An integrated epigenomic-transcriptomic landscape of lung cancer reveals novel methylation driver genes of diagnostic and therapeutic relevance. Theranostics 2021;11(11):5346-5364
Date
04/17/2021Pubmed ID
33859751Pubmed Central ID
PMC8039961DOI
10.7150/thno.58385Scopus ID
2-s2.0-85102449346 (requires institutional sign-in at Scopus site) 20 CitationsAbstract
Background: Aberrant DNA methylation occurs commonly during carcinogenesis and is of clinical value in human cancers. However, knowledge of the impact of DNA methylation changes on lung carcinogenesis and progression remains limited. Methods: Genome-wide DNA methylation profiles were surveyed in 18 pairs of tumors and adjacent normal tissues from non-small cell lung cancer (NSCLC) patients using Reduced Representation Bisulfite Sequencing (RRBS). An integrated epigenomic-transcriptomic landscape of lung cancer was depicted using the multi-omics data integration method. Results: We discovered a large number of hypermethylation events pre-marked by poised promoter in embryonic stem cells, being a hallmark of lung cancer. These hypermethylation events showed a high conservation across cancer types. Eight novel driver genes with aberrant methylation (e.g., PCDH17 and IRX1) were identified by integrated analysis of DNA methylome and transcriptome data. Methylation level of the eight genes measured by pyrosequencing can distinguish NSCLC patients from lung tissues with high sensitivity and specificity in an independent cohort. Their tumor-suppressive roles were further experimentally validated in lung cancer cells, which depend on promoter hypermethylation. Similarly, 13 methylation-driven ncRNAs (including 8 lncRNAs and 5 miRNAs) were identified, some of which were co-regulated with their host genes by the same promoter hypermethylation. Finally, by analyzing the transcription factor (TF) binding motifs, we uncovered sets of TFs driving the expression of epigenetically regulated genes and highlighted the epigenetic regulation of gene expression of TCF21 through DNA methylation of EGR1 binding motifs. Conclusions: We discovered several novel methylation driver genes of diagnostic and therapeutic relevance in lung cancer. Our findings revealed that DNA methylation in TF binding motifs regulates target gene expression by affecting the binding ability of TFs. Our study also provides a valuable epigenetic resource for identifying DNA methylation-based diagnostic biomarkers, developing cancer drugs for epigenetic therapy and studying cancer pathogenesis.
Author List
Sun X, Yi J, Yang J, Han Y, Qian X, Liu Y, Li J, Lu B, Zhang J, Pan X, Liu Y, Liang M, Chen E, Liu P, Lu YMESH terms used to index this publication - Major topics in bold
A549 CellsBasic Helix-Loop-Helix Transcription Factors
Carcinoma, Non-Small-Cell Lung
Cell Line, Tumor
Computational Biology
DNA Methylation
Epigenesis, Genetic
Epigenomics
Gene Expression
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
Humans
Lung Neoplasms
MicroRNAs
Promoter Regions, Genetic
RNA, Long Noncoding
RNA, Untranslated
Transcription Factors
Transcriptome