Multi-Platform Classification of IDH-Wild-Type Glioblastoma Based on ERK/MAPK Pathway: Diagnostic, Prognostic and Therapeutic Implications

Abstract

Glioblastoma is the most aggressive and frequent glioma in the adult population. Because current therapy regimens confer only minimal survival benefit, molecular subgrouping to stratify patient prognosis and therapy design is warranted. This study presents a multi-platform classification of glioblastoma by analyzing a large, ethnicity-inclusive 101-adult-patient cohort. It defines seven non-redundant IDH-wild-type glioblastoma molecular subgroups, G1–G7, corresponding to the upstream receptor tyrosine kinase (RTK) and RAS-RAF segment of the ERK/MAPK signal transduction pathway. These glioblastoma molecular subgroups are classified as G1/EGFR, G2/FGFR3, G3/NF1, G4/RAF, G5/PDGFRA, G6/Multi-RTK, and G7/Other. The comprehensive genomic analysis was refined by expression landscaping of all RTK genes, as well as of the major associated growth pathway mediators, and used to hierarchically cluster the subgroups. Parallel demographic, clinical, and histologic pattern analyses were merged with the molecular subgrouping to yield the first inclusive multi-platform classification for IDH-wild-type glioblastoma. This straightforward classification with diagnostic and prognostic significance may be readily used in neuro-oncological practice and lays the foundation for personalized targeted therapy approaches.

Novel neoplasms associated with syndromic pediatric medulloblastoma: integrated pathway delineation for personalized therapy

“…4 B, 5 G), sharing with the MB-SHH cluster similar NTRK1 and INSRR overexpression, and much higher EPH RTK overexpression, especially of EPHA3/7 . In the M6 prolactinoma, MET was the only RTK with relative high overexpression, although the absolute levels were average in comparison to other CNS tumors, such as glioblastoma [ 14 ].…”

“…Formalin-fixed paraffin-embedded (FFPE) sections were stained with hematoxylin–eosin (H&E). Images were acquired with Nikon Eclipse Ci microscope equipped with Nikon Digital Sight DS-Fi2 camera (Nikon Instruments Inc., Melville, NY), as previously described [ 14 , 15 ]. IHC was performed on selected sections, by using the heat-induced epitope retrieval method at 95 °C in CC1 solution for 8 min on a Ventana Benchmark Ultra platform (Roche/Ventana Medical Systems Inc., Tucson, AZ), as previously described [ 12 , 15 ].…”

“…The tumor mutation burden (TMB) is expressed as single-nucleotide protein-altering mutations per megabase DNA. Whole transcriptome RNA sequencing with RNA fusion detection was performed at Tempus Labs for all samples from FFPE sections [ 11 , 14 ]. For each case, the same FFPE block was used for DNA and RNA extraction to allow direct comparison of results.…”

“…Absolute expression levels of selected overexpressed genes from syndromic tumors were compared against an internal mRNA expression database, MG-eDB1. The MG-eDB1 database comprises the expression profiles of a total of 278 various primary and metastatic brain tumors, including the syndromic tumors described in this study, processed and sequenced under the same experimental conditions [ 11 , 14 , 16 , 17 ]. For the high-grade sarcoma clinical diagnostic workup, a methylation test was performed in St. Jude Children’s Research Hospital (Memphis, TN) on an Infinium MethylationEPIC BeadChip array (850 k array) targeting 862,927 CpG sites across the genome (Illumina Inc, San Diego, CA).…”

“…Hierarchical clustering was performed as described [ 14 ], by using Instant Clue software [ 18 ]. Gene category overexpression median ranking was assessed by using non-parametric, two-tailed Wilcoxon matched-pairs signed rank test, as described [ 11 ].…”