Therapeutic targeting of SMARCAL1 in therapy-resistant gliomas

10-15% of all cancers achieve replicative immortality through a telomerase-independent mechanism of telomere maintenance, termed Alternative Lengthening of Telomeres (ALT). ALT+ cancer cells exhibit high levels of DNA replication stress, which promotes telomere length maintenance via break-induced replication. While ALT is an adaptive mechanism by which cancer cells achieve replicative immortality, the high levels of DNA replication stress in ALT+ cancer cells constitutes a targetable therapeutic vulnerability. However, ALT-targeted therapeutic strategies remain poorly defined, and there are currently no approved anti-cancer therapies targeting ALT. /DH-mutant astrocytomas are incurable brain tumors that are characterized by co-occurring mutations in the IDH1, A TRX, and TP53 genes. A TRX loss-of-function mutations promote ALT activation in nearly all /DH-mutant astrocytomas. Despite treatment with IDH-mutant inhibitors (IDHi) and radiation-chemotherapy, /DH-mutant astrocytomas inevitably recur and progress to high-grade tumors that are therapy-resistant and lethal. There is a critical need to define novel therapeutic targets and improved therapeutic strategies for these ALT+ tumors. SMARCAL 1 is an annealing helicase that catalyzes the reversal of stalled replication forks within difficult-toreplicate DNA sequences to facilitate fork repair and re-start. In this proposal, we provide evidence that SMARCAL 1 is a highly specific synthetic lethal vulnerability in ALT+ cancers. Preliminary data demonstrate that inducible SMARCAL 1 depletion drastically increases the abundance and intensity of ALT-associated biomarkers in /DH-mutant astrocytoma cells and that depletion of SMARCAL 1 prolongs survival of mice bearing orthotopic xenografts derived from high-grade chemotherapy-resistant tumors. Moreover, our data show that SMARCAL 1 depletion in /DH-mutant astrocytoma cells induces the expression of genes involved in the activation of antitumor immunity, such as inflammatory cytokines, NK cell ligands, and antigen presentation and processing genes. These data suggest that SMARCAL 1-targeting in /DH-mutant astrocytomas induces both synthetic lethal cytotoxicity and immune-stimulatory gene expression changes that can be leveraged to elicit anti-tumor immunity. We hypothesize that ALT+ /DH-mutant astrocytomas require SMARCAL 1 in order to limit excessive ALT activity, thus preventing intolerable levels of ALT-associated replication stress. We propose that SMARCAL 1 depletion leads to excessive ALT activity, unsustainable telomeric replication stress, and cytotoxicity in a manner that stimulates tumor-intrinsic and -extrinsic inflammation and anti-tumor immunity. Aim 1 studies will define the mechanisms conferring a synthetic lethal vulnerability to SMARCAL 1 inhibition in /DH-mutant astrocytomas by defining the role of SMARCAL 1 in modulating ALT telomere synthesis, DNA replication, and genomic instability. Aim 2 will determine the efficacy and immune-stimulatory potential of SMARCAL 1-targeting in combination with vorasidenib, an FDA-approved IDHi, in immune competent glioma models. Results from this project will validate and mechanistically define new therapeutic strategies for /DH-mutant astrocytomas and other ALT+ cancers. Project Number: 1R37CA307076-01 | Fiscal Year: 2026 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Matthew Waitkus | Institution: DUKE UNIVERSITY, DURHAM, NC | Award Amount: $395,846 | Activity Code: R37 | Study Section: Mechanisms of Cancer Therapeutics C Study Section [MCTC] View on NIH RePORTER: https://reporter.nih.gov/project-details/11270910