Defining Determinants of Primary Drug Resistance in Precision Cancer Therapies

The dramatic expansion of genomic sequencing methodologies, applications and efforts has empowered our abilities to deepen the conceptual understanding of complex biological processes, including diseases like cancer. Through our accumulated understanding of cancer genomics, targeted therapies, which inhibit the specific driver oncogenes and pathophysiological processes that underlie cancer progression, have been developed. However, in modern precision oncology and therapeutics, cancer drug resistance, both primary and secondary, has greatly limited the potential of targeted therapies to improve patients’ lives. Here, we systematically define combination treatment strategies by using unbiased pharmacological and functional genetic screening approaches to overcome the persistent problem of primary drug resistance in two cancer contexts: (1) epidermal growth factor receptor (EGFR)-driven triple-negative breast cancer (TNBC) and (2) PIK3CA mutant gastric cancer. Particularly, in the first context, using a candidate drug screen, we discovered that inhibition of cyclin-dependent kinase (CDK) 12 dramatically sensitizes diverse models of TNBC to EGFR blockade. Instead of functioning through CDK12’s well-established transcriptional roles, this combination therapy drives cell death through the 4E-BP1-dependent suppression of the translation and consequent stability of driver oncoproteins, including MYC. Further, with mechanistic intent, using a genome-wide CRISPR/Cas9 screen, we identified the CCR4-NOT complex as a major determinant of sensitivity to the combination therapy whose loss renders 4E-BP1 unresponsive to drug-induced dephosphorylation, rescuing MYC translational suppression and stability. Thus, by revealing a long debated EGFR dependence in TNBC, we have identified a therapeutic approach that functions through the cooperative regulation of translation-coupled oncoprotein stability and holds promising translational potential for the treatment of this difficult-to-treat disease subtype. In the second context, despite extensive molecular characterization of gastric cancer, personalized treatment approaches to improve patient survival outcomes are still lacking. Motivated by this unmet need, we performed drug sensitizer screens with a PI3K-alpha isoform-specific inhibitor, BYL719, in multiple PIK3CA wild-type (WT) and mutant cell lines, including those derived from gastric cancers, head and neck squamous cell carcinomas (HNSCCs), and colorectal cancers using a miniaturized CRISPR/Cas9 library targeting key druggable nodes of cellular survival pathways. This work led to the promising findings that intrinsic resistance to PI3K-alpha inhibition specifically in gastric cancer may be mediated by BCL-xL and NEDD9. Sensitization to PI3K-alpha inhibition by BCL-xL specific inhibitor revealed a novel targeted approach for the treatment of EBV+ PIK3CA mutant gastric cancers, thereby overcoming a perplexing obstacle to the effective targeting of PI3K oncogenic dependency in this cancer subtype. Collectively, our work demonstrated the ability and applicability of screening approaches to define the determinants of primary drug resistance in precision cancer therapies across diverse cancer contexts.