Genome-wide association studies (GWASs) have produced large numbers of disease associated single-nucleotide polymorphisms (SNPs). However, many of these studies have failed to identify causative mutations. This may be due to the complexity of the disease; or in part, due to many associated SNPs lying outside of gene coding regions. A recent assessment of GWASs illustrated that 45% of disease or trait associated SNPs fell in introns, while 43% lie in intergenic regions. Global methods for determining chromatin states have shown that associated SNPs can overlap regulatory regions. We have constructed enhancer maps based H3K4me1 localization in isolated, human T cells, which were activated, or polarized toward Th1 or Th2 lineages. We focused on an early time point of polarization to determine the cis-regulome of early T cell differentiation and regulation f T cell fate commitment. To determine if rheumatoid arthritis-associated SNPs are potentially rSNPs, we analyzed the vicinities of associated SNPs from the NHGRI GWAS catalog for overlap with our global T helper cell enhancer predictions. Goal: Having identified 440 potential regulatory SNPs within enhancers driving early T cell fates, our goal is to functionally validate RA-associated rSNPs through a series of high-throughput assays and systematic evaluation to determine the most functionally relevant rSNPs. Through this process we will also determine the target genes of enhancers harboring rSNPs in order to identify new genes important in the etiology of RA pathogenesis. We will do so through the following specific aims.
Specific Aim 1. Determine the effect of rSNPs on enhancer activity.
Specific Aim 2. Identification of TFs and their disrupted binding at enhancer SNPs.
Specific Aim 3. Identification of target genes for enhancers harboring associated SNPs

Public Health Relevance

We are employing genome-wide epigenomic approaches to map regulatory elements in human T cells at an early time point of lineage commitment. We have identified enhancers that overlap rheumatoid arthritis-associated SNPs. We will functionally validate enhancer SNPs by several high-throughput methods to tests for enhancer activity, transcription factor binding, and to determine enhancer gene targets.

Agency
National Institute of Health (NIH)
Institute
National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
Type
Research Project (R01)
Project #
5R01AR065952-04
Application #
9446772
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Wang, Yan Z
Project Start
2015-03-01
Project End
2019-01-31
Budget Start
2018-02-01
Budget End
2019-01-31
Support Year
4
Fiscal Year
2018
Total Cost
Indirect Cost
Name
University of Washington
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
605799469
City
Seattle
State
WA
Country
United States
Zip Code
98195
Mishra, Arpit; Hawkins, R David (2017) Three-dimensional genome architecture and emerging technologies: looping in disease. Genome Med 9:87
Pasumarthy, Kalyan K; Doni Jayavelu, Naresh; Kilpinen, Lotta et al. (2017) Methylome Analysis of Human Bone Marrow MSCs Reveals Extensive Age- and Culture-Induced Changes at Distal Regulatory Elements. Stem Cell Reports 9:999-1015