Project Details
Projekt
Cell-state specific tissue proteomes in AKI
Subject Area
Nephrology
Term
since 2025
Project identifier
Deutsche Forschungsgemeinschaft (DFG) - Project number 445703531
Acute kidney injury (AKI) causes profound morphological and molecular changes in tubular epithelial cells (TECs) and is a risk factor for chronic kidney disease (CKD). In the previous funding period, using a murine model of AKI, we found that healthy TECs can transiently transdifferentiate into various injury-related molecular cell states, emphasizing the plasticity of mature TECs. Our proteomic analysis of the transdifferentiated TECs revealed protein kinase, X-linked (PRKX) as one of the most upregulated proteins. This serine/threonine kinase plays a role in tubulogenesis, but its roles in tubule remodeling after AKI and potential as a cell-state marker are unknown. Also, little is known about the molecular profiles of specific TEC states, and how these profiles associate with morphological alterations during tubule remodeling in AKI. We hypothesize that combining spatial proteomics with morphological analysis will better define injury-related cell states of TECs and potential markers, like PRKX, leading to improved tissue diagnostics of tubular injury and potentially new therapeutic approaches to AKI. To tackle this, we will combine our expertise in proteomics (Jankowski) with expertise in clinical nephrology and tubule remodeling in AKI (Saritas). In WP1, we will establish an integrated workflow combining mass spectrometric imaging (MSI), pathomics (with P4) and multiplexed immunofluorescence microscopy (with P9), enabling cell-type segmentation and identification based on pathomics and immunofluorescence data followed by the mining of cell type or cell-cluster-associated proteomic signatures. This workflow will be applied to time courses of various rodent AKI models (re-using samples from P2, P6 and P9) to identify distinctive protein signatures and expression of PRKX. In WP2, due to the lack of human tissue samples in many AKI cases, we will collect kidney samples through our rapid post-mortem autopsy program (with P10) and analyze them using MSI, transcriptomics (with P2), and pathomics (with P4). In WP3, in close collaboration with P2, we will perform clonal phenotypic analysis of tubule remodeling in AKI using a transgenic reporter mouse model and integrate single-cell transcriptomes as an additional layer to our combined imaging workflow to uncover the gene regulatory network within PRKX-expressing cells and other clonally expanded TECs in AKI. In WP4, we will provide functional insights and validate the role of identified molecules, including PRKX. We will use CRISPR/Cas9 technology to manipulate the respective gene expression in vitro in injured human tubular cells and organoids (with P1 and P10). In conclusion, our work will reveal the cell-state-specific proteomes in situ and their association with tubule morphology, potentially facilitating tissue diagnostics of TEC injury. It will provide spatial proteomic information to the consortium for joint multi-modal characterization of tubul
DFG Programme
Clinical Research Units
