A prognostic signature of G2 checkpoint function in melanoma cell lines

Bernard Omolo, Craig Carson, Haitao Chu, Yingchun Zhou, Dennis A. Simpson, Jill E. Hesse, Richard S. Paules, Kristine C. Nyhan, Joseph G. Ibrahim, William K. Kaufmann

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


As DNA damage checkpoints are barriers to carcinogenesis, G2 checkpoint function was quantified to test for override of this checkpoint during melanomagenesis. Primary melanocytes displayed an effective G2 checkpoint response to ionizing radiation (IR)-induced DNA damage Thirty-seven percent of melanoma cell lines displayed a significant defect in G2 checkpoint function. Checkpoint function was melanoma subtype-specific with "epithelial-like" melanoma lines, with wild type NRAS and BRAF displaying an effective checkpoint, while lines with mutant NRAS and BRAF displayed defective checkpoint function. Expression of oncogenic B-Raf in a checkpoint-effective melanoma attenuated G2 checkpoint function significantly but modestly. Other alterations must be needed to produce the severe attenuation of G2 checkpoint function seen in some BRAF-mutant melanoma lines. Quantitative trait analysis tools identified mRNA species whose expression was correlated with G2 checkpoint function in the melanoma lines. A 165 gene signature was identified with a high correlation with checkpoint function (p < 0.004) and low false discovery rate (≤ 0.077). The G2 checkpoint gene signature predicted G2 checkpoint function with 77-94% accuracy. The signature was enriched in lysosomal genes and contained numerous genes that are associated with regulation of chromatin structure and cell cycle progression. The core machinery of the cell cycle was not altered in checkpoint-defective lines but rather numerous mediators of core machinery function were. When applied to an independent series of primary melanomas, the predictive G2 checkpoint signature was prognostic of distant metastasis-free survival. These results emphasize the value of expression profiling of primary melanomas for understanding melanoma biology and disease prognosis.

Original languageEnglish (US)
Pages (from-to)1071-1082
Number of pages12
JournalCell Cycle
Issue number7
StatePublished - Apr 1 2013

Bibliographical note

Funding Information:
We are grateful to Drs. Jayne Boyer and Leena Nylander-French for providing primary melanocyte cultures. Supported in part by PHS grants ES10126, CA16086 and ES014635. This research was supported in part by the Intramural Research Program of the NIH, National Institute of Environmental Health Sciences.


  • Ionizing radiation
  • Melanoma
  • Microarray
  • Oncogene


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