Defective cell cycle checkpoint functions in melanoma are associated with altered patterns of gene expression.
Defects in DNA damage responses may underlie genetic instability and malignant progression in melanoma. Cultures of normal human melanocytes (NHMs) and melanoma lines were analyzed to determine whether global patterns of gene expression could predict the efficacy of DNA damage cell cycle checkpoints that arrest growth and suppress genetic instability. NHMs displayed effective G1 and G2 checkpoint responses to ionizing radiation-induced DNA damage. A majority of melanoma cell lines (11/16) displayed significant quantitative defects in one or both checkpoints. Melanomas with B-RAF mutations as a class displayed a significant defect in DNA damage G2 checkpoint function. In contrast the epithelial-like subtype of melanomas with wild-type N-RAS and B-RAF alleles displayed an effective G2 checkpoint but a significant defect in G1 checkpoint function. RNA expression profiling revealed that melanoma lines with defects in the DNA damage G1 checkpoint displayed reduced expression of p53 transcriptional targets, such as CDKN1A and DDB2, and enhanced expression of proliferation-associated genes, such as CDC7 and GEMININ. A Bayesian analysis tool was more accurate than significance analysis of microarrays for predicting checkpoint function using a leave-one-out method. The results suggest that defects in DNA damage checkpoints may be recognized in melanomas through analysis of gene expression.
Kaufmann
William K
WK
Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. wkarlk@med.unc.edu
Nevis
Kathleen R
KR
Qu
Pingping
P
Ibrahim
Joseph G
JG
Zhou
Tong
T
Zhou
Yingchun
Y
Simpson
Dennis A
DA
Helms-Deaton
Jennifer
J
Cordeiro-Stone
Marila
M
Moore
Dominic T
DT
Thomas
Nancy E
NE
Hao
Honglin
H
Liu
Zhi
Z
Shields
Janiel M
JM
Scott
Glynis A
GA
Sharpless
Norman E
NE
D018797:Cell Cycle Proteins / Q000235:genetics; D045744:Cell Line, Tumor; D002478:Cells, Cultured; D043171:Chromosomal Instability; D050759:Cyclin-Dependent Kinase Inhibitor p21 / Q000235:genetics; D053903:DNA Breaks, Double-Stranded; D004249:DNA Damage; D004268:DNA-Binding Proteins / Q000235:genetics; D016193:G1 Phase / Q000502:physiology*; D016195:G2 Phase / Q000502:physiology*; D064248:Geminin; D020869:Gene Expression Profiling; D006801:Humans; D008544:Melanocytes / Q000166:cytology; D008545:Melanoma / Q000235:genetics / Q000378:metabolism / Q000473:pathology*; D009154:Mutation; D010766:Phosphorylation; D017346:Protein Serine-Threonine Kinases / Q000235:genetics; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics; D016159:Tumor Suppressor Protein p53 / Q000502:physiology
C493956:CDKN1A protein, human; D018797:Cell Cycle Proteins; D050759:Cyclin-Dependent Kinase Inhibitor p21; C117669:DDB2 protein, human; D004268:DNA-Binding Proteins; C577995:GMNN protein, human; D064248:Geminin; D016159:Tumor Suppressor Protein p53; C068619:CDC7 protein, human; C482119:BRAF protein, human; D017346:Protein Serine-Threonine Kinases; D048493:Proto-Oncogene Proteins B-raf