Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA237203 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We investigated whether methylation in primary melanomas is associated with tumor pathologic features or defines subgroups of primary melanomas 47 primary cutaneous melanomas were analyzed using the Illumina GoldenGate Cancer Panel I methylation array
2015-06-15 | E-GEOD-54623 | biostudies-arrayexpress
Project description:Epigenetic alterations play significant roles in the melanoma tumorigenesis and malignant progression. We profiled genome-wide promoter DNA methylation patterns of melanoma cells deribed from primary lesions of Radial Growrth phase (RGP) and Vertical Growth Phase (VGP), metastatic lesions, and primary normal melanocytes by interrogating 14,495 genes using Illumina bead chip technology. By comparative analysis of the promoter methylation profiles, we identified epigenetically silenced gene signatures that potentially associated with malignant melanoma progression. Bisulphite converted genomic DNA from a group of melanoma cells representing pathologic stages of melanoma progression (3 cell lines derived from RGP melanoma lesions, 4 cell lines derived from VGP lesions, and 3 melastatic melanomas) and normal human primary melanocytes isolated from lightly pigmented adult skin were hybridized to Illumina's Infinium HumanMethylation27 BeadChips
2013-12-20 | E-GEOD-53516 | biostudies-arrayexpress
Project description:We investigated whether methylation in primary melanomas is associated with tumor pathologic features or defines subgroups of primary melanomas
2015-06-15 | GSE54623 | GEO
Project description:The implication of epigenetic alterations in the pathogenesis of melanoma is increasingly recognized. Here we performed genome-wide DNA methylation analysis of primary cutaneous melanoma and benign melanocytic naevus interrogating 14,495 genes using beadchip technology. This first genome-wide view of promoter methylation in primary cutaneous melanoma revealed an array of recurrent DNA methylation alterations with potential diagnostic applications. Among 106 frequently hypermethylated genes there were many novel methylation targets and tumor suppressor genes. Highly recurrent methylation of the HOXA9, MAPK13, CDH11, PLEKHG6, PPP1R3C and CLDN11genes was established. Promoter methylation of MAPK13, encoding p38?, was present in 67% of primary and 85% of metastatic melanomas. Restoration of MAPK13 expression in melanoma cells exhibiting epigenetic silencing of this gene reduced proliferation, indicative of tumor suppressive functions. This study demonstrates that DNA methylation alterations are widespread in melanoma and suggests that epigenetic silencing of MAPK13 contributes to melanoma progression. Bisulphite converted genomic DNA from 5 fresh-frozen benign naevus and 24 fresh-frozen primary melanoma biopsy samples were hybridised to Illumina's Infinium HumanMethylation27 Beadchips
2013-04-24 | E-GEOD-45266 | biostudies-arrayexpress
Project description:In this experiment, FFPE samples of 41 primary cutaneous melanoma, 2 metastatic melanoma and 6 normal skin were used for DNA extraction and genotyping by Affymetrix OncoScan FFPE Assay, in order to define chromosomal alterations in copy number and loss of heterozygosity. Genomic damage was then correlated with clinical features of melanoma.
2015-11-01 | E-MTAB-3481 | biostudies-arrayexpress
Project description:The implication of epigenetic alterations in the pathogenesis of melanoma is increasingly recognized. Here we performed genome-wide DNA methylation analysis of primary cutaneous melanoma and benign melanocytic naevus interrogating 14,495 genes using beadchip technology. This first genome-wide view of promoter methylation in primary cutaneous melanoma revealed an array of recurrent DNA methylation alterations with potential diagnostic applications. Among 106 frequently hypermethylated genes there were many novel methylation targets and tumor suppressor genes. Highly recurrent methylation of the HOXA9, MAPK13, CDH11, PLEKHG6, PPP1R3C and CLDN11genes was established. Promoter methylation of MAPK13, encoding p38?, was present in 67% of primary and 85% of metastatic melanomas. Restoration of MAPK13 expression in melanoma cells exhibiting epigenetic silencing of this gene reduced proliferation, indicative of tumor suppressive functions. This study demonstrates that DNA methylation alterations are widespread in melanoma and suggests that epigenetic silencing of MAPK13 contributes to melanoma progression.
2013-04-24 | GSE45266 | GEO
Project description:Epigenetic alterations play significant roles in the melanoma tumorigenesis and malignant progression. We profiled genome-wide promoter DNA methylation patterns of melanoma cells deribed from primary lesions of Radial Growrth phase (RGP) and Vertical Growth Phase (VGP), metastatic lesions, and primary normal melanocytes by interrogating 14,495 genes using Illumina bead chip technology. By comparative analysis of the promoter methylation profiles, we identified epigenetically silenced gene signatures that potentially associated with malignant melanoma progression.
2013-12-20 | GSE53516 | GEO
Project description:Brain metastases of melanoma are associated with therapy resistance and poor prognosis. It is not fully understood whether and how the selection of cells capable of metastasizing into the brain is accompanied by the establishment of specific features. For the investigation of these questions, we made use of previously described xenograft mouse models for primary human melanoma cells distinguishing cutaneous from cerebellar metastases from the same genetic background. Previous experiments suggested that cultured cells derived from these xenografts still maintain properties characteristic for the microenvironment of the originating metastases. Such corresponding pairs of metastatic cells were obtained from four individual donors, resulting in eight cell-lines presently investigated with regard to molecular properties characteristic for metastasis. Label free proteome profiling revealed significant alterations when comparing corresponding pairs of cutaneous and cerebellar metastases from the same donor. Molecules previously associated with metastasis such as cell adhesion molecules, immune regulators, epithelial mesenchymal transition markers, stem cell markers, redox regulators and cytokines were found differently expressed. This was also observed with regard to eicosanoids considered relevant for metastasis such as PGE2 and 12-HETE. However, no commonalities in the molecular characteristics of cerebellar metastases were identified in all four donors. Multiparametric morphological analysis of cells also revealed alterations associated with the kind of metastases, while lacking uniformity. In conclusion, here we describe that xenografted melanoma cells derived from two different microenvironments, i.e. cutaneous and cerebellar metastases, display significant alterations in the expression of molecules associated with metastastic properties. The observed lack of uniformity suggests that metastatic cells may find individual strategies to adapt to their microenvironmental challenges accompanied by the establishment of individual cell characteristics.
2020-01-08 | PXD013765 | Pride
Project description:Genomic profiles comparing 23 nevi with a pool of primary cutaneous melanoma
2009-04-16 | E-TABM-3 | biostudies-arrayexpress
Project description:Melanoma is one of the most aggressive and treatment-resistant cancers. It represents the most life-threatening neoplasm of the skin, and its incidence has been increasing for the last three decades. Melanoma evolves from the local transformation of melanocytes to primary tumors, which can metastasize to multiple organs. Brain metastases represent one of the most significant causes of death in cutaneous melanoma patients. Despite aggressive multi-modality threapy, patients with melanoma brain metastasis have a median survival of less than a year, with a majority of these patients dying as a result of their intracranial disease. We aimed to find brain metastasis-specific molecular markers. To identify alterations in DNA methylation related to brain metastasis, we used Illumina 450K BeadChips to assess differentially methylated regions in melanocytes, primary melanomas, lymph node metastases, and brain metastases. Bisulphite-converted DNA from 40 specimens was hybridised to the Illumina Infinium 450k Human Methylation BeadChip.
2013-09-19 | E-GEOD-44661 | biostudies-arrayexpress