MYLK* FLNB and DOCK1* LAMA2 gene-gene interactions associated with rheumatoid arthritis in the focal adhesion pathway

Abstract

Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disease caused by a combination of genetic and environmental factors. Rare variants with low predicted effects in genes participating in the same biological function might be involved in developing complex diseases such as RA. From whole-exome sequencing (WES) data, we identified genes containing rare non-neutral variants with complete penetrance and no phenocopy in at least one of nine French multiplex families. Further enrichment analysis highlighted focal adhesion as the most significant pathway. We then tested if interactions between the genes participating in this function would increase or decrease the risk of developing RA disease. The model-based multifactor dimensionality reduction (MB-MDR) approach was used to detect epistasis in a discovery sample (19 RA cases and 11 healthy individuals from 9 families and 98 unrelated CEU controls from the International Genome Sample Resource). We identified 9 significant interactions involving 11 genes (MYLK, FLNB, DOCK1, LAMA2, RELN, PIP5K1C, TNC, PRKCA, VEGFB, ITGB5, and FLT1). One interaction (MYLK*FLNB) increasing RA risk and one interaction decreasing RA risk (DOCK1*LAMA2) were confirmed in a replication sample (200 unrelated RA cases and 91 GBR unrelated controls). Functional and genomic data in RA samples or relevant cell types argue the key role of these genes in RA.

Keywords: familial sample; gene–gene interaction; pathway enrichment analysis; rare variants; rheumatoid arthritis.

FIGURE 1

Enrichment analysis results of rare variants carried by all RA cases in at least one multiplex family. Barplot representing the number of genes carrying a rare variant (with complete penetrance and no phenocopy in nine multiplex families) by the significant biological pathway (FDR <5%). The color represents the false discovery rate (FDR) value (Benjamini–Hochberg procedure) of the enrichment analysis.