In a study published in Annals of the Rheumatic Diseases, researchers from the University of Washington (UW) and Benaroya Research Institute (BRI) have uncovered how subtle differences in noncoding regions of DNA — areas that do not code for proteins — can contribute to rheumatoid arthritis (RA) by disrupting the regulation of immune genes.
The study was led by R. David Hawkins at UW Medicine, PhD, along with Jane Buckner, MD, and Karen Cerosaletti, PhD, at BRI. The research team used a high-throughput functional screening method to evaluate more than 1,700 genetic variants found in enhancer regions of activated CD4+ T cells, immune cells that recognize pathogen and self antigens and orchestrate the protective immune response. These enhancer regions are known to play a critical role in turning genes on or off and are increasingly recognized as hotspots for genetic risk in autoimmune diseases. Samples were provided by the BRI biorepository, which were essential for this work. BRI scientists, Naresh Doni Jayavelu, PhD, and Arpit Mishra, PhD, from the Buckner and Cerosaletti labs worked closely with Dr. Hawkins, providing genotyping data and isolating the T cell populations of interest.
“Genome-wide association studies have revealed hundreds of genetic regions linked to RA, but many of these are in noncoding parts of the genome,” said Dr. Naresh Doni Jayavelu. “This study bridges the gap by identifying which of these variants are functionally active and how they may contribute to disease.”
Using a technique called massively parallel reporter assay (MPRA), the researchers identified 17 noncoding variants that significantly alter enhancer activity. These functional variants influence the expression of genes important for immune cell function, many of which have been previously implicated in RA or other autoimmune diseases.
To determine how these variants affect gene expression, the team mapped enhancers to their target genes, then used CRISPR-Cas9 genome editing in primary human T cells to confirm that deleting these enhancers disrupted their target genes. One striking finding was that certain combinations of five functional enhancer genotypes were found exclusively in RA patients, but not in healthy controls, suggesting a multiple-gene model of disease predisposition.
“Our data suggest that RA doesn’t result from a single causative gene, but from combinations of small genetic changes that together disrupt immune regulation,” said Dr. Jane Buckner, president of BRI and co-author on the study. “Understanding these combinations can help us pinpoint which immune pathways are most involved and how we might intervene.”
This study also identified new therapeutic opportunities. Many of the genes linked to these enhancer variants are targets of existing drugs or small molecules, highlighting the possibility of drug repurposing, combination therapy approaches or the development of new precision therapies.
For more information about BRI, visit www.benaroyaresearch.org.
Research reported in this press release was supported by the National Institute of Arthritis and Musculoskeletal and Skin Diseases of the National Institutes of Health under award number R01AR065952. This project was financed with 100% of funding from the National Institutes of Health.
The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
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