Exome Capture Sequencing of Adenoma Reveals Genetic Alterations in Multiple Cellular Pathways at the Early Stage of Colorectal Tumorigenesis

Donger Zhou,Weiting Ge,Huanming Yang,Shu Zheng,Mingming Liu,Jinghong Xu,Xueda Hu,Yong Zhang,Yanqin Huang,Hanguang Hu,Liu Yang,Liangtao Zheng,Hang Zhang,Hao Zhang,Dan Li,Zhibo Gao,Lei Zheng,Hassan Brim

doi:10.1371/journal.pone.0053310

Abstract

Most of colorectal adenocarcinomas are believed to arise from adenomas, which are premalignant lesions. Sequencing the whole exome of the adenoma will help identifying molecular biomarkers that can predict the occurrence of adenocarcinoma more precisely and help understanding the molecular pathways underlying the initial stage of colorectal tumorigenesis. We performed the exome capture sequencing of the normal mucosa, adenoma and adenocarcinoma tissues from the same patient and sequenced the identified mutations in additional 73 adenomas and 288 adenocarcinomas. Somatic single nucleotide variations (SNVs) were identified in both the adenoma and adenocarcinoma by comparing with the normal control from the same patient. We identified 12 nonsynonymous somatic SNVs in the adenoma and 42 nonsynonymous somatic SNVs in the adenocarcinoma. Most of these mutations including OR6X1, SLC15A3, KRTHB4, RBFOX1, LAMA3, CDH20, BIRC6, NMBR, GLCCI1, EFR3A, and FTHL17 were newly reported in colorectal adenomas. Functional annotation of these mutated genes showed that multiple cellular pathways including Wnt, cell adhesion and ubiquitin mediated proteolysis pathways were altered genetically in the adenoma and that the genetic alterations in the same pathways persist in the adenocarcinoma. CDH20 and LAMA3 were mutated in the adenoma while NRXN3 and COL4A6 were mutated in the adenocarcinoma from the same patient, suggesting for the first time that genetic alterations in the cell adhesion pathway occur as early as in the adenoma. Thus, the comparison of genomic mutations between adenoma and adenocarcinoma provides us a new insight into the molecular events governing the early step of colorectal tumorigenesis.

Highlights

Colorectal cancer (CRC) is the third most commonly diagnosed cancer in males and the second in females in the world [1]
The adenoma had a smaller number of somatic mutations but demonstrating a similar pattern of enrichment in nucleotide transitions and involving similar functional pathways as the adenocarcinoma from the same patient
LAMA3 is involved in cell adhesion, signal transduction and differentiation and its mutations were previously reported in brain cancer [29], ovary cancer [15] and melanoma [30]

Summary

Introduction

Colorectal cancer (CRC) is the third most commonly diagnosed cancer in males and the second in females in the world [1]. The CRC development involves multiple genetic alterations including both oncogenic mutations and loss of tumor suppressor genes [3,4]. Among these genetic alterations, inactivation of the APC gene was often detected in small adenomas, the early stage of CRC development. KRAS mutations were detected when a small adenoma grows into a large adenoma (.1 cm diameter) [5]; and alterations in PIK3CA and TP53 or other genes [6,7,8,9] occurred during the development of invasive adenocarcinoma. With advances in sequencing technology, the whole exomes and even the whole genomes of individual colorectal adenocarcinomas have been sequenced and a comprehensive landscape of genetic alterations was delineated [10,11,12]

Methods

Results

Conclusion