Assessing pathogenicity of germline ATM variation and mechanisms maintaining genomic integrity for response to therapy in a melanoma model

The Ataxia-Telangiectasia Mutated (ATM) protein kinase plays a key role in the DNA damage response (DDR). It is activated by DNA double-strand breaks (DSB) and initiates repair processes by phosphorylating several key proteins involved in DNA repair, including those in the homologous recombination (HR) pathway. HR-deficient tumors are more susceptible to specific therapies, such as Poly ADP-Ribose Polymerase inhibitors (PARPi), which exploit the DNA repair defects to induce synthetic lethality. Studies have shown that ATM pathogenic variants can contribute to homologous recombination deficiency (HRD) in various cancers. Little is known about melanoma. We observed that germline variants are enriched in melanoma patients, but to clarify their potential effect in melanoma, a careful functional assessment and classification of the variants is needed, considering that ATM is a hypermutated gene, posing a challenge for their interpretation. Here, we aimed to functionally assess germline ATM variants in melanoma by establishing primary cell line models to test Loss of Heterozygosity (LOH), HRD, activation of DDR downstream pathway, and response to inhibition of DNA damage repair by PARPi as a potential therapeutic approach. Despite proven LOH, lack of ATM protein, HRD (determined by the absence of RAD51 foci), and downstream pathway dysregulation, our model did not show sensitivity to PARPi. Therefore, we assessed the potential role of the Schlafen family member 11 (SLFN11), a helicase involved in regulating cell proliferation, differentiation, and immune response, whose expression sensitizes tumors to PARP inhibitors. Our ATM mutant cell line lacked SLFN11 protein and featured hypermethylation-mediated silencing of the SLFN11 promoter. Our findings provide functional evidence for the pathogenicity of the germline ATM variation in melanoma through disruption of mechanisms maintaining genomic integrity and show lack of sensitivity to PARPi despite HRD. SLFN11 appears to play a role in regulating sensitivity to agents targeting HR in our model.