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

Marc Warmoes,Janneke E Jaspers,Thang V Pham,Sander R Piersma,Gideon Oudgenoeg,Maarten P.G Massink,Quinten Waisfisz,Sven Rottenberg,Epie Boven,Jos Jonkers,Connie R Jimenez

doi:10.1074/mcp.m111.013334

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.

Highlights

From the ‡Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands, the §Division of Molecular Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands, and the ¶Department Clinical Genetics, VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands
We report a BRCA1 deficiency signature based on 45 proteins with DNA repair(-associated) functions that can enrich for homology-directed DNA repair-deficient tumors and identify breast cancer patients with a poor prognosis in various publicly available breast cancer gene expression data sets
Protein Regulations in BRCA1-deficient versus Proficient Mouse Mammary Tumors—For comparative protein profiling, we employed a label-free workflow based on protein fractionation by gel electrophoresis coupled to nano-LC-MS/MS of

Summary

Introduction

We employed state of the art mass spectrometry-based proteomics to identify proteins associated with BRCA1-deficient breast tumors. To this end, we made use of inbred mouse models that display a minimal amount of genetic variability. As a model for human breast cancers deficient in BRCA1, we analyzed mouse mammary tumors harboring conditional tissue-specific mutations in BRCA1 and p53 [24] The majority of these tumors are highly similar to their human counterpart with respect to histological and molecular characteristics and show a high level of genomic instability. We report a BRCA1 deficiency signature based on 45 proteins with DNA repair(-associated) functions that can enrich for homology-directed DNA repair-deficient tumors and identify breast cancer patients with a poor prognosis in various publicly available breast cancer gene expression data sets

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