Abstract 4327: MSI cancer associated DNA (TA)n-dinucleotide repeat expansions and implications for Werner synthetic lethality

Microsatellite instability (MSI) is caused by deficient DNA mismatch repair (MMR) and is a ubiquitous feature of cancer. Werner syndrome (WRN) helicase is involved in genome stability and DNA repair. We identified WRN as a synthetic-lethal target in dMMR/MSI cancers and highlighted WRN inhibition as a therapeutic option for dMMR/MSI cancers refractory to available therapies. A previously unappreciated genetic feature of dMMR/MSI cancer cells, DNA (TA)n-dinucleotide repeat expansions, were recently reported to cause vulnerability to WRN depletion. Our mechanistic understanding of TA-dinucleotide repeat expansion biology is limited, and their potential therapeutic implications are unclear. To investigate the landscape of these alterations in cancer, we inferred (TA)-dinucleotide repeat expansions by performing coverage analysis in a collection of hundreds of preclinical cancer models and human tumors (PCAWG) profiled by whole genome sequencing (WGS). We validated our findings in cancer cell lines and organoid cultures by performing long-read WGS. Furthermore, we investigated TA-expansions in single-cell-derived clones from human MSI tumors and cancer organoids. Finally, we inferred TA repeats in laser capture microdissection (LCMB)-derived samples obtained from patients affected by familial cancer predisposition syndromes. Our analysis unveils the landscape of TA-repeats alterations in a large collection of tumors and preclinical models, informing on the level of inter-tumor heterogeneity and their association with variable levels of WRN dependency. In addition, we investigated intra-patient tumor heterogeneity of TA-repeats length both within clonal organoids expanded from normal and neoplastic colorectal stem cells, and within different subclones derived from MSI cancer organoids. Furthermore, analysis of non-neoplastic and neoplastic tissues from patients affected by familial cancer predisposition syndromes revealed the pattern of TA-repeats expansions associated with various DNA-repair pathway alterations. Finally, we will discuss the clinical implications of our findings, as TA-repeats heterogeneity may affect sensitivity and resistance to the future generation of WRN inhibitors. Our data provide fresh insights into the inter and intra-tumoral heterogeneity of TA-dinucleotide repeat expansions in human cancers. These data contribute to understanding the role of MMR in cancer and exploiting Werner as a therapeutic target in cancer. Citation Format: Gabriele Picco, Shriram Bhosle, Maria Kalyva, Elena Grassi, Freddy Gibson, Angham Al Saedi, Sara Vieira, Mathijs Sanders, Livio Trusolino, Andrea Bertotti, Isidro Cortes-Ciriano, Mathew Garnett. MSI cancer associated DNA (TA)n-dinucleotide repeat expansions and implications for Werner synthetic lethality. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4327.