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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

Published on: September 18, 2020

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A novel reannotation strategy for dissecting DNA methylation patterns of human long intergenic non-coding RNAs in

Hui Zhi1, Shangwei Ning1, Xiang Li1

  • 1College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.

Nucleic Acids Research
|July 12, 2014
PubMed

Insights

This study reveals distinct deoxyribonucleic acid (DNA) methylation patterns in long intergenic non-coding ribonucleic acids (lincRNAs) across various cancers. These findings offer new avenues for developing cancer biomarkers and therapeutic targets.

Area of Science:

  • Oncology
  • Epigenetics
  • Molecular Biology

Background:

  • Long intergenic non-coding ribonucleic acids (lincRNAs) are increasingly recognized as cancer modulators.
  • However, their deoxyribonucleic acid (DNA) methylation patterns in cancer remain underexplored.

Purpose of the Study:

  • To comprehensively profile DNA methylation patterns of lincRNAs in diverse human cancers.
  • To identify lincRNAs with aberrant methylation associated with cancer status, subtype, and prognosis.
  • To explore the role of aberrantly methylated lincRNAs in cancer development.

Main Methods:

  • Reannotation of DNA methylation array data from 4629 tumors and 705 normal tissues across 20 cancer types.
  • Classification of lincRNAs based on promoter methylation patterns.
  • Integration of cancer subtype and clinical data.
  • Network analysis of aberrantly methylated lincRNAs.

Main Results:

  • Identified distinct promoter methylation patterns for lincRNAs in cancer compared to normal tissues.
  • Classified 2461 lincRNAs into categories based on methylation patterns, with some showing conserved regulatory regions and ubiquitous expression in normal tissues.
  • Discovered associations between lincRNA promoter methylation patterns and cancer status, subtype, or prognosis in several cancer types.
  • Network analysis suggested involvement of aberrantly methylated lincRNAs in cancer progression.

Conclusions:

  • Aberrant DNA methylation of lincRNAs is a significant feature across multiple human cancers.
  • Methylated and demethylated lincRNAs identified represent potential novel biomarkers for cancer detection and patient stratification.
  • These lincRNAs may also serve as promising therapeutic targets for cancer treatment.

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