Ajay Jajodia, Arpit Mishra, Naresh Doni Jayavelu, Katharina Lambert, Nicholas Moss et al.
Non-coding variants are critical to our understanding of the genetic basis of diseases and disorders such as rheumatoid arthritis (RA). While genome-wide association studies have identified regions of the genome associated with disease, functional studies are still lagging that can identify potentially causative variants. In order to functionally fine-map RA-associated variants, we identified variants at enhancers marked in primary activated T helper cells and conducted massively parallel reporter assay in these cells. We find that combinations of functional variant genotypes are often exclusive to RA patients. We leveraged 3D genome architecture and eQTL data to identify target genes of enhancers exhibiting allelic differences in activity. We confirmed enhancer activity and target-gene interactions by CRISPR deletion in primary T cells. The identification of functional enhancer variants suggests possible causal variants, and their target genes reveal known and novel genes as likely drivers of RA, as well as a means for therapeutic intervention.
Ajay Jajodia, Arpit Mishra, Naresh Doni Jayavelu, Katharina Lambert, Nicholas Moss, Zongchen Yang, Karen Cerosaletti, Jane H Buckner, R David Hawkins. Functional dissection of noncoding variants associated with rheumatoid arthritis. 2025-05-03. https://doi.org/10.1016/j.ard.2025.04.001
A synthetic 230-nucleotide reference/alternate allele library covering 1,765 RA-associated variants at 611 H3K4me1-marked enhancers was cloned into a STARR-seq-derived episomal reporter plasmid and electroporated into activated primary human CD4+ T cells. RNA and plasmid DNA readouts were analyzed with QuASAR-MPRA to estimate allele-specific enhancer activity.
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