Meta-Analysis and Gene Set Enrichment Relative to ER Status Reveal Elevated Activity of MYC and E2F in the “Basal” Breast Cancer Subgroup

Background Breast cancers lacking the estrogen receptor (ER) can be distinguished from other breast cancers on the basis of poor prognosis, high grade, distinctive histopathology and unique molecular signatures. These features further distinguish estrogen receptor negative (ER−) tumor subtypes, but targeted therapy is currently limited to tumors over-expressing the ErbB2 receptor. Methodology/Principal Findings To uncover the pathways against which future therapies could be developed we undertook a meta-analysis of gene expression from five large microarray datasets relative to ER status. A measure of association with ER status was calculated for every Affymetrix HG-U133A probe set and the pathways that distinguished ER− tumors were defined by testing for enrichment of biologically defined gene sets using Gene Set Enrichment Analysis (GSEA). As expected, the expression of the direct transcriptional targets of the ER was muted in ER− tumors, but the expression of genes indirectly regulated by estrogen was enhanced. We also observed enrichment of independent MYC- and E2F-driven transcriptional programs. We used a cell model of estrogen and MYC action to define the interaction between estrogen and MYC transcriptional activity in breast cancer. We found that the basal subgroup of ER− breast cancer showed a strong MYC transcriptional response that reproduced the indirect estrogen response seen in estrogen receptor positive (ER+) breast cancer cells. Conclusions/Significance Increased transcriptional activity of MYC is a characteristic of basal breast cancers where it mimics a large part of an estrogen response in the absence of the ER, suggesting a mechanism by which these cancers achieve estrogen-independence and providing a potential therapeutic target for this poor prognosis sub group of breast cancer.

[1]  Steven C. Lawlor,et al.  GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways , 2002, Nature Genetics.

[2]  R. Bernards,et al.  Re-Evaluating Cell-Cycle Regulation by E2Fs , 2006, Cell.

[3]  D. Liao,et al.  Correlation of amplification and overexpression of the c-myc oncogene in high-grade breast cancer: FISH, in situ hybridisation and immunohistochemical analyses , 2004, British Journal of Cancer.

[4]  Sven Bilke,et al.  The gene expression response of breast cancer to growth regulators: patterns and correlation with tumor expression profiles. , 2003, Cancer research.

[5]  Mike West,et al.  Distinctions in the specificity of E2F function revealed by gene expression signatures. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Clifford A. Meyer,et al.  Genome-wide analysis of estrogen receptor binding sites , 2006, Nature Genetics.

[7]  Y Wang,et al.  Effects of chemotherapy and hormonal therapy for early breast cancer on recurrence and 15-year survival: an overview of the randomised trials , 2005, The Lancet.

[8]  Peter Regitnig,et al.  Identification and meta‐analysis of a small gene expression signature for the diagnosis of estrogen receptor status in invasive ductal breast cancer , 2006, International journal of cancer.

[9]  David M. Livingston,et al.  A Complex with Chromatin Modifiers That Occupies E2F- and Myc-Responsive Genes in G0 Cells , 2002, Science.

[10]  A. Efstratiadis,et al.  Notch, Myc and Breast Cancer , 2007, Cell cycle.

[11]  Arul M Chinnaiyan,et al.  Genes regulated by estrogen in breast tumor cells in vitro are similarly regulated in vivo in tumor xenografts and human breast tumors , 2006, Genome Biology.

[12]  Robin L. Jones,et al.  MYC amplification in breast cancer: a chromogenic in situ hybridisation study , 2006, Journal of Clinical Pathology.

[13]  Martín C Abba,et al.  Gene expression signature of estrogen receptor α status in breast cancer , 2005, BMC Genomics.

[14]  A. Howell,et al.  Origins of breast cancer subtypes and therapeutic implications , 2007, Nature Clinical Practice Oncology.

[15]  Norhanom Abdul Wahab,et al.  Protein expression and molecular analysis of c-myc gene in primary breast carcinomas using immunohistochemistry and differential polymerase chain reaction. , 2002, International journal of molecular medicine.

[16]  P. Hall,et al.  An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[17]  R. Tibshirani,et al.  Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[18]  M E Greenberg,et al.  Myc requires distinct E2F activities to induce S phase and apoptosis. , 2001, Molecular cell.

[19]  Yudong D. He,et al.  Gene expression profiling predicts clinical outcome of breast cancer , 2002, Nature.

[20]  Daniel J Schaid,et al.  ERBB2, TBX2, RPS6KB1, and MYC alterations in breast tissues of BRCA1 and BRCA2 mutation carriers , 2004, Genes, chromosomes & cancer.

[21]  Jorge S. Reis-Filho,et al.  Molecular Cytogenetic Identification of Subgroups of Grade III Invasive Ductal Breast Carcinomas with Different Clinical Outcomes , 2004, Clinical Cancer Research.

[22]  Allen Chong,et al.  Discovery of estrogen receptor α target genes and response elements in breast tumor cells , 2004, Genome Biology.

[23]  M. J. van de Vijver,et al.  Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. , 2006, Journal of the National Cancer Institute.

[24]  Anthony Scime,et al.  Pocket Protein Complexes Are Recruited to Distinct Targets in Quiescent and Proliferating Cells , 2005, Molecular and Cellular Biology.

[25]  K. Lindblad-Toh,et al.  Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals , 2005, Nature.

[26]  T. Barrette,et al.  Molecular concepts analysis links tumors, pathways, mechanisms, and drugs. , 2007, Neoplasia.

[27]  Duonan Yu,et al.  Functional Validation of Genes Implicated in Lymphomagenesis: An in Vivo Selection Assay Using a Myc‐Induced B‐Cell Tumor , 2005, Annals of the New York Academy of Sciences.

[28]  Brad T. Sherman,et al.  DAVID: Database for Annotation, Visualization, and Integrated Discovery , 2003, Genome Biology.

[29]  Harry Bartelink,et al.  Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas , 2007, Breast Cancer Research.

[30]  Robert Tibshirani,et al.  Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene‐expression subtypes of breast cancer , 2006, Genes, chromosomes & cancer.

[31]  Sangsoo Kim,et al.  Combining multiple microarray studies and modeling interstudy variation , 2003, ISMB.

[32]  Y. Benjamini,et al.  THE CONTROL OF THE FALSE DISCOVERY RATE IN MULTIPLE TESTING UNDER DEPENDENCY , 2001 .

[33]  Jeffrey T. Chang,et al.  Oncogenic pathway signatures in human cancers as a guide to targeted therapies , 2006, Nature.

[34]  Andy J. Minn,et al.  Genes that mediate breast cancer metastasis to lung , 2005, Nature.

[35]  T. Sørlie,et al.  Distinct molecular mechanisms underlying clinically relevant subtypes of breast cancer: gene expression analyses across three different platforms , 2006, BMC Genomics.

[36]  Margaret Gardiner-Garden,et al.  Identification of Functional Networks of Estrogen- and c-Myc-Responsive Genes and Their Relationship to Response to Tamoxifen Therapy in Breast Cancer , 2008, PloS one.

[37]  D. Easton,et al.  Specific morphological features predictive for the basal phenotype in grade 3 invasive ductal carcinoma of breast , 2006, Histopathology.

[38]  Shridar Ganesan,et al.  X chromosomal abnormalities in basal-like human breast cancer. , 2006, Cancer cell.

[39]  R. Sutherland,et al.  c-Myc or Cyclin D1 Mimics Estrogen Effects on Cyclin E-Cdk2 Activation and Cell Cycle Reentry , 1998, Molecular and Cellular Biology.

[40]  L. Holmberg,et al.  Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts , 2005, Breast Cancer Research.

[41]  Catherine Legrand.  1687Effects of chemotherapy and hormonal therapy for early breast cancer on recurrence and 15-year survival: an overview of the randomised trials : Early Breast Cancer Trialists' Collaborative Group (EBCTCG) , 2005 .

[42]  Zhiping Weng,et al.  Global mapping of c-Myc binding sites and target gene networks in human B cells , 2006, Proceedings of the National Academy of Sciences.

[43]  Gordon K. Smyth,et al.  limma: Linear Models for Microarray Data , 2005 .

[44]  S. Culine,et al.  Relating genotype and phenotype in breast cancer: an analysis of the prognostic significance of amplification at eight different genes or loci and of p53 mutations. , 2000, Cancer research.

[45]  Kristian Helin,et al.  Identification of Target Genes of the p16INK4A-pRB-E2F Pathway* , 2003, Journal of Biological Chemistry.

[46]  Terence P. Speed,et al.  A comparison of normalization methods for high density oligonucleotide array data based on variance and bias , 2003, Bioinform..

[47]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[48]  David Cameron,et al.  Identification of molecular apocrine breast tumours by microarray analysis , 2005, Oncogene.

[49]  J. Foekens,et al.  Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer , 2005, The Lancet.

[50]  Sridhar Ramaswamy,et al.  Loss of Heterozygosity and Its Correlation with Expression Profiles in Subclasses of Invasive Breast Cancers , 2004, Cancer Research.

[51]  Margaret Gardiner-Garden,et al.  c-Myc overexpression and endocrine resistance in breast cancer , 2006, The Journal of Steroid Biochemistry and Molecular Biology.

[52]  T. Volkert,et al.  E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. , 2002, Genes & development.

[53]  Carsten O. Peterson,et al.  Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. , 2001, Cancer research.