ArticlePloS one2011
Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers, 1 of them a synthesis that pooled it.
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Who cites it
83 citing papers in PubMed, 1 synthesis or guideline pooled it, 145 citations in OpenAlex.
- Aberrant promoter methylation of HIN-1 gene may contribute to the pathogenesis of breast cancer: a meta-analysis.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2014Pooled it
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- A multi-organization epigenetic age prediction based on a channel attention perceptron networks.Frontiers in genetics · 2024Article
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- Cigarette Smoke Regulates the Expression of EYA4 via Alternation of DNA Methylation Status.BioMed research international · 2022Article
- Coordinated regulation of WNT/β-catenin, c-Met, and integrin signalling pathways by miR-193b controls triple negative breast cancer metastatic traits.BMC cancer · 2021Article
- High endogenous CCL2 expression promotes the aggressive phenotype of human inflammatory breast cancer.Nature communications · 2021Article
- An epigenomic landscape of cervical intraepithelial neoplasia and cervical cancer using single-base resolution methylome and hydroxymethylome.Clinical and translational medicine · 2021Article
- Epigenetically regulated digital signaling defines epithelial innate immunity at the tissue level.Nature communications · 2021Article
- miRNA expression profiling of hereditary breast tumors from BRCA1- and BRCA2-germline mutation carriers in Brazil.BMC cancer · 2020Article
- Oxidative stress in the aging substantia nigra and the etiology of Parkinson's disease.Aging cell · 2019Review
- Epigenetic upregulation of FKBP5 by aging and stress contributes to NF-κB-driven inflammation and cardiovascular risk.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Expression level of ACOT7 influences the prognosis in acute myeloid leukemia patients.Cancer biomarkers : section A of Disease markers · 2019Article
- Hemimethylation Patterns in Breast Cancer Cell Lines.Cancer informatics · 2019Article
- Identification of Biomarkers Based on Differentially Expressed Genes in Papillary Thyroid Carcinoma.Scientific reports · 2018Article
- Dissecting the sources of gene expression variation in a pan-cancer analysis identifies novel regulatory mutations.Nucleic acids research · 2018Article
- Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
13 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We used deep sequencing technology to profile the transcriptome, gene copy number, and CpG island methylation status simultaneously in eight commonly used breast cell lines to develop a model for how these genomic features are integrated in estrogen receptor positive (ER+) and negative breast cancer. Total mRNA sequence, gene copy number, and genomic CpG island methylation were carried out using the Illumina Genome Analyzer. Sequences were mapped to the human genome to obtain digitized gene expression data, DNA copy number in reference to the non-tumor cell line (MCF10A), and methylation status of 21,570 CpG islands to identify differentially expressed genes that were correlated with methylation or copy number changes. These were evaluated in a dataset from 129 primary breast tumors. Gene expression in cell lines was dominated by ER-associated genes. ER+ and ER- cell lines formed two distinct, stable clusters, and 1,873 genes were differentially expressed in the two groups. Part of chromosome 8 was deleted in all ER- cells and part of chromosome 17 amplified in all ER+ cells. These loci encoded 30 genes that were overexpressed in ER+ cells; 9 of these genes were overexpressed in ER+ tumors. We identified 149 differentially expressed genes that exhibited differential methylation of one or more CpG islands within 5 kb of the 5' end of the gene and for which mRNA abundance was inversely correlated with CpG island methylation status. In primary tumors we identified 84 genes that appear to be robust components of the methylation signature that we identified in ER+ cell lines. Our analyses reveal a global pattern of differential CpG island methylation that contributes to the transcriptome landscape of ER+ and ER- breast cancer cells and tumors. The role of gene amplification/deletion appears to more modest, although several potentially significant genes appear to be regulated by copy number aberrations.
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