Unravelling the landscape of genomic alterations in Malaysian colorectal cancer patients using whole genome sequencing

Abstract

Over the past few years, colorectal cancer (CRC) remains the third most common cancer worldwide, and the incidence is increasing continuously in some areas of the world, including Malaysia. The rise in the number of CRC cases in Malaysia underlines the importance of understanding this cancer by genetically profiling the genome of our local CRC patients. In this study, we aimed to characterize the landscape of somatic mutations using a whole-genome sequencing approach and provide a better insight into the key molecular networks involved in Malaysian CRC patients. With at least 30× coverage, whole-genome sequencing was performed on the genomic DNA obtained from 50 CRC patients. Identified variants were validated using Sanger sequencing. We detected all types of somatic mutations, including single nucleotide variants (SNVs), insertions and deletion (indels), structural variants (SVs) and copy number alterations (CNAs) involving the coding region of the genome. With the mutation rate range from 0.83 to 243.97 mutations per Mb, we obtained an average of 40, 666 somatic variants. We discovered five top significantly mutated genes (p<0.001 and q<1.0), which are APC, TP53, KRAS, TCF7L2 and ACVR2A. A total of five novel, non-synonymous variants which led to amino acid changes had not been reported previously in either COSMIC or dbSNP. These variants were identified in four genes; KDM4E, MUC16, POTED and KRTAP10-4. At least one druggable somatic alteration was identified in 88% of our patients. Among them were two RNF43 variants, which were predicted to have responsive effects against the Wnt pathway inhibitor. CRC cell line expressing RNF43 p.G156Afs*11 and p.P192Gfs*2 promoted cell proliferation, increased sensitivity towards LGK974 drug treatment and caused G1 cell cycle arrest. Additionally, both RNF43 mutant proteins had longer protein half-lives as compared to the wild-type protein. In conclusion, this study uncovered the genomic landscape of local CRC patients and suggested an alternative treatment targeting the Wnt/Beta Catenin signalling pathway, which could benefit CRC patients.