Mutation Profiling of Premalignant Colorectal Neoplasia

Abstract

Accumulation of allelic variants in genes that regulate cellular proliferation, differentiation, and apoptosis may result in expansion of the aberrant intestinal epithelium, generating adenomas. Herein, we compared the mutation profiles of conventional colorectal adenomas (CNADs) across stages of progression towards early carcinoma. DNA was isolated from 17 invasive adenocarcinomas (ACs) and 58 large CNADs, including 19 with low-grade dysplasia (LGD), 21 with LGD adjacent to areas of high-grade dysplasia and/or carcinoma (LGD-H), and 28 with high-grade dysplasia (HGD). Ion AmpliSeq Comprehensive Cancer Panel libraries were prepared and sequenced on the Ion Proton. We identified 956 unique allelic variants; of these, 499 were considered nonsynonymous variants. Eleven genes (APC, KRAS, SYNE1, NOTCH4, BLNK, FBXW7, GNAS, KMT2D, TAF1L, TCF7L2, and TP53) were mutated in at least 15% of all samples. Out of frequently mutated genes, TP53 and BCL2 had a consistent trend in mutation prevalence towards malignancy, while two other genes (HNF1A and FBXW7) exhibited the opposite trend. HGD adenomas had significantly higher mutation rates than LGD adenomas, while LGD-H adenomas exhibited mutation frequencies similar to those of LGD adenomas. A significant increase in copy number variant frequency was observed from LGD through HGD to malignant samples. The profiling of advanced CNADs demonstrated variations in mutation patterns among colorectal premalignancies. Only limited numbers of genes were repeatedly mutated while the majority were altered in single cases. Most genetic alterations in adenomas can be considered early contributors to colorectal carcinogenesis.

Discovering the Mutational Profile of Early Colorectal Lesions: A Translational Impact

“…The pivotal role of alterations in the Wnt-pathway related genes in colorectal tumorigenesis was also supported in a retrospective analysis of 58 CNADs with different grades of dysplasia, 17 of which were classified as adenocarcinomas [ 58 ]. APC gene mutations frequently occurred in this study (76.5% of cases).…”

“…The following are available online at https://www.mdpi.com/article/10 .3390/cancers13092081/s1, Table S1: Studies evaluating cumulative CRC risk in Lynch syndrome in relation to germline mutations in MMR gene; Table S2: Studies evaluating somatic mutations in sporadic CRC. References [49][50][51][52]58,59,63,68,69,74] are cited in the Supplementary Material. Funding: This research was funded by the AIRC Foundation for Cancer Research (Grant number: IG 21723 to L.R.…”

“…TP53 mutations are also traditionally associated with TGF-β , SMAD4 and PI3KCA mutations during the later phases of adenoma-carcinoma transition [ 55 ]. Despite being more frequent in the advanced stages of colorectal tumorigenesis, there is also evidence of TP53 mutations in normal colon epithelial stem cells [ 56 ], as well as in early and premalignant colorectal adenomas [ 57 , 58 , 59 ].…”

“…KRAS mutations were found in most of the adenomas analyzed (62.4% of cases), particularly in pre-malignant and high-grade dysplasia adenomas. Mutations in other genes, including BCL2 , FBXW7 , GNAS , HNF1A , MLL2/KMT2D , MLL3/KMT2C , SYNE1 , TCF7L2 , NOTCH1 , PBRM1 , RET , RARA , and FN1, were also detected [ 58 ] ( Table 2 ). Mutations in the Wnt-related genes CTNNB1 , EP300 , TCF7L2 , and the AMER1 genes were also observed, but at a lower frequency, in accordance with previous data on adenomas with high grade dysplasia [ 65 ].…”

Clinical significance of FBXW7 tumor suppressor gene mutations and expression in human colorectal cancer: a systemic review and meta-analysis

“…CRC harbors the second most frequent FBXW7 mutations (7.73%) among different cancer types [ 9 ]. Moreover, FBXW7 is one of the most frequently mutated genes during CRC initiation and progression [ 10 ]. Altered FBXW7 status (mutation and/or low expression) may be associated with prognosis in CRC, however, the results vary among different studies [ 11 – 20 ].…”