title: A prognostic signature of G(2) checkpoint function in melanoma cell lines.
abstract: As DNA damage checkpoints are barriers to carcinogenesis, G(2) checkpoint function was quantified to test for override of this checkpoint during melanomagenesis. Primary melanocytes displayed an effective G(2) checkpoint response to ionizing radiation (IR)-induced DNA damage. Thirty-seven percent of melanoma cell lines displayed a significant defect in G(2) 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 G(2) checkpoint function significantly but modestly. Other alterations must be needed to produce the severe attenuation of G(2) checkpoint function seen in some BRAF-mutant melanoma lines. Quantitative trait analysis tools identified mRNA species whose expression was correlated with G(2) 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 G(2) checkpoint gene signature predicted G(2) 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 G(2) 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.
authors: Division of Mathematics and Computer Science, University of South Carolina Upstate, Spartanburg, SC, USA.
authors: Bernard
authors: B
authors: Omolo
authors: Craig
authors: C
authors: Carson
authors: Haitao
authors: H
authors: Chu
authors: Yingchun
authors: Y
authors: Zhou
authors: Dennis A
authors: DA
authors: Simpson
authors: Jill E
authors: JE
authors: Hesse
authors: Richard S
authors: RS
authors: Paules
authors: Kristine C
authors: KC
authors: Nyhan
authors: Joseph G
authors: JG
authors: Ibrahim
authors: William K
authors: WK
authors: Kaufmann
mesh_terms: D002460:Cell Line; D004249:DNA Damage / Q000528:radiation effects; D059565:G2 Phase Cell Cycle Checkpoints / Q000528:radiation effects; D020558:GTP Phosphohydrolases / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008544:Melanocytes / Q000166:cytology / Q000378:metabolism* / Q000528:radiation effects; D008545:Melanoma / Q000378:metabolism* / Q000473:pathology; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics / Q000378:metabolism; D011839:Radiation, Ionizing; D059467:Transcriptome
chemical_list: D008565:Membrane Proteins; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf; D020558:GTP Phosphohydrolases; C579846:NRAS protein, human
keywords: G2 checkpoint; ionizing radiation; melanoma; microarray; oncogene