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A validated gene regulatory network and GWAS identifies early regulators of T cell-associated diseases
Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
Karolinska Institute, Sweden.
University of Calif San Francisco, CA, USA.
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2015 (English)In: Science Translational Medicine, ISSN 1946-6234, E-ISSN 1946-6242, Vol. 7, no 313, 313ra178Article in journal (Refereed) PublishedText
Abstract [en]

Early regulators of disease may increase understanding of disease mechanisms and serve as markers for presymptomatic diagnosis and treatment. However, early regulators are difficult to identify because patients generally present after they are symptomatic. We hypothesized that early regulators of T cell-associated diseases could be found by identifying upstream transcription factors (TFs) in T cell differentiation and by prioritizing hub TFs that were enriched for disease-associated polymorphisms. A gene regulatory network (GRN) was constructed by time series profiling of the transcriptomes and methylomes of human CD4(+) T cells during in vitro differentiation into four helper T cell lineages, in combination with sequence-based TF binding predictions. The TFs GATA3, MAF, and MYB were identified as early regulators and validated by ChIP-seq (chromatin immunoprecipitation sequencing) and small interfering RNA knockdowns. Differential mRNA expression of the TFs and their targets in T cell-associated diseases supports their clinical relevance. To directly test if the TFs were altered early in disease, T cells from patients with two T cell-mediated diseases, multiple sclerosis and seasonal allergic rhinitis, were analyzed. Strikingly, the TFs were differentially expressed during asymptomatic stages of both diseases, whereas their targets showed altered expression during symptomatic stages. This analytical strategy to identify early regulators of disease by combining GRNs with genome-wide association studies may be generally applicable for functional and clinical studies of early disease development.

Place, publisher, year, edition, pages
AMER ASSOC ADVANCEMENT SCIENCE , 2015. Vol. 7, no 313, 313ra178
National Category
Biological Sciences Clinical Medicine
URN: urn:nbn:se:liu:diva-123522DOI: 10.1126/scitranslmed.aad2722ISI: 000365237400003PubMedID: 26560356OAI: diva2:886275

Funding Agencies|Cancer fund, Swedish Medical Research Council [K2013-61X-22310-01-04, 2012-3168]; Academy of Finland Centre of Excellence in Molecular Systems Immunology and Physiology Research [250114]; Sigrid Juselius Foundation; Generalitat de Catalunya AGAUR [2014-SGR364]; Spanish Association Against Cancer; Spanish Ministry of Health ISCIII FIS [PI12/01528]; RTICC [RD12/0036/0008]

Available from: 2015-12-22 Created: 2015-12-21 Last updated: 2016-03-11Bibliographically approved

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Gustafsson, MikaGawel, DanutaBlomgran, RobertHellberg, SandraEklund, DanielErnerudh, JanLentini, AntonioMellergård, JohanWang, HuiZhang, HuanNestor, ColmBenson, Mikael
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