Germline and Somatic Whole-Exome Sequencing Identifies New Candidate Genes Involved in Familial Predisposition to Serrated Polyposis Syndrome

SIMPLE SUMMARY: Cancer is the second leading cause of death worldwide. Serrated polyposis syndrome (SPS) is characterized by the presence of serrated lesions in the colon and a higher colorectal cancer (CRC) risk. An important part of risk is due to the alteration of certain genes, which will be transmitted from one generation to another in the same family. Our main objective was to identify alterations of the human genome relevant to the hereditary predisposition to SPS, by focusing on families with several cases of this disease (familial SPS) and by using massive sequencing techniques to decode the genome. Our strategy allowed us to suggest the implication of 14 new genes in SPS predisposition. Identifying the inherited genetic factors involved in SPS can be useful to identify those families with medium-high CRC risk and, therefore, implement more targeted, intensive preventive measures for this group of patients. ABSTRACT: The serrated polyposis syndrome (SPS) is the most common and yet underdiagnosed colorectal polyposis syndrome. It is characterized by multiple and/or large colonic serrated polyps and a higher associated risk for colorectal cancer (CRC). The main objective of this study was to identify new candidate genes involved in the germline predisposition to SPS/CRC. Thirty-nine SPS patients from 16 families (≥2 patients per family) were recruited without alterations in well-known hereditary CRC genes, and germline and somatic whole-exome sequencing were performed. Germline rare variants with plausible pathogenicity, located in genes involved in cancer development, senescence and epigenetic regulation were selected. Somatic mutational profiling and signature analysis was pursued in one sample per family, when possible. After data filtering, ANXA10, ASXL1, CFTR, DOT1L, HIC1, INO80, KLF3, MCM3AP, MCM8, PDLIM2, POLD1, TP53BP1, WNK2 and WRN were highlighted as the more promising candidate genes for SPS germline predisposition with potentially pathogenic variants shared within families. Somatic analysis characterized mutational profiles in advanced serrated polyps/tumors, revealing a high proportion of hypermutated samples, with a prevalence of clock-like mutational signatures in most samples and the presence of DNA mismatch repair-defective signatures in some cases. In conclusion, we identified new candidate genes to be involved in familial SPS. Further functional studies and replication in additional cohorts are required to confirm the selected candidates.