Multi-population GWAS meta-analysis identifies novel bladder cancer susceptibility loci and highlights the genetic regulation of smoking-related risk

Urinary bladder cancer (BC) is the ninth most common malignancy worldwide. We conducted a meta-analysis of genome-wide association studies for BC risk in 32,470 cases and 1,753,462 controls, identifying 70 independent genome-wide significant loci, including 43 novel signals. A 70-marker polygenic risk score was strongly associated with BC risk (hazard ratio=1.61 (1.50-1.73) per standard deviation), substantially improving the area under the curve (AUC) when added to a model with age, sex, and smoking status (AUC=0.75 vs. 0.70, p=4.49E-20). BC risk variants (n=4,196 at p<5.0E-8) were enriched in regions of open chromatin in bladder tissue. Integrated germline, transcriptomic, and proteomic analyses nominated additional susceptibility genes and pathways, particularly related to xenobiotic metabolism. We detected a novel BC signal within a known smoking-related locus at 15q25.1 (rs7173514-C, OR=1.07, p=9.64E-10 for BC risk overall, OR Never-Smoker =1.00 and OR Ever-Smoker =1.14). This signal was primarily driven by an insertion/deletion variant within CHRNA3 -3'UTR rs71581744/rs10637216 (A/ACCCC, r 2 =0.78 with rs7173514 in Europeans) linked with smoking cessation, with an additional contribution from a known lead variant for smoking intensity (rs16969968-G/A, D398N within CHRNA5 ). Further analyses revealed significant heterogeneity for rs71581744 by BC subtype (muscle-invasiveness), particularly among current smokers (OR Muscle Invasive =1.42 vs. OR Non-muscle Invasive =1.11, p heterogeneity =1.84E-02), consistent with epidemiologic observations that current smokers have a higher risk of muscle-invasive bladder cancer. Our in-vitro reporter assays for rs71581744-A/ACCCC demonstrated allele-specific effects on mRNA stability in several cell lines. Since neuronally expressed CHRNA5 and CHRNA3 encode subunits of the nicotinic acetylcholine receptors (nAChR) that regulate smoking behavior, we investigated their expression in normal brain tissues in GTEx. The BC risk signal colocalized with a top CHRNA3 eQTL in one brain area, with variable allelic expression imbalance for CHRNA3 in several brain areas from the same donors. Our results implicate rs71581744-A/ACCCC as a functional variant contributing to BC risk via regulation of CHRNA3 mRNA stability in specific brain areas, affecting nicotine reward/aversion circuits and possibly bladder function. Overall, our study provides new insights into BC genetics and etiology with relevant clinical implications.