Basic Study
Copyright ©The Author(s) 2024. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Gastrointest Oncol. Feb 15, 2024; 16(2): 414-435
Published online Feb 15, 2024. doi: 10.4251/wjgo.v16.i2.414
Early results of the integrative epigenomic-transcriptomic landscape of colorectal adenoma and cancer
You-Wang Lu, Zhao-Li Ding, Rui Mao, Gui-Gang Zhao, Yu-Qi He, Xiao-Lu Li, Jiang Liu
You-Wang Lu, Department of Dermatology and Venereology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan Province, China
Zhao-Li Ding, Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Public Technical Service Center, Kunming Institute of Zoology, Kunming 650223, Yunnan Province, China
Rui Mao, School of Stomatology, Kunming Medical University, Kunming 650500, Yunnan Province, China
Gui-Gang Zhao, Yu-Qi He, Xiao-Lu Li, Genome Center of Biodiversity, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, Yunnan Province, China
Jiang Liu, Department of Reproduction and Genetics, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan Province, China
Co-first authors: You-Wang Lu and Zhao-Li Ding.
Author contributions: Liu J contributed to the conceptualization of this study; Ding ZL and Zhao GG involved in the investigation of this article; Lu YW and Mao R took part in the formal analysis of this manuscript; Lu YW and Liu J participated in the writing - original draft of this manuscript; He YQ and Li XL contributed to the writing - review & editing of this article.
Supported by the National Natural Science Foundation of China, No. 81960504; the “Xingdian Talents” Support Project of Yunnan Province, No. RLQB20200002; the Medical Discipline Reserve Talents of Yunnan Province, No. H-2018015; the Applied Basic Research Projects-Union Foundation of Kunming Medical University, No. 2017FE467(-132); and the Talent Introduction Project of Hubei Polytechnic University, No. 21xjz34R.
Institutional review board statement: This study was approved by the Ethics Committee of the First Affiliated Hospital of Kunming Medical University.
Conflict-of-interest statement: All the authors report no relevant conflicts of interest for this article.
Data sharing statement: All the raw data for WGBS and RNA-Seq have been deposited in the SRA database (BioProject Number:PRJNA996378). Technical appendix, and statistical code available from the corresponding author at
Open-Access: This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See:
Corresponding author: Jiang Liu, PhD, Senior Scientist, Department of Reproduction and Genetics, The First Affiliated Hospital of Kunming Medical University, No. 295 Xichang Road, Kunming 650032, Yunnan Province, China.
Received: August 17, 2023
Peer-review started: August 17, 2023
First decision: November 6, 2023
Revised: November 24, 2023
Accepted: December 22, 2023
Article in press: December 22, 2023
Published online: February 15, 2024
Research background

Aberrant methylation is a common occurrence in colorectal cancer (CRC) initiation and progression, with clinical implications for early detection during CRC formation.

Research motivation

Addressing the critical need to identify specific DNA methylation markers for both adenoma (ADE) and CRC, the aim of this study was to unravel key molecular signatures associated with ADE and CRC.

Research objectives

Utilizing SeqCap targeted bisulfite sequencing and RNA-seq analysis, the goal of this study was to comprehensively profile the epigenomic-transcriptomic landscapes of colorectal ADE and CRC samples.

Research methods

The research involved a detailed examination, through SeqCap targeted bisulfite sequencing and RNA-seq analysis, shedding light on the distinctive epigenomic and transcriptomic characteristics of colorectal ADE and CRC. Public The Cancer Genome Atlas datasets were mined to explored the clinical implications of those methylation makers.

Research results

The comparative analysis of 22 CRC and 25 ADE samples revealed higher global methylation in CRC, with both exhibiting similar methylation patterns in differentially methylated positions, gene locations, chromatin signatures, and repeated elements. Integration with RNA-seq data identified 14 methylation-regulated differentially expressed genes, highlighting the prognostic significance of AGTR1 and NECAB1 methylation.

Research conclusions

This study revealed genome-wide alterations in DNA methylation during early CRC stages. It further identified distinctive methylation signatures associated with colorectal ADEs and CRC. Notably, AGTR1 and NECAB1 methylation emerged as potential prognostic biomarkers for CRC.

Research perspectives

The findings provide a foundation for future investigations into the clinical utility of identified methylation markers and the development of new targets for CRC treatment.