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

Cell Biology and Toxicology, vol. 41, pp. 49

Abstract

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.

Authors 17

1. Lukas S. Wijaya corresponding Aachen Division of Drug Discovery and Safety Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands

2. Steven J. Kunnen corresponding Aachen Division of Drug Discovery and Safety Leiden Academic Centre for Drug Research

   Leiden University

   Affiliation as printed

   Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands

3. Panuwat Trairatphisan corresponding

   AbbVie (Germany) · Sanofi (Germany)

   Affiliation as printed

   , Sanofi, Frankfurt, Hesse, Germany

   Abbvie Deutschland, GmbH & Co KG, Ludwigshafen, Germany

   Sanofi, Frankfurt, Hesse, Germany

4. Ciaran P. Fisher corresponding

   GlaxoSmithKline (United Kingdom)

   Affiliation as printed

   GlaxoSmithKline Plc, Stevenage, England, UK

5. Meredith E. Crosby corresponding

   Regeneron (United States) · AbbVie (United States)

   Affiliation as printed

   Drug Safety and Pharmacometrics, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA

   Global Pharmaceutical Research and Development, AbbVie, North Chicago, IL, USA

6. Kai Schaefer corresponding

   AbbVie (Germany)

   Affiliation as printed

   Abbvie Deutschland, GmbH & Co KG, Ludwigshafen, Germany

7. Karen Bodié corresponding

   AbbVie (Germany)

   Affiliation as printed

   Abbvie Deutschland, GmbH & Co KG, Ludwigshafen, Germany

8. Erin E Vaughan corresponding

   AbbVie (United States)

   Affiliation as printed

   Global Pharmaceutical Research and Development, AbbVie, North Chicago, IL, USA

9. Laura Breidenbach corresponding

   AbbVie (Germany)

   Affiliation as printed

   Abbvie Deutschland, GmbH & Co KG, Ludwigshafen, Germany

10. Thomas Reich corresponding

    AbbVie (Germany)

    Affiliation as printed

    Abbvie Deutschland, GmbH & Co KG, Ludwigshafen, Germany

11. Diana Clausznitzer corresponding

    AbbVie (Germany)

    Affiliation as printed

    Abbvie Deutschland, GmbH & Co KG, Ludwigshafen, Germany

12. Sylvestre A. Bonnet corresponding Aachen

    Leiden University

    Affiliation as printed

    Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands

13. Sipeng Zheng corresponding Aachen

    Leiden University

    Affiliation as printed

    Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands

14. Chantal Pont corresponding Aachen Division of Drug Discovery and Safety Leiden Academic Centre for Drug Research

    Leiden University

    Affiliation as printed

    Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands

15. James L. Stevens corresponding Aachen Division of Drug Discovery and Safety Leiden Academic Centre for Drug Research

    Leiden University

    Affiliation as printed

    Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands

16. Sylvia E. Le Dévédec corresponding Aachen Division of Drug Discovery and Safety Leiden Academic Centre for Drug Research

    Leiden University

    Affiliation as printed

    Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands

17. Bob van de Water corresponding Aachen Division of Drug Discovery and Safety Leiden Academic Centre for Drug Research

    Leiden University

    Affiliation as printed

    Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands. b.water@lacdr.leidenuniv.nl

    Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands