| | - Susan M Goodman
- Hospital for Special Surgery, New York, NY, 10021, USA.,Weill Cornell Medical College, New York, NY, 10065, USA
| | | | - Paul J Utz
- Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - James A Lederer
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Brendan F Boyce
- University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA.,Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | | | - Peter K Gregersen
- The Feinstein Institute for Medical Research, Manhasset, NY, 11030, USA
| | - Gary S Firestein
- University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Soumya Raychaudhuri
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Larry W Moreland
- University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - V Michael Holers
- University of Colorado of Denver School of Medicine, Aurora, CO, 80045, USA
| | - Vivian P Bykerk
- Hospital for Special Surgery, New York, NY, 10021, USA.,Weill Cornell Medical College, New York, NY, 10065, USA
| | - Andrew Filer
- University of Birmingham, Queen Elizabeth Hospital, B15 2WB, Birmingham, UK
| | - David L Boyle
- University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Michael B Brenner
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
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