Functional dissection of noncoding variants associated with rheumatoid arthritis

Area of Science:

• Genetics
• Immunology
• Molecular Biology

Background:

• Noncoding variants play a crucial role in diseases like rheumatoid arthritis (RA).
• Genome-wide association studies (GWAS) have identified disease-associated genomic regions, but functional validation of variants is often lacking.
• Understanding the functional impact of noncoding variants is essential for pinpointing disease mechanisms.

Purpose of the Study:

• To functionally fine-map rheumatoid arthritis-associated variants within noncoding regions.
• To identify specific variants at enhancers that influence gene regulation in T helper cells.
• To uncover the target genes regulated by these functional variants.

Main Methods:

• Identification of variants located at enhancers in primary activated T helper cells.
• Massively parallel reporter assays (MPRAs) were performed in T helper cells to assess variant function.
• Integration of 3D genome architecture and expression quantitative trait loci (eQTL) data to link enhancers to target genes.
• Validation of enhancer activity and target gene interactions using CRISPR-Cas9 deletion in primary T cells.

Main Results:

• Combinations of functional variant genotypes were found to be specific to rheumatoid arthritis patients.
• Allelic differences in enhancer activity were identified, suggesting differential gene regulation.
• Target genes of these enhancers were pinpointed using genomic and eQTL data.
• CRISPR-Cas9 experiments confirmed the regulatory role of identified enhancers and their interaction with target genes.

Conclusions:

• The study identified functional enhancer variants that are potential causal variants for rheumatoid arthritis.
• The identified target genes include both known and novel genes implicated in RA pathogenesis.
• These findings provide a basis for developing novel therapeutic interventions for rheumatoid arthritis.