Jenkins, Robert B.

Abstract Ganglioglioma (GG) with anaplasia (anaplastic ganglioglioma) is a rare and controversial diagnosis. When present, anaplasia involves the glial component of the tumor, either at presentation or at recurrence. To date, most published cases lack molecular characterization. We describe the histologic and molecular features of 3 patients presenting with BRAF p. V600E-mutant GG (CNS WHO grade 1) with high-grade glial transformation at recurrence. The tumors occurred in pediatric patients (age 9–16 years) with time to recurrence from 20 months to 7 years. At presentation, each tumor was low-grade, with a BRAFV600E-positive ganglion cell component and a glial component resembling pleomorphic xanthoastrocytoma (PXA) or fibrillary astrocytoma. At recurrence, tumors resembled anaplastic PXA or high-grade astrocytomas without neuronal differentiation. CDKN2A homozygous deletion (HD) was absent in all primary tumors. At recurrence, 2 cases acquired CDKN2A HD; the third case showed loss of p16 and MTAP immunoexpression, but no CDKN2A/B HD or mutation was identified. By DNA methylation profiling, all primary and recurrent tumors either grouped or definitely matched to different methylation classes. Our findings indicate that malignant progression of the glial component can occur in GG and suggest that CDKN2A/B inactivation plays a significant role in this process.

Abstract Clinical management of IDH wildtype glioblastoma (GBM) and tumefactive multiple sclerosis (tMS) is drastically different. GBM requires maximal safe resection followed by chemoradiation, while tMS outcome is worsened by surgery and radiotherapy. Misdiagnosis of brain lesions may expose patients to unnecessary anxiety, surgery, or radiotherapy. Noninvasive methods to help with accurate diagnosis of tumor and non-tumor etiologies are needed. tMS subjects were identified by the Mayo Clinic Center for Multiple Sclerosis and Autoimmune Neurology (CMSAN). GBM subjects were matched to tMS by age at diagnosis, index MRI date, and sex. Inclusion criteria included one cm minimal lesion size and pre-operative post-contrast T1 and T2 images available for analysis. To identify potential experimental design bias, MRI technology and clinical characteristics were compared across groups. A 3D-DenseNet121 was used to develop a classification model using prespecified parameters: 600 epochs, batch size 16, learning rate 10-3, cross entropy loss, and AdamW optimizer. The stopping rule was defined as three sequential epoch cross entropy loss < 0.02. Five-fold cross validation (CV) was utilized to obtain an unbiased estimate of predictive performance (overfitting) and sensitivity of the 3D-DenseNet121 algorithm was evaluated. 224 subjects (114 GBM, 110 tMS) were analyzed: 40% male, median age 46. After one round of CV, the average unbiased estimate of sensitivity and specificity for predicting GBM from the final classification model was 0.86 and 0.73, respectively. To assess the reproducibility of the deep learning algorithm (3D-DenseNet121), the exact same CV folds were rerun resulting in average sensitivity and specificity of 0.82 and 0.75, respectively. Obtaining unbiased estimates of model performance using internal validation is critical before evaluating a final model on an external dataset. Understanding sensitivity of a deep learning algorithm is important for model validity. Differentiation of GBM and tMS appears reasonable with MRI; external validation is in progress.

Abstract Glioblastoma (GBM), IDH-wildtype (WT) is currently defined as an IDH-WT and H3-WT diffuse astrocytic glioma with molecular diagnostic features including whole +7/−10, TERT promoter (TERTp) mutation, and EGFR amplification and/or morphological diagnostic features such as necrosis and microvascular proliferation. To further understand the diversity of copy number signatures of GBM, IDHWT and evaluate the diagnostic utility of other recurrent copy number changes, we analyzed paired chromosomal microarray and next-generation sequencing mutational profiling data from 418 adult IDH-WT and H3-WT tumors with GBM morphological diagnostic features. The most common molecular features were TERTp mutations (85%), CDKN2A/B heterozygous/homozygous deletion (78%/66%), +7/-10 (63%), EGFR amplification (41%), +19 (36%), PTEN mutations (35%), partial -13 (33%), partial -14 (33%), +20 (32%), TP53 mutations (32%), and partial -22 (29%). At least one molecular diagnostic biomarker was present in 92% (n=385) of cases, and 29% (n=121) of cases had all three. The +7/-10 biomarker was the most frequent chromosomes 7/10 copy number change (68%, n=265). Other +7/-10 patterns were seen in 30% (n=125) of cases and included isolated +7 or -10, combinations of +7 and -10 with partial +7, partial -10 or 10 copy neutral loss of heterozygosity (cnLOH). Overall, 93% (390/418) of cases had whole and other chromosome 7/10 copy number changes. In comparison to tumors with +7/-10, tumors with other +7/-10 patterns were significantly enriched for partial 13 loss (Bonferroni adjusted p=0.04) but were not associated with significant difference in patient overall survival (p=0.30, 158/418 had available survival data). Our findings reiterate and expand the spectrum of copy number changes associated with GBM, IDH-WT. The similar overall survival rates between cases with the +7/-10 biomarker and those with other +7/-10 patterns suggest that other +7/-10 patterns may be functionally equivalent to +7/-10 and diagnostically relevant as a molecular diagnostic biomarker for this tumor type.

Abstract INTRODUCTION Prior to 2021, (classic) glioblastoma (GBM) required absence of IDH mutation and histologic features of hypercellularity, nuclear atypia, microvascular proliferation (MVP), and necrosis. Absence of histologic features can be a result of undersampling, with molecular, radiologic, and clinical features consistent with GBM. Accordingly, WHO 2021 defined molecular glioblastoma as diffuse glioma IDHwt, H3wt, with one or more of MVP, necrosis, TERT promoter mutation, EGFR gene amplification (EGFRamp), and/or +7/−10. We hypothesized that there is clinical and radiographic heterogeneity among tumors defined as molecular GBM. METHODS We identified 121 patients that met the criteria for molecular GBM. 121 Classic GBM, defined as IDHwt with hypercellularity, MVP or necrosis, were matched to molecular GBM cases by age, sex, and diagnosis date. All cases were reviewed for relevant histologic features and molecular features. Examined clinical variables included: first symptom, time from first symptom to date of pathological diagnosis, date of first MRI, tumor location, radiographic features of enhancement, diffusion or mass effect, time to progression and overall survival. Clinical, radiologic, and molecular features were compared between classic and molecular GBM. RESULTS Currently,160 cases have been reviewed. Preliminary results show that there is a longer time from first symptom to diagnosis for molecular GBM. Molecular GBM is significantly more likely to be discovered coincidentally, and without enhancement or radiographic necrosis. Classic GBM is significantly more likely to present with focal neurologic deficit as first symptom, regional mass effect on index imaging and have monosomy 10. CONCLUSION While pathologic undersampling accounts for a significant proportion of molecular GBM, our data suggest that there are significant clinical, radiographic, and outcome differences between classical and molecular GBM. Final analysis of the entire cohort will help better define this clinical spectrum.

Abstract BACKGROUND The diagnosis and management of patients with brain tumors currently uses WHO defined morphologic and molecular features. However, neuro-oncology practice in low resource settings relies on histomorphology. This study aims to reclassify glioma cases diagnosed in the Department of Anatomic and Molecular Pathology Lagos University Teaching Hospital using the 2021 WHO classification. METHODS Fifty-six cases of glioma diagnosed between 2013 to 2021 were evaluated. Morphologic diagnosis was reassessed. Five-micron sections were obtained for immunohistochemistry (IHC), and genetic testing (DNA and RNA); after manual macrodissection for tumor enrichment using 10μm sections. IHC for IDH1-R132H, ATRX, BRAFV600E, P53,Ki67, and H3K27M and OncoScan chromosomal microarray analysis were performed. NGS mutation/fusion analysis and EPIC methylation array profiling are in progress. RESULTS Of 56 cases evaluated, median age was 22 years (range=1-60 years); 71% were males. The initial morphologic diagnosis include 21 pilocytic astrocytoma, 11 glioblastoma, 9 ependymoma, 7 diffuse astrocytoma, 3 anaplastic astrocytoma, 2 high-grade gliomas, 1 oligodendroglioma, 1 diffuse midline glioma, and 1 pleomorphic xanthoastrocytoma (PXA). Histomorphologic re-evaluation revealed discordant diagnosis in 29% (16/56) of cases. Of the 56 cases, 73% (41/56) had usable DNA yield and 38% (21/56) had DNA yield of ≥ 750ng. Chromosomal microarray analysis was completed for 50% (28/56) cases. The revised 2021 WHO diagnosis were: 5 glioblastoma, IDH-wildtype, 5 pilocytic astrocytoma, 4 glioma NEC, 3 posterior fossa ependymoma, group B, 3 PXAs, 3 astrocytoma, IDH-mutant, 2 pediatric low-grade glioma, 2 supratentorial ependymoma, ZFTA fusion-positive, 1 posterior fossa ependymoma, group A. In 71% (20/28) of cases, diagnosis was revised using the 2021 WHO criteria. CONCLUSION Most cases had usable DNA yield. Overall, hsitologic re-evaluation and molecular testing based on the 2021 WHO classification guidelines refined the diagnosis in 48% (27/56) of cases.

Abstract INTRODUCTION Brain tumors constitute significant morbidity and mortality in sub-Saharan Africa (SSA). Improvements in neuro-oncology practice and research have seen increased diagnosis of brain tumors. However, to our knowledge, there have been no previous projects on brain tumor genetics in SSA. To understand the feasibility of developing brain tumor biobanking and registries, this project aims to start by mapping out the current neuro-oncology capacity in terms of workforce and available services. METHODOLOGY We will conduct a descriptive questionnaire-based online survey among a cross section of neuro-oncology practitioners spread across SSA countries. The dissemination of the survey questionnaire will be facilitated by the Society for Neuro-oncology in SSA (SNOSSA). The Google designed questionnaire will capture information on the distribution, and number of available neuro-oncology care practitioners, capacity for brain tumor diagnosis and management, cancer registration, tumor biobanking, and research. CLINICAL IMPACT AND CONCLUSION This study will generate robust data from SSA, which can be used to improve future research and promote advocacy towards brain tumor diagnosis and management. This work will also serve as a pilot study for subsequent research that will focus on the development of brain tumor-specific registries and biorepositories in SSA.

Abstract BACKGROUND The diagnosis and management of patients with brain tumors currently uses WHO defined morphologic and molecular features. However, neuro-oncology practice in low resource settings relies solely on histomorphology. This study aims to reclassify glioma cases diagnosed in the Department of Anatomic and Molecular Pathology Lagos University Teaching Hospital using the WHO 2021 classification. METHODS Fifty-six cases of glioma diagnosed between 2013 to 2021 were evaluated. Morphologic diagnosis was reassessed. Five-micron sections were obtained for immunohistochemistry (IHC), and genetic testing (DNA and RNA) after manual macrodissection for tumor enrichment used 10-µm sections. IHC for IDH1-R132H, ATRX, BRAF-V600E, p53, Ki67 and H3-K27M and Oncoscan chromosomal microarray analysis were performed. NGS mutation/fusion analysis and EPIC methylation array profiling are in progress. RESULTS Of the 56 cases evaluated, median age was 22 years (range, 1-60); 71% were male. The initial morphologic diagnoses included 21 pilocytic astrocytoma, 11 glioblastoma, 9 ependymoma, 7 diffuse astrocytoma, 3 anaplastic astrocytoma, 2 high-grade gliomas, 1 oligodendroglioma, 1 diffuse midline glioma, and 1 pleomorphic xanthoastrocytoma (PXA). Histomorphologic re-evaluation revealed discordant diagnosis in 29% (16/56) of cases. Of the 56 cases, 73% (41/56) had usable DNA yield and 38% (21/56) had DNA yield of ≥750ng. Chromosomal microarray analysis was completed for 50% (28/56) cases. The revised WHO 2021 diagnosis was: 5 glioblastoma IDH-wildtype, 5 pilocytic astrocytoma, 4 glioma NEC, 3 posterior fossa ependymoma, group B, 3 PXA, 3 astrocytoma IDH-mutant, 2 pediatric low-grade gliomas, 2 supratentorial ependymoma, ZFTA fusion-positive, 1 posterior fossa ependymoma, group A. In 71% (20/28) of cases with molecular testing, diagnosis was revised using WHO 2021 criteria. CONCLUSION Most cases had usable DNA. Overall, histologic re-evaluation and molecular based on the WHO 2021 criteria refined the diagnosis in 48% (27/56) of cases.