Transcriptome-wide association study identifies susceptibility genes for rheumatoid arthritis

Abstract

Abstract Objective To identify rheumatoid arthritis (RA)-associated susceptibility genes and pathways through integrating genome-wide association study (GWAS) and gene expression profile data. Methods A transcriptome-wide association study (TWAS) was conducted by the FUSION software for RA considering EBV-transformed lymphocytes (EL), transformed fibroblasts (TF), peripheral blood (NBL), and whole blood (YBL). GWAS summary data was driven from a large-scale GWAS, involving 5539 autoantibody-positive RA patients and 20,169 controls. The TWAS-identified genes were further validated using the mRNA expression profiles and made a functional exploration. Results TWAS identified 692 genes with P TWAS values < 0.05 for RA. CRIPAK (P EL = 0.01293, P TF = 0.00038, P NBL = 0.02839, P YBL = 0.0978), MUT (P EL = 0.00377, P TF = 0.00076, P NBL = 0.00778, P YBL = 0.00096), FOXRED1 (P EL = 0.03834, P TF = 0.01120, P NBL = 0.01280, P YBL = 0.00583), and EBPL (P EL = 0.00806, P TF = 0.03761, P NBL = 0.03540, P YBL = 0.04254) were collectively expressed in all the four tissues/cells. Eighteen genes, including ANXA5, AP4B1, ATIC (P TWAS = 0.0113, downregulated expression), C12orf65, CMAH, PDHB, RUNX3 (P TWAS = 0.0346, downregulated expression), SBF1, SH2B3, STK38, TMEM43, XPNPEP1, KIAA1530, NUFIP2, PPP2R3C, RAB24, STX6, and TLR5 (P TWAS = 0.04665, upregulated expression), were validated with integrative analysis of TWAS and mRNA expression profiles. TWAS-identified genes functionally involved in endoplasmic reticulum organization, regulation of cytokine production, TNF signaling pathway, immune response-regulating signaling pathway, regulation of autophagy, etc. Conclusion We identified multiple candidate genes and pathways, providing novel clues for the genetic mechanism of RA.

Keywords

• Rheumatoid arthritis (RA)
• Transcriptome-wide association study (TWAS)
• Genome wide association study (GWAS)
• Susceptibility genes