RNA-seq of PRSS23 knockdown in ovarian cancer cell lines JHOC-5 and OVCA420
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE315399 | GEO | 2026/01/07
REPOSITORIES: GEO
Similar Datasets
Project description:To find new genes that might be targeted for reduction of Copper (Cu) toxicity in Wilson disease we employed genome-wide shRNA screening in ATP7B-KO HepG2 cells, a bona fide WD cell model. Cells were screened using the Dharmacon™ Decode™ Pooled Lentiviral shRNA Screening Library targeting 18205 human genes (Dharmacon #RHS6083). The Lentiviral RNAi screening library is made of 10 pools of 9570 GIPZ short hairpin RNAs (shRNAs) packaged into high-titer lentiviral particles. Genomic DNA was isolated from the cells and read counts for each shRNAs were obtained by deep sequencing to determine the abundance of each shRNA in the Cu-treated cells compared to controls. This analysis allowed the identification of genes whose downregulation promoted survival of ATP7B-KO cells upon Cu overload. To exclude that some shRNAs would have been responsible for ATP7B-KO survival by suppressing generic proapoptotic genes, we run the same screening with the proapoptotic drug vinblastine instead of CuCl2. Genes, whose suppression allowed cell to resist Cu but not vinblastine were considered as Cu-specific hits and through this approach we identified PrP as a suitable target for reduction of Cu toxicity in WD. Indeed, we found that Cu accumulation in ATP7B-KO cells stimulates expression of PrP, which brings to toxic Cu overload while PrP suppression significantly reduces Cu accumulation and toxicity in ATP7B-deficient cells. In sum our data highlight an important regulatory role of PrP in copper metabolism and as a therapeutic tool for Wilson disease.
2024-12-09 | GSE260454 | GEO
Project description:To find new genes that might be targeted for reduction of Copper (Cu) toxicity in Wilson disease we employed genome-wide shRNA screening in ATP7B-KO HepG2 cells, a bona fide WD cell model. Cells were screened using the Dharmacon™ Decode™ Pooled Lentiviral shRNA Screening Library targeting 18205 human genes (Dharmacon #RHS6083). The Lentiviral RNAi screening library is made of 10 pools of 9570 GIPZ short hairpin RNAs (shRNAs) packaged into high-titer lentiviral particles. Genomic DNA was isolated from the cells and read counts for each shRNAs were obtained by deep sequencing to determine the abundance of each shRNA in the Cu-treated cells compared to controls. This analysis allowed the identification of genes whose downregulation promoted survival of ATP7B-KO cells upon Cu overload. To exclude that some shRNAs would have been responsible for ATP7B-KO survival by suppressing generic proapoptotic genes, we run the same screening with the proapoptotic drug vinblastine instead of CuCl2. Genes, whose suppression allowed cell to resist Cu but not vinblastine were considered as Cu-specific hits and through this approach we identified PrP as a suitable target for reduction of Cu toxicity in WD. Indeed, we found that Cu accumulation in ATP7B-KO cells stimulates expression of PrP, which brings to toxic Cu overload while PrP suppression significantly reduces Cu accumulation and toxicity in ATP7B-deficient cells. In sum our data highlight an important regulatory role of PrP in copper metabolism and as a therapeutic tool for Wilson disease.
2024-12-09 | GSE277865 | GEO
Project description:We collected 3 paired ovarian tumor tissues and ovarian normal tissues. Total RNA was extracted from tissues using Trizol reagent. Then total RNA was processed and circRNAs were profiled using RNA-seq technique. Raw read counts were filtered to remove the genes with a zero read count in 3 or more samples, and then normalized with DESeq2 in the statistical program R (version 4.0.1). Differentially expressed genes were screened using following criterions: fold change was larger than 2 and adjusted P value was less than 0.05.
2021-12-28 | GSE192410 | GEO
Project description:G9a depleted SKCO3 cells were used to identify genes regulated by G9a-dependent epigenetic regulations We used microarrays to detail the global programme of gene expression underlying paritoneal dissemination and identified distinct classes of G9a-regulated genes during this process. SKOV3 cells receiving G9a-specific shRNAs were analyzed compare to cells receiving control shRNA
2013-07-18 | E-GEOD-41226 | biostudies-arrayexpress
Project description:CHSY1 has high expression in malignant tumor cells, such as colorectal cancer and ovarian cancer, and is associated with poor prognosis.The proliferation and invasion of ovarian cancer cells are weakened after knocking down CHSY1 with shRNA transfected We used microarrays to detail the global programme of gene expression underlying CHSY1 knockdown and identified distinct classes of up-regulated and down-regulated genes.
2024-05-01 | GSE232722 | GEO
Project description:We had previously discovered that the transcription factor OVO-like 1 (OVOL1) was highly induced during trophoblast differentiation. In this study, we used an lentiviral shRNA strategy to decrease OVOL1 expression in BeWo trophoblast cells. Control cells were transduced with shRNAs targeting no known mammalian transcript (shCont). Following stimulation of differentiation (48h exposure to 8-bromo-cyclic adenosine monophosphate), a RNA-seq approach was used to determine global transcript differences in OVOL1-knockdown cells compared to control cells. Trophoblast cells transduced with control shRNAs were used as controls. Cells transduced with shRNAs targeting OVOL1 were used as treatment. All cells received 250 uM 8-bromo-cyclic adenosine monophosphate to stimulate differentiation. Three independent replicates of control and treatment groups were analyzed.
2015-08-01 | E-GEOD-66962 | biostudies-arrayexpress
Project description:We had previously discovered that the transcription factor OVO-like 1 (OVOL1) was highly induced during trophoblast differentiation. In this study, we used an lentiviral shRNA strategy to decrease OVOL1 expression in BeWo trophoblast cells. Control cells were transduced with shRNAs targeting no known mammalian transcript (shCont). Following stimulation of differentiation (48h exposure to 8-bromo-cyclic adenosine monophosphate), a RNA-seq approach was used to determine global transcript differences in OVOL1-knockdown cells compared to control cells.
2015-08-01 | GSE66962 | GEO
Project description:This experiment was designed to investigate the effect of PDK1 silencing on tumor growth, metabolism, and microenvironment modulation in vivo. Tumors were established in NOD/SCID mice by subcutaneous (s.c.) injection of an highly glycolytic ovarian cancer cell line (OVCAR3) transduced with lentiviral vectors encoding PDK1-specific shRNA and selected in puromycin-containing medium. These cells had >70% reduced expression of PDK1 protein in vitro. OVCAR3 cells transduced with a scrambled shRNA lentiviral vector were used as control. Total RNA was extracted from tumor samples and hybridized on Affymetrix GeneChip™ PrimeView™ Human Gene Expression Arrays. Transcriptome analysis was performed with RNA purified from 5 different tumor samples per group (n=5 mice/shRNA and n=5 mice/shPDHK1), obtained from different mice sacrificed at equivalent tumor volumes (200 mm3).
2020-12-31 | E-MTAB-9877 | biostudies-arrayexpress
Project description:To investigate the function of STXBP6 in the regulation of ovarian cancer, we established SKOV3 cell lines in which STXBP6 gene has been knocked down by shRNA.
2025-11-01 | GSE281337 | GEO
Project description:PAX2 is one of nine PAX genes that regulate tissue development and cellular differentiation in embryos. PAX2 promotes cell proliferation, oncogenic transformation, cell lineage specification, migration, and survival. In our previous study, we found that PAX2 is highly expressed in low-grade ovarian serous carcinoma, but its expression in clear cell, endometrioid, and mucinous cell ovarian carcinomas have not been studied. More importantly, the functional role of PAX2 in ovarian cancer is not known. Downregulation of PAX2 in PAX2-expressing ovarian cancer cells inhibits cell proliferation and migration. This growth inhibition is due to the upregulation of the tumor suppressor gene G0S2 and subsequent induction of apoptosis. The PAX2 pathway thus represents a potential therapeutic target for PAX2-expressing ovarian carcinomas. Knockdown PAX2 expression in these cell lines was achieved by lentiviral shRNAs targeting the PAX2 gene. PAX2 stable knockdown cells were characterized for cell proliferation, migration, apoptosis, and gene expression profiles.
2011-12-05 | E-GEOD-30501 | biostudies-arrayexpress