title: Proteomics of mouse BRCA1-deficient mammary tumors identifies DNA repair proteins with potential diagnostic and prognostic value in human breast cancer.
abstract: 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.
authors.affiliation: Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands.
authors.forename: Marc
authors.initials: M
authors.lastname: Warmoes
authors.forename: Janneke E
authors.initials: JE
authors.lastname: Jaspers
authors.forename: Thang V
authors.initials: TV
authors.lastname: Pham
authors.forename: Sander R
authors.initials: SR
authors.lastname: Piersma
authors.forename: Gideon
authors.initials: G
authors.lastname: Oudgenoeg
authors.forename: Maarten P G
authors.initials: MP
authors.lastname: Massink
authors.forename: Quinten
authors.initials: Q
authors.lastname: Waisfisz
authors.forename: Sven
authors.initials: S
authors.lastname: Rottenberg
authors.forename: Epie
authors.initials: E
authors.lastname: Boven
authors.forename: Jos
authors.initials: J
authors.lastname: Jonkers
authors.forename: Connie R
authors.initials: CR
authors.lastname: Jimenez
mesh_terms: D000818:Animals; D019313:BRCA1 Protein / Q000172:deficiency / Q000235:genetics*; D014408:Biomarkers, Tumor / Q000235:genetics*; D001943:Breast Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000401:mortality; D004260:DNA Repair; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D015674:Mammary Neoplasms, Animal / Q000175:diagnosis / Q000235:genetics*; D051379:Mice; D046228:Microarray Analysis; D005810:Multigene Family; D009154:Mutation; D009363:Neoplasm Proteins / Q000235:genetics*; D025941:Protein Interaction Mapping; D020543:Proteome; D040901:Proteomics; D017386:Sequence Homology, Amino Acid; D016019:Survival Analysis; D053719:Tandem Mass Spectrometry
chemical_list: D019313:BRCA1 Protein; C492913:BRCA1 protein, human; D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins; D020543:Proteome