Multi-omics profiling and targeting of EMT/ZEB1-driven DNA damage response plasticity

• Applicant: Dr. Harald Schuhwerk
• Subject Area: Pathology
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 555537070

Therapy resistance is a major problem in cancer medicine that is strongly facilitated by the partial execution of ‘epithelial-to-mesenchymal-transition’ (EMT) in tumor cells. One key inducer of EMT in tumor cells is the transcription factor ZEB1, a well-known plasticity factor, but the underlying mechanisms of ZEB1/EMT-driven resistance remain poorly understood. We discovered that ZEB1 shows remarkable intercellular heterogeneity in expression across mammalian cancers in vitro and in vivo and that it induces adaptive rewiring of the DNA damage response (DDR). In this proof-of concept study, the selective targeting of one particular DDR alteration pre-existing prior to therapy prevented tumor cell sub-populations expressing high levels of ZEB1 (ZEB1hi) from establishing a chemoresistant fraction within tumors, thereby eliciting partial chemosensitization. Although this suggests the biological and translational relevance of the phenomenon ‘DDR plasticity’ as well as its therapeutic potential, its specific phenotypic manifestations, and the mechanisms underlying its acquisition and/or maintenance remain elusive. In the proposed project, we will thus investigate DDR plasticity in the context of standard chemotherapies in detail. To this end, single-cell transcriptomes and epigenetic processes will be determined in so-called ‘persister cells’ which initially survive therapies and are enriched in ZEB1hi cells, as we demonstrated before, in comparison to untreated cells. In parallel, an independent genome-wide CRISPR-Cas9 dropout screen will be conducted to identify essential genes in persister cells directly. Potential key effectors and signaling pathways pinpointed from these approaches will be functionally validated systematically in vitro and in vivo. Altogether, this study will help understanding the translationally relevant phenomenon of EMT-/ZEB1-associated DDR plasticity, thereby shedding light on persistence and establishing its effector mechanisms. As these effectors may represent not only novel biomarkers but also therapeutic vulnerabilities, we will selectively target them to eliminate persistence, aiming to sensitize to chemotherapies and envisioning to thereby prevent fatal resistance-driven relapses in the future.

• DFG Programme: Research Grants