Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Deep proteomic mapping of the human podocyte proteome

ABSTRACT: We subjected differentiated and undifferentiated podocytes to deep proteomics analysis by tryptic digestion and SCX fractionation.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Kidney

SUBMITTER: Markus Rinschen

LAB HEAD: Markus Rinschen

PROVIDER: PXD007075 | Pride | 2018-05-01

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20160425_AWH_ColID_143_Koehler_Benzing_SyKo_SCX_S01.raw	Raw
	20160425_AWH_ColID_143_Koehler_Benzing_SyKo_SCX_S02.raw	Raw
	20160425_AWH_ColID_143_Koehler_Benzing_SyKo_SCX_S03.raw	Raw
	20160425_AWH_ColID_143_Koehler_Benzing_SyKo_SCX_S04.raw	Raw
	20160425_AWH_ColID_143_Koehler_Benzing_SyKo_SCX_S05.raw	Raw

Items per page:

1 - 5 of 37

Publications

Protein half-life determines expression of proteostatic networks in podocyte differentiation.

Schroeter Christina B CB Koehler Sybille S Kann Martin M Schermer Bernhard B Benzing Thomas T Brinkkoetter Paul T PT Rinschen Markus M MM

FASEB journal : official publication of the Federation of American Societies for Experimental Biology 20180425 9

Podocytes are highly specialized, epithelial, postmitotic cells, which maintain the renal filtration barrier. When adapting to considerable metabolic and mechanical stress, podocytes need to accurately maintain their proteome. Immortalized podocyte cell lines are a widely used model for studying podocyte biology in health and disease in vitro. In this study, we performed a comprehensive proteomic analysis of the cultured human podocyte proteome in both proliferative and differentiated conditions ...[more]

PMID: 29694247

Similar Datasets

Deep mapping of the mouse podocyte proteome

Project description:We analyzed the proteome of mouse FACS-sorted podocytes. We compared podocytes ("green cells") with non-podocyte ("red cells") cells of the glomerulus.

2018-06-21 | PXD003306 | Pride

Analysis of the effect of CHX on the cultured podocyte proteome

Project description:We analyzed the effect of Cycloheximide (CHX) on the podocyte proteome in both the differentiated and undifferentiated state.

2018-05-01 | PXD006886 | Pride

Analysis of the cultured podocyte phosphoproteome

Project description:The renal filtration barrier is critically maintained by the renal podocyte, a postmitotic, neuron-like epithelial cell type. Cultured podocyte cell lines – both in the differentiated and undifferentiated state - are a widely utilized tool to estimate cytoskeletal rearrangement processes in vitro. Here, we mapped the podocyte proteome at a depth of more than 7000 proteins. The data dissects the dynamic range of the podocyte proteome during differentiation. The data also demonstrates an absolute quantitative analysis of proteins mutated in forms of hereditary disease and demonstrates expression of several proteins not expressed in other, standard cell lines. We validated differentially regulated proteins using immunoblot and functional assays estimating lysosomal and proteasomal function. Comparison with deep mapping RNAseq data from the native podocyte, preliminary fingerprint data from the native proteome and staining intensities from the human protein atlas was performed to estimate similiarities between the cultured and native podocyte proteome, unravelling that at least 26 high-abundant native, podocyte-specific proteins, were not identified in the dataset. Notably, this data detected general perturbations in proteostatic mechanisms as a key alteration during podocyte differentiation, with increased proteasome activity in the undifferentiated state and markedly increased expression of lysosomal proteins in the differentiated state. We also performed a comparative phosphoproteomic analysis with published data from the native glomerul. These data also suggests a preference of phosphorylation of actin associated proteins in the differentiated state. The dataset obtained here, a valuable resource, warrants and provides the means for deep mapping of the native podocyte proteome and phosphoproteome in a similar manner.

2016-07-04 | PXD004013 | Pride

Analysis of isotope incorporation in differentiated and undifferentiated podocytes

Project description:We subjected podocytes (either differentiated or undifferentiated) to a pulse with stable isotope labeled amino acids for 24, 48, 72 and 96h.

2018-05-01 | PXD006887 | Pride

Gene expression in a conditionally immortalized mouse podocyte cell line

Project description:The specialized glomerular epithelial cell (podocyte) of the kidney is a complex cell that is often damaged in glomerular diseases. Study of this cell type is facilitated by an in vitro system of propagation of conditionally immortalized podocytes. Here, genes that are differentially expressed in this in vitro model of podocyte differentiation are evaluated. Conditionally immortalized undifferentiated mouse podocytes were cultured under permissive conditions at 33*C. Podocytes that were differentiated at the non-permissive conditions at 37*C were used for comparison.

2010-08-28 | E-GEOD-23856 | biostudies-arrayexpress

Proteomics analysis of podocytes with alpha-galactosidase knockdown

Project description:We subjected human podocytes with and without alpha-Galactosidase knockdown to proteomic analysis.

2018-10-17 | PXD007080 | Pride

Glucocorticoid therapy regulates podocyte motility by inhibition of Rac1

Project description:Nephrotic syndrome (NS) occurs when the glomerular filtration barrier becomes excessively permeable leading to massive proteinuria. In childhood NS, dysregulation of the immune system has been implicated and increasing evidence points to the central role of podocytes in the pathogenesis. Children with NS are typically treated with an empiric course of glucocorticoid (Gc) therapy; a class of steroids that are activating ligands for the glucocorticoid receptor (GR) transcription factor. Although Gc-therapy has been the cornerstone of NS management for decades, the mechanism of action, and target cell, remain poorly understood. We tested the hypothesis that Gc acts directly on the podocyte to produce clinically useful effects without involvement of the immune system. In human podocytes, we demonstrated that the basic GR-signalling mechanism is intact and that Gc induced an increase in podocyte barrier function. To gain mechanistic insight we performed RNA microarray and ChIP-sequencing and identified Gc regulation of motility genes.

2017-07-17 | E-MTAB-5235 | biostudies-arrayexpress

Role of calcium/calmodulin-dependent kinase type IV in podocyte function in lupus nephritis

Project description:Kidney podocytes and their slit diaphragms contribute to prevent urinary protein loss. T cell from patients with systemic lupus erythematosus display increased expression of calcium/calmodulin kinase IV (CaMKIV). Here we evaluated the functional role of CaMKIV in lupus nephritis (LN) using kidney biopsy specimens and human podocyte cell line (AB8/13). We found that exposure of podocytes to IgG from LN patients resulted in entry of IgG into the cytoplasm. CaMKIV expression was found to be increased in podocytes of LN kidney biopsy specimens and exposure to IgG from LN patients. IgG entered podocytes using the FcRn receptor because when podocytes where treated with FcRn siRNA less IgG was found in the cytoplasm. The DNA microarray studies of podocytes exposed to LN IgG revealed that genes that are related to the activation of immune cells or podocyte damage were upregulated. These genes included CD86, CaMKIV, PTPN22, PDE5A, CD47 and MALT1. Interestingly, CD86 expression decreased after silencing CaMKIV in podocytes. Also, in situ hybridization experiments showed that the expression of CD86 was reduced in podocytes from MRL/lpr.camkivM-bM-^HM-^R/M-bM-^HM-^R mice. IgG from LN patients may enter podocytes through the FcRn and causes the upregulation of a distinct set of genes which may alter podocyte function. Upregulation of CaMKIV appears to precede that of genes known to be linked to podocyte damage such as CD86. These findings may indicate that inhibition of CaMKIV may prove of clinical use in patients with LN. IgG Purification Kits (Dojindo Molecular Technologies, Inc.) are used for isolation and purification of immunoglobulin G of healthy and normal individual according to the manufacturerM-bM-^@M-^Ys protocol. Flow through the column was used for non IgG binding samples. Cultured human podocytes with IgG purified from sera of normal individuals and LN patient for 24 hr were collected for RNA.

2014-08-01 | E-GEOD-55768 | biostudies-arrayexpress

Analysis of MOF under stress conditions

Project description:We analyzed the role of MOF in primary MEFs and differentiated podocytes in response to Adriamycin. Mof was deleted in MEFs using the Cre-ERT2 trasgene, while Mof was knockdown in podocytes using shRNA infection. Samples were treated with Adriamycin for 24 hours and gene expression changes analysed. Analysis of gene expression changes upon Mof depletion in two cell lines, MEFs and podocytes, with and without Adriamycin

2015-07-10 | E-GEOD-70706 | biostudies-arrayexpress

Mouse Podocyte Proteome - ARP3 Controls the Podocyte Architecture at the Kidney Filtration Barrier

Project description:Label-free expression proteomics analysis of FACS-sorted mouse podocytes versus non-podocytes

2018-12-14 | PXD010601 | Pride