Genomic and epigenetic instability in colorectal cancer pathogenesis

Abstract

Colorectal cancer arises as a consequence of the accumulation of genetic alterations (gene mutations, gene amplification, and so on) and epigenetic alterations (aberrant DNA methylation, chromatin modifications, and so on) that transform colonic epithelial cells into colon adenocarcinoma cells. The loss of genomic stability and resulting gene alterations are key molecular pathogenic steps that occur early in tumorigenesis; they permit the acquisition of a sufficient number of alterations in tumor suppressor genes and oncogenes that transform cells and promote tumor progression. Two predominant forms of genomic instability that have been identified in colon cancer are microsatellite instability and chromosome instability. Substantial progress has been made to identify causes of chromosomal instability in colorectal cells and to determine the effects of the different forms of genomic instability on the biological and clinical behavior of colon tumors. In addition to genomic instability, epigenetic instability results in the aberrant methylation of tumor suppressor genes. Determining the causes and roles of genomic and epigenomic instability in colon tumor formation has the potential to yield more effective prevention strategies and therapeutics for patients with colorectal cancer.

Figure 1

Depiction of colorectal tumor progression in sporadic and high-risk genetic syndromes. The general paradigm is that a tumor is initiated from a normal colonocyte stem cell that has sustained genetic damage over time due to the local environment and any germline genetic mutation that has been inherited. The damaged DNA provides a growth advantage that drives tumor progression as successive clonal outgrowths are generated, ultimately forming carcinoma. In FAP, tumor initiation is accelerated with the inheritance of a germline APC mutation; in Lynch syndrome, tumor intitiation might be normal to slightly accelerated, but tumor progression is greatly accelerated due to the hypermutable phenotype that occurs with loss of DNA MMR. Photomicrographs depict, in order, normal colon, tubular adenoma, high-grade dysplasia, and cancer.

Figure 2

Schematic of DNA MMR. The MMR heterodimer hMSH2-hMSH6 (hMutSα) recognizes single nucleotide mispairs and will bind to DNA as a sliding clamp. The heterodimer hMLH1-hPMS2 (hMutLα) then binds to hMutSα to eventually guide an exonuclease to remove several bases from the newly synthesized DNA strand, with eventual resynthesis of DNA with the correct base pairing. At microsatellite sequences, insertion-deletion loops of one nucleotide are typically recognized by hMutSβ (upper panel), but larger insertion-deletion lops are recognized by the heterodimer hMSH2-hMSH3 (hMutSβ) (lower panel), followed by binding by hMutLα, excision, and resynthesis as described previously. The roles of hMLH1-hPMS1 and hMLH1-hMLH3 in human MMR function are not entirely clear. When the MutS complexes bind DNA, they exchange ADP for ATP. For the MMR proteins to be released from DNA, ATP is hydrolyzed to ADP.

Figure 3

Progression of colorectal tumors with MSI. MSI tumors, whether sporadic or from patients with Lynch syndrome, lose MMR function early in the polyp → cancer progression sequence. Sporadic tumors almost uniformly lose MMR function due to hypermethylation of the promoter of hMLH1, whereas patients with Lynch syndrome have a germline mutation in one of the MMR genes. It is generally believed that Wnt signaling, the gatekeeper for colorectal neoplasia, is affected, but the full mechanisms are not clear and include mutation of CTNNB1, the gene encoding β-catenin in some cases of Lynch syndrome. The serrated adenoma may be one histologic form for MSI colorectal tumors. In the milieu of MMR absence, a hypermutable phenotype develops in which multiple mutations occur in DNA. Although most mutations occur in noncoding sequences such as intronic DNA microsatellites, certain genes such as TGFBR2, ACVR2, BAX, hMSH3, hMSH6, and others that have coding microsatellite sequences become frameshifted in the absence of DNA MMR. These mutations help drive the progression of the tumor. BRAF mutations are principally found in sporadic tumors with MSI and not tumors from patients with Lynch syndrome and can be used to differentiate these 2 groups of tumors. Notably, in MSI and non-MSI tumors, signaling through the TGF-β superfamily is altered to favor tumor promotion in a not yet fully understood fashion.

Figure 4

Progression of colorectal tumors with CIN. The hallmark of the CIN pathway is aneuploidy. Initiation of neoplasia in this pathway occurs with interruption of components of the Wnt signaling pathway, including somatic mutation in one allele and loss of heterozygosity of the second normal allele of the APC gene, and is seen in dysplastic ACF histologically. Progression is then driven by successive waves of cellular clonal expansion that acquire enhanced growth characteristics and include mutational activation of the proto-oncogene KRAS and mutation of TP53 with subsequent loss of heterozygosity of the normal remaining TP53 allele to allow carcinoma formation. In some colorectal tumors, mutational activation of PIK3CA occurs late in the adenoma-carcinoma sequence. Several TGF-β signaling molecules are also affected in CIN progression, including mutations of the kinase domain of TGFBR2 and loss of heterozygosity at chromosome 18q, the site of SMAD4 and SMAD2. Several genes are believed to be involved in metastasis and include gene amplification of PRL3.

Figure 5

Schematic diagram of cell cycle checkpoints in relation to cell cycle phases. The DNA damage, DNA replication, and mitotic/spindle-kinetochore checkpoints are shown with a corresponding list of a subset of human and S cerevisiae genes that function at each of the checkpoints. The sensor proteins and downstream signal transduction and effector proteins are listed for the DNA replication checkpoints in S phase. The proteins listed at the other checkpoints operate as sensor, transducers, or effector proteins.

Figure 6

Conceptual progression of colorectal tumors with CpG island Methylator Phenotype. The hallmark of the CIMP pathway is abnormal methylation of several promoter sequences of tumor suppressor genes. This pathway in part overlaps with sporadic MSI tumors because the MMR gene hMLH1 is targeted for hypermethylation, which causes loss of MMR function. Although a full understanding of the CIMP is not clear, including the mechanism for hypermethylation of genes that is observed, we propose the following adenoma-carcinoma sequence based on studies published to date. Instead of dysplastic ACF with interrupted Wnt signaling, hyperplastic ACF may be the initial lesion in this pathway. Methylated promoters of MGMT, EVL, HLTF, SFRP2, SLC5A8, and MINT1 develop during the initiation phase of colorectal tumor development. hMLH1 promoter hypermethylation might correspond to the development of a serrated adenoma, with methylated TSP1 and TIMP3 helping to drive the progression of the CIMP tumor.