Proteomics of Mouse BRCA1-deficient Mammary Tumors Identifies DNA Repair Proteins with Potential Diagnostic and Prognostic Value in Human Breast Cancer*

Breast cancer 1, early onset (BRCA1) hereditary breast cancer, a type of cancer with defects in the homology-directed DNA repair pathway, would benefit from the identification of proteins for diagnosis, which might also be of potential use as screening, prognostic, or predictive markers. Sporadic breast cancers with defects in the BRCA1 pathway might also be diagnosed. We employed proteomics based on one-dimensional gel electrophoresis in combination with nano-LC-MS/MS and spectral counting to compare the protein profiles of mammary tumor tissues of genetic mouse models either deficient or proficient in BRCA1. We identified a total of 3,545 proteins, of which 801 were significantly differentially regulated between the BRCA1-deficient and -proficient breast tumors. Pathway and protein complex analysis identified DNA repair and related functions as the major processes associated with the up-regulated proteins in the BRCA1-deficient tumors. In addition, by selecting highly connected nodes, we identified a BRCA1 deficiency signature of 45 proteins that enriches for homology-directed DNA repair deficiency in human gene expression breast cancer data sets. This signature also exhibits prognostic power across multiple data sets, with optimal performance in a data set enriched in tumors deficient in homology-directed DNA repair. In conclusion, by comparing mouse proteomes from BRCA1-proficient and -deficient mammary tumors, we were able to identify several markers associated with BRCA1 deficiency and a prognostic signature for human breast cancer deficient in homology-directed DNA repair.

[1]  J. Peterse,et al.  Somatic loss of BRCA1 and p53 in mice induces mammary tumors with features of human BRCA1-mutated basal-like breast cancer , 2007, Proceedings of the National Academy of Sciences.

[2]  A. Ashworth,et al.  Hallmarks of 'BRCAness' in sporadic cancers , 2004, Nature Reviews Cancer.

[3]  L. Goldstein,et al.  Prognostic and predictive factors in early-stage breast cancer. , 2004, The oncologist.

[4]  Maria P. Pavlou,et al.  Nipple aspirate fluid proteome of healthy females and patients with breast cancer. , 2010, Clinical chemistry.

[5]  Annuska M. Glas,et al.  The 70-gene signature as a response predictor for neoadjuvant chemotherapy in breast cancer , 2010, Breast Cancer Research and Treatment.

[6]  M. Imieliński,et al.  In Situ Proteomic Analysis of Human Breast Cancer Epithelial Cells Using Laser Capture Microdissection: Annotation by Protein Set Enrichment Analysis and Gene Ontology* , 2010, Molecular & Cellular Proteomics.

[7]  A. Witteveen,et al.  Converting a breast cancer microarray signature into a high-throughput diagnostic test , 2006, BMC Genomics.

[8]  M. Cronin,et al.  A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. , 2004, The New England journal of medicine.

[9]  M. Kubbutat,et al.  Workflow comparison for label-free, quantitative secretome proteomics for cancer biomarker discovery: method evaluation, differential analysis, and verification in serum. , 2010, Journal of proteome research.

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

[11]  A. Tutt,et al.  Oral poly(ADP-ribose) polymerase inhibitor olaparib in patients with BRCA1 or BRCA2 mutations and recurrent ovarian cancer: a proof-of-concept trial , 2010, The Lancet.

[12]  R. Donnelly,et al.  Identification of Toposome, A Novel Multisubunit Complex Containing Topoisomerase II-alpha , 2004, Cell cycle.

[13]  Meng Qiao,et al.  Quantitative proteomics study of breast cancer cell lines isolated from a single patient: Discovery of TIMM17A as a marker for breast cancer , 2010, Proteomics.

[14]  W. Earnshaw,et al.  Condensin I interacts with the PARP-1-XRCC1 complex and functions in DNA single-strand break repair. , 2006, Molecular cell.

[15]  C. D. Salcido,et al.  Brca1 breast tumors contain distinct CD44+/CD24- and CD133+ cells with cancer stem cell characteristics , 2008, Breast Cancer Research.

[16]  M. Ringnér,et al.  Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics , 2010, Breast Cancer Research.

[17]  I. Ellis,et al.  A gene-expression signature to predict survival in breast cancer across independent data sets , 2007, Oncogene.

[18]  Fatima Cardoso,et al.  The MINDACT trial: The first prospective clinical validation of a genomic tool , 2007, Molecular oncology.

[19]  K. Sandelin,et al.  Proteomic Characterization of the Interstitial Fluid Perfusing the Breast Tumor Microenvironment , 2004, Molecular & Cellular Proteomics.

[20]  David R. Croucher,et al.  Tyrosine phosphorylation profiling reveals the signaling network characteristics of Basal breast cancer cells. , 2010, Cancer research.

[21]  Yi-Wen Chen,et al.  Secretomic and proteomic analysis of potential breast cancer markers by two-dimensional differential gel electrophoresis. , 2010, Journal of proteome research.

[22]  N. Cordes.  Integrin-mediated cell-matrix interactions for prosurvival and antiapoptotic signaling after genotoxic injury. , 2006, Cancer letters.

[23]  J. Jonkers,et al.  Therapeutic options for triple-negative breast cancers with defective homologous recombination. , 2009, Biochimica et biophysica acta.

[24]  Lisa H. Cazares,et al.  Surfaced-Enhanced Laser Desorption/Ionization Time-of-Flight (SELDI-TOF) Differentiation of Serum Protein Profiles of BRCA-1 and Sporadic Breast Cancer , 2004, Annals of Surgical Oncology.

[25]  J. Berg,et al.  DNA Replication, Recombination, and Repair , 2002 .

[26]  S. Elledge,et al.  BASC, a super complex of BRCA1-associated proteins involved in the recognition and repair of aberrant DNA structures. , 2000, Genes & development.

[27]  Van,et al.  A gene-expression signature as a predictor of survival in breast cancer. , 2002, The New England journal of medicine.

[28]  Min-Sung Kim,et al.  COFECO: composite function annotation enriched by protein complex data , 2009, Nucleic Acids Res..

[29]  B. Karlan,et al.  Gene expression profile of BRCAness that correlates with responsiveness to chemotherapy and with outcome in patients with epithelial ovarian cancer. , 2010, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[30]  M. Mann,et al.  Super-SILAC mix for quantitative proteomics of human tumor tissue , 2010, Nature Methods.

[31]  Jos Jonkers,et al.  Selective induction of chemotherapy resistance of mammary tumors in a conditional mouse model for hereditary breast cancer , 2007, Proceedings of the National Academy of Sciences.

[32]  Keli Ou,et al.  Novel breast cancer biomarkers identified by integrative proteomic and gene expression mapping. , 2008, Journal of proteome research.

[33]  Christian von Mering,et al.  STRING 8—a global view on proteins and their functional interactions in 630 organisms , 2008, Nucleic Acids Res..

[34]  A. Vincent-Salomon,et al.  High frequency of TP53 mutation in BRCA1 and sporadic basal-like carcinomas but not in BRCA1 luminal breast tumors. , 2009, Cancer research.

[35]  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.

[36]  J. Reis-Filho,et al.  Basal-like breast cancer and the BRCA1 phenotype , 2006, Oncogene.

[37]  A. Ashworth,et al.  The roles of BRCA1 and BRCA2 and associated proteins in the maintenance of genomic stability , 2006, Oncogene.

[38]  M. J. van de Vijver,et al.  An aCGH classifier derived from BRCA1-mutated breast cancer and benefit of high-dose platinum-based chemotherapy in HER2-negative breast cancer patients , 2010, Annals of oncology : official journal of the European Society for Medical Oncology.

[39]  R. Aebersold,et al.  A statistical model for identifying proteins by tandem mass spectrometry. , 2003, Analytical chemistry.

[40]  Alexey I Nesvizhskii,et al.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. , 2002, Analytical chemistry.

[41]  Baocun Sun,et al.  Identification of Metastasis-Related Proteins and Their Clinical Relevance to Triple-Negative Human Breast Cancer , 2008, Clinical Cancer Research.

[42]  Thomas Helleday,et al.  DNA repair pathways as targets for cancer therapy , 2008, Nature Reviews Cancer.

[43]  Connie R. Jimenez,et al.  On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics , 2010, Bioinform..

[44]  Jos Jonkers,et al.  Somatic inactivation of E-cadherin and p53 in mice leads to metastatic lobular mammary carcinoma through induction of anoikis resistance and angiogenesis. , 2006, Cancer cell.

[45]  Ljiljana Paša-Tolić,et al.  Identification of a Putative Protein Profile Associated with Tamoxifen Therapy Resistance in Breast Cancer*S⃞ , 2009, Molecular & Cellular Proteomics.

[46]  Toyoko Tsukuda,et al.  ATP-dependent chromatin remodeling factors and DNA damage repair. , 2007, Mutation research.

[47]  L. Pannell,et al.  Identification of differentially secreted biomarkers using LC-MS/MS in isogenic cell lines representing a progression of breast cancer. , 2007, Journal of proteome research.

[48]  Jeremy M. Stark,et al.  53BP1 Inhibits Homologous Recombination in Brca1-Deficient Cells by Blocking Resection of DNA Breaks , 2010, Cell.

[49]  M. Pajic,et al.  Sensitivity and acquired resistance of BRCA1;p53-deficient mouse mammary tumors to the topoisomerase I inhibitor topotecan. , 2010, Cancer research.

[50]  Stephen Fox,et al.  Subtypes of familial breast tumours revealed by expression and copy number profiling , 2010, Breast Cancer Research and Treatment.

[51]  P. Borst,et al.  High sensitivity of BRCA1-deficient mammary tumors to the PARP inhibitor AZD2281 alone and in combination with platinum drugs , 2008, Proceedings of the National Academy of Sciences.

[52]  P. Nederlof,et al.  Genomic signature of BRCA1 deficiency in sporadic basal‐like breast tumors , 2011, Genes, chromosomes & cancer.

[53]  D. Adams,et al.  53BP1 loss rescues BRCA1 deficiency and is associated with triple-negative and BRCA-mutated breast cancers , 2010, Nature Structural &Molecular Biology.

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

[55]  P. Nederlof,et al.  High incidence of protein-truncating TP53 mutations in BRCA1-related breast cancer. , 2009, Cancer research.

[56]  A. Ashworth,et al.  Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers. , 2009, The New England journal of medicine.

[57]  R. Kennedy,et al.  BRCA1 transcriptionally regulates genes associated with the basal-like phenotype in breast cancer , 2010, Breast Cancer Research and Treatment.

[58]  A. Shevchenko,et al.  Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. , 1996, Analytical chemistry.

[59]  C Caldas,et al.  Proliferation markers and survival in early breast cancer: a systematic review and meta-analysis of 85 studies in 32,825 patients. , 2008, Breast.