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Homo sapiens

ABSTRACT: Gene expression comparison in control and DEK oncogene depleted human melanoma cell lines

OTHER RELATED OMICS DATASETS IN: PXD003112

PROVIDER: PRJNA326505 | ENA |

REPOSITORIES: ENA

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Gene expression comparison in control and DEK oncogene depleted human melanoma cell lines

Project description:Gene expression SK-Mel-103 melanoma cell line to find genes controled by DEK oncogene

2017-12-21 | GSE83614 | GEO

Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1

Project description:Melanomas are well-known for their altered mRNA expression profiles. Yet, the specific contribution of mRNA binding proteins (mRBPs) to melanoma development remains unclear. Here we identify a cluster of melanoma-enriched genes under the control of CUGBP Elav-like family member 1 (CELF1). CELF1 was discovered with a distinct prognostic value in melanoma after mining the genomic landscape of the 692 known mRBPs across different cancer types. Genome-wide transcriptomic, proteomic, and RNA-immunoprecipitation studies, together with loss-of-function analyses in cell lines, and histopathological evaluation in clinical biopsies, revealed an intricate repertoire of CELF1-RNA interactors with minimal overlap with other malignancies. This systems approach uncovered the oncogene DEK as an unexpected target and downstream effector of CELF1. Importantly, CELF1 and DEK were found to represent early-induced melanoma genes and adverse indicators of overall patient survival. These results underscore novel roles of CELF1 in melanoma, illustrating tumor type-restricted functions of RBPs in cancer.

2017-12-22 | GSE83678 | GEO

Gene expression changes upon knockdown of DEK in the U937 cell line

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Project description:We analyzed the transcriptional response of the human melanoma cell line Ma-Mel-15 either transfected with control siRNA (siNT = non-targeting siRNA) or transfected with siRNAs (pool of 4 active and independent siRNAs) directed against the melanocytic transcription factor and lineage oncogene MITF (Microphthalmia-associated transcription factor). The experiment was performed as biological duplicates and RNA was isolated 48 hours after siRNA transfection. We aimed to determine novel markers and pathways of melanoma cell plasticity. Total RNA was obtained from siRNA-treated Ma-Mel-15 melanoma cell lines and global gene expression profiling was done using the Illumina Human HT12 v4 platform.

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Dek overexpression under the environment exposed to carcinogen in oral squamous cell.

Project description:Oral squamous cell carcinoma (OSCC) develop multi-step carcinogenesis, including the concept of the field cancerization. DEK gene is considered to be a proto-oncogene, has multifaceted functions, such as replication, transcription, and chromatin remodeling, and also affects oncogenic process, such as cellular proliferation, differentiation, senescence, and apoptosis. DEK overexpression has proposed to be closely associated with many malignancies, however, functional mechanisms and crucial roles are still unclear. DEK-expressing cells significantly increased in human oral squamous cell carcinogenesis. We generated ubiquitous and squamous cell-specific Doxycycline (DOX)- inducible Dek mice (iDek and iDek-e mice, respectively). DOX administrated (DOX+) iDek mice promoted field cancerization and the development of OSCC in the environment exposed to carcinogen. By the microarray expression profiling analysis, the promotion of the filed cancerization by Dek overexpression was mediated by the upregulation of DNA replication- and cell cycle (G1 to S phase transition)-related genes. Further, Dek-overexpressed tongue tumors were progressed by proliferating cell nuclear antigen (Pcna) and the elongator complex protein 3 (Elp3). Our data suggest that, by DEK overexpression enhances the carcinogenesis, including field cancerization, of OSCC stimulating the G1-to-S phase transition in the cell-cycle and DNA replication, even after carcinogen-exposed environment, and offers a fascinating target for treatment and prevention of OSCC.

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Project description:Melanoma cell lines

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