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Series GSE31879 Query DataSets for GSE31879
Status Public on Dec 31, 2012
Title Alterations of methylome and transcriptome in human melanoma: the inverse relationship between epigenome integrity and BRAF mutation
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Expression profiling by array
Summary Melanoma is the deadliest form of skin cancer with rising incidence and mortality rates. Oncogenic mutation in BRAF gene is the single most frequent genetic alteration in human melanoma; however, this event per se is not sufficient to produce melanoma in vivo. We have investigated whether epigenetic changes, specifically aberrant DNA methylation and dysregulation of gene expression, alone or in combination with this genetic event, are involved in the genesis of human melanoma. We have constructed the whole ‘‘of primary human melanomas in relation to their BRAF mutational status. Our methylation profiling identified a large number of hyper- or hypomethylated genes in melanoma tumors, many of which being novel and having the potential to serve as biomarkers. Gene ontology analysis revealed that gene categories involved in neuronal cell morphology and development, and skin and neurological disorders were highly enriched. Frequently methylated targets included developmental regulatory transcription factors and homeobox genes, which are mostly subjected to bivalent histone marking and Polycomb occupancy in embryonic stem cells. Notably, several genes involved in the MEK-ERK and the PI3K pathways, two of the most frequently perturbed pathways in human melanoma, showed extensive methylation changes. Gene expression profiling identified a long list of dysregulated genes, many of which being involved in melanocytes development and differentiation, and showing concomitant aberrant DNA methylation. Sub-typing of the melanoma tumors based on BRAF mutational status revealed that tumors with a mutated BRAF had distinctive and more pronounced changes in both DNA methylation and gene expression profiles than tumors carrying the wildtype BRAF. The differentially compromised methylome and transcriptome of melanomas (dependent on BRAF mutation) deserves special attention because many epigenetic alterations, including DNA methylation-mediated regulation of gene expression, are potentially reversible. The dichotomous integrity of epigenome in human melanoma holds great promise for the field of personalized medicine.
Overall design Methylome: Eleven primary human melanoma speciemens versus five normal human melanocyte samples. Transcriptome: Ten primary human melanoma speciemens versus four normal human melanocyte samples
Contributor(s) Tommasi S, Zheng A, Li AX, Wu X, Besaratinia A
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Submission date Sep 06, 2011
Last update date Mar 25, 2019
Contact name Arthur Li
Organization name City of Hope
Street address 1500 E Duarte Rd
City Duarte
ZIP/Postal code 91010
Country USA
Platforms (2)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
GPL13118 NimbleGen Human DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Array [100718_HG18_CpG_Refseq_Prom_MeDIP]
Samples (30)
GSM790527 Melanoma (methylome) Mel.1
GSM790528 Melanoma (methylome) Mel.2
GSM790529 Melanoma (methylome) Mel.3
BioProject PRJNA145237

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE31879_RAW.tar 724.5 Mb (http)(custom) TAR (of CEL, GFF, PAIR)
GSE31879_mutational_status.pdf.gz 85.5 Kb (ftp)(http) PDF
Processed data included within Sample table

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