Uncovering cancer vulnerabilities through novel non-coding, multidimensional, and phenotypic screening technologies
Juan José Montero Valderrama
Institute of Molecular Oncology and Functional Genomics (IMO), Technical University of Munich (TUM). Munich
Despite significant advancements in cancer treatment - most notably in targeted therapies and immunotherapies - many malignancies still show only modest improvements in patient outcomes. Consequently, the discovery of novel therapeutic strategies remains critical. In this context, my research centers on developing and applying screening technologies to reveal cancer vulnerabilities. This includes identifying non-coding genes as antineoplastic targets, repurposing established drugs for combination therapies, and discovering genetic and chemical perturbations to alter cancer plasticity, specifically Epithelial-to-mesenchymal transition (EMT). i) Although lncRNA genes constitute the majority of the genome and are implicated in various diseases, including cancer, their functional validation has been challenging due to limitations of traditional genomic tools in perturbing them effectively. I optimized the RNA nuclease CasRx to directly interrogate lncRNA functions and evolved the system for high-throughput applicability, which allowed me to perform genome-scale pooled CRISPR screens, enabling the identification of novel lncRNA vulnerabilities across tumors. This methodology have set the stage for the systematic exploration of lncRNA biology in health and disease, which we are already exploiting to generate a pan-cancer atlas of lncRNA vulnerabilities. ii) Cancer therapies rely on additive or synergistic drug combinations to enhance efficacy and reduce toxicity. However, systematic discovery of synergies has been impeded by the immense number of possible drug combinations, which cannot be tested pharmacologically. I address this problem by developing screening methodology that enables global mapping of genetic interactions within the druggable genome that can be used as a proxy for drug synergy as we later validated using chemical screens. Our results not only reveal new combinatorial drug therapy options for several tumor types with high clinical, such as pancreatic cancer, but also created an unparalleled data resource of thousands of druggable genetic interactions that can be used for rapid drug repurposing. iii) EMT is a process in which epithelial cells lose polarity and adhesion, playing a critical role in health and disease. For example, in cancer, it can contribute to metastasis and drug resistance. Despite being well-studied, tools for the genetic and chemical modulation of EMT remain limited. I developed a FACS-based CRISPR screening, which allowed me to identify hundreds of EMT modulators, including drug target genes, in PDAC. I validated the molecular mechanisms of a dozen of these genes and demonstrated that modulating EMT can sensitize tumors to standard chemotherapy in PDAC.