ELF4 in NK Cells Is an Important Mediator of Fibroinflammation in Mice and Patients

Background: Inflammation plays a key role in tissue fibrosis. However, the pathways that orchestrate the inflammatory response are poorly understood. Using genome-wide comparative transcriptomics, we identified ELF4 as a conserved transcription factor upregulated in mouse kidney fibrosis models and human chronic kidney disease (CKD) samples. Methods: We analyzed gene expression profiles of kidneys from five mouse fibrosis models and human CKD samples to identify conserved transcriptional regulators. The functional role of the identified transcription factor ELF4 was studied using genetic modified mice, single cell RNA-seq, chromatin immunoprecipitation and in vivo antibody mediated cell-depletion and cytokine neutralization. Results: Overlap analysis of differentially expressed genes identified ELF4 as a conserved upregulated transcription factor in kidney fibrosis. Mice with genetic deletion of ELF4 were protected from folic acid induced kidney fibrosis, showing reduced collagen accumulation and expression of pro-fibrotic genes. Single cell RNA-seq and immunofluorescence indicated that ELF4 was primarily expressed by NK cells in the mouse kidney. ChIP-seq and scRNA-seq revealed that ELF4 directly regulates IFNG expression in NK cells. In vivo, loss of ELF4 reduced IFNG expression by NK cells and altered macrophage polarization in an IFNG dependent manner, which further confirmed by NK cell depletion and IFNG neutralization experiments. Antisense oligonucleotide mediated ELF4 knockdown also protected mice from kidney fibrosis, recapitulating the genetic deletion phenotype. Moreover, in vitro studies showed that ELF4 knock out macrophages had normal IFNG response, indicating an indirect regulation of macrophages by ELF4 in vivo. Conclusion: We identified ELF4 as a conserved transcription factor induced in kidney fibrosis. ELF4 expressed by NK cells directly regulates IFNG expression and indirectly alters macrophage polarization and fibrogenesis. Inhibiting ELF4 expression might provide new therapeutic opportunities for kidney fibrosis. Funding: NIDDK Support