Genome-wide association study reveals a novel tuberculosis susceptibility locus in multiple East Asian and European populations

Abstract Background Tuberculosis (TB) continues to be a leading cause of morbidity and mortality worldwide. Although numerous genome-wide association studies (GWAS) have explored TB susceptibility across various ethnic groups, multi-population replication of findings has been very limited, particularly outside the HLA region, and a significant portion of TB heritability remains unexplained. Methods We conducted GWAS in the Singapore Chinese and Vietnamese, followed by a comprehensive meta-analysis incorporating 4 independent East Asian datasets ( N = 11,841 cases; N = 197,373 controls). The transferability of any identified association was assessed using summary statistics from independent European populations. Potential candidate genes were prioritized using gene-based association testing and integrative bioinformatic database mining, followed by functional validation through assessment of Mycobacterium marinum ( M.marinum ) infection burden in CRISPR-Cas9-edited zebrafish embryos. Results We identified a novel susceptibility locus for pulmonary TB (PTB) at 22q12.2 in East Asians [rs6006426, OR (95%Cl) = 1.097(1.066, 1.130), P meta =3.31 × 10 − 10 ]. The association was further validated in Europeans [OR (95%Cl) = 1.101(1.002, 1.211), P = 0.046] and was strengthened in the combined meta-analysis including a total of 12,736 PTB cases and 673,864 controls [OR (95%Cl) = 1.098 (1.068, 1.129); P meta =4.33 × 10 − 11 ]. Gene-based association test identified Oncostatin M ( OSM ) to be significantly associated with PTB (ZSTAT = 5.013; P = 2.68 × 10 − 7 ; P adj =0.005). The lead SNP rs6006426 affected Splicing factor 3a subunit 1 ( SF3A1 ) expression in various immune cells ( P from 0.003 to 6.17 × 10 − 18 ) and OSM expression in monocytes post lipopolysaccharide stimulation ( P = 5.57 × 10 − 4 ) as reported in the eQTL Catalogue. CRISPR-Cas9 edited zebrafish embryos with osm depletion resulted in decreased burden of M.marinum in infected embryos ( P = 0.047). Conclusions Our findings offer novel insights into the genetic factors underlying TB and reveals new avenues for understanding its etiology.