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

ABSTRACT: We report gene expression data for human melanoma cell lines using RNAseq.

ORGANISM(S): Homo sapiens

PROVIDER: GSE75354 | GEO | 2016/02/01

SECONDARY ACCESSION(S): PRJNA304002

REPOSITORIES: GEO

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A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation.

Project description:The "cancerized field" concept posits that cancer-prone cells in a given tissue share an oncogenic mutation, but only discreet clones within the field initiate tumors. Most benign nevi carry oncogenic BRAF(V600E) mutations but rarely become melanoma. The zebrafish crestin gene is expressed embryonically in neural crest progenitors (NCPs) and specifically reexpressed in melanoma. Live imaging of transgenic zebrafish crestin reporters shows that within a cancerized field (BRAF(V600E)-mutant; p53-deficient), a single melanocyte reactivates the NCP state, revealing a fate change at melanoma initiation in this model. NCP transcription factors, including sox10, regulate crestin expression. Forced sox10 overexpression in melanocytes accelerated melanoma formation, which is consistent with activation of NCP genes and super-enhancers leading to melanoma. Our work highlights NCP state reemergence as a key event in melanoma initiation.

| S-EPMC4868069 | biostudies-literature

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

Project description:We report the distribution of H3K27Ac histone marks in a zebrafish melanoma cell line and a zebrafish primary melanoma tumor with the aim of identifying super-enhancer regions and regions of interest. We also report sox10 ChIP-Seq on the same zebrafish melanoma cell line.

2016-02-01 | GSE75353 | 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

A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation [ATAC-Seq]

Project description:We report the locations of accessible/open chromatin as assayed by ATAC-Seq on two zebrafish melanoma cell lines, zcrest 1 and zcrest 2.

2016-02-01 | GSE75351 | GEO

A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-02-01 | GSE75356 | GEO

A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation [zebrafish RNA-Seq]

Project description:We report gene expression data for FACS sorted zebrafish crestin_1kb:EGFP + cells collected at 15 somite stage (SS).

2016-02-01 | GSE75355 | GEO

Emergence of neural crest identity is a key early step in melanoma formation [Affymetrix]

Project description:The “cancerized field” concept posits that cells of a given tissue share a potentially oncogenic mutation or insult and are thus cancer-prone, yet only discreet clones within the field initiate tumor formation. In melanoma, tumors frequently (~50%) carry the oncogenic BRAFV600E mutation that is also nearly always present in benign nevi that rarely become melanoma. The zebrafish crestin gene is expressed embryonically in neural crest progenitors and is then specifically re-expressed in melanoma tumors. Here, we show by live imaging transgenic zebrafish crestin reporters that single melanocytes in a cancerized field with oncogenic BRAFV600E and p53 tumor suppressor loss undergo a change that recapitulates the neural crest progenitor (NCP) state, and patches of these cells initiate early melanoma. The crestin element is regulated by the NCP transcription factor sox10. Forced sox10 overexpression in melanocytes accelerated melanoma formation, consistent with reprogramming to the NCP state and activation of super-enhancers that lead to melanoma. Our work highlights the importance of the reemergence of the NCP state as a barrier to melanoma initiation.

2016-06-08 | GSE61823 | GEO

Emergence of neural crest identity is a key early step in melanoma formation [ChIP-Seq]

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Functional in vivo characterization of zebrafish sox10 enhancers in melanoma and neural crest

Project description:We analyzed the epigenetic landscape of five bulk (unsorted) melanoma tumors in a zebrafish melanoma model using ATAC-seq. We find that areas of open chromatin are consistent between tumor samples.

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Expression of neural crest markers GLDC and ERRFI1 is correlated with melanoma prognosis

Project description:Regulation of particular genes during the formation of neural crest (NC) cells is also described during progression of malignant melanoma. In this context it is of paramount importance to develop neural crest models allowing the identification of candidate genes, which could be used as biomarkers for melanoma prognosis. Here, we used a human iPSC-based approach to present novel NC-associated genes, expression of which was upregulated in melanoma. A list of 8 candidate genes, based on highest upregulation, was tested for prognostic value in a tissue microarray analysis containing samples from advanced melanoma (good versus bad prognosis) as well as from high-risk primary melanomas (early metastasizing versus non or late-metastasizing). CD271, GLDC and ERRFI1 showed significantly higher expression in metastatic patients who died early than the one who survived at least 30 months. In addition, GLDC and TWIST showed a significant higher IHC score in primary melanomas from patients who developed metastases within 12 months versus those who did not develop metastases in 30 months. In conclusion, our iPSC-based study reveals a significant association of NC marker GLDC protein expression with melanoma prognosis.

2019-02-07 | GSE123686 | GEO

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