RNA-sequencing of CCN2 knockout and wild type mice following 4 hours after IRI
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA773391 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16520762.fastq.gz | Fastqsanger.gz | |||
| SRR16520763.fastq.gz | Fastqsanger.gz | |||
| SRR16520764.fastq.gz | Fastqsanger.gz | |||
| SRR16520765.fastq.gz | Fastqsanger.gz | |||
| SRR16520766.fastq.gz | Fastqsanger.gz |
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Project description:GPX3 is primarily synthesized and secreted by renal tubular epithelial cells and serves as the main source of GPX3 in plasma. A portion of GPX3 adheres to the renal basement membrane, suggesting that GPX3 may also regulate renal cell physiological functions. Our previous work has found that GPX3 expression is downregulated in the renal tubular epithelial cells of mice that have undergone ischemia-reperfusion-induced acute kidney injury, but the specific impact of this downregulation remains unclear. To address this, we constructed mice with specific deletion of GPX3 in renal tubular epithelial cells and subjected them to ischemia-reperfusion modeling. We reported the protective role of native GPX3 in the kidneys under IRI-AKI conditions in mitigating oxidative stress and mitochondrial damage in tubular epithelial cells. The deletion of GPX3 in tubular epithelial cells exacerbated oxidative stress, apoptosis, and mitochondrial dysfunction in IRI-AKI. Renal cortex tissue from control and IRI-modeled mice was used for RNA sequencing. Overall, our data provide an overview of the genetic changes in the kidneys of mice with GPX3 knockout in both non-modeled and IRI-AKI-modeled conditions, laying the groundwork for studying the specific mechanisms by which GPX3 regulates renal function.
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Project description:The cellular communication network (CCN) 2, also known as CTGF, is a secreted matricellular protein with regulatory functions in vasoproliferative and fibrotic diseases. Although CCN2 functions extend to developmental processes, the impact of CCN2/CTGF expression, or lack thereof, during retinogenesis is unknown. Herein, we used bulk RNA-sequencing to determine the transcriptomic changes associated with global deletion of CCN2 in E18.5 mouse retinas. we show that CCN2 signals act on intrinsic signal transduction pathway genes and induce genetic reprogramming of retinal progenitor cells endowing these cells with neurogenic and gliogenic potentials.
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Project description:To identify the direct m6A demethylation targets of ALKBH5 at the onset of renal IRI, we performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) using RNA isolated from IRI mouse kidney of WT and KO mice 24h after I/R (WT n=3 vs. KO n=3)
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Project description:Antiphospholipid syndrome (APS)-associated vasculopathy is heralded by abnormal proliferation of endothelial and smooth muscle cells, leading to small blood vessel occlusion in the skin, kidneys, and heart, amongst other organs. The underlying mechanisms remain unclear, and targeted treatment options for patients with APS are lacking. To identify and analyze APS microvascular endothelial cells (MVECs), skin biopsies of patients with APS complicated by livedo racemosa were characterized using single-cell RNA sequencing (scRNA-seq). Increased expression of CCN1 and CCN2 were discovered and further confirmed in APS skin by microscopy, and in APS plasma by ELISA. Exposure of healthy MVECs to patient IgG triggered CCN1 and CCN2 upregulation via yes-associated protein (YAP1)-mediated signaling. CCN2 originating from APS IgG-stimulated MVECs led to the proliferation and migration of vascular smooth muscle cells, which were blocked by the anti-CCN2 antibody, pamrevlumab. We further observed increased expression of CCN1 and CCN2, along with evidence of YAP1 nuclear translocation, in kidney vessels of APS nephropathy biopsies. Finally, CCN2 inhibition with pamrevlumab significantly reduced neointima thickening and cell proliferation in a mouse model of APS IgG-accelerated neointima formation. Together, this study revealed activation of YAP1-mediated signaling in APS dermal microvessels and demonstrated that the YAP1 target CCN2 plays a role in facilitating pro-proliferative communication between MVECs and VSMCs. These findings offer insights into the cellular and molecular mechanisms underlying APS vasculopathy and provide potential therapeutic targets for patients.
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Project description:TGF-β stimulates CCN2 expression which in turn amplifies TGF-β signaling. This process promotes extracellular matrix production and accelerates the pathological progression of fibrotic diseases. Alternative splicing plays an important role in multiple disease development, while U2 small nuclear RNA auxiliary factor 2 (U2AF2) is an essential factor in the early steps of pre-mRNA splicing. However, the molecular mechanism underlying abnormal CCN2 expression upon TGF-β stimulation remains unclear. This study elucidates that SIRT4 acts as a master regulator for CCN2 expression in response to TGF-β by modulating U2AF2-mediated alternative splicing. Analyses of renal biopsy specimens from patients with CKD and mouse fibrotic kidney tissues revealed marked nuclear accumulation of SIRT4. The tubulointerstitial fibrosis was alleviated by global deletion or tubular epithelial cell (TEC)-specific knockout of Sirt4, and aggravated by adeno-associated virus-mediated SIRT4 overexpression in TECs. Furthermore, SIRT4 was found to translocate from the mitochondria to the cytoplasm through the BAX/BAK pore under TGF-β stimulation. In the cytoplasm, TGF-β activated the ERK pathway and induced the phosphorylation of SIRT4 at Ser36, which further promoted its interaction with importin α1 and subsequent nuclear translocation. In the nucleus, SIRT4 was found to deacetylate U2AF2 at K413, facilitating the splicing of CCN2 pre-mRNA to promote CCN2 protein expression. Importantly, exosomes containing anti-SIRT4 antibodies were found to effectively mitigate the UUO-induced kidney fibrosis in mice. Collectively, these findings indicated that SIRT4 plays a role in kidney fibrosis by regulating CCN2 expression via the pre-mRNA splicing.
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