Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic analysis of murine kidney proximal tubule sub-segment derived cell lines reveals preferences in mitochondrial pathway activity

ABSTRACT: The proximal tubule (PT) is a highly energetic segment of the nephron, responsible for the majority of solute and water reabsorption in the kidney. Each of its sub-segments have specialized functions; however, little is known about the genes and proteins that determine the oxidative phosphorylation capacity of the PT sub-segments. This information is a critical deficit in understanding kidney function and to develop a fuller comprehensive landscape of renal cell adaptations to injury, toxins, physiologic stressors, and development. In this study, three immortalized murine renal cell lines (PT S1,S2 and S3 segments) were analyzed for protein content and compared to a murine fibroblast cell line. All three proximal tubule cell lines generate ATP predominantly by oxidative phosphorylation while the fibroblast cell line is glycolytic. The proteomic data demonstrates that the most striking difference in proteomic signatures between the cell lines are differences in nuclear proteins followed by differences in mitochondria proteome. The mitochondria physiologic profile is also determined in the cell lines to provide physiologic context to the proteomic dataset. This data set will allow researchers to study differences in nephron-specific cell lines, differences between epithelial and fibroblast cells, and differences between actively respiring cells and glycolytic cells.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

SUBMITTER: Robert L Bacallao

PROVIDER: MSV000089838 | MassIVE | Thu Jul 07 08:14:00 BST 2022

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

GNPS - Proteomic analysis of murine kidney proximal tubule sub-segment derived cell lines reveals preferences in mitochondrial pathway activity

Project description:The proximal tubule (PT) is a highly energetic segment of the nephron, responsible for the majority of solute and water reabsorption in the kidney. Each of its sub-segments have specialized functions; however, little is known about the genes and proteins that determine the oxidative phosphorylation capacity of the PT sub-segments. This information is a critical deficit in understanding kidney function and to develop a fuller comprehensive landscape of renal cell adaptations to injury, toxins, physiologic stressors, and development. In this study, three immortalized murine renal cell lines (PT S1,S2 and S3 segments) were analyzed for protein content and compared to a murine fibroblast cell line. All three proximal tubule cell lines generate ATP predominantly by oxidative phosphorylation while the fibroblast cell line is glycolytic. The proteomic data demonstrates that the most striking difference in proteomic signatures between the cell lines are differences in nuclear proteins followed by differences in mitochondria proteome. The mitochondria physiologic profile is also determined in the cell lines to provide physiologic context to the proteomic dataset. This data set will allow researchers to study differences in nephron-specific cell lines, differences between epithelial and fibroblast cells, and differences between actively respiring cells and glycolytic cells.

2022-07-07 | MSV000089838 | GNPS

RNA-seq profiling of microdissected rat renal tubule segments

Project description:We sequenced mRNAs from glomeruli and 14 different rat renal tubule segments collected by hand microdissection. Collagenase-digested rat renal tubule segments were collected by hand microdissection. Poly(A)-mRNAs were captured from cell lysate and sequenced using paired-end protocol.

2015-03-31 | E-GEOD-56743 | biostudies-arrayexpress

RNA-seq profiling of microdissected rat renal tubule segments

Project description:We sequenced mRNAs from glomeruli and 14 different rat renal tubule segments collected by hand microdissection.

2015-03-31 | GSE56743 | GEO

Tacrolimus TK173 RPTEC

Project description:Confluent cultures of a human renal fibroblast cell line (TK-173) and a human renal proximal tubule epithelial cell line (RPTEC/TERT1) were treated with 10 micromolar tacrolimus (FK-506) for one and three days.

2012-01-01 | E-MTAB-778 | biostudies-arrayexpress

PPARs and c-Myc regulate metabolism of renal tubules

Project description:Different segments of renal tubules have distinct metabolic features and functions, and defective metabolism in renal tubules is involved in the pathobiology of kidney diseases. However, the mechanisms underlying the metabolic regulation in renal tubules remain to be defined. We demonstrated that the renal proximal tubule (PT) has high expression of fatty acid and lipid metabolism enzymes, which is transcriptionally upregulated by abundantly expressed peroxisome proliferator-activated receptor (PPAR)/γ to support active lipid metabolism. In contrast, the renal distal tubule (DT) has elevated glycolytic enzyme expression corresponding with high rates of glycolysis, and this increased expression is mediated by abundantly expressed c-Myc. In addition, Nrf2 upregulated glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, and NADP-dependent malic enzyme 1 expression for NADPH production and antioxidation in the DT. Highly expressed PPARγ transcriptionally enhanced expression of the protease iRhom2 in the PT, which suppressed epidermal growth factor (EGF) expression and secretion, inhibiting EGF receptor activation-dependent glycolytic gene expression and maintaining the low level of glycolysis. PPARγ inhibition reduced iRhom2 expression and increased EGF and GLUT1 expression in the PT in mice, resulting in hypertrophy of renal tubules and inhibited kidney functions, which can be rescued by inhibition of glycolysis via treatment with 2-deoxy-D-glucose. These findings delineate instrumental molecular mechanisms underlying the active lipid metabolism and suppressed glycolysis in the PT and active glycolysis in the DT and reveal critical roles for PPARs and c-Myc in maintaining metabolic homeostasis in the kidney

2018-11-15 | PXD007828 | Pride

Targeted single-cell RNA-seq identifies minority cell types of kidney distal nephron & A Comprehensive Map of mRNAs and Their Isoforms across All 14 Renal Tubule Segments of Mouse

Project description:Characterization of gene expression for each renal cell type is essential for identifying mechanisms underlying kidney physiology and pathophysiology. Here, we built a transcriptome landscape mouse renal epithelial cells by deep sequencing of all 14 mouse renal segments, upon which we developed an enrichment protocol to characterize distal nephron cells by single-cell RNA-seq. Our renal tubule expression atlas provided landscapes of gene expression and alternative splicing along the renal tubule segments. We identified, and integrated segment-specific genes with human gene nomenclature to understand the gene function and conservation. We further developed an enrichment strategy for single-cell analysis of distal nephron cells. The analysis revealed heterogeneous gene expression in DCT1-DCT2-CNT. Moreover, we identified two mosaic cell types in thick ascending limb and verified their presence in mouse kidney tissue. Our data provides a rich resource for kidney research and we provide our data user-friendly at https://esbl.nhlbi.nih.gov/MRECA/Nephron/ and https://esbl.nhlbi.nih.gov/MRECA/DCT/.

2020-11-18 | GSE150338 | GEO

Rattus norvegicus

Project description:RNA-seq profiling of microdissected rat renal tubule segments

| PRJNA244440 | ENA

Proteomics of Rat Proximal-Tubule Cell-Culture Models

Project description: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. New tools for transcriptomic and proteomic profiling using RNA-sequencing (RNA-Seq) and mass spectrometry make it possible to catalog expressed genes in each cell line. This data set is the protoemic data of Rat NRK-52E cell line. We concludeno cell line fully 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.

2020-10-15 | PXD021160 | Pride

Expression data from NRK-52E cells treated with aristolochic acids for 6h, 24h and 72h

Project description:In this study we have examined the effect of sub-cytotoxic exposure to aristolochic acids (1.65µM) at 6h, 24h and 72h on the whole-genome expression profile in a rat proximal renal tubule cell line (NRK-52E). We used microarrays to detail the mechanism of toxicity and possibly carcinogenicity of aristolochic acids in rat renal proximal cells.

2015-07-02 | GSE68687 | GEO

Multi-omics Analyses Reveal Sex Differences in Mouse Renal Proximal Tubules

Project description:Sex differences have been increasingly recognized to play an important role in kidney physiology and pathophysiology, but limited resources are available for comprehensive interrogation of sex differences. Here, we coupled renal tubule microdissection with RNA-seq and ATAC-seq with a focus on proximal tubules that exhibited the greatest sex differences and carried out whole-kidney proteomics to build a comprehensive sex difference landscape between male and female mouse kidneys. The transcriptomic data indicate that the major sex differences are in S2 and S3 of proximal tubule segments, where signaling pathways including monocarboxylic acid metabolic process, organic anion transport, and organic acid transport display the greatest differences. We develop an ATAC-seq method on microdissected tubules to capture chromatin accessibility differences between sexes. The analysis reveals that major sex differences are in autosomes instead of sex chromosomes, and many of them are in S2/S3 segments related to the signaling pathways identified by transcriptomic analysis. Motif analysis identifies several transcription factors (Tead1, Nfia/b, and Pou3f3) whose interplay with other transcription factors (e.g. Hnf1b, Hnf4a) may contribute to sex differences. Finally, whole-kidney quantitative proteomics analysis correlates with the transcriptome analysis and identifies a large number of proteins (Cyp2e1, Acsm2/3) that are sex-dependent. We develop a knowledge portal to promote our understanding of sex differences in kidneys in kidneys at https://esbl.nhlbi.nih.gov/MRECA/PT/.

2022-11-21 | GSE212213 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data