Genomic and Transcriptomic Differences at the Pyruvate Kinase M (PKM) Locus in Patient-Derived Glioblastoma Multiforme (GBM) Cell Lines

Abstract

Glioblastoma multiforme (GBM), a particularly devastating primary CNS tumor, alters the expression and activity of multiple metabolic genes to enhance its ability to grow and divide, buffer against oxidative stress, and resist apoptosis. The shift from oxidative metabolism in the mitochondria to aerobic glycolysis is known as the Warburg effect, a phenomenon mediated by gene expression changes like the isoform switch at the pyruvate kinase muscle-type (PKM) locus from PKM1 to PKM2. Novel pharmaceuticals targeting this tumor-specific isoform have entered clinical trials, but the effect of genetic or transcriptomic background on the effectiveness of these drugs is unknown. The purpose of this work is to characterize the PKM locus at the level of DNA and mRNA.Our lab has previously collected and curated patient-derived GBM cell lines and characterized them with high-throughput transcriptome sequencing (RNA-seq). Herein, RNA-seq reads were mapped to the genome. Limiting analysis to the PKM locus, variant calling including single nucleotide polymorphism (SNP) calling is performed, and absolute expression and relative isoform abundance is measured and compared across lines.In this analysis of 16 GBM cell lines, multiple SNPs are identified that are predicted to be deleterious to the function of the protein. Additionally, concordant with previous findings in astrocytomas, the PKM2 isoform is the dominant pyruvate kinase transcript in all cell lines profiled. One cell line, in particular, had substantially higher PKM expression compared to the other cell lines.Previous studies have queried the mutational burden of PKM in other cancer types, but no mutational analysis has been performed on GBM. This work suggests genetic variation at this important locus. Targeting tumor-specific metabolism can increase the effectiveness of current standard-of-care therapies while leaving normal tissue intact. This characterization of the PKM locus at the level of DNA variants and gene expression will inform planned future work using a novel pharmaceutical targeting PKM2.K.J. Lee: None. C. Willey: None.