Mutation Profiling of Premalignant Colorectal Neoplasia

Jakub Karczmarski; Krzysztof Goryca; Jacek Pachlewski; Michalina Dabrowska; Kazimiera Pysniak; Agnieszka Paziewska; Maria Kulecka; Malgorzata Lenarcik; Andrzej Mroz; Michal Mikula; Jerzy Ostrowski

doi:10.1155/2019/2542640

Mutation Profiling of Premalignant Colorectal Neoplasia

Gastroenterol Res Pract. 2019 Nov 12:2019:2542640. doi: 10.1155/2019/2542640. eCollection 2019.

Authors

Affiliations

¹ Department of Genetics, Maria Sklodowska-Curie Institute-Oncology Center, 02-781 Warsaw, Poland.
² Department of Gastroenterology, Hepatology and Clinical Oncology, Center for Postgraduate Medical Education, 01-813 Warsaw, Poland.
³ Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Institute-Oncology Center, 02-781 Warsaw, Poland.
⁴ Department of Pathomorphology, Center for Postgraduate Medical Education, 01-813 Warsaw, Poland.

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.