Rapid Intraoperative Molecular Characterization of Glioma

Shankar, Ganesh M.; Francis, Joshua M.; Rinne, Mikael L.; Ramkissoon, Shakti; Huang, Franklin W.; Venteicher, Andrew S.; Akama-Garren, Elliot H.; Kang, Yun Jee; Lelic, Nina; Kim, James C.; Brown, Loreal; Charbonneau, Sarah; Golby, Alexandra J.; Pedamallu, Chandra Sekhar; Hoang, Mai P.; Sullivan, Ryan J.; Cherniack, Andrew D.; Garraway, Levi A.; Stemmer‐Rachamimov, Anat; Reardon, David A.; Wen, Patrick Y.; Brastianos, Priscilla K.; Curry, William T.; Barker, Frederick G.; Hahn, William C.; Nahed, Brian V.; Ligon, Keith L.; Louis, David N.; Cahill, Daniel P.; Meyerson, Matthew

doi:10.1001/jamaoncol.2015.0917

Cited by 72 publications

(55 citation statements)

References 15 publications

(21 reference statements)

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“…A mutation-specific telomerase promoter PCR quantifies tumor purity Although allele-specific PCR has been used qualitatively for genotyping glioma (25), it can also be performed quantitatively for allele frequency estimation (26). To sensitively detect telomerase promoter mutations, we established an allele-specific quantitative real-time PCR (qAS-PCR) assay for the two commonly observed hotspot mutations (chr5:1,295,228G>A and chr5:1,295,250G>A) in the TERT promoter (Fig.…”

Section: Resultsmentioning

confidence: 99%

Prognostic Relevance of Tumor Purity and Interaction with MGMT Methylation in Glioblastoma

Heuling

Knab

Radke

et al. 2017

Molecular Cancer Research

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Promoter methylation status of O-6-methylguanine-DNA methyltransferase (MGMT), a DNA repair enzyme, is a critical biomarker in glioblastoma (GBM), as treatment decisions and clinical trial inclusion rely on its accurate assessment. However, interpretation of results is complicated by poor interassay reproducibility as well as a weak correlation between methylation status and expression levels of MGMT. This study systematically investigates the influence of tumor purity on tissue subjected to MGMT analysis. A quantitative, allele-specific realtime PCR (qAS-PCR) assay was developed to determine genotype and mutant allele frequency of telomerase promoter (pTERT) mutations as a direct measure of tumor purity. We studied tumor purity, pTERT mutation by Sanger sequencing, MGMT methylation by pyrosequencing, IDH1 mutation status, and clinical parameters in a cohort of high-grade gliomas (n ¼ 97). The qAS-PCR reliably predicted pTERT genotype and tumor purity compared with independent methods. Tumor purity positively and significantly correlated with the extent of methylation in MGMT methylated GBMs. Extent of MGMT methylation differed significantly with respect to pTERT mutation hotspot (C228T vs. C250T). Interestingly, frontal lobe tumors showed greater tumor purity than those in other locations. Above all, tumor purity was identified as an independent prognostic factor in GBM. In conclusion, we determined mutual associations of tumor purity with MGMT methylation and pTERT mutations and found that the extent of MGMT methylation reflects tumor purity. In turn, tumor purity is prognostic in IDH1 wild-type GBM.Implications: Tumor purity is an independent prognostic marker in glioblastoma and is associated with the extent of MGMT methylation. Mol Cancer Res; 15(5); 532-40. Ó2017 AACR.

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Section: Resultsmentioning

confidence: 99%

Prognostic Relevance of Tumor Purity and Interaction with MGMT Methylation in Glioblastoma

Heuling

Knab

Radke

et al. 2017

Molecular Cancer Research

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“…Moreover, specimens may be small and not representative, hampering correct diagnosis or even necessitating multiple surgical samplings to clarify final pathologic diagnosis. In addition, the surgical intervention strategy and assessment of the surgical risk-benefit balance depend on the glioma subtype (1, [9][10][11]. This implies that an intraoperative histologic diagnosis may be required, possibly delaying the surgical procedure.…”

Section: Introductionmentioning

confidence: 99%

Molecular Diagnosis of Diffuse Gliomas through Sequencing of Cell-Free Circulating Tumor DNA from Cerebrospinal Fluid

Martínez‐Ricarte

Mayor²,

Martínez‐Sáez

et al. 2018

Clinical Cancer Research

141

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Purpose: Diffuse gliomas are the most common primary tumor of the brain and include different subtypes with diverse prognosis. The genomic characterization of diffuse gliomas facilitates their molecular diagnosis. The anatomical localization of diffuse gliomas complicates access to tumor specimens for diagnosis, in some cases incurring high-risk surgical procedures and stereotactic biopsies. Recently, cell-free circulating tumor DNA (ctDNA) has been identified in the cerebrospinal fluid (CSF) of patients with brain malignancies. Experimental Design: We performed an analysis of IDH1, IDH2, TP53, TERT, ATRX, H3F3A, and HIST1H3B gene mutations in two tumor cohorts from The Cancer Genome Atlas (TCGA) including 648 diffuse gliomas. We also performed targeted exome sequencing and droplet digital PCR (ddPCR) analysis of these seven genes in 20 clinical tumor specimens and CSF from glioma patients and performed a histopathologic characterization of the tumors. Results: Analysis of the mutational status of the IDH1, IDH2, TP53, TERT, ATRX, H3F3A, and HIST1H3B genes allowed the classification of 79% of the 648 diffuse gliomas analyzed, into IDH-wild-type glioblastoma, IDH-mutant glioblastoma/diffuse astrocytoma and oligodendroglioma, each subtype exhibiting diverse median overall survival (1.1, 6.7, and 11.2 years, respectively). We developed a sequencing platform to simultaneously and rapidly genotype these seven genes in CSF ctDNA allowing the subclassification of diffuse gliomas. Conclusions: The genomic analysis of IDH1, IDH2, TP53, ATRX, TERT, H3F3A, and HIST1H3B gene mutations in CSF ctDNA facilitates the diagnosis of diffuse gliomas in a timely manner to support the surgical and clinical management of these patients. Clin Cancer Res; 24(12); 2812–9. ©2018 AACR.

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“…Genetic testing remains timeconsuming [reporting of isocitrate dehydrogenase (IDH) mutation status, a prognostic marker, can take weeks], creating delay in pathologic diagnosis and rendering treatment. However, recently, Shankar et al (17) reported a genotyping method for IDH and telomerase reverse transcriptase mutations, with results available in 60 min.…”

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confidence: 99%

Lipid and metabolite profiles of human brain tumors by desorption electrospray ionization-MS

Jarmusch

Pirro

Baird

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

179

166

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Examination of tissue sections using desorption electrospray ionization (DESI)-MS revealed phospholipid-derived signals that differ between gray matter, white matter, gliomas, meningiomas, and pituitary tumors, allowing their ready discrimination by multivariate statistics. A set of lower mass signals, some corresponding to oncometabolites, including 2-hydroxyglutaric acid and N-acetylaspartic acid, was also observed in the DESI mass spectra, and these data further assisted in discrimination between brain parenchyma and gliomas. The combined information from the lipid and metabolite MS profiles recorded by DESI-MS and explored using multivariate statistics allowed successful differentiation of gray matter (n = 223), white matter (n = 66), gliomas (n = 158), meningiomas (n = 111), and pituitary tumors (n = 154) from 58 patients. A linear discriminant model used to distinguish brain parenchyma and gliomas yielded an overall sensitivity of 97.4% and a specificity of 98.5%. Furthermore, a discriminant model was created for tumor types (i.e., glioma, meningioma, and pituitary), which were discriminated with an overall sensitivity of 99.4% and a specificity of 99.7%. Unsupervised multivariate statistics were used to explore the chemical differences between anatomical regions of brain parenchyma and secondary infiltration. Infiltration of gliomas into normal tissue can be detected by DESI-MS. One hurdle to implementation of DESI-MS intraoperatively is the need for tissue freezing and sectioning, which we address by analyzing smeared biopsy tissue. Tissue smears are shown to give the same chemical information as tissue sections, eliminating the need for sectioning before MS analysis. These results lay the foundation for implementation of intraoperative DESI-MS evaluation of tissue smears for rapid diagnosis. ambient ionization | MS imaging | multivariate statistics | pathology | neurosurgery M S is increasingly being used in medicine (e.g., in clinical chemistry, pharmaceutical development, and proteomics). Ambient ionization methods generate ions under atmospheric conditions, with minimal to no sample preparation (1). Desorption electrospray ionization (DESI), an ambient method that uses a spray of charged solvent as the projectile, provides rapid chemical information while preserving tissue and cellular morphology, allowing subsequent histopathology on the same specimen (2). This feature allows integration of DESI-MS into current workflows and postacquisition pathology. DESI-MS has been used to study prostate cancer (3), bladder cancer (4), kidney cancer (5), seminoma (6), lymphoma (7), gastrointestinal cancer (8), and others. In each case, the recorded pattern of lipid signals allows the differentiation of cancer from normal tissue. DESI-MS has been previously used to explore chemical differences among glioma subtypes, grades, and tumor cell concentrations (relative percentage of tumor compared with parenchyma) (9, 10). Meningiomas have also been studied previously and were distinguished from normal dura mater (11).T...

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Rapid Intraoperative Molecular Characterization of Glioma

Cited by 72 publications

References 15 publications

Prognostic Relevance of Tumor Purity and Interaction with MGMT Methylation in Glioblastoma

Prognostic Relevance of Tumor Purity and Interaction with MGMT Methylation in Glioblastoma

Molecular Diagnosis of Diffuse Gliomas through Sequencing of Cell-Free Circulating Tumor DNA from Cerebrospinal Fluid

Lipid and metabolite profiles of human brain tumors by desorption electrospray ionization-MS

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