Melan-OMICS: whole-exome and transcriptome sequencing to dissect molecular complexity of cutaneous malignant melanoma

Cutaneous melanoma is the most fatal skin cancer and, although some effective molecular therapies exist, novel targets and drugs are still needed. To provide new insights for novel targets discovery, we performed an extensive characterization by next-generation sequencing (NGS) of a collection of melanoma cell lines derived from metastatic cases. Samples were profiled by whole-exome sequencing (WES) and RNA-sequencing using Illumina technology. Starting from WES data, we developed a bioinformatics pipeline to catalogue 2,172 novel mutations affecting genes in melanoma key pathways targeted by current therapies (MAPK and glutamate pathways) as well as genes never described for melanoma [Cifola, 2013]. Moreover, WES data were used to perform copy number alteration (CNA) analysis using a novel software developed by us, called Excavator, which is very sensitive and precise in DNA copies estimation even in situations of great sample heterogeneity [Magi, 2013]. CNA results were concordant with 250K SNP Array data and used to explore CN state of mutated genes. To collect and share these results, we created a Melanoma Exome Database (https://155.253.6.64/ MExDB/). On the same samples, we also carried out RNA-sequencing and performed both a traditional gene expression analysis and more sophisticated structural evaluations. Focusing on fusion transcripts, we identified 72 putative events generated by either inter-chromosomal translocations or intra-chromosomal rearrangements, recently defined “conjoined genes” and representing an additional gene regulation mechanism. Globally, NGS proved to be extremely powerful to dissect cancer complexity at both genomic and transcriptomic levels, and to identify novel potential targets for personalized treatment of cutaneous melanoma.