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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome profile of silenced MCF-7 using ASO mediated knock-down for three lncRNAs

ABSTRACT: RNA-Seq of MCF-7 knock-down cells for PVT1, FGD5-AS1, and EPB41L4A-AS1. Cells were treated with ASO or scramble as negative control.

INSTRUMENT(S): Illumina NovaSeq 6000, none, DELL PRICISION T7500

ORGANISM(S): Homo sapiens

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PROVIDER: E-MTAB-14148 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): E-MTAB-14147

REPOSITORIES: biostudies-arrayexpress

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PVT1

Project description:Homo sapiens PVT1, Pvt1 oncogene [Source:HGNC Symbol;Acc:HGNC:9709], is differentially expressed in 155 experiment(s);

| ENSG00000249859 | ExpressionAtlas

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Project description:Mus musculus Pvt1, Pvt1 oncogene [Source:MGI Symbol;Acc:MGI:97824], is differentially expressed in 106 experiment(s);

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PVT1

Project description:Homo sapiens PVT1, Pvt1 oncogene [Source:HGNC Symbol;Acc:HGNC:9709], is expressed in 39 baseline experiment(s);

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Pvt1

Project description:Mus musculus Pvt1, Pvt1 oncogene [Source:MGI Symbol;Acc:MGI:97824], is expressed in 34 baseline experiment(s);

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Long non-coding RNA PVT1 is overexpressed in cutaneous squamous cell carcinoma and exon 2 is critical for its oncogenicity

Project description:Background Cutaneous squamous cell carcinoma (cSCC) is one of the most common and fastest increasing forms of cancer worldwide with metastatic potential. Long non-coding RNAs (lncRNAs) are a group of RNA-molecules with essential regulatory functions for both physiological and pathological processes. Objectives To investigate the function and mode of action of lncRNA plasmacytoma variant translocation 1 (PVT1) in cSCC. Methods The expression level of PVT1 was quantified in healthy skin, benign skin diseases and cSCCs by qRT-PCR and single molecule in situ hybridization. The function of PVT1 in cSCC was investigated both in vivo (tumour xenograft) and in vitro (competitive cell growth assay, EdU-incorporation assay, colony formation assay and tumour spheroid formation assay) by CRISPR-Cas9-mediated PVT1 or PVT1 exon 2 knockout and by locked nucleic acid (LNA) GapmeR-mediated PVT1-knockdown. RNAseq-analysis was conducted to identify genes and processes regulated by PVT1. Results We identified PVT1 as a lncRNA upregulated in cutaneous squamous cell carcinoma in situ (cSCCIS) and cSCC and associated with oncogenic phenotype of cSCC. The increased expression of PVT1 in cSCC was regulated by MYC. Both CRISPR-Cas9-deletion of the entire PVT1 locus and LNA GapmeR-mediated knockdown of PVT1-transcript impaired malignant behaviour of cSCC cells which suggested that PVT1 is an oncogenic transcript in cSCC. Furthermore, knockout of PVT1 exon 2 inhibited cSCC tumour growth both in vivo and in vitro demonstrating that exon 2 is a critical element for the oncogenic role of PVT1. Mechanistically, we show that PVT1 is localized in the cell nucleus and acts as a suppressor of cellular senescence by inhibiting CDKN1A expression and preventing cell cycle arrest. Conclusions Our study reveals a previously unrecognized role for exon 2 of PVT1 in its oncogenic role and that PVT1 suppresses cellular senescence. PVT1 may be a biomarker and therapeutic target in cSCC.

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