Riku Takei, Megan Leask, Tony Merriman
Affiliation(s):
University of Alabama at Birmingham, AL, 35233, United States
Objective: Activity-By-Contact (ABC) enhancers identify enhancer regions that physically connect to a gene promoter region1. Using ABC enhancer data, we investigated whether immune cell-related ABC enhancers in stimulated innate immune cells overlap with genetic loci identified in a genome-wide association study (GWAS) of gout.
Methodology: An ABC enhancer-gene connection dataset1 was downloaded. ABC enhancer regions were restricted to those with ABC-score ≥0.0151 and from 57 (31 stimulated and 26 unstimulated) immune cells or cell-lines. Lead variants from a gout GWAS2 were tested for genetic colocalization (using the “coloc” package in R3) with Genotype-Tissue Expression (GTEx)4 expression quantitative trait loci (eQTL) dataset to identify variants that may affect risk of gout via gene expression. The threshold for posterior probability for hypothesis 4 (PPH4) was set at ≥0.8, which indicates strong evidence of shared signal between gout and the eQTL. The eQTL-colocalized gout variants were overlapped with the ABC enhancer regions to assess whether the variants lay within the ABC enhancers.
Results: Out of 340 lead gout variants tested, 273 variants (80.3%) genetically colocalized (PPH4 ≥0.8) with eQTL for at least one gene in cis or trans. In total, 29 variants (10.6%) that colocalized with eQTL were within an ABC enhancer region for 177 genes. For stimulated innate immune cells and cell lines, 14 variants were within an ABC enhancer for 85 genes. Among these genes was CSF1, where the lead gout variant rs2938616 is within an ABC enhancer region for the gene and also a colocalized eQTL of CSF1. In addition to CSF1, CSF1R also had a lead gout variant (rs2282804) within its ABC enhancer region, although it did not colocalize with an eQTL for CSF1R. ABC enhancer regions for both CSF1 and CSF1R were exclusive to stimulated innate immune cells.
Conclusions: Through enhancer activity estimates and three-dimensional connection frequencies, ABC enhancers provide valuable information on how a gene may be regulated. Acute gout inflammation results from an innate immune response to monosodium urate (MSU) crystals. By focusing on stimulated innate immune cell types, we were able to identify gout eQTL variants that were within an ABC enhancer, indicating that these genes may be regulated through these enhancer regions in immune cell types.
In particular, the gene for colony stimulating factor 1, CSF1, was amongst the genes that had colocalized eQTL and the promoter was contacted by an ABC enhancer region for the same gene. CSF1 controls the differentiation and proliferation of monocytes and macrophages5, indicating its possible role in gouty inflammation. In addition to CSF1, its receptor, CSF1R, showed evidence of ABC enhancer-gene connections, and the ABC enhancer regions for both CSF1 and CSF1R are binding sites for the transcription factors nuclear factor kappa B (NF-κB) and repressor element 1 silencing transcription factor (REST). A recent study of gout in an adolescent Chinese cohort6 showed genetic association with REST corepressor 1 (RCOR1) and suppression of REST expression reduced the production of pro-interleukin-1β (pro-IL-1β) in THP-1 cells after MSU crystal stimulation, further supporting the potential involvement of CSF1/CSF1R in gouty inflammation.
References:
1. Nasser, J. et al. Genome-wide enhancer maps link risk variants to disease genes. Nature 1–6 (2021).
2. Major, T. J. et al. A genome-wide association analysis of 2,622,830 individuals reveals new pathogenic pathways in gout. Preprint at https://doi.org/10.1101/2022.11.26.22281768 (2022).
3. Giambartolomei, C. et al. Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics. PLOS Genetics 10, e1004383 (2014).
4. Lonsdale, J. et al. The Genotype-Tissue Expression (GTEx) project. Nat Genet 45, 580–585 (2013).
5.Sehgal, A., Irvine, K. M. & Hume, D. A. Functions of macrophage colony-stimulating factor (CSF1) in development, homeostasis, and tissue repair. Seminars in Immunology 54, 101509 (2021).
6. Ji, A. et al. Novel genetic loci in early-onset gout derived from whole genome sequencing of an adolescent gout cohort. Arthr. Rheum. In press