Interleukin enhancer binding factor 2 (Ilf2) and kidney epithelial stress resilience

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Item Type:	Preprint
Title:	Interleukin enhancer binding factor 2 (Ilf2) and kidney epithelial stress resilience
Creators Name:	Cao, Shuang, López-Cayuqueo, Karen I., Leiz, Janna, Boivin, Felix J., Markó, Lajos, Hinze, Christian and Schmidt-Ott, Kai
Abstract:	INTRODUCTION: In the kidney, epithelial cells of medullary collecting ducts (MCD) are exposed to a harsh microenvironment characterized by hyperosmolality, hypoxia, and oxidative stress. Still, under physiological conditions, they show no apparent signs of cellular injury. We hypothesized that the study of transcription factors (TFs) enriched in MCD cells might identify pathways of stress resilience. METHODS: We generated single-cell expression data from mouse kidneys and predicted in silico candidate TFs with MCD-enriched expression and activity. To investigate the transcriptomic effects of perturbing these candidate TFs, we devised a single-cell CRISPR interference (CRISPRi) screen in mouse inner medullary collecting duct (IMCD3) cells. RESULTS: We found that perturbation of interleukin enhancer-binding factor 2 (Ilf2), Krueppellike factor 5 (Klf5), and JunB proto-oncogene (Junb), significantly impacted IMCD3 cells’ gene expression programs, including genes involved in proliferation, apoptosis, and stress-related intracellular signaling, highlighting these TFs as potential regulators of cell-specific resilience. We then focused on Ilf2, validated its impact on gene expression signatures by RNA sequencing, and identified a further role of Ilf2 in the splicing of genes involved in epithelial cellular dynamics and stress responses. Loss of Ilf2 function in IMCD3 cells resulted in nuclear atypia, reduced proliferative capacity, and increased cell death in response to osmotic stress. Ilf2 was upregulated in mouse kidneys during the repair phase following ischemia-reperfusion injury (IRI), as were Ilf2-regulated transcripts and splicing events, suggesting that Ilf2 might serve as a post-ischemic signal to facilitate epithelial stress resilience. CONCLUSIONS: Our approach nominates novel pathways of cellular resilience in kidney tubular cells and highlights Ilf2 as a potential target for kidney protection.
Keywords:	Kidney Medullary Epithelial Cells, Stress Resilience, Nuclear Integrity, RNA Splicing, Proliferation, Repair, Animals, Mice
Source:	bioRxiv
Publisher:	Cold Spring Harbor Laboratory Press
Article Number:	2025.08.12.667599v2
Date:	9 September 2025
Additional Information:	External datasets in Gene Expression Omnibus (GEO) are currently private and scheduled to be released on Jun 30, 2027. Reviewer tokens are the following: GSE299239 (reviewer token onwzwycqtvmntgl), GSE299244 (reviewer token gxibwcquhngpnml), GSE299248 (reviewer token qtklsmwqffwppsz), GSE299251 (reviewer token GSE299251), and GSE299249 (reviewer token edutiqmqxhqxnqp).
Official Publication:	https://doi.org/10.1101/2025.08.12.667599
Related to:	URL URL Type https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE299239 External Dataset https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE299244 External Dataset https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE299248 External Dataset https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE299251 External Dataset https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE299249 External Dataset https://doi.org/10.26068/mhhrpm/20250530-000 External Dataset https://github.com/shuangcao-mhh/Perturb-seq-screening-in-IMCD3-cells Software

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