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Transcription profiling of normal human melanocytes and melanoma cell lines from advanced lesions

ABSTRACT: Affymetrix oligonucleotide microarrays were used to assess global differential gene expression comparing normal human melanocytes with six independent melanoma cell strains from advanced lesions. The data, validated at the protein level for selected genes, confirmed the overexpression in melanoma cells relative to normal melanocytes of several genes in the growth factor/receptor family that confer growth advantage and metastasis. In addition, novel pathways and patterns of associated expression in melanoma cells not reported before emerged.

ORGANISM(S): Homo sapiens

DISEASE(S): melanoma

SUBMITTER: Keith Hoek

PROVIDER: E-GEOD-4570 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas.

Hoek Keith K Rimm David L DL Williams Kenneth R KR Zhao Hongyu H Ariyan Stephan S Lin Aiping A Kluger Harriet M HM Berger Aaron J AJ Cheng Elaine E Trombetta E Sergio ES Wu Terence T Niinobe Michio M Yoshikawa Kazuaki K Hannigan Gregory E GE Halaban Ruth R

Cancer research 20040801 15

Affymetrix and spotted oligonucleotide microarrays were used to assess global differential gene expression comparing normal human melanocytes with six independent melanoma cell strains from advanced lesions. The data, validated at the protein level for selected genes, confirmed the overexpression in melanoma cells relative to normal melanocytes of several genes in the growth factor/receptor family that confer growth advantage and metastasis. In addition, novel pathways and patterns of associated ...[more]

PMID: 15289333

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Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas.

Project description:Affymetrix oligonucleotide microarrays were used to assess global differential gene expression comparing normal human melanocytes with six independent melanoma cell strains from advanced lesions. The data, validated at the protein level for selected genes, confirmed the overexpression in melanoma cells relative to normal melanocytes of several genes in the growth factor/receptor family that confer growth advantage and metastasis. In addition, novel pathways and patterns of associated expression in melanoma cells not reported before emerged. Keywords: class comparison study (melanoma vs melanocyte)

2006-03-30 | GSE4570 | GEO

Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas. II

Project description:Spotted oligonucleotide microarrays were used to assess global differential gene expression comparing normal human melanocytes with six independent melanoma cell strains from advanced lesions. The data, validated at the protein level for selected genes, confirmed the overexpression in melanoma cells relative to normal melanocytes of several genes in the growth factor/receptor family that confer growth advantage and metastasis. In addition, novel pathways and patterns of associated expression in melanoma cells not reported before emerged. Keywords: class comparison study (melanoma vs melanocyte)

2006-03-31 | GSE4576 | GEO

Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas. II

Project description:Spotted oligonucleotide microarrays were used to assess global differential gene expression comparing normal human melanocytes with six independent melanoma cell strains from advanced lesions. The data, validated at the protein level for selected genes, confirmed the overexpression in melanoma cells relative to normal melanocytes of several genes in the growth factor/receptor family that confer growth advantage and metastasis. In addition, novel pathways and patterns of associated expression in melanoma cells not reported before emerged. Six melanoma cultures and two melanocyte cultures. The melanoma cultures are considered, for the purposes of this investigation, replicates from the point of view that they are all melanomas. Three of the melanomas were replicated once or twice in addition.

2010-07-01 | E-GEOD-4576 | biostudies-arrayexpress

UV effects in mouse melanocytes

Project description:Ultraviolet (UV) radiation is a major melanoma risk factor, yet underlying mechanisms remain poorly understood. Here we introduce a mouse model permitting fluorescence-aided melanocyte imaging and isolation following in vivo UV irradiation. We use expression profiling to show that activated neonatal skin melanocytes isolated following a melanomagenic UVB dose bear a distinct, persistent interferon-response signature, including genes associated with immunoevasion. UVB-induced melanocyte activation, characterized by aberrant growth and migration, was abolished by antibody-mediated systemic blockade of interferon-gamma (IFN-gamma), but not type-I interferons. IFN-gamma was produced by macrophages recruited to neonatal skin by UVB-induced chemokine receptor Ccr2 ligands. Admixed recruited skin macrophages enhanced transplanted melanoma growth by inhibiting apoptosis; notably, IFN-gamma blockade abolished macrophage-associated melanoma growth and survival. IFN-gamma-producing macrophages were identified in 70% of human melanomas examined. Our data reveal an unanticipated role for IFN-gamma in promoting melanocytic cell survival/immunoevasion, and suggest IFN-gamma-R signaling represents a novel therapeutic melanoma target. Biologic replicates of UVA- and UVB-treated mouse melanocytes, as well as untreated mouse melanocytes and mouse keratinocytes, were used to define melanocyte expression signatures associated with UV treatment.

2011-01-01 | E-GEOD-25164 | biostudies-arrayexpress

Differential expression analysis of RNA-seq data from melanocytes driven by tumor cell-derived exosomes

Project description:Exosomes (40–100 nm) are organelle-like membranous structures shed into interstitial spaces and body fluids under diverse pathophysiologic conditions, including tumor development. The tumor microenvironment is abundant with exosomes secreted by the cancer cells themselves. Studies have shown that tumor-derived exosomes can transport RNA and active molecules to other cells to promote tumor growth. Exosomes are increasingly being recognized as a major contributor in the progression of malignant neoplasms. We have found that normal melanocytes can acquire invasiveness through the internalization of melanoma cell-derived exosomes. However, little is known about how the exosomes modulate the melanocytes in the microenvironment to optimize conditions for tumor progression and metastasis. We hypothesize that melanoma cell-derived exosomes can drive the dysregulation of transcriptomes in normal melanocytes and facilitate melanoma progression. Our objective is to identify differentially expressed genes in melanocytes driven by tumor cell-derived exosomes through RNA sequencing and translate those genes as therapeutic targets for melanoma metastasis.

2019-11-06 | GSE84683 | GEO

Genome-wide promoter methylation analysis of human melanocytes and melanoma cell lines

Project description:DNA methylation profiling of human melanocytes and melanoma cell lines. Goal was to identify hypermethylated gene promoters in melanoma Genomic DNA from 4 human melanoma cell lines and normal human epidermal melanocytes was subjected to methylated DNA immunoprecipitation (MeDIP) and hybridized to Agilent's G4489A Human Promoter ChIP-on-Chip Set 244K

2014-08-01 | E-GEOD-53801 | biostudies-arrayexpress

Next generation sequencing analysis in uveal melanoma cells and normal melanocytes.

Project description:Study the RNA expression differences in uveal melanoma cells and normal melanocytes, providing new insights into the tumorgenesis of uveal melanoma.

2021-06-08 | GSE176345 | GEO

expression 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 HumanHT-12_v4 BeadChip

2018-11-29 | GSE122907 | GEO