Title |
A validated gene regulatory network and GWAS identifies early regulators of T cell–associated diseases
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Published in |
Science Translational Medicine, November 2015
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DOI | 10.1126/scitranslmed.aad2722 |
Pubmed ID | |
Authors |
Mika Gustafsson, Danuta R Gawel, Lars Alfredsson, Sergio Baranzini, Janne Björkander, Robert Blomgran, Sandra Hellberg, Daniel Eklund, Jan Ernerudh, Ingrid Kockum, Aelita Konstantinell, Riita Lahesmaa, Antonio Lentini, H Robert I Liljenström, Lina Mattson, Andreas Matussek, Johan Mellergård, Melissa Mendez, Tomas Olsson, Miguel A Pujana, Omid Rasool, Jordi Serra-Musach, Margaretha Stenmarker, Subhash Tripathi, Miro Viitala, Hui Wang, Huan Zhang, Colm E Nestor, Mikael Benson |
Abstract |
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. |
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Geographical breakdown
Country | Count | As % |
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United States | 12 | 32% |
Canada | 2 | 5% |
Spain | 1 | 3% |
Saudi Arabia | 1 | 3% |
Argentina | 1 | 3% |
Malaysia | 1 | 3% |
France | 1 | 3% |
Israel | 1 | 3% |
Brazil | 1 | 3% |
Other | 1 | 3% |
Unknown | 16 | 42% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 24 | 63% |
Scientists | 11 | 29% |
Science communicators (journalists, bloggers, editors) | 2 | 5% |
Practitioners (doctors, other healthcare professionals) | 1 | 3% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United Kingdom | 2 | 1% |
United States | 2 | 1% |
Spain | 1 | <1% |
Sweden | 1 | <1% |
Unknown | 174 | 97% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 55 | 31% |
Student > Ph. D. Student | 31 | 17% |
Student > Master | 15 | 8% |
Student > Bachelor | 11 | 6% |
Other | 10 | 6% |
Other | 34 | 19% |
Unknown | 24 | 13% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 48 | 27% |
Biochemistry, Genetics and Molecular Biology | 33 | 18% |
Medicine and Dentistry | 30 | 17% |
Immunology and Microbiology | 16 | 9% |
Computer Science | 4 | 2% |
Other | 15 | 8% |
Unknown | 34 | 19% |