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Copyright ©The Author(s) 2022. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Gastrointest Oncol. Apr 15, 2022; 14(4): 935-946
Published online Apr 15, 2022. doi: 10.4251/wjgo.v14.i4.935
Genome-wide methylation profiling of early colorectal cancer using an Illumina Infinium Methylation EPIC BeadChip
Yu-Ling Wu, Tao Jiang, Wei Huang, Xing-Yu Wu, Peng-Jun Zhang, Ya-Ping Tian
Yu-Ling Wu, Wei Huang, Medical School of Chinese PLA, Beijing 100853, China
Tao Jiang, Ya-Ping Tian, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing 100853, China
Xing-Yu Wu, Nankai University School of Medicine, Tianjin 300071, China
Peng-Jun Zhang, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Interventional Therapy Department, Peking University Cancer Hospital and Institute, Beijing 100142, China
Author contributions: Wu YL, Jiang T, Zhang PJ and Tian YP designed the study; Wu YL performed the research, wrote the paper; Wu YL and Jiang T analyzed the data, and revised the manuscript for final submission; Huang W, Wu XY participated in the processing of bioinformatic analysis; Wu YL and Jiang T contributed equally to this study; Zhang PJ and Tian YP are the co-corresponding authors; and all authors have read and approve the final manuscript.
Supported by National Natural Science Foundation of China, No. 81972010; the National Key Research and Development Program of China, No. 2020YFC2002700, and No. 2020YFC2004604.
Institutional review board statement: The study was reviewed and approved by the Medical Ethics Committee of PLA General Hospital.
Clinical trial registration statement: We declared that this study has been reviewed and approved by the Medical Ethics Committee of PLA General Hospital. The number was S2022-003-01.
Informed consent statement: All study participants, or their legal guardian, provided informed written consent prior to study enrollment.
Conflict-of-interest statement: We declare that we have no financial or personal relationships with other individuals or organizations that can inappropriately influence our work and that there is no professional or other personal interest of any nature in any product, service and/or company that could be construed as influencing the position presented in or the review of the manuscript.
Data sharing statement: No additional data are available.
CONSORT 2010 statement: The authors have read the CONSORT 2010 statement, and the manuscript was prepared and revised according to the CONSORT 2010 statement.
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: https://creativecommons.org/Licenses/by-nc/4.0/
Corresponding author: Ya-Ping Tian, MD, Professor, Medical Innovation Research Division, Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing 100853, China. tianyp@301hospital.com.cn
Received: December 19, 2021
Peer-review started: December 19, 2021
First decision: February 21, 2022
Revised: February 21, 2022
Accepted: April 3, 2022
Article in press: April 3, 2022
Published online: April 15, 2022
Processing time: 116 Days and 20.4 Hours
ARTICLE HIGHLIGHTS
Research background

DNA methylation is closely related to the growth and development of colorectal cancer (CRC). Circulating tumor DNA (ctDNA) in plasma also has tumor-specific methylation patterns, the methylation status of ctDNA might serve as a potential biomarker.

Research motivation

In this study, we investigated the different methylation pattern between early CRC and colorectal adenoma.

Research objectives

This study aimed to analyze the genomic methylation status of CRC and discover potential methylated biomarkers for CRC diagnosis by Illumina Infinium Human Methylation 850K BeadChip.

Research methods

We used 850K Methylation BeadChip and enrichment analysis to select the differentially methylated sites of early CRC patients (n = 5) and colorectal adenoma patients (n = 5). Then, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed.

Research results

We found 1865 methylated sites with significant differences (676 hypermethylated sites and 1189 hypomethylated sites). The distribution of these sites covered from the 1st to 22nd chromosomes and are mainly distributed on the gene body and gene promoter region. GO and KEGG enrichment analysis identified that the functions of these genes were related to biological regulation, molecular binding, transcription factor activity and signal transduction pathway.

Research conclusions

The Illumina Infinium Human Methylation 850K BeadChip can be used to investigate genome-wide methylation status of plasma DNA to select potential methylated biomarkers for CRC diagnosis.

Research perspectives

Genome-wide methylation analysis of early CRC and screening of biomarkers by 850K Methylation BeadChip provided a new possibility for early diagnosis of CRC.