1
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Chan A, Naarmann-de Vries IS, Scheitl CPM, Höbartner C, Dieterich C. Detecting m 6A at single-molecular resolution via direct RNA sequencing and realistic training data. Nat Commun 2024; 15:3323. [PMID: 38637518 PMCID: PMC11026524 DOI: 10.1038/s41467-024-47661-2] [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: 08/28/2023] [Accepted: 04/05/2024] [Indexed: 04/20/2024] Open
Abstract
Direct RNA sequencing offers the possibility to simultaneously identify canonical bases and epi-transcriptomic modifications in each single RNA molecule. Thus far, the development of computational methods has been hampered by the lack of biologically realistic training data that carries modification labels at molecular resolution. Here, we report on the synthesis of such samples and the development of a bespoke algorithm, mAFiA (m6A Finding Algorithm), that accurately detects single m6A nucleotides in both synthetic RNAs and natural mRNA on single read level. Our approach uncovers distinct modification patterns in single molecules that would appear identical at the ensemble level. Compared to existing methods, mAFiA also demonstrates improved accuracy in measuring site-level m6A stoichiometry in biological samples.
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Affiliation(s)
- Adrian Chan
- Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Isabel S Naarmann-de Vries
- Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK)-Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | | | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Würzburg, Germany
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany.
- German Centre for Cardiovascular Research (DZHK)-Partner Site Heidelberg/Mannheim, Heidelberg, Germany.
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2
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Jakab M, Lee KH, Uvarovskii A, Ovchinnikova S, Kulkarni SR, Jakab S, Rostalski T, Spegg C, Anders S, Augustin HG. Lung endothelium exploits susceptible tumor cell states to instruct metastatic latency. Nat Cancer 2024:10.1038/s43018-023-00716-7. [PMID: 38308117 DOI: 10.1038/s43018-023-00716-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/15/2023] [Indexed: 02/04/2024]
Abstract
In metastasis, cancer cells travel around the circulation to colonize distant sites. Due to the rarity of these events, the immediate fates of metastasizing tumor cells (mTCs) are poorly understood while the role of the endothelium as a dissemination interface remains elusive. Using a newly developed combinatorial mTC enrichment approach, we provide a transcriptional blueprint of the early colonization process. Following their arrest at the metastatic site, mTCs were found to either proliferate intravascularly or extravasate, thereby establishing metastatic latency. Endothelial-derived angiocrine Wnt factors drive this bifurcation, instructing mTCs to follow the extravasation-latency route. Surprisingly, mTC responsiveness towards niche-derived Wnt was established at the epigenetic level, which predetermined tumor cell behavior. Whereas hypomethylation enabled high Wnt activity leading to metastatic latency, methylated mTCs exhibited low activity and proliferated intravascularly. Collectively the data identify the predetermined methylation status of disseminated tumor cells as a key regulator of mTC behavior in the metastatic niche.
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Affiliation(s)
- Moritz Jakab
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany.
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany.
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
| | - Ki Hong Lee
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Alexey Uvarovskii
- Center for Molecular Biology, Heidelberg University, Heidelberg, Germany
- Evotec SE, Göttingen, Germany
| | - Svetlana Ovchinnikova
- Center for Molecular Biology, Heidelberg University, Heidelberg, Germany
- Bioquant Center, Heidelberg University, Heidelberg, Germany
| | - Shubhada R Kulkarni
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany
| | - Sevinç Jakab
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Till Rostalski
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany
| | - Carleen Spegg
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany
| | - Simon Anders
- Center for Molecular Biology, Heidelberg University, Heidelberg, Germany
- Bioquant Center, Heidelberg University, Heidelberg, Germany
| | - Hellmut G Augustin
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany.
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany.
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3
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Köppke J, Keller LE, Stuck M, Arnow ND, Bannert N, Doellinger J, Cingöz O. Direct translation of incoming retroviral genomes. Nat Commun 2024; 15:299. [PMID: 38182622 PMCID: PMC10770327 DOI: 10.1038/s41467-023-44501-7] [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: 04/29/2023] [Accepted: 12/15/2023] [Indexed: 01/07/2024] Open
Abstract
Viruses that carry a positive-sense, single-stranded (+ssRNA) RNA translate their genomes soon after entering the host cell to produce viral proteins, with the exception of retroviruses. A distinguishing feature of retroviruses is reverse transcription, where the +ssRNA genome serves as a template to synthesize a double-stranded DNA copy that subsequently integrates into the host genome. As retroviral RNAs are produced by the host cell transcriptional machinery and are largely indistinguishable from cellular mRNAs, we investigated the potential of incoming retroviral genomes to directly express proteins. Here we show through multiple, complementary methods that retroviral genomes are translated after entry. Our findings challenge the notion that retroviruses require reverse transcription to produce viral proteins. Synthesis of retroviral proteins in the absence of productive infection has significant implications for basic retrovirology, immune responses and gene therapy applications.
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Affiliation(s)
- Julia Köppke
- Robert Koch Institute, Department of Infectious Diseases, Unit of Sexually Transmitted Bacterial Pathogens and HIV (FG18), Berlin, Germany
| | - Luise-Elektra Keller
- Robert Koch Institute, Department of Infectious Diseases, Unit of Sexually Transmitted Bacterial Pathogens and HIV (FG18), Berlin, Germany
- Institute of Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt, Germany
| | - Michelle Stuck
- Robert Koch Institute, Department of Infectious Diseases, Unit of Sexually Transmitted Bacterial Pathogens and HIV (FG18), Berlin, Germany
- Department of Chemistry, Heidelberg University, Heidelberg, Germany
| | - Nicolas D Arnow
- Robert Koch Institute, Department of Infectious Diseases, Unit of Sexually Transmitted Bacterial Pathogens and HIV (FG18), Berlin, Germany
| | - Norbert Bannert
- Robert Koch Institute, Department of Infectious Diseases, Unit of Sexually Transmitted Bacterial Pathogens and HIV (FG18), Berlin, Germany
| | - Joerg Doellinger
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
| | - Oya Cingöz
- Robert Koch Institute, Department of Infectious Diseases, Unit of Sexually Transmitted Bacterial Pathogens and HIV (FG18), Berlin, Germany.
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4
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Mukesh S, Mukherjee G, Singh R, Steenbuck N, Demidova C, Joshi P, Sangamwar AT, Wade RC. Comparative analysis of drug-salt-polymer interactions by experiment and molecular simulation improves biopharmaceutical performance. Commun Chem 2023; 6:201. [PMID: 37749228 PMCID: PMC10519957 DOI: 10.1038/s42004-023-01006-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 09/14/2023] [Indexed: 09/27/2023] Open
Abstract
The propensity of poorly water-soluble drugs to aggregate at supersaturation impedes their bioavailability. Supersaturated amorphous drug-salt-polymer systems provide an emergent approach to this problem. However, the effects of polymers on drug-drug interactions in aqueous phase are largely unexplored and it is unclear how to choose an optimal salt-polymer combination for a particular drug. Here, we describe a comparative experimental and computational characterization of amorphous solid dispersions containing the drug celecoxib, and a polymer, polyvinylpyrrolidone vinyl acetate (PVP-VA) or hydroxypropyl methylcellulose acetate succinate, with or without Na+/K+ salts. Classical models for drug-polymer interactions fail to identify the best drug-salt-polymer combination. In contrast, more stable drug-polymer interaction energies computed from molecular dynamics simulations correlate with prolonged stability of supersaturated amorphous drug-salt-polymer systems, along with better dissolution and pharmacokinetic profiles. The celecoxib-salt-PVP-VA formulations exhibit excellent biopharmaceutical performance, offering the prospect of a low-dosage regimen for this widely used anti-inflammatory, thereby increasing cost-effectiveness, and reducing side-effects.
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Affiliation(s)
- Sumit Mukesh
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Sector-67, Mohali, Punjab, 160062, India
| | - Goutam Mukherjee
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - Ridhima Singh
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Sector-67, Mohali, Punjab, 160062, India
| | - Nathan Steenbuck
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Carolina Demidova
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
- Faculty of Chemistry, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Prachi Joshi
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Sector-67, Mohali, Punjab, 160062, India
| | - Abhay T Sangamwar
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Sector-67, Mohali, Punjab, 160062, India.
| | - Rebecca C Wade
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, Heidelberg, Germany.
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5
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Richter-Pechanski P, Wiesenbach P, Schwab DM, Kiriakou C, He M, Allers MM, Tiefenbacher AS, Kunz N, Martynova A, Spiller N, Mierisch J, Borchert F, Schwind C, Frey N, Dieterich C, Geis NA. A distributable German clinical corpus containing cardiovascular clinical routine doctor's letters. Sci Data 2023; 10:207. [PMID: 37059736 PMCID: PMC10104831 DOI: 10.1038/s41597-023-02128-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/31/2023] [Indexed: 04/16/2023] Open
Abstract
We present CARDIO:DE, the first freely available and distributable large German clinical corpus from the cardiovascular domain. CARDIO:DE encompasses 500 clinical routine German doctor's letters from Heidelberg University Hospital, which were manually annotated. Our prospective study design complies well with current data protection regulations and allows us to keep the original structure of clinical documents consistent. In order to ease access to our corpus, we manually de-identified all letters. To enable various information extraction tasks the temporal information in the documents was preserved. We added two high-quality manual annotation layers to CARDIO:DE, (1) medication information and (2) CDA-compliant section classes. To the best of our knowledge, CARDIO:DE is the first freely available and distributable German clinical corpus in the cardiovascular domain. In summary, our corpus offers unique opportunities for collaborative and reproducible research on natural language processing models for German clinical texts.
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Affiliation(s)
- Phillip Richter-Pechanski
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, DE, Germany.
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, DE, Germany.
- German Center for Cardiovascular Research (DZHK) - Partner site Heidelberg/Mannheim, Heidelberg, DE, Germany.
- Informatics for Life, Heidelberg, DE, Germany.
| | - Philipp Wiesenbach
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, DE, Germany
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, DE, Germany
- Informatics for Life, Heidelberg, DE, Germany
| | - Dominic M Schwab
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, DE, Germany
| | - Christina Kiriakou
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, DE, Germany
| | - Mingyang He
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, DE, Germany
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, DE, Germany
| | - Michael M Allers
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, DE, Germany
| | - Anna S Tiefenbacher
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, DE, Germany
| | - Nicola Kunz
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, DE, Germany
| | - Anna Martynova
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, DE, Germany
| | - Noemie Spiller
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, DE, Germany
| | - Julian Mierisch
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, DE, Germany
| | - Florian Borchert
- Digital Health Center, Hasso Plattner Institute, University of Potsdam, Potsdam, DE, Germany
| | - Charlotte Schwind
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, DE, Germany
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, DE, Germany
| | - Norbert Frey
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, DE, Germany
- German Center for Cardiovascular Research (DZHK) - Partner site Heidelberg/Mannheim, Heidelberg, DE, Germany
- Informatics for Life, Heidelberg, DE, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, DE, Germany
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, DE, Germany
- German Center for Cardiovascular Research (DZHK) - Partner site Heidelberg/Mannheim, Heidelberg, DE, Germany
- Informatics for Life, Heidelberg, DE, Germany
| | - Nicolas A Geis
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, DE, Germany
- Informatics for Life, Heidelberg, DE, Germany
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6
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Rennekamp B, Karfusehr C, Kurth M, Ünal A, Monego D, Riedmiller K, Gryn'ova G, Hudson DM, Gräter F. Collagen breaks at weak sacrificial bonds taming its mechanoradicals. Nat Commun 2023; 14:2075. [PMID: 37045839 PMCID: PMC10097693 DOI: 10.1038/s41467-023-37726-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 10/17/2022] [Accepted: 03/29/2023] [Indexed: 04/14/2023] Open
Abstract
Collagen is a force-bearing, hierarchical structural protein important to all connective tissue. In tendon collagen, high load even below macroscopic failure level creates mechanoradicals by homolytic bond scission, similar to polymers. The location and type of initial rupture sites critically decide on both the mechanical and chemical impact of these micro-ruptures on the tissue, but are yet to be explored. We here use scale-bridging simulations supported by gel electrophoresis and mass spectrometry to determine breakage points in collagen. We find collagen crosslinks, as opposed to the backbone, to harbor the weakest bonds, with one particular bond in trivalent crosslinks as the most dominant rupture site. We identify this bond as sacrificial, rupturing prior to other bonds while maintaining the material's integrity. Also, collagen's weak bonds funnel ruptures such that the potentially harmful mechanoradicals are readily stabilized. Our results suggest this unique failure mode of collagen to be tailored towards combatting an early onset of macroscopic failure and material ageing.
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Affiliation(s)
- Benedikt Rennekamp
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing, Heidelberg University, INF 205, 69120, Heidelberg, Germany
- Max Planck School Matter to Life, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Christoph Karfusehr
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
- Max Planck School Matter to Life, Jahnstrasse 29, 69120, Heidelberg, Germany
- Physics Department and ZNN, Technical University Munich, Coulombwall 4a, 85748, Garching, Germany
| | - Markus Kurth
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing, Heidelberg University, INF 205, 69120, Heidelberg, Germany
| | - Aysecan Ünal
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing, Heidelberg University, INF 205, 69120, Heidelberg, Germany
- Max Planck School Matter to Life, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Debora Monego
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - Kai Riedmiller
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - Ganna Gryn'ova
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing, Heidelberg University, INF 205, 69120, Heidelberg, Germany
| | - David M Hudson
- Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.
- Interdisciplinary Center for Scientific Computing, Heidelberg University, INF 205, 69120, Heidelberg, Germany.
- Max Planck School Matter to Life, Jahnstrasse 29, 69120, Heidelberg, Germany.
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7
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Schulz AM, Zebley CC, Youngblood B, Zehn D. Tapping the keg of discovery to advance T cell therapy. Nat Immunol 2023; 24:213-215. [PMID: 36631639 PMCID: PMC9838262 DOI: 10.1038/s41590-022-01401-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Anna M Schulz
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany.
| | - Caitlin C Zebley
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ben Youngblood
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Dietmar Zehn
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany.
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8
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Reiser P, Neubert M, Eberhard A, Torresi L, Zhou C, Shao C, Metni H, van Hoesel C, Schopmans H, Sommer T, Friederich P. Graph neural networks for materials science and chemistry. Commun Mater 2022; 3:93. [PMID: 36468086 PMCID: PMC9702700 DOI: 10.1038/s43246-022-00315-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/07/2022] [Indexed: 05/14/2023]
Abstract
Machine learning plays an increasingly important role in many areas of chemistry and materials science, being used to predict materials properties, accelerate simulations, design new structures, and predict synthesis routes of new materials. Graph neural networks (GNNs) are one of the fastest growing classes of machine learning models. They are of particular relevance for chemistry and materials science, as they directly work on a graph or structural representation of molecules and materials and therefore have full access to all relevant information required to characterize materials. In this Review, we provide an overview of the basic principles of GNNs, widely used datasets, and state-of-the-art architectures, followed by a discussion of a wide range of recent applications of GNNs in chemistry and materials science, and concluding with a road-map for the further development and application of GNNs.
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Affiliation(s)
- Patrick Reiser
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Marlen Neubert
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
| | - André Eberhard
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
| | - Luca Torresi
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
| | - Chen Zhou
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
| | - Chen Shao
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
- Present Address: Institute for Applied Informatics and Formal Description Systems, Karlsruhe Institute of Technology, Kaiserstr. 89, 76133 Karlsruhe, Germany
| | - Houssam Metni
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
- ECPM, Université de Strasbourg, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Clint van Hoesel
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
- Department of Applied Physics, Eindhoven University of Technology, Groene Loper 19, 5612 AP Eindhoven, The Netherlands
| | - Henrik Schopmans
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Timo Sommer
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
- Institute for Theory of Condensed Matter, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- Present Address: School of Chemistry, Trinity College Dublin, College Green, Dublin 2, Ireland
| | - Pascal Friederich
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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9
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Wild B, Dormagen DM, Zachariae A, Smith ML, Traynor KS, Brockmann D, Couzin ID, Landgraf T. Social networks predict the life and death of honey bees. Nat Commun 2021; 12:1110. [PMID: 33597518 PMCID: PMC7889932 DOI: 10.1038/s41467-021-21212-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 08/28/2020] [Accepted: 01/19/2021] [Indexed: 12/22/2022] Open
Abstract
In complex societies, individuals' roles are reflected by interactions with other conspecifics. Honey bees (Apis mellifera) generally change tasks as they age, but developmental trajectories of individuals can vary drastically due to physiological and environmental factors. We introduce a succinct descriptor of an individual's social network that can be obtained without interfering with the colony. This 'network age' accurately predicts task allocation, survival, activity patterns, and future behavior. We analyze developmental trajectories of multiple cohorts of individuals in a natural setting and identify distinct developmental pathways and critical life changes. Our findings suggest a high stability in task allocation on an individual level. We show that our method is versatile and can extract different properties from social networks, opening up a broad range of future studies. Our approach highlights the relationship of social interactions and individual traits, and provides a scalable technique for understanding how complex social systems function.
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Affiliation(s)
- Benjamin Wild
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
| | - David M Dormagen
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | | | - Michael L Smith
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Kirsten S Traynor
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
- Global Biosocial Complexity Initiative, Arizona State University, Tempe, FL, USA
| | - Dirk Brockmann
- Robert Koch Institute, Berlin, Germany
- Institute for Theoretical Biology, Humboldt University Berlin, Berlin, Germany
| | - Iain D Couzin
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Tim Landgraf
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
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Kaiser RWJ, Ignarski M, Van Nostrand EL, Frese CK, Jain M, Cukoski S, Heinen H, Schaechter M, Seufert L, Bunte K, Frommolt P, Keller P, Helm M, Bohl K, Höhne M, Schermer B, Benzing T, Höpker K, Dieterich C, Yeo GW, Müller RU, Fabretti F. A protein-RNA interaction atlas of the ribosome biogenesis factor AATF. Sci Rep 2019; 9:11071. [PMID: 31363146 PMCID: PMC6667500 DOI: 10.1038/s41598-019-47552-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 01/03/2019] [Accepted: 07/19/2019] [Indexed: 01/08/2023] Open
Abstract
AATF is a central regulator of the cellular outcome upon p53 activation, a finding that has primarily been attributed to its function as a transcription factor. Recent data showed that AATF is essential for ribosome biogenesis and plays a role in rRNA maturation. AATF has been implicated to fulfil this role through direct interaction with rRNA and was identified in several RNA-interactome capture experiments. Here, we provide a first comprehensive analysis of the RNA bound by AATF using CLIP-sequencing. Interestingly, this approach shows predominant binding of the 45S pre-ribosomal RNA precursor molecules. Furthermore, AATF binds to mRNAs encoding for ribosome biogenesis factors as well as snoRNAs. These findings are complemented by an in-depth analysis of the protein interactome of AATF containing a large set of proteins known to play a role in rRNA maturation with an emphasis on the protein-RNA-complexes known to be required for the generation of the small ribosomal subunit (SSU). In line with this finding, the binding sites of AATF within the 45S rRNA precursor localize in close proximity to the SSU cleavage sites. Consequently, our multilayer analysis of the protein-RNA interactome of AATF reveals this protein to be an important hub for protein and RNA interactions involved in ribosome biogenesis.
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Affiliation(s)
- Rainer W J Kaiser
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
| | - Michael Ignarski
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Christian K Frese
- Proteomics Core Facility, Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
| | - Manaswita Jain
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937, Cologne, Germany
| | - Sadrija Cukoski
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937, Cologne, Germany
| | - Heide Heinen
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937, Cologne, Germany
| | - Melanie Schaechter
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937, Cologne, Germany
| | - Lisa Seufert
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
| | - Konstantin Bunte
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937, Cologne, Germany
- Bioinformatics Core Facility, Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
| | - Peter Frommolt
- Bioinformatics Core Facility, Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
| | - Patrick Keller
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Katrin Bohl
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
- Systems Biology of Ageing Cologne, University of Cologne, 50931, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
- Systems Biology of Ageing Cologne, University of Cologne, 50931, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
- Systems Biology of Ageing Cologne, University of Cologne, 50931, Cologne, Germany
| | - Katja Höpker
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
| | - Christoph Dieterich
- German Center for Cardiovascular Research (DZHK), Partner site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Roman-Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937, Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany.
- Systems Biology of Ageing Cologne, University of Cologne, 50931, Cologne, Germany.
| | - Francesca Fabretti
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50937, Cologne, Germany
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