ArticleNature communications2024
The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis.
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Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33citing papers in PubMed
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Who cites it
33 citing papers in PubMed.
- Immune-mediated rheumatoid arthritis: from single-cell genomics to new therapies.Nature immunology · 2026Review
- Condensates and cell states: A new paradigm for understanding tumor biology.Biophysical journal · 2026Review
- Multi-level transcriptional control of specific macrophage responses.The EMBO journal · 2026Review
- Systematic investigation reveals extensive Epstein-Barr virus transcriptional regulation of the human genome.Cell genomics · 2026Article
- Accurate, sensitive, and efficient chromatin accessibility quantification at target loci using UNIChro-seq.Nature communications · 2026Article
- Targeting the cytokine-epigenetic axis: a new paradigm and prospects for disease treatment.European cytokine network · 2026Review
- Targeting fibroblasts in immune mediated inflammatory diseases: a cellular basis for cure?Rheumatology (Oxford, England) · 2026Review
- From undruggable to degradable: A deep learning-enabled framework for precision orthopaedic protein degradation.Journal of orthopaedic translation · 2026Review
- Single-cell and spatial profiling of peripheral blood and synovium unveils pro-arthritis CNBPJournal of translational medicine · 2026Article
- Spatial patterning of fibroblast TGFβ signaling underlies treatment resistance in rheumatoid arthritis.Nature immunology · 2026Article
- Impact of disease-associated chromatin accessibility QTLs across immune cell types and contexts.Cell genomics · 2026Article
- Computational approaches to multimodal data integration in rheumatoid arthritis: from data landscape to clinical translation.Briefings in bioinformatics · 2026Review
- Immune signaling as a determinant of cellular identity and tissue function.Frontiers in immunology · 2026Review
- Epigenetic alterations in rheumatoid arthritis: multilayer mechanisms and translational opportunities.Frontiers in immunology · 2026Review
- B cell receptor signaling in autoimmune rheumatic diseases: regulatory mechanisms and therapeutic targeting.Frontiers in immunology · 2026Review
- Salidroside: A Potential Drug Candidate to Treat Rheumatoid Arthritis.Molecules (Basel, Switzerland) · 2025Review
- Ectopic Nociceptor Sprouting as a Key Peripheral Driver of Pain in Rheumatoid Arthritis.Current rheumatology reports · 2025Review
- Current state and future directions of basic research in rheumatoid arthritis.Journal of rheumatic diseases · 2025Review
- Narrowing Down Key Players in Autoimmunity via Single-Cell Multiomics.European journal of immunology · 2025Review
- Understanding rheumatic disease through continuous cell state analysis.Nature reviews. Rheumatology · 2025Review
Corrections and comments
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Authors and funding
15 authors.
Kathryn WeinandDivision of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-8491-7251
Saori SakaueDivision of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0003-3618-9717
Aparna NathanDivision of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0002-5975-2851
Anna Helena JonssonDivision of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0002-9558-2474
Fan ZhangDivision of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0002-6102-2970
Gerald F M WattsDivision of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Majd Al SuqriDivision of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0009-0006-8818-1329
Zhu ZhuDivision of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Accelerating Medicines Partnership Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Network
Deepak A RaoDivision of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-9672-7746
Jennifer H AnolikDivision of Allergy, Immunology and Rheumatology, Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA.ORCID http://orcid.org/0000-0002-1450-1549
Michael B BrennerDivision of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-6202-8445
Laura T DonlinHospital for Special Surgery, New York, NY, USA.ORCID http://orcid.org/0000-0002-1428-090X
Kevin WeiDivision of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0002-1821-167X
Soumya RaychaudhuriDivision of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA. soumya@broadinstitute.org.ORCID http://orcid.org/0000-0002-1901-8265
Funding
Role of fibroblastic stromal cells and notch signaling in tissue inflammation in RA and SLEP01AI148102 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI Michael B. Brenner · 2021 to 2026
$17.3MTraining Program in Bioinformatics and Integrative GenomicsT32HG002295 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Peter J Park · 2001 to 2026
$15.8MMECHANISMS OF ARTHRITIC &DERMATOLOGY DISORDERST32AR007530 · NIAMS · BRIGHAM AND WOMEN'S HOSPITAL · PI Michael B. Brenner, Ellen M Gravallese · 1986 to 2026
$10.4MTissue Acquisition Research GroupUM2AR067678 · NIAMS · STANFORD UNIVERSITY · PI HOLERS, VERNON MICHAEL, UTZ, PAUL JOSEPH · 2014 to 2020
$8.2MPain and synovial pathotypes in AMP AIMUC2AR081025 · NIAMS · UNIVERSITY OF ROCHESTER · PI Jennifer Howitt Anolik, Laura T. Donlin · 2022 to 2026
$7.2MResearch Training in Rheumatology at Massachusetts General HospitalT32AR007258 · NIAMS · MASSACHUSETTS GENERAL HOSPITAL · PI ANDREW D LUSTER · 1986 to 2026
$6.9MEvolving Adaptive and Effector Mechanisms from Pre-RA Through Established DiseaseUH2AR067681 · NIAMS · UNIVERSITY OF COLORADO DENVER · PI HOLERS, VERNON MICHAEL · 2014 to 2020
$5.5MDiscovery and Functional Impact of Common and Rare Variants in RAR01AR063759 · NIAMS · BRIGHAM AND WOMEN'S HOSPITAL · PI Soumya Raychaudhuri · 2013 to 2026
$5.4MMolecular and Cellular Dissection of Early Rheumatoid ArthritisUH2AR067694 · NIAMS · FEINSTEIN INSTITUTE FOR MEDICAL RESEARCH · PI BRENNER, MICHAEL B., GREGERSEN, PETER K. · 2014 to 2020
$5.4MIntegrative analysis of high dimensional tissue molecular data to define key biological systems in autoimmune diseases (SBC)UC2AR081023 · NIAMS · BRIGHAM AND WOMEN'S HOSPITAL · PI Soumya Raychaudhuri · 2022 to 2026
$4.8MRA-SLE Molecular Deconstruction Leadership CenterUH2AR067677 · NIAMS · BRIGHAM AND WOMEN'S HOSPITAL · PI BRENNER, MICHAEL B., RAYCHAUDHURI, SOUMYA · 2014 to 2020
$4.3MCellular Dynamics at the Synovium-Bone interface in RAUH2AR067690 · NIAMS · UNIVERSITY OF ROCHESTER · PI ANOLIK, JENNIFER HOWITT · 2014 to 2020
$3.0MNHGRI NIH HHS T32 HG002295NHGRI NIH HHS U01 HG009379NIAID NIH HHS P01 AI148102NIAID NIH HHS R01 AI175212NIAMS NIH HHS K08 AR077037NIAMS NIH HHS R01 AR063759NIAMS NIH HHS R01 AR078769NIAMS NIH HHS R21 AR071670NIAMS NIH HHS T32 AR007258NIAMS NIH HHS T32 AR007530NIAMS NIH HHS UC2 AR081023NIAMS NIH HHS UC2 AR081025NIAMS NIH HHS UH2 AR067676NIAMS NIH HHS UH2 AR067677NIAMS NIH HHS UH2 AR067679NIAMS NIH HHS UH2 AR067681NIAMS NIH HHS UH2 AR067685NIAMS NIH HHS UH2 AR067690NIAMS NIH HHS UH2 AR067691NIAMS NIH HHS UH2 AR067694NIAMS NIH HHS UM2 AR067678U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) T32HG002295U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) U01HG009379U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) 1UH2AR067677-01U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) AR078769U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) K08AR077037U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) T32AR007530U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) UC2AR081023
Abstract
Synovial tissue inflammation is a hallmark of rheumatoid arthritis (RA). Recent work has identified prominent pathogenic cell states in inflamed RA synovial tissue, such as T peripheral helper cells; however, the epigenetic regulation of these states has yet to be defined. Here, we examine genome-wide open chromatin at single-cell resolution in 30 synovial tissue samples, including 12 samples with transcriptional data in multimodal experiments. We identify 24 chromatin classes and predict their associated transcription factors, including a CD8 + GZMK+ class associated with EOMES and a lining fibroblast class associated with AP-1. By integrating with an RA tissue transcriptional atlas, we propose that these chromatin classes represent 'superstates' corresponding to multiple transcriptional cell states. Finally, we demonstrate the utility of this RA tissue chromatin atlas through the associations between disease phenotypes and chromatin class abundance, as well as the nomination of classes mediating the effects of putatively causal RA genetic variants.
Indexed as
Arthritis, RheumatoidChromatinSynovial MembraneCD8-Positive T-LymphocytesEpigenesis, GeneticFibroblastsHumansSingle-Cell AnalysisT-Box Domain ProteinsTranscription Factor AP-1Transcription FactorsTranscription, GeneticChromatinEOMES protein, humanT-Box Domain ProteinsTranscription Factor AP-1Transcription Factors
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.