Systematic functional mapping and interrogation of oncogenic intrinsically disordered regions

The origins of cancer lie in genetic mutations, but these mutations ultimately impact protein function, and most proteins in turn form intricate protein complexes and signaling networks to regulate cellular activity and phenotypes. Just as in-depth study of the landscape of driver genes and mutations has led to the development of targeted therapies, profiling protein interactions to identify those most critical for promoting oncogenic signaling in specific mutational contexts has the potential to reveal cancer cell vulnerabilities and mechanisms of drug resistance. In this regard, intrinsically disordered regions (IDRs) of several cancer drivers have emerged as central mediators of oncogenic signaling, protein-protein interactions (PPIs), post-translational modifications and drug resistance. However, systematic and at scale functional mapping and mechanistic dissection of IDRs is challenging. Towards this, we propose to utilize a panel of novel and complementary high throughput functional screening technologies developed by us that enable systematic protein perturbation at protein domain resolution and residue resolution, as well as a computational framework to convert these data to interpretable maps of oncogenic dependencies. Specifically, we will functionally map IDRs of all high confidence human and viral derived cancer drivers (~1000 proteins) across a panel of clinically relevant melanoma cancer cell lines (wild- type and mutant NRAS), and in the presence and absence of BRAF inhibitors. Integrating resulting large-scale IDR perturbation data with available protein interaction information and novel computational analyses, we will systematically interrogate underlying IDR driven oncogenic networks and their rewiring across the above cell states. Our hypothesis is that comprehensive domain and residue level perturbation screening of IDRs across all annotated cancer drivers will enable us to systematically uncover their mechanisms of action and reveal the most critical IDRs in drug sensitive and resistant contexts, thus informing more effective selection and development of cancer drugs. Project Number: 1R01CA310063-01 | Fiscal Year: 2026 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Prashant Mali (+1 co-PI) | Institution: UNIVERSITY OF CALIFORNIA, SAN DIEGO, LA JOLLA, CA | Award Amount: $661,721 | Activity Code: R01 | Study Section: Special Emphasis Panel[ZRG1 BTC-Y (02)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11319585