High-Resolution Genomic Copy Number Profiling of Glioblastoma Multiforme by Single Nucleotide Polymorphism DNA Microarray

Abstract

Glioblastoma multiforme (GBM) is an extremely malignant brain tumor. To identify new genomic alterations in GBM, genomic DNA of tumor tissue/explants from 55 individuals and 6 GBM cell lines were examined using single nucleotide polymorphism DNA microarray (SNP-Chip). Further gene expression analysis relied on an additional 56 GBM samples. SNP-Chip results were validated using several techniques, including quantitative PCR (Q-PCR), nucleotide sequencing, and a combination of Q-PCR and detection of microsatellite markers for loss of heterozygosity with normal copy number [acquired uniparental disomy (AUPD)]. Whole genomic DNA copy number in each GBM sample was profiled by SNP-Chip. Several signaling pathways were frequently abnormal. Either the p16(INK4A)/p15(INK4B)-CDK4/6-pRb or p14(ARF)-MDM2/4-p53 pathways were abnormal in 89% (49 of 55) of cases. Simultaneous abnormalities of both pathways occurred in 84% (46 of 55) samples. The phosphoinositide 3-kinase pathway was altered in 71% (39 of 55) GBMs either by deletion of PTEN or amplification of epidermal growth factor receptor and/or vascular endothelial growth factor receptor/platelet-derived growth factor receptor α. Deletion of chromosome 6q26-27 often occurred (16 of 55 samples). The minimum common deleted region included PARK2, PACRG, QKI, and PDE10A genes. Further reverse transcription Q-PCR studies showed that PARK2 expression was decreased in another collection of GBMs at a frequency of 61% (34 of 56) of samples. The 1p36.23 region was deleted in 35% (19 of 55) of samples. Notably, three samples had homozygous deletion encompassing this site. Also, a novel internal deletion of a putative tumor suppressor gene, LRP1B, was discovered causing an aberrant protein.AUPDs occurred in 58% (32 of 55) of the GBM samples and five of six GBM cell lines. A common AUPD was found at chromosome 17p13.3-12 (included p53 gene) in 13 of 61 samples and cell lines. Single-strand conformational polymorphism and nucleotide sequencing showed that 9 of 13 of these samples had homozygous p53 mutations, suggesting that mitotic recombination duplicated the abnormal p53 gene, probably providing a growth advantage to these cells. A significantly shortened survival time was found in patients with 13q14 (RB) deletion or 17p13.1 (p53) deletion/AUPD. Taken together, these results suggest that this technique is a rapid, robust, and inexpensive method to profile genome-wide abnormalities in GBM. (Mol Cancer Res 2009;7(5):665-77)

STAR RNA-binding protein Quaking suppresses cancer via stabilization of specific miRNA

“…As a first step in prioritizing such putative p53 targets for further study, their potential cancer relevance was determined through examination of various cancer genome data sets. These analyses revealed strikingly frequent focal deletions of chromosome 6q26-27, which includes QKI, in human primary GBM that are present in several of our array-CGH data sets (Maher et al 2006;Wiedemeyer et al 2008;Yin et al 2009). Subsequent analysis of the extensive multidimensional TCGA data sets showed loss of QKI expression in 92 out of 420 (22%) transcriptional profiles, deletion of QKI in 85 out of 420 (20%) array-CGH profiles, and QKI methylation (chromosome 6, base 163,755,107) in 50 out of 250 (20%) methylation profiles; mutation data for QKI have not been completed.…”

“…The Cancer Genome Atlas Project (TCGA) (The Cancer Genome Atlas Research Network 2008) has compiled a large collection of highresolution genomic data from clinically annotated tumor samples, providing an unprecedented framework for the rapid discovery of novel cancer genes guided by cancer gene alterations across multiple dimensions of the genome. Here, in the course of conducting a functional genomic screen for p53 targets and mining the TCGA glioblastoma multiforme (GBM) data set and others (Mulholland et al 2006;Wiedemeyer et al 2008;Yin et al 2009), we identified Quaking (QKI) as a potential tumor suppressor gene that is frequently deleted in GBM. The potential importance of QKI in GBM pathogenesis is further elevated by its direct regulation by the TP53 tumor suppressor, the most commonly mutated gene in primary GBM .…”

QKI-Mediated Alternative Splicing of the Histone Variant MacroH2A1 Regulates Cancer Cell Proliferation

“…This hypothesis finds additional support in two prior studies. First, the QKI gene is found on a region of chromosome 6 often deleted in glioblastoma multiforme (51). Additionally, QKI suppresses the growth of colon cancer cells in culture, which is exactly the phenotype we would expect from a splicing factor that enhances the splicing of macroH2A1.1 (50).…”

“…5B and C; also see Table S2 at the URL above). Second, two recent reports implicate QKI as a potential tumor suppressor (50,51). Finally, an interaction between QKI and macroH2A1 pre-mRNA was recently reported in a genome-wide screen for site-specific interactions between RNA-binding factors and total RNA called PAR-CLIP (27).…”

Alterações metabólicas e o papel da mitocôndria no processo de tumorigênese de astrocitomas humanos

“…Importantes vias, como a de p53, possuem anormalidades genéticas em 87% das amostras em GBMs secundários detectadas por microarray de DNA de polimorfismo (SNP-Chip) (Yin et al, 2009). As mutações somáticas de TP53 foram detectadas em 7,4% de GBM analisados, 27,3% em astrocitomas anaplásicos e 43% em astrocitomas de baixo grau em pacientes brasileiros (Uno et al, 2005).…”