A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastoma.
A novel genome-wide screen that combines patient outcome analysis with array comparative genomic hybridization and mRNA expression profiling was developed to identify genes with copy number alterations, aberrant mRNA expression, and relevance to survival in glioblastoma. The method led to the discovery of physical gene clusters within the cancer genome with boundaries defined by physical proximity, correlated mRNA expression patterns, and survival relatedness. These boundaries delineate a novel genomic interval called the functional common region (FCR). Many FCRs contained genes of high biological relevance to cancer and were used to pinpoint functionally significant DNA alterations that were too small or infrequent to be reliably identified using standard algorithms. One such FCR contained the EphA2 receptor tyrosine kinase. Validation experiments showed that EphA2 mRNA overexpression correlated inversely with patient survival in a panel of 21 glioblastomas, and ligand-mediated EphA2 receptor activation increased glioblastoma proliferation and tumor growth via a mitogen-activated protein kinase-dependent pathway. This novel genome-wide approach greatly expanded the list of target genes in glioblastoma and represents a powerful new strategy to identify the upstream determinants of tumor phenotype in a range of human cancers.
Liu
Fenghua
F
Department of Neurological Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Park
Peter J
PJ
Lai
Weil
W
Maher
Elizabeth
E
Chakravarti
Arnab
A
Durso
Laura
L
Jiang
Xiuli
X
Yu
Yi
Y
Brosius
Amanda
A
Thomas
Meredith
M
Chin
Lynda
L
Brennan
Cameron
C
DePinho
Ronald A
RA
Kohane
Isaac
I
Carroll
Rona S
RS
Black
Peter M
PM
Johnson
Mark D
MD
D001932:Brain Neoplasms / Q000201:enzymology* / Q000235:genetics* / Q000473:pathology; D048708:Cell Growth Processes / Q000235:genetics; D015894:Genome, Human; D005909:Glioblastoma / Q000201:enzymology* / Q000235:genetics* / Q000473:pathology; D006801:Humans; D020928:Mitogen-Activated Protein Kinases / Q000378:metabolism; D005810:Multigene Family; D009693:Nucleic Acid Hybridization; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D036104:Receptor, EphA2 / Q000096:biosynthesis / Q000235:genetics*
D012333:RNA, Messenger; D036104:Receptor, EphA2; D020928:Mitogen-Activated Protein Kinases