Cancer-associated SMARCAL1 loss-of-function mutations promote alternative lengthening of telomeres and tumorigenesis in telomerase-negative glioblastoma cells

Abstract

Background Telomere maintenance mechanisms are required to enable the replicative immortality of malignant cells. While most cancers activate the enzyme telomerase, a subset of cancers use telomerase-independent mechanisms termed alternative lengthening of telomeres (ALT). ALT occurs via homology directed-repair mechanisms and is frequently associated with ATRX mutations. We previously showed that a subset of adult GBM patients with ATRX-expressing ALT-positive tumors harbored loss-of-function mutations in the SMARCAL1 gene, which encodes an annealing helicase involved in replication fork remodeling and the resolution of replication stress. However, the causative relationship between SMARCAL1 deficiency, tumorigenesis, and de novo telomere synthesis is not understood. Methods We used a patient-derived ALT-positive GBM cell line with native SMARCAL1 deficiency to investigate the role of SMARCAL1 in ALT-mediated de novo telomere synthesis, replication stress, and gliomagenesis in vivo. Results Inducible rescue of SMARCAL1 expression suppresses ALT indicators and inhibits de novo telomere synthesis in GBM and osteosarcoma cells, suggesting that SMARCAL1 deficiency plays a functional role in ALT induction in cancers that natively lack SMARCAL1 function. SMARCAL1-deficient ALT-positive cells can be serially propagated in vivo in the absence of detectable telomerase activity, demonstrating that the SMARCAL1-deficient ALT phenotype maintains telomeres in a manner that promotes tumorigenesis. Conclusions SMARCAL1 deficiency is permissive to ALT and promote gliomagenesis. Inducible rescue of SMARCAL1 in ALT-positive cell lines permits the dynamic modulation of ALT activity, which will be valuable for future studies aimed at understanding the mechanisms of ALT and identifying novel anti-cancer therapeutics that target the ALT phenotype.

Characterization of the mutational landscape of high-grade gliomas in a Latin American cohort

“…ATRX and SMARCAL1 mutations are linked to telomerase-independent telomere maintenance in glioblastoma (Brosnan-Cashman et al, 2021; Diplas et al, 2018; Liu et al, 2023; Nandakumar et al, 2017; Qin et al, 2022). While ATRX mutations are typically present in about 20% of high-grade gliomas (Haase et al, 2018), our study identified a lower-than-expected frequency corresponding to 10% (7 out of 70), and none of the most reported alterations were present in our cohort.…”

Profound synthetic lethality between SMARCAL1 and FANCM

“…Interestingly, this role of SMARCAL1 does not involve its RPA-interacting domain 58 but involves its ATP-dependent translocase, suggesting that the role of SMARCAL1 in suppressing telomeric DNA replication stress may be instructive for understanding its role in FANCM -/- cells. Perhaps paradoxically, SMARCAL1 mutations are also found in a subset of ALT tumors, such as in TERT promoter wild type glioblastoma 61, 62 , suggesting that under some contexts SMARCAL1 is a barrier to ALT initiation or maintenance. We expect that loss of FANCM will be particularly detrimental for SMARCAL1 -mutated ALT tumors, and while this should be formally tested, we note that FANCM is essential in a wide range of SMARCAL1 wild type ALT cell lines 63, 64 .…”