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. 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. 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. 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. 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.
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. 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. These efforts uncovered multiple novel “BRCAness” genes to which current BRCA-targeted therapy could be applied. Furthermore, this approach identified a novel protein (Spinophilin) which interacts with BRCA1. 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. Phospho-proteomic analysis indicates that Spinophilin dephosphorylates and thus modulates BRCA1 functions via direct interaction. 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%). Our finding suggests that Spinophilin-amplified tumors may arise due to abnormal regulation of DDR.
Rational Repurposing of Kinase Inhibitors for SARS-CoV-2 Combination Therapy
The development of therapeutic strategies against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an urgent global research priority. Identifying host targets of SARS-CoV-2 offers the potential to develop efficient therapies with a fast development timeline by avoiding viral escape mechanisms and utilizing repurposed FDA-approved drugs. We recently identified 332 host factors that interact with SARS-CoV-2, including 66 that are targeted by 109 FDA-approved drugs, investigational new drugs (INDs), and preclinical compounds. Among these, inhibitors of mRNA translation and predicted regulators of the Sigma1 and Sigma2 receptors demonstrated antiviral activity in vitro. To obtain additional potential drug targets, we utilized the orthogonal approach of global phosphorylation proteomic profiling upon SARS-CoV-2 infection in Vero E6 cells to gain a snapshot of signaling pathways that are rewired during virus infection. Profiling of differentially regulated kinase activities and pathways revealed 87 kinase inhibitors, with inhibitors of p38, CK2, CDKs, AXL, and PIKFYVE kinases all showing in vitro antiviral activity. We will further expand on the portfolio of pharmacological interventions and drug repurposing by analyzing the proteome-wide impact of SARS-CoV-2 on protein abundance and phosphorylation over a clinically relevant time-course of infection in human cells.