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DNA-FISH analysis of non-EGFR-amplified GBM CTCs.

Summary of clinically informative (TARGET) genes.

Supplementary Methods, Figures S1 - S20. Figure S1. Branched evolution leads to tissue-sampling bias in primary tumor samples. Figure S2. Results of ABSOLUTE on samples from patient 418. Figure S3. 2D Bayesian clustering analysis of point-mutation CCF distributions in case 418. Figure S4. Bayesian clustering of private point-mutation CCF distributions in all sequenced tissue samples from case 418. Figure S5. Genetic alterations supporting phylogeny construction in case 418. Figure S6. Phylogenetic tree for case 418 Figure S7. Evolutionary relationships between primary tumor-samples and brain metastasis samples Figure S8. Detection of homozygous deletion in CDKN2A in the brain metastasis of case 24. Figure S9. Amplification of FGFR1 and MYC detected in the brain metastasis of case 331. Figure S10. Additional alterations under investigation for association with various targeted therapies. Figure S11. Power for paired-detection of somatic mutations. Figure S12. Amplification of CCNE1 detected in the brain metastasis of case 314. Figure S13. Amplification of EGFR detected in the brain metastasis of case 314. Figure S14. Amplification of MYC detected in the brain metastasis of case 308. Figure S15. Amplification of MYC detected in the brain metastasis of case 138. Figure S16. Amplifications of CDK6 and MET detected in the brain metastasis of case 138. Figure S17. Amplifications of CCNE1 and AKT2 detected in the brain metastasis of case 138. Figure S18. Amplification of EGFR detected in a regional lymph node from case 296. Figure S19. Power for somatic mutation detection in 86 matched primary-tumor and brain-metastasis samples. Figure S20. Calling of amplifications in primary-tumor samples and paired brain metastases.

Immunohistologic and DNA-FISH analysis of tumor cells and CTCs from a patient with metastatic GBM.

Supplementary File 1. Power for detection of somatic point mutations in coding exons of TARGET genes. The description for the plots in Supplementary File 1 can be found in the Legend of Supplementary Figure S1.

Methods and Supplementary Figure Legends

STEAM cocktail staining specifically identifies GBM cells.

Clinical association of CTC frequency

Data describing results of deep targeted sequencing.

Unsupervised hierarchical clustering analysis of patient and xenograft single cell qRT-PCR expression data.

GBM8 and GBM24 growth in culture.

Tumor genotypes and CTC frequency

Supplementary File 3. Detailed plots of the data used for phylogenetic inference in each case. The description for the plots in Supplementary File 3 can be found in the Legend of Supplementary Figure S13-S17.

Clinical characteristics of the 86 patients.

Supplementary File 2. Detailed plots of SCNA calls in TARGET genes. The description for the plots in Supplementary File 2 can be found in the Legend of Supplementary Figure S3.

PDF file - 102KB, Supplementary Figure S6. Sphere formation assay of MGG152 expressing N-MYC shRNA.

Figure S3

Purpose: Recurrent malignant glioma carries a dismal prognosis, and novel therapies are needed. We examined the feasibility and safety of vaccination with irradiated autologous glioma cells mixed with irradiated GM-K562 cells in patients undergoing craniotomy for recurrent malignant glioma.Experimental Design: We initiated a phase I study examining the safety of 2 doses of GM-K562 cells mixed with autologous cells. Primary endpoints were feasibility and safety. Feasibility was defined as the ability for 60% of enrolled subjects to initiate vaccination. Dose-limiting toxicity was assessed via a 3+3 dose-escalation format, examining irradiated tumor cells mixed with 5 × 106 GM-K562 cells or 1 × 107 GM-K562 cells. Eligibility required a priori indication for resection of a recurrent high-grade glioma. We measured biological activity by measuring delayed type hypersensitivity (DTH) responses, humoral immunity against tumor-associated antigens, and T-lymphocyte activation.Results: Eleven patients were enrolled. Sufficient numbers of autologous tumor cells were harvested in 10 patients, all of whom went on to receive vaccine. There were no dose-limiting toxicities. Vaccination strengthened DTH responses to irradiated autologous tumor cells in most patients, and vigorous humoral responses to tumor-associated angiogenic cytokines were seen as well. T-lymphocyte activation was seen with significantly increased expression of CTLA-4, PD-1, 4-1BB, and OX40 by CD4+ cells and PD-1 and 4-1BB by CD8+ cells. Activation was coupled with vaccine-associated increase in the frequency of regulatory CD4+ T lymphocytes.Conclusions: Vaccination with irradiated autologous tumor cells mixed with GM-K562 cells is feasible, well tolerated, and active in patients with recurrent malignant glioma. Clin Cancer Res; 22(12); 2885–96. ©2016 AACR.

Supplementary Table 2. Relationship of NAMPT inhibitor sensitivity, MYC/MYCN amplification, and Myc/N-Myc protein expression status in glioblastoma tumorsphere lines

''Temozolomide induced PARP activation deregulates NAD metabolism. Additive cytotoxic effect of TMZ and NAMPT inhibitors in IDH1 mutant cancers. NAD and cell viability effects with TMZ and NAMPT inhibitors in endogenous IDH1 mutant cancers. Combination treatment with TMZ and NAMPT inhibitor in IDH1 mutant and wild-type cells. Cell death mechanisms that underlie combined TMZ and NAMPT inhibitor treatment in IDH1 mutant cells. In vivo effects of combined TMZ and NAMPT inhibitor treatment for endogenous IDH1 mutant cancer.''

PDF file - 266KB, Supplementary Figure S5. Maintenance of genotype upon serial xenotransplantation.

Extended methods for flow cytometry for lymphocyte phenotyping.

Figure S1

Figure S4

Extended methods for ELISA assay for angiogenic cytokines.

'Temozolomide induced PARP activation deregulates NAD metabolism. Additive cytotoxic effect of TMZ and NAMPT inhibitors in IDH1 mutant cancers. NAD and cell viability effects with TMZ and NAMPT inhibitors in endogenous IDH1 mutant cancers. Combination treatment with TMZ and NAMPT inhibitor in IDH1 mutant and wild-type cells. Cell death mechanisms that underlie combined TMZ and NAMPT inhibitor treatment in IDH1 mutant cells. In vivo effects of combined TMZ and NAMPT inhibitor treatment for endogenous IDH1 mutant cancer.'

Supplementary Figure S1. Nampt inhibitor effects in glioblastoma tumorsphere cells. Supplementary Figure S2. Characterization of Nampt inhibitor effects in MYC/MYCN driven glioblastoma cells. Supplementary Figure S3. Characterization of NAD+-synthesis pathways in glioblastoma cells. Supplementary Figure S4. Nampt inhibitors induce apoptosis and disrupt intracellular metabolism pathways in MYC/MYCN amplified glioblastoma cells. Supplementary Figure S5. Fluorescent in situ hybridization (FISH) for MYC and MYCN in standard cancer cell lines. Supplementary Figure S6. Effect of Nampt inhibitors in Myc-driven standard cancer cell lines. Supplementary Figure S7. In vivo efficacy of Nampt inhibitor in MYC amplified H1975 xenografts. Supplementary Figure S8. NAMPT inhibitors were well tolerated in SCID mice bearing flank or orthotopic xenografts.

PDF file - 404KB, Supplementary Figure S2. IDH1-mutant glioma orthotopic xenografts recapitulate histopathological features of the respective patient tumors.

Purpose: Glioblastomas are treated by surgical resection followed by radiotherapy [X-ray therapy (XRT)] and the alkylating chemotherapeutic agent temozolomide. Recently, inactivating mutations in the mismatch repair gene MSH6 were identified in two glioblastomas recurrent post-temozolomide. Because mismatch repair pathway inactivation is a known mediator of alkylator resistance in vitro, these findings suggested that MSH6 inactivation was causally linked to these two recurrences. However, the extent of involvement of MSH6 in glioblastoma is unknown. We sought to determine the overall frequency and clinical relevance of MSH6 alterations in glioblastomas.Experimental Design: The MSH6 gene was sequenced in 54 glioblastomas. MSH6 and O6-methylguanine methyltransferase (MGMT) immunohistochemistry was systematically scored in a panel of 46 clinically well-characterized glioblastomas, and the corresponding patient response to treatment evaluated.Results:MSH6 mutation was not observed in any pretreatment glioblastoma (0 of 40), whereas 3 of 14 recurrent cases had somatic mutations (P = 0.015). MSH6 protein expression was detected in all pretreatment (17 of 17) cases examined but, notably, expression was lost in 7 of 17 (41%) recurrences from matched post–XRT + temozolomide cases (P = 0.016). Loss of MSH6 was not associated with O6-methylguanine methyltransferase status. Measurements of in vivo tumor growth using three-dimensional reconstructed magnetic resonance imaging showed that MSH6-negative glioblastomas had a markedly increased rate of growth while under temozolomide treatment (3.17 versus 0.04 cc/mo for MSH6-positive tumors; P = 0.020).Conclusions: Loss of MSH6 occurs in a subset of post–XRT + temozolomide glioblastoma recurrences and is associated with tumor progression during temozolomide treatment, mirroring the alkylator resistance conferred by MSH6 inactivation in vitro. MSH6 deficiency may therefore contribute to the emergence of recurrent glioblastomas during temozolomide treatment.

PDF file - 347KB, Supplementary Figure S3. Proliferation index of IDH1-mutant glioma orthotopic xenografts (MIB-1).

XLS file - 24KB, Supplementary Table S2. Primers used for sequencing.

Supplemental Table S1 Putative Metabolites

Purpose: Measurements of objective response rates are critical to evaluate new glioma therapies. The hallmark metabolic alteration in gliomas with mutant isocitrate dehydrogenase (IDH) is the overproduction of oncometabolite 2-hydroxyglutarate (2HG), which plays a key role in malignant transformation. 2HG represents an ideal biomarker to probe treatment response in IDH-mutant glioma patients, and we hypothesized a decrease in 2HG levels would be measureable by in vivo magnetic resonance spectroscopy (MRS) as a result of antitumor therapy.Experimental Design: We report a prospective longitudinal imaging study performed in 25 IDH-mutant glioma patients receiving adjuvant radiation and chemotherapy. A newly developed 3D MRS imaging was used to noninvasively image 2HG. Paired Student t test was used to compare pre- and posttreatment tumor 2HG values. Test–retest measurements were performed to determine the threshold for 2HG functional spectroscopic maps (fSM). Univariate and multivariate regression were performed to correlate 2HG changes with Karnofsky performance score (KPS).Results: We found that mean 2HG (2HG/Cre) levels decreased significantly (median = 48.1%; 95% confidence interval = 27.3%–56.5%; P = 0.007) in the posttreatment scan. The volume of decreased 2HG correlates (R2 = 0.88, P = 0.002) with clinical status evaluated by KPS.Conclusions: We demonstrate that dynamic measurements of 2HG are feasible by 3D fSM, and the decrease of 2HG levels can monitor treatment response in patients with IDH-mutant gliomas. Our results indicate that quantitative in vivo 2HG imaging may be used for precision medicine and early response assessment in clinical trials of therapies targeting IDH-mutant gliomas. Clin Cancer Res; 22(7); 1632–41. ©2015 AACR.

PDF file - 791KB, Supplementary Figure S1. Additional mouse orthotopic xenografts generated from patient IDH1 R132H-mutant gliomas.

Supplementary document

Figure S2

Purpose:Dopamine receptor D2 (DRD2) is a G protein–coupled receptor antagonized by ONC201, an anticancer small molecule in clinical trials for high-grade gliomas and other malignancies. DRD5 is a dopamine receptor family member that opposes DRD2 signaling. We investigated the expression of these dopamine receptors in cancer and their influence on tumor cell sensitivity to ONC201.Experimental Design:The Cancer Genome Atlas was used to determine DRD2/DRD5 expression broadly across human cancers. Cell viability assays were performed with ONC201 in >1,000 Genomic of Drug Sensitivity in Cancer and NCI60 cell lines. IHC staining of DRD2/DRD5 was performed on tissue microarrays and archival tumor tissues of glioblastoma patients treated with ONC201. Whole exome sequencing was performed in RKO cells with and without acquired ONC201 resistance. Wild-type and mutant DRD5 constructs were generated for overexpression studies.Results:DRD2 overexpression broadly occurs across tumor types and is associated with a poor prognosis. Whole exome sequencing of cancer cells with acquired resistance to ONC201 revealed a de novo Q366R mutation in the DRD5 gene. Expression of Q366R DRD5 was sufficient to induce tumor cell apoptosis, consistent with a gain-of-function. DRD5 overexpression in glioblastoma cells enhanced DRD2/DRD5 heterodimers and DRD5 expression was inversely correlated with innate tumor cell sensitivity to ONC201. Investigation of archival tumor samples from patients with recurrent glioblastoma treated with ONC201 revealed that low DRD5 expression was associated with relatively superior clinical outcomes.Conclusions:These results implicate DRD5 as a negative regulator of DRD2 signaling and tumor sensitivity to ONC201 DRD2 antagonism.

Supplementary Table 1 Primers used for PCR amplification and sequencing Supplementary Table 2 Results of Multiplex PCR based MGH SNAPShot assay, Pyrosequencing and Sanger sequencing in YMG6 patient and xenograft cells Supplementary Table 3 Analysis of microsatellite instability in YMG6 parent and xenograft tumors Supplementary Table 4 Quantitative analysis for MGMT methylation status in YMG6 cells Supplementary Table 5 Multiplex PCR based MGH SnaPShot assay for oligodendroglial tumors Supplementary Table 6 Correlation of xenograft lethality and phosphorylation of PI3K pathway protein Supplementary Table 7 Phosphorylation in PI3K pathway in oligodendroglioma xenograft model Supplementary Table 8 Clinical characteristics in oligodendroglial tumor patients

Table S1

Supplementary Figure S1-S7

Supplemental Figure: Mean plasma concentrations of vandetanib.

This file contains 3 Tables and 9 Figures with additional results and details of analysis related to the main results presented in the manuscript. The complete list of figures and tables is provided below. Table 1S. Baseline metabolite levels relative to creatine. Table 2S. Demographic, genomic, molecular, histological, radiological and clinical data. Table 3S. Fractional changes for all imaging biomarkers. Table 4S. General Linear Model with change of KPS as dependent variable and grade, age and fractional volume of decreased 2HG/Cre as covariates. Figure 1S. 3D MRSI pulse sequence for 2HG imaging, detailed diagram. Figure 2S. Quantum mechanics simulations of 2HG spectral editing for MEGA-LASER, MEGA-PRESS and PRESS-97 sequences. Figure 3S. Simulations of 2HG editing for MEGA-LASER and PRESS-97 sequences in the presence of B1 field inhomogeneity. Figure 4S. Mitigation of subtraction artifacts caused by motion and scanner instability in J-difference MR spectroscopy using real-time prospective motion correction, shim update and reacquisition. Figure 5S. Metabolic maps before image interpolation. Figure 6S. Examples of OFF and difference (DIFF) MEGA-LASER spectra from 3D MRSI voxels located in the tumor and contralateral normal appearing white matter, pre- and post-treatment respectively. Figure 7S. Distributions of Δ2HG/Cre in the test-retest and post-pre longitudinal data sets. Figure 8S. Comparison of functional spectroscopic maps (fSM) and functional diffusion maps (fDM). Figure 9S. Relation between residual tumor measured by FLAIR hyperintensity volume and the SNR and CRLB of 2HG. Notes. Details related to data analysis in Figures 7S and 9S.

Supplemental Tables 1-3. Supplementary Table 1: Correlations in the vandetanib/RT/TMZ arm between best radiographic responses with pre-treatment and on-treatment changes in blood biomarkers. Supplementary Table 2: Correlations in the vandetanib/RT/TMZ arm between overall survival with pre-treatment and on-treatment changes in blood biomarkers. Supplementary Table 3: Comparison of PFS or OS by log-rank p-value based on tissue biomarker analysis

PDF file - 323KB, Supplementary Figure S4. Sequencing of the IDH1 R132 locus in IDH1-mutant glioma xenografts.

Purpose: Isocitrate dehydrogenase (IDH) gene mutations occur in low-grade and high-grade gliomas. We sought to identify the genetic basis of malignant phenotype heterogeneity in IDH-mutant gliomas.Methods: We prospectively implanted tumor specimens from 20 consecutive IDH1-mutant glioma resections into mouse brains and genotyped all resection specimens using a CLIA-certified molecular panel. Gliomas with cancer driver mutations were tested for sensitivity to targeted inhibitors in vitro. Associations between genomic alterations and outcomes were analyzed in patients.Results: By 10 months, 8 of 20 IDH1-mutant gliomas developed intracerebral xenografts. All xenografts maintained mutant IDH1 and high levels of 2-hydroxyglutarate on serial transplantation. All xenograft-producing gliomas harbored “lineage-defining” mutations in CIC (oligodendroglioma) or TP53 (astrocytoma), and 6 of 8 additionally had activating mutations in PIK3CA or amplification of PDGFRA, MET, or N-MYC. Only IDH1 and CIC/TP53 mutations were detected in non–xenograft-forming gliomas (P = 0.0007). Targeted inhibition of the additional alterations decreased proliferation in vitro. Moreover, we detected alterations in known cancer driver genes in 13.4% of IDH-mutant glioma patients, including PIK3CA, KRAS, AKT, or PTEN mutation or PDGFRA, MET, or N-MYC amplification. IDH/CIC mutant tumors were associated with PIK3CA/KRAS mutations whereas IDH/TP53 tumors correlated with PDGFRA/MET amplification. Presence of driver alterations at progression was associated with shorter subsequent progression-free survival (median 9.0 vs. 36.1 months; P = 0.0011).Conclusion: A subset of IDH-mutant gliomas with mutations in driver oncogenes has a more malignant phenotype in patients. Identification of these alterations may provide an opportunity for use of targeted therapies in these patients. Clin Cancer Res; 20(11); 2898–909. ©2014 AACR.

Purpose: Deregulated Myc drives an oncogenic metabolic state, including pseudohypoxic glycolysis, adapted for the constitutive production of biomolecular precursors to feed rapid tumor cell growth. In glioblastoma, Myc facilitates renewal of the tumor-initiating cell reservoir contributing to tumor maintenance. We investigated whether targeting the Myc-driven metabolic state could be a selectively toxic therapeutic strategy for glioblastoma.Experimental Design: The glycolytic dependency of Myc-driven glioblastoma was tested using 13C metabolic flux analysis, glucose-limiting culture assays, and glycolysis inhibitors, including inhibitors of the NAD+ salvage enzyme nicotinamide phosphoribosyl-transferase (NAMPT), in MYC and MYCN shRNA knockdown and lentivirus overexpression systems and in patient-derived glioblastoma tumorspheres with and without MYC/MYCN amplification. The in vivo efficacy of glycolyic inhibition was tested using NAMPT inhibitors in MYCN-amplified patient-derived glioblastoma orthotopic xenograft mouse models.Results: Enforced Myc overexpression increased glucose flux and expression of glycolytic enzymes in glioblastoma cells. Myc and N-Myc knockdown and Myc overexpression systems demonstrated that Myc activity determined sensitivity and resistance to inhibition of glycolysis. Small-molecule inhibitors of glycolysis, particularly NAMPT inhibitors, were selectively toxic to MYC/MYCN–amplified patient-derived glioblastoma tumorspheres. NAMPT inhibitors were potently cytotoxic, inducing apoptosis and significantly extended the survival of mice bearing MYCN-amplified patient-derived glioblastoma orthotopic xenografts.Conclusions: Myc activation in glioblastoma generates a dependency on glycolysis and an addiction to metabolites required for glycolysis. Glycolytic inhibition via NAMPT inhibition represents a novel metabolically targeted therapeutic strategy for MYC or MYCN-amplified glioblastoma and potentially other cancers genetically driven by Myc. Clin Cancer Res; 22(17); 4452–65. ©2016 AACR.

Figure S5