Colorectal cancer: genetic abnormalities, tumor progression, tumor heterogeneity, clonal evolution and tumor-initiating cells

Abstract

Colon cancer is the third most common cancer worldwide. Most colorectal cancer occurrences are sporadic, not related to genetic predisposition or family history; however, 20-30% of patients with colorectal cancer have a family history of colorectal cancer and 5% of these tumors arise in the setting of a Mendelian inheritance syndrome. In many patients, the development of a colorectal cancer is preceded by a benign neoplastic lesion: either an adenomatous polyp or a serrated polyp. Studies carried out in the last years have characterized the main molecular alterations occurring in colorectal cancers, showing that the tumor of each patient displays from two to eight driver mutations. The ensemble of molecular studies, including gene expression studies, has led to two proposed classifications of colorectal cancers, with the identification of four/five non-overlapping groups. The homeostasis of the rapidly renewing intestinal epithelium is ensured by few stem cells present at the level of the base of intestinal crypts. Various experimental evidence suggests that colorectal cancers may derive from the malignant transformation of intestinal stem cells or of intestinal cells that acquire stem cell properties following malignant transformation. Colon cancer stem cells seem to be involved in tumor chemoresistance, radioresistance and relapse.

Keywords: adenomatous polyp; cancer stem cells; colorectal cancer; gene expression profiling; gene sequencing; serrated polyp; tumor xenotrasplantation assay.

Figure 1

Schematic representation of the large intestine crypt. Each crypt comprises a bottom region, containing crypt base columnar (CBC) cells. These cells are intestinal cycling stem cells, leucine-rich repeat-containing G-protein coupled receptor 5 (LGR5)⁺ and generate all major intestinal lineages, including secretory cells and enterocytes. Crypts also contain Paneth cells, the only mature cells that do not migrate upwards and that remain at the base of crypts, near to LGR5⁺ cells. The +4 region contains a population of quiescent stem cells, identified as Bmi1, LRIG1 or label-retaining cells (LRC). A transit-amplifying (TA) region contains differentiating progenitors/precursors. A top region, corresponding to the tip of villi, contains mature elements (enterocytes, goblet cells, Tuft cells and enteroendocrine cells).

Figure 2

The LGR5⁺ stem cell compartment is heterogeneous, comprising a majority of LGR5⁺ cycling intestinal stem cells and a minority of LGR5⁺/Mex3a⁺ quiescent, chemotherapy- and radiation-resistant intestinal stem cells. TAC: transit amplifying cell; ISC: intestinal stem cell.

Figure 3

Outline of the three main pathways of colon carcinogenesis. A classic, conventional pathway is initiated by APC mutations and progresses through the sequential accumulation of genetic mutations and chromosomal instability (CIN), causing microsatellite stable (MSS) tumors. The germline mutation pathway is related to germline mutation of mis-match repair (MMR) genes, seen in Lynch syndrome (hereditary non-polyposis coli) and leads to microsatellite instability (MSI-H). The sessile-serrated-methylation pathway is heterogeneous: a traditional serrated pathway, related to KRAS/BRAF mutations, leading to MSS tumors, with a variable CpG island methylator phenotype (CIMP); a traditional serrated pathway, comprising three subgroups: one leading to MSS and CIMP⁺ tumors, one associated with BRAF mutated and KRAS-WT and hypermethylation of MGMT and p16 gene promoters; the two others leading to MSI-H and CIMP⁺ tumors, one associated with BRAF-mutations and KRAS-WT and hypermethylation of the MLH1 gene promoter and the other one associated with BRAF-WT and KRAS-mutated and hypermethylation of the MLH1 gene promoter.

Figure 4

Genes most frequently mutated in colorectal cancer. (A) Frequently mutated genes in non-hypermutated colon cancer. (B) Recurrently mutated genes in hypermutated colon cancers. (C) Frequency of signaling pathway alterations observed in hypermutated and non-hypermutated colorectal cancers. (D) Frequency of microsatellite instability (MSI-High), CpG island methylator phenotype (CIMP-High) and MLH1 gene epigenetic silencing in hypermutated and non-hypermutated colorectal cancers. (E) Mutations in mismatch repair genes and POLE among the hypermutated colorectal cancers. The figure shows the data reported in the The Cancer Genoma Atlas (TCGA) study [99].

Figure 5

Distribution of somatic mutations in colorectal cancers subdivided into four tumor groups: double mutant (i.e., colorectal cancer samples containing two or more somatic mutations in genes encoding mismatch repair proteins), Lynch syndrome, MLH1-hypermethylated, microsatellite stability (MSS). The upper panel (A) shows the data reported by Cohen and coworkers [114] and the lower panel (B) the data reported in the TCGA study [99].

Figure 6

Frequent genetic alterations, CIMP-H and MLH1-methylated in hyperplastic polyps (A), traditional serrated adenomas (TSA) (B), and sessile serrated adenomas/polyps (SSA/P) (C). The data are reported by Sekine and coworkers [184].

Figure 7

Recurrently altered genes in advanced colorectal patients. (A) Frequency of mutations of the whole population of MSS colorectal cancers. (B) Frequency of mutations in MSS colorectal cancer subdivided into left and right according to tumor location. The figure shows the data reported by Yaeger et al. [201].

Figure 8

(A) Relative prevalence of key oncogenic alterations at specific primary tumor locations in patients with metastatic colon cancer. Panels 1 to 3 from the top to the bottom: frequency of BRAFV600, TP53, SMAD4, CTNNB1, PIK3CA and KRAS/NRAS alterations in primary tumor locations. Bottom pane: frequency of the main oncogenic alterations, consensus molecular subtypes and CIMP-H at the level of right-side colorectal cancer (RSC), left-side colorectal cancer (LSC) and rectum-located colorectal cancers. The data are reported by Loree et al. [242]; (B) Relative prevalence of consensus molecular subtypes (CMS) at specific tumor locations. The data are reported by Loree and coworkers [242].

Figure 8

(A) Relative prevalence of key oncogenic alterations at specific primary tumor locations in patients with metastatic colon cancer. Panels 1 to 3 from the top to the bottom: frequency of BRAFV600, TP53, SMAD4, CTNNB1, PIK3CA and KRAS/NRAS alterations in primary tumor locations. Bottom pane: frequency of the main oncogenic alterations, consensus molecular subtypes and CIMP-H at the level of right-side colorectal cancer (RSC), left-side colorectal cancer (LSC) and rectum-located colorectal cancers. The data are reported by Loree et al. [242]; (B) Relative prevalence of consensus molecular subtypes (CMS) at specific tumor locations. The data are reported by Loree and coworkers [242].

Figure 9

Gene expression-based classification of colorectal cancers into four types according to Guinney et al. [251]: consensus molecular subtype 1 (CMS1), CMS2, CMS3 and CMS4. (A): Activation of some signaling pathways in the four CMS subtypes. (B) Distribution of some molecular abnormalities in the four CMS subtytes. (C): Recurrent gene mutations in the four CMS subtypes. CIMP: CpG island methylator phenotype; hypermutation; SNCA high: single copy number alteration high.

Figure 10

Classification of colorectal cancers into five tumor archetypes. This classification is based on gene expression data on the cancer cell and tumor microenvironment. This classification system is based on the study of Bramsen et al. [264]. SSC: serrated similar cancer; dARE: depleted AU-rich elements; CIN: chromosomal instability.

Figure 11

Recurrent genetic abnormalities observed in small bowel adenocarcinoma. (A): Frequency of genomic alterations in small bowel adenocarcinoma (SB), colorectal cancer (CRC) and gastric cancer (GC). (B): Frequency of genomic alterations in SB adenocarcinomas, subdivided according to tumor location. These data are reported in Schrock et al. [342].