title: Quantitative assessment of intragenic receptor tyrosine kinase deletions in primary glioblastomas: their prevalence and molecular correlates.
abstract: Intragenic deletion is the most common form of activating mutation among receptor tyrosine kinases (RTK) in glioblastoma. However, these events are not detected by conventional DNA sequencing methods commonly utilized for tumor genotyping. To comprehensively assess the frequency, distribution, and expression levels of common RTK deletion mutants in glioblastoma, we analyzed RNA from a set of 192 glioblastoma samples from The Cancer Genome Atlas for the expression of EGFRvIII, EGFRvII, EGFRvV (carboxyl-terminal deletion), and PDGFRAΔ8,9. These mutations were detected in 24, 1.6, 4.7, and 1.6 % of cases, respectively. Overall, 29 % (55/189) of glioblastomas expressed at least one RTK intragenic deletion transcript in this panel. For EGFRvIII, samples were analyzed by both quantitative real-time PCR (QRT-PCR) and single mRNA molecule counting on the Nanostring nCounter platform. Nanostring proved to be highly sensitive, specific, and linear, with sensitivity comparable or exceeding that of RNA seq. We evaluated the prognostic significance and molecular correlates of RTK rearrangements. EGFRvIII was only detectable in tumors with focal amplification of the gene. Moreover, we found that EGFRvIII expression was not prognostic of poor outcome and that neither recurrent copy number alterations nor global changes in gene expression differentiate EGFRvIII-positive tumors from tumors with amplification of wild-type EGFR. The wide range of expression of mutant alleles and co-expression of multiple EGFR variants suggests that quantitative RNA-based clinical assays will be important for assessing the relative expression of intragenic deletions as therapeutic targets and/or candidate biomarkers. To this end, we demonstrate the performance of the Nanostring assay in RNA derived from routinely collected formalin-fixed paraffin-embedded tissue.
authors.affiliation: Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
authors.forename: Edward R
authors.initials: ER
authors.lastname: Kastenhuber
authors.forename: Jason T
authors.initials: JT
authors.lastname: Huse
authors.forename: Samuel H
authors.initials: SH
authors.lastname: Berman
authors.forename: Alicia
authors.initials: A
authors.lastname: Pedraza
authors.forename: Jianan
authors.initials: J
authors.lastname: Zhang
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Suehara
authors.forename: Agnes
authors.initials: A
authors.lastname: Viale
authors.forename: Magali
authors.initials: M
authors.lastname: Cavatore
authors.forename: Adriana
authors.initials: A
authors.lastname: Heguy
authors.forename: Nicholas
authors.initials: N
authors.lastname: Szerlip
authors.forename: Marc
authors.initials: M
authors.lastname: Ladanyi
authors.forename: Cameron W
authors.initials: CW
authors.lastname: Brennan
mesh_terms: D001932:Brain Neoplasms / Q000175:diagnosis / Q000453:epidemiology / Q000235:genetics* / Q000378:metabolism; D056915:DNA Copy Number Variations; D066246:ErbB Receptors / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods; D005909:Glioblastoma / Q000175:diagnosis / Q000453:epidemiology / Q000235:genetics* / Q000378:metabolism; D009154:Mutation; D015995:Prevalence; D011379:Prognosis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D017384:Sequence Deletion; D016019:Survival Analysis
chemical_list: D012333:RNA, Messenger; C410723:epidermal growth factor receptor VIII; C512478:EGFR protein, human; D066246:ErbB Receptors; D020794:Receptor Protein-Tyrosine Kinases