Pan-cancer analysis of the DNA methylation patterns of long non-coding RNA

Shijia Wang; Rendong Wang; Fang Gao; Jun Huang; Xiaoxiao Zhao; Dongguo Li

doi:10.1016/j.ygeno.2022.110377

Pan-cancer analysis of the DNA methylation patterns of long non-coding RNA

Genomics. 2022 Jul;114(4):110377. doi: 10.1016/j.ygeno.2022.110377. Epub 2022 May 2.

Authors

Shijia Wang¹, Rendong Wang¹, Fang Gao², Jun Huang¹, Xiaoxiao Zhao¹, Dongguo Li³

Affiliations

¹ School of Biomedical Engineering, Capital Medical University, 10 You An Men Wai, Xi Tou Tiao, Beijing 100069, China; Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing 100069, China.
² Health Management Center, Binzhou People's Hospital, Shandong Province, China.
³ School of Biomedical Engineering, Capital Medical University, 10 You An Men Wai, Xi Tou Tiao, Beijing 100069, China; Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing 100069, China. Electronic address: ldg213@ccmu.edu.cn.

PMID: 35513292
DOI: 10.1016/j.ygeno.2022.110377

Abstract

Long non-coding RNA (lncRNA) regulated by abnormal DNA methylation (ADM-lncRNA) emerges as a biomarker for cancer diagnosis and treatment. This study comprehensively described the methylation patterns of lncRNA in pan-cancer using the cancer data set in The Cancer Genome Atlas (TCGA). Based on the cancer heterogeneity of ADM-lncRNA in pan-cancer, we constructed a co-expression network of pan-cancer ADM-lncRNA (pADM-lncRNA) in 10 cancers, highlighting the combined action mode of abnormal DNA methylation, and indicating the internal connection among different cancers. Functional analysis revealed the pan-carcinogenic pathway of pADM-lncRNA and suggested potential factors for cancer heterogeneity and tumor immune microenvironment changes. Survival analysis showed the potential of pADM-lncRNA-mRNA co-expression pair as cancer biomarkers. Revealing the action mode of lncRNA and DNA methylation in cancer may help understand the key molecular mechanisms of cell carcinogenesis.

Keywords: Co-expression network; DNA methylation; Long non-coding RNA; Pan-cancer; TCGA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biomarkers, Tumor / genetics
Biomarkers, Tumor / metabolism
DNA Methylation
Gene Expression Regulation, Neoplastic
Humans
Neoplasms* / genetics
RNA, Long Noncoding* / genetics
RNA, Long Noncoding* / metabolism
Survival Analysis
Tumor Microenvironment / genetics

Substances

Biomarkers, Tumor
RNA, Long Noncoding