Journal Article

Spatio-temporal transcriptomic analysis reveals distinct nephrotoxicity, DNA damage, and regeneration response after cisplatin

Wijaya, Lukas S., Pont, Chantal, Le Dévédec, Sylvia E., Crosby, Meredith E., Zheng, Sipeng, Trairatphisan, Panuwat, Breidenbach, Laura, Kunnen, Steven J., Schaefer, Kai, Clausznitzer, Diana, Bonnet, Sylvestre, Stevens, James L., Fisher, Ciarán P., Vaughan, Erin E., Reich, Thomas, van de Water, Bob, Bodié, Karen

2025

Overview

Nephrotoxicity caused by drug or chemical exposure involves complex mechanisms as well as a temporal integration of injury and repair responses in different nephron segments. Distinct cellular transcriptional programs regulate the time-dependent tissue injury and regeneration responses. Whole kidney transcriptome analysis cannot dissect the complex spatio-temporal injury and regeneration responses in the different nephron segments. Here, we used laser capture microdissection of formalin-fixed paraffin embedded sections followed by whole genome targeted RNA-sequencing-TempO-Seq and co-expression gene-network (module) analysis to determine the spatial–temporal responses in rat kidney glomeruli (GM), cortical proximal tubules (CPT) and outer-medulla proximal tubules (OMPT) comparison with whole kidney, after a single dose of the nephrotoxicant cisplatin. We demonstrate that cisplatin induced early onset of DNA damage in both CPT and OMPT, but not GM. Sustained DNA damage response was strongest in OMPT coinciding with OMPT specific inflammatory signaling, actin cytoskeletal remodeling and increased glycolytic metabolism with suppression of mitochondrial activity. Later responses reflected regeneration-related cell cycle pathway activation and ribosomal biogenesis in the injured OMPT regions. Activation of modules containing kidney injury biomarkers was strongest in OMPT, with OMPT Clu expression highly correlating with urinary clusterin biomarker measurements compared the correlation of Kim1. Our findings also showed that whole kidney responses were less sensitive than OMPT. In conclusion, our LCM-TempO-Seq method reveals a detailed spatial mechanistic understanding of renal injury/regeneration after nephrotoxicant exposure and identifies the most representative mechanism-based nephron segment specific renal injury biomarkers. Graphical Abstract Highlights • Different nephron segments exhibit distinct transcriptomic perturbation with different degrees of sensitivity. • Sustained activation of DNA damage responses upon cisplatin exposure is linked to progressive outcomes of injured nephron regions. • Mechanistic kidney injury biomarkers such as urinary clusterin outperform conventional biomarkers in reflecting the condition of the damaged nephron segments.

• Publisher: Springer Netherlands,Springer Nature B.V
• Subject: Actin / Animals / Biochemistry / Biomarkers / Biomedical and Life Sciences / Cell activation / Cell Biology / Cell cycle / Cisplatin / Cisplatin - toxicity / Clusterin / Cytoskeleton / Damage / Deoxyribonucleic acid / DNA / DNA damage / DNA Damage - drug effects / Exposure / Gene expression / Gene Expression Profiling - methods / Gene sequencing / Glomerulus / Glycolysis / Injuries / Injury analysis / Kidney - drug effects / Kidney - metabolism / Kidney - pathology / Kidney Glomerulus - drug effects / Kidney Glomerulus - metabolism / Kidney Glomerulus - pathology / Kidneys / Life Sciences / Male / Modules / Pharmacology/Toxicology / Proximal tubules / Rats / Rats, Sprague-Dawley / Regeneration / Regeneration - drug effects / Regeneration - genetics / Segments / Transcriptome - drug effects / Transcriptomes / Transcriptomics