HGG-57. Whole-Genome Sequencing, Methylation Analysis, and Single-Cell Rna-Seq Define Unique Characteristics of Pediatric Treatment-Induced High-Grade Glioma and Suggest Oncogenic Mechanisms

Abstract

BACKGROUND Pediatric treatment-induced high-grade glioma (TIHGG) is among the most severe late effects observed in childhood cancer survivors and is uniformly fatal. We previously showed that TIHGG are divergent from de novo pediatric high-grade glioma (pHGG) and cluster into two gene expression subgroups, one stemlike and the other inflammatory. Here we systematically compared TIHGG molecular profiles to pHGG and evaluated expression and single cell sequencing profiles in order to identify oncogenic mechanisms and the cellular basis for the observed TIHGG gene expression subgroups. MATERIALS/ METHODS 450/850K methylation and mutational signature analysis was conducted in 36 TIHGG samples. Resultant data were analyzed for the presence of chromothripsis, distinct molecular alterations, and mutational signatures in a subset of 10 samples with whole genome sequencing data. Five TIHGGs underwent single-cell RNA-Seq analysis (scRNAseq). RESULTS 26/36 TIHGG clustered with the pedRTK1 methylation class. TIHGG were characterized by an increased frequency of chromothripsis relative to pHGG (67% vs. 31%, p=0.036). FISH and WGS revealed frequent PDGFRA amplification secondary to enrichment in ecDNA. TIHGG were enriched for COSMIC mutational signatures 5 and 19 (p=0.0003) relative to pHGG. scRNAseq data showed that TIHGG tumors are composed of stem-like, neuronal, and inflammatory cell populations which may contribute to the previously described dominant expression profiles. CONCLUSIONS TIHGG represents a distinct molecular subtype of pHGG. Chromothripsis, leading to enriched expression of genes in extrachromosomal DNA, likely contribute to TIHGG oncogenesis. The dominant cell type (stem-like vs. inflammatory) may define the expression subgroup derived from bulk RNA-seq in heterogeneous tumors.

Defining the molecular features of radiation-induced glioma: A systematic review and meta-analysis

“…The correlation of recurrent RIG genetic alterations with those observed in the methylation subclass pedGBM_RTK1, and the positive association of the TK-RIG915 PDX with this methylation class, raises the question of whether other RIGs would cluster similarly using DNA methylation-based techniques. Furthermore, preliminary data by Lucas et al 90 corroborate our assessment, where they report that RIG DNA methylation profiles are similar to pedGBM_RTK1 methylation subgroup tumors. Additional research using a larger number of samples is essential to determine whether RIGs truly are genetically similar to pediatric GBM or if they represent a unique tumor subclass.…”

“…Preliminary data from others support this correlation, with 26 out of 36 gliomas that developed after therapy clustering with the pedGBM_RTK1 subgroup by methylation array. 90 In summary, despite most RIGs being diagnosed in adulthood, 16 our comparisons of cranial RIGs with multiple other types of glioma revealed that these tumors most closely resemble the pedGBM_RTK1 molecular subgroup of pediatric gliomas (depicted in Figure 5 ).…”

“… 5 , 8 Given these inconsistent findings in the literature, we cannot rule out the possibility that chemotherapy may have contributed to the effects of radiation in the initiation of the glioma cases we report here, despite satisfaction of Cahan’s criteria in most cases. For this review, we have chosen to retain the more widely-used term “radiation-induced glioma”, but acknowledge that broader terms such as “radiation-associated” 98 or “treatment-induced” 90 may prove to be more accurate should chemotherapy be shown to be a contributing factor in the development of these tumors in the future.…”

“…This can only be achieved by increasing the number of samples comprehensively analyzed at the genetic, epigenetic and transcriptional level in a patient-specific manner, an opinion supported by other research groups. 90 , 99 This large-scale analysis will help the field conclusively determine if RIGs are molecularly distinct from, or should be considered synonymous with, the pedGBM_RTK1 tumors. Proposed plans to distinguish between pediatric and adult diffuse HGG in the next edition of the WHO classification of CNS tumors may assist further with a more accurate diagnosis of these tumors.…”