Enhancing diagnosis, prognosis, and therapeutic outcome prediction of gliomas using genomics

Abstract

Malignant gliomas are the most frequent type of primary brain tumors. Patients' outcome has not improved despite new therapeutics, thus underscoring the need for a better understanding of their genetics and a fresh approach to treatment. The lack of reproducibility in the classification of many gliomas presents an opportunity where genomics may be paramount for accurate diagnosis and therefore best for therapeutic decisions. The aim of this work is to identify large and focal copy number abnormalities (CNA) and loss of heterozygosity (LOH) events in a malignant glioma population. We hypothesized that these explorations will allow discovery of genetic markers that may improve diagnosis and predict outcome. DNA from glioma specimens were subjected to CNA and LOH analyses. Our studies revealed more than 4000 CNA and several LOH loci. Losses of chromosomes 1p and/or 19q, 10, 13, 14, and 22 and gains of 7, 19, and 20 were found. Several of these alterations correlated significantly with histology and grade. Further, LOH was detected at numerous chromosomes. Interestingly, several of these loci harbor genes with potential or reported tumor suppressor properties. These novel genetic signatures may lead to critical insights into diagnosis, classification, prognosis, and design of individualized therapies.

FIG. 1.

Frequency of major chromosome alterations in the studied glioma population. Chi-square test was used to determine statistically significant copy number changes by glioma subtype. ACG, astrocytoma grade II; AAC, anaplastic astrocytoma grade III; GBM, glioblastoma grade IV; ODG, oligodendroglioma grade II; AOD, anaplastic oligodendroglioma grade III.

FIG. 2.

Summary of gain (red) and loss (blue) events observed in selected chromosomes that showed highly statistically significance associations with diagnosis (p<0.0001, ANOVA); chromosome 1, chromosome 7, chromosome 9, chromosome 10, chromosome 19, and chromosome 20 are shown. Specific genetic losses or gains have been detected and shown to correlate significantly with histology and subtype.

FIG. 3.

Kaplan-Meier estimates of probability of survival stratified according to chr.1p deletion signature (A), to chr.19 gain or chr.19q loss status signature (B), and to chr.1p/chr.19q losses signature (C).

FIG. 4.

EGFR, EGFRv3, and MGMT gene expressions comparisons in representative specimens using semiquantitative RT-PCR showing variable levels of expression depending on chr.7 and chr.10 status. GAPDH serves as a housekeeping gene for normalization.

FIG. 5.

(A) PTPRK gene expression comparison in representative specimens using real-time Q-PCR showing lower levels of PTPRK expression in various tumor specimen compared to nontumor brain samples (epilepsy biopsies; CNTR). ACG, astrocytoma grade II (n=5); AAC, anaplastic astrocytoma grade III (n=13); GBM, glioblastoma grade IV (n=29); ODG: oligodendroglioma grade II (n=6); AOD, anaplastic oligodendroglioma grade III (n=7). (B) Kaplan-Meier estimates of probability of survival stratified according to PTPRK genomic status.