Comprehensive molecular characterization of multifocal glioblastoma proves its monoclonal origin and reveals novel insights into clonal evolution and heterogeneity of glioblastomas

Abstract

Background.The evolution of primary glioblastoma (GBM) is poorly understood. Multifocal GBM (ie, multiple synchronous lesions in one patient) could elucidate GBM development.Methods.We present the first comprehensive study of 12 GBM foci from 6 patients using array-CGH, spectral karyotyping, gene expression arrays, and next-generation sequencing.Results.Multifocal GBMs genetically resemble primary GBMs. Comparing foci from the same patient proved their monoclonal origin. All tumors harbored alterations in the 3 GBM core pathways: RTK/PI3K, p53, and RB regulatory pathways with aberrations of EGFR and CDKN2A/B in all (100%) patients. This unexpected high frequency reflects a distinct genetic signature of multifocal GBMs and might account for their highly malignant and invasive phenotype. Surprisingly, the types of mutations in these genes/pathways were different in tumor foci from the same patients. For example, we found distinct mutations/aberrations in PTEN, TP53, EGFR, and CDKN2A/B, which therefore must have occurred independently and late during tumor development. We also identified chromothripsis as a late event and in tumors with wild-type TP53. Only 2 events were found to be early in all patients: single copy loss of PTEN and TERT promoter point mutations.Conclusions.Multifocal GBMs develop through parallel genetic evolution. The high frequency of alterations in 3 main pathways suggests that these are essential steps in GBM evolution; however, their late occurrence indicates that they are not founder events but rather subclonal drivers. This might account for the marked genetic heterogeneity seen in primary GBM and therefore has important implications for GBM therapy.

Tumor heterogeneity assessed by sequencing and fluorescencein situhybridization (FISH) data

“…We observe a pattern of focal CNAs consistent with those described previously in [21] based only on bulk and SCS data. Previous work showed that glioblastomas tend to display at least some chromosome-scale CNAs, such as chromosome 7 gain, chromosome 9p loss and chromosome 10 loss [11,12,1]. The inferred cell components here all show gain of chromosome 7 and loss of chromosome 9p, suggesting these are early events in the tumor's evolution.…”

“…We give it a probability β 2 of tetraploidy, corresponding top ii = 1. We then allow a probability β 3 (= 1 − β 1 − β 2 ) of some other ploidy, selected uniformly from [1,3,5,6,7,8]. Currently, β 1 = 60%, β 2 = 30%, β 3 = 10%.…”

Multifocal primary neuroblastoma tumor heterogeneity in siblings with co‐occurring PHOX2B and NF1 genetic aberrations

“…Despite the common somatic 17q gain, we found significant divergence of somatic CN and mutational variants across samples, similar to what has been described in multifocal lung cancer, 21 prostate cancer, 22 and glioblastoma, 23 suggesting true multifocal primary sites of disease with independent development of tumors rather than oligometastatic spread. All somatic mutations identified were present in no more than two samples, although several have been described to have oncogenic potential and relevance in neuroblastoma, including FBN1, 24,25 FLT4/VEGFR3, 26 and N4BP1 27 (Table S1).…”

The biology and mathematical modelling of glioma invasion: a review

“…It is commonly assumed that tumour heterogeneity arises either from a self-renewing cancer stem cell population or due to clonal competition for common resources driven by the acquisition and expansion of mutations in cancer cells [61,[69][70][71]. Recent clinical and experimental findings have revealed extensive genetic variations in glioma cells due to intra-tumoural evolution [63,64,67,72]. Besides the large genetic heterogeneity, interactions between glioma cells and with the surrounding brain parenchyma lead to functional and phenotypic diversity.…”