Genomic approaches to guide the molecular classification of glioma

Malignant gliomas account for more than 80% of all primary brain malignancies and 14,000 deaths in the U.S. annually. Despite aggressive treatment, malignant gliomas are largely fatal, as their invasive nature renders them prone to rapid recurrence. Gliomas are classified according to histopathologic criteria which are critical to treatment planning, as certain subtypes show increased sensitivity to particular therapeutic agents. However, gliomas often exhibit extensive tumor heterogeneity and ambiguity among histologic features, leading to subjectivity in diagnosis and low concordance rates among neuropathologists.

Recently, a number of large-scale genomic studies identified mutations in the TERT promoter and IDH1/2 in ~80% of all gliomas. Based on the occurrence of these mutations, gliomas can be classified into objective molecular subtypes that stratify patients into clear prognostic subgroups more effectively than by histology alone. However, current sequencing-based methods to identify these alterations are limited by low sensitivity (40% tumor cellularity), a major constraint on their clinical utility in the context of diffusely infiltrative gliomas. Importantly, this work also revealed that 20% of glioblastomas lack these alterations, delineating a subset of tumors known as the TERT promoter wildtype-IDH wildtype (TERTpWT-IDHWT) glioblastomas.

Preliminary studies indicate that TERT promoter and IDH mutations can effectively stratify the majority (80%) of patients into clinically-relevant genetic subtypes, however current mutation detection methods lack sensitivity (Sanger sequencing) or are overly time-consuming (next-generation sequencing). Here, we report the development of a qPCR-based approach which can provide more sensitive and rapid detection of these mutations and practical utility in glioma diagnosis by detecting low-abundance mutations (e.g., poorly sampled tumors). Finally, we report the genetic landscape of TERTpWT-IDHWT glioblastomas using whole exome and whole genome sequencing, revealing that these tumors harbor a unique set of genetic alterations and exhibit distinct genetic mechanisms of telomere maintenance from other known subgroups of GBM, including recurrent SMARCAL1 mutations and rearrangements upstream of TERT. Using cell-based assays and markers of alternative lengthening of telomeres (ALT), we provide evidence showing that SMARCAL1 acts as a tumor and ALT suppressor and that loss of function cancer-associated mutations are involved in ALT mechanism of telomere maintenance.

These studies have identified the key underlying genetic alterations that characterize TERTpWT-IDHWT glioblastomas, and can serve as biomarkers for more accurate diagnosis and treatment of this glioma subgroup. By developing a sensitive diagnostic for the critical TERTp and IDH alterations, we facilitate accurate diagnosis and prognostication of glioma patients.