Translational profiling of proximal tubule in fibrotic kidney
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA514912 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Injury to the proximal tubule plays a central role in the initiation and progression of kidney fibrosis, and rates of chronic kidney disease progresses approximately 50% faster in males compared to females. We applied Translating Ribosome Affinity Purification (TRAP) followed by RNA-sequencing to characterize the cell-specific proximal tubule transcriptional landscape during fibrosis in male vs. female mice.
2019-09-21 | GSE125015 | GEO
Project description:Global gene expression in the primary cultured mouse kidney proximal tubule cells treated either DMSO or 1uM GW4064 (a FXR agonist) was compared. Results provide insight into mechanisms underlying effects of FXR activation on gene expression in mouse kidney proximal tubule cells. Male C57/BJ mice aged 6 weeks were sacrificed under anesthesia and kidney proximal tubule cells were cultured until confluent. Cells were treated with either GW4064 (1uM) or equal amount of DMSO and incubated for 24 hours. 4 total RNA samples per group were analyzed and gene expression was compared between the groups.
2015-06-26 | E-GEOD-70296 | biostudies-arrayexpress
Project description:Global gene expression in primary cultured mouse kidney proximal tubule cells treated with either DMSO or 1uM GW4064 (an FXR agonist) was compared. Results provide insight into mechanisms underlying effects of FXR activation on gene expression in mouse kidney proximal tubule cells.
2015-06-26 | GSE70296 | GEO
Project description:Freshly isolated rat kidney proximal tubules were subjected for transcript profiling. Three microarray experiments were done to obtain the kidney proxmial tubule transcriptome.
2009-01-26 | E-GEOD-13668 | biostudies-arrayexpress
Project description:Metabolic programming drives proximal tubule differentiation and kidney dysfunction
| PRJNA640369 | ENA
Project description:Purpose:Cultured cell lines are widely used for research in the physiology, pathophysiology, toxicology and pharmacology of the renal proximal tubule. The lines that are most appropriate for a given use depend on the genes expressed.We have used modern RNA-sequencing techniques to identify the gene expression profile of 14 different cell lines plus primary cultures of mouse proximal tubule and compare them to transcriptomes of native kidney proximal tubules. Methods: 14 different proximal tubule cell lines were grown on permeable supports under conditions specific for the respective lines. RNA-Seq followed standard procedures. Results and conclusion: Transcripts expressed in cell lines showed variable match to transcripts selectively expressed in native proximal tubule. Opossum kidney (OK) cells displayed the highest percentage match (45%) with pig kidney cells (LLC-PK1) close behind (39%). Much lower percentage matches were seen for various human lines including HK-2 cells (26%) and lines from rodent kidneys (18-23%).An online resource (https://esbl.nhlbi.nih.gov/JBrowse/KCT/) has been created for interrogation of the data.No cell line closely matched the transcriptome of native proximal tubule cells. However, some of the lines tested are suitable for the study of particular metabolic and transport processes seen in the proximal tubule.
2020-10-14 | GSE135441 | GEO
Project description:We sequenced mRNAs in microdissected glomeruli and S1 proximal tubule segments and the whole remnant kidney of uninephrectomized rats.
2017-06-17 | GSE70012 | GEO
Project description:Acute kidney injury (AKI) is a major health care concern. There are no therapies for the treatment of AKI. The primary site of damage during AKI is the proximal tubule, which are highly metabolically active cells that rely upon fatty acids for energy. Proximal tubules are notably mitochondria- and peroxisomes-rich cell type that mediate fatty acid oxidation (FAO). Sirtuins reverse post-translational lysine acylation and control many biological processes including FAO. Sirtuin1 and sirtuin3 are protective against AKI. However, the role of the mitochondrial Sirtuin5 (Sirt5) during AKI has yet to be determined. We found Sirt5 to be highly expressed in the proximal tubule. At baseline Sirtuin5 knockout (Sirt5-/-) animals had modestly decreased mitochondrial function but significantly increased FAO, which was localized to the peroxisome. While no overt kidney phenotype was observed in SIRT5-/- mice, following ischemia reperfusion injury Sirt5-/- animals had significantly improved kidney function and less tissue damage. This coincided with increased peroxisomal activity in the Sirt5-/- proximal tubules in preference to the mitochondria. Here we have identified a novel mechanism driving protection of kidneys from ischemic injury. If this can be harnessed it may prove to be an effective therapeutic.
2019-02-13 | MSV000083439 | MassIVE
Project description:We performed a mild-to-moderate ischemia reperfusion injury (IRI) to model injury responses reflective of kidney injury in a variety of clinical settings. Single-nuclear RNA-sequencing (snRNA-seq) of genetically labeled injured PTCs at 7-days (“early”) and 28-days (“late”) time points post-IRI identified specific gene and pathway activity in the injury-repair transition. In particular, we identified Vcam1+/Ccl2+ proximal tubule cells at a late injury stage distinguished by marked activation of NF-kB-, TNF- and AP-1-signaling pathways. This population of PTCs showed features of a senescence-associated secretory phenotype but did not exhibit G2/M cell cycle arrest. These pro-inflammatory, pro-fibrotic proximal tubule cells are likely triggers for chronic disease progression.
2021-06-16 | GSE171417 | GEO
Project description:Pentraxin-2 (PTX-2) is a constitutive, anti-inflammatory, innate immune plasma protein whose circulating level is decreased in chronic human fibrotic diseases. Recent studies indicate that systemic delivery of recombinant PTX-2 inhibits inflammatory diseases associated with fibrosis by blocking pro-fibrotic macrophage activation and promoting anti-inflammatory and regulatory macrophages. Here we show that recombinant human PTX-2 (rhPTX-2) retards the progression of chronic kidney disease in Col4a3 mutant mice that develop Alport syndrome, reducing blood markers of kidney failure, enhancing lifespan by 20%, and improving histological signs of disease. Exogenously-delivered rhPTX-2 is detected in macrophages but is also found in tubular epithelial cells where it counteracts macrophage activation and is cytoprotective for the epithelium. We performed transcriptional profiling of whole kidney homogenates and human proximal tubule epithelial cells (PTECs) to identify pathways differentially activated or suppressed in response to treatment with PTX-2. Computational analysis of genes regulated by rhPTX-2 identified the transcriptional regulator c-Jun and its binding partners, which form AP-1 complexes, as a central target for the function of rhPTX-2. Accordingly, PTX-2 attenuates c-Jun activation and reduces expression of AP-1 dependent inflammatory genes in both monocytes and epithelium. Our studies therefore identify rhPTX-2 as a potential therapy for chronic fibrotic disease of the kidney and an important inhibitor of pathological c-Jun signaling in this setting. 1. Total RNA from whole kidney homogenates of wildtype (Col4a3+/+) and knockout (Col4a3-/-) mice treated with PTX-2 was isolated and hybidized to Illumina Mouse WG-6 v2 Expression BeadChips. 2. Total RNA from human proximal tubules treated with plasma and PTX-2 was isolated and hybidized to Illumina HumanHT-12 v4 Expression BeadChips.
2016-08-11 | E-GEOD-85409 | biostudies-arrayexpress