<p>PDF file - 1353K, Supplementary Table S1. Patient and tumor characteristics from the 22 bevacizumab-resistant versus 22 bevacizumab-na�ve glioblastomas from whom paired pre-treatment tissue was available. Supplementary Table S2. Altered transcripts in 15 bevacizumab-resistant glioblastomas compared to before treatment. Supplementary Table S3. Altered transcripts in 15 bevacizumab-resistant glioblastomas compared to before treatment. Supplementary Table S4. Altered transcripts in bevacizumab-naive recurrent glioblastomas compared to their paired glioblastomas at diagnosis. Supplemetary Table S5. FISH Results. Supplementary Table S6. Patient and tumor characteristics from 22 bevacizumab-na�ve recurrent glioblastomas (control group) from whom paired pre-treatment tissue was available.</p>
High-grade astrocytomas (HGAs), corresponding to World Health Organization grades III (anaplastic astrocytoma) and IV (glioblastoma; GBM), are biologically aggressive, and their molecular classification is increasingly relevant to clinical management. PDGFRA amplification is common in HGAs, although its prognostic significance remains unclear. Using fluorescence in situ hybridization (FISH), the most sensitive technique for detecting PDGFRA copy number gains, we determined PDGFRA amplification status in 123 pediatric and 263 adult HGAs. A range of PDGFRA FISH patterns were identified and cases were scored as non-amplified (normal and polysomy) or amplified (low-level and high-level). PDGFRA amplification was frequent in pediatric (29.3%) and adult (20.9%) tumors. Amplification was not prognostic in pediatric HGAs. In adult tumors diagnosed initially as GBM, the presence of combined PDGFRA amplification and isocitrate dehydrogenase 1 (IDH1)(R132H) mutation was a significant independent prognostic factor (P = 0.01). In HGAs, PDGFRA amplification is common and can manifest as high-level and focal or low-level amplifications. Our data indicate that the latter is more prevalent than previously reported with copy number averaging techniques. To our knowledge, this is the largest survey of PDGFRA status in adult and pediatric HGAs and suggests PDGFRA amplification increases with grade and is associated with a less favorable prognosis in IDH1 mutant de novo GBMs.
Significance Identifying the drivers of tumorigenesis provides insight into mechanisms of transformation and can suggest novel therapeutic targets. IDH1 mutations in gliomas are one such promising target. Drivers of tumor initiation may be distinct from those at tumor recurrence, however. Here, we demonstrate that in a subset of initially IDH1 mutant gliomas IDH1 is deleted or amplified at recurrence, yielding a higher grade tumor with a reprogrammed epigenome. We also report systematic selection for cells with IDH1 CNA in vitro and in vivo. Thus, while IDH1 mutation likely initiates gliomagenesis, neither mutant IDH1 nor the oncometabolite 2HG that it produces are required at recurrence. These findings have important implications for emerging therapeutic strategies targeting mutant IDH1.
Mutations in IDH1 are the most common genetic alteration in low-grade gliomas (LGGs) and lead to overproduction of the oncometabolite 2-hydroxyglutarate (2HG) and altered DNA methylation (glioma CpG island methylator phenotype or G-CIMP). While mutant IDH1 likely initiates tumorigenesis, its role in tumor progression is less clear. We and others have previously found that mutations in IDH1 are maintained at recurrence, but several case reports have noted the loss of either the mutant or wild-type allele of IDH1 in vitro and in vivo. We therefore undertook a longitudinal analysis of copy number at the IDH1 locus in a cohort of 50 patients with IDH1-mutant LGG and patient-matched recurrences of all grades. We identified six cases (12%) in which the ratio of the mutant to wild-type allele was altered. Deletion or amplification of the mutant allele both coincided with malignant progression and resulted in decreased 2HG. While G-CIMP was uniformly maintained, there was extreme DNA hypomethylation outside CpG islands. The clonal expansion of tumor cells in the absence of mutant IDH1 and 2HG suggests that initially IDH1-mutant LGG can undergo malignant progression without mutant IDH1. These results have implications for therapeutic inhibition of mutant IDH1, and provide evidence that a driver of gliomagenesis may not be required for malignant progression in vivo.
