Association of twelve polymorphisms in three onco-lncRNA genes with hepatocellular cancer risk and prognosis:A case-control study

AIM To evaluate the association of 12 tag single nucleotide polymorphisms(tag SNPs) in three onco-long non-coding RNA(lnc RNA) genes(HOTTIP,CCAT2,MALAT1) with the risk and prognosis of hepatocellular cancer(HCC). METHODS Twelve tag SNPs covering the three onco-lnc RNAs were genotyped by the KASP method in a total of 1338 samples,including 521 HCC patients and frequencymatched 817 controls. The samples were obtained from an unrelated Chinese population at the First Hospital ofChina Medical University from 2012-2015. The expression quantitative trait loci(e QTL) analyses were conducted to explore further the potential function of the promising SNPs. RESULTS Three SNPs in HOTTIP,one promoter SNP in MALAT1,and one haplotype of HOTTIP were associated with HCC risk. The HOTTIP rs17501292,rs2067087,and rs17427960 SNPs were increased to 1.55-,1.20-,and 1.18-fold HCC risk under allelic models(P = 0.012,0.017 and 0.049,respectively). MALAT1 rs4102217 SNP was increased to a 1.32-fold HCC risk under dominant models(P = 0.028). In addition,the two-way interaction of HOTTIP rs17501292-MALAT1 rs619586 polymorphisms showed a decreased effect on HCC risk(P interaction = 0.028,OR = 0.30) and epistasis with each other. HOTTIP rs3807598 variant genotype showed significantly longer survival time in HBV negative subgroup(P = 0.049,HR = 0.12),and MALAT1 rs591291 showed significantly better prognosis in female and HBV negative subgroups(P = 0.022,HR = 0.37; P = 0.042,HR = 0.25,respectively). In the study,no significant effect was observed in e QTL analysis. CONCLUSION Specific lnc RNA(HOTTIP and MALAT1) SNPs have potential to be biomarkers for HCC risk and prognosis.