Elucidating the Cellular Mechanism of Action of Poly(ADP-Ribose) Polymerase (PARP) Inhibitors

• Applicant: Dr. Alissa Miriam Drees
• Subject Area: General Genetics and Functional Genome Biology ; Biochemistry
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 564159720

Poly(ADP-ribose) polymerase inhibitors (PARPi) are a class of chemotherapy drugs that have emerged over the last two decades. They inhibit the PARP-1-mediated repair of single-strand breaks in DNA, causing double-strand breaks to form during DNA replication. PARPi are synthetically lethal: if cells have an impaired homology recombination repair (HRR), as it is in BRCA-mutated breast cancers, these double-strand breaks cannot be efficiently repaired and become lethal to the cell. Many PARPi show encouraging preclinical efficacy, and four entered clinic applications, where they have become a mainstay of cancer treatment for breast and ovarian cancers, with an annual revenue of 7.2 bn USD in 2024. However, despite this clinical success, PARPi are still limited by an often insufficient anti-tumour efficacy and cytotoxicity in HRR-sufficient cells. To enable the development of PARPi with improved characteristics, we have to understand their detailed mechanism of action in a way which goes beyond merely understanding the molecular interactions of the inhibitors with PARP-1, to encompass how the inhibitors actually function within a cell. To this end, I aim to map the binding sites of PARPi-bound PARP-1 on the genome of cancer cells. For this, I want to develop a novel approach to enable the co-mapping of the binding sites of PARPi-bound PARP-1 and DNA damage sites in live cells, to follow their distribution and effects over time. As a foundation, I will use the Chem-map method, developed by the Balasubramanian lab in 2023, which maps small molecule binding sites to the genome of fixed cells with unprecedented sensitivity and resolution. By comparing the genomic binding sites of inhibited PARP-1 in HRR-deficient and HRR-sufficient cells after treatment with different PARPi, important insights in the mechanism of action of different PARPi could be gained. In particular, under consideration of the structural, biophysical, and clinical characteristics of the mapped PARPi, the importance of currently hypothesized mode of actions, for example trapping of PARP-1 on DNA or inducing transcription-replication conflicts, can be inferred, since these would cause different genomic distributions. Knowing the mode of action will aid determining the desired PARPi characteristics that lead to an increased anti-tumor efficacy and to decreased cytotoxicity. Hence, mapping the genomic position and number of binding sites of PARPi will form the basis for the development of PARPi with improved clinical efficacy and fewer side effects.

• DFG Programme: WBP Fellowship
• International Connection: United Kingdom
• Host: Professor Shankar Balasubramanian, Ph.D.