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Original Contribution
July 15, 2009

A Network Model of a Cooperative Genetic Landscape in Brain Tumors

Author Affiliations

Author Affiliations: Department of Neurological Surgery, Northwestern Brain Tumor Institute, Lurie Center for Cancer Genetics Research and Center for Genetic Medicine (Drs M. Bredel, Chandler, and Yadav and Ms Renfrow), and Department of Preventive Medicine (Dr Scholtens), Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; Department of Neurosurgery (Drs M. Bredel and Harsh), Oncology Division, and Departments of Medicine (Drs C. Bredel and Sikic), Pathology (Dr Vogel), and Health Research and Policy and Statistics (Dr Tibshirani), Stanford University School of Medicine, Stanford, California; Department of General Neurosurgery, Neurocenter and Comprehensive Cancer Center Freiburg, University of Freiburg, Freiburg, Germany (Drs M. Bredel and C. Bredel); and Ina Levine Brain Tumor Center, Neuro-Oncology and Neurosurgery Research, Barrow Neurological Institute of St Joseph's Medical Center, Phoenix, Arizona (Dr Scheck).

JAMA. 2009;302(3):261-275. doi:10.1001/jama.2009.997
Abstract

Context  Gliomas, particularly glioblastomas, are among the deadliest of human tumors. Gliomas emerge through the accumulation of recurrent chromosomal alterations, some of which target yet-to-be-discovered cancer genes. A persistent question concerns the biological basis for the coselection of these alterations during gliomagenesis.

Objectives  To describe a network model of a cooperative genetic landscape in gliomas and to evaluate its clinical relevance.

Design, Setting, and Patients  Multidimensional genomic profiles and clinical profiles of 501 patients with gliomas (45 tumors in an initial discovery set collected between 2001 and 2004 and 456 tumors in validation sets made public between 2006 and 2008) from multiple academic centers in the United States and The Cancer Genome Atlas Pilot Project (TCGA).

Main Outcome Measures  Identification of genes with coincident genetic alterations, correlated gene dosage and gene expression, and multiple functional interactions; association between those genes and patient survival.

Results  Gliomas select for a nonrandom genetic landscape—a consistent pattern of chromosomal alterations—that involves altered regions (“territories”) on chromosomes 1p, 7, 8q, 9p, 10, 12q, 13q, 19q, 20, and 22q (false-discovery rate–corrected P<.05). A network model shows that these territories harbor genes with putative synergistic, tumor-promoting relationships. The coalteration of the most interactive of these genes in glioblastoma is associated with unfavorable patient survival. A multigene risk scoring model based on 7 landscape genes (POLD2, CYCS, MYC, AKR1C3, YME1L1, ANXA7, and PDCD4) is associated with the duration of overall survival in 189 glioblastoma samples from TCGA (global log-rank P = .02 comparing 3 survival curves for patients with 0-2, 3-4, and 5-7 dosage-altered genes). Groups of patients with 0 to 2 (low-risk group) and 5 to 7 (high-risk group) dosage-altered genes experienced 49.24 and 79.56 deaths per 100 person-years (hazard ratio [HR], 1.63; 95% confidence interval [CI], 1.10-2.40; Cox regression model P = .02), respectively. These associations with survival are validated using gene expression data in 3 independent glioma studies, comprising 76 (global log-rank P = .003; 47.89 vs 15.13 deaths per 100 person-years for high risk vs low risk; Cox model HR, 3.04; 95% CI, 1.49-6.20; P = .002) and 70 (global log-rank P = .008; 83.43 vs 16.14 deaths per 100 person-years for high risk vs low risk; HR, 3.86; 95% CI, 1.59-9.35; P = .003) high-grade gliomas and 191 glioblastomas (global log-rank P = .002; 83.23 vs 34.16 deaths per 100 person-years for high risk vs low risk; HR, 2.27; 95% CI, 1.44-3.58; P<.001).

Conclusions  The alteration of multiple networking genes by recurrent chromosomal aberrations in gliomas deregulates critical signaling pathways through multiple, cooperative mechanisms. These mutations, which are likely due to nonrandom selection of a distinct genetic landscape during gliomagenesis, are associated with patient prognosis.

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