| Abstract: |
Much emphasis has been placed on the identification, functional characterization, and therapeutic potential of somatic variants in tumor genomes. However, the majority of somatic variants lie outside coding regions and their role in cancer progression remains to be determined. In order to establish a system to test the functional importance of non-coding somatic variants in cancer, we created a low-passage cell culture of a metastatic melanoma tumor sample. As a foundation for interpreting functional assays, we performed whole-genome sequencing and analysis of this cell culture, the metastatic tumor from which it was derived, and the patient-matched normal genomes. When comparing somatic mutations identified in the cell culture and tissue genomes, we observe concordance at the majority of single nucleotide variants, whereas copy number changes are more variable. To understand the functional impact of non-coding somatic variation, we leveraged functional data generated by the ENCODE Project Consortium. We analyzed regulatory regions derived from multiple different cell types and found that melanocyte-specific regions are among the most depleted for somatic mutation accumulation. Significant depletion in other cell types suggests the metastatic melanoma cells de-differentiated to a more basal regulatory state. Experimental identification of genome-wide regulatory sites in two different melanoma samples supports this observation. Together, these results show that mutation accumulation in metastatic melanoma is nonrandom across the genome and that a de-differentiated regulatory architecture is common among different samples. Our findings enable identification of the underlying genetic components of melanoma and define the differences between a tissue-derived tumor sample and the cell culture created from it. Such information helps establish a broader mechanistic understanding of the linkage between non-coding genomic variations and the cellular evolution of cancer. © 2012 This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. |
| Keywords: |
adult; controlled study; human tissue; gene mutation; human cell; somatic mutation; missense mutation; polymorphism, single nucleotide; case report; gene; melanoma; melanocytes; genetic association; genetic variability; genome-wide association study; gene function; tumor cells, cultured; mutational analysis; carcinogenesis; cell specificity; cell type; genome analysis; gene identification; neoplasm metastasis; genome, human; genetic linkage; dna copy number variations; tissue specificity; regulatory sequences, nucleic acid; metastatic melanoma; copy number variation; cell dedifferentiation; focal adhesion kinase 2; a disintegrin and metalloproteinase 29 gene; protein tyrosine kinase 2b gene; somatic single nucleotide variant; dna, intergenic; primary cell culture
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