ArticleJournal of translational medicine2017
Individualized analysis reveals CpG sites with methylation aberrations in almost all lung adenocarcinoma tissues.
Article in Journal of translational medicine, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 42 citations in OpenAlex.
- Genome-Wide DNA methylation profiling of tissue-plasma pairs identifies Novel cfDNA biomarkers for the diagnosis of gastric cancer.PLoS genetics · 2026Article
- Metabolic signature of phosphoethanolamine and arginine pathways predicts prognosis and immunotherapy resistance in lung adenocarcinoma.Translational cancer research · 2026Article
- Correlating obstructive sleep apnea and lung adenocarcinoma using hub gene signatures and molecular mechanisms.Discover oncology · 2026Article
- A liquid biopsy-based multi-methylation marker panel for minimally invasive gastric cancer screening.Clinical epigenetics · 2026Article
- Integrative multi-omics reveals common and distinct pathogenic mechanisms and preoperative diagnostic signatures in breast fibroepithelial lesions.Breast cancer research : BCR · 2025Article
- DNMT3B blocks TAL1-mediated PKM2 transcriptional repression to promote non-small cell lung cancer progression through inducing glycolysis.Cell division · 2025Article
- Association of FANCD2, TFPI, and CD33 genes with prognosis of lung adenocarcinoma: a bioinformatics study.Discover oncology · 2025Article
- Applications of gene pair methods in clinical research: advancing precision medicine.Molecular biomedicine · 2025Review
- Identification of cellular senescence-associated genes for predicting the diagnosis, prognosis and immunotherapy response in lung adenocarcinoma via a 113-combination machine learning framework.Discover oncology · 2025Article
- Blood-based biomarkers derived from tumor-informed DNA methylation analysis for lung adenocarcinoma.Heliyon · 2025Article
- Blood Leukocyte DNA Methylation Markers of Periodontal Disease and Risk of Lung Cancer in a Case-Control Study Nested in the CLUE II Cohort.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2024Article
- RankCompV3: a differential expression analysis algorithm based on relative expression orderings and applications in single-cell RNA transcriptomics.BMC bioinformatics · 2024Article
- Flipping the script: Advances in understanding how and why P4-ATPases flip lipid across membranes.Biochimica et biophysica acta. Molecular cell research · 2024Review
- Functional impact of multi-omic interactions in lung cancer.Frontiers in genetics · 2024Article
- SCN4B inhibits the progression of lung adenocarcinoma and is associated with better prognosis.The clinical respiratory journal · 2023Article
- Multi-omics integration analysis unveils heterogeneity in breast cancer at the individual level.Cell cycle (Georgetown, Tex.) · 2023Article
- Type IV P-Type ATPases: Recent Updates in Cancer Development, Progression, and Treatment.Cancers · 2023Review
- Assessing the Differential Methylation Analysis Quality for Microarray and NGS Platforms.International journal of molecular sciences · 2023Article
- CircSCN8A suppresses malignant progression and induces ferroptosis in non-small cell lung cancer by regulating miR-1290/ACSL4 axis.Cell cycle (Georgetown, Tex.) · 2023Article
- Current and future applications of liquid biopsy in non-small-cell lung cancer-a narrative review.Translational lung cancer research · 2023Review
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDue to the heterogeneity of cancer, identifying differentially methylated (DM) CpG sites between a set of cancer samples and a set of normal samples cannot tell us which patients have methylation aberrations in a particular DM CpG site.
methodsWe firstly showed that the relative methylation-level orderings (RMOs) of CpG sites within individual normal lung tissues are highly stable but widely disrupted in lung adenocarcinoma tissues. This finding provides the basis of using the RankComp algorithm, previously developed for differential gene expression analysis at the individual level, to identify DM CpG sites in each cancer tissue compared with its own normal state. Briefly, through comparing with the highly stable normal RMOs predetermined in a large collection of samples for normal lung tissues, the algorithm finds those CpG sites whose hyper- or hypo-methylations may lead to the disrupted RMOs of CpG site pairs within a disease sample based on Fisher's exact test.
resultsEvaluated in 59 lung adenocarcinoma tissues with paired adjacent normal tissues, RankComp reached an average precision of 94.26% for individual-level DM CpG sites. Then, after identifying DM CpG sites in each of the 539 lung adenocarcinoma samples from TCGA, we found five and 44 CpG sites hypermethylated and hypomethylated in above 90% of the disease samples, respectively. These findings were validated in 140 publicly available and eight additionally measured paired cancer-normal samples. Gene expression analysis revealed that four of the five genes, HOXA9, TAL1, ATP8A2, ENG and SPARCL1, each harboring one of the five frequently hypermethylated CpG sites within its promoters, were also frequently down-regulated in lung adenocarcinoma.
conclusionsThe common DNA methylation aberrations in lung adenocarcinoma tissues may be important for lung adenocarcinoma diagnosis and therapy.
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