Multi-omics profiling reveals EMT-driven fibroblast activation in the renal injury niche

Persistent renal injury creates conditions for activating fibroblasts. However, due to the complexity of the renal injury microenvironment, the mechanisms driving fibroblast activation remain poorly understood. Here, we use single-nucleus RNA sequencing data and spatial transcriptomic data to investigate the mechanisms of fibroblast activation in renal injury. By integrating 619,137 single-cell nuclei from 80 samples, we identify 10 fibroblast subtypes within the renal injury environment. The FIB_EMT (Epithelial-Mesenchymal Transitional Fibroblast) subtype is characterized by elevated scores in EMT-related gene programs, TGF-β signaling pathway, and extracellular matrix (ECM) evaluation, and it is also linked to poorer renal function. Our analysis suggests that SOX4 may promote the activation of FIB_EMT subtype by upregulating EMT and ECM-associated pathways. The interaction between the FIB_EMT subtype and the CYP24A1⁺ descending thin limb cell (DTL) subtype with mesenchymal cell characteristics is enhanced in acute injury. Additionally, the analysis of spatial transcriptomic data further reveals that the FIB_EMT subtype, along with EMT and ECM features, as well as CYP24A1⁺ DTL subtype, are primarily concentrated in the renal papilla region. These findings offer critical insights into the mechanisms of fibroblast activation in renal injury.