Dataset Information

Proteomic profiling of melanoma progression

ABSTRACT: Melanoma is one of the most aggressive malignancies. It is the second most common tumor in patients at the ages of 20-35 with increased prevalence in western countries. Patient prognosis largely depends on the tumor stage upon diagnosis, which is determined based on the depth of the primary tumor, ulceration and metastases. To date, only a few studies profiled melanoma proteomes. Here we assembled a panel of nine cell lines, including two melanocyte cultures, two cell lines originating from primary tumors, and five cell lines from metastatic lesions. We identified in total more than 9,000 proteins, and identified the processes that change during melanoma progression.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Melanocyte, Cell Culture

DISEASE(S): Melanoma

SUBMITTER: Tamar Geiger

LAB HEAD: Tamar Geiger

PROVIDER: PXD001048 | Pride | 2020-07-07

REPOSITORIES: Pride

ACCESS DATA

Similar Datasets

Project description:Melanoma genomes are often characterized by large numbers of sunlight-induced mutations. However, epigenetic alterations, in the form of aberrant DNA methylation patterns, are also abundant. Using MIRA-seq, we have carried out a comprehensive characterization of the DNA methylome in a series of metastatic melanoma samples and catalogued the methylation changes relative to normal melanocytes, the presumed cells of origin for these tumors. Individual melanoma tumors contained up to several thousand hypermethylated regions. We discovered 179 tumor-specific methylation peaks that were present in all (27/27) melanomas and may lend themselves as effective disease biomarkers, and 3124 methylation peaks were present in >40% of the tumors. We specifically examined the relationship between presence of the Polycomb mark, H3K27me3 in melanocytes and tumor-specific DNA methylation in melanoma. We found that 150 of the approximately 1,200 tumor-associated methylation peaks near transcription start sites (TSS) were H3K27me3-marked in melanocytes. Notably, DNA methylation in melanoma was specific for distinct H3K27me3 peaks rather than for H3K27me3-enriched regions with broad genomic coverage. Yet, there were also numerous H3K27me3 peak-associated TSS regions that were completely resistant to DNA methylation in tumors. Furthermore, a rather large group of genes became methylated in melanoma but lacked H3K27me3 in melanocytes. There was no relationship between presence of BRAF V600 mutations and the number of methylation peaks in individual tumors. Gene expression analysis showed a strong signature of upregulated immune response genes in melanomas presumably as a result of lymphocyte infiltration. Genes down-regulated in tumors were enriched for melanocyte differentiation and pigmentation factors. Overall, there was limited correlation between tumor-associated DNA methylation changes and changes in gene expression although distinct melanocyte differentiation genes including KIT, PAX3 and SOX10 became methylated and downregulated in melanoma. Genome-wide gene expression analysis of 17 melanomas and 3 melanocyte samples

Dataset Information

Proteomic profiling of melanoma progression

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure