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Gene expression changes associated with knockdown of lncRNA PVT1 in ovarian cancer cell line SK-OV3

ABSTRACT: Gene expression changes associated with knockdown of lncRNA PVT1 in ovarian cancer cell line SK-OV3

PROVIDER: PRJNA771390 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16345353.fastq.gz	Fastqsanger.gz
	SRR16345354.fastq.gz	Fastqsanger.gz
	SRR16345355.fastq.gz	Fastqsanger.gz
	SRR16345356.fastq.gz	Fastqsanger.gz
	SRR16345357.fastq.gz	Fastqsanger.gz

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Gene expression changes associated with knockdown of lncRNA PVT1 in ovarian cancer cell line SK-OV3

Project description:lncRNA PVT1 is an emerging lncRNA of significance in cancer due to alterations in both the RNA and genomic locus in multiple cancers and its established relationship to the oncogene MYC. Several recent studies have documented potential important roles for the lncRNA in ovarian cancer. Herein RNA sequencing was performed to determine the impact of PVT1 on global gene expression by performing RNA sequencing in SK-OV3 cells after silencing PVT1 (siPVT1) of cells grown upon transient knockdown of the lncRNA PVT1. SK-OV3 cells were cultured to 50% confluence in 6 well plates. Pooled siRNA’s to human PVT1 or non targeting control siRNA’s from Dharmacon were used to transfect SK-OV3 cells for 48 hrs in full serum media carefully maintaining cell confluence to not exceed approximately 80%. This was followed by RNA extraction and verification of knockdown using primers to PVT1 followed by sequencing. We find that 450 protein coding genes were differentially expressed between control (siControl) and siPVT1 cells with 50 additional found to be non-protein coding. The top 50 differentially expressed genes include 12 that were downregulated by siPVT1 and 32 that were upregulated. Several pathways associated with metabolic and stress processes, ribosome biogenesis and ncRNA processing were altered based on GO pathway analysis. Additional pathways included pathways associated with cell motility and differentiation.

2022-07-06 | GSE185933 | GEO

N6-methyladenosine Modification of lncRNA Pvt1 Governs Epidermal Stemness

Project description:Dynamic chemical modifications of RNA represent novel and fundamental mechanisms that regulate stemness and tissue homeostasis. Rejuvenation and wound repair of mammalian skin are sustained by epidermal progenitor cells, which are localized within the basal layer of the skin epidermis. N6-methyladenosine (m6A) is one of the most abundant modifications found in eukaryotic mRNA and lncRNA (long non-coding RNA). In this report, we survey changes of m6A RNA methylomes upon epidermal differentiation, and identify Pvt1, a lncRNA whose m6A modification is critically involved in sustaining stemness of epidermal progenitor cells. With genome-editing and a mouse genetics approach, we show that ablation of m6A methyltransferase or Pvt1 impairs the self-renewal and wound healing capability of skin. Mechanistically, methylation of Pvt1 transcripts enhances its interaction with MYC and stabilizes the MYC protein in epidermal progenitor cells. Our study presents a global view of epitranscriptomic dynamics that occur during epidermal differentiation and identifies the m6A modification of Pvt1 as a key signaling event involved in skin tissue homeostasis and wound repair.

2021-02-01 | GSE165912 | GEO

The whole transcriptome expression profiling comparison between the Pin1 knockIn in Hose cells and Pin1 knockdown in ovarian cancer MCAS and SK-OV-3 cells

Project description:To discover the abnormal regulatory role of Pin1 in the ovarian cancer, The Pin1 full cDNA was knockIn (KI) the normal ovarian epithelium (Hose), and parallelly Pin1 was knockdown in the Ovarian cancer cells MCAS and sk-ov-3, and then compared the expression profiles of them to discovery the key features regulated by Pin1.

2018-01-04 | GSE84539 | GEO

LncRNA PVT1 and miR-214 in hepatocellular carcinoma

Project description:LncRNA PVT1 and miR-214 in hepatocellular carcinoma

| PRJNA509671 | ENA

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.

2023-11-30 | GSE235606 | GEO

N6-methyladenosine Modification of lncRNA Pvt1 Governs Epidermal Stemness

Project description:N6-methyladenosine Modification of lncRNA Pvt1 Governs Epidermal Stemness

| PRJNA698564 | ENA

Pvt1 silencing in C2C12 cell cultures

Project description:In order to understand the role of lncRNA Pvt1 in skeletal muscle physiopathology we silenced this transcript in-vitro, using C2C12 cell cultures, and in-vivo, in leg muscles of CD1 wild-type and denervated mice.

2019-01-07 | GSE112881 | GEO

LncRNA PVT1 and miR-214 in hepatocellular carcinoma

Project description:We aimed to detect the mRNA expression levels in HepG2 cells after trasfection with NC RNA, miR-214 mimics or PVT1 siRNAs.

2020-12-12 | GSE123745 | GEO

Promoter of lncRNA gene *PVT1* is a tumor suppressor DNA element

Project description:Promoter of lncRNA gene *PVT1* is a tumor suppressor DNA element

| PRJNA382623 | ENA

Effect of PAI-1 knockdown on gene expression in SK-OV-3 cells, and effect of platelets on gene expression in SK-OV-3 cells.

Project description:To investigate the role of PAI-1 (SERPIN E1) in ovarian cancer, we performed several in vitro assays using SK-OV-3 cells in which PAI-1 had been knocked down by siRNA, treated with platelets, or both. We then performed a comparative gene expression analysis using RNA-Seq data from untreated cells, PAI-1 siRNA knockdown or negative control, each with and without incubation with healthy donor platelets.

2023-11-29 | GSE223654 | GEO

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