1. Research Background

Chronic kidney disease (CKD) affects an increasingly large proportion of the aging population in industrialized countries, with a prevalence exceeding 13%. Beyond its progression to end-stage renal disease requiring dialysis or transplantation, CKD is now recognized as a major cardiovascular risk factor and one of the most impactful non-neoplastic diseases affecting overall life expectancy. Despite advances, the pathogenesis of CKD and age-related renal decline remains incompletely understood, with both genetic and environmental factors playing significant roles. Our laboratory investigates the molecular mechanisms underlying kidney disease, with a particular focus on age-associated renal pathologies. Our primary aim is to advance the understanding of age-associated kidney disease to promote healthy aging. Rather than focusing on extending lifespan, we are committed to preserving renal function and improving quality of life in aging populations.

2. Research questions addressed by the group:

A. Primaryciliaandrenal ciliopathies

Cilia are sensory organelles present on the surface of most mammalian cells. In recent years, we and others have demonstrated the essential role of primary cilia and cilia-mediated signaling in maintaining kidney architecture and function. Mutations in genes encoding proteins localized to renal primary cilia represent a major cause of polycystic kidney disease and other degenerative renal disorders in humans. These conditions are collectively termed ciliopathies. Notably, the renal degeneration observed in ciliopathies shows striking similarities to the pathological changes associated with chronic kidney disease arising from natural aging.

Research questions (selection):

• (1) What is the role of R-loop metabolism in ciliopathies and CKD?
• (2) How does genome instability promote CKD development?
• (3) How do regulated cell death (RCD) pathways contribute to kidney degeneration in ciliopathies and CKD? ¹

B. Glomerular diseases and the (patho-) physiology of filtration

The majority of kidney diseases affect glomeruli, the microvascular subunits of the kidney. Here, primary urine, which is almost free of proteins, is generated by a complex filtration process. One essential part of the glomerular filter is podocytes, highly specialized epithelial cells that enwrap the glomerular capillaries. Injury and loss of podocytes lead to the clinical symptom of proteinuria and glomerular sclerosis (FSGS). To gain insights into the filtration process, we used CRISPR/Cas9 to generate knock-in mouse models mimicking late-onset human glomerular disease ². With superresolution imaging (STED) ³ and mathematical modeling ⁴ we suggested a novel model for the understanding of the filtration barrier in the kidney ^2,5.

Research questions (selection):

• (1) Decipher the ultrastructure of the mechanosensor complex at the kidney filtration barrier.
• (2) Understand transcriptional and epigenetic networks and their alterations in FSGS and the aging kidney.
• (3) Investigate the regulation of YAP/TAZ signaling in podocytes.

3. Possible project(s):

Possible projects for Ph.D. candidates include, but are not limited to the following topics:

• Deciphering the initial (and still reversible) steps in the pathogenesis of glomerular diseases using single-cell RNA-Seq and AI-based imaging analyses.
• The role of YAP/TAZ signaling in the pathogenesis of FSGS and of age-related glomerular disease (based on models from^2,6). Following up on our recent snRNA- Seq study ⁷ we now focus on LLPS formation and the Ajuba/YAP/TAZ module.
• Mechanisms of premature aging in ciliopathy models and mice lacking cilia (including the model from⁸): Impact of R-loops on disease progression.

Details will be discussed and developed together with the Ph.D. candidate.

4. Applied Methods and model organisms:

• Models and model organisms: M. musculus, human and murine cell lines, primary cells, iPSCs, 3D kidney organoids, human biopsy material.
• Methods (selection, depending on the specific project): 2D/3D cell culture; genome editing primarily based on CRISPR/Cas9 in mice, iPSCs and cultured human cells; lenti-/retroviral gene transfer; molecular cloning; FACS; genomics (RNA-seq, ChIP-seq, Cut&Tag); proteomics; confocal imaging; super-resolution microscopy (STED/GSD); 2P- intra vital-imaging of the kidney; hybridoma techniques; etc.

5. Desirable skills and qualifications:

We are searching for a highly motivated scientist with great enthusiasm for biomedical research and with the qualities of a great team player.

6. References and key publications:

1. Kieckhofer, E., Slaats, G.G., Ebert, L.K., Albert, M.C., Dafinger, C., Kashkar, H., Benzing, T., and Schermer, B. (2022). Primary cilia suppress Ripk3-mediated necroptosis. Cell Death Discov 8, 477. 10.1038/s41420-022-01272-2.
2. Butt, L., Unnersjo-Jess, D., Hohne, M., Edwards, A., Binz-Lotter, J., Reilly, D., Hahnfeldt, R., Ziegler, V., Fremter, K., Rinschen, M.M., Helmstadter, M., Ebert, L.K., Castrop, H., Hackl, M.J., Walz, G., Brinkkoetter, P.T., Liebau, M.C., Tory, K., Hoyer, P.F., Beck, B.B., Brismar, H., Blom, H., Schermer, B., and Benzing, T. (2020). A molecular mechanism explaining albuminuria in kidney disease. Nat Metab 2, 461-474. 10.1038/s42255-020-0204-y.
3. Unnersjo-Jess, D., Butt, L., Hohne, M., Witasp, A., Kuhne, L., Hoyer, P.F., Patrakka, J., Brinkkotter, P.T., Wernerson, A., Schermer, B., Benzing, T., Scott, L., Brismar, H., and Blom, H. (2021). A fast and simple clearing and swelling protocol for 3D in-situ imaging of the kidney across scales. Kidney Int. 99, 1010-1020. 10.1016/j.kint.2020.10.039.
4. Butt, L., Unnersjo-Jess, D., Hohne, M., Schermer, B., Edwards, A., and Benzing, T. (2021). A mathematical estimation of the physical forces driving podocyte detachment. Kidney Int. 100, 1054-1062. 10.1016/j.kint.2021.06.040.
5. Benzing, T., and Salant, D. (2021). Insights into Glomerular Filtration and Albuminuria. N. Engl. J. Med. 384, 1437-1446. 10.1056/NEJMra1808786.
6. Rinschen, M.M., Grahammer, F., Hoppe, A.K., Kohli, P., Hagmann, H., Kretz, O., Bertsch, S., Hohne, M., Gobel, H., Bartram, M.P., Gandhirajan, R.K., Kruger, M., Brinkkoetter, P.T., Huber, T.B., Kann, M., Wickstrom, S.A., Benzing, T., and Schermer, B. (2017). YAP-mediated mechanotransduction determines the podocyte's response to damage. Sci Signal 10. 10.1126/scisignal.aaf8165.
7. Ester, L., Wiesner, E., Chen, H., Ventzke, M., Diefenhardt, P., Mandel, A.M., Fabretti, F., Brinkkoetter, P.T., Benzing, T., Habbig, S., Kann, M., Cabrita, I., and Schermer, B. (2025). Transcriptional Regulators YAP and TAZ Have Distinct Abilities to Compensate for One Another in Podocytes. J. Am. Soc. Nephrol. 10.1681/ASN.0000000689.
8. Jain, M., Kaiser, R.W.J., Bohl, K., Hoehne, M., Gobel, H., Bartram, M.P., Habbig, S., Muller, R.U., Fogo, A.B., Benzing, T., Schermer, B., Hopker, K., and Slaats, G.G. (2019). Inactivation of Apoptosis Antagonizing Transcription Factor in tubular epithelial cells induces accumulation of DNA damage and nephronophthisis. Kidney Int. 95, 846-858. 10.1016/j.kint.2018.10.034.