Identification of Excellent Prognosis IDH Wildtype Glioblastomas Using Genomic and Metabolic Profiling

PURPOSE/OBJECTIVE(S)

High grade gliomas (HGGs) are aggressive brain tumors with altered cellular metabolism. HGGs can carry mutations in the tricarboxylic acid (TCA) cycle enzyme isocitrate dehydrogenase 1 (IDH1), conferring distinct biology and improved patient prognosis compared to IDH wildtype (wt) tumors. Using metabolomic analyses of tumor tissue, we previously showed that IDH wt and IDH mutant (IDH mut) tumors have unique metabolomic signatures that correlate with different survival outcomes. Among this cohort of 69 HGG samples, we identified two unique patient tumors that metabolically clustered with IDH mut tumors, but lacked both the IDH mutation and its product 2-hydroxyglutarate. We aimed to discover unique mutations in these two tumors that may impart an IDH mutant-like phenotype in the absence of an IDH1 or IDH2 mutation.

MATERIALS/METHODS

Whole exome sequencing (WES) was performed on frozen tumor samples from two patients diagnosed as glioblastoma (GBM), IDH wt via Agilent v5 + IncRNA platform. Alignment to the hg38 genome and variant calling were completed using an accelerated implementation of GATK's BWA and MuTect2 algorithms from Sentieon. Variants were filtered based on supporting reads and variant allele thresholds, with synonymous variants and common SNPs removed. High-confidence variants were further filtered by membership in the four KEGG pathways associated with IDH1 and IDH2. Identified variants were corroborated with metabolomics data from the two unique IDH wt tumors compared with classical GBM IDH wt, oligodendrogliomas IDH mut and astrocytomas IDH mut to identify putative drivers of an IDH mutant-like metabolomic phenotype in these unique IDH wt tumors.

RESULTS

Despite the lack of an IDH mutation, one patient survived 45.6 months and the other patient remains alive at last follow up 64 months post diagnosis, much longer than the 16-18-month median survival typical of patients with GBM IDH wt. WES of outlier IDH wt tumor samples revealed 65 unique mutations in the queried KEGG pathways, of which 34 had a variant allele frequency > = 0.15. These variants were processed in Gprofiler, confirming expected enrichment of the carboxylic acid metabolic biologic process, a functional gene set consisting of TCA genes, among these variants (p = 0.002, 3.6-fold enrichment). Accordingly, metabolite levels of intermediates of the TCA cycle, including malate and isocitrate were decreased in the outlier tumor samples compared to classic GBMs IDH wt (p<0.001). Presence of genetic alterations in key variants of the carboxylic acid metabolic biologic process (including ME1, GYP4F3, PTGIS, PFKL, PSPH, AKR1A1, HK2, NOS1) correlated with improved overall survival among GBM patients in the TCGA (p = 0.04). Laboratory validation of these findings in preclinical GBM models is ongoing.

CONCLUSION

Disruption of the TCA cycle independent of an IDH mutation is associated with favorable survival in GBM. Pharmacologic inhibition of these pathways may be a promising strategy to improve GBM outcomes.

Fine needle aspiration diagnosis of ipsilateral synchronous neoplasm - mucoepidermoid carcinoma with warthin tumor in parotid gland

Warthin tumor (WT) owing to its heterogeneous appearance, biological behavior and multicentricity poses a diagnostic challenge to cytologists worldwide. We report a rare double pathology of mucoepidermoid carcinoma (MEC) with WT which was diagnosed by fine needle aspiration (FNA). Cytological smears revealed sheets of epithelial cells and small clusters of squamous cells in a background of mucoid material along with a few small groups and scattered oncocytic cells and inflammatory cells (mainly lymphocytes). In view of the cytological findings various differentials such as oncocytic lesions, benign lesions of the parotid with extensive lymphoid reaction, necrotizing sialometaplasia, WT with extensive squamous/mucoid metaplasia, metastatic squamous cell carcinoma (SCC) with or without cystic change, oncocytic variant of MEC and a possibility of a synchronous MEC with WT were considered. By means of extensive review of the smears and clinic-pathological meets as discussed below, 2 differential diagnoses were given- MEC with WT versus an oncocytic variant of MEC with "?" lymphoid (tumor response) reaction. Subsequent histopathological examination confirmed the diagnosis of MEC with WT. Recent discovery of t(11; 19) translocation generating a novel fusion gene CRTC1/MAML2 which has been demonstrated in both MEC and WT has helped in providing the missing link in confirming the genetic relatedness and proof of development of a subset of WT with concomitant MEC. The case discusses the FNA findings of a rare collision tumor (MEC with WT), its possible differentials and highlights the importance of noting the background material in a case of double pathology on FNA.

Mature ovarian teratoma with gliomatosis peritonei--a case report

Gliomatosis peritonei (GP), a rare condition related to ovarian teratomas, is characterized by miliary implants of mature glial tissues on the peritoneum or omentum. We report herein a case of mature teratoma of the ovary with GP with imaging features and pathological correlation.

Sarcoglycanopathies: a clinicopathological study of 13 cases [corrected]

BACKGROUND

Limb girdle muscular dystrophy (LGMD) is a phenotypic expression of a heterogeneous group of diseases and sarcoglycanopathy is one of the causes of LGMD. There is only one study on sarcoglycanopathies in the Indian literature. No data is available from northern India.

MATERIALS AND METHODS

All cases of muscular dystrophies, which were diagnosed in our laboratory in the last six years, were reviewed. Immunohistochemistry for various sarcoglycan proteins was done. Clinical features and pathological findings of the cases that were diagnosed as sarcoglycanopathies were reviewed.

RESULTS

In the last 6 (1/2) years (1998-June 2004), we received 1435 muscle biopsies, of which 498 cases were of muscular dystrophies, and 13 cases were of sarcoglycanopathies (8 of gamma, 3 of alpha, 1 of both alpha and gamma, and 1 with absence of all four sarcoglycans). Sarcoglycanopathies comprised 2.6% of all muscular dystrophies, 11.8% of LGMD and 0.90% of all muscle diseases diagnosed in our laboratory. The mean age of onset was 7.2 years and the M:F ratio was 1.1:1. Most of them presented with difficulty in getting up, climbing stairs, calf hypertrophy and markedly raised CPK levels. Histological features were like dystrophinopathies.

CONCLUSION

Sarcoglycanopathies are a relatively rare cause of LGMD and should be confirmed by immunohistochemistry as it will facilitate counseling and also prognostification. Although rare, in patients with muscle weakness, calves hypertrophy and raised CPK levels this possibility should be considered and needs to be differentiated from dystrophinopathies.