Nfkb1 Removal from Proximal Tubule Cells Improves Renal Tubular Outcomes Following Ischemia Reperfusion Injury

Shun-Yang Cheng; Kari Koppitch; Jinjin Guo; Nathan Moy; Taylor L Simonian; Parker C Wilson; Andrew P McMahon

doi:10.34067/KID.0000000868

Nfkb1 Removal from Proximal Tubule Cells Improves Renal Tubular Outcomes Following Ischemia Reperfusion Injury

Kidney360. 2025 Jun 4. doi: 10.34067/KID.0000000868. Online ahead of print.

Authors

Shun-Yang Cheng¹, Kari Koppitch¹, Jinjin Guo¹, Nathan Moy¹, Taylor L Simonian¹, Parker C Wilson², Andrew P McMahon^{1

3}

Affiliations

¹ Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for 8 Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
² Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, PA, USA.
³ Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.

PMID: 40465395
DOI: 10.34067/KID.0000000868

Abstract

Background: CKD is a significant global health burden. AKI is a risk factor for progression to CKD. Recent studies have linked a failure in proximal tubule repair as a potential contributing factor to CKD in mouse and human studies. Failed repair proximal tubule cells (FR-PTCs), initially present at the site of maximal sensitivity to ischemia reperfusion injury and spreading to more cortical regions over time, adopt a senescence-associated secretory phenotype (SASP) linked to activation of the NF-kB pathway. Several transcriptional regulatory factors mediate NF-kB pathway action. Of these, Nfkb1 is prominent within FR-PTCs and chromatin studies predict Nfkb1 interactions with pathology-associated gene targets.

Methods: To examine the role of NF-kB in nephron injury outcomes, we removed Nfkb1 activity within the nephron lineage of the mouse kidney and examined the kidney's response to bilateral ischemia reperfusion injury (Bi-IRI).

Results: Single cell transcriptional analysis showed a significant reduction of inflammation-associated gene expression, including Ccl2, Birc3, Spp1, Cd47, and Traf1, in Nfkb1 deficient FR-PTCs. A reduced pathological signature correlated with normalized expression of genes associated with healthy proximal tubule function including Cubn, Kap, and a number of solute carriers. Single-nucleus ATAC-seq analysis linked transcriptomic changes to enhancer regulation, in particular, marked opening of chromatin for targets of HNF-family members associated with normal regulation of gene expression in PTCs.

Conclusions: Examining ATAC-seq motif predictions and performing direct immunolabelling studies suggested Relb, another transcriptional mediator of NF-κB transcriptional responses with overlapping targeting specificity to Nfkb1, may partially compensate for the loss of Nfkb1. These studies support future efforts to remove ongoing NF-κB signaling within nephrons as a potential therapeutic strategy to target the AKI-to-CKD transition.