Proteomic analysis of mouse podocytes

ABSTRACT: 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 glomeruli, revealing a strong fuzziness of phosphorylation process as compared to the native podocyte phosphoproteome. The 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Glomerular Visceral Epithelial Cell, Kidney

SUBMITTER: Markus Rinschen  

LAB HEAD: Markus Rinschen

PROVIDER: PXD004040 | Pride | 2016-07-04

REPOSITORIES: pride