Biomarkers For BRCA1-Deficient Cancers

ABSTRACT Each year an estimated 275,000 new cases of invasive breast cancer will be diagnosed in the US. Despite major advances being made to improve breast cancer treatment, the disease still accounts for over 40,000 deaths annually. Research in the past decades has helped to identify inherited BRCA1 and BRCA2 pathogenic variants. These variants are often associated with an aggressive form of breast cancer as well as ovarian cancer. Although treatments are available for BRCA1-mutant breast and ovarian cancers, most breast cancer patients will relapse within 9 months of therapy due to resistance to the treatment. Therefore, more treatment options are needed. We have recently established a connection between BRCA1 protein and the Unfolded Protein Response (UPR). We found that BRCA1 is an E3 ligase in the endoplasmic reticulum (ER). Furthermore, our study also reveals that the UPR stress sensors, PERK and IRE1, are endogenous protein substrates targeted by BRCA1 for ubiquitination. Our data shows that both PERK and IRE1 proteins are expressed at a much higher level in the BRCA1-deficient (def) cancer cells than in the BRCA1-proficent cancer cells, probably due to under- ubiquitination from the lack of a functional BRCA1 protein. Subsequently, we discovered that BRCA1-def cancer cells (in vitro) and BRCA1-def tumors (in vivo) can be targeted by depleting specific components of the UPR signaling pathway. Since our proposed treatment is most effective in targeting BRCA1-def cancer, therefore, it will be imperative to identify patients that will be most benefit from the treatment. Currently there is no definitive means to identify a loss of E3 ligase function BRCA1 variant. With this new information from our study, we plan to explore the potential of using proteins that are ubiquitination substrates of BRCA1 (e.g., PERK and IRE1) as biomarkers to identify patients who have an E3 ligase-deficient (E3D) BRCA1. Our study shows that PERK and IRE1 proteins are consistently overexpressed in BRCA1-def cancer cells so we hypothesize that we will be able to differentiate the BRCA1-proficient and BRCA1-def tumors by examining the quantitative densitometric staining intensity difference in the protein expression profile of PERK and IRE1 via immunohistochemical staining or by ELISA/Mass Spectrophotometric analysis if flash frozen samples are available. We will examine the protein levels of PERK, IRE1 and other components of the UPR signaling pathway in patient tumor biospecimens and will evaluate whether any of them can be used as valid biomarkers to screen for patients who have a BRCA1 variant that has caused a loss of E3 ligase function of the BRCA1 protein. In this study we propose an exploratory measure of the integrity of E3 ligase function of BRCA1 by profiling the expression pattern of PERK and/or IRE1 protein. We will also study the correlation between high UPR activity and tumor’s responsiveness to the UPR target therapy. We will address the following questions in this proposal: (1) How does BRCA1 mediate protein homeostasis in cancer cells? (2) Can we apply UPR sensors/effectors as biomarkers to differentiate BRCA1-proficient and BRCA1-def tumors? (3) How do we identify UPR-dependent cancers?