Home LiteratureArticle Details
PMID: 21364760 Published · epublish English Journal Article Research Support, Non-U.S. Gov't Validation Study

Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing.

PloS one ·Vol. 6 ·No. 2 ·2011-02-25 ·Pages e17490

Sun Z, Asmann YW, Kalari KR, Bot B, Eckel-Passow JE, Baker TR, Carr JM, Khrebtukova I, Luo S, Zhang L, Schroth GP, Perez EA, Thompson EA

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.

MeSH Terms
Breast Neoplasms/genetics,metabolism,pathology Carcinoma/genetics,metabolism,pathology Cell Line, Tumor Cells, Cultured Cluster Analysis CpG Islands/genetics DNA Methylation/physiology Female Gene Dosage/physiology Gene Expression Profiling/methods Gene Expression Regulation, Neoplastic High-Throughput Nucleotide Sequencing/methods Humans Sequence Analysis, DNA/methods Systems Integration
Authors & Affiliations
13 authors, click to expand affiliations / ORCID
Sun Zhifu
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America.
Asmann Yan W
Kalari Krishna R
Bot Brian
Eckel-Passow Jeanette E
Baker Tiffany R
Carr Jennifer M
Khrebtukova Irina
Luo Shujun
Zhang Lu
Schroth Gary P
Perez Edith A
Thompson E Aubrey
References (34)
34 references, click to expand
  1. Estrogen and progesterone receptor status affect genome-wide DNA methylation profile in breast cancer.
    Hum Mol Genet. 2010 Nov 1;19(21):4273-7 PMID: 20724461
  2. Fast and accurate short read alignment with Burrows-Wheeler transform.
    Bioinformatics. 2009 Jul 15;25(14):1754-60 PMID: 19451168
  3. CNV-seq, a new method to detect copy number variation using high-throughput sequencing.
    BMC Bioinformatics. 2009 Mar 06;10:80 PMID: 19267900
  4. Gene expression profiling predicts clinical outcome of breast cancer.
    Nature. 2002 Jan 31;415(6871):530-6 PMID: 11823860
  5. Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data.
    Bioinformatics. 2002 Nov;18(11):1462-9 PMID: 12424117
  6. Ancestry-shift refinement mapping of the C6orf97-ESR1 breast cancer susceptibility locus.
    PLoS Genet. 2010 Jul 22;6(7):e1001029 PMID: 20661439
  7. Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns.
    Cancer Res. 2001 Aug 15;61(16):5979-84 PMID: 11507038
  8. Selective estrogen receptor modulators: discrimination of agonistic versus antagonistic activities by gene expression profiling in breast cancer cells.
    Cancer Res. 2004 Feb 15;64(4):1522-33 PMID: 14973112
  9. Supervised risk predictor of breast cancer based on intrinsic subtypes.
    J Clin Oncol. 2009 Mar 10;27(8):1160-7 PMID: 19204204
  10. Cross-study analysis of gene expression data for intermediate neuroblastoma identifies two biological subtypes.
    BMC Cancer. 2007 May 25;7:89 PMID: 17531100
  11. LYN is a mediator of epithelial-mesenchymal transition and a target of dasatinib in breast cancer.
    Cancer Res. 2010 Mar 15;70(6):2296-306 PMID: 20215510
  12. Gene expression profiling identifies lobe-specific and common disruptions of multiple gene networks in testosterone-supported, 17beta-estradiol- or diethylstilbestrol-induced prostate dysplasia in Noble rats.
    Neoplasia. 2008 Jan;10(1):20-40 PMID: 18231636
  13. Gene expression profile for predicting survival in advanced-stage serous ovarian cancer across two independent datasets.
    PLoS One. 2010 Mar 12;5(3):e9615 PMID: 20300634
  14. Coregulator small nuclear RING finger protein (SNURF) enhances Sp1- and steroid receptor-mediated transcription by different mechanisms.
    J Biol Chem. 2000 Jan 7;275(1):571-9 PMID: 10617653
  15. Defining the galaxy of gene expression in breast cancer.
    Breast Cancer Res. 2002;4(4):141-4 PMID: 12100738
  16. Breast cancer classification and prognosis based on gene expression profiles from a population-based study.
    Proc Natl Acad Sci U S A. 2003 Sep 2;100(18):10393-8 PMID: 12917485
  17. Association between invasive ovarian cancer susceptibility and 11 best candidate SNPs from breast cancer genome-wide association study.
    Hum Mol Genet. 2009 Jun 15;18(12):2297-304 PMID: 19304784
  18. GATA3 in development and cancer differentiation: cells GATA have it!
    J Cell Physiol. 2010 Jan;222(1):42-9 PMID: 19798694
  19. Molecular portraits of human breast tumours.
    Nature. 2000 Aug 17;406(6797):747-52 PMID: 10963602
  20. Transcriptional coregulator SNURF (RNF4) possesses ubiquitin E3 ligase activity.
    FEBS Lett. 2004 Feb 27;560(1-3):56-62 PMID: 14987998
  21. Predicting features of breast cancer with gene expression patterns.
    Breast Cancer Res Treat. 2008 Mar;108(2):191-201 PMID: 18297396
  22. GATA-3 as a marker of hormone response in breast cancer.
    J Surg Res. 2009 Dec;157(2):290-5 PMID: 19059610
  23. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
    Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50 PMID: 16199517
  24. Genome-wide association study identifies a new breast cancer susceptibility locus at 6q25.1.
    Nat Genet. 2009 Mar;41(3):324-8 PMID: 19219042
  25. Copine-III interacts with ErbB2 and promotes tumor cell migration.
    Oncogene. 2010 Mar 18;29(11):1598-610 PMID: 20010870
  26. Molecular characterization of breast cancer with high-resolution oligonucleotide comparative genomic hybridization array.
    Clin Cancer Res. 2009 Jan 15;15(2):441-51 PMID: 19147748
  27. A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer.
    Clin Cancer Res. 2010 Nov 1;16(21):5222-32 PMID: 20837693
  28. Oestrogen receptors and small nuclear ring finger protein 4 (RNF4) in malignant ovarian germ cell tumours.
    Mol Cell Endocrinol. 2009 Aug 13;307(1-2):205-10 PMID: 19524139
  29. Daxx-mediated transcriptional repression of MMP1 gene is reversed by SPOP.
    Biochem Biophys Res Commun. 2004 Jul 30;320(3):760-5 PMID: 15240113
  30. Statistical significance for genomewide studies.
    Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9440-5 PMID: 12883005
  31. The hereditary renal cell carcinoma 3;8 translocation fuses FHIT to a patched-related gene, TRC8.
    Proc Natl Acad Sci U S A. 1998 Aug 4;95(16):9572-7 PMID: 9689122
  32. Linear models and empirical bayes methods for assessing differential expression in microarray experiments.
    Stat Appl Genet Mol Biol. 2004;3:Article3 PMID: 16646809
  33. Gene expression signature of estrogen receptor alpha status in breast cancer.
    BMC Genomics. 2005 Mar 11;6:37 PMID: 15762987
  34. A hedgehog-induced BTB protein modulates hedgehog signaling by degrading Ci/Gli transcription factor.
    Dev Cell. 2006 Jun;10(6):719-29 PMID: 16740475
Article Info
Journal
PloS one
Abbr.
PLoS One
ISSN
1932-6203
DOI
10.1371/journal.pone.0017490
Published
2011-02-25
Epub
2011-00-25
Pages
e17490
Language
English
Region
United States
NLM ID
101285081
PMCID
PMC3045451
Subset
IM
External Links
PubMed source DOI: 10.1371/journal.pone.0017490 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2