1
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Węgrzyn E, Mejdrová I, Müller FM, Nainytė M, Escobar L, Carell T. RNA-Templated Peptide Bond Formation Promotes L-Homochirality. Angew Chem Int Ed Engl 2024; 63:e202319235. [PMID: 38407532 DOI: 10.1002/anie.202319235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
The world in which we live is homochiral. The ribose units that form the backbone of DNA and RNA are all D-configured and the encoded amino acids that comprise the proteins of all living species feature an all-L-configuration at the α-carbon atoms. The homochirality of α-amino acids is essential for folding of the peptides into well-defined and functional 3D structures and the homochirality of D-ribose is crucial for helix formation and base-pairing. The question of why nature uses only encoded L-α-amino acids is not understood. Herein, we show that an RNA-peptide world, in which peptides grow on RNAs constructed from D-ribose, leads to the self-selection of homo-L-peptides, which provides a possible explanation for the homo-D-ribose and homo-L-amino acid combination seen in nature.
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Affiliation(s)
- Ewa Węgrzyn
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Ivana Mejdrová
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Felix M Müller
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Milda Nainytė
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Luis Escobar
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Thomas Carell
- Department of Chemistry, Institute for Chemical Epigenetics (ICE-M), Ludwig-Maximilians-Universität (LMU) München, Butenandtstrasse 5-13, 81377, Munich, Germany
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2
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Tölke AJ, Gaisbauer JF, Gärtner YV, Steigenberger B, Holovan A, Streshnev F, Schneider S, Müller M, Carell T. Efficient Tandem Cu-Catalyzed Click Synthesis of Multi-Sugar-Modified Oligonucleotides. Angew Chem Int Ed Engl 2024:e202405161. [PMID: 38606873 DOI: 10.1002/anie.202405161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/13/2024]
Abstract
Nucleic acids in the form of siRNA, antisense oligonucleotides or mRNA are currently explored as new promising modalities in the pharmaceutical industry. Particularly, the success of mRNA-vaccines against SARS-CoV-2, along with the successful development of the first sugar-modified siRNA therapeutics has inspired the field. The development of nucleic acid therapeutics requires efficient chemistry to link oligonucleotides to chemical structures that can improve stability, boost cellular uptake, or enable specific targeting. For the siRNA therapeutics currently in use, modification of the 3'-end of the oligonucleotides with triple-N-acetylgalactosamine (GalNAc)3 was shown to be of significance. This modification is currently achieved via a cumbersome multi-step synthesis and subsequent loading onto the solid support material. Here, we report the development of a bifunctional click-reactive linker that allows the modification of oligonucleotides in a tandem click reaction with multiple sugars, regardless of the position within the oligonucleotide, with remarkable efficiency and in a one-pot reaction.
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Affiliation(s)
| | | | | | | | - Anna Holovan
- Ludwig-Maximilians-Universität München, Chemie, GERMANY
| | | | | | - Markus Müller
- Ludwig-Maximilians-Universität München, Chemie, GERMANY
| | - Thomas Carell
- Ludwig-Maximilians-Universitat Munchen, Department of Chemistry and Biochemistry, Butenandtstraße 5-13, 81377, München, GERMANY
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3
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Schönegger ES, Crisp A, Radukic M, Burmester J, Frischmuth T, Carell T. Orthogonal End Labelling of Oligonucleotides through Dual Incorporation of Click-Reactive NTP Analogues. Chembiochem 2024; 25:e202300701. [PMID: 37861375 DOI: 10.1002/cbic.202300701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 10/20/2023] [Indexed: 10/21/2023]
Abstract
Post-synthetic modification of nucleic acid structures with clickable functionality is a versatile tool that facilitates many emerging applications, including immune evasion, enhancements in stability, fluorescent labelling, chemical 5'-RNA-capping and the development of functional aptamers. While certain chemoenzymatic approaches for 3'-azido and alkynyl labelling are known, equivalent 5'-strategies are either inefficient, complex, or require harsh chemical conditions. Here, we present a modular and facile technology to consecutively modify DNA and RNA strands at both ends with click-modifiable functional groups. Our approach using γ-modified ATP analogues facilitates T4 PNK-catalysed 5'-modification of oligonucleotides, a process that is compatible with TdT-catalysed 3'-elongation using 3'-azido-2',3'-ddGTP. Finally, we demonstrate that our approach is suitable for both oligo-oligo ligations, as well ssDNA circularization. We anticipate that such approaches will pave the way for the synthesis of highly functionalised oligonucleotides, improving the therapeutic and diagnostic applicability of oligonucleotides such as in the realm of next-generation sequencing.
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Affiliation(s)
- Eva S Schönegger
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
- baseclick GmbH, Floriansbogen 2-4, 82061, Neuried, Germany
| | - Antony Crisp
- baseclick GmbH, Floriansbogen 2-4, 82061, Neuried, Germany
| | - Marco Radukic
- Technische Fakultät, Universität Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany
| | | | | | - Thomas Carell
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
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4
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Helm M, Bohnsack MT, Carell T, Dalpke A, Entian KD, Ehrenhofer-Murray A, Ficner R, Hammann C, Höbartner C, Jäschke A, Jeltsch A, Kaiser S, Klassen R, Leidel SA, Marx A, Mörl M, Meier JC, Meister G, Rentmeister A, Rodnina M, Roignant JY, Schaffrath R, Stadler P, Stafforst T. Experience with German Research Consortia in the Field of Chemical Biology of Native Nucleic Acid Modifications. ACS Chem Biol 2023; 18:2441-2449. [PMID: 37962075 DOI: 10.1021/acschembio.3c00586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The chemical biology of native nucleic acid modifications has seen an intense upswing, first concerning DNA modifications in the field of epigenetics and then concerning RNA modifications in a field that was correspondingly rebaptized epitranscriptomics by analogy. The German Research Foundation (DFG) has funded several consortia with a scientific focus in these fields, strengthening the traditionally well-developed nucleic acid chemistry community and inciting it to team up with colleagues from the life sciences and data science to tackle interdisciplinary challenges. This Perspective focuses on the genesis, scientific outcome, and downstream impact of the DFG priority program SPP1784 and offers insight into how it fecundated further consortia in the field. Pertinent research was funded from mid-2015 to 2022, including an extension related to the coronavirus pandemic. Despite being a detriment to research activity in general, the pandemic has resulted in tremendously boosted interest in the field of RNA and RNA modifications as a consequence of their widespread and successful use in vaccination campaigns against SARS-CoV-2. Funded principal investigators published over 250 pertinent papers with a very substantial impact on the field. The program also helped to redirect numerous laboratories toward this dynamic field. Finally, SPP1784 spawned initiatives for several funded consortia that continue to drive the fields of nucleic acid modification.
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Affiliation(s)
- Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Alexander Dalpke
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe-University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | | | - Ralf Ficner
- Institute for Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Christian Hammann
- Department of Medicine, HMU Health and Medical University, 14471 Potsdam, Germany
| | - Claudia Höbartner
- Institute for Organic Chemistry, Julius-Maximilians-University of Würzburg, 97074 Würzburg, Germany
| | - Andres Jäschke
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University Heidelberg, 69120 Heidelberg, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Stefanie Kaiser
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Roland Klassen
- Institute for Biology - Microbiology, University of Kassel, 34132 Kassel, Germany
| | - Sebastian A Leidel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Andreas Marx
- Department of Chemistry - Organic/Cellular Chemistry, University of Constance, 78457 Constance, Germany
| | - Mario Mörl
- Institute of Biochemistry, University of Leipzig, 04103 Leipzig, Germany
| | - Jochen C Meier
- Department of Cell Physiology, Technical University of Braunschweig, 38106 Brunswick, Germany
| | - Gunter Meister
- Institute of Biochemistry, Genetics and Microbiology - Biochemistry I, University of Regensburg, 93053 Regensburg, Germany
| | - Andrea Rentmeister
- Institute for Biochemistry, Westphalian Wilhelms University Münster, 48149 Münster, Germany
| | - Marina Rodnina
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Jean-Yves Roignant
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
- Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Raffael Schaffrath
- Institute for Biology - Microbiology, University of Kassel, 34132 Kassel, Germany
| | - Peter Stadler
- Institute for Computer Science - Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Thorsten Stafforst
- Interfaculty Institute for Biochemistry, Eberhard Karls University Tübingen, 72074 Tübingen, Germany
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5
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Pichler A, Hillmeier M, Heiss M, Peev E, Xefteris S, Steigenberger B, Thoma I, Müller M, Borsò M, Imhof A, Carell T. Synthesis and Structure Elucidation of Glutamyl-Queuosine. J Am Chem Soc 2023; 145:25528-25532. [PMID: 37967838 PMCID: PMC10690763 DOI: 10.1021/jacs.3c10075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/17/2023]
Abstract
Queuosine is one of the most complex hypermodified RNA nucleosides found in the Wobble position of tRNAs. In addition to Queuosine itself, several further modified derivatives are known, where the cyclopentene ring structure is additionally modified by a galactosyl-, a mannosyl-, or a glutamyl-residue. While sugar-modified Queuosine derivatives are found in the tRNAs of vertebrates, glutamylated Queuosine (gluQ) is only known in bacteria. The exact structure of gluQ, particularly with respect to how and where the glutamyl side chain is connected to the Queuosine cyclopentene side chain, is unknown. Here we report the first synthesis of gluQ and, using UHPLC-MS-coinjection and NMR studies, we show that the isolated natural gluQ is the α-allyl-connected gluQ compound.
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Affiliation(s)
- Alexander Pichler
- Department
of Chemistry, Institute of Chemical Epigenetics,
Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Markus Hillmeier
- Department
of Chemistry, Institute of Chemical Epigenetics,
Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Matthias Heiss
- Department
of Chemistry, Institute of Chemical Epigenetics,
Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Elsa Peev
- Department
of Chemistry, Institute of Chemical Epigenetics,
Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Stylianos Xefteris
- Department
of Chemistry, Institute of Chemical Epigenetics,
Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Barbara Steigenberger
- Mass
Spectrometry Core Facility, Max Planck Institute
of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Planegg, Germany
| | - Ines Thoma
- Department
of Chemistry, Institute of Chemical Epigenetics,
Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Markus Müller
- Department
of Chemistry, Institute of Chemical Epigenetics,
Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Marco Borsò
- Department
of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, Martinsried, 82152 Planegg, Germany
| | - Axel Imhof
- Department
of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, Martinsried, 82152 Planegg, Germany
| | - Thomas Carell
- Department
of Chemistry, Institute of Chemical Epigenetics,
Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
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6
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Karousi P, Samiotaki M, Makridakis M, Zoidakis J, Sideris DC, Scorilas A, Carell T, Kontos CK. 3'-tRF-Cys GCA overexpression in HEK-293 cells alters the global expression profile and modulates cellular processes and pathways. Funct Integr Genomics 2023; 23:341. [PMID: 37987851 PMCID: PMC10663186 DOI: 10.1007/s10142-023-01272-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
tRNA fragments (tRFs) are small non-coding RNAs generated through specific cleavage of tRNAs and involved in various biological processes. Among the different types of tRFs, the 3'-tRFs have attracted scientific interest due to their regulatory role in gene expression. In this study, we investigated the role of 3'-tRF-CysGCA, a tRF deriving from cleavage in the T-loop of tRNACysGCA, in the regulation of gene expression in HEK-293 cells. Previous studies have shown that 3'-tRF-CysGCA is incorporated into the RISC complex and interacts with Argonaute proteins, suggesting its involvement in the regulation of gene expression. However, the general role and effect of the deregulation of 3'-tRF-CysGCA levels in human cells have not been investigated so far. To fill this gap, we stably overexpressed 3'-tRF-CysGCA in HEK-293 cells and performed transcriptomic and proteomic analyses. Moreover, we validated the interaction of this tRF with putative targets, the levels of which were found to be affected by 3'-tRF-CysGCA overexpression. Lastly, we investigated the implication of 3'-tRF-CysGCA in various pathways using extensive bioinformatics analysis. Our results indicate that 3'-tRF-CysGCA overexpression led to changes in the global gene expression profile of HEK-293 cells and that multiple cellular pathways were affected by the deregulation of the levels of this tRF. Additionally, we demonstrated that 3'-tRF-CysGCA directly interacts with thymopoietin (TMPO) transcript variant 1 (also known as LAP2α), leading to modulation of its levels. In conclusion, our findings suggest that 3'-tRF-CysGCA plays a significant role in gene expression regulation and highlight the importance of this tRF in cellular processes.
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Affiliation(s)
- Paraskevi Karousi
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center, "Alexander Fleming", Vari, Greece
| | - Manousos Makridakis
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Jerome Zoidakis
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Diamantis C Sideris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
| | - Thomas Carell
- Department for Chemistry, Institute for Chemical Epigenetics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece.
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7
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Witzenberger M, Burczyk S, Settele D, Mayer W, Welp L, Heiss M, Wagner M, Monecke T, Janowski R, Carell T, Urlaub H, Hauck S, Voigt A, Niessing D. Human TRMT2A methylates tRNA and contributes to translation fidelity. Nucleic Acids Res 2023; 51:8691-8710. [PMID: 37395448 PMCID: PMC10484741 DOI: 10.1093/nar/gkad565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023] Open
Abstract
5-Methyluridine (m5U) is one of the most abundant RNA modifications found in cytosolic tRNA. tRNA methyltransferase 2 homolog A (hTRMT2A) is the dedicated mammalian enzyme for m5U formation at tRNA position 54. However, its RNA binding specificity and functional role in the cell are not well understood. Here we dissected structural and sequence requirements for binding and methylation of its RNA targets. Specificity of tRNA modification by hTRMT2A is achieved by a combination of modest binding preference and presence of a uridine in position 54 of tRNAs. Mutational analysis together with cross-linking experiments identified a large hTRMT2A-tRNA binding surface. Furthermore, complementing hTRMT2A interactome studies revealed that hTRMT2A interacts with proteins involved in RNA biogenesis. Finally, we addressed the question of the importance of hTRMT2A function by showing that its knockdown reduces translation fidelity. These findings extend the role of hTRMT2A beyond tRNA modification towards a role in translation.
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Affiliation(s)
- Monika Witzenberger
- Institute of Structural Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Sandra Burczyk
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
| | - David Settele
- Institute of Structural Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Wieland Mayer
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
| | - Luisa M Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Matthias Heiss
- Department of Chemistry and Biochemistry, Ludwig-Maximilians University Munich, München, Germany
| | - Mirko Wagner
- Department of Chemistry and Biochemistry, Ludwig-Maximilians University Munich, München, Germany
| | - Thomas Monecke
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
| | - Robert Janowski
- Institute of Structural Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Carell
- Department of Chemistry and Biochemistry, Ludwig-Maximilians University Munich, München, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Stefanie M Hauck
- Metabolomics and Proteomics Core, Research Unit Protein Science, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Aaron Voigt
- Department of Neurology, Faculty of Medicine, RWTH Aachen, Aachen, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
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8
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Nieborak A, Lukauskas S, Capellades J, Heyn P, Santos GS, Motzler K, Zeigerer A, Bester R, Protzer U, Schelter F, Wagner M, Carell T, Hruscha A, Schmid B, Yanes O, Schneider R. Depletion of pyruvate kinase (PK) activity causes glycolytic intermediate imbalances and reveals a PK-TXNIP regulatory axis. Mol Metab 2023:101748. [PMID: 37290673 DOI: 10.1016/j.molmet.2023.101748] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/14/2023] [Accepted: 05/31/2023] [Indexed: 06/10/2023] Open
Abstract
OBJECTIVE Cancer cells convert more glucose into lactate than healthy cells, what results in their growth advantage. Pyruvate kinase (PK) is a key rate limiting enzyme in this process, what makes it a promising potential therapeutic target. However, currently it is still unclear what consequences the inhibition of PK has on cellular processes. Here, we systematically investigate the consequences of PK depletion for gene expression, histone modifications and metabolism. METHODS Epigenetic, transcriptional and metabolic targets were analysed in different cellular and animal models with stable knockdown or knockout of PK. RESULTS Depleting PK activity reduces the glycolytic flux and causes accumulation of glucose-6-phosphate (G6P). Such metabolic perturbation results in stimulation of the activity of a heterodimeric pair of transcription factors MondoA and MLX but not in a major reprogramming of the global H3K9ac and H3K4me3 histone modification landscape. The MondoA:MLX heterodimer upregulates expression of thioredoxin-interacting protein (TXNIP) - a tumour suppressor with multifaceted anticancer activity. This effect of TXNIP upregulation extends beyond immortalised cancer cell lines and is applicable to multiple cellular and animal models. CONCLUSIONS Our work shows that actions of often pro-tumorigenic PK and anti-tumorigenic TXNIP are tightly linked via a glycolytic intermediate. We suggest that PK depletion stimulates the activity of MondoA:MLX transcription factor heterodimers and subsequently, increases cellular TXNIP levels. TXNIP-mediated inhibition of thioredoxin (TXN) can reduce the ability of cells to scavenge reactive oxygen species (ROS) leading to the oxidative damage of cellular structures including DNA. These findings highlight an important regulatory axis affecting tumour suppression mechanisms and provide an attractive opportunity for combination cancer therapies targeting glycolytic activity and ROS-generating pathways.
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Affiliation(s)
- Anna Nieborak
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Saulius Lukauskas
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jordi Capellades
- Universitat Rovira i Virgili, Department of Electronic Engineering, IISPV, Tarragona, Spain; CIBER on Diabetes and Associated Metabolic Diseases (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Patricia Heyn
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Gabriela Silva Santos
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Karsten Motzler
- Institute for Diabetes and Cancer, Helmholtz Center Munich, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
| | - Anja Zeigerer
- Institute for Diabetes and Cancer, Helmholtz Center Munich, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, Heidelberg, Germany
| | - Romina Bester
- Institute of Virology, Technical University of Munich, School of Medicine / Helmholtz Munich, Trogerstr. 30, 81675 Munich, Germany
| | - Ulrike Protzer
- Institute of Virology, Technical University of Munich, School of Medicine / Helmholtz Munich, Trogerstr. 30, 81675 Munich, Germany
| | - Florian Schelter
- Ludwig-Maximilians-Universität München, Institute for Chemical Epigenetics Munich, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Mirko Wagner
- Ludwig-Maximilians-Universität München, Institute for Chemical Epigenetics Munich, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Thomas Carell
- Ludwig-Maximilians-Universität München, Institute for Chemical Epigenetics Munich, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Alexander Hruscha
- German Center for Neurodegenerative Diseases (DZNE) Munich, 81377 Munich, Germany
| | - Bettina Schmid
- German Center for Neurodegenerative Diseases (DZNE) Munich, 81377 Munich, Germany
| | - Oscar Yanes
- Universitat Rovira i Virgili, Department of Electronic Engineering, IISPV, Tarragona, Spain; CIBER on Diabetes and Associated Metabolic Diseases (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
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9
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Searle B, Müller M, Carell T, Kellett A. Third-Generation Sequencing of Epigenetic DNA. Angew Chem Int Ed Engl 2023; 62:e202215704. [PMID: 36524852 DOI: 10.1002/anie.202215704] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
The discovery of epigenetic bases has revolutionised the understanding of disease and development. Among the most studied epigenetic marks are cytosines covalently modified at the 5 position. In order to gain insight into their biological significance, the ability to determine their spatiotemporal distribution within the genome is essential. Techniques for sequencing on "next-generation" platforms often involve harsh chemical treatments leading to sample degradation. Third-generation sequencing promises to further revolutionise the field by providing long reads, enabling coverage of highly repetitive regions of the genome or structural variants considered unmappable by next generation sequencing technology. While the ability of third-generation platforms to directly detect epigenetic modifications is continuously improving, at present chemical or enzymatic derivatisation presents the most convenient means of enhancing reliability. This Review presents techniques available for the detection of cytosine modifications on third-generation platforms.
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Affiliation(s)
- Bethany Searle
- SSPC, the SFI Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Dublin, Ireland
| | - Markus Müller
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Andrew Kellett
- SSPC, the SFI Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Dublin, Ireland
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10
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Singer JN, Müller FM, Węgrzyn E, Hölzl C, Hurmiz H, Liu C, Escobar L, Carell T. Loading of Amino Acids onto RNA in a Putative RNA‐Peptide World. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202302360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Affiliation(s)
- Johannes N. Singer
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen Department of Chemistry GERMANY
| | - Felix M. Müller
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen Department of Chemistry GERMANY
| | - Ewa Węgrzyn
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen Department of Chemistry GERMANY
| | - Christina Hölzl
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen Department of Chemistry GERMANY
| | - Hans Hurmiz
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen Department of Chemistry GERMANY
| | - Chuyi Liu
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen Department of Chemistry GERMANY
| | - Luis Escobar
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen Department of Chemistry Butenandtstrasse 5-13 81377 Munich GERMANY
| | - Thomas Carell
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen Department of Chemistry GERMANY
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11
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Singer JN, Müller FM, Węgrzyn E, Hölzl C, Hurmiz H, Liu C, Escobar L, Carell T. Loading of Amino Acids onto RNA in a Putative RNA-Peptide World. Angew Chem Int Ed Engl 2023; 62:e202302360. [PMID: 36881520 DOI: 10.1002/anie.202302360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/08/2023]
Abstract
RNA is a molecule that can both store genetic information and perform catalytic reactions. This observed dualism places RNA into the limelight of concepts about the origin of life. The RNA world concept argues that life started from self-replicating RNA molecules, which evolved toward increasingly complex structures. Recently, we demonstrated that RNA, with the help of conserved non-canonical nucleosides, which are also putative relics of an early RNA world, had the ability to grow peptides covalently connected to RNA nucleobases, creating RNA-peptide chimeras. It is conceivable that such molecules, which combined the information-coding properties of RNA with the catalytic potential of amino acid side chains, were once the structures from which life emerged. Herein, we report prebiotic chemistry that enabled the loading of both nucleosides and RNAs with amino acids as the first step toward RNA-based peptide synthesis in a putative RNA-peptide world.
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Affiliation(s)
- Johannes N Singer
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Department of Chemistry, GERMANY
| | - Felix M Müller
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Department of Chemistry, GERMANY
| | - Ewa Węgrzyn
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Department of Chemistry, GERMANY
| | - Christina Hölzl
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Department of Chemistry, GERMANY
| | - Hans Hurmiz
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Department of Chemistry, GERMANY
| | - Chuyi Liu
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Department of Chemistry, GERMANY
| | - Luis Escobar
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Department of Chemistry, Butenandtstrasse 5-13, 81377, Munich, GERMANY
| | - Thomas Carell
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Department of Chemistry, GERMANY
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12
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Kuhl N, Linder A, Philipp N, Nixdorf D, Fischer H, Veth S, Kuut G, Xu TT, Theurich S, Carell T, Subklewe M, Hornung V. STING agonism turns human T cells into interferon-producing cells but impedes their functionality. EMBO Rep 2023; 24:e55536. [PMID: 36705069 PMCID: PMC9986811 DOI: 10.15252/embr.202255536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/28/2023] Open
Abstract
The cGAS-STING (cyclic GMP-AMP synthase-stimulator of interferon genes) axis is the predominant DNA sensing system in cells of the innate immune system. However, human T cells also express high levels of STING, while its role and physiological trigger remain largely unknown. Here, we show that the cGAS-STING pathway is indeed functional in human primary T cells. In the presence of a TCR-engaging signal, both cGAS and STING activation switches T cells into type I interferon-producing cells. However, T cell function is severely compromised following STING activation, as evidenced by increased cell death, decreased proliferation, and impaired metabolism. Interestingly, these different phenotypes bifurcate at the level of STING. While antiviral immunity and cell death require the transcription factor interferon regulatory factor 3 (IRF3), decreased proliferation is mediated by STING independently of IRF3. In summary, we demonstrate that human T cells possess a functional cGAS-STING signaling pathway that can contribute to antiviral immunity. However, regardless of its potential antiviral role, the activation of the cGAS-STING pathway negatively affects T cell function at multiple levels. Taken together, these results could help inform the future development of cGAS-STING-targeted immunotherapies.
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Affiliation(s)
- Niklas Kuhl
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Department of Medicine II, University HospitalLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Andreas Linder
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Department of Medicine II, University HospitalLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Nora Philipp
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Department of Medicine III, University HospitalLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Daniel Nixdorf
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Department of Medicine III, University HospitalLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Hannah Fischer
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Simon Veth
- Department of Chemistry and Center for NanoScience (CeNS)Ludwig‐Maximilians‐Universität MünchenMunichGermany
| | - Gunnar Kuut
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Teng Teng Xu
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Department of Medicine III, University HospitalLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Sebastian Theurich
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Department of Medicine III, University HospitalLudwig‐Maximilians‐Universität MünchenMunichGermany
- German Cancer Consortium (DKTK), Partner site MunichHeidelbergGermany
- German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Thomas Carell
- Department of Chemistry and Center for NanoScience (CeNS)Ludwig‐Maximilians‐Universität MünchenMunichGermany
| | - Marion Subklewe
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Department of Medicine III, University HospitalLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Veit Hornung
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
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13
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Montiel L, Spada F, Crisp A, Serdjukow S, Carell T, Frischmuth T. Divergent Synthesis of Ultrabright and Dendritic Xanthenes for Enhanced Click-Chemistry-Based Bioimaging. Chemistry 2023; 29:e202202633. [PMID: 36317813 PMCID: PMC10107433 DOI: 10.1002/chem.202202633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Indexed: 12/13/2022]
Abstract
Biorthogonal labelling with fluorescent small molecules is an indispensable tool for diagnostic and biomedical applications. In dye-based 5-ethynyl-2'-deoxyuridine (EdU) cell proliferation assays, augmentation of the fluorescent signal entails an overall enhancement in the sensitivity and quality of the method. To this end, a rapid, divergent synthetic procedure that provides ready-to-click pH-insensitive rhodamine dyes exhibiting outstanding brightness was established. Compared to the shortest available synthesis of related high quantum-yielding rhodamines, two fewer synthetic steps are required. In a head-to-head imaging comparison involving copper(I)-catalyzed azide alkyne cycloaddition reactions with in vitro administered EdU, our new 3,3-difluoroazetidine rhodamine azide outperformed the popular 5-TAMRA-azide, making it among the best available choices when it comes to fluorescent imaging of DNA. In a further exploration of the fluorescence properties of these dyes, a set of bis-MPA dendrons carrying multiple fluorescein or rhodamine units was prepared by branching click chemistry. Fluorescence self-quenching of fluorescein- and rhodamine-functionalized dendrons limited the suitability of the dyes as labels in EdU-based experiments but provided new insights into these effects.
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Affiliation(s)
- Luis Montiel
- Baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (Munich), Germany.,Department of Chemistry, Institut für Chemische Epigenetik München (ICEM), Ludwig-Maximilians-Universität München (LMU), Butenandtstr. 5-13, 81377, Munich, Germany
| | - Fabio Spada
- Baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (Munich), Germany
| | - Antony Crisp
- Baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (Munich), Germany
| | - Sascha Serdjukow
- Baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (Munich), Germany
| | - Thomas Carell
- Department of Chemistry, Institut für Chemische Epigenetik München (ICEM), Ludwig-Maximilians-Universität München (LMU), Butenandtstr. 5-13, 81377, Munich, Germany
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14
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Searle B, Müller M, Carell T, Kellett A. Third Generation Sequencing of Epigenetic DNA. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202215704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | - Markus Müller
- LMU München: Ludwig-Maximilians-Universitat Munchen Institute of Chemical Epigenetics Munich GERMANY
| | - Thomas Carell
- LMU München: Ludwig-Maximilians-Universitat Munchen Institute for Chemical Epigenetics Munich GERMANY
| | - Andrew Kellett
- Dublin City University Chemical Sciences Glasnevin D9 Dublin IRELAND
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15
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Xu F, Crisp A, Schinkel T, Dubini RCA, Hübner S, Becker S, Schelter F, Rovó P, Carell T. Isoxazole Nucleosides as Building Blocks for a Plausible Proto-RNA. Angew Chem Int Ed Engl 2022; 61:e202211945. [PMID: 36063071 PMCID: PMC9828505 DOI: 10.1002/anie.202211945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Indexed: 01/12/2023]
Abstract
The question of how RNA, as the principal carrier of genetic information evolved is fundamentally important for our understanding of the origin of life. The RNA molecule is far too complex to have formed in one evolutionary step, suggesting that ancestral proto-RNAs (first ancestor of RNA) may have existed, which evolved over time into the RNA of today. Here we show that isoxazole nucleosides, which are quickly formed from hydroxylamine, cyanoacetylene, urea and ribose, are plausible precursors for RNA. The isoxazole nucleoside can rearrange within an RNA-strand to give cytidine, which leads to an increase of pairing stability. If the proto-RNA contains a canonical seed-nucleoside with defined stereochemistry, the seed-nucleoside can control the configuration of the anomeric center that forms during the in-RNA transformation. The results demonstrate that RNA could have emerged from evolutionarily primitive precursor isoxazole ribosides after strand formation.
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Affiliation(s)
- Felix Xu
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Antony Crisp
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Thea Schinkel
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Romeo C. A. Dubini
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Sarah Hübner
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Sidney Becker
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany,Current address: Max Planck Institute of Molecular PhysiologyOtto-Hahn-Straße 1144227DortmundGermany
| | - Florian Schelter
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Petra Rovó
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany,Current address: Institute of Science and Technology Austria (ISTA)Am Campus 13400KlosterneuburgAustria
| | - Thomas Carell
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
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16
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Stazzoni S, Böhmer DFR, Hernichel F, Özdemir D, Pappa A, Drexler D, Bauernfried S, Witte G, Wagner M, Veth S, Hopfner K, Hornung V, König LM, Carell T. Novel Poxin Stable cGAMP-Derivatives Are Remarkable STING Agonists. Angew Chem Int Ed Engl 2022; 61:e202207175. [PMID: 35876840 PMCID: PMC9804856 DOI: 10.1002/anie.202207175] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 01/09/2023]
Abstract
2',3'-cGAMP is a cyclic A- and G-containing dinucleotide second messenger, which is formed upon cellular recognition of foreign cytosolic DNA as part of the innate immune response. The molecule binds to the adaptor protein STING, which induces an immune response characterized by the production of type I interferons and cytokines. The development of STING-binding molecules with both agonistic as well as antagonistic properties is currently of tremendous interest to induce or enhance antitumor or antiviral immunity on the one hand, or to treat autoimmune diseases on the other hand. To escape the host innate immune recognition, some viruses encode poxin endonucleases that cleave 2',3'-cGAMP. Here we report that dideoxy-2',3'-cGAMP (1) and analogs thereof, which lack the secondary ribose-OH groups, form a group of poxin-stable STING agonists. Despite their reduced affinity to STING, particularly the compound constructed from two A nucleosides, dideoxy-2',3'-cAAMP (2), features an unusually high antitumor response in mice.
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Affiliation(s)
- Samuele Stazzoni
- New address: Monoclonal Antibody Discovery (MAD) LabFondazione Toscana Life Sciences53100SienaItaly,Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Daniel F. R. Böhmer
- Division of Clinical PharmacologyUniversity HospitalLudwig-Maximilians-Universität MünchenLindwurmstr. 2a80337MunichGermany
| | - Fabian Hernichel
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Dilara Özdemir
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Aikaterini Pappa
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - David Drexler
- Gene Center and Department of BiochemistryLudwig-Maximilians-Universität MünchenFeodor-Lynen-Str. 2581377MunichGermany
| | - Stefan Bauernfried
- Gene Center and Department of BiochemistryLudwig-Maximilians-Universität MünchenFeodor-Lynen-Str. 2581377MunichGermany
| | - Gregor Witte
- Gene Center and Department of BiochemistryLudwig-Maximilians-Universität MünchenFeodor-Lynen-Str. 2581377MunichGermany
| | - Mirko Wagner
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Simon Veth
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Karl‐Peter Hopfner
- Gene Center and Department of BiochemistryLudwig-Maximilians-Universität MünchenFeodor-Lynen-Str. 2581377MunichGermany
| | - Veit Hornung
- Gene Center and Department of BiochemistryLudwig-Maximilians-Universität MünchenFeodor-Lynen-Str. 2581377MunichGermany
| | - Lars M. König
- Division of Clinical PharmacologyUniversity HospitalLudwig-Maximilians-Universität MünchenLindwurmstr. 2a80337MunichGermany
| | - Thomas Carell
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
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17
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Schönegger ES, Crisp A, Müller M, Fertl J, Serdjukow S, Croce S, Kollaschinski M, Carell T, Frischmuth T. Click Chemistry Enables Rapid Amplification of Full-Length Reverse Transcripts for Long-Read Third Generation Sequencing. Bioconjug Chem 2022; 33:1789-1795. [PMID: 36154005 DOI: 10.1021/acs.bioconjchem.2c00353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here we describe the development of a novel click chemistry-based method for the generation and amplification of full-length cDNA libraries from total RNA, while avoiding the need for problematic template-switching (TS) reactions. Compared with prior efforts, our method involves neither random priming nor stochastic cDNA termination, thus enabling amplification of transcripts that were previously inaccessible via related click chemistry-based RNA sequencing techniques. A key modification involving the use of PCR primers containing two overhanging 3'-nucleotides substantially improved the read-through compatibility of the 1,4-disubstituted 1,2,3-triazole-containing cDNA, where such modifications typically hinder amplification. This allowed us to more than double the possible insert size compared with the state-of-the art click chemistry-based technique, PAC-seq. Furthermore, our method performed on par with a commercially available PCR-cDNA RNA sequencing kit, as determined by Oxford Nanopore sequencing. Given the known advantages of PAC-seq, namely, suppression of PCR artifacts, we anticipate that our contribution could enable diverse applications including improved analyses of mRNA splicing variants and fusion transcripts.
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Affiliation(s)
- Eva S Schönegger
- Ludwig-Maximilians-Universität München, Institute for Chemical Epigenetics Munich, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Antony Crisp
- baseclick GmbH, Floriansbogen 2-4, 82061 Neuried (Munich), Germany
| | - Markus Müller
- Ludwig-Maximilians-Universität München, Institute for Chemical Epigenetics Munich, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Jessica Fertl
- baseclick GmbH, Floriansbogen 2-4, 82061 Neuried (Munich), Germany
| | - Sascha Serdjukow
- baseclick GmbH, Floriansbogen 2-4, 82061 Neuried (Munich), Germany
| | - Stefano Croce
- baseclick GmbH, Floriansbogen 2-4, 82061 Neuried (Munich), Germany
| | | | - Thomas Carell
- Ludwig-Maximilians-Universität München, Institute for Chemical Epigenetics Munich, Butenandtstr. 5-13, 81377 Munich, Germany
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18
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Traube FR, Stern M, Tölke AJ, Rudelius M, Mejías‐Pérez E, Raddaoui N, Kümmerer BM, Douat C, Streshnev F, Albanese M, Wratil PR, Gärtner YV, Nainytė M, Giorgio G, Michalakis S, Schneider S, Streeck H, Müller M, Keppler OT, Carell T. Suppression of SARS‐CoV‐2 Replication with Stabilized and Click‐Chemistry Modified siRNAs. Angew Chem Int Ed Engl 2022; 61:e202204556. [PMID: 35802496 PMCID: PMC9350007 DOI: 10.1002/anie.202204556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Franziska R. Traube
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Marcel Stern
- Max von Pettenkofer Institute and Gene Center Ludwig-Maximilians-Universität München Feodor-Lynen-Straße 25 81377 Munich Germany
| | - Annika J. Tölke
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Martina Rudelius
- Institute of Pathology Ludwig-Maximilians-Universität München Marchioninistr. 68 81377 Munich Germany
| | - Ernesto Mejías‐Pérez
- Max von Pettenkofer Institute and Gene Center Ludwig-Maximilians-Universität München Feodor-Lynen-Straße 25 81377 Munich Germany
| | - Nada Raddaoui
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Beate M. Kümmerer
- Institute of Virology Universitätsklinikum Bonn Venusberg-Campus 1 53127 Bonn Germany
- German Center for Infection Research (DZIF) Partner Site Cologne/Bonn 53127 Bonn Germany
| | - Céline Douat
- Department of Pharmacy Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Filipp Streshnev
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Manuel Albanese
- Max von Pettenkofer Institute and Gene Center Ludwig-Maximilians-Universität München Feodor-Lynen-Straße 25 81377 Munich Germany
| | - Paul R. Wratil
- Max von Pettenkofer Institute and Gene Center Ludwig-Maximilians-Universität München Feodor-Lynen-Straße 25 81377 Munich Germany
| | - Yasmin V. Gärtner
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Milda Nainytė
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Grazia Giorgio
- Department of Ophthalmology University Hospital Ludwig-Maximilians-Universität München 80336 Munich Germany
| | - Stylianos Michalakis
- Department of Ophthalmology University Hospital Ludwig-Maximilians-Universität München 80336 Munich Germany
| | - Sabine Schneider
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Hendrik Streeck
- Institute of Virology Universitätsklinikum Bonn Venusberg-Campus 1 53127 Bonn Germany
| | - Markus Müller
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Oliver T. Keppler
- Max von Pettenkofer Institute and Gene Center Ludwig-Maximilians-Universität München Feodor-Lynen-Straße 25 81377 Munich Germany
| | - Thomas Carell
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
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19
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Xu F, Crisp A, Schinkel T, Dubini RCA, Hübner S, Becker S, Schelter F, Rovó P, Carell T. Isoxazole Nucleosides as Building Blocks for a Plausible Proto‐RNA. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202211945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Felix Xu
- Ludwig-Maximilians-Universitat Munchen Fakultat fur Chemie und Pharmazie Chemistry GERMANY
| | - Antony Crisp
- Ludwig Maximillians University Munich: Ludwig-Maximilians-Universitat Munchen Chemistry GERMANY
| | - Thea Schinkel
- Ludwig-Maximilians-Universitat Munchen Fakultat fur Chemie und Pharmazie Chemistry GERMANY
| | | | - Sarah Hübner
- Ludwig-Maximilians-Universität München Fakultät für Chemie und Pharmazie: Ludwig-Maximilians-Universitat Munchen Fakultat fur Chemie und Pharmazie Chemistry GERMANY
| | - Sidney Becker
- Ludwig-Maximilians-Universitat Munchen Fakultat fur Chemie und Pharmazie Chemistry GERMANY
| | - Florian Schelter
- Ludwig-Maximilians-Universitat Munchen Fakultat fur Chemie und Pharmazie Chemistry GERMANY
| | - Petra Rovó
- Ludwig-Maximilians-Universitat Munchen Fakultat fur Chemie und Pharmazie Chemistry GERMANY
| | - Thomas Carell
- Ludwig-Maximilians-Universitat Munchen Department of Chemistry and Biochemistry Butenandtstraße 5-13 81377 München GERMANY
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20
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Arroyo M, Hastert FD, Zhadan A, Schelter F, Zimbelmann S, Rausch C, Ludwig AK, Carell T, Cardoso MC. Isoform-specific and ubiquitination dependent recruitment of Tet1 to replicating heterochromatin modulates methylcytosine oxidation. Nat Commun 2022; 13:5173. [PMID: 36056023 PMCID: PMC9440122 DOI: 10.1038/s41467-022-32799-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/15/2022] [Indexed: 01/26/2023] Open
Abstract
Oxidation of the epigenetic DNA mark 5-methylcytosine by Tet dioxygenases is an established route to diversify the epigenetic information, modulate gene expression and overall cellular (patho-)physiology. Here, we demonstrate that Tet1 and its short isoform Tet1s exhibit distinct nuclear localization during DNA replication resulting in aberrant cytosine modification levels in human and mouse cells. We show that Tet1 is tethered away from heterochromatin via its zinc finger domain, which is missing in Tet1s allowing its targeting to these regions. We find that Tet1s interacts with and is ubiquitinated by CRL4(VprBP). The ubiquitinated Tet1s is then recognized by Uhrf1 and recruited to late replicating heterochromatin. This leads to spreading of 5-methylcytosine oxidation to heterochromatin regions, LINE 1 activation and chromatin decondensation. In summary, we elucidate a dual regulation mechanism of Tet1, contributing to the understanding of how epigenetic information can be diversified by spatio-temporal directed Tet1 catalytic activity.
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Affiliation(s)
- María Arroyo
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Florian D. Hastert
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany ,grid.425396.f0000 0001 1019 0926Section AIDS and newly emerging pathogens, Paul Ehrlich Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany
| | - Andreas Zhadan
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Florian Schelter
- grid.5252.00000 0004 1936 973XDepartment of Chemistry, Ludwig Maximilians University, Butenandstr. 5-13, 81377 Munich, Germany
| | - Susanne Zimbelmann
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Cathia Rausch
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany ,grid.16008.3f0000 0001 2295 9843Present Address: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Anne K. Ludwig
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany ,grid.5253.10000 0001 0328 4908Present Address: Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Thomas Carell
- grid.5252.00000 0004 1936 973XDepartment of Chemistry, Ludwig Maximilians University, Butenandstr. 5-13, 81377 Munich, Germany
| | - M. Cristina Cardoso
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
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21
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Stazzoni S, Böhmer DF, Hernichel F, Özdemir D, Pappa A, Drexler D, Bauernfried S, Witte G, Wagner M, Veth S, Hopfner KP, Hornung V, König LM, Carell T. Novel Poxin Stable cGAMP‐Derivatives Are Remarkable STING Agonists. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Daniel F.R. Böhmer
- Klinikum der Universität München: Klinikum der Universitat Munchen Klinische Pharmakologie GERMANY
| | | | - Dilara Özdemir
- LMU: Ludwig-Maximilians-Universitat Munchen Chemistry GERMANY
| | | | - David Drexler
- LMU: Ludwig-Maximilians-Universitat Munchen Biochemistry GERMANY
| | | | - Gregor Witte
- LMU: Ludwig-Maximilians-Universitat Munchen Biochemistry GERMANY
| | - Mirko Wagner
- LMU: Ludwig-Maximilians-Universitat Munchen Chemistry GERMANY
| | - Simon Veth
- LMU Munich Faculty for Chemistry and Pharmacy: Ludwig-Maximilians-Universitat Munchen Fakultat fur Chemie und Pharmazie Chemistry GERMANY
| | | | - Veit Hornung
- LMU: Ludwig-Maximilians-Universitat Munchen Biochemistry GERMANY
| | - Lars M. König
- Klinikum der Universität München: Klinikum der Universitat Munchen Klinische Pharmakologie GERMANY
| | - Thomas Carell
- Ludwig-Maximilians-Universitat Munchen Department of Chemistry and Biochemistry Butenandtstraße 5-13 81377 München GERMANY
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22
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Traube FR, Stern M, Tölke AJ, Rudelius M, Mejías-Pérez E, Raddaoui N, Kümmerer BM, Douat C, Streshnev F, Albanese M, Wratil PR, Gärtner YV, Nainytė M, Giorgio G, Michalakis S, Schneider S, Streeck H, Müller M, Keppler OT, Carell T. Suppression of SARS‐CoV‐2 Replication with Stabilized and Click‐Chemistry Modified siRNAs. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Franziska R. Traube
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Marcel Stern
- LMU München: Ludwig-Maximilians-Universitat Munchen Max von Pettenkopfer Institute and Gene Center, Virology GERMANY
| | - Annika J. Tölke
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Martina Rudelius
- LMU München: Ludwig-Maximilians-Universitat Munchen Institute of Pathology GERMANY
| | - Ernesto Mejías-Pérez
- LMU München: Ludwig-Maximilians-Universitat Munchen Max von Pettenkofer Institute and Gene Center, Virology GERMANY
| | - Nada Raddaoui
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Beate M. Kümmerer
- Universität Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Institute of Virology GERMANY
| | - Céline Douat
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Filipp Streshnev
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Manuel Albanese
- LMU München: Ludwig-Maximilians-Universitat Munchen Max von Pettenkofer Institute and Gene Center, Virology GERMANY
| | - Paul R. Wratil
- LMU München: Ludwig-Maximilians-Universitat Munchen Max von Pettenkofer Institute and Gene Center, Virology GERMANY
| | - Yasmin V. Gärtner
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Milda Nainytė
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Grazia Giorgio
- LMU München: Ludwig-Maximilians-Universitat Munchen Department of Ophthalmology, University Hospital GERMANY
| | - Stylianos Michalakis
- LMU München: Ludwig-Maximilians-Universitat Munchen Department of Ophthalmology, University Hospital GERMANY
| | - Sabine Schneider
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Hendrick Streeck
- Universität Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Institute of Virology GERMANY
| | - Markus Müller
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Oliver T. Keppler
- LMU München: Ludwig-Maximilians-Universitat Munchen Max von Pettenkofer Institute and Gene Center, Virology GERMANY
| | - Thomas Carell
- Ludwig-Maximilians-Universitat Munchen Department of Chemistry and Biochemistry Butenandtstraße 5-13 81377 München GERMANY
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23
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Czuppa M, Dhingra A, Zhou Q, Schludi C, König L, Scharf E, Farny D, Dalmia A, Täger J, Castillo-Lizardo M, Katona E, Mori K, Aumer T, Schelter F, Müller M, Carell T, Kalliokoski T, Messinger J, Rizzu P, Heutink P, Edbauer D. Drug screen in iPSC-Neurons identifies nucleoside analogs as inhibitors of (G 4C 2) n expression in C9orf72 ALS/FTD. Cell Rep 2022; 39:110913. [PMID: 35675776 DOI: 10.1016/j.celrep.2022.110913] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 12/22/2021] [Accepted: 05/12/2022] [Indexed: 11/03/2022] Open
Abstract
An intronic (G4C2)n expansion in C9orf72 causes amyotrophic lateral sclerosis and frontotemporal dementia primarily through gain-of-function mechanisms: the accumulation of sense and antisense repeat RNA foci and dipeptide repeat (DPR) proteins (poly-GA/GP/GR/PA/PR) translated from repeat RNA. To therapeutically block this pathway, we screen a library of 1,430 approved drugs and known bioactive compounds in patient-derived induced pluripotent stem cell-derived neurons (iPSC-Neurons) for inhibitors of DPR expression. The clinically used guanosine/cytidine analogs decitabine, entecavir, and nelarabine reduce poly-GA/GP expression, with decitabine being the most potent. Hit compounds nearly abolish sense and antisense RNA foci and reduce expression of the repeat-containing nascent C9orf72 RNA transcript and its mature mRNA with minimal effects on global gene expression, suggesting that they specifically act on repeat transcription. Importantly, decitabine treatment reduces (G4C2)n foci and DPRs in C9orf72 BAC transgenic mice. Our findings suggest that nucleoside analogs are a promising compound class for therapeutic development in C9orf72 repeat-expansion-associated disorders.
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Affiliation(s)
- Mareike Czuppa
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Ashutosh Dhingra
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
| | - Qihui Zhou
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Carina Schludi
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Laura König
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Elisabeth Scharf
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Daniel Farny
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Anupriya Dalmia
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Joachim Täger
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | | | - Eszter Katona
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Kohji Mori
- Psychiatry, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Tina Aumer
- Ludwig-Maximilians-University Munich, Faculty of Chemistry and Pharmacy, Munich, Germany
| | - Florian Schelter
- Ludwig-Maximilians-University Munich, Faculty of Chemistry and Pharmacy, Munich, Germany
| | - Markus Müller
- Ludwig-Maximilians-University Munich, Faculty of Chemistry and Pharmacy, Munich, Germany
| | - Thomas Carell
- Ludwig-Maximilians-University Munich, Faculty of Chemistry and Pharmacy, Munich, Germany
| | | | - Josef Messinger
- Orion Corporation Orion Pharma, Medicine Design, Espoo, Finland
| | - Patrizia Rizzu
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany; Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Dieter Edbauer
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Ludwig-Maximilians-University Munich, Graduate School of Systemic Neurosciences (GSN), Munich, Germany.
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24
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Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovó P. 1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives. ACS Phys Chem Au 2022; 2:237-246. [PMID: 35637781 PMCID: PMC9137243 DOI: 10.1021/acsphyschemau.1c00050] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 11/29/2022]
Abstract
![]()
5-Carboxycytosine
(5caC) is a rare epigenetic modification found
in nucleic acids of all domains of life. Despite its sparse genomic
abundance, 5caC is presumed to play essential regulatory roles in
transcription, maintenance and base-excision processes in DNA. In
this work, we utilize nuclear magnetic resonance (NMR) spectroscopy
to address the effects of 5caC incorporation into canonical DNA strands
at multiple pH and temperature conditions. Our results demonstrate
that 5caC has a pH-dependent global destabilizing and a base-pair
mobility enhancing local impact on dsDNA, albeit without any detectable
influence on the ground-state B-DNA structure. Measurement of hybridization
thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted
how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded
structure by ∼10–20 kJ mol–1 at 37
°C when compared to the same sample at neutral pH. Protonation
of 5caC results in a lower activation energy for the dissociation
process and a higher barrier for annealing. Studies on conformational
exchange on the microsecond time scale regime revealed a sharply localized
base-pair motion involving exclusively the modified site and its immediate
surroundings. By direct comparison with canonical and 5-formylcytosine
(5fC)-edited strands, we were able to address the impact of the two
most oxidized naturally occurring cytosine derivatives in the genome.
These insights on 5caC’s subtle sensitivity to acidic pH contribute
to the long-standing questions of its capacity as a substrate in base
excision repair processes and its purpose as an independent, stable
epigenetic mark.
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Affiliation(s)
- Romeo C. A. Dubini
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
- Center for Nanoscience (CeNS), Faculty of Physics, Ludwig-Maximilians-Universität München, Schellingstraße 4, 5th floor, 80799 Munich, Germany
| | - Eva Korytiaková
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Thea Schinkel
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Pia Heinrichs
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Thomas Carell
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Petra Rovó
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
- Center for Nanoscience (CeNS), Faculty of Physics, Ludwig-Maximilians-Universität München, Schellingstraße 4, 5th floor, 80799 Munich, Germany
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
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25
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Traube FR, Brás NF, Roos WP, Sommermann CC, Diehl T, Mayer RJ, Ofial AR, Müller M, Zipse H, Carell T. Epigenetic Anti‐Cancer Treatment With a Stabilized Carbocyclic Decitabine Analogue. Chemistry 2022; 28:e202200640. [PMID: 35285586 PMCID: PMC9314125 DOI: 10.1002/chem.202200640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Indexed: 11/23/2022]
Abstract
5‐Aza‐2’‐deoxycytidine (Decitabine, AzadC) is a nucleoside analogue, which is in clinical use to treat patients with myelodysplastic syndrome or acute myeloid leukemia. Its mode of action is unusual because the compound is one of the few drugs that act at the epigenetic level of the genetic code. AzadC is incorporated as an antimetabolite into the genome and creates covalent, inhibitory links to DNA methyltransferases (DNMTs) that methylate 2’‐deoxycytidine (dC) to 5‐methyl‐dC (mdC). Consequently, AzadC treatment leads to a global loss of mdC, which presumably results in a reactivation of silenced genes, among them tumor suppressor and DNA damage response genes. Because AzadC suffers from severe instability, which limits its use in the clinic, a more sophisticated AzadC derivative would be highly valuable. Here, we report that a recently developed carbocyclic AzadC analogue (cAzadC) blocks DNMT1 in the AML cell line MOLM‐13 as efficient as AzadC. Moreover, cAzadC has a surprisingly strong anti‐proliferative effect and leads to a significantly higher number of double strand breaks compared to AzadC, while showing less off‐target toxicity. These results show that cAzadC triggers more deleterious repair and apoptotic pathways in cancer cells than AzadC, which makes cAzadC a promising next generation epigenetic drug.
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Affiliation(s)
- Franziska R. Traube
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Natércia F. Brás
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
- LAQV-REQUIMTEDepartamento de Química e Bioquímica, Faculdade de CiênciasUniversidade do PortoRua do Campo Alegre s/n4169-007PortoPortugal
| | - Wynand P. Roos
- Institut für ToxikologieUniversitätsmedizin MainzObere Zahlbacher Str. 6755131MainzGermany
| | - Corinna C. Sommermann
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Tamara Diehl
- Institut für ToxikologieUniversitätsmedizin MainzObere Zahlbacher Str. 6755131MainzGermany
| | - Robert J. Mayer
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
- Present address: Institut des Science et d'Ingénierie Supramoléculaires (ISIS)Université des Strasbourg & CNRS8 Allée Gaspard Monge67000StrasbourgFrance
| | - Armin R. Ofial
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Markus Müller
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Hendrik Zipse
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Thomas Carell
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MunichGermany
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26
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Veth S, Fuchs A, Özdemir D, Dialer C, Drexler DJ, Knechtel F, Witte G, Hopfner KP, Carell T, Ploetz E. Chemical synthesis of the fluorescent, cyclic dinucleotides cthGAMP. Chembiochem 2022; 23:e202200005. [PMID: 35189023 PMCID: PMC9310808 DOI: 10.1002/cbic.202200005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/12/2022] [Indexed: 11/15/2022]
Abstract
The cGAS‐STING pathway is known for its role in sensing cytosolic DNA introduced by a viral infection, bacterial invasion or tumorigenesis. Free DNA is recognized by the cyclic GMP‐AMP synthase (cGAS) catalyzing the production of 2’,3’‐cyclic guanosine monophosphate‐adenosine monophosphate (2’,3’‐cGAMP) in mammals. This cyclic dinucleotide acts as a second messenger, activating the stimulator of interferon genes (STING) that finally triggers the transcription of interferon genes and inflammatory cytokines. Due to the therapeutic potential of this pathway, both the production and the detection of cGAMP via fluorescent moieties for assay development is of great importance. Here, we introduce the paralleled synthetic access to the intrinsically fluorescent, cyclic dinucleotides 2’3’‐cthGAMP and 3’3’‐cthGAMP based on phosphoramidite and phosphate chemistry, adaptable for large scale synthesis. We examine their binding properties to murine and human STING and confirm biological activity including interferon induction by 2’3’‐cthGAMP in THP‐1 monocytes. Two‐photon imaging revealed successful cellular uptake of 2’3’‐cthGAMP in THP‐1 cells.
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Affiliation(s)
- Simon Veth
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Adrian Fuchs
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Dilara Özdemir
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Clemens Dialer
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - David Jan Drexler
- Ludwig-Maximilians-Universität München Genzentrum: Ludwig-Maximilians-Universitat Munchen Genzentrum, Biochemistry, GERMANY
| | - Fabian Knechtel
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Gregor Witte
- Ludwig-Maximilians-Universität München Genzentrum: Ludwig-Maximilians-Universitat Munchen Genzentrum, Biochemistry, GERMANY
| | - Karl-Peter Hopfner
- Ludwig-Maximilians-Universität München Genzentrum: Ludwig-Maximilians-Universitat Munchen Genzentrum, Biochemistry, GERMANY
| | - Thomas Carell
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Evelyn Ploetz
- Ludwig-Maximilians-Universitat Munchen, Chemistry, Butenandtstr 11, 81377, Muenchen, GERMANY
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27
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Margreiter MA, Witzenberger M, Wasser Y, Davydova E, Janowski R, Metz J, Habib P, Sahnoun SEM, Sobisch C, Poma B, Palomino-Hernandez O, Wagner M, Carell T, Jon Shah N, Schulz JB, Niessing D, Voigt A, Rossetti G. Small-molecule modulators of TRMT2A decrease PolyQ aggregation and PolyQ-induced cell death. Comput Struct Biotechnol J 2022; 20:443-458. [PMID: 35070167 PMCID: PMC8759985 DOI: 10.1016/j.csbj.2021.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 11/17/2022] Open
Abstract
Polyglutamine (polyQ) diseases are characterized by an expansion of cytosine-adenine-guanine (CAG) trinucleotide repeats encoding for an uninterrupted prolonged polyQ tract. We previously identified TRMT2A as a strong modifier of polyQ-induced toxicity in an unbiased large-scale screen in Drosophila melanogaster. This work aimed at identifying and validating pharmacological TRMT2A inhibitors as treatment opportunities for polyQ diseases in humans. Computer-aided drug discovery was implemented to identify human TRMT2A inhibitors. Additionally, the crystal structure of one protein domain, the RNA recognition motif (RRM), was determined, and Biacore experiments with the RRM were performed. The identified molecules were validated for their potency to reduce polyQ aggregation and polyQ-induced cell death in human HEK293T cells and patient derived fibroblasts. Our work provides a first step towards pharmacological inhibition of this enzyme and indicates TRMT2A as a viable drug target for polyQ diseases.
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Affiliation(s)
- Michael A Margreiter
- Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Juelich GmbH, Germany.,Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, 52425 Aachen, Germany
| | - Monika Witzenberger
- Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Institute of Structural Biology, 85764 Neuherberg, Germany
| | - Yasmine Wasser
- Department of Neurology, RWTH University Aachen, Faculty of Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Elena Davydova
- Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Institute of Structural Biology, 85764 Neuherberg, Germany
| | - Robert Janowski
- Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Institute of Structural Biology, 85764 Neuherberg, Germany
| | - Jonas Metz
- Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Juelich GmbH, Germany
| | - Pardes Habib
- Department of Neurology, RWTH University Aachen, Faculty of Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany.,JARA - BRAIN - Translational Medicine, Aachen, Germany
| | - Sabri E M Sahnoun
- Department of Nuclear Medicine, University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany
| | - Carina Sobisch
- Department of Neurology, RWTH University Aachen, Faculty of Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Benedetta Poma
- Department of Neurology, RWTH University Aachen, Faculty of Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Oscar Palomino-Hernandez
- Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Juelich GmbH, Germany.,Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, 52425 Aachen, Germany
| | - Mirko Wagner
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 München, Germany
| | - Thomas Carell
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 München, Germany
| | - N Jon Shah
- JARA - BRAIN - Translational Medicine, Aachen, Germany.,Institute of Neuroscience and Medicine (INM-4), Forschungszentrum Juelich GmbH, Germany.,Institute of Neuroscience and Medicine (INM-11), Forschungszentrum Juelich GmbH, Germany
| | - Jörg B Schulz
- Department of Neurology, RWTH University Aachen, Faculty of Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany.,JARA - BRAIN - Translational Medicine, Aachen, Germany.,Institute of Neuroscience and Medicine (INM-11), Forschungszentrum Juelich GmbH, Germany
| | - Dierk Niessing
- Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Institute of Structural Biology, 85764 Neuherberg, Germany.,Institute of Pharmaceutical Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Aaron Voigt
- Department of Neurology, RWTH University Aachen, Faculty of Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany.,JARA - BRAIN - Translational Medicine, Aachen, Germany
| | - Giulia Rossetti
- Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Juelich GmbH, Germany.,Department of Neurology, RWTH University Aachen, Faculty of Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany.,Juelich Supercomputing Center (JSC), Forschungszentrum Juelich GmbH, Germany.,Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstr. 30, 52074 Aachen, Germany
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28
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Hillmeier M, Wagner M, Ensfelder T, Korytiakova E, Thumbs P, Müller M, Carell T. Synthesis and structure elucidation of the human tRNA nucleoside mannosyl-queuosine. Nat Commun 2021; 12:7123. [PMID: 34880214 PMCID: PMC8654956 DOI: 10.1038/s41467-021-27371-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 11/11/2021] [Indexed: 11/09/2022] Open
Abstract
Queuosine (Q) is a structurally complex, non-canonical RNA nucleoside. It is present in many eukaryotic and bacterial species, where it is part of the anticodon loop of certain tRNAs. In higher vertebrates, including humans, two further modified queuosine-derivatives exist - galactosyl- (galQ) and mannosyl-queuosine (manQ). The function of these low abundant hypermodified RNA nucleosides remains unknown. While the structure of galQ was elucidated and confirmed by total synthesis, the reported structure of manQ still awaits confirmation. By combining total synthesis and LC-MS-co-injection experiments, together with a metabolic feeding study of labelled hexoses, we show here that the natural compound manQ isolated from mouse liver deviates from the literature-reported structure. Our data show that manQ features an α-allyl connectivity of its sugar moiety. The yet unidentified glycosylases that attach galactose and mannose to the Q-base therefore have a maximally different constitutional connectivity preference. Knowing the correct structure of manQ will now pave the way towards further elucidation of its biological function.
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Affiliation(s)
- Markus Hillmeier
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Mirko Wagner
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Timm Ensfelder
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Eva Korytiakova
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Peter Thumbs
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Markus Müller
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Thomas Carell
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany.
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29
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Kabaciński P, Romanelli M, Ponkkonen E, Jaiswal VK, Carell T, Garavelli M, Cerullo G, Conti I. Unified Description of Ultrafast Excited State Decay Processes in Epigenetic Deoxycytidine Derivatives. J Phys Chem Lett 2021; 12:11070-11077. [PMID: 34748341 PMCID: PMC8607503 DOI: 10.1021/acs.jpclett.1c02909] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Epigenetic DNA modifications play a fundamental role in modulating gene expression and regulating cellular and developmental biological processes, thereby forming a second layer of information in DNA. The epigenetic 2'-deoxycytidine modification 5-methyl-2'-deoxycytidine, together with its enzymatic oxidation products (5-hydroxymethyl-2'-deoxycytidine, 5-formyl-2'-deoxycytidine, and 5-carboxyl-2'-deoxycytidine), are closely related to deactivation and reactivation of DNA transcription. Here, we combine sub-30-fs transient absorption spectroscopy with high-level correlated multiconfigurational CASPT2/MM computational methods, explicitly including the solvent, to obtain a unified picture of the photophysics of deoxycytidine-derived epigenetic DNA nucleosides. We assign all the observed time constants and identify the excited state relaxation pathways, including the competition of intersystem crossing and internal conversion for 5-formyl-2'-deoxycytidine and ballistic decay to the ground state for 5-carboxy-2'-deoxycytidine. Our work contributes to shed light on the role of epigenetic derivatives in DNA photodamage as well as on their possible therapeutic use.
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Affiliation(s)
- Piotr Kabaciński
- IFN-CNR,
Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Marco Romanelli
- Dipartimento
di Chimica Industriale, Università
degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Eveliina Ponkkonen
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, Butenandtstrasse 5-13, Munich 81377, Germany
| | - Vishal Kumar Jaiswal
- Dipartimento
di Chimica Industriale, Università
degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Thomas Carell
- Department
of Chemistry, Ludwig-Maximilians-Universität
München, Butenandtstrasse 5-13, Munich 81377, Germany
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale, Università
degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Giulio Cerullo
- IFN-CNR,
Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Irene Conti
- Dipartimento
di Chimica Industriale, Università
degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
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30
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Abstract
Cellular DNA is composed of four canonical nucleosides (dA, dC, dG and T), which form two Watson-Crick base pairs. In addition, 5-methylcytosine (mdC) may be present. The methylation of dC to mdC is known to regulate transcriptional activity. Next to these five nucleosides, the genome, particularly of stem cells, contains three additional dC derivatives, which are formed by stepwise oxidation of the methyl group of mdC with the help of Tet enzymes. These are 5-hydroxymethyl-dC (hmdC), 5-formyl-dC (fdC), and 5-carboxy-dC (cadC). It is believed that fdC and cadC are converted back into dC, which establishes an epigenetic control cycle that starts with methylation of dC to mdC, followed by oxidation and removal of fdC and cadC. While fdC was shown to undergo intragenomic deformylation to give dC directly, a similar decarboxylation of cadC was postulated but not yet observed on the genomic level. By using metabolic labelling, we show here that cadC decarboxylates in several cell types, which confirms that both fdC and cadC are nucleosides that are directly converted back to dC within the genome by C-C bond cleavage.
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Affiliation(s)
- Ewelina Kamińska
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Eva Korytiaková
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Andreas Reichl
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Markus Müller
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Thomas Carell
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
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31
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Kamińska E, Korytiaková E, Reichl A, Müller M, Carell T. Intragenomische Decarboxylierung von 5‐Carboxy‐2′‐desoxycytidin. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ewelina Kamińska
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Eva Korytiaková
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Andreas Reichl
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Markus Müller
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Thomas Carell
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
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32
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Schmidl D, Jonasson NSW, Korytiaková E, Carell T, Daumann LJ. Biomimetic Iron Complex Achieves TET Enzyme Reactivity**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- David Schmidl
- Department Chemie Ludwig-Maximilians-University München Butenandtstr. 5–13, Haus D München Germany
| | - Niko S. W. Jonasson
- Department Chemie Ludwig-Maximilians-University München Butenandtstr. 5–13, Haus D München Germany
| | - Eva Korytiaková
- Department Chemie Ludwig-Maximilians-University München Butenandtstr. 5–13, Haus D München Germany
| | - Thomas Carell
- Department Chemie Ludwig-Maximilians-University München Butenandtstr. 5–13, Haus D München Germany
| | - Lena J. Daumann
- Department Chemie Ludwig-Maximilians-University München Butenandtstr. 5–13, Haus D München Germany
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33
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Schmidl D, Jonasson NSW, Korytiaková E, Carell T, Daumann LJ. Biomimetic Iron Complex Achieves TET Enzyme Reactivity*. Angew Chem Int Ed Engl 2021; 60:21457-21463. [PMID: 34181314 PMCID: PMC8518650 DOI: 10.1002/anie.202107277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/23/2021] [Indexed: 12/12/2022]
Abstract
The epigenetic marker 5-methyl-2'-deoxycytidine (5mdC) is the most prevalent modification to DNA. It is removed inter alia via an active demethylation pathway: oxidation by Ten-Eleven Translocation 5-methyl cytosine dioxygenase (TET) and subsequent removal via base excision repair or direct demodification. Recently, we have shown that the synthetic iron(IV)-oxo complex [FeIV (O)(Py5 Me2 H)]2+ (1) can serve as a biomimetic model for TET by oxidizing the nucleobase 5-methyl cytosine (5mC) to its natural metabolites. In this work, we demonstrate that nucleosides and even short oligonucleotide strands can also serve as substrates, using a range of HPLC and MS techniques. We found that the 5-position of 5mC is oxidized preferably by 1, with side reactions occurring only at the strand ends of the used oligonucleotides. A detailed study of the reactivity of 1 towards nucleosides confirms our results; that oxidation of the anomeric center (1') is the most common side reaction.
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Affiliation(s)
- David Schmidl
- Department ChemieLudwig-Maximilians-University MünchenButenandtstr. 5–13, Haus DMünchenGermany
| | - Niko S. W. Jonasson
- Department ChemieLudwig-Maximilians-University MünchenButenandtstr. 5–13, Haus DMünchenGermany
| | - Eva Korytiaková
- Department ChemieLudwig-Maximilians-University MünchenButenandtstr. 5–13, Haus DMünchenGermany
| | - Thomas Carell
- Department ChemieLudwig-Maximilians-University MünchenButenandtstr. 5–13, Haus DMünchenGermany
| | - Lena J. Daumann
- Department ChemieLudwig-Maximilians-University MünchenButenandtstr. 5–13, Haus DMünchenGermany
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34
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Runtsch LS, Stadlmeier M, Schön A, Müller M, Carell T. Comparative Nucleosomal Reactivity of 5-Formyl-Uridine and 5-Formyl-Cytidine. Chemistry 2021; 27:12747-12752. [PMID: 34152627 PMCID: PMC8518870 DOI: 10.1002/chem.202102159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Indexed: 11/21/2022]
Abstract
5‐Formyl‐deoxyuridine (fdU) and 5‐formyl‐deoxycytidine (fdC) are formyl‐containing nucleosides that are created by oxidative stress in differentiated cells. While fdU is almost exclusively an oxidative stress lesion formed from deoxythymidine (T), the situation for fdC is more complex. Next to formation as an oxidative lesion, it is particularly abundant in stem cells, where it is more frequently formed in an epigenetically important oxidation reaction performed by α‐ketoglutarate dependent TET enzymes from 5‐methyl‐deoxycytidine (mdC). Recently, it was shown that genomic fdC and fdU can react with the ϵ‐aminogroups of nucleosomal lysines to give Schiff base adducts that covalently link nucleosomes to genomic DNA. Here, we show that fdU features a significantly higher reactivity towards lysine side chains compared with fdC. This result shows that depending on the amounts of fdC and fdU, oxidative stress may have a bigger impact on nucleosome binding than epigenetics.
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Affiliation(s)
- Leander Simon Runtsch
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Michael Stadlmeier
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Alexander Schön
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Markus Müller
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
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35
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Abstract
Epigenetic programming of cells requires methylation of deoxycytidines (dC) to 5-methyl-dC (mdC) followed by oxidation to 5-hydroxymethyl-dC (hmdC), 5-formyl-dC (fdC), and 5-carboxy-dC (cadC). Subsequent transformation of fdC and cadC back to dC by various pathways establishes a chemical intra-genetic control circle. One of the discussed pathways involves the Tdg-independent deformylation of fdC directly to dC. Here we report the synthesis of a fluorinated fdC feeding probe (F-fdC) to study direct deformylation to F-dC. The synthesis was performed along a novel pathway that circumvents any F-dC as a reaction intermediate to avoid contamination interference. Feeding of F-fdC and observation of F-dC formation in vivo allowed us to gain insights into the Tdg-independent removal process. While deformylation was shown to occur in stem cells, we here provide data that prove deformylation also in different somatic cell types. We also investigated active demethylation in a non-dividing neurogenin-inducible system of iPS cells that differentiate into bipolar neurons.
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Affiliation(s)
- Eva Korytiaková
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Ewelina Kamińska
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Markus Müller
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
| | - Thomas Carell
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstrasse 5–1381377MunichGermany
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36
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Jütte BB, Krollmann C, Cieslak K, Koerber RM, Boor P, Graef CM, Bartok E, Wagner M, Carell T, Landsberg J, Aymans P, Wenzel J, Brossart P, Teichmann LL. Intercellular cGAMP transmission induces innate immune activation and tissue inflammation in Trex1 deficiency. iScience 2021; 24:102833. [PMID: 34368651 PMCID: PMC8326191 DOI: 10.1016/j.isci.2021.102833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/17/2021] [Accepted: 07/07/2021] [Indexed: 11/24/2022] Open
Abstract
Intercellular transmission of the second messenger 2′,3′-cGAMP, synthesized by the viral DNA sensor cGAMP synthase (cGAS), is a potent mode of bystander activation during host defense. However, whether this mechanism also contributes to cGAS-dependent autoimmunity remains unknown. Here, using a murine bone marrow transplantation strategy, we demonstrate that, in Trex1−/−-associated autoimmunity, cGAMP shuttling from radioresistant to immune cells induces NF-κB activation, interferon regulatory factor 3 (IRF3) phosphorylation, and subsequent interferon signaling. cGAMP travel prevented myeloid cell and lymphocyte death, promoting their accumulation in secondary lymphoid tissue. Nonetheless, it did not stimulate B cell differentiation into autoantibody-producing plasmablasts or aberrant T cell priming. Although cGAMP-mediated bystander activation did not induce spontaneous organ disease, it did trigger interface dermatitis after UV light exposure, similar to cutaneous lupus erythematosus. These findings reveal that, in Trex1-deficiency, intercellular cGAMP transfer propagates cGAS signaling and, under conducive conditions, causes tissue inflammation. In Trex1−/−-associated autoimmunity radioresistant cells transfer cGAMP to immune cells cGAMP shuttling induces NF-κB activation, IRF3 and IFN signaling in vivo Intercellular cGAMP transmission is sufficient to cause UV skin inflammation
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Affiliation(s)
- Bianca B. Jütte
- Department of Medicine III, University Hospital Bonn, Bonn, Germany
| | - Calvin Krollmann
- Department of Medicine III, University Hospital Bonn, Bonn, Germany
| | - Kevin Cieslak
- Department of Medicine III, University Hospital Bonn, Bonn, Germany
| | | | - Peter Boor
- Institute of Pathology and Division of Nephrology, University Hospital of the RWTH Aachen, Aachen, Germany
| | - Claus M. Graef
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany
| | - Eva Bartok
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
- Unit of Experimental Immunology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Mirko Wagner
- Department of Chemistry, Ludwig Maximilians University Munich, Munich, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig Maximilians University Munich, Munich, Germany
| | | | - Pia Aymans
- Department of Dermatology, University Hospital Bonn, Bonn, Germany
| | - Jörg Wenzel
- Department of Dermatology, University Hospital Bonn, Bonn, Germany
| | - Peter Brossart
- Department of Medicine III, University Hospital Bonn, Bonn, Germany
| | - Lino L. Teichmann
- Department of Medicine III, University Hospital Bonn, Bonn, Germany
- Corresponding author
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37
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Traube FR, Özdemir D, Sahin H, Scheel C, Glück AF, Geserich AS, Oganesian S, Kostidis S, Iwan K, Rahimoff R, Giorgio G, Müller M, Spada F, Biel M, Cox J, Giera M, Michalakis S, Carell T. Redirected nuclear glutamate dehydrogenase supplies Tet3 with α-ketoglutarate in neurons. Nat Commun 2021; 12:4100. [PMID: 34215750 PMCID: PMC8253819 DOI: 10.1038/s41467-021-24353-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/11/2021] [Indexed: 12/14/2022] Open
Abstract
Tet3 is the main α-ketoglutarate (αKG)-dependent dioxygenase in neurons that converts 5-methyl-dC into 5-hydroxymethyl-dC and further on to 5-formyl- and 5-carboxy-dC. Neurons possess high levels of 5-hydroxymethyl-dC that further increase during neural activity to establish transcriptional plasticity required for learning and memory functions. How αKG, which is mainly generated in mitochondria as an intermediate of the tricarboxylic acid cycle, is made available in the nucleus has remained an unresolved question in the connection between metabolism and epigenetics. We show that in neurons the mitochondrial enzyme glutamate dehydrogenase, which converts glutamate into αKG in an NAD+-dependent manner, is redirected to the nucleus by the αKG-consumer protein Tet3, suggesting on-site production of αKG. Further, glutamate dehydrogenase has a stimulatory effect on Tet3 demethylation activity in neurons, and neuronal activation increases the levels of αKG. Overall, the glutamate dehydrogenase-Tet3 interaction might have a role in epigenetic changes during neural plasticity. α-ketoglutarate (αKG) is an intermediate in the tricarboxylic acid cycle that is required in the nucleus for genomic DNA demethylation by Tet3. Here, the authors show that the enzyme glutamate dehydrogenase, which converts glutamate to αKG, is redirected from the mitochondria to the nucleus.
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Affiliation(s)
- Franziska R Traube
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dilara Özdemir
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hanife Sahin
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Constanze Scheel
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andrea F Glück
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anna S Geserich
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sabine Oganesian
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sarantos Kostidis
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands
| | - Katharina Iwan
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - René Rahimoff
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Grazia Giorgio
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Markus Müller
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabio Spada
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin Biel
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jürgen Cox
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Martin Giera
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands
| | - Stylianos Michalakis
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany. .,Department of Ophthalmology, University Hospital, LMU Munich, Munich, Germany.
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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38
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Affiliation(s)
- Eva Korytiaková
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Ewelina Kamińska
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Markus Müller
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
| | - Thomas Carell
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13 81377 München Deutschland
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39
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Schelter F, Kirchner A, Traube FR, Müller M, Steglich W, Carell T. 5-Hydroxymethyl-, 5-Formyl- and 5-Carboxydeoxycytidines as Oxidative Lesions and Epigenetic Marks. Chemistry 2021; 27:8100-8104. [PMID: 33769637 PMCID: PMC8252671 DOI: 10.1002/chem.202100551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Indexed: 01/20/2023]
Abstract
The four non-canonical nucleotides in the human genome 5-methyl-, 5-hydroxymethyl-, 5-formyl- and 5-carboxydeoxycytidine (mdC, hmdC, fdC and cadC) form a second layer of epigenetic information that contributes to the regulation of gene expression. Formation of the oxidized nucleotides hmdC, fdC and cadC requires oxidation of mdC by ten-eleven translocation (Tet) enzymes that require oxygen, Fe(II) and α-ketoglutarate as cosubstrates. Although these oxidized forms of mdC are widespread in mammalian genomes, experimental evidence for their presence in fungi and plants is ambiguous. This vagueness is caused by the fact that these oxidized mdC derivatives are also formed as oxidative lesions, resulting in unclear basal levels that are likely to have no epigenetic function. Here, we report the xdC levels in the fungus Amanita muscaria in comparison to murine embryonic stem cells (mESCs), HEK cells and induced pluripotent stem cells (iPSCs), to obtain information about the basal levels of hmdC, fdC and cadC as DNA lesions in the genome.
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Affiliation(s)
- Florian Schelter
- Ludwigs-Maximilian-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Angie Kirchner
- Ludwigs-Maximilian-Universität MünchenButenandtstr. 5–1381377MunichGermany
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeCB2 0REUK
| | | | - Markus Müller
- Ludwigs-Maximilian-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Wolfgang Steglich
- Ludwigs-Maximilian-Universität MünchenButenandtstr. 5–1381377MunichGermany
| | - Thomas Carell
- Ludwigs-Maximilian-Universität MünchenButenandtstr. 5–1381377MunichGermany
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40
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Thilgen C, Wennemers H, Carell T. François Diederich (1952-2020): 40 Years of Organic Chemistry. Angew Chem Int Ed Engl 2021; 60:11562-11567. [PMID: 33909942 DOI: 10.1002/anie.202101232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
François Diederich, Professor of Organic Chemistry and long-time Chair of the Editorial Board of Angewandte Chemie, sadly passed away on September 23, 2020. He will be remembered for his groundbreaking research in the chemistry of fullerenes and carbon-rich molecules, in supramolecular and medicinal chemistry, as an engaging teacher, and as a generous and fascinating human being.
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Affiliation(s)
- Carlo Thilgen
- Departement für Chemie und Angewandte Biowissenschaften, ETH Zürich, Switzerland
| | - Helma Wennemers
- Departement für Chemie und Angewandte Biowissenschaften, ETH Zürich, Switzerland
| | - Thomas Carell
- Department für Chemie, Ludwig-Maximilians-Universität München, Germany
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41
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Thilgen C, Wennemers H, Carell T. François Diederich (1952–2020): 40 Jahre Organische Chemie. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Carlo Thilgen
- Departement für Chemie und Angewandte Biowissenschaften ETH Zürich
| | - Helma Wennemers
- Departement für Chemie und Angewandte Biowissenschaften ETH Zürich
| | - Thomas Carell
- Department für Chemie Ludwig-Maximilians-Universität München
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42
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Fugger K, Bajrami I, Silva Dos Santos M, Young SJ, Kunzelmann S, Kelly G, Hewitt G, Patel H, Goldstone R, Carell T, Boulton SJ, MacRae J, Taylor IA, West SC. Targeting the nucleotide salvage factor DNPH1 sensitizes BRCA-deficient cells to PARP inhibitors. Science 2021; 372:156-165. [PMID: 33833118 PMCID: PMC7610649 DOI: 10.1126/science.abb4542] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 12/31/2020] [Accepted: 02/24/2021] [Indexed: 12/13/2022]
Abstract
Mutations in the BRCA1 or BRCA2 tumor suppressor genes predispose individuals to breast and ovarian cancer. In the clinic, these cancers are treated with inhibitors that target poly(ADP-ribose) polymerase (PARP). We show that inhibition of DNPH1, a protein that eliminates cytotoxic nucleotide 5-hydroxymethyl-deoxyuridine (hmdU) monophosphate, potentiates the sensitivity of BRCA-deficient cells to PARP inhibitors (PARPi). Synthetic lethality was mediated by the action of SMUG1 glycosylase on genomic hmdU, leading to PARP trapping, replication fork collapse, DNA break formation, and apoptosis. BRCA1-deficient cells that acquired resistance to PARPi were resensitized by treatment with hmdU and DNPH1 inhibition. Because genomic hmdU is a key determinant of PARPi sensitivity, targeting DNPH1 provides a promising strategy for the hypersensitization of BRCA-deficient cancers to PARPi therapy.
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Affiliation(s)
- Kasper Fugger
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | | | | | | | | | - Geoff Kelly
- MRC Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Graeme Hewitt
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Harshil Patel
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Thomas Carell
- Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, Building F, 81377 Munich, Germany
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - James MacRae
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ian A Taylor
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephen C West
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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43
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Schön A, Kaminska E, Schelter F, Ponkkonen E, Korytiaková E, Schiffers S, Carell T. Berichtigung: Analyse des aktiven Deformylierungsmechanismus von 5‐Formyl‐2′‐Desoxycytidin in Stammzellen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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44
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Schön A, Kaminska E, Schelter F, Ponkkonen E, Korytiaková E, Schiffers S, Carell T. Corrigendum: Analysis of an Active Deformylation Mechanism of 5‐Formyl‐deoxycytidine (fdC) in Stem Cells. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/anie.202100271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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45
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Koch M, Scheel C, Ma H, Yang F, Stadlmeier M, Glück AF, Murenu E, Traube FR, Carell T, Biel M, Ding XQ, Michalakis S. The cGMP-Dependent Protein Kinase 2 Contributes to Cone Photoreceptor Degeneration in the Cnga3-Deficient Mouse Model of Achromatopsia. Int J Mol Sci 2020; 22:E52. [PMID: 33374621 PMCID: PMC7793084 DOI: 10.3390/ijms22010052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 12/21/2022] Open
Abstract
Mutations in the CNGA3 gene, which encodes the A subunit of the cyclic guanosine monophosphate (cGMP)-gated cation channel in cone photoreceptor outer segments, cause total colour blindness, also referred to as achromatopsia. Cones lacking this channel protein are non-functional, accumulate high levels of the second messenger cGMP and degenerate over time after induction of ER stress. The cell death mechanisms that lead to loss of affected cones are only partially understood. Here, we explored the disease mechanisms in the Cnga3 knockout (KO) mouse model of achromatopsia. We found that another important effector of cGMP, the cGMP-dependent protein kinase 2 (Prkg2) is crucially involved in cGMP cytotoxicity of cones in Cnga3 KO mice. Virus-mediated knockdown or genetic ablation of Prkg2 in Cnga3 KO mice counteracted degeneration and preserved the number of cones. Analysis of markers of endoplasmic reticulum stress and unfolded protein response confirmed that induction of these processes in Cnga3 KO cones also depends on Prkg2. In conclusion, we identified Prkg2 as a novel key mediator of cone photoreceptor degeneration in achromatopsia. Our data suggest that this cGMP mediator could be a novel pharmacological target for future neuroprotective therapies.
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Affiliation(s)
- Mirja Koch
- Department of Pharmacy—Center for Drug Research, Ludwig-Maximilians-University, 81377 Munich, Germany; (M.K.); (C.S.); (E.M.); (M.B.)
| | - Constanze Scheel
- Department of Pharmacy—Center for Drug Research, Ludwig-Maximilians-University, 81377 Munich, Germany; (M.K.); (C.S.); (E.M.); (M.B.)
| | - Hongwei Ma
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (H.M.); (F.Y.); (X.-Q.D.)
| | - Fan Yang
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (H.M.); (F.Y.); (X.-Q.D.)
| | - Michael Stadlmeier
- Department of Chemistry, Ludwig-Maximilians-University, 81377 Munich, Germany; (M.S.); (A.F.G.); (F.R.T.); (T.C.)
| | - Andrea F. Glück
- Department of Chemistry, Ludwig-Maximilians-University, 81377 Munich, Germany; (M.S.); (A.F.G.); (F.R.T.); (T.C.)
| | - Elisa Murenu
- Department of Pharmacy—Center for Drug Research, Ludwig-Maximilians-University, 81377 Munich, Germany; (M.K.); (C.S.); (E.M.); (M.B.)
- Department of Ophthalmology, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - Franziska R. Traube
- Department of Chemistry, Ludwig-Maximilians-University, 81377 Munich, Germany; (M.S.); (A.F.G.); (F.R.T.); (T.C.)
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-University, 81377 Munich, Germany; (M.S.); (A.F.G.); (F.R.T.); (T.C.)
| | - Martin Biel
- Department of Pharmacy—Center for Drug Research, Ludwig-Maximilians-University, 81377 Munich, Germany; (M.K.); (C.S.); (E.M.); (M.B.)
| | - Xi-Qin Ding
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (H.M.); (F.Y.); (X.-Q.D.)
| | - Stylianos Michalakis
- Department of Pharmacy—Center for Drug Research, Ludwig-Maximilians-University, 81377 Munich, Germany; (M.K.); (C.S.); (E.M.); (M.B.)
- Department of Ophthalmology, Ludwig-Maximilians-University, 80336 Munich, Germany
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46
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Spada F, Schiffers S, Kirchner A, Zhang Y, Arista G, Kosmatchev O, Korytiakova E, Rahimoff R, Ebert C, Carell T. Active turnover of genomic methylcytosine in pluripotent cells. Nat Chem Biol 2020; 16:1411-1419. [PMID: 32778844 DOI: 10.1038/s41589-020-0621-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 07/08/2020] [Indexed: 12/20/2022]
Abstract
Epigenetic plasticity underpins cell potency, but the extent to which active turnover of DNA methylation contributes to such plasticity is not known, and the underlying pathways are poorly understood. Here we use metabolic labeling with stable isotopes and mass spectrometry to quantitatively address the global turnover of genomic 5-methyl-2'-deoxycytidine (mdC), 5-hydroxymethyl-2'-deoxycytidine (hmdC) and 5-formyl-2'-deoxycytidine (fdC) across mouse pluripotent cell states. High rates of mdC/hmdC oxidation and fdC turnover characterize a formative-like pluripotent state. In primed pluripotent cells, the global mdC turnover rate is about 3-6% faster than can be explained by passive dilution through DNA synthesis. While this active component is largely dependent on ten-eleven translocation (Tet)-mediated mdC oxidation, we unveil additional oxidation-independent mdC turnover, possibly through DNA repair. This process accelerates upon acquisition of primed pluripotency and returns to low levels in lineage-committed cells. Thus, in pluripotent cells, active mdC turnover involves both mdC oxidation-dependent and oxidation-independent processes.
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Affiliation(s)
- Fabio Spada
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany.
| | - Sarah Schiffers
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
- National Cancer Institute, Center for Cancer Research, Bethesda, MD, USA
| | - Angie Kirchner
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Yingqian Zhang
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
- State Key Laboratory of Elemento-organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, China
| | - Gautier Arista
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
| | - Olesea Kosmatchev
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
| | - Eva Korytiakova
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
| | - René Rahimoff
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
- Department of Chemistry, University of California, Los Angeles, Berkeley, CA, USA
| | - Charlotte Ebert
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig Maximilians University Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany.
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47
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Mulholland CB, Nishiyama A, Ryan J, Nakamura R, Yiğit M, Glück IM, Trummer C, Qin W, Bartoschek MD, Traube FR, Parsa E, Ugur E, Modic M, Acharya A, Stolz P, Ziegenhain C, Wierer M, Enard W, Carell T, Lamb DC, Takeda H, Nakanishi M, Bultmann S, Leonhardt H. Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals. Nat Commun 2020; 11:5972. [PMID: 33235224 PMCID: PMC7686362 DOI: 10.1038/s41467-020-19603-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. Here, we describe a recently evolved pathway in which global hypomethylation is achieved by the coupling of active and passive demethylation. TET activity is required, albeit indirectly, for global demethylation, which mostly occurs at sites devoid of TET binding. Instead, TET-mediated active demethylation is locus-specific and necessary for activating a subset of genes, including the naïve pluripotency and germline marker Dppa3 (Stella, Pgc7). DPPA3 in turn drives large-scale passive demethylation by directly binding and displacing UHRF1 from chromatin, thereby inhibiting maintenance DNA methylation. Although unique to mammals, we show that DPPA3 alone is capable of inducing global DNA demethylation in non-mammalian species (Xenopus and medaka) despite their evolutionary divergence from mammals more than 300 million years ago. Our findings suggest that the evolution of Dppa3 facilitated the emergence of global DNA demethylation in mammals.
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Affiliation(s)
- Christopher B Mulholland
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Joel Ryan
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Merve Yiğit
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ivo M Glück
- Physical Chemistry, Department of Chemistry, Center for Nanoscience, Nanosystems Initiative Munich and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Carina Trummer
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Weihua Qin
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael D Bartoschek
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Franziska R Traube
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Edris Parsa
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Enes Ugur
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Miha Modic
- The Francis Crick Institute and UCL Queen Square Institute of Neurology, London, UK
| | - Aishwarya Acharya
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Paul Stolz
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Christoph Ziegenhain
- Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Wolfgang Enard
- Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Thomas Carell
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience, Nanosystems Initiative Munich and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Sebastian Bultmann
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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48
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Lauria T, Slator C, McKee V, Müller M, Stazzoni S, Crisp AL, Carell T, Kellett A. A Click Chemistry Approach to Developing Molecularly Targeted DNA Scissors. Chemistry 2020; 26:16782-16792. [PMID: 32706904 DOI: 10.1002/chem.202002860] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/23/2020] [Indexed: 12/21/2022]
Abstract
Nucleic acid click chemistry was used to prepare a family of chemically modified triplex forming oligonucleotides (TFOs) for application as a new gene-targeted technology. Azide-bearing phenanthrene ligands-designed to promote triplex stability and copper binding-were 'clicked' to alkyne-modified parallel TFOs. Using this approach, a library of TFO hybrids was prepared and shown to effectively target purine-rich genetic elements in vitro. Several of the hybrids provide significant stabilisation toward melting in parallel triplexes (>20 °C) and DNA damage can be triggered upon copper binding in the presence of added reductant. Therefore, the TFO and 'clicked' ligands work synergistically to provide sequence-selectivity to the copper cutting unit which, in turn, confers high stabilisation to the DNA triplex. To extend the boundaries of this hybrid system further, a click chemistry-based di-copper binding ligand was developed to accommodate designer ancillary ligands such as DPQ and DPPZ. When this ligand was inserted into a TFO, a dramatic improvement in targeted oxidative cleavage is afforded.
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Affiliation(s)
- Teresa Lauria
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Creina Slator
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Vickie McKee
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland.,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Markus Müller
- Department of Chemistry, Ludwig-Maximilians-Universität, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Samuele Stazzoni
- Department of Chemistry, Ludwig-Maximilians-Universität, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Antony L Crisp
- Department of Chemistry, Ludwig-Maximilians-Universität, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-Universität, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland.,CÚRAM, Centre for Research in Medical Devices, Dublin City University, Glasnevin, Dublin, 9, Ireland
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49
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Alberge JB, Magrangeas F, Wagner M, Denié S, Guérin-Charbonnel C, Campion L, Attal M, Avet-Loiseau H, Carell T, Moreau P, Minvielle S, Sérandour AA. DNA hydroxymethylation is associated with disease severity and persists at enhancers of oncogenic regions in multiple myeloma. Clin Epigenetics 2020; 12:163. [PMID: 33138842 PMCID: PMC7607866 DOI: 10.1186/s13148-020-00953-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/19/2020] [Indexed: 12/29/2022] Open
Abstract
Background Multiple myeloma (MM) is a heterogeneous plasma cell malignancy that remains challenging to cure. Global hypomethylation correlates with an aggressive phenotype of the disease, while hypermethylation is observed at particular regions of myeloma such as B cell-specific enhancers. The recently discovered active epigenetic mark 5-hydroxymethylCytosine (5hmC) may also play a role in tumor biology; however, little is known about its level and distribution in myeloma. In this study, we investigated the global level and the genomic localization of 5hmC in myeloma cells from 40 newly diagnosed patients, including paired relapses, and of control individuals.
Results Compared to normal plasma cells, we found global 5hmC levels to be lower in myeloma (P < 0.001). Higher levels of 5hmC were found in lower grades of the International Staging System prognostic index (P < 0.05) and tend to associate with a longer overall survival (P < 0.1). From the hydroxymethylome data, we observed that the remaining 5hmC is organized in large domains overlapping with active chromatin marks and chromatin opening. We discovered that 5hmC strongly persists at key oncogenic genes such as CCND1, CCND2 and MMSET and characterized domains that are specifically hydroxymethylated in myeloma subgroups. Novel 5hmC-enriched domains were found at putative enhancers of CCND2 and MYC in newly diagnosed patients. Conclusions 5hmC level is associated with clinical aspects of MM. Mapping 5hmC at a genome-wide level provides insights into the disease biology directly from genomic DNA, which makes it a potent mark to study epigenetics on large patient cohorts.
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Affiliation(s)
- Jean-Baptiste Alberge
- Université de Nantes, CNRS, Inserm, CRCINA, Nantes, France.,Site de Recherche Intégrée Sur Le Cancer (SIRIC) ILIAD, INCA-DGOS-Inserm 12558, Nantes, France
| | - Florence Magrangeas
- Université de Nantes, CNRS, Inserm, CRCINA, Nantes, France.,Site de Recherche Intégrée Sur Le Cancer (SIRIC) ILIAD, INCA-DGOS-Inserm 12558, Nantes, France.,Hematology Department, University Hospital, Nantes, France
| | - Mirko Wagner
- Ludwig Maximilian Universität München, Munich, Germany
| | - Soline Denié
- Université de Nantes, CNRS, Inserm, CRCINA, Nantes, France
| | - Catherine Guérin-Charbonnel
- Université de Nantes, CNRS, Inserm, CRCINA, Nantes, France.,Site de Recherche Intégrée Sur Le Cancer (SIRIC) ILIAD, INCA-DGOS-Inserm 12558, Nantes, France.,Institut de cancérologie de L'Ouest Site René-Gauducheau, Saint-Herblain, France
| | - Loïc Campion
- Université de Nantes, CNRS, Inserm, CRCINA, Nantes, France.,Site de Recherche Intégrée Sur Le Cancer (SIRIC) ILIAD, INCA-DGOS-Inserm 12558, Nantes, France.,Institut de cancérologie de L'Ouest Site René-Gauducheau, Saint-Herblain, France
| | - Michel Attal
- Centre de Recherche en Cancérologie de Toulouse, Institut National de la Santé et de la Recherche Médicale U1037, Toulouse, France.,Unit for Genomics in Myeloma, Institut Universitaire du Cancer de Toulouse-Oncopole, University Hospital, Toulouse, France
| | - Hervé Avet-Loiseau
- Centre de Recherche en Cancérologie de Toulouse, Institut National de la Santé et de la Recherche Médicale U1037, Toulouse, France.,Unit for Genomics in Myeloma, Institut Universitaire du Cancer de Toulouse-Oncopole, University Hospital, Toulouse, France
| | - Thomas Carell
- Ludwig Maximilian Universität München, Munich, Germany
| | - Philippe Moreau
- Université de Nantes, CNRS, Inserm, CRCINA, Nantes, France.,Site de Recherche Intégrée Sur Le Cancer (SIRIC) ILIAD, INCA-DGOS-Inserm 12558, Nantes, France.,Hematology Department, University Hospital, Nantes, France
| | - Stéphane Minvielle
- Université de Nantes, CNRS, Inserm, CRCINA, Nantes, France. .,Site de Recherche Intégrée Sur Le Cancer (SIRIC) ILIAD, INCA-DGOS-Inserm 12558, Nantes, France. .,Hematology Department, University Hospital, Nantes, France.
| | - Aurélien A Sérandour
- Université de Nantes, CNRS, Inserm, CRCINA, Nantes, France. .,École Centrale de Nantes, Nantes, France.
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Nainytė M, Müller F, Ganazzoli G, Chan CY, Crisp A, Globisch D, Carell T. Amino Acid Modified RNA Bases as Building Blocks of an Early Earth RNA-Peptide World. Chemistry 2020; 26:14856-14860. [PMID: 32573861 PMCID: PMC7756884 DOI: 10.1002/chem.202002929] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Indexed: 12/14/2022]
Abstract
Fossils of extinct species allow us to reconstruct the process of Darwinian evolution that led to the species diversity we see on Earth today. The origin of the first functional molecules able to undergo molecular evolution and thus eventually able to create life, are largely unknown. The most prominent idea in the field posits that biology was preceded by an era of molecular evolution, in which RNA molecules encoded information and catalysed their own replication. This RNA world concept stands against other hypotheses, that argue for example that life may have begun with catalytic peptides and primitive metabolic cycles. The question whether RNA or peptides were first is addressed by the RNA‐peptide world concept, which postulates a parallel existence of both molecular species. A plausible experimental model of how such an RNA‐peptide world may have looked like, however, is absent. Here we report the synthesis and physicochemical evaluation of amino acid containing adenosine bases, which are closely related to molecules that are found today in the anticodon stem‐loop of tRNAs from all three kingdoms of life. We show that these adenosines lose their base pairing properties, which allow them to equip RNA with amino acids independent of the sequence context. As such we may consider them to be living molecular fossils of an extinct molecular RNA‐peptide world.
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Affiliation(s)
- Milda Nainytė
- Department of Chemistry, LMU München, Butenandtstr. 5-13, 81377, München, Germany
| | - Felix Müller
- Department of Chemistry, LMU München, Butenandtstr. 5-13, 81377, München, Germany
| | - Giacomo Ganazzoli
- Department of Chemistry, LMU München, Butenandtstr. 5-13, 81377, München, Germany
| | - Chun-Yin Chan
- Department of Chemistry, LMU München, Butenandtstr. 5-13, 81377, München, Germany
| | - Antony Crisp
- Department of Chemistry, LMU München, Butenandtstr. 5-13, 81377, München, Germany
| | - Daniel Globisch
- Department of Medicinal Chemistry, Uppsala University, Husargatan 3, 75123, Uppsala, Sweden
| | - Thomas Carell
- Department of Chemistry, LMU München, Butenandtstr. 5-13, 81377, München, Germany
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