Genome instability in colorectal cancer

Abstract

Four main forms of genomic instability have been described in colorectal cancer (CRC): microsatellite instability (MSI), chromosomal instability (CIN), epigenome abnormalities (CIMP), and hypermutation-ultramutation. The present thesis was focused on the two better characterized forms of genome instability: MSI and CIN. The aim of the present work was to set up a new classification based on MSI and CIN and to analyze gene expression profiles of the newly defined groups. Microsatellite testing classifies tumor samples in two fundamental types: microsatellite-instable (MSI) and microsatellite-stable (MSS) tumors. This classification is well-established according to routine methodology and widely accepted guidelines (Boland et al., 1998). In the present thesis a detailed mutational profile analysis was performed for DNA mismatch repair (MMR) genes, the catalytic subunit of proofreading polymerases (POLE and POLD1) and a selected group of 50 among oncogenes and tumor suppressors, for a more accurate molecular description of MSI tumors. Classification based on chromosomal instability is much less standardized and affected by some technical difficulties. In the present thesis, the recent proposal about the use of somatic broad copy number abnormalities (BCNAs) (Barresi et al., 2017) was adopted in order to identify and sub-classify CRC tumors. According to the proposed methodology and to new criteria established in the present work, MSS tumors were subdivided into high-BCNA (HB) and low-BCNA (LB) tumors. A mutational profile analysis - with the same methodology used for MSI tumors was also applied to the LB group. A further step of the present work was to correlate the classification based on microsatellite status and on the number of BCNAs with gene expression profiles from cancer samples. HB tumors showed upregulation of intestinal epithelial genes, such as NOX1, AREG, EREG. LB tumors and MSI tumors shared a pattern of upregulation of REG4, AGR2, SPP1, CD55, MUC5B, although expression of such genes was higher for MSI samples. Upregulation of these genes had previously been described for mucinous tumors. Indeed, LB and MSI groups were enriched for mucin-producing tumors. In conclusion, taking into account the number of BCNAs, along with MSI status and with the mutational profile, two groups of MSS samples can be distinguished: HB tumors, characterized by the expression of a subset of epithelial genes, some of them involved in EGF signaling; and LB tumors, enriched for mucin-producing tumors, which resemble MSI tumors for what concerns upregulation of a subset of genes involved in the colon mucus barrier and other cell-precursor markers