Abstract 3234: Comparative oncogenomics: identifying melanoma drivers from zebrafish to humans.
Authors: Richard M. White, Erin Langdon, Charles Kaufman, Ellen van Rooijen, Jennifer Yen, Peter Van Loo, Leonard Zon
Journal: Cancer Research (2013)

Abstract The elucidation of core networks driving tumorigenesis is greatly enhanced by studying tumors from multiple species. A comparison of tumors between evolutionarily distant organisms such as humans and fish offers a particularly powerful method to identify such core functionalities. In the past several years, the zebrafish has emerged as an important vertebrate model of cancer because it develops tumors that are histologically and functionally similar to the human disease. Overexpression of the BRAFV600E oncogene under the melanocyte-specific mitf promoter leads to a 100% penetrant melanoma in the context of p53 loss of function. We have previously shown that these zebrafish tumors exhibit characteristics of neural crest progenitors, rather than differentiated melanocytes, similar to many human melanomas which also overexpress the neural crest markers sox10 and ednrb. To identify the genomic lesions that are common to both species, we are performing RNA and DNA-sequencing of the zebrafish tumors and comparing them to human melanoma resequencing samples to identify common driver events. To facilitate this, we have developed technologies for both short and long term culture of zebrafish melanoma cell lines, along with normal tissue from each individual animal. One such melanoma line, ZMEL1, has been comprehensively characterized. RNA-seq demonstrated upregulation of neural crest genes such as ednrb, and pathway analysis indicated enrichment for ERK/MAP kinase and PI3K/AKT signaling pathways, and these tumors are sensitive to inhibition by the BRAF inhibitor PLX4720. Whole-genome sequencing (WGS) was performed on tumor cell line and matched normal tissue to a depth of 39X coverage on the Illumina platform. A total of 5193 single basepair mutations were identified, of which 2% were found in the coding region, 41% in intronic regions and 56% in the intergenic DNA. Within the coding region, 25% were G&amp;gt;C and 18% T&amp;gt;C substitutions, with approximately equal number of non-synonymous to silent mutations. Coding mutations in several genes such as rps6kb1b and plb1 are of particular interest because of their reported mutation in human cancer as well. 35 regions of copy number changes were found, comprising over 600 genes, and these include amplification of known oncogenes such as SETDB1. Functional analysis of the genomic changes common to both zebrafish and human tumors is now being undertaken using in vitro and in vivo melanoma models. In summary, comparative oncogenomics between zebrafish and human melanoma provides a powerful method for filtering the vast number of changes down to a list of manageable, testable hypotheses. This method can be broadly applied to other tumors types. Citation Format: Richard M. White, Erin Langdon, Charles Kaufman, Ellen van Rooijen, Jennifer Yen, Peter Van Loo, Leonard Zon. Comparative oncogenomics: identifying melanoma drivers from zebrafish to humans. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3234. doi:10.1158/1538-7445.AM2013-3234 Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.