title: Quantitative deep mapping of the cultured podocyte proteome uncovers shifts in proteostatic mechanisms during differentiation.
abstract: The renal filtration barrier is maintained by the renal podocyte, an epithelial postmitotic cell. Immortalized mouse podocyte cell lines-both in the differentiated and undifferentiated state-are widely utilized tools to estimate podocyte injury and cytoskeletal rearrangement processes in vitro. Here, we mapped the cultured podocyte proteome at a depth of more than 8,800 proteins and quantified 7,240 proteins. Copy numbers of proteins mutated in forms of hereditary nephrotic syndrome or focal segmental glomerulosclerosis (FSGS) were assessed. We found that cultured podocytes express abundant copy numbers of endogenous receptors, such as tyrosine kinase membrane receptors, the G protein-coupled receptor (GPCR), NPR3 (ANP receptor), and several poorly characterized GPCRs. The data set was correlated with deep mapping mRNA sequencing ("mRNAseq") data from the native mouse podocyte, the native mouse podocyte proteome and staining intensities from the human protein atlas. The generated data set was similar to these previously published resources, but several native and high-abundant podocyte-specific proteins were not identified in the data set. Notably, this data set detected general perturbations in proteostatic mechanisms as a dominant alteration during podocyte differentiation, with high proteasome activity in the undifferentiated state and markedly increased expression of lysosomal proteins in the differentiated state. Phosphoproteomics analysis of mouse podocytes at a resolution of more than 3,000 sites suggested a preference of phosphorylation of actin filament-associated proteins in the differentiated state. The data set obtained here provides a resource and provides the means for deep mapping of the native podocyte proteome and phosphoproteome in a similar manner.
authors.affiliation: Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany; and Systems Biology of Ageing Cologne, SybaCol, Cologne, Germany markus.rinschen@uk-koeln.de.
authors.forename: Markus M
authors.initials: MM
authors.lastname: Rinschen
authors.affiliation: Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany;
authors.forename: Christina B
authors.initials: CB
authors.lastname: Schroeter
authors.affiliation: Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany;
authors.forename: Sybille
authors.initials: S
authors.lastname: Koehler
authors.affiliation: Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany;
authors.forename: Christina
authors.initials: C
authors.lastname: Ising
authors.affiliation: Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany; and Systems Biology of Ageing Cologne, SybaCol, Cologne, Germany.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Schermer
authors.affiliation: Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany;
authors.forename: Martin
authors.initials: M
authors.lastname: Kann
authors.affiliation: Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany; and Systems Biology of Ageing Cologne, SybaCol, Cologne, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Benzing
authors.affiliation: Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany;
authors.forename: Paul T
authors.initials: PT
authors.lastname: Brinkkoetter
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000502:physiology*; D002460:Cell Line; D005923:Glomerulosclerosis, Focal Segmental / Q000378:metabolism; D006801:Humans; D007668:Kidney / Q000378:metabolism / Q000502:physiology; D051379:Mice; D010766:Phosphorylation / Q000502:physiology; D050199:Podocytes / Q000378:metabolism* / Q000502:physiology*; D011506:Proteins / Q000378:metabolism; D020543:Proteome / Q000378:metabolism*
chemical_list: D011506:Proteins; D020543:Proteome; C018589:lysosomal proteins
keywords: database; podocyte; proteomics; systems biology; transcriptomics