Genome-wide association studies (GWAS) have revealed that 25 regions in 24 genes are associated with adult diffuse glioma development. These regions were identified by performing GWAS of glioma overall and GWAS by pathology (GBM and nonGBM). Subsequently, these regions have been evaluated for associations with specific molecular subtypes. The 2016 WHO Classification of Tumors of the Central Nervous System utilizes two somatic alterations to molecularly-classify adult diffuse glioma: IDH mutation and 1p/19q codeletion. TERT promoter mutation has also been shown to be associated with age at diagnosis and patient outcome. We hypothesized that germline variants may increase susceptibility to, or interact with, these somatic alterations to accelerate the development of specific molecular subtypes of glioma. To test our hypothesis, we performed a GWAS by glioma molecular subtype – as defined by presence or absence of IDH and TERT somatic mutation and 1p/19q codeletion – utilizing a two-stage design and subsequent meta analysis that included 3001 total glioma cases and 2697 total controls. Data were imputed using the Michigan Server and logistic regression was used, adjusting for age and sex. The Cancer Genome Atlas (TCGA) data were used to perform an expression quantitative trait loci (eQTL) analysis on candidate germline variants. Variants in 2q37 and 7p22 were associated with IDH-mutated glioma (meta analysis p< 5x10-8). The eQTL analyses demonstrated significant associations between 2q37 variants and expression of nearby genes as well as associations between 7p22 variants and nearby genes (p< 0.0001). In conclusion, we identified and validated novel germline variants in two genes that are associated with etiology of IDH-mutated adult diffuse glioma.

Background ETS gene fusions and PTEN loss are the most common genomic alteration events in prostate cancer that stratify patients into molecularly distinct subtypes. Recently, a commercially available genomic classifier (GC, DecipherTM) has been validated to predict metastasis in patients with high-risk prostate cancer. In this study we evaluated the robustness of the GC model in the light of prostate cancer molecular heterogeneity. Methods: Analysis of PTEN expression loss, ERG overexpression and GC scores were performed on a previously reported genome-wide microarray dataset (Karnes et al., 2013). Microarray probesets mapping to exons of PTEN were benchmarked to identify a representative exon whose loss of expression was highly correlated to FISH analysis for PTEN deletion (PTEN-loss) performed on an independent dataset. ERG overexpression (ERG+) was determined similarly and the microarray probesets that best correlate with the FISH status (in independent dataset) were used to annotate the ERG status of the samples in this study. Receiver operating characteristic area under the curve (AUC), and multivariable regression analysis were used to assess GC performance for predicting metastasis in subsets of patient tumors with genomic alterations. Results Using the microarray method 42% of the tumors had ERG overexpression, 23% had PTEN-loss and 11% had both events. ERG+ and PTEN-loss were not on their own predictive of metastasis with AUCs of 0.52 (CI:0.44-0.6) and 0.47(CI 0.39-0.56), respectively. In ERG+ tumors GC had an AUC of 0.82 (p=4e-7) and high GC score ERG+ patients had a hazard ratio (HR) of 100 (p=6e-7) for metastasis. Similarly, in PTEN-loss tumors GC had an AUC of 0.83 (p=7.9e-5) and high GC score PTEN-loss patients had an HR of 62 (p=1.8e-4) for metastasis. When GC was evaluated in patient tumors with both ERG+ and PTEN-loss the AUC was 0.85 (p=2e-15) and high GC score patients had an HR of 95 (p=4e-4) for metastasis. In multivariable analysis, Decipher was the only significant risk factor with an HR of 55 (CI 12.2-249, p=1.8e-7) for metastasis after adjusting for ERG+, PTEN-loss, Gleason score, PSA, tumor stage, margins and adjuvant treatment. Conclusion The Decipher genomic classifier is a powerful prognostic marker that retains its significance for predicting metastasis in subsets of patients with tumors that harbor common genomic alterations. Patients with high GC scores and these alterations may represent an extremely high-risk subset of prostate cancer. Citation Format: Mohammed Alshalalfa, Ismael Vergara, Nicholas Erho, Elai Davicioni, Robert Jenkins, Kollmeyer Thomas. Evaluation of a genomic classifier (Decipher®) in subsets of primary tumors with common prostate cancer genomic alterations. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4720. doi:10.1158/1538-7445.AM2014-4720

NEURO-ONCOLOGY • NOVEMBER 2017 spheres. By a high throughput screening using the natural product libraries, we found several HDAC inhibitors selectively eliminate MES but not PN glioma spheres and block the intercellular signals from MES glioma spheres to promote aggressiveness of PN cells. To translate these pre-clinical data to the clinic, we focused on characterization of the newly developed pan-HDACi, AR42 in GSCs. AR42 treatment to the patient-derived MES glioma spheres attenuated their in vitro clonogenicity, in vivo tumor propagation and radio-resistance. Beyond direct tumor cell cytotoxicity, HDACi elevated the expression of adaptive immune checkpoint PD-L1 in a class I HDAC dependent way. Mechanistically, after HDAC inhibition, we observed an increase in binding of transcription factor STAT1 to PD-L1 promoter, which was attributed to increased histone acetylation. A combination of HDACi and anti-PD1 antibody improved the survival and reduced tumor burden in our syngeneic murine GBM models, with higher PD-L1 expression and cytotoxic T cell infiltration in mouse tumor tissue. Collectively, the results shed light on potential combinatorial therapeutic approaches, providing the rationale to combine AR42 with Nivolumab in the future clinical therapeutic development for GBM. The current status of the clinical development of AR42 for GBM will be discussed in detail.

BACKGROUND Determination of the causation of germline single nucleotide polymorphisms (SNPs) located in non-coding regions of the genome is challenging. The genomic region of 8q24 has been identified as important in many kinds of cancer, linked to a topologically associated domain (TAD) encompassing MYC; this TAD contains a GWAS SNP (rs55705857) associated with IDH-mutant glioma. METHODS Germline genotyping data from 622 IDH-mutant glioma and 668 controls were used to fine map the rs55705857 locus by detailed haplotype analysis. Chromatin immunoprecipitation sequencing (ChIP-seq) of histone markers H3K4me1, H3K4me3, H3K27ac and H3K36me3 was performed on normal brain samples (n=8) and human glioma samples (n=11 IDH-wt and 52 IDH-mut). RNAseq from 9 normal and 83 brain tumors (n=26 IDH-wt and 55 IDH-mut) were used to assess differential gene expression. RESULTS Fine-mapping identified rs55705857 SNP as the most likely causative allele (OR=8.69; p&lt;0.001) within 8q24 for the development of IDH-mutant glioma. At rs55705857, both H3K27ac and H3K4me1 in IDH-mutant vs IDH-wt tumors were increased 3.05- and 1.58-fold, respectively (DiffBind; p=5.81×10-7 and p=2.31×10-3). ChromHMM analysis of the marks indicated that promoter and enhancer functions were significantly increased, and the activity broadened at rs55705857 in IDH-mut gliomas compared to IDH-wt tumors and normal brain samples. This enhancement correlated with significant increased MYC expression in IDH-mut gliomas (p=3.1×10-13), as well as alterations of Myc signaling targets. Publicly available ATACseq, ChIPseq and long-range DNA interaction data demonstrated that the rs55705857 locus is open and interacts with the MYC promoter. CONCLUSIONS Fine-mapping of the 8q24 locus provided strong evidence that rs55705857 is the causative 8q24 locus associated with IDH-mut glioma. Functional experiments suggest that IDH mutation facilitates rs55705857 interaction with MYC to alter downstream MYC targets.