Melanoma genome evolution across species.

TitleMelanoma genome evolution across species.
Publication TypeJournal Article
Year of Publication2017
AuthorsKansler ER, Verma A, Langdon EM, Simon-Vermot T, Yin A, Lee W, Attiyeh M, Elemento O, White RM
JournalBMC Genomics
Date Published2017 02 07
KeywordsAnimals, Cell Transformation, Neoplastic, Cluster Analysis, Disease Models, Animal, Drug Resistance, Neoplasm, Evolution, Molecular, Genetic Association Studies, Genetic Predisposition to Disease, Genome, Genomics, High-Throughput Nucleotide Sequencing, Humans, Melanoma, Mutation, Signal Transduction, Species Specificity, Zebrafish

BACKGROUND: Cancer genomes evolve in both space and time, which contributes to the genetic heterogeneity that underlies tumor progression and drug resistance. In human melanoma, identifying mechanistically important events in tumor evolution is hampered due to the high background mutation rate from ultraviolet (UV) light. Cross-species oncogenomics is a powerful tool for identifying these core events, in which transgenically well-defined animal models of cancer are compared to human cancers to identify key conserved alterations.

RESULTS: We use a zebrafish model of tumor progression and drug resistance for cross-species genomic analysis in melanoma. Zebrafish transgenic tumors are initiated with just 2 genetic lesions, BRAF and p53, yet take 4-6 months to appear, at which time whole genome sequencing demonstrated >3,000 new mutations. An additional 4-month exposure to the BRAF inhibitor vemurafenib resulted in a highly drug resistant tumor that showed 3 additional new DNA mutations in the genes BUB1B, PINK1, and COL16A1. These genetic changes in drug resistance are accompanied by a massive reorganization of the transcriptome, with differential RNA expression of over 800 genes, centered on alterations in cAMP and PKA signaling. By comparing both the DNA and mRNA changes to a large panel of human melanomas, we find that there is a highly significant enrichment of these alterations in human patients with vemurafenib resistant disease.

CONCLUSIONS: Our results suggest that targeting of alterations that are conserved between zebrafish and humans may offer new avenues for therapeutic intervention. The approaches described here will be broadly applicable to the diverse array of cancer models available in the zebrafish, which can be used to inform human cancer genomics.

Alternate JournalBMC Genomics
PubMed ID28173755
PubMed Central IDPMC5297047