Analysis Of Early-onset Colorectal Carcinoma With Paired Liver Metastases Using Exome Sequencing

Colorectal carcinoma (CRC) is one of the most common malignant neoplasm and death results from the formation of metastases in most cases. Moreover, the molecular mechanisms underlying the early-onset CRC is still unclear. This study was conducted to determine the genomic discordance and evaluate clonal structures in matched primary colorectal tumors and metastases, as well as the molecular events involved in early-onset CRC. We performed exome sequencing and SNP array to profile somatic mutations and copy number variations (CNVs) in patients. First, our exome sequencing result from 4 patients showed that known driver genes involved in oncogenesis of CRC, for example, APC, TP53, KRAS, PIK3CA, SMAD4, ATM, PTEN, were found in some but not all patients. Although mutated genes found in patients were different, the enrichment result exhibited high similarity among known pathways that were deregulated, including WNT, TGF-β, PI3K, RAS and P53 pathways. By analyzing CNV among 4 cases, we showed that 13q amplification was the only shared broad CNV. Furthermore, the identification of common fragile sites located in focal CNVs indicated that the presence of DNA replication stress in tumor. Second, intratumor heterogeneity (ITH) was observed in all cases. We noticed the discordance in KRAS and PIK3CA mutational status between primary tumor and metastases in case 1. In case 2, multiple regions from primary tumor showed heterogenous mutations and copy number variation profiles. Based on the mutational distribution, we speculated that the three metastases were offspring of different primary tumor regions. Third, although heterogeneity was seen, in same patient, all known driver mutations were shared by all sampling tumors. We constructed phylogenetic tree of tumors by applying mutations, broad CNVs, focal CNVs and CNV breakpoints, the result supported branching evolution and tumors in same patient shared same ancestral clone. Clonal composition analysis suggested that the major clone observed in primary tumor sections was also dominant in metastases. Last, we observed high proportional of CNVs accompanied by frequent chromosomal regions of loss of heterozygosity (LOH) in early-onset CRC as well as the enrichment of T to G mutation in CpTpT context. Furthermore, APC 5 bp deletion at codon 1309 arose as a somatic mosaic at early stage and might played a dominant role in triggering tumorigenesis, which explains the development of early-onset CRC in patient 2.