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Dederer V, Sanz Murillo M, Karasmanis EP, Hatch KS, Chatterjee D, Preuss F, Abdul Azeez KR, Nguyen LV, Galicia C, Dreier B, Plückthun A, Versees W, Mathea S, Leschziner AE, Reck-Peterson SL, Knapp S. A designed ankyrin-repeat protein that targets Parkinson's disease-associated LRRK2. J Biol Chem 2024; 300:107469. [PMID: 38876305 DOI: 10.1016/j.jbc.2024.107469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
Leucine rich repeat kinase 2 (LRRK2) is a large multidomain protein containing two catalytic domains, a kinase and a GTPase, as well as protein interactions domains, including a WD40 domain. The association of increased LRRK2 kinase activity with both the familial and sporadic forms of Parkinson's disease has led to an intense interest in determining its cellular function. However, small molecule probes that can bind to LRRK2 and report on or affect its cellular activity are needed. Here, we report the identification and characterization of the first high-affinity LRRK2-binding designed ankyrin-repeat protein (DARPin), named E11. Using cryo-EM, we show that DARPin E11 binds to the LRRK2 WD40 domain. LRRK2 bound to DARPin E11 showed improved behavior on cryo-EM grids, resulting in higher resolution LRRK2 structures. DARPin E11 did not affect the catalytic activity of a truncated form of LRRK2 in vitro but decreased the phosphorylation of Rab8A, a LRRK2 substrate, in cells. We also found that DARPin E11 disrupts the formation of microtubule-associated LRRK2 filaments in cells, which are known to require WD40-based dimerization. Thus, DARPin E11 is a new tool to explore the function and dysfunction of LRRK2 and guide the development of LRRK2 kinase inhibitors that target the WD40 domain instead of the kinase.
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Affiliation(s)
- Verena Dederer
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Goethe-Universität, Frankfurt, Germany; Aligning Science Across Parkinson's (ASAP), Chevy Chase, Maryland, USA
| | - Marta Sanz Murillo
- Aligning Science Across Parkinson's (ASAP), Chevy Chase, Maryland, USA; Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Eva P Karasmanis
- Aligning Science Across Parkinson's (ASAP), Chevy Chase, Maryland, USA; Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Kathryn S Hatch
- Aligning Science Across Parkinson's (ASAP), Chevy Chase, Maryland, USA; Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Deep Chatterjee
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Goethe-Universität, Frankfurt, Germany; Aligning Science Across Parkinson's (ASAP), Chevy Chase, Maryland, USA
| | - Franziska Preuss
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Goethe-Universität, Frankfurt, Germany
| | - Kamal R Abdul Azeez
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Goethe-Universität, Frankfurt, Germany; Aligning Science Across Parkinson's (ASAP), Chevy Chase, Maryland, USA
| | - Landon Vu Nguyen
- Aligning Science Across Parkinson's (ASAP), Chevy Chase, Maryland, USA; Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Christian Galicia
- VIB-VUB Center for Structural Biology, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Wim Versees
- VIB-VUB Center for Structural Biology, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sebastian Mathea
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Goethe-Universität, Frankfurt, Germany; Aligning Science Across Parkinson's (ASAP), Chevy Chase, Maryland, USA
| | - Andres E Leschziner
- Aligning Science Across Parkinson's (ASAP), Chevy Chase, Maryland, USA; Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Samara L Reck-Peterson
- Aligning Science Across Parkinson's (ASAP), Chevy Chase, Maryland, USA; Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, California, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Goethe-Universität, Frankfurt, Germany; Aligning Science Across Parkinson's (ASAP), Chevy Chase, Maryland, USA.
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Strubel A, Münick P, Hartmann O, Chaikuad A, Dreier B, Schaefer JV, Gebel J, Osterburg C, Tuppi M, Schäfer B, Buck V, Rosenfeldt M, Knapp S, Plückthun A, Diefenbacher ME, Dötsch V. DARPins detect the formation of hetero-tetramers of p63 and p73 in epithelial tissues and in squamous cell carcinoma. Cell Death Dis 2023; 14:674. [PMID: 37828008 PMCID: PMC10570377 DOI: 10.1038/s41419-023-06213-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/15/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023]
Abstract
The two p53 homologues p63 and p73 regulate transcriptional programs in epithelial tissues and several cell types in these tissues express both proteins. All members of the p53 family form tetramers in their active state through a dedicated oligomerization domain that structurally assembles as a dimer of dimers. The oligomerization domain of p63 and p73 share a high sequence identity, but the p53 oligomerization domain is more divergent and it lacks a functionally important C-terminal helix present in the other two family members. Based on these structural differences, p53 does not hetero-oligomerize with p63 or p73. In contrast, p63 and p73 form hetero-oligomers of all possible stoichiometries, with the hetero-tetramer built from a p63 dimer and a p73 dimer being thermodynamically more stable than the two homo-tetramers. This predicts that in cells expressing both proteins a p632/p732 hetero-tetramer is formed. So far, the tools to investigate the biological function of this hetero-tetramer have been missing. Here we report the generation and characterization of Designed Ankyrin Repeat Proteins (DARPins) that bind with high affinity and selectivity to the p632/p732 hetero-tetramer. Using these DARPins we were able to confirm experimentally the existence of this hetero-tetramer in epithelial mouse and human tissues and show that its level increases in squamous cell carcinoma.
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Affiliation(s)
- Alexander Strubel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Philipp Münick
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Oliver Hartmann
- Department of Biochemistry and Molecular Biology I, University of Würzburg, 97074, Würzburg, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University, 60438, Frankfurt, Germany
- Structural Genomics Consortium, Goethe University, 60438, Frankfurt, Germany
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Jakob Gebel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Christian Osterburg
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Marcel Tuppi
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Birgit Schäfer
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany
| | - Viktoria Buck
- Department of Pathology, University of Würzburg, 97074, Würzburg, Germany
| | - Mathias Rosenfeldt
- Department of Pathology, University of Würzburg, 97074, Würzburg, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University, 60438, Frankfurt, Germany
- Structural Genomics Consortium, Goethe University, 60438, Frankfurt, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Markus E Diefenbacher
- Department of Biochemistry and Molecular Biology I, University of Würzburg, 97074, Würzburg, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438, Frankfurt, Germany.
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Smirnov A, Melino G, Candi E. Gene expression in organoids: an expanding horizon. Biol Direct 2023; 18:11. [PMID: 36964575 PMCID: PMC10038780 DOI: 10.1186/s13062-023-00360-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/20/2023] [Indexed: 03/26/2023] Open
Abstract
Recent development of human three-dimensional organoid cultures has opened new doors and opportunities ranging from modelling human development in vitro to personalised cancer therapies. These new in vitro systems are opening new horizons to the classic understanding of human development and disease. However, the complexity and heterogeneity of these models requires cutting-edge techniques to capture and trace global changes in gene expression to enable identification of key players and uncover the underlying molecular mechanisms. Rapid development of sequencing approaches made possible global transcriptome analyses and epigenetic profiling. Despite challenges in organoid culture and handling, these techniques are now being adapted to embrace organoids derived from a wide range of human tissues. Here, we review current state-of-the-art multi-omics technologies, such as single-cell transcriptomics and chromatin accessibility assays, employed to study organoids as a model for development and a platform for precision medicine.
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Affiliation(s)
- Artem Smirnov
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Eleonora Candi
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.
- Biochemistry Laboratory, Istituto Dermopatico Immacolata (IDI-IRCCS), 00166, Rome, Italy.
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Logotheti S, Pavlopoulou A, Marquardt S, Takan I, Georgakilas AG, Stiewe T. p73 isoforms meet evolution of metastasis. Cancer Metastasis Rev 2022; 41:853-869. [PMID: 35948758 DOI: 10.1007/s10555-022-10057-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/30/2022] [Indexed: 01/25/2023]
Abstract
Cancer largely adheres to Darwinian selection. Evolutionary forces are prominent during metastasis, the final and incurable disease stage, where cells acquire combinations of advantageous phenotypic features and interact with a dynamically changing microenvironment, in order to overcome the metastatic bottlenecks, while therapy exerts additional selective pressures. As a strategy to increase their fitness, tumors often co-opt developmental and tissue-homeostasis programs. Herein, 25 years after its discovery, we review TP73, a sibling of the cardinal tumor-suppressor TP53, through the lens of cancer evolution. The TP73 gene regulates a wide range of processes in embryonic development, tissue homeostasis and cancer via an overwhelming number of functionally divergent isoforms. We suggest that TP73 neither merely mimics TP53 via its p53-like tumor-suppressive functions, nor has black-or-white-type effects, as inferred by the antagonism between several of its isoforms in processes like apoptosis and DNA damage response. Rather, under dynamic conditions of selective pressure, the various p73 isoforms which are often co-expressed within the same cancer cells may work towards a common goal by simultaneously activating isoform-specific transcriptional and non-transcriptional programs. Combinatorial co-option of these programs offers selective advantages that overall increase the likelihood for successfully surpassing the barriers of the metastatic cascade. The p73 functional pleiotropy-based capabilities might be present in subclonal populations and expressed dynamically under changing microenvironmental conditions, thereby supporting clonal expansion and propelling evolution of metastasis. Deciphering the critical p73 isoform patterns along the spatiotemporal axes of tumor evolution could identify strategies to target TP73 for prevention and therapy of cancer metastasis.
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Affiliation(s)
- Stella Logotheti
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), 15780, Zografou, Greece.
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center (IBG), 35340, Balcova, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340, Balcova, Izmir, Turkey
| | - Stephan Marquardt
- Institute of Translational Medicine for Health Care Systems, Medical School Berlin, Hochschule Für Gesundheit Und Medizin, 14197, Berlin, Germany
| | - Işıl Takan
- Izmir Biomedicine and Genome Center (IBG), 35340, Balcova, Izmir, Turkey.,Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340, Balcova, Izmir, Turkey
| | - Alexandros G Georgakilas
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), 15780, Zografou, Greece
| | - Thorsten Stiewe
- Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University, Marburg, Germany.,Institute of Lung Health, Giessen, Germany.,German Center for Lung Research (DZL), Philipps-University, Marburg, Germany
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