EGFRvIII expression and isocitrate dehydrogenase mutations in patients with glioma

Abstract

Molecular pathology and personalized medicine are still being evolved in Saudi Arabia, and genetic testing for the detection of mutations as cancer markers have not been established in the diagnostics laboratories in Saudi Arabia. The aim of the present study was to determine the prevalence of isocitrate dehydrogenase (IDH1 and IDH2) mutations and epidermal growth factor receptor variant (EGFRv)III transcript expression in Saudi Arabian patients with glioma. Out of 117 brain tumors tested by reverse transcription-quantitative PCR for EGFRvIII, 41 cases tested positive. In the glioblastoma (GBM) category, 28/55 tumors were positive, in astrocytoma tumors 5/22, and in oligodendrogliomas 4/13 cases were positive respectively. EGFRvIII transcript was sequenced by capillary electrophoresis to demonstrate the presence of EGFRvIII-specific junction where exons 2-7 were deleted. In the present study 106 tumors were sequenced for IDH1 exon-4 mutations using the capillary sequencing method. The most common substitution missense mutation c.395G>A was found in 16 tumors. In the case of adamantinomatous craniopharyngioma, a novel missense mutation in c.472C>T was detected in IDH2 gene. Using next-generation sequencing (NGS), 74 tumors were sequenced for the IDH1 gene, and a total of 8 missense variants were identified in 36 tumors in a population of Saudi Arabia. The missense mutation (c.395G>A) was detected in 29/36 of tumors. A novel intronic mutation in c.414+9T>A was found in 13 cases in the IDH1 gene. In addition, one case exhibited a novel synonymous mutation in c.369A>G. Eleven tumors were found to have compound mutations in the IDH1 gene. In IDH2 gene, out of a total of 16 variants found in 6 out of 45 tumors, nine were missense, five were synonymous and one was intronic. This is the first report from Saudi Arabian laboratories analyzing glioma tumors for EGFRvIII expression, and the first study from Saudi Arabia to analyze IDH mutations in gliomas using the capillary and NGS methods.

IDH Mutations in Glioma: Double-Edged Sword in Clinical Applications?

“…They can be targeted by the genetically modified chimeric antigen receptor (CAR) T cells or oncolytic viral therapy, in which viruses are genetically engineered in order to selectively infect and replicate in tumor cells, therefore resulting in not only cellular lysis, but also the activation of immunogenic cell death pathways [118,119]. Even if EGFRvIII is mostly associated with IDH-wildtype gliomas, there are some cases in which IDH mutation and EGFRvIII are found together [120,121]. Alternatively, PDGFRA, which is known to be upregulated in IDH-mutant gliomas [122], has recently been shown to be targeted by CAR T cell therapy in other cancer types [123].…”

Supratentorial Sporadic Hemangioblastoma: A Case Report With Mutation Profiling Using Next-Generation DNA Sequencing

“…Compared with the Ion AmpliSeq Comprehensive Cancer Panel and Ion AmpliSeq Cancer HotSpot Panel, the custom panel used in the present NGS analysis (Ion AmpliSeq Cancer Panel v1) contains primers for only 46 genes, as shown in Table 1 . The IDH1 intronic mutation (c.414+9T>A) was previously reported in this HBL tumor by us; however, no missense mutations were detected in IDH1 and IDH2 genes in this tumor [ 28 ]. Ion AmpliSeq™ Cancer Panel v1 contains the primers for the VHL gene; however, no VHL mutations were detected in this tumor.…”

“…4471262) consists of 50 oncogenes and tumor suppressor genes that are frequently mutated in several types of cancers. The mutation profiling of a-CPP, MPE, and other brain tumors was reported in previous studies using these custom gene panels on the Ion Proton instrument [ 20 - 23 , 28 ]. Compared with the Ion AmpliSeq Comprehensive Cancer Panel and Ion AmpliSeq Cancer HotSpot Panel, the custom panel used in the present NGS analysis (Ion AmpliSeq Cancer Panel v1) contains primers for only 46 genes, as shown in Table 1 .…”

“…for further mutation identification. The VCF file data were analyzed using Ion Reporter v5.18.4.0 (Thermo Fisher Scientific, Inc.), which calculated allele coverage, allele frequency, allele ratio, variant impact, clinical significance, Polymorphism Phenotyping v2 (PolyPhen-2) score, Phred score, Sorting Intolerant from Tolerant (SIFT) score, Grantham score, and Functional Analysis Through Hidden Markov Models (FATHMM) score [ 22 , 28 ]. The PolyPhen-2 score predicts the potential impact of substitution in the variant on the structural and functional aspects of the protein.…”

“…True mutations were considered based on a Phred quality score >20 and mutations with a p‑value <0.05 were considered significant. Variants that do not fall into this criterion were filtered out [ 22 , 28 ].…”