Center for Molecular Medicine Cologne

Bernhard Schermer | Max C Liebau - C 14

Discovering novel diseases mechanisms of human ciliopathies using proximity labelling technologies

Introduction

The overarching aim of our project is to gain novel insights in the disease mechanisms of a large heterogeneous group of severe human diseases termed ciliopathies.

While individual ciliopathies are rare conditions, they collectively struck a large number of individuals. We expect our studies to challenge and expand several current pathophysiological concepts in the large field of ciliopathy research.

This will be important for many medical disciplines since ciliopathies manifest in multiple organs (e.g. kidney, brain, eyes, pancreas, liver). Ultimately, we hope to provide novel key mechanisms and potential therapeutic targets to the pathogenesis of ciliopathies.

Groundbreaking work of the last two decades has revealed that mutations in genes encoding for proteins localized to primary cilia are causative for a large number of different human diseases, nowadays subsumed as a group termed ciliopathies.

A hallmark of most ciliopathies is the development of cystic kidneys caused by altered function and proliferation of epithelial cells. Multiple other tissues can also be severely affected. Beyond hereditary ciliopathies, there is accumulating evidence that cilia may be involved in the pathogenesis of various acquired diseases including diabetes and cancer.

Primary cilia are sensory organelles that, like antennae, project from the surface of virtually all mammalian cells explaining the broad spectrum of defects and clinical symptoms observed in ciliopathies. To exert their signaling functions, cilia are covered by a specialized compartment of the plasma membrane and the entry of proteins into the ciliary compartment and the ciliary membrane is strictly regulated.

While basic mechanisms of ciliogenesis, ciliary disassembly, ciliary targeting, intra-flagellar transport and ‘classical’ ciliary signaling such as Hedgehog or WNT signaling have been extensively studied in the recent past, the exact molecular alterations of primary cilia in human ciliopathies have not been identified so far due to technical limitations. Since the vast majority of ciliopathy-causing mutations do not result in the loss of ciliogenesis, a detailed understanding of the subtle and largely unknown alterations of cilia in ciliopathies is urgently needed to decipher the mechanisms of disease.

To break down technical limitations in studying ciliary protein composition we fused the engineered peroxidase APEX2 to a ciliary targeting motiv and used proximity labeling and pulldowns followed by MS/MS analyses to explore the ciliary membrane associated proteome.

This approach revealed numerous novel ciliary proteins unexpectedly including actin-binding proteins and even more unforeseen families of proteins.

The overarching goal of the at hand project is to use and expand this technology to get a deeper understanding of the molecular composition of cilia and their alterations in ciliopathies both in patient derived cells and model organisms.

Previous Work

To overcome limitations in the analysis of the ciliary proteome we used APEX-based proximity labeling1 to biotinylate and pull down ciliary membrane associated proteins for subsequent MS/MS analysis (‘ciliary membrane APEX’ (cmAPEX);2). With this approach we identified numerous novel ciliary proteins in renal epithelial cells. Among those we found actin binding proteins to be very prominent. Following up on this, we could demonstrate that myosin 5a is essential for ciliogenesis by using knockout (KO) cell lines generated with CRISPR/Cas9. This function has been confirmed independently by another lab.3

We recently used the same experimental approach to study ciliary disassembly. In brief, we induced ciliogenesis by serum starvation for 48 h and stimulated ciliary disassembly by serum addition. The ciliary proteome was determined at 45 min, 2 h and 8 h after serum addition. Interestingly, within these datasets, a number of proteins related to unexpected biological processes were detectable with an increased abundance. We are currently following up on these hits and hope to obtain a deeper understanding of the interplay of cilia with other processes and structures of cellular biology. In summary, ciliary proximity labeling allows the comprehensively analysis of the ciliary proteome with very high sensitivity and provided some more evidence on a potential role of cilia in cellular biology.

Project Related Publications

  1. 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.: Inactivation of Apoptosis Antagonizing Transcription Factor in tubular epithelial cells induces accumulation of DNA damage and nephronophthisis. Kidney Int. (2019);  95: 846-858.
  2. Dafinger, C., Rinschen, M.M., Borgal, L., Ehrenberg, C., Basten, S.G., Franke, M., Hohne, M., Rauh, M., Gobel, H., Bloch, W., Wunderlich, F.T., Peters, D.J.M., Tasche, D., Mishra, T., Habbig, S., Dotsch, J., Muller, R.U., Bruning, J.C., Persigehl, T., Giles, R.H., Benzing, T., Schermer, B.*, and Liebau, M.C.*: Targeted deletion of the AAA-ATPase Ruvbl1 in mice disrupts ciliary integrity and causes renal disease and hydrocephalus. Exp Mol Med. (2018);  50: 75.  (*equal contribution)
  3. Burgmaier K, Kunzmann K, Ariceta G, Bergmann C, Buescher AK, Burgmaier M, Dursun I, Duzova A, Eid L, Feldkoetter M, Gessner M, Gokce I, Haffner D, Hooman N, Hoppe B, Jankauskiene A, Klaus G, König J, Litwin M, Massella L, Mekahli D, Melek E, Mir S, Pape L, Prikhodina L, Ranchin B, Schild R, Seeman T, Sever L, Shroff R, Soliman NA, Stabouli S, Stanczyk M, Tabel Y, Taranta-Janusz K, Testa S, Thumfart J, Topaloglu R, Weber LT, Wicher D, Wühl E, Wygoda S, Yilmaz A, Zachwieja K, Zagozdzon I, Zerres K, ESCAPE Study Group, GPN Study Group, Dötsch J, Schaefer F, Liebau MC for the ARegPKD consortium. “Risk Factors for Early Dialysis Dependency in ARPKD”; J Peds 2018 Aug;199:22-28.e6.
  4. Höhne M, Frese CK, Grahammer F, Dafinger C, Ciarimboli G, Butt L, Binz J, Hackl MJ, Rahmatollahi M, Kann M, Schneider S, Altintas MM, Schermer B, Reinheckel T, Göbel H, Reiser J, Huber TB, Kramann R, Seeger-Nukpezah T, Liebau MC, Beck BB, Benzing T, Beyer A, Rinschen MM. “Individual nephron proteomes connect morphology and function in proteinuric kidney disease”; Kidney Int 2018 Jun;93(6):1308-1319.
  5. 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.: YAP-mediated mechanotransduction determines the podocyte's response to damage. Sci Signal. (2017);  10.
  6. Kohli, P., Hohne, M., Jungst, C., Bertsch, S., Ebert, L.K., Schauss, A.C., Benzing, T., Rinschen, M.M., and Schermer, B.: The ciliary membrane-associated proteome reveals actin-binding proteins as key components of cilia. EMBO Rep. (2017);  18: 1521-1535.
  7. Gandhirajan, R.K., Jain, M., Walla, B., Johnsen, M., Bartram, M.P., Huynh Anh, M., Rinschen, M.M., Benzing, T., and Schermer, B.: Cysteine S-Glutathionylation Promotes Stability and Activation of the Hippo Downstream Effector Transcriptional Co-activator with PDZ-binding Motif (TAZ). J Biol Chem. (2016);  291: 11596-607.
  8. Borgal, L., Rinschen, M.M., Dafinger, C., Liebrecht, V.I., Abken, H., Benzing, T., and Schermer, B.: Jade-1S phosphorylation induced by CK1alpha contributes to cell cycle progression. Cell Cycle. (2016);  15: 1034-45.
  9. Kohli, P., Bartram, M.P., Habbig, S., Pahmeyer, C., Lamkemeyer, T., Benzing, T., Schermer, B.*, and Rinschen, M.M.*: Label-free quantitative proteomic analysis of the YAP/TAZ interactome. Am J Physiol Cell Physiol. (2014);  306: C805-18. (*equal contribution)
  10. Borgal, L., Rinschen, M.M., Dafinger, C., Hoff, S., Reinert, M.J., Lamkemeyer, T., Lienkamp, S.S., Benzing, T., and Schermer, B.: Casein kinase 1 alpha phosphorylates the Wnt regulator Jade-1 and modulates its activity. J Biol Chem. (2014);  289: 26344-56.

References

  1. Rhee H-W, Zou P, Udeshi ND, et al. Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. Science 2013;339(6125):1328–31.
  2. Kohli P, Höhne M, Jüngst C, et al. The ciliary membrane-associated proteome reveals actin-binding proteins as key components of cilia. EMBO Rep 2017;18(9):1521–35.
  3. Wu C-T, Chen H-Y, Tang TK. Myosin-Va is required for preciliary vesicle transportation to the mother centriole during ciliogenesis. Nat Cell Biol 2018;20(2):175–85.

 

Prof. Dr. Bernhard Schermer CMMC Cologne
Prof. Dr. Bernhard Schermer

Dept. II of Internal Medicine / RG location - CECAD Building

Principal Investigator - C 14
Executive Board Member

 

+49 221 478 89030

+49 221 478 6360

Dept. II of Internal Medicine / RG location - CECAD Building

Joseph-Stelzmann-Str. 26

50931 Cologne

http://www.kidneyresearchcenter.org/52/Research/Cystic-Kidney-Diseases-and-Cilia-Biology/Cilia-Biology-and-Cystic-Kidney-Disease-%E2%80%93-Bernhard-Schermer.htm

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Publications - Bernhard Schermer

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PD Dr. Max C Liebau CMMC Cologne
PD Dr. Max C Liebau

Dept. of Children and Adolescent Medicine / RG location - CECAD Building

Co-Principal Investigator - C 14

+49 221 478 4359

+49 221 478 97295

Dept. of Children and Adolescent Medicine / RG location - CECAD Building

Kerpener Straße 62

50937 Cologne

http://www.kidneyresearchcenter.org/49/Research/Cystic-Kidney-Diseases-and-Cilia-Biology/Molecular-pathogenesis-of-ARPKD-%E2%80%93-Max-Liebau.htm

CMMC Profile Page

Publications - Max C Liebau

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Figure 1