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An epigenetic gene signature underlies phenotype switching in early stage melanomas [ChIP-seq]

ABSTRACT: A 122-epigenetic gene signature distinguished low- versus high-risk early stage melanomas. We sought to validate the signature, examined clinical correlates in a cohort of primary melanomas of the skin, and studied the underlying transcriptomic aberrations and changes in chromatin in cell lines representing these two groups. H3K27Ac ChipSeq profiles of primary human melanoma cell lines (n=4) as well as corresponding input samples were generated by deep sequencing using Illumina NextSeq500. Purpose: The goals of this study are to identify H3K27Ac differential peak expression between two groups of melanoma cell lines (Epgn1 and Epgn3) and relate this data to RNASeq. Methods: H3K27Ac ChipSeq was performed on 4 melanoma cell lines by deep sequencing 75bp single end reads using Illumina NextSeq500. Reads were aligned and counts called using____. The sequence reads that passed quality filters were analyzed. Results: Using an optimized data analysis workflow, we mapped about 40 million reads per Chip sample and 60 million reads per input sample to the human genome (build _____). Conclusions: Our study allowed us to identify differentially expressed peaks between two classes of melanoma cell lines and relate this information to differential gene expression. Further in vitro and in vivo assays using some of the candidate genes identified will allow us to more fully understand primary melanoma progression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE197235 | GEO | 2024/05/08

REPOSITORIES: GEO

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Next Generation Sequencing of Primary Melanocytes, Epgn1, and Epgn3 Melanoma Cell lines [RNA-seq]

Project description:Purpose: The goals of this study are to identify differentially expressed genes between two groups of melanoma cell lines (Epgn1 and Epgn3) as compared to control melanocytes. Methods: Melanoma cell line profiles of control melanocytes and primary human cell lines were generated by deep sequencing 75bp paired end reads, in triplicate, using Illumina NextSeq500. Reads were aligned and counts called using STAR. The sequence reads that passed quality filters were analyzed at the transcript isoform level. Results: Using an optimized data analysis workflow, we mapped about 35 million reads per sample to the human genome (build hg37). We identified 4566 transcripts which showed differential expression between groups Epgn1 and Epgn2, with a log fold change ≥2 and p value <=0.005. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to melanoma progression. Conclusions: Our study allowed us to identify differentially expressed genes between two classes of melanoma cell lines as well as control melanocytes. Further in vitro and in vivo assays using some of the candidate genes identified will allow us to more fully understand primary melanoma progression.

2024-05-08 | GSE198425 | GEO

A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation [human cell line ChIP-seq]

Project description:We report the distribution of H3K27Ac histone marks in multiple human melanoma cell lines with the aim of identifying super-enhancer regions and regions of interest. Also performed ChipSeq for H3K4Me1 to identify active enhancers in a representative human melanoma cell line, A375.

2016-02-01 | GSE75352 | GEO

SATB2 induces transcriptional programs in melanoma that lead to metastatic behavior [ChIP-Seq]

Project description:We report the distribution of human SATB2 in a primary zebrafish melanoma that overexpresses human SATB2, and H3K27Ac histone marks in zebrafish melanomas overexpressing either EGFP (control) or human SATB2.

2021-02-08 | GSE77921 | GEO

A novel epigenetic regulated gene and involved in phenotypic switch classifies primary melanomas depending on the aggressiveness grade (gene expression)

Project description:Loss of methylation of a GTPase-activating protein in melanoma mediates higher proliferation, lower migration, and agressiveness of primary melanomas. Gene wide expression analysis of melanoma and breast primary and metastatic related tumorigenic cell lines.

2015-05-11 | E-GEOD-46521 | biostudies-arrayexpress

A novel epigenetic regulated gene and involved in phenotypic switch classifies primary melanomas depending on the aggressiveness grade (Illumina)

Project description:Loss of methylation of a GTPase-activating protein in melanoma mediates higher proliferation, lower migration, and aggressiveness of primary melanomas. Sequencing of bisulfite converted DNA and array based analysis of melanoma, breast, and colon primary and metastatic related tumorigenic cell lines.

2015-05-11 | E-GEOD-46419 | biostudies-arrayexpress

Treatment of melanoma cell lines with CCG-222740

Project description:The Ras/MEK/ERK pathway has been the primary focus of targeted therapies in melanoma, given that it is aberrantly activated in almost 80% of human cutaneous melanomas (~50% BRAFV600 mutations and ~30% NRAS mutations). While targeted therapies have yielded success in BRAFV600 mutant melanoma patients, such therapies have been ineffective in NRAS mutant melanomas in part due to their cytostatic effects and primary resistance in this patient population. Here, we demonstrate that increased Rho/MRTF-pathway activation correlates with high intrinsic resistance to trametinib, a MEK inhibitor, in a panel of NRAS mutant melanoma cell lines. Combination of trametinib with the Rho/MRTF-pathway inhibitor, CCG-222740, synergistically reduced cell viability in NRAS mutant melanoma cell lines in vitro. Furthermore, the combination of CCG-222740 with trametinib induced apoptosis and reduced clonogenicity in the highly trametinib-resistant SK-Mel-147 cells. These findings suggest a role of the Rho/MRTF-pathway in high intrinsic trametinib resistance to a subset of NRAS mutant melanoma cell lines and highlights the potential of concurrently targeting the Rho/MRTF-pathway and MEK in NRAS mutant melanomas.

2019-07-16 | GSE134320 | GEO

Treatment of melanoma cell lines with CCG-222740

2018-12-30 | GSE115938 | GEO

Genome-wide promoter methylation analysis associated with malignant melanoma progression

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

methylation analysis in melanomas and melanocytes from the same patient

Project description:DNA methylation is considered the primary epigenetic mechanism underlying the development of malignant melanoma. Since DNA methylation can be influenced by environmental factors, it is preferable to compare cancer and normal cells from the same patient. Here, we employed a novel epidermal sheet cultivation technique to isolate normal melanocytes from unaffected sites of melanoma patients and compared the methylation status with melanoma tissues from the same individuals. We also analyzed primary and metastatic melanoma samples, three commercially available melanocytes, and four melanoma cell lines. Cluster analysis of DNA methylation data classified freshly isolated melanomas and melanocytes into the same group, whereas the four melanoma cell lines were clustered together in a distant clade. Moreover, our analysis discovered methylation at several novel loci (KRTCAP3, AGAP2, ZNF490), in addition to those identified in previous studies (COL1A2, GPX3); however, the latter two were not observed in fresh melanoma samples. Subsequent studies revealed that NPM2 was hypermethylated and downregulated in melanomas, which was consistent with previous reports and indicated that NPM2 immunoreactivity could be used to differentiate melanomas from normal melanocytes or benign disease. Our results highlight the importance of using matched fresh melanoma and melanocyte samples in epigenetic studies. Illumina Infinium 450k Human Methylation Beadchip

2018-11-29 | GSE122909 | GEO

expression analysis in melanomas and melanocytes from the same patient

2018-11-29 | GSE122907 | GEO

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