1. Research Background:

Kidney disease is a very common aging-associated disorder and is a major risk factor for cardiovascular morbidity and mortality. We study the molecular mechanisms involved in the pathogenesis of renal function decline and aim to identify novel strategies to prevent and/or cure 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. 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 interactions in kidney disease, we have a special interest in RNA-biology. 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 addressed by the group:

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

3. Possible project:

Riboregulation of the aldolase family in kidney disease and nephroprotection

This project will follow-up on our recent observation that aldolases, well-described enzymes of glycolysis and gluconeogenesis, have the capacity to bind RNA. Aldolases bind RNAs differentially based on the level of cellular oxygenation. We therefore hypothesize that the aldolase family is subjected to riboregulation resulting in adaptation of the glycolysis pathway in acute kidney injury (AKI). Considering the importance of metabolic processes for the pathogenesis of AKI the project is structured to achieve three major aims:

1. Identification of RNA-binding regions and characterization of transcripts interacting with Aldoa and Aldob.
2. Analysis of the impact of RNA-binding on the enzymatic activity of aldolases and its effects on the glycolytic pathway.
3. Unraveling the role of riboregulatory effects of the aldolase family and protective preconditioning strategies in mouse models of AKI.

We expect that this project will significantly enhance the understanding of riboregulatory processes in metabolic pathways and shed light on new entry points for pharmacological treatment.

4. Applied Methods and model organisms:

• Model organisms: cell culture, C. elegans and mouse (including models of kidney disease)
• Standard methods in molecular and cellular biology
• State-of-the-art methods regarding proteomics, RNA-sequencing (including single- cell RNAseq), RNA-protein interactions, e.g. CLIPseq (crosslinking and immunoprecipitation), RIC (RNA-interactome capture)
• Transgenesis and CRISPR-Cas9 mediated genome editing
• 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 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 and key publications:

• Seufert L, Benzing T, Ignarski M, Müller RU. RNA-binding proteins and their role in kidney disease. Nat Rev Nephrol. 2022 Mar;18(3):153-170. doi: 10.1038/s41581- 021-00497-1.
• Ignarski M, Rill C, Kaiser RWJ, Kaldirim M, Neuhaus R, Esmaillie R, Li X, Klein C, Bohl K, Petersen M, Frese CK, Höhne M, Atanassov I, Rinschen MM, Höpker K, Schermer B, Benzing T, Dieterich C, Fabretti F, Müller RU. The RNA-Protein Interactome of Differentiated Kidney Tubular Epithelial Cells. J Am Soc Nephrol. 2019 Apr;30(4):564-576. doi: 10.1681/ASN.2018090914.
• Kaiser RWJ, Ignarski M, Van Nostrand EL, Frese CK, Jain M, Cukoski S, Heinen H, Schaechter M, Seufert L, Bunte K, Frommolt P, Keller P, Helm M, Bohl K, Höhne M, Schermer B, Benzing T, Höpker K, Dieterich C, Yeo GW, Müller RU, Fabretti F. A protein-RNA interaction atlas of the ribosome biogenesis factor AATF. Sci Rep. 2019 Jul 30;9(1):11071. doi: 10.1038/s41598-019-47552-3.
• Esmaillie R, Ignarski M, Bohl K, Krüger T, Ahmad D, Seufert L, Schermer B, Benzing T, Müller RU, Fabretti F. Activation of Hypoxia-Inducible Factor Signaling Modulates the RNA Protein Interactome in Caenorhabditis elegans. iScience. 2019 Dec 20;22:466-476. doi: 10.1016/j.isci.2019.11.039.
• Huppertz I, Perez-Perri JI, Mantas P, Sekaran T, Schwarzl T, Russo F, Ferring-Appel D, Koskova Z, Dimitrova-Paternoga L, Kafkia E, Hennig J, Neveu PA, Patil K, Hentze MW. Riboregulation of Enolase 1 activity controls glycolysis and embryonic stem cell differentiation. Mol Cell. 2022 Jul 21;82(14):2666-2680.e11. doi: 10.1016/j.molcel.2022.05.019.