Lentiviral-mediated small hairpin RNAs (shRNAs)-based knockdown of OLFM2 or PKP2 in human adipocytes
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ABSTRACT:
PROVIDER: PRJNA755335 | ENA |
REPOSITORIES: ENA
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Project description:We introduced into subcutaneous fully-differentiated human adipocytes from the same subject small hairpin RNAs (shRNAs) against two genes, thus enabling the study of functional consequences of sustained OLFM2 (shOLFM2; n=3 biological replicates) and PKP2 (shPKP2; n=3) knockdown in these cells. The lentiviral-based transfection was used to provide a long-lasting, convenient, reliable and efficient knockdown into in vitro cultured and fully differentiated adipocytes maintained for 6 d after reaching fully differentiation. A non-targeting shRNA was used as control (shCTRL; n=4) and reference for both modifications.
2021-12-28 | GSE182229 | GEO
Project description:We introduced into subcutaneous fully-differentiated human adipocytes from the same subject short interfering RNAs (siRNAs), thus enabling the study of functional consequences of OLFM2 (siOLFM2; n=3 biological replicates) and PKP2 (siPKP2; n=3) knockdown in these cells. A lipid-based transfection reagent (i.e. Lipofectamine 3000 reagent) was used to provide a transient (72h), convenient, reliable and efficient transfection into in vitro cultured and fully differentiated adipocytes. A non-targeting siRNA was used as control (siCTRL; n=4) for both modifications.
2021-12-28 | GSE182231 | GEO
Project description:To explore the downstream genes of PKP2,we performed RNA-seq to screen after overexpression of PKP2 in A549 cells.
2023-08-05 | GSE155759 | GEO
Project description:Short interfering RNAs (siRNAs)-based knockdown of OLFM2 or PKP2 in human adipocytes
| PRJNA755338 | ENA
Project description:Whole transcriptome of IRF3-depleted myeloma cells was analysed using a high-throughput RNA-seq approach. IRF3 was depleted by 2 different shRNAs in MM1.S cells, and total RNA was isolated on day 4 post-lentiviral transduction. Poly A-tail enriched RNA was sequenced and the analysis of commonly regulated genes by both shRNAs from 2 independent experiments revealed that IRF3 regulates genes that are involved in cell cycle regulation.
2021-02-28 | GSE163482 | GEO
Project description:Background: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a familial cardiac disease associated with ventricular arrhythmias and an increased risk of sudden cardiac death. Currently, there are no approved treatments that address the underlying genetic cause of this disease, representing a significant unmet need. Mutations in Plakophilin-2 (PKP2), encoding a desmosomal protein, account for approximately 40% of ARVC cases and result in reduced gene expression. Methods: Our goal is to examine the feasibility and the efficacy of adeno-associated virus 9 (AAV9)-mediated restoration of PKP2 expression in a cardiac specific knock-out mouse model of Pkp2. Results: We show that a single dose of AAV9:PKP2 gene delivery prevents disease development before the onset of cardiomyopathy and attenuates disease progression after overt cardiomyopathy. Restoration of PKP2 expression leads to a significant extension of lifespan by restoring cellular structures of desmosomes and gap junctions, preventing or halting decline in left ventricular ejection fraction, preventing or reversing dilation of the right ventricle, ameliorating ventricular arrhythmia event frequency and severity, and preventing adverse fibrotic remodeling. RNA sequencing analyses show that restoration of PKP2 expression leads to highly coordinated and durable correction of PKP2-associated transcriptional networks beyond desmosomes, revealing a broad spectrum of biological perturbances behind ARVC disease etiology. Conclusions: We identify fundamental mechanisms of PKP2-associated ARVC beyond disruption of desmosome function. The observed PKP2 dose-function relationship indicates that cardiac-selective AAV9:PKP2 gene therapy may be a promising therapeutic approach to treat ARVC patients with PKP2 mutations.
2024-02-23 | GSE253223 | GEO
Project description:We explored a gene editing approach to depleting ephrinB2 from colorectal cancer cells using an inducible lentiviral vector encoding a short hairpin (sh) RNA for ephrinB2 silencing via RNA interference. We discovered that lentiviral integration in the host DNA frequently drives divergent gene transcription generating antisense reads by forcing splicing and read-through into the host DNA resulting in expression of chimeric vector/host transcripts.
2022-05-25 | GSE186796 | GEO
Project description:Background: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a familial cardiac disease associated with ventricular arrhythmias and an increased risk of sudden cardiac death. Currently, there are no approved treatments that address the underlying genetic cause of this disease, representing a significant unmet need. Mutations in Plakophilin-2 (PKP2), encoding a desmosomal protein, account for approximately 40% of ARVC cases and result in reduced gene expression. Methods: Our goal is to examine the feasibility and the efficacy of adeno-associated virus 9 (AAV9)-mediated restoration of PKP2 expression in a cardiac specific knock-out mouse model of Pkp2. Results: We show that a single dose of AAV9:PKP2 gene delivery prevents disease development before the onset of cardiomyopathy and attenuates disease progression after overt cardiomyopathy. Restoration of PKP2 expression leads to a significant extension of lifespan by restoring cellular structures of desmosomes and gap junctions, preventing or halting decline in left ventricular ejection fraction, preventing or reversing dilation of the right ventricle, ameliorating ventricular arrhythmia event frequency and severity, and preventing adverse fibrotic remodeling. RNA sequencing analyses show that restoration of PKP2 expression leads to highly coordinated and durable correction of PKP2-associated transcriptional networks beyond desmosomes, revealing a broad spectrum of biological perturbances behind ARVC disease etiology. Conclusions: We identify fundamental mechanisms of PKP2-associated ARVC beyond disruption of desmosome function. The observed PKP2 dose-function relationship indicates that cardiac-selective AAV9:PKP2 gene therapy may be a promising therapeutic approach to treat ARVC patients with PKP2 mutations.
2024-02-23 | GSE253224 | GEO
Project description:MiRNA isoforms (isomiRs) are single stranded small RNAs originating from the same pri-miRNA hairpin as a result of cleavage by Drosha and Dicer enzymes. Variations at the 5’-end of a miRNA alter the seed region of the molecule, thus affecting the targetome of the miRNA. MDA-MB-231 cells were transduced with shRNAs against ELOVL5 and luciferase genes. Small RNA sequencing was used to study the cleavage profiles of shRNAs.
2021-05-03 | GSE173709 | GEO
Project description:Background: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a familial cardiac disease associated with ventricular arrhythmias and an increased risk of sudden cardiac death. Currently, there are no approved treatments that address the underlying genetic cause of this disease, representing a significant unmet need. Mutations in Plakophilin-2 (PKP2), encoding a desmosomal protein, account for approximately 40% of ARVC cases and result in reduced gene expression. Methods: Our goal is to examine the feasibility and the efficacy of adeno-associated virus 9 (AAV9)-mediated restoration of PKP2 expression in a cardiac specific knock-out mouse model of Pkp2. Results: We show that a single dose of AAV9:PKP2 gene delivery prevents disease development before the onset of cardiomyopathy and attenuates disease progression after overt cardiomyopathy. Restoration of PKP2 expression leads to a significant extension of lifespan by restoring cellular structures of desmosomes and gap junctions, preventing or halting decline in left ventricular ejection fraction, preventing or reversing dilation of the right ventricle, ameliorating ventricular arrhythmia event frequency and severity, and preventing adverse fibrotic remodeling. RNA sequencing analyses show that restoration of PKP2 expression leads to highly coordinated and durable correction of PKP2-associated transcriptional networks beyond desmosomes, revealing a broad spectrum of biological perturbances behind ARVC disease etiology. Conclusions: We identify fundamental mechanisms of PKP2-associated ARVC beyond disruption of desmosome function. The observed PKP2 dose-function relationship indicates that cardiac-selective AAV9:PKP2 gene therapy may be a promising therapeutic approach to treat ARVC patients with PKP2 mutations.
2024-02-23 | GSE253225 | GEO