Abstract 4291: Inhibition of FANCM helicase activity confers synthetic lethality in alternative lengthening of telomeres (ALT) positive cancers

Abstract FANCM (Fanconi anemia, complementation group M) is a human gene that encodes a protein that plays a key role in DNA repair and genome maintenance. Alternative lengthening of telomeres (ALT) is a mechanism that allows cancer cells to maintain telomere length without using telomerase. A synthetic lethal relationship between ALT status and FANCM levels was uncovered by analyzing CRISPR Screens in DepMap database. By using telomerase (TERT) as a biomarker which is negative in ALT positive tumors, cell lines without TERT or ALT+ were found to be sensitive to FANCM knockdown. This synthetic lethal relationship was validated in cell lines with different status of ALT by targeting FANCM with siRNA pool and CRISPR-Cas9. Knock-in of K117K silent mutation, but not K117A/R mutations in catalytic domain of FANCM “rescued” the growth of ALT positive FANCM KO SAOS2 cell. Depletion or deletion of FANCM using siRNA/ CRISPR Cas9 led to the increase in the intensity/distribution of PML and TRF foci. ALT positive cell lines have significantly higher amount of C circle DNA compared to telomerase positive or ALT negative cell lines. Loss of FANCM leads to increase in the levels of C circles. Our results further validate FANCM as a target for ALT cancers and suggest inhibiting its helicase activity as a strategy to treat ALT cancer. Citation Format: Youyou Zhang, Raghuvar Dronamraju, Tom Berrodin, Kevin Coleman, Benjamin Schwartz. Inhibition of FANCM helicase activity confers synthetic lethality in alternative lengthening of telomeres (ALT) positive cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4291.