Gene-Based Genome-Wide Association Analysis in European and Asian Populations Identified Novel Genes for Rheumatoid Arthritis

<div><p>Objective</p><p>Rheumatoid arthritis (RA) is a complex autoimmune disease. Using a gene-based association research strategy, the present study aims to detect unknown susceptibility to RA and to address the ethnic differences in genetic susceptibility to RA between European and Asian populations.</p><p>Methods</p><p>Gene-based association analyses were performed with KGG 2.5 by using publicly available large RA datasets (14,361 RA cases and 43,923 controls of European subjects, 4,873 RA cases and 17,642 controls of Asian Subjects). For the newly identified RA-associated genes, gene set enrichment analyses and protein-protein interactions analyses were carried out with DAVID and STRING version 10.0, respectively. Differential expression verification was conducted using 4 GEO datasets. The expression levels of three selected ‘highly verified’ genes were measured by ELISA among our in-house RA cases and controls.</p><p>Results</p><p>A total of 221 RA-associated genes were newly identified by gene-based association study, including 71‘overlapped’, 76 ‘European-specific’ and 74 ‘Asian-specific’ genes. Among them, 105 genes had significant differential expressions between RA patients and health controls at least in one dataset, especially for 20 genes including 11 ‘overlapped’ (<i>ABCF1</i>, <i>FLOT1</i>, <i>HLA-F</i>, <i>IER3</i>, <i>TUBB</i>, <i>ZKSCAN4</i>, <i>BTN3A3</i>, <i>HSP90AB1</i>, <i>CUTA</i>, <i>BRD2</i>, <i>HLA-DMA)</i>, 5 ‘European-specific’ <i>(PHTF1</i>, <i>RPS18</i>, <i>BAK1</i>, <i>TNFRSF14</i>, <i>SUOX)</i> and 4 ‘Asian-specific’ (<i>RNASET2</i>, <i>HFE</i>, <i>BTN2A2</i>, <i>MAPK13</i>) genes whose differential expressions were significant at least in three datasets. The protein expressions of two selected genes <i>FLOT1</i> (P value = 1.70E-02) and <i>HLA-DMA</i> (P value = 4.70E-02) in plasma were significantly different in our in-house samples.</p><p>Conclusion</p><p>Our study identified 221 novel RA-associated genes and especially highlighted the importance of 20 candidate genes on RA. The results addressed ethnic genetic background differences for RA susceptibility between European and Asian populations and detected a long list of overlapped or ethnic specific RA genes. The study not only greatly increases our understanding of genetic susceptibility to RA, but also provides important insights into the ethno-genetic homogeneity and heterogeneity of RA in both ethnicities.</p></div

The flow chart of data analysis.

<p>European-specific and Asian-specific multivariate gene-based association tests were conducted separately by using extended Simes procedure (GATES) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0167212#pone.0167212.ref009" target="_blank">9</a>], KGG 2.5, using raw data of 18 European GWASs and 4 Asian GWASs. The 221novel genes were screened from 402gene-based detected genes. Among the 221genes, the differential expression of 105 genes was verified at least in one of four GEO datasets. The differential expressions of 20 genes were verified at least in three of four GEO datasets. Three genes encoding secretory proteins were selected from the 11 ‘highly’ verified ‘overlapped’ genes. GWASs: genome-wide association studies; PheGenI: Phenotype-Genotype Integrator<a href="http://www.ncbi.nlm.nih.gov/gap/phegeni/;GEO" target="_blank">http://www.ncbi.nlm.nih.gov/gap/phegeni/;GEO</a>: gene expression omnibus.</p

The 20 ‘highly verified’ RA-associated genes newly identified by gene-based association study.

<p>The 20 ‘highly verified’ RA-associated genes newly identified by gene-based association study.</p

Clinical characteristics and ELISA test results of all patients and controls.

<p>Clinical characteristics and ELISA test results of all patients and controls.</p

PPI network analysis for the 221‘novel’RA-associated genes.

<p>This is the confidence view of protein-protein interactions produced by STRING for(A) 221 total, (B) 71 overlapped, (C) 76 European-specific and (D)74 Asian-specific gene-based RA-associated genes whose integrated scores are bigger than 0.4. The disconnected nodes are not shown in the figure. Stronger associations are represented by thicker lines. The most visible gene set is mainly composed by histone 1H family both in (A) and (D).</p