Consensus draft of the native mouse podocyte-ome

The podocyte is a key cell in maintaining renal filtration barrier integrity. Several recent studies have analyzed the genome and tran-scriptome in the podocyte at deep resolution. This avenue of podocyte-ome research was enabled by a variety of techniques, including 1) single-cell transcriptomics, 2) FACS with and without genetically encoded markers, and 3) deep proteomics. However, data across various omics techniques and studies are currently not well integrated with each other. Here, we aimed to establish a common, simplified knowledge base for the mouse podocyte-ome by integrating bulk RNA sequencing, bulk proteomics of FACS-sorted podocytes, and single-cell transcriptomics. Three publicly available datasets of each omics technique from different laboratories were bioinformatically integrated and visualized. Our approach not only revealed conserved processes of podocytes but also sheds light on the benefits and limitations of the used technologies. We identified that high expression of glycan glycosylphosphatidylinositol anchor synthesis and turnover, as well as retinol metabolism, were relatively understudied features of podocytes. In addition, actin -binding molecules were organized in a podocyte-specific manner, as evidenced by differential expression in podocytes compared with other glomerular cells. We compiled a Web-based PodIent application that illustrates the features of the integrated dataset. This enables user-driven exploratory analysis by querying genes of interest for podocyte identity in absolute and relative quantifica-tion while also linking to functional annotation using keywords, Gene Ontology terms, and gene set enrichments. This consensus draft is a first step toward common molecular omics knowledge of kidney cells.NEW & NOTEWORTHY Podocytes are key components of glomerular filtration and are affected in various kidney diseases. Here, we present an integrated, robust definition of molecular identity across proteomic, single-cell transcriptomics, and bulk transcriptomic studies on native mouse podocytes. We created the PodIdent app, a novel knowledge base promoting access to the presence and expression of specific proteins for podocytes.

Automated summary

This study integrates bulk RNA sequencing, bulk proteomics of FACS-sorted podocytes, and single-cell transcriptomics to establish a common, simplified knowledge base for the mouse podocyte-ome. The findings reveal conserved processes and shed light on the benefits and limitations of the used technologies. A Web-based application, PodIdent, is developed to facilitate user-driven exploratory analysis.