Association of survival and disease progression with chromosomal instability: a genomic exploration of colorectal cancer.
During disease progression the cells that comprise solid malignancies undergo significant changes in gene copy number and chromosome structure. Colorectal cancer provides an excellent model to study this process. To indentify and characterize chromosomal abnormalities in colorectal cancer, we performed a statistical analysis of 299 expression and 130 SNP arrays profiled at different stages of the disease, including normal tissue, adenoma, stages 1-4 adenocarcinoma, and metastasis. We identified broad (> 1/2 chromosomal arm) and focal (< 1/2 chromosomal arm) events. Broad amplifications were noted on chromosomes 7, 8q, 13q, 20, and X and broad deletions on chromosomes 4, 8p, 14q, 15q, 17p, 18, 20p, and 22q. Focal events (gains or losses) were identified in regions containing known cancer pathway genes, such as VEGFA, MYC, MET, FGF6, FGF23, LYN, MMP9, MYBL2, AURKA, UBE2C, and PTEN. Other focal events encompassed potential new candidate tumor suppressors (losses) and oncogenes (gains), including CCDC68, CSMD1, POLR1D, and PMEPA1. From the expression data, we identified genes whose expression levels reflected their copy number changes and used this relationship to impute copy number changes to samples without accompanying SNP data. This analysis provided the statistical power to show that deletions of 8p, 4p, and 15q are associated with survival and disease progression, and that samples with simultaneous deletions in 18q, 8p, 4p, and 15q have a particularly poor prognosis. Annotation analysis reveals that the oxidative phosphorylation pathway shows a strong tendency for decreased expression in the samples characterized by poor prognosis.
Sheffer
Michal
M
Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel.
Bacolod
Manny D
MD
Zuk
Or
O
Giardina
Sarah F
SF
Pincas
Hanna
H
Barany
Francis
F
Paty
Philip B
PB
Gerald
William L
WL
Notterman
Daniel A
DA
Domany
Eytan
E
D043171:Chromosomal Instability / Q000235:genetics*; D002872:Chromosome Deletion; D015179:Colorectal Neoplasms / Q000235:genetics* / Q000473:pathology*; D018450:Disease Progression; D000089703:Fibroblast Growth Factor-23; D018628:Gene Dosage / Q000235:genetics; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D010084:Oxidation-Reduction; D010766:Phosphorylation; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics; D015996:Survival Rate
C000717427:FGF23 protein, human; D022661:RNA, Untranslated; D000089703:Fibroblast Growth Factor-23