Polymorphic variants involved in methylation regulation: a new strategy to discover risk loci for pancreatic ductal adenocarcinoma

Introduction: The genetic susceptibility of pancreatic ductal adeno- carcinoma (PDAC) is poorly understood and population stratification ac- cording to the risk of pancreatic cancer development is a very hard challenge. Genome-wide association studies (GWAS) have identified several single nucleotide polymorphisms (SNPs) as susceptibility loci in non-coding regions of the genome, highlighting the importance of regu- latory region in cancer etiology. Given the importance of DNA methylation in cancer development, functional characterization of non-coding SNPs located inside methylated regions (such as correlated sequences of inter- individual variation (CoRSIV)),or SNPs that influence DNA methylation (methylation quantitative trait loci (meQTL)), could represent a good strategy to improve the knowledge of PDAC susceptibility. Purpose: The purpose of this project was to identify if meQTL or SNPs inside CORSiV regions could affect the risk of developing PDAC. Materials and methods: We searched cis-meQTLs in the whole genome and SNPs inside CORSiV, and performed an association study in a total of 21,954 individuals. In particular, we used the Pancreatic Cancer Cohort Consortium (PanScan) I-III and the Pancreatic Cancer Case-Control Consortium (PanC4) GWAS data as discovery phase (8738 cases and 7034 controls) and the PANcreatic Disease ReseArch (PANDoRA) consortium as replication phase (3047 cases and 3135 controls). Two SNPs (15q26.1- rs12905855 and 15q15.1-rs3751653), that regulate the methylation and the expression of the RCCD1 and ZFYVE19 genes, were selected for repli- cation. Furthermore, a meta-analysis was performed between the two phases. Results: The C allele of 15q15.1-rs3751653 showed an association with an increase of PDAC risk development with OR¼1.09 95% CI 1.05-1.13 and p¼1.59„10-5, very close to the Bonferroni-corrected threshold (p¼1.33„10- 5). 15q15.1-rs3751653 increases the methylation of a CpG site located in the promoter region of the ZFYVE19 gene and decreases the expression of the same gene. A lower expression of ZFYVE19 is known to be associated with DNA damage and aneuploidy, processes that are known to promote carcinogenesis also in PDAC cells. The other selected SNP (15q26.1- rs12905855) did not show an association in the replication phase. Conclusions: Our study identified a novel PDAC risk locus on chro- mosome 15, that might act by modifying gene expression through meth- ylation.