Cytogenetic and genomic profiles of 5 cancer stem-like cell lines from glioblastoma multiforme

Glioblastoma multiforme (GBM) is one of the most malignant brain tumors and is characterized by multiple genomic alterations such as chromosomal rearrangements and DNA copy number variations. Recent genome-wide studies show a remarkable genomic heterogeneity in GBM and the importance of giving an insight in cancer genome. We analyzed a small subpopulation of cells within the tumor, called cancer stem cells (CSCs), that are able to initiate and sustain tumor growth and recurrence. In particular, we analyzed five cancer stem-like cell lines from GBM to conventional cytogenetics (QFQ banding) and molecular cytogenetics techniques (FISH array, Human Genome CGH microarray kit 44K, Agilent Technologies). This approach allows evaluating recurrent cytogenetic and genomic alterations and also new aberrations in order to identify novel putative loci involved in GBMpathogenesis. The evaluation of chromosome number confirmed tumor heterogeneity as the modal number varied from near-diploid to tetraploid and allowed investigating cell line stability in vitro. Moreover, the karyotype analysis identified the most common chromosomal aberrations in GBM, such as polisomy of chromosome 7 (5/5) and loss of chromosome 10 (3/5). Molecular karyotype confirmed the conventional cytogenetic data and revealed, within the genomic heterogeneity, the presence of specific copy number alterations (CNAs). These CNAs map in loci usually associated with peculiar pathways involved in GBMpathogenesis: gain of whole chromosome 7 (5/5) and amplification of EGFR, complete loss of 9p21.3 (CDKN2A and CDKN2B genes, 4/5), pseudomonosomy for whole chromosome 10 loss (3/5), gain of 1q32.1 (MDM4, 2/5) and amplification of PDGFR gene (4q12, 2/5). This methodological approach allowed integrating different dimensions in genome study and delineating the major aberrations in the cytogenetic and genomic profiles of CSC from GBM