ArticleNucleic acids research2014
Aberrant transcriptional regulations in cancers: genome, transcriptome and epigenome analysis of lung adenocarcinoma cell lines.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed, 120 citations in OpenAlex.
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- Cancer-associated fibroblast-derived acetate promotes pancreatic cancer development by altering polyamine metabolism via the ACSS2-SP1-SAT1 axis.Nature cell biology · 2024Article
- An improved method for the highly specific detection of transcription start sites.Nucleic acids research · 2024Article
- Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma.Nature communications · 2023Article
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- Preliminary Study of Whole-Genome Bisulfite Sequencing and Transcriptome Sequencing in VHL Disease-Associated ccRCC.Molecular diagnosis & therapy · 2023Article
- An ATR-PrimPol pathway confers tolerance to oncogenic KRAS-induced and heterochromatin-associated replication stress.Nature communications · 2023Article
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- Regulation of immunological tolerance by the p53-inhibitor iASPP.Cell death & disease · 2023Article
- Classification and characterization of alternative promoters in 26 lung adenocarcinoma cell lines.Japanese journal of clinical oncology · 2023Article
- UPF1-From mRNA Degradation to Human Disorders.Cells · 2023Review
- Identification of tumor antigens and immune landscapes for bladder urothelial carcinoma mRNA vaccine.Frontiers in immunology · 2023Article
- Phasing analysis of lung cancer genomes using a long read sequencer.Nature communications · 2022Article
- HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples.Genome biology · 2022Article
- Identification of Tissue-Specific Gene Clusters Induced by DNA Demethylation in Lung Adenocarcinoma: More Than Germline Genes.Cancers · 2022Article
- Inflammatory Immune-Associated eRNA: Mechanisms, Functions and Therapeutic Prospects.Frontiers in immunology · 2022Review
- Extrachromosomal Circular DNA: A New Target in Cancer.Frontiers in oncology · 2022Review
- Clinicopathological implications of lncRNAs, immunotherapy and DNA methylation in lung squamous cell carcinoma: a narrative review.Translational cancer research · 2021Review
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here we conducted an integrative multi-omics analysis to understand how cancers harbor various types of aberrations at the genomic, epigenomic and transcriptional levels. In order to elucidate biological relevance of the aberrations and their mutual relations, we performed whole-genome sequencing, RNA-Seq, bisulfite sequencing and ChIP-Seq of 26 lung adenocarcinoma cell lines. The collected multi-omics data allowed us to associate an average of 536 coding mutations and 13,573 mutations in promoter or enhancer regions with aberrant transcriptional regulations. We detected the 385 splice site mutations and 552 chromosomal rearrangements, representative cases of which were validated to cause aberrant transcripts. Averages of 61, 217, 3687 and 3112 mutations are located in the regulatory regions which showed differential DNA methylation, H3K4me3, H3K4me1 and H3K27ac marks, respectively. We detected distinct patterns of aberrations in transcriptional regulations depending on genes. We found that the irregular histone marks were characteristic to EGFR and CDKN1A, while a large genomic deletion and hyper-DNA methylation were most frequent for CDKN2A. We also used the multi-omics data to classify the cell lines regarding their hallmarks of carcinogenesis. Our datasets should provide a valuable foundation for biological interpretations of interlaced genomic and epigenomic aberrations.
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