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Chromatin activity at GWAS loci identifies T cell states driving complex immune diseases

bioRxiv, ISSN: 2692-8205
2019
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    Citations
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Metric Options:   Counts1 Year3 Year

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  • Citations
    2
    • Citation Indexes
      2
      • CrossRef
        2
  • Social Media
    202
    • Shares, Likes & Comments
      202
      • Facebook
        202

Article Description

Complex immune disease variants are enriched in active chromatin regions of T cells and macrophages. However, whether these variants function in specific cell states or stages of cell activation is unknown. We stimulated T cells and macrophages in the presence of thirteen different cytokine cocktails linked to immune diseases and profiled active enhancers and promoters together with regions of open chromatin. We observed that T cell activation induced major chromatin remodelling, while additional exposure to cytokines fine-tuned the magnitude of these changes. Therefore, we developed a new statistical method that accounts for subtle changes in chromatin landscape to identify SNP enrichment across cell states. Our results point towards the role of immune disease variants in early rather than late activation of memory CD4+ T cells, and with limited differences across polarizing cytokines. Furthermore, we demonstrate that inflammatory bowel disease variants are enriched in chromatin regions active in Th1 cells, while asthma variants overlap regions active in Th2 cells. We also show that Alzheimer’s disease variants are enriched in different macrophage cell states. Our results represent the first in-depth analysis of immune disease variants across a comprehensive panel of activation states of T cells and macrophages.

Bibliographic Details

Soskic, Blagoje; Cano Gamez, Eddie; Smith, Deborah J; Rowan, Wendy C; Nakic, Nikolina; Esparza-Gordillo, Jorge; Bossini-Castillo, Lara; Tough, David F; Larminie, Christopher G. C.; Bronson, Paola G.; Wille, David; Trynka, Gosia

Cold Spring Harbor Laboratory

Biochemistry, Genetics and Molecular Biology; Agricultural and Biological Sciences; Immunology and Microbiology; Neuroscience; Pharmacology, Toxicology and Pharmaceutics

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