Importantly, Spinophilin is frequently amplified in ~8% (87 out of 1093) of sequenced breast cancer patient tumors (TCGA Study), which is higher than the alteration frequency of BRCA1 (3%) and BRCA2 (4%). Phospho-proteomic analysis indicates that Spinophilin dephosphorylates and thus modulates BRCA1 functions via direct interaction. Both knockdown and overexpression of Spinophilin led to significant impairment in DNA double-strand break repair by homologous recombination and single-strand annealing pathways, establishing that this protein has a defined role in DNA repair. Furthermore, this approach identified a novel protein (Spinophilin) which interacts with BRCA1. These efforts uncovered multiple novel “BRCAness” genes to which current BRCA-targeted therapy could be applied. To define functional DDR interactome, we identified 240 proteins that physically interact with 10 breast cancer susceptible DNA repair proteins (BRCA1, BRCA2, BRIP1, CHEK2, PALB2, RAD51C, RAD51D, MLH1, MSH2, XPC), and assessed the role of these interacting proteins in DDR by analyzing cellular response to DDR-targeting drugs (cisplatin and olaparib) upon knocking these genes out by CRISPR/Cas9. Functional Interactome of DNA Damage Response-Deficient Breast Cancer The DNA damage response (DDR) requires the interaction of proteins involved in DNA repair, and that the coordinated regulation of these interactions is fundamental to maintain genome stability.
Thus, cancer protein interaction landscapes provide a framework to recognize oncogenic drivers and drug vulnerabilities, for which new and effective therapeutic strategies could be developed. Indeed, our analysis identifies novel PIK3CA-interacting proteins which repress PI3K-AKT signaling, and UBE2N as a BRCA1 interactor predictive of clinical response to inhibition of PARP in the context of the I-SPY 2 clinical trial.
We investigate protein-protein and genetic interactions, using the large-scale proteomics and genomics, to dissect functions of protein complexes and biological pathways during cellular proliferation and/or tumorigenesis as they are formed and turned on. Notably, different genetic drivers of a trait often aggregate, rather than randomly located, in the molecular networks such as those that underlie protein complexes or signaling pathways, emphasizing the importance of network-based approaches in cancer research. Physical and Genetic Interaction Networks Governing Pathway Deregulation in Cancer Cancers have been associated with diverse sets of genomic alterations, many of which have unidentified roles in tumorigenesis.