Integrative Genome Comparison of Primary and Metastatic Melanomas

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Integrative Genome Comparison of Primary and Metastatic Melanomas

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Title: Integrative Genome Comparison of Primary and Metastatic Melanomas
Author: Kabbarah, Omar; Nogueira, Cristina; Feng, Bin; Bosenberg, Marcus; Scott, Kenneth L.; Xiao, Yonghong; Cordon-Cardo, Carlos; Wagner, Stephan N.; Brennan, Cameron; Nazarian, Rosalynn; Wu, Min; Kwong, Lawrence Noc-Woon; Granter, Scott R.; Ramaswamy, Sridhar; Golub, Todd R.; Duncan, Lyn M.; Chin, Lynda

Note: Order does not necessarily reflect citation order of authors.

Citation: Kabbarah, Omar, Cristina Nogueira, Bin Feng, Rosalynn M. Nazarian, Marcus Bosenberg, Min Wu, Kenneth L. Scott, et al. 2010. Integrative genome comparison of primary and metastatic melanomas. PLoS ONE 5(5): e10770.
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Abstract: A cardinal feature of malignant melanoma is its metastatic propensity. An incomplete view of the genetic events driving metastatic progression has been a major barrier to rational development of effective therapeutics and prognostic diagnostics for melanoma patients. In this study, we conducted global genomic characterization of primary and metastatic melanomas to examine the genomic landscape associated with metastatic progression. In addition to uncovering three genomic subclasses of metastastic melanomas, we delineated 39 focal and recurrent regions of amplification and deletions, many of which encompassed resident genes that have not been implicated in cancer or metastasis. To identify progression-associated metastasis gene candidates, we applied a statistical approach, Integrative Genome Comparison (IGC), to define 32 genomic regions of interest that were significantly altered in metastatic relative to primary melanomas, encompassing 30 resident genes with statistically significant expression deregulation. Functional assays on a subset of these candidates, including MET, ASPM, AKAP9, IMP3, PRKCA, RPA3, and SCAP2, validated their pro-invasion activities in human melanoma cells. Validity of the IGC approach was further reinforced by tissue microarray analysis of Survivin showing significant increased protein expression in thick versus thin primary cutaneous melanomas, and a progression correlation with lymph node metastases. Together, these functional validation results and correlative analysis of human tissues support the thesis that integrated genomic and pathological analyses of staged melanomas provide a productive entry point for discovery of melanoma metastases genes.
Published Version: doi://10.1371/journal.pone.0010770
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