DNAR-07. SMARCAL1 inhibition synergizes with TOP1 inhibitors to induce replication catastrophe and inflammation in ALT+ gliomas

Abstract Alternative lengthening of telomeres (ALT) is a homologous recombination-based mechanism of telomere maintenance that promotes replicative immortality. ALT is common in high-grade gliomas (HGGs) and is associated with elevated baseline DNA damage. Despite this, ALT+ HGGs remain immunologically cold, limiting the effectiveness of current therapies. Topoisomerase I (TOP1) inhibition has been explored as a strategy to induce lethal DNA damage in gliomas. However, clinical trials using the TOP1 inhibitor irinotecan failed to improve survival in glioblastoma, partly due to poor blood–brain barrier penetration and lack of molecularly-guided patient selection. Newer TOP1 inhibitors with improved pharmacologic profiles and updated biomarker-guided tumor stratification offer renewed potential. We found ALT+ glioma cells, relative to telomerase+, are specifically vulnerable to either TOP1i or depletion of SMARCAL1, an annealing helicase involved in replication fork reversal. Replication fork reversal is a primary mechanism of the DNA damage response to TOP1 trapping; therefore, we hypothesized these strategies would synergize to amplify DNA damage and enhance immunogenicity in ALT+ HGGs. We utilized doxycycline inducible shRNAs to deplete SMARCAL1 over multiple cell cycles in ALT+ and telomerase+ HGG cell lines. In patient-derived ALT+ cell lines, SMARCAL1 depletion led to increased DNA double-strand breaks and ALT-associated PML bodies (APBs), as shown by immunofluorescence and FISH. Flow cytometry revealed that this damage includes excessive RPA binding and replication catastrophe preferentially in ALT+ cells. Combining SMARCAL1 depletion with TOP1 inhibition produced a synergistic increase in DNA damage. Importantly, SMARCAL1 loss also upregulated inflammatory signaling and immune receptor expression in ALT+ cells, enhancing recognition by phagocytes. These findings establish SMARCAL1 as a critical regulator of DNA repair and immune suppression in ALT+ HGGs. Its inhibition presents a promising therapeutic approach, either alone or in combination with TOP1 inhibitors, to increase tumor cell death and boost anti-tumor immunity in this challenging glioma subtype.