1. Research Background:

Kidney disease is a very common ageing-associated disorder and is a major risk factor for cardiovascular morbidity and mortality¹. We study the molecular mechanisms involved in the pathogenesis of renal function decline and aim to identify novel strategies to prevent kidney disease. In this context, modulation of cellular metabolism as a strategy to increase stress resistance and treat kidney disease is the central focus of our work. In this context, we have a special interest in RNA-biology considering both the growing body of evidence regarding the impact of RNA-binding proteins in metabolic processes and the lack of knowledge regarding non-coding RNAs and RNA-protein interactions². Consequently, this research harbors a great potential to identify novel pathomechanisms and therapeutic targets. Importantly, all basic research in our lab is accompanied by clinical trials translating the findings from bench to bedside.

2. Research questions addresses by the group:

• How do interventions that mediate longevity and stress resistance modulate cellular metabolism?
• Which metabolic pathways are crucial to organ protection? Which metabolites are involved and how do they mediate their effect?
• How do non-coding RNAs and RNA-binding proteins modulate ageing-associated phenotypes and renal function decline? Is this effect dependent on cell-type specific expression and functions?
• Which RNA-protein binding events are altered by kidney disease and can be therapeutically targeted?
• How do RNA-binding proteins influence cellular metabolism?
• Can RNA-protein binding be targeted therapeutically to protect from kidney injury?

3. Possible projects:

• Project 1:
  Metabolic modulation as a novel strategy for the treatment of polycystic kidney disease
  Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic cause of end-stage kidney failure with a lifetime prevalence of ~1/1,000 and affects more than 7 Mio. people worldwide. Currently, therapeutic strategies are limited³⁴. Cyst-lining epithelial cells in polycystic kidney disease have an altered metabolism involving aerobic glycolysis and defective fatty acid oxidation⁵. Interestingly, dietary approaches (including the induction of ketosis) have been found to be extremely potent therapeutic strategies in animal models of PKD⁶. We are currently running the very first clinical trials testing these approaches in humans. This project will focus (1) on the optimization of these approaches in rodent models of PKD by comparing different dietary regimens, (2) use human biosamples to examine metabolic consequences of the dietary interventions employed in the trials and (3) aim to elucidate the molecular mechanisms involved in the dietary amelioration of ADPKD. In this context, we will focus on the impact of enigmRBPs⁷ as modulators of cellular metabolism in ADPKD.
• Project 2:
  RNA-binding proteins as modulators of cellular metabolism in renal organ protection
  Using RNAseq datasets of the kidney after cisplatin⁸ and ischemia-reperfusion induced acute kidney injury in a mouse model combined with datasets on mice pre-treated by caloric restriction, hypoxic preconditioning and prolyl hydroxylase inhibitors we were able to identify a number of RNA-binding proteins (RBPs) to be significantly dysregulated as candidates to be involved in the protection from acute kidney injury. Interestingly, several of these RBPs appear to be enzymes associated with metabolic processes known to be involved in acute renal damage. We will now study these RBPs in detail focusing on the following questions: How does cell-type specific expression change upon renal damage and preconditioning (using snRNAseq⁹)? Which RNA targets do these RBPs bind to (using eCLIP)? What is the impact of RNA-binding on the activity of the associated metabolic pathways? Can modulation of RNA-binding be used as a therapeutic strategy in acute kidney injury?

4. Applied Methods and model organisms:

• model organisms: cell culture^10,11, C. elegans^12–14 and mouse^8,15
• all standard methods in molecular and cellular biology (such as molecular cloning, Western Blotting, Immunofluorescence etc.)
• state-of-the-art methods regarding RNA-RNA and RNA-protein interactions, e.g. CLIP (crosslinking and immunoprecipitation)^10–12, CHART-MS, RNA interactome capture, proteomics⁸, RNA-sequencing (including single-cell RNAseq)^9,15, RNA modifications¹⁶
• transgenesis and CRISPR-Cas9 mediated genome editing
• several mouse models of kidney disease
• bioinformatics analysis of the datasets obtained

5. Desirable skills and qualifications:

• good training in and understanding of standard techniques in molecular and cellular biology
• interest in tackling clinically relevant questions using these techniques in cell culture and model organisms
• FELASA certificate would be desirable, but can also be obtained the project
• basic bioinformatics skills would be desirable, but can also be obtained during the first months of the project. However, an interest in the analysis of large-scale datasets under the supervision of a bioinformatician is required

6. References:

1. Hsu, R. K., McCulloch, C. E., Dudley, R. A., Lo, L. J. & Hsu, C. Temporal changes in incidence of dialysis-requiring AKI. J. Am. Soc. Nephrol. JASN24, 37–42 (2013).
2. Seufert, L., Benzing, T., Ignarski, M. & Müller, R.-U. RNA-binding proteins and their role in kidney disease. Nat. Rev. Nephrol. 1–18 (2021) doi:10.1038/s41581-021-00497-1.
3. Müller, R.-U. et al. An update on the use of tolvaptan for autosomal dominant polycystic kidney disease: consensus statement on behalf of the ERA Working Group on Inherited Kidney Disorders, the European Rare Kidney Disease Reference Network and Polycystic Kidney Disease International. Nephrol. Dial. Transplant.37, 825–839 (2022).
4. Müller, R.-U. & Benzing, T. Management of autosomal-dominant polycystic kidney disease—state-of-the-art. Clin. Kidney J.11, i2–i13 (2018).
5. Haumann, S., Müller, R.-U. & Liebau, M. C. Metabolic Changes in Polycystic Kidney Disease as a Potential Target for Systemic Treatment. Int. J. Mol. Sci.21, (2020).
6. Torres, J. A. et al. Ketosis ameliorates renal cyst growth in polycystic kidney disease. Cell Metab, in press (2019).
7. Castello, A., Hentze, M. W. & Preiss, T. Metabolic Enzymes Enjoying New Partnerships as RNA-Binding Proteins. Trends Endocrinol. Metab. TEM26, 746–757 (2015).
8. Späth, M. R. et al. The proteome microenvironment determines the protective effect of preconditioning in cisplatin-induced acute kidney injury. Kidney Int.95, 333–349 (2019).
9. Karaiskos, N. et al. A Single-Cell Transcriptome Atlas of the Mouse Glomerulus. J. Am. Soc. Nephrol. JASN29, 2060–2068 (2018).
10. Ignarski, M. et al. The RNA-Protein Interactome of Differentiated Kidney Tubular Epithelial Cells. J. Am. Soc. Nephrol. JASN30, 564–576 (2019).
11. Kaiser, R. W. J. et al. A protein-RNA interaction atlas of the ribosome biogenesis factor AATF. Sci. Rep.9, 11071 (2019).
12. Esmaillie, R. et al. Activation of Hypoxia-Inducible Factor Signaling Modulates the RNA Protein Interactome in Caenorhabditis elegans. iScience22, 466–476 (2019).
13. Gharbi, H. et al. Loss of the Birt-Hogg-Dubé gene product folliculin induces longevity in a hypoxia-inducible factor-dependent manner. Aging Cell12, 593–603 (2013).
14. Müller, R.-U. et al. The von Hippel Lindau tumor suppressor limits longevity. J. Am. Soc. Nephrol. JASN20, 2513–2517 (2009).
15. Johnsen, M. et al. The Integrated RNA Landscape of Renal Preconditioning against Ischemia-Reperfusion Injury. J. Am. Soc. Nephrol. JASN31, 716–730 (2020).
16. Dal Magro, C. et al. A Vastly Increased Chemical Variety of RNA Modifications Containing a Thioacetal Structure. Angew. Chem. Int. Ed Engl.57, 7893–7897 (2018).