Alternative Splicing Related Genetic Variants in lncRNA BCLETare Associated with Bladder Cancer Risk in the Chinese Population

Background: Although thousands of alternative splicing related single nucleotide polymorphisms (AS-SNPs) have been uncovered in human tumors, the potential function of AS-SNPs involved in bladder cancer is rarely reported. Here we identified bladder cancer risk-associated AS-SNPs and revealed its underlying causal mechanism in bladder carcinogenesis.Methods: Variants with annotation of “splice-3” or “splice-5” were extracted as AS-SNPs through the database of Single Nucleotide Polymorphism (dbSNP). Two-stage case-control studies comprising 1,630 cases and 2,504 controls were conducted to assess the association between the AS-SNPs and bladder cancer risk. A series of experiments including luciferase reporter assays, RNA immunoprecipitation, and malignant phenotype were performed to comprehensively investigate the genetic and epigenetic biological effects of AS-SNPs in the development of bladder cancer.Results: We identified the potential causal variant rs558814 A>G located in intron of lncRNA BCLET (Bladder Cancer Low-Expressed Transcript) was significantly associated with a reduced risk of bladder cancer [odds ratio (OR) = 0.84, 95% confidence interval (CI) = 0.76 to 0.92, P = 3.26 × 10−4]. The SNP rs558814 exerted transcriptional activity regulatory effect and thus facilitated the expression of BCLET transcripts including BCLET-long and BCLET-short. In addition, both BCLET transcripts overexpression remarkably inhibited in vitro and in vivo bladder cancer phenotypes including cell proliferation, clone formation, invasion, migration and apoptosis. Mechanistically, lncRNA BCLET bound to MSANTD2 mRNA, masked splicing site of MSANTD2 mRNA, and thereby facilitated the expression of MSANTD2-004 transcript, which lacks the first exon and remarkably inhibited the progression of bladder cancer.Conclusions: Our findings not only revealed the important role of AS related genetic variants rs558814 and its associated gene BCLET in bladder cancer progression, but also provided the perspective to understand the etiology and pathology of cancers from the alternative splicing regulation mechanism.