IDH-mutant Glioblastomas Research Articles

Gamma distribution model of diffusion MRI for evaluating the isocitrate dehydrogenase mutation status of glioblastomas.

To determine whether the γ distribution (GD) model of diffusion MRI is useful in the evaluation of the isocitrate dehydrogenase (IDH) mutation status of glioblastomas. 12 patients with IDH-mutant glioblastomas and 54 patients with IDH-wildtype glioblastomas were imaged with diffusion-weighted imaging using 13 b-values from 0 to 1000 s/mm2. The shape parameter (κ) and scale parameter (θ) were obtained with the GD model. Fractions of three different areas under the probability density function curve (f1, f2, f3) were defined as follows: f1, diffusion coefficient (D) < 1.0×10-3 mm2/s; f2, D > 1.0×10-3 and <3.0×10-3 mm2/s; f3, D > 3.0 × 10-3 mm2/s. The GD model-derived parameters measured in gadolinium-enhancing lesions were compared between the IDH-mutant and IDH-wildtype groups. Receiver operating curve analyses were performed to assess the parameters' diagnostic performances. The IDH-mutant group's f1 (0.474 ± 0.143) was significantly larger than the IDH-wildtype group's (0.347 ± 0.122, p = 0.0024). The IDH-mutant group's f2 (0.417 ± 0.131) was significantly smaller than the IDH-wildtype group's (0.504 ± 0.126, p = 0.036). The IDH-mutant group's f3 (0.109 ± 0.060) was significantly smaller than the IDH-wildtype group's (0.149 ± 0.063, p = 0.0466). The f1 showed the best diagnostic performance among the GD model-derived parameters with the area under the curve value of 0.753. The GD model could well describe the pathological features of IDH-mutant and IDH-wildtype glioblastomas, and was useful in the differentiation of these tumors. Diffusion MRI based on the γ distribution model could well describe the pathological features of IDH-mutant and IDH-wildtype glioblastomas, and its use enabled the significant differentiation of these tumors. The γ distribution model may contribute to the non-invasive identification of the IDH mutation status based on histological viewpoint.

NIMG-19. SYNTHETIC ISOCITRATE DEHYDROGENASE-MUTANT GLIOBLASTOMAS FROM GENERATIVE ADVERSARIAL NETWORK PROVIDE MORPHOLOGIC VARIABILITY AND DIAGNOSTIC PERFORMANCE SIMILAR TO REAL DATA: DEVELOPMENT AND VALIDATION

Abstract BACKGROUND Generative adversarial network (GAN) creates synthetic MRI data that may provide morphologic variability to assess molecular characteristics of glioblastomas. PURPOSE To investigate the ability of GAN-based generation of isocitrate dehydrogenase (IDH)-mutant glioblastomas to provide morphologic variability and improve molecular prediction. METHODS GAN was retrospectively trained on 110 IDH-mutant high-grade gliomas. Paired contrast-enhanced T1-weighted and FLAIR synthetic MRI data were generated. Diagnostic models were developed from 80 IDH-wild type glioblastomas and 38 IDH-mutant patients, (real model), 38 IDH-mutant GAN-generated synthetic data (synthetic model), or both combined (augmented model). Two neuroradiologists independently assessed real and morphologic characteristics of contrast-enhancement patterns, the presence of necrosis, and margins and type of non-enhancing region. Significant predictors of IDH mutation were selected from multivariable logistic regression, and diagnostic performance was validated in 44 separate patients, 33 with IDH-wild type and 11 with IDH-mutant glioblastomas. RESULTS Synthetic IDH-mutant glioblastomas were similar to real tumors on Turing tests, with an area under the curve (AUC) of 0.67–0.71. Significant predictors of a more frontal or insular location (odds ratio [OR], 1.34 vs. 1.52; highest P = .04) and distinct non-enhancing tumor margins (OR, 2.68 vs. 3.88; P &amp;lt; .001) were similar for the real and synthetic models, with the synthetic (AUC, 0.958) and augmented (AUC, 0.899) models having higher diagnostic performance than the real model (AUC, 0.864) in the training set. The diagnostic accuracy was higher for the synthetic and augmented models (90.9% [40/44] each for both observers) than for the real model (84.1% [37/44] for one observer and 86.4% [38/44] for the other). CONCLUSIONS The GAN-based synthetic images yield morphologically variable IDH-mutant glioblastomas and may be useful as realistic training sets.

Generative adversarial network for glioblastoma ensures morphologic variations and improves diagnostic model for isocitrate dehydrogenase mutant type

Generative adversarial network (GAN) creates synthetic images to increase data quantity, but whether GAN ensures meaningful morphologic variations is still unknown. We investigated whether GAN-based synthetic images provide sufficient morphologic variations to improve molecular-based prediction, as a rare disease of isocitrate dehydrogenase (IDH)-mutant glioblastomas. GAN was initially trained on 500 normal brains and 110 IDH-mutant high-grade astocytomas, and paired contrast-enhanced T1-weighted and FLAIR MRI data were generated. Diagnostic models were developed from real IDH-wild type (n = 80) with real IDH-mutant glioblastomas (n = 38), or with synthetic IDH-mutant glioblastomas, or augmented by adding both real and synthetic IDH-mutant glioblastomas. Turing tests showed synthetic data showed reality (classification rate of 55%). Both the real and synthetic data showed that a more frontal or insular location (odds ratio [OR] 1.34 vs. 1.52; P = 0.04) and distinct non-enhancing tumor margins (OR 2.68 vs. 3.88; P < 0.001), which become significant predictors of IDH-mutation. In an independent validation set, diagnostic accuracy was higher for the augmented model (90.9% [40/44] and 93.2% [41/44] for each reader, respectively) than for the real model (84.1% [37/44] and 86.4% [38/44] for each reader, respectively). The GAN-based synthetic images yield morphologically variable, realistic-seeming IDH-mutant glioblastomas. GAN will be useful to create a realistic training set in terms of morphologic variations and quality, thereby improving diagnostic performance in a clinical model.

Predictive value of MGMT promoter methylation on the survival of TMZ treated IDH-mutant glioblastoma.

Objective:O6methylguanine-DNA methyltransferase (MGMT) promoter methylation is a biomarker widely used to predict the sensitivity of IDH-wildtype glioblastoma to temozolomide therapy. Given that the IDH status has critical effects on the survival and epigenetic features of glioblastoma, we aimed to assess the role of MGMT promoter methylation in IDH-mutant glioblastoma.Methods:This study included 187 IDH-mutant glioblastomas and used 173 IDH-wildtype glioblastomas for comparison. Kaplan-Meier curves and multivariate Cox regression were used to study the predictive effects.Results:Compared with IDH-wildtype glioblastomas, IDH-mutant glioblastomas showed significantly higher (P < 0.0001) MGMT promoter methylation. We demonstrated that MGMT promoter methylation status, as determined by a high cutoff value (≥30%) in pyrosequencing, could be used to significantly stratify the survival of 50 IDH-mutant glioblastomas receiving temozolomide therapy (cohort A); this result was validated in another cohort of 25 IDH-mutant glioblastomas (cohort B). The median progression-free survival and median overall survival in cohort A were 9.33 and 13.76 months for unmethylated cases, and 18.37 and 41.61 months for methylated cases, and in cohort B were 6.97 and 9.10 months for unmethylated cases, and 23.40 and 26.40 months for methylated cases. In addition, we confirmed that the MGMT promoter methylation was significantly (P = 0.0001) correlated with longer OS in IDH-mutant patients with GBM, independently of age, gender distribution, tumor type (primary or recurrent/secondary), and the extent of resection.Conclusions:MGMT promoter methylation has predictive value in IDH-mutant glioblastoma, but its cutoff value should be higher than that for IDH-wildtype glioblastoma.

Characteristics of diffuse hemispheric gliomas, H3 G34-mutant in adults.

BackgroundDiffuse hemispheric gliomas, H3 G34-mutant (DHG H3G34-mutant) constitute a distinct type of aggressive brain tumors. Although initially described in children, they can also affect adults. The aims of this study were to describe the characteristics of DHG H3G34-mutant in adults and to compare them to those of established types of adult WHO grade IV gliomas.MethodsThe characteristics of 17 adult DHG H3G34-mutant, 32 H3.3 K27M-mutant diffuse midline gliomas (DMG), 100 IDH-wildtype, and 36 IDH-mutant glioblastomas were retrospectively analyzed.ResultsMedian age at diagnosis in adult DHG H3G34-mutant was 25 years (range: 19–33). All tumors were hemispheric. For 9 patients (56%), absent or faint contrast enhancement initially suggested another diagnosis than a high-grade glioma, and diffusion-weighted imaging seemed retrospectively more helpful to suspect an aggressive tumor than MR-spectroscopy and perfusion MRI. All cases were IDH-wildtype. Most cases were immunonegative for ATRX (93%) and Olig2 (100%) and exhibited MGMT promoter methylation (82%). The clinical and radiological presentations of adult DHG H3G34-mutant were different from those of established types of adult grade IV gliomas. Median overall survival of adult DHG H3G34-mutant was 12.4 months compared to 19.6 months (P = .56), 11.7 months (P = .45), and 50.5 months (P = .006) in H3.3 K27M-mutant DMG, IDH-wildtype, and IDH-mutant glioblastomas, respectively.ConclusionsAdult DHG H3G34-mutant are associated with distinct characteristics compared to those of established types of adult WHO grade IV gliomas. This study supports considering these tumors as a new type of WHO grade IV glioma in future classifications.

Molecular Classification of Gliomas is Associated with Seizure Control: A Retrospective Analysis.

Classically, histologic grading of gliomas has been used to predict seizure association, with low-grade gliomas associated with an increased incidence of seizures compared to high-grade gliomas. In 2016, WHO reclassified gliomas based on histology and molecular characteristics. We sought to determine whether molecular classification of gliomas is associated with preoperative seizure presentation and/or post-operative seizure control across multiple glioma subtypes. All gliomas operated at our institution from 2007 to 2017 were identified based on ICD 9 and 10 billing codes and were retrospectively assessed for molecular classification of the IDH1 mutation, and 1p/19q codeletion. Logistic regression models were performed to assess associations of seizures at presentation as well as post-operative seizures with IDH status and the new WHO integrated classification. Our study included 376 patients: 82 IDH mutant and 294 IDH wildtype. The presence of IDH mutation was associated with seizures at presentation [OR 3.135 (1.818-5.404), p<0.001]. IDH-mutant glioblastomas presented with seizures less often than other IDH-mutant glioma subtypes grade II and III [OR 0.104 (0.032-0.340), p<0.001]. IDH-mutant tumors were associated with worse post-operative seizure outcomes, demonstrated by Engel Class [OR 2.666 (1.592-4.464), p<0.001]. IDH mutation in gliomas is associated with an increased risk of seizure development and worse post-operative seizure control, in all grades except for GBM.

PATH-23. GENOMIC LANDSCAPE OF IDH-MUTANT PRIMARY GLIOBLASTOMAS SHOWS DISTINCT CLINICAL AND MOLECULAR FEATURES AND THAT CDKN2A SHOULD BE SUPPLEMENTED WITH MGMTp AND G-CIMP FOR PRECISE PROGNOSTICATION

Abstract There have only been rare studies of IDH-mutant primary glioblastomas (IDH-mutant astrocytoma IV); there were one or two studies on secondary glioblastomas. In a cohort of 70 cases, we conducted clinical analysis, methylation profiling, RNA sequencing, targeted sequencing, and TERTp seqeuncing on available FFPE tissues. Median follow-up was 58.2 months (n= 60). IDH-mutant primary glioblastomas had longer median OS (30.4 months) and median PFS (25.9 months) than IDH-mutant secondary glioblastomas as in the literature or established databases. MGMTp methylated cases had better OS (p= 0.001) and it was an independent prognosticator. We previously showed G-CIMP to be an independent prognostic marker for IDH-mutant glioblastomas (NOA 2019). Although CDKN2A deletion was an independent prognostic marker for poorer OS (p= 0.036) and PFS (p= 0.005), MGMTp methylation had a trend of superseding CDKN2A deletion (p= 0.055) for prognostication and G-CIMP subgroups could similarly partially supersede CDKN2A deletion (p= 0.582). Hence, CDKN2A deletion should be supplemented with these two biomarkers for finer prognostication. Targeted sequencing (n= 55) showed that there were more ATRX (35/55, 64%), TP53 (31/55, 56%), KMT2D (18/55, 33%), POLE (11/55, 20%) and MSH6 (7/55, 13%) mutations, but fewer TERTp (3/69, 4%) and PTEN (1/55, 2%) mutations than IDH-wildtype glioblastomas as from literature and databases. CNVs revealed by methylomes (n= 53) and mutations (n= 55) showed that there were more PDGFRA (amplification: 9/53, 17%, mutation: 10/55, 18%) alterations, but fewer MET (amplification: 3/53, 6%, mutation: 4/55, 7%) alterations and hypermutated (6/55, 11%) cases than IDH-mutant secondary glioblastomas from literature. GISTIC analysis revealed amplifications of CCND2, CDK4, MYC, and PDGFRA, deletions of CDKN2A, RB1, and chromosome 10q to be significant CNVs (q&amp;lt; 0.05). There were few EGFR amplifications (2/53, 4%), which was different from regular glioblastomas. RNA sequencing (n= 42) showed few fusions (4/42, 10%), which was different from IDH-mutant secondary glioblastomas.

H3 G34-mutant high-grade glioma.

H3F3A G34 (H3.3 G34)-mutant high-grade gliomas (HGG) are rare, and newly recognized infiltratinggliomasof the cerebral hemisphere. Here, we report the clinicopathological and molecular characteristics of four H3.3 G34-mutant gliomas in terms of its biological behavior compared to those of glioblastomas (GBMs) and H3 K27M-mutant diffuse midline gliomas (DMGs) of our hospital. The median age of the four patients with H3.3 G34 HGG was 44.5years (14-66years). Three patients had tumors in the cerebral hemisphere, whereas one patient had synchronous double tumors in the cerebral hemisphere and posterior fossa. All these tumors were high-grade glioma, but neither microvascular proliferation nor necrosis. They displayed uniform genetic and epigenetic signatures; ATRX-mutant, MGMT promoter-methylated, Olig2-negative, but IDH- and TERT promoter-wildtype. The median survival rate of H3.3 G34-mutant HGGs, IDH-was 23.5months. In conclusion, H3.3 G34-mutant gliomas were unique HGGs with uniform genetic and epigenetic abnormalities, which suggested a single phylogenic origin. The median survival of H3.3 G34-mutant HGGs was better than those of IDH-wildtype GBMs and H3 K27M-mutant DMGs, but worse than that of IDH-mutant GBM. The tumor-infiltrating area and resectability may be the crucial parameters for the prognosis of the patients.

Glioblastomas harboring gene fusions detected by next-generation sequencing.

Oncogenic gene fusions have been reported in diffuse gliomas and may serve as potential therapeutic targets. Here, using next-generation sequencing analysis (Illumina TruSight Tumor 170 panel), we analyzed a total of 356 diffuse gliomas collected from 2017 to 2019 to evaluate clinical, pathological, and genetic features of gene fusion. We found 53 cases of glioblastomas harboring the following oncogenic gene fusions: MET (n = 18), EGFR (n = 14), FGFR (n = 12), NTRK (n = 5), RET (n = 2), AKT3 (n = 1), and PDGFRA fusions (n = 1). Gene fusions were consistently observed in both IDH-wildtype and IDH-mutant glioblastomas (8.8% and 9.4%, p = 1.000). PTPRZ1-MET fusion was the only fusion that genetically resembled secondary glioblastomas (i.e., high frequency of IDH mutation, ATRX loss, TP53 mutation, and absence of EGFR amplification), whereas other gene fusion types were similar to primary glioblastomas (i.e., high frequency of IDH-wildtype, TERT mutation, EGFR amplification, and PTEN mutation). In IDH-wildtype glioblastoma patients, multivariable analysis revealed that the PTPRZ1-MET fusion was associated with poor progression-free survival (HR [95% CI]: 5.42 (1.72-17.05), p = 0.004). Additionally, we described two novel cases of CCDC6-RET fusion in glioma. Collectively, our findings indicate that targetable gene fusions are associated with aggressive biological behavior and can aid the clinical treatment strategy for glioma patients.

PATH-15. IDENTIFICATION OF SUBSETS OF IDH-MUTANT GLIOBLASTOMAS WITH DISTINCT EPIGENETIC AND COPY NUMBER ALTERATIONS AND STRATIFIED CLINICAL RISKS

Abstract IDH-mutant glioblastoma is classified by the 2016 CNS WHO as a group with good prognosis. However, the actual number of cases examined in the literature is relatively small. We hypothesize that IDH-mutant glioblastoma is not a uniform group and should be further stratified. We conducted methylation profiles and estimated copy number variations of 57 IDH-mutant glioblastomas. Our results showed that 59.6%, and 40.4% of tumors belonged to G-CIMP-high and G-CIMP-low methylation subgroups, respectively. G-CIMP-low subgroup was associated with significantly worse OS as compared to G-CIMP-high (P=0.005). CDKN2A deletion (42.1%) was the most common gene copy number variation, and was significantly associated with G-CIMP-low subgroup (P=0.004). Other frequent copy number changes included MET (5.3%), CCND2 (19.3%), PDGFRA (14.0%), CDK4 (12.3%), and EGFR (12.3%) amplification. Both CDKN2A deletion (P=0.036) and MET amplification (P&lt; 0.001) were associated with poor OS in IDH-mutant glioblastomas. Combined epigenetic signatures and gene copy number variations separated IDH-mutant glioblastomas into Group 1 (G-CIMP-high), Group 2 (G-CIMP-low without CDKN2A nor MET alterations), and Group 3 (G-CIMP-low with CDKN2A and/or MET alterations). Survival analysis revealed Groups 1 and 2 exhibited a favorable OS (median survival: 619 days (20.6 months), and 655 days (21.8 months), respectively). Group 3 exhibited a significant shorter OS (median survival: 252 days (8.4 months)). Multivariable analysis confirmed the independent prognostic significance of our Groups. IDH-mutant glioblastomas should be stratified for risk with combined epigenetic signature and CDKN2A/MET status and some cases have poor outcome.

Combined epigenetic signature and gene copy number variations in IDH-mutant glioblastomas showed varied risk stratification

Abstract The number of IDH-mutant glioblastoma examined in the literature and TCGA is few. We used Infinium MethylationEPIC BeadChip array to classify 64 IDH-mutant-GBM into methylation groups. Gene copy number variations were determined from methylation. 53.1%, 35.9%, and 10.9% of tumors belonged to G-CIMP-high, G-CIMP-low and codel groups respectively. G-CIMP-low group of IDH-mutant glioblastoma was associated with worse survival as compared to G-CIMP-high (p=0.005) and Codel groups (p=0.009). CDKN2A deletion (24/64; 37.5%) was the most common gene copy number variation, and was significantly associated with GCIMP-low subgroup (p=0.001). Amplification of MET was identified in 3/64 (9.4%), CCND2 11/64 (17.2%), PDGFRA 9/64 (14.1%), CDK4 8/64 (12.5%) and EGFR 8/64 cases (12.5%). Both CDKN2A deletion (p=0.008) and MET amplification (p&lt;0.001) were associated with poor survival. Combined methylation signature and gene copy number variations separated IDH-mutant glioblastoma into Group 1 (codeleted), Group 2 (GCIMP-high without CDKN2A deletion), Group 3 (GCIMP-high with CDKN2A deletion), Group 4 (GCIMP-low without CDKN2A and MET alterations), and Group 5 (GCIMP-low with CDKN2A and/or MET alterations). Group 1 had a favorable overall survival with a median survival of 1240 days. Groups 2, 3, and 4 exhibited an intermediate outcome with a median survival of 536, 619, and 655 days respectively. Group 5 exhibited a poor outcome with a median survival of 255 days. Groups based on combined methylation signature and CDKN2A/MET status are an independent prognostic factor. Conclusion: IDH mutant glioblastomas should be stratified for risk with combined epigenetic signature and CDKN2A/MET status and some cases have unfavorable outcomes.

P14.48 Identification of subsets of IDH-mutant glioblastomas with distinct epigenetic and copynumber alterations and stratified clinical risks

Abstract BACKGROUND IDH-mutant glioblastoma is classified by the 2016 CNS WHO as a group with good prognosis. However, the actual number of cases examined in the literature is relatively small. We hypothesize that IDH-mutant glioblastoma is not a uniform group and should be further stratified. MATERIAL AND METHODS We conducted methylation profiles and estimated copy number variations in 64 IDH-mutant glioblastomas. RESULTS Our results showed that 10.9%, 53.1%, and 35.9% of tumors belonged to Codel, G-CIMPhigh, and G-CIMP-low methylation subgroups, respectively. G-CIMP-low subgroup was associated with significantly worse OS as compared to G-CIMP-high (P=0.005) and Codel groups (P=0.009). CDKN2A deletion (37.5%) was the most common gene copy number variation, and was associated with G-CIMP-low subgroup (P=0.001). Other frequent copy number changes included MET (4.7%), CCND2 (17.2%), PDGFRA (14.1%), CDK4 (12.5%), and EGFR (12.5%) amplification. Both CDKN2A deletion (P=0.008) and MET amplification (P&lt;0.001) were associated with poor OS in IDH-mutant glioblastomas. Combined epigenetic signatures and gene copy number variations separated IDH-mutant glioblastomas into Group 1 (Codel), Group 2 (GCIMP- high), Group 3 (G-CIMP-low without CDKN2A and MET alterations), and Group 4 (G-CIMP-low with CDKN2A/MET alteration). Survival analysis revealed Group 1 had a favorable OS (median survival: 41.3 months), while Groups 2 and 3 exhibited an intermediate OS (median survival: 20.6 and 21.8 months, respectively). Group 4 exhibited the worst OS (median survival: 8.4 months). Multivariable analysis confirmed the independent prognostic significance of our Groups. CONCLUSION IDH-mutant glioblastomas should be stratified for risk with combined epigenetic signature and CDKN2A/MET status and some cases have poor outcome.

OS5.5 Characteristics of high-grade gliomas with H3 G34 mutation in adults

Abstract BACKGROUND H3 G34-mutant high-grade gliomas occur primarily in children but can also be encountered in adults. The aim of the present study was to describe the characteristics of H3 G34-mutant high-grade gliomas in adults. MATERIAL AND METHODS We analysed the characteristics of 17 adult H3 G34-mutant high-grade gliomas and compared them with those of adult grade IV gliomas with H3 K27M mutation (n=21), IDH mutation (n=42) and TERT promoter (pTERT) mutation (n=88). RESULTS Median age at diagnosis in H3 G34-mutant gliomas was 25 years (range: 19–33 y). All tumors had a hemispheric location. The radiological presentation was suggestive of a high-grade glioma in 6 patients but in 10 patients it initially suggested another diagnosis due to absent or faint contrast enhancement (n=9) or the presence of an initial intratumoral haemorrhage (n=1). In non- or faint contrast-enhancing cases, diffusion-weighted imaging (DWI) was more helpful to suspect an aggressive tumor than MR spectroscopy and perfusion MRI. All H3 G34-mutant gliomas were classified as IDH wildtype glioblastomas. PNET-like foci were observed in 8 cases and most cases were immunonegative for ATRX (92%) and Olig2 (81%) and demonstrated MGMT promoter methylation (82%). The clinical, radiological and histological presentation of H3 G34-mutant gliomas was different from that of midline H3 K27M-mutant diffuse gliomas and from that of IDH-mutant and IDH-wildtype pTERT-mutant glioblastomas. Median overall survival of G34-mutant gliomas was 23.9 months compared to 19.6 months (p=0.16), 13.7 months (p=0.45) and 58 months (p=2.3x10-10) in H3 K27M-mutant diffuse gliomas, IDHwt pTERT-mutant and IDH-mutant glioblastomas, respectively. CONCLUSION Adults H3 G34-mutant high-grade gliomas are associated with distinct characteristics and a poor prognosis. DWI seems helpful to identify cases that present as non-contrast enhancing lesions and can wrongly suggest another diagnosis in these young patients.

P14.13 Incidence of pseudoprogression in high-grade IDH-mutant gliomas

Abstract BACKGROUND Pseudoprogression (PsP) is a well-known concern in IDH-wildtype glioblastomas. The aim of the present study was to describe its incidence in high-grade IDH-mutant gliomas. MATERIAL AND METHODS We retrospectively analyzed the characteristics of a consecutive series of high-grade IDH-mutant gliomas treated with radiotherapy (RT) with or without chemotherapy between March 2009 and September 2017. PsP was defined as a new enhanced lesion that occurred after RT and subsequently disappeared or remained stable during follow-up for a least 6 months. RESULTS The study population consisted of 38 anaplastic IDH-mutant and 1p/19q codeleted oligodendrogliomas, 34 IDH-mutant anaplastic astrocytomas and 18 IDH-mutant glioblastomas. Treatment consisted of radiotherapy alone (n=8, 9%), radiotherapy and PCV chemotherapy (n=63, 70%) and temozolomide radiochemotherapy (n=19, 21%). After a median follow-up of 3.5 years (range 1–8 years), 24 patients (28%) presented a PsP that occurred after a median delay of 10 months after radiotherapy (2 to 32 months). PsP was more frequent in patients treated with RT+PCV than in those treated with RT+TMZ (34% vs 10%, p=0.05). During the first two years after RT completion, 19 patients (21%) presented a PsP and 15 patients (17%) a true progression. At last follow-up, 1 patient (4%) in the PsP group had died compared to 10 patients (16%) in the group of patients without PsP. CONCLUSION PsP is a frequent issue in IDH-mutant high-grade gliomas. Its timing of onset is delayed compared to the timing of PsP onset reported in IDH-wildtype glioblastomas. The association between the use of PCV chemotherapy and PsP requires validation in an independent series.

A preliminary comprehensive molecular-based nomogram for individualized estimation of survival in patients with newly diagnosed glioblastoma utilizing global microRNA expression data.

2044 Background: Glioblastoma (GBM) is the most aggressive and common primary brain tumor. Nomograms are prediction models that help form individualized risk scores for cancer patients, which are valuable for treatment decision-making. The aim of this study is to create a refined nomogram by including novel molecular variables beyond MGMT promoter methylation. Methods: Clinical data and miRNA expression data were obtained from 226 newly diagnosed GBM patients. Clinical data included age at diagnosis, sex, Karnofsky performance status (KPS), extent of resection, O6-methylguanine-DNA methyltransferase ( MGMT) promoter methylation status, IDH mutation status and overall survival. Due to low representation of less than 13 cases each, IDH mutant glioblastomas and patients submitted to biopsy-only were excluded. Total RNA was isolated from formalin-fixed paraffin-embedded (FFPE) tissues; miRNA expression was subsequently measured using the NanoString human miRNA v3a assay. A Cox regression model was developed using glmnet R package with the elastic net penalty while adjusting for known prognostic factors. A dichotomized genomic score was created by finding the optimal cutpoint (maximum association with survival) of the linear combination of the selected. A nomogram was generated using known clinical prognostic factors, specifically age, sex, KPS, and MGMT status along with the dichotomized genomic score. Results: Four novel miRNAs were found to significantly correlate with overall survival and were used to create the dichotomized miRNA genomic score (GS). This score split the cohort into a poor performing group (GS_high) and a better performing group (GS_low) (p = 0.0031). A final nomogram was created using the Cox proportional hazards model (Figure 1). Factors that correlated with improved survival included younger age, KPS &gt; 70, MGMT methylation and a low genomic score. Conclusions: This study is a proof of concept demonstrating that integration of molecular variables beyond MGMT methylation improve existing nomograms to provide individualized information about patient prognosis. Future directions include a more comprehensive analysis, including proteomic and methylation data, and subsequent validation in an external cohort. Finally, network analysis integrating molecular signatures of poor performers will help identify therapeutic targets.

Identification of subsets of IDH-mutant glioblastomas with distinct epigenetic and copy number alterations and stratified clinical risks.

Background IDH-mutant glioblastoma is classified by the 2016 CNS WHO as a group with good prognosis. However, the actual number of cases examined in the literature is relatively small. We hypothesize that IDH-mutant glioblastoma is not a uniform group and should be further stratified.MethodsWe conducted methylation profiles and estimated copy number variations of 57 IDH-mutant glioblastomas.ResultsOur results showed that 59.6% and 40.4% of tumors belonged to glioma-CpG island methylator phenotype (G-CIMP)-high and G-CIMP-low methylation subgroups, respectively. G-CIMP-low subgroup was associated with significantly worse overall survival (OS) as compared to G-CIMP-high (P = .005). CDKN2A deletion (42.1%) was the most common gene copy number variation, and was significantly associated with G-CIMP-low subgroup (P = .004). Other frequent copy number changes included mesenchymal–epithelial transition (MET) (5.3%), CCND2 (19.3%), PDGFRA (14.0%), CDK4 (12.3%), and EGFR (12.3%) amplification. Both CDKN2A deletion (P = .036) and MET amplification (P < .001) were associated with poor OS in IDH-mutant glioblastomas. Combined epigenetic signature and gene copy number variations separated IDH-mutant glioblastomas into Group 1 (G-CIMP-high), Group 2 (G-CIMP-low without CDKN2A nor MET alteration), and Group 3 (G-CIMP-low with CDKN2A and/or MET alteration). Survival analysis revealed Groups 1 and 2 exhibited a favorable OS (median survival: 619 d [20.6 mo] and 655 d [21.8 mo], respectively). Group 3 exhibited a significant shorter OS (median survival: 252 d [8.4 mo]). Multivariable analysis confirmed the independent prognostic significance of our Groups.Conclusions IDH-mutant glioblastomas should be stratified for risk with combined epigenetic signature and CDKN2A/MET status and some cases have poor outcome.

DNA demethylation is associated with malignant progression of lower-grade gliomas

To elucidate the mechanisms of malignant progression of lower-grade glioma, molecular profiling using methylation array, whole-exome sequencing, and RNA sequencing was performed for 122, 36 and 31 gliomas, respectively. This cohort included 24 matched pairs of initial lower-grade gliomas and recurrent tumors, most of which showed malignant progression. Nearly half of IDH-mutant glioblastomas that had progressed from lower-grade gliomas exhibited characteristic partial DNA demethylation in previously methylated genomic regions of their corresponding initial tumors, which had the glioma CpG island methylator phenotype (G-CIMP). In these glioblastomas, cell cycle-related genes, RB and PI3K-AKT pathway genes were frequently altered. Notably, late-replicating domain was significantly enriched in the demethylated regions that were mostly located in non-regulatory regions, suggesting that the loss of DNA methylation during malignant transformation may involve mainly passive demethylation due to a delay in maintenance of methylation during accelerated cell division. Nonetheless, a limited number of genes including IGF2BP3, which potentially drives cell proliferation, were presumed to be upregulated due to demethylation of their promoter. Our data indicated that demethylation of the G-CIMP profile found in a subset of recurrent gliomas reflects accelerated cell divisions accompanied by malignant transformation. Oncogenic genes activated by such epigenetic change represent potential therapeutic targets.

Molecular classification of IDH-mutant glioblastomas based on gene expression profiles.

Isocitrate dehydrogenase (IDH) mutant glioblastoma (GBM), accounts for ~10% GBMs, arises from lower grade diffuse glioma and preferentially appears in younger patients. Here, we aim to establish a robust gene expression-based molecular classification of IDH-mutant GBM. A total of 33 samples from the Chinese Glioma Genome Atlas RNA-sequencing data were selected as training set, and 21 cases from Chinese Glioma Genome Atlas microarray data were used as validation set. Consensus clustering identified three groups with distinguished prognostic and molecular features. G1 group, with a poorer clinical outcome, mainly contained TERT promoter wild-type and male cases. G2 and G3 groups had better prognosis differed in gender. Gene ontology analysis showed that genes enriched in G1 group were involved in DNA replication, cell division and cycle. On the basis of the differential genes between G1 and G2/G3 groups, a six-gene signature was developed with a Cox proportional hazards model. Kaplan–Meier analysis found that the acquired signature could differentiate the outcome of low- and high-risk cases. Moreover, the signature could also serve as an independent prognostic factor for IDH-mutant GBM in the multivariate Cox regression analysis. Gene ontology and gene set enrichment analyses revealed that gene sets correlated with high-risk group were involved in cell cycle, cell proliferation, DNA replication and repair. These finding highlights heterogeneity within IDH-mutant GBMs and will advance our molecular understanding of this lethal cancer.

Integrated molecular characterization of IDH-mutant glioblastomas.

Mutations of isocitrate dehydrogenase (IDH)1/2 affect almost all astrocytomas of WHO grade II and III. A subset of IDH-mutant astrocytic tumours progresses to IDH-mutant glioblastoma or presents with the histology of a glioblastoma at first presentation. We set out here to assess the molecular spectrum of IDH-mutant glioblastomas. We performed an integrated molecular analysis of a mono-centric cohort (n=97); assessed through genome-wide DNA methylation analysis, copy-number profiling and targeted next generation sequencing using a neurooncology-tailored gene panel. Of these 97 IDH-mutant glioblastomas, 68 had a glioblastoma at first presentation ('de novo' IDH-mutant glioblastoma) and 29 emerged from a prior low-grade lesion ('evolved' IDH-mutant glioblastoma). Unsupervised hierarchical clustering of DNA methylation data disclosed that IDH-mutant glioblastoma ('de novo' and 'evolved') formed a distinct group separate from other diffuse glioma subtypes. Homozygous deletions of CDKN2A/B were found to be associated with shorter survival. This study demonstrates DNA methylation patterns in IDH-mutant glioblastoma to be distinct from lower-grade astrocytic counterparts but homogeneous within de novo and evolved IDH-mutant glioblastomas, and identifies CDKN2A as a marker for possible genetic sub-stratification.

BTC1.04 Genomic profiling of IDH-wildtype and IDH-mutant initial and matched recurrent glioblastomas reveals clinically actionable mutations (e.g. BRCA1/2) and resistance signatures

Abstract: Background: Glioblastomas account for 90% of all adult brain tumours. Patient survival remains low because treatments are ineffective against this lethal disease. Understanding the genes and pathways altered in subtypes is necessary for therapeutic intervention. Material and Methods: Tumours from 41 patients, 8 with matched initial and recurrent glioblastomas were genomically profiled. Some 130 clinically relevant neuro-oncology genes were assessed using an NGS-based diagnostic panel. Single nucleotide variants (SNVs), copy number variations (CNVs) and potentially clinically actionable mutations were described for initial and recurrent IDH-wildtype (n=38) and IDH-mutant glioblastomas (n=3). Results: The mutational landscape revealed discrete differences and similarities between subtypes. TSC2, MSH6, TP53, CREBBP and IDH1 were co-mutated and putatively pathogenic in both subtypes, suggesting they are driver mutations. Recurrent tumours were not hypermutated and matched analysis revealed inter-tumour heterogeneity. IDH-wildtype: SNVs (145) impacted 55 genes in the RTK/Ras/PI(3)K (82%), p53 (63%), WNT (58%), SHH (13%), NOTCH (11%), Rb (5%) and G-protein (8%) pathways. SNV burden was a predictor of overall survival (P=0.003) but no particular pathway was individually responsible. SNVs (40) in BRAF, DAXX, EGFR, FGFR2, JAK2, MYB, PIK3CA, PIK3R1, PTEN, ATM, BRCA1, CHEK2, PPM1D, PTCH1 and SMO were also putatively pathogenic. Many initial tumours had BRCA1 (21%) and BRCA2 (18%) variants, including previously confirmed somatic mutations in haemangioblastoma, and also WNT variants (58%). Recurrent tumours had fewer pathways (RTK/Ras/PI(3)K, p53, WNT, G-protein) impacted by genetic alterations. Possible tumour resistance signatures included a private SNV in PIK3C2G and CNV gains (BRCA2, GNAS, EGFR) and losses (TERT, SMARCA4). Survival analysis suggested GNAS variation was prognostic (P