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Yin K, Büttner M, Deligiannis IK, Strzelecki M, Zhang L, Talavera-López C, Theis F, Odom DT, Martinez-Jimenez CP. Polyploidisation pleiotropically buffers ageing in hepatocytes. J Hepatol 2024:S0168-8278(24)00227-7. [PMID: 38583492 DOI: 10.1016/j.jhep.2024.03.043] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND & AIMS Polyploidy in hepatocytes has been proposed as a genetic mechanism to buffer against transcriptional dysregulation. Here, we aim to demonstrate the role of polyploidy in modulating gene regulatory networks in hepatocytes during ageing. METHODS We performed single-nucleus RNA-sequencing in hepatocyte nuclei of different ploidy levels isolated from young and old wild-type mice. Changes in the gene expression and regulatory network were compared to three independent haploinsufficient strains for HNF4A, CEBPA or CTCF, representing non-deleterious perturbations. Phenotypic characteristics of the liver section were additionally evaluated histologically, whereas the genomic allele composition of hepatocytes was analysed by BaseScope. RESULTS We observed that ageing in wild-type mice results in nuclei polyploidy and marked increase in steatosis. Haploinsufficiency of liver-specific master regulators (HFN4A or CEBPA) results in the enrichment of hepatocytes with tetraploid nuclei at a young age, affecting the genomic regulatory network, and dramatically suppressing ageing-related steatosis tissue-wide. Notably, these phenotypes are not the result of subtle disruption to liver-specific transcriptional networks, since haploinsufficiency in CTCF insulator protein resulted in the same phenotype. Further quantification of genotypes of tetraploid hepatocytes in young and old HFN4A haploinsufficient mice revealed that during ageing, tetraploid hepatocytes lead to the selection of wild-type alleles, restoring non-deleterious genetic perturbation. ConclusionsOur results suggest a model whereby polyploidisation leads to fundamentally different cell states. Polyploid conversion enables pleiotropic buffering against age-related decline via non-random allelic segregation to restore a wild-type genome.
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Affiliation(s)
- Kelvin Yin
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany
| | - Maren Büttner
- Institute of Computational Biology, Computational Health Department, Helmholtz Munich, Neuherberg, Germany
| | | | - Mateusz Strzelecki
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany; German Cancer Research Centre, Heidelberg, Germany
| | - Liwei Zhang
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany
| | - Carlos Talavera-López
- Institute of Computational Biology, Computational Health Department, Helmholtz Munich, Neuherberg, Germany; TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Fabian Theis
- Institute of Computational Biology, Computational Health Department, Helmholtz Munich, Neuherberg, Germany; Würzburg Institute for Systems Immunology, Faculty of Medicine, Julius-Maximilian-Universität, Würzburg, Germany
| | - Duncan T Odom
- Technical University of Munich, Department of Mathematics, 85748 Garching. Munich, Germany
| | - Celia P Martinez-Jimenez
- Helmholtz Pioneer Campus (HPC), Helmholtz Munich, Neuherberg, Germany; German Cancer Research Centre, Heidelberg, Germany; Institute of Biotechnology and Biomedicine (BIOTECMED), Department of Biochemistry and Molecular Biology, University of Valencia, Burjassot, Spain.
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2
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Eckardt F, Mittas R, Horlava N, Schiefelbein J, Asani B, Michalakis S, Gerhardt M, Priglinger C, Keeser D, Koutsouleris N, Priglinger S, Theis F, Peng T, Schworm B. Deep Learning-Based Retinal Layer Segmentation in Optical Coherence Tomography Scans of Patients with Inherited Retinal Diseases. Klin Monbl Augenheilkd 2024. [PMID: 38086412 DOI: 10.1055/a-2227-3742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
BACKGROUND In optical coherence tomography (OCT) scans of patients with inherited retinal diseases (IRDs), the measurement of the thickness of the outer nuclear layer (ONL) has been well established as a surrogate marker for photoreceptor preservation. Current automatic segmentation tools fail in OCT segmentation in IRDs, and manual segmentation is time-consuming. METHODS AND MATERIAL Patients with IRD and an available OCT scan were screened for the present study. Additionally, OCT scans of patients without retinal disease were included to provide training data for artificial intelligence (AI). We trained a U-net-based model on healthy patients and applied a domain adaption technique to the IRD patients' scans. RESULTS We established an AI-based image segmentation algorithm that reliably segments the ONL in OCT scans of IRD patients. In a test dataset, the dice score of the algorithm was 98.7%. Furthermore, we generated thickness maps of the full retinal thickness and the ONL layer for each patient. CONCLUSION Accurate segmentation of anatomical layers on OCT scans plays a crucial role for predictive models linking retinal structure to visual function. Our algorithm for segmentation of OCT images could provide the basis for further studies on IRDs.
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Affiliation(s)
- Franziska Eckardt
- Department of Ophthalmology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Robin Mittas
- Institute for Computational Biology, Helmholtz Munich, Munich, Germany
| | - Nastassya Horlava
- Institute for Computational Biology, Helmholtz Munich, Munich, Germany
| | | | - Ben Asani
- Department of Ophthalmology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Stylianos Michalakis
- Department of Ophthalmology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Maximilian Gerhardt
- Department of Ophthalmology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Claudia Priglinger
- Department of Ophthalmology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Daniel Keeser
- Department of Psychiatry und Psychotherapy, LMU University Hospital, LMU Munich, Munich, Germany
| | - Nikolaos Koutsouleris
- Department of Psychiatry und Psychotherapy, LMU University Hospital, LMU Munich, Munich, Germany
| | - Siegfried Priglinger
- Department of Ophthalmology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Fabian Theis
- Institute for Computational Biology, Helmholtz Munich, Munich, Germany
| | - Tingying Peng
- Institute for Computational Biology, Helmholtz Munich, Munich, Germany
| | - Benedikt Schworm
- Department of Ophthalmology, LMU University Hospital, LMU Munich, Munich, Germany
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3
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Rosowski S, Remmert C, Marder M, Akishiba M, Bushe J, Feuchtinger A, Platen A, Ussar S, Theis F, Wiedenmann S, Meier M. Single-cell characterization of neovascularization using hiPSC-derived endothelial cells in a 3D microenvironment. Stem Cell Reports 2023; 18:1972-1986. [PMID: 37714147 PMCID: PMC10656300 DOI: 10.1016/j.stemcr.2023.08.008] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 09/17/2023] Open
Abstract
The formation of vascular structures is fundamental for in vitro tissue engineering. Vascularization can enable the nutrient supply within larger structures and increase transplantation efficiency. We differentiated human induced pluripotent stem cells toward endothelial cells in 3D suspension culture. To investigate in vitro neovascularization and various 3D microenvironmental approaches, we designed a comprehensive single-cell transcriptomic study. Time-resolved single-cell transcriptomics of the endothelial and co-evolving mural cells gave insights into cell type development, stability, and plasticity. Transfer to a 3D hydrogel microenvironment induced neovascularization and facilitated tracing of migrating, coalescing, and tubulogenic endothelial cell states. During maturation, we monitored two pericyte subtypes evolving mural cells. Profiling cell-cell interactions between pericytes and endothelial cells revealed angiogenic signals during tubulogenesis. In silico discovered ligands were tested for their capability to attract endothelial cells. Our data, analyses, and results provide an in vitro roadmap to guide vascularization in future tissue engineering.
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Affiliation(s)
- Simon Rosowski
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Caroline Remmert
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Maren Marder
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Misao Akishiba
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Judith Bushe
- Research Unit Analytical Pathology, Helmholtz München, 85764 Neuherberg, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz München, 85764 Neuherberg, Germany
| | - Alina Platen
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Siegfried Ussar
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany; Department of Mathematics, Technical University of Munich, 85748 Garching bei München, Germany
| | - Sandra Wiedenmann
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Matthias Meier
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany; University Leipzig, Center for Biotechnology and Biomedicine, Institute of Biochemistry, Leipzig, Germany.
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4
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Henao JD, Lauber M, Azevedo M, Grekova A, Theis F, List M, Ogris C, Schubert B. Multi-omics regulatory network inference in the presence of missing data. Brief Bioinform 2023; 24:bbad309. [PMID: 37670505 PMCID: PMC10516394 DOI: 10.1093/bib/bbad309] [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: 12/08/2022] [Revised: 05/06/2023] [Accepted: 05/29/2023] [Indexed: 09/07/2023] Open
Abstract
A key problem in systems biology is the discovery of regulatory mechanisms that drive phenotypic behaviour of complex biological systems in the form of multi-level networks. Modern multi-omics profiling techniques probe these fundamental regulatory networks but are often hampered by experimental restrictions leading to missing data or partially measured omics types for subsets of individuals due to cost restrictions. In such scenarios, in which missing data is present, classical computational approaches to infer regulatory networks are limited. In recent years, approaches have been proposed to infer sparse regression models in the presence of missing information. Nevertheless, these methods have not been adopted for regulatory network inference yet. In this study, we integrated regression-based methods that can handle missingness into KiMONo, a Knowledge guided Multi-Omics Network inference approach, and benchmarked their performance on commonly encountered missing data scenarios in single- and multi-omics studies. Overall, two-step approaches that explicitly handle missingness performed best for a wide range of random- and block-missingness scenarios on imbalanced omics-layers dimensions, while methods implicitly handling missingness performed best on balanced omics-layers dimensions. Our results show that robust multi-omics network inference in the presence of missing data with KiMONo is feasible and thus allows users to leverage available multi-omics data to its full extent.
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Affiliation(s)
- Juan D Henao
- Helmholtz Zentrum München, Computational Health Department, Ingolstädter Landstraße 1, 85764 Munich, Germany, Member of the German Center for Lung Research (DZL)
| | - Michael Lauber
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising
| | - Manuel Azevedo
- Helmholtz Zentrum München, Computational Health Department, Ingolstädter Landstraße 1, 85764 Munich, Germany, Member of the German Center for Lung Research (DZL)
| | - Anastasiia Grekova
- Helmholtz Zentrum München, Computational Health Department, Ingolstädter Landstraße 1, 85764 Munich, Germany, Member of the German Center for Lung Research (DZL)
| | - Fabian Theis
- Helmholtz Zentrum München, Computational Health Department, Ingolstädter Landstraße 1, 85764 Munich, Germany, Member of the German Center for Lung Research (DZL)
- Department of Mathematics, Technical University of Munich, 85748 Garching bei München, Germany
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising
| | - Christoph Ogris
- Helmholtz Zentrum München, Computational Health Department, Ingolstädter Landstraße 1, 85764 Munich, Germany, Member of the German Center for Lung Research (DZL)
| | - Benjamin Schubert
- Helmholtz Zentrum München, Computational Health Department, Ingolstädter Landstraße 1, 85764 Munich, Germany, Member of the German Center for Lung Research (DZL)
- Department of Mathematics, Technical University of Munich, 85748 Garching bei München, Germany
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5
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Polychronidou M, Hou J, Babu MM, Liberali P, Amit I, Deplancke B, Lahav G, Itzkovitz S, Mann M, Saez-Rodriguez J, Theis F, Eils R. Single-cell biology: what does the future hold? Mol Syst Biol 2023:e11799. [PMID: 37318792 DOI: 10.15252/msb.202311799] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/16/2023] Open
Affiliation(s)
| | | | - M Madan Babu
- Center for Data Driven Discovery, Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Ido Amit
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Bart Deplancke
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, USA
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Matthias Mann
- Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Julio Saez-Rodriguez
- Faculty of Medicine, Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany
| | | | - Roland Eils
- Berlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin, Germany
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6
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Bhatia HS, Brunner AD, Öztürk F, Kapoor S, Rong Z, Mai H, Thielert M, Ali M, Al-Maskari R, Paetzold JC, Kofler F, Todorov MI, Molbay M, Kolabas ZI, Negwer M, Hoeher L, Steinke H, Dima A, Gupta B, Kaltenecker D, Caliskan ÖS, Brandt D, Krahmer N, Müller S, Lichtenthaler SF, Hellal F, Bechmann I, Menze B, Theis F, Mann M, Ertürk A. Spatial proteomics in three-dimensional intact specimens. Cell 2022; 185:5040-5058.e19. [PMID: 36563667 DOI: 10.1016/j.cell.2022.11.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/13/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022]
Abstract
Spatial molecular profiling of complex tissues is essential to investigate cellular function in physiological and pathological states. However, methods for molecular analysis of large biological specimens imaged in 3D are lacking. Here, we present DISCO-MS, a technology that combines whole-organ/whole-organism clearing and imaging, deep-learning-based image analysis, robotic tissue extraction, and ultra-high-sensitivity mass spectrometry. DISCO-MS yielded proteome data indistinguishable from uncleared samples in both rodent and human tissues. We used DISCO-MS to investigate microglia activation along axonal tracts after brain injury and characterized early- and late-stage individual amyloid-beta plaques in a mouse model of Alzheimer's disease. DISCO-bot robotic sample extraction enabled us to study the regional heterogeneity of immune cells in intact mouse bodies and aortic plaques in a complete human heart. DISCO-MS enables unbiased proteome analysis of preclinical and clinical tissues after unbiased imaging of entire specimens in 3D, identifying diagnostic and therapeutic opportunities for complex diseases. VIDEO ABSTRACT.
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Affiliation(s)
- Harsharan Singh Bhatia
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Andreas-David Brunner
- Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Str. 65, D-88400 Biberach Riss, Germany
| | - Furkan Öztürk
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Saketh Kapoor
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Zhouyi Rong
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Munich Medical Research School (MMRS), 80336 Munich, Germany
| | - Hongcheng Mai
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Munich Medical Research School (MMRS), 80336 Munich, Germany
| | - Marvin Thielert
- Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Mayar Ali
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Graduate School of Neuroscience (GSN), 82152 Munich, Germany
| | - Rami Al-Maskari
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Center for Translational Cancer Research (TranslaTUM) of the TUM, 81675 Munich, Germany; Image-Based Biomedical Modeling, Department of Informatics, Technical University of Munich, 85748 Garching, Germany
| | - Johannes Christian Paetzold
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Center for Translational Cancer Research (TranslaTUM) of the TUM, 81675 Munich, Germany; Image-Based Biomedical Modeling, Department of Informatics, Technical University of Munich, 85748 Garching, Germany; Biomedical Image Analysis Group, Department of Computing, Imperial College London, London SW7 2AZ, UK
| | - Florian Kofler
- Center for Translational Cancer Research (TranslaTUM) of the TUM, 81675 Munich, Germany; Image-Based Biomedical Modeling, Department of Informatics, Technical University of Munich, 85748 Garching, Germany; Helmholtz AI, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Department of Neuroradiology, Klinikum rechts der Isar, 81675 Munich, Germany
| | - Mihail Ivilinov Todorov
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Muge Molbay
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Munich Medical Research School (MMRS), 80336 Munich, Germany
| | - Zeynep Ilgin Kolabas
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Graduate School of Neuroscience (GSN), 82152 Munich, Germany
| | - Moritz Negwer
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Luciano Hoeher
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Hanno Steinke
- Institute of Anatomy, University of Leipzig, 04109 Leipzig, Germany
| | - Alina Dima
- Center for Translational Cancer Research (TranslaTUM) of the TUM, 81675 Munich, Germany; Image-Based Biomedical Modeling, Department of Informatics, Technical University of Munich, 85748 Garching, Germany
| | - Basavdatta Gupta
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Doris Kaltenecker
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Institute for Diabetes and Cancer, Helmholz Zentrum München, 85764 Neuherberg, Germany
| | - Özüm Sehnaz Caliskan
- Institute for Diabetes and Obesity, Helmholz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research, Helmholz Zentrum München, 85764 Neuherberg, Germany
| | - Daniel Brandt
- Institute for Diabetes and Obesity, Helmholz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research, Helmholz Zentrum München, 85764 Neuherberg, Germany
| | - Natalie Krahmer
- Institute for Diabetes and Obesity, Helmholz Zentrum München, 85764 Neuherberg, Germany; German Center for Diabetes Research, Helmholz Zentrum München, 85764 Neuherberg, Germany
| | - Stephan Müller
- German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Neuroproteomics, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Stefan Frieder Lichtenthaler
- Graduate School of Neuroscience (GSN), 82152 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Neuroproteomics, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany
| | - Farida Hellal
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Ingo Bechmann
- Institute of Anatomy, University of Leipzig, 04109 Leipzig, Germany
| | - Bjoern Menze
- Center for Translational Cancer Research (TranslaTUM) of the TUM, 81675 Munich, Germany; Image-Based Biomedical Modeling, Department of Informatics, Technical University of Munich, 85748 Garching, Germany; Department for Quantitative Biomedicine, University of Zurich, 8006 Zurich, Switzerland
| | - Fabian Theis
- Institute of Computational Biology, Helmholz Zentrum München, 85764 Neuherberg, Germany; TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany; Department of Mathematics, Technical University of Munich, 85748 Garching, Germany
| | - Matthias Mann
- Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Ali Ertürk
- Insititute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany; Graduate School of Neuroscience (GSN), 82152 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany.
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7
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Schäbitz A, Hillig C, Mubarak M, Jargosch M, Farnoud A, Scala E, Kurzen N, Pilz AC, Bhalla N, Thomas J, Stahle M, Biedermann T, Schmidt-Weber CB, Theis F, Garzorz-Stark N, Eyerich K, Menden MP, Eyerich S. Spatial transcriptomics landscape of lesions from non-communicable inflammatory skin diseases. Nat Commun 2022; 13:7729. [PMID: 36513651 PMCID: PMC9747967 DOI: 10.1038/s41467-022-35319-w] [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: 09/24/2021] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Abundant heterogeneous immune cells infiltrate lesions in chronic inflammatory diseases and characterization of these cells is needed to distinguish disease-promoting from bystander immune cells. Here, we investigate the landscape of non-communicable inflammatory skin diseases (ncISD) by spatial transcriptomics resulting in a large repository of 62,000 spatially defined human cutaneous transcriptomes from 31 patients. Despite the expected immune cell infiltration, we observe rather low numbers of pathogenic disease promoting cytokine transcripts (IFNG, IL13 and IL17A), i.e. >125 times less compared to the mean expression of all other genes over lesional skin sections. Nevertheless, cytokine expression is limited to lesional skin and presented in a disease-specific pattern. Leveraging a density-based spatial clustering method, we identify specific responder gene signatures in direct proximity of cytokines, and confirm that detected cytokine transcripts initiate amplification cascades of up to thousands of specific responder transcripts forming localized epidermal clusters. Thus, within the abundant and heterogeneous infiltrates of ncISD, only a low number of cytokine transcripts and their translated proteins promote disease by initiating an inflammatory amplification cascade in their local microenvironment.
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Affiliation(s)
- A. Schäbitz
- grid.4714.60000 0004 1937 0626Division of Dermatology and Venereology, Department of Medicine Solna, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - C. Hillig
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München—German Research Centre for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - M. Mubarak
- grid.6936.a0000000123222966Center for Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Biedersteinerstrasse 29, 80802 Munich, Germany
| | - M. Jargosch
- grid.6936.a0000000123222966Center for Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Biedersteinerstrasse 29, 80802 Munich, Germany ,grid.6936.a0000000123222966Department of Dermatology and Allergy, Technical University of Munich, Biedersteinerstrasse 29, 80802 Munich, Germany
| | - A. Farnoud
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München—German Research Centre for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - E. Scala
- grid.4714.60000 0004 1937 0626Division of Dermatology and Venereology, Department of Medicine Solna, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden ,grid.5963.9Department of Dermatology and Venerology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - N. Kurzen
- grid.6936.a0000000123222966Center for Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Biedersteinerstrasse 29, 80802 Munich, Germany
| | - A. C. Pilz
- grid.6936.a0000000123222966Department of Dermatology and Allergy, Technical University of Munich, Biedersteinerstrasse 29, 80802 Munich, Germany ,grid.5963.9Department of Dermatology and Venerology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - N. Bhalla
- grid.5037.10000000121581746Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - J. Thomas
- grid.6936.a0000000123222966Center for Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Biedersteinerstrasse 29, 80802 Munich, Germany
| | - M. Stahle
- grid.4714.60000 0004 1937 0626Division of Dermatology and Venereology, Department of Medicine Solna, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - T. Biedermann
- grid.6936.a0000000123222966Department of Dermatology and Allergy, Technical University of Munich, Biedersteinerstrasse 29, 80802 Munich, Germany
| | - C. B. Schmidt-Weber
- grid.6936.a0000000123222966Center for Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Biedersteinerstrasse 29, 80802 Munich, Germany
| | - F. Theis
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München—German Research Centre for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - N. Garzorz-Stark
- grid.4714.60000 0004 1937 0626Division of Dermatology and Venereology, Department of Medicine Solna, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden ,grid.6936.a0000000123222966Department of Dermatology and Allergy, Technical University of Munich, Biedersteinerstrasse 29, 80802 Munich, Germany
| | - K. Eyerich
- grid.4714.60000 0004 1937 0626Division of Dermatology and Venereology, Department of Medicine Solna, and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden ,grid.5963.9Department of Dermatology and Venerology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.24381.3c0000 0000 9241 5705Department of Dermatology and Venereology, Unit of Dermatology, Karolinska University Hospital, Stockholm, Sweden
| | - M. P. Menden
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München—German Research Centre for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany ,grid.5252.00000 0004 1936 973XDepartment of Biology, Ludwig-Maximilians University, Goßhadernerstrasse 2, Martinsried, 82152 Germany ,grid.452622.5German Center for Diabetes Research (DZD e.V.), Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - S. Eyerich
- grid.6936.a0000000123222966Center for Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Biedersteinerstrasse 29, 80802 Munich, Germany
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8
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Pardo M, Offer S, Hartner E, Di Bucchianico S, Bisig C, Bauer S, Pantzke J, Zimmermann EJ, Cao X, Binder S, Kuhn E, Huber A, Jeong S, Käfer U, Schneider E, Mesceriakovas A, Bendl J, Brejcha R, Buchholz A, Gat D, Hohaus T, Rastak N, Karg E, Jakobi G, Kalberer M, Kanashova T, Hu Y, Ogris C, Marsico A, Theis F, Shalit T, Gröger T, Rüger CP, Oeder S, Orasche J, Paul A, Ziehm T, Zhang ZH, Adam T, Sippula O, Sklorz M, Schnelle-Kreis J, Czech H, Kiendler-Scharr A, Zimmermann R, Rudich Y. Exposure to naphthalene and β-pinene-derived secondary organic aerosol induced divergent changes in transcript levels of BEAS-2B cells. Environ Int 2022; 166:107366. [PMID: 35763991 DOI: 10.1016/j.envint.2022.107366] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/13/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
The health effects of exposure to secondary organic aerosols (SOAs) are still limited. Here, we investigated and compared the toxicities of soot particles (SP) coated with β-pinene SOA (SOAβPin-SP) and SP coated with naphthalene SOA (SOANap-SP) in a human bronchial epithelial cell line (BEAS-2B) residing at the air-liquid interface. SOAβPin-SP mostly contained oxygenated aliphatic compounds from β-pinene photooxidation, whereas SOANap-SP contained a significant fraction of oxygenated aromatic products under similar conditions. Following exposure, genome-wide transcriptome responses showed an Nrf2 oxidative stress response, particularly for SOANap-SP. Other signaling pathways, such as redox signaling, inflammatory signaling, and the involvement of matrix metalloproteinase, were identified to have a stronger impact following exposure to SOANap-SP. SOANap-SP also induced a stronger genotoxicity response than that of SOAβPin-SP. This study elucidated the mechanisms that govern SOA toxicity and showed that, compared to SOAs derived from a typical biogenic precursor, SOAs from a typical anthropogenic precursor have higher toxicological potency, which was accompanied with the activation of varied cellular mechanisms, such as aryl hydrocarbon receptor. This can be attributed to the difference in chemical composition; specifically, the aromatic compounds in the naphthalene-derived SOA had higher cytotoxic potential than that of the β-pinene-derived SOA.
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Affiliation(s)
- Michal Pardo
- Department of Earth and Planetary Sciences, Faculty of Chemistry, Weizmann Institute of Science, 234 Herzl Street, POB 26, ISR-7610001 Rehovot, Israel.
| | - Svenja Offer
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Elena Hartner
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Sebastiano Di Bucchianico
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Christoph Bisig
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Stefanie Bauer
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Jana Pantzke
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Elias J Zimmermann
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Xin Cao
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Stephanie Binder
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Evelyn Kuhn
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Anja Huber
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Seongho Jeong
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Uwe Käfer
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Eric Schneider
- Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Arunas Mesceriakovas
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70210 Kuopio, Finland
| | - Jan Bendl
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; University of the Bundeswehr Munich, Institute for Chemistry and Environmental Engineering, Werner- Heisenberg-Weg 39, D-85577 Neubiberg, Germany; Institute for Environmental Studies, Faculty of Science, Charles University, Albertov 6, CZE-12800 Prague, Czech Republic
| | - Ramona Brejcha
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Angela Buchholz
- Department of Applied Physics, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70210 Kuopio, Finland
| | - Daniela Gat
- Department of Earth and Planetary Sciences, Faculty of Chemistry, Weizmann Institute of Science, 234 Herzl Street, POB 26, ISR-7610001 Rehovot, Israel
| | - Thorsten Hohaus
- Institute of Energy and Climate Research, Troposphere (IEK-8), Forschungszentrum Jülich GmbH, Wilhelm-Johen-Str., D-52428 Jülich, Germany
| | - Narges Rastak
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Erwin Karg
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Gert Jakobi
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Markus Kalberer
- Department of Environmental Sciences, University of Basel, Klingelbergstr. 27, CH-4056 Basel, Switzerland
| | - Tamara Kanashova
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Robert-Rössle-Str. 10, D-13125 Berlin, Germany
| | - Yue Hu
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Christoph Ogris
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Annalisa Marsico
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Tali Shalit
- The Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Thomas Gröger
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Christopher P Rüger
- Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Sebastian Oeder
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Jürgen Orasche
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Andreas Paul
- Institute of Energy and Climate Research, Troposphere (IEK-8), Forschungszentrum Jülich GmbH, Wilhelm-Johen-Str., D-52428 Jülich, Germany
| | - Till Ziehm
- Institute of Energy and Climate Research, Troposphere (IEK-8), Forschungszentrum Jülich GmbH, Wilhelm-Johen-Str., D-52428 Jülich, Germany
| | - Zhi-Hui Zhang
- Department of Environmental Sciences, University of Basel, Klingelbergstr. 27, CH-4056 Basel, Switzerland
| | - Thomas Adam
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; University of the Bundeswehr Munich, Institute for Chemistry and Environmental Engineering, Werner- Heisenberg-Weg 39, D-85577 Neubiberg, Germany
| | - Olli Sippula
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70210 Kuopio, Finland
| | - Martin Sklorz
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Jürgen Schnelle-Kreis
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Hendryk Czech
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Astrid Kiendler-Scharr
- Institute of Energy and Climate Research, Troposphere (IEK-8), Forschungszentrum Jülich GmbH, Wilhelm-Johen-Str., D-52428 Jülich, Germany
| | - Ralf Zimmermann
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Joint Mass Spectrometry Center (JMSC) at Analytical Chemistry, Institute of Chemistry, University of Rostock, Dr.-Lorenz-Weg 2, D-18059 Rostock, Germany
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Faculty of Chemistry, Weizmann Institute of Science, 234 Herzl Street, POB 26, ISR-7610001 Rehovot, Israel
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9
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Slob EMA, Faiz A, van Nijnatten J, Vijverberg SJH, Longo C, Kutlu M, Chew FT, Sio YY, Herrera-Luis E, Espuela-Ortiz A, Perez-Garcia J, Pino-Yanes M, Burchard EG, Potočnik U, Gorenjak M, Palmer C, Maroteau C, Turner S, Verhamme K, Karimi L, Mukhopadhyay S, Timens W, Hiemstra PS, Pijnenburg MW, Neighbors M, Grimbaldeston MA, Tew GW, Brandsma CA, Berce V, Aliee H, Theis F, Sin DD, Li X, van den Berge M, Maitland-van der Zee AH, Koppelman GH. Association of bronchial steroid inducible methylation quantitative trait loci with asthma and chronic obstructive pulmonary disease treatment response. Clin Transl Allergy 2022; 12:e12173. [PMID: 36036237 PMCID: PMC9421427 DOI: 10.1002/clt2.12173] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Elise M A Slob
- Department of Respiratory Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Department of Paediatric Pulmonology, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Department of Clinical Pharmacy, Haaglanden Medical Center, The Hague, The Netherlands
| | - Alen Faiz
- Department of Pulmonology, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Jos van Nijnatten
- Department of Pulmonology, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Susanne J H Vijverberg
- Department of Respiratory Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Department of Paediatric Pulmonology, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Cristina Longo
- Department of Respiratory Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Merve Kutlu
- Department of Respiratory Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Fook Tim Chew
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - Yang Yie Sio
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - Esther Herrera-Luis
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Antonio Espuela-Ortiz
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Javier Perez-Garcia
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, California, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Mario Gorenjak
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Colin Palmer
- Population Pharmacogenetics Group, Biomedical Research Institute, University of Dundee, Dundee, UK
| | - Cyrielle Maroteau
- Population Pharmacogenetics Group, Biomedical Research Institute, University of Dundee, Dundee, UK
| | - Steve Turner
- Child Health, University of Aberdeen, Aberdeen, UK
| | - Katia Verhamme
- Department of Medical Informatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Leila Karimi
- Department of Medical Informatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Wim Timens
- Department of Pulmonology, University Medical Center Groningen, Groningen, The Netherlands.,Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Pieter S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Mariëlle W Pijnenburg
- Department of Pediatrics, Pediatric Pulmonology and Allergology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Margaret Neighbors
- OMNI Biomarker Development, Genentech Inc, South San Francisco, California, USA
| | | | - Gaik W Tew
- Product Development Immunology, Infectious Disease & Ophtalmology, Genentech Inc, South San Francisco, California, USA
| | - Corry A Brandsma
- Department of Pulmonology, University Medical Center Groningen, Groningen, The Netherlands.,Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Vojko Berce
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Department of Pediatrics, University Medical Centre Maribor, Maribor, Slovenia
| | - Hananeh Aliee
- Institute of Computational Biology, Helmholtz Center, Munich, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Center, Munich, Germany.,Department of Mathematics, Technical University of Munich, Munich, Germany
| | - Don D Sin
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Xuan Li
- Centre for Heart Lung Innovation, St. Paul's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Maarten van den Berge
- Department of Pulmonology, University Medical Center Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Department of Paediatric Pulmonology, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Department of Pediatric Pulmonology and Pediatric Allergology, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Groningen, The Netherlands
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10
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Hu B, Lelek S, Spanjaard B, El-Sammak H, Simões MG, Mintcheva J, Aliee H, Schäfer R, Meyer AM, Theis F, Stainier DYR, Panáková D, Junker JP. Origin and function of activated fibroblast states during zebrafish heart regeneration. Nat Genet 2022; 54:1227-1237. [PMID: 35864193 PMCID: PMC7613248 DOI: 10.1038/s41588-022-01129-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [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: 02/15/2022] [Accepted: 06/09/2022] [Indexed: 12/12/2022]
Abstract
The adult zebrafish heart has a high capacity for regeneration following injury. However, the composition of the regenerative niche has remained largely elusive. Here, we dissected the diversity of activated cell states in the regenerating zebrafish heart based on single-cell transcriptomics and spatiotemporal analysis. We observed the emergence of several transient cell states with fibroblast characteristics following injury, and we outlined the proregenerative function of collagen-12-expressing fibroblasts. To understand the cascade of events leading to heart regeneration, we determined the origin of these cell states by high-throughput lineage tracing. We found that activated fibroblasts were derived from two separate sources: the epicardium and the endocardium. Mechanistically, we determined Wnt signalling as a regulator of the endocardial fibroblast response. In summary, our work identifies specialized activated fibroblast cell states that contribute to heart regeneration, thereby opening up possible approaches to modulating the regenerative capacity of the vertebrate heart. Single-cell RNA sequencing and spatiotemporal analysis of the regenerating zebrafish heart identify transient proregenerative fibroblast-like cells that are derived from the epicardium and the endocardium. Wnt signalling regulates the endocardial fibroblast response.
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Affiliation(s)
- Bo Hu
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Sara Lelek
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research) partner site, Berlin, Germany
| | - Bastiaan Spanjaard
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Hadil El-Sammak
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,DZHK (German Centre for Cardiovascular Research) partner site Rhine/Main, Frankfurt, Germany
| | - Mariana Guedes Simões
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Janita Mintcheva
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Hananeh Aliee
- Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Munich, Germany
| | - Ronny Schäfer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Alexander M Meyer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Fabian Theis
- Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Munich, Germany
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,DZHK (German Centre for Cardiovascular Research) partner site Rhine/Main, Frankfurt, Germany
| | - Daniela Panáková
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany. .,DZHK (German Centre for Cardiovascular Research) partner site, Berlin, Germany.
| | - Jan Philipp Junker
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany. .,DZHK (German Centre for Cardiovascular Research) partner site, Berlin, Germany.
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11
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Ruecker FG, Corbacioglu A, Theis F, Christopeit M, Germing U, Wulf G, Abu Samra M, Teichmann L, Lübbert M, Kühn MW, Bentz M, Westermann J, Bullinger L, Gaidzik VI, Jahn E, Gröger M, Kapp-Schwoerer S, Weber D, Thol F, Heuser M, Ganser A, Döhner H, Döhner K. P448: PROGNOSTIC IMPACT OF SOMATIC CEBPA BZIP DOMAIN MUTATIONS IN ACUTE MYELOID LEUKEMIA. Hemasphere 2022. [DOI: 10.1097/01.hs9.0000844680.77570.26] [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: 11/25/2022] Open
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Offer S, Hartner E, Di Bucchianico S, Bisig C, Bauer S, Pantzke J, Zimmermann EJ, Cao X, Binder S, Kuhn E, Huber A, Jeong S, Käfer U, Martens P, Mesceriakovas A, Bendl J, Brejcha R, Buchholz A, Gat D, Hohaus T, Rastak N, Jakobi G, Kalberer M, Kanashova T, Hu Y, Ogris C, Marsico A, Theis F, Pardo M, Gröger T, Oeder S, Orasche J, Paul A, Ziehm T, Zhang ZH, Adam T, Sippula O, Sklorz M, Schnelle-Kreis J, Czech H, Kiendler-Scharr A, Rudich Y, Zimmermann R. Effect of Atmospheric Aging on Soot Particle Toxicity in Lung Cell Models at the Air–Liquid Interface: Differential Toxicological Impacts of Biogenic and Anthropogenic Secondary Organic Aerosols (SOAs). Environ Health Perspect 2022; 130:27003. [PMID: 35112925 PMCID: PMC8812555 DOI: 10.1289/ehp9413] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Background: Secondary organic aerosols (SOAs) formed from anthropogenic or biogenic gaseous precursors in the atmosphere substantially contribute to the ambient fine particulate matter [PM ≤2.5μm in aerodynamic diameter (PM2.5)] burden, which has been associated with adverse human health effects. However, there is only limited evidence on their differential toxicological impact. Objectives: We aimed to discriminate toxicological effects of aerosols generated by atmospheric aging on combustion soot particles (SPs) of gaseous biogenic (β-pinene) or anthropogenic (naphthalene) precursors in two different lung cell models exposed at the air–liquid interface (ALI). Methods: Mono- or cocultures of lung epithelial cells (A549) and endothelial cells (EA.hy926) were exposed at the ALI for 4 h to different aerosol concentrations of a photochemically aged mixture of primary combustion SP and β-pinene (SOAβPIN-SP) or naphthalene (SOANAP-SP). The internally mixed soot/SOA particles were comprehensively characterized in terms of their physical and chemical properties. We conducted toxicity tests to determine cytotoxicity, intracellular oxidative stress, primary and secondary genotoxicity, as well as inflammatory and angiogenic effects. Results: We observed considerable toxicity-related outcomes in cells treated with either SOA type. Greater adverse effects were measured for SOANAP-SP compared with SOAβPIN-SP in both cell models, whereas the nano-sized soot cores alone showed only minor effects. At the functional level, we found that SOANAP-SP augmented the secretion of malondialdehyde and interleukin-8 and may have induced the activation of endothelial cells in the coculture system. This activation was confirmed by comet assay, suggesting secondary genotoxicity and greater angiogenic potential. Chemical characterization of PM revealed distinct qualitative differences in the composition of the two secondary aerosol types. Discussion: In this study using A549 and EA.hy926 cells exposed at ALI, SOA compounds had greater toxicity than primary SPs. Photochemical aging of naphthalene was associated with the formation of more oxidized, more aromatic SOAs with a higher oxidative potential and toxicity compared with β-pinene. Thus, we conclude that the influence of atmospheric chemistry on the chemical PM composition plays a crucial role for the adverse health outcome of emissions. https://doi.org/10.1289/EHP9413
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Affiliation(s)
- Svenja Offer
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Elena Hartner
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Sebastiano Di Bucchianico
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Christoph Bisig
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Stefanie Bauer
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jana Pantzke
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Elias J. Zimmermann
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Xin Cao
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Stefanie Binder
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Evelyn Kuhn
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Anja Huber
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Seongho Jeong
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Uwe Käfer
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Patrick Martens
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Arunas Mesceriakovas
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jan Bendl
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute for Chemistry and Environmental Engineering, University of the Bundeswehr Munich, Neubiberg, Germany
- Institute for Environmental Studies, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ramona Brejcha
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Angela Buchholz
- Department of Applied Physics, University of Eastern Finland, Kuopio, Finland
| | - Daniella Gat
- Department of Earth and Planetary Sciences, Faculty of Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Thorsten Hohaus
- Institute of Energy and Climate Research, Troposphere, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Narges Rastak
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gert Jakobi
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Markus Kalberer
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | | | - Yue Hu
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Christoph Ogris
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Annalisa Marsico
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michal Pardo
- Department of Earth and Planetary Sciences, Faculty of Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Thomas Gröger
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Sebastian Oeder
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jürgen Orasche
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Andreas Paul
- Institute of Energy and Climate Research, Troposphere, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Till Ziehm
- Institute of Energy and Climate Research, Troposphere, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Zhi-Hui Zhang
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Thomas Adam
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute for Chemistry and Environmental Engineering, University of the Bundeswehr Munich, Neubiberg, Germany
| | - Olli Sippula
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Martin Sklorz
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jürgen Schnelle-Kreis
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Hendryk Czech
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Astrid Kiendler-Scharr
- Institute of Energy and Climate Research, Troposphere, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Faculty of Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Ralf Zimmermann
- Joint Mass Spectrometry Center (JMSC) at Comprehensive Molecular Analytics, Helmholtz Zentrum München, Neuherberg, Germany
- JMSC at Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
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Puchinger K, Castelletti N, Rubio-Acero R, Geldmacher C, Eser TM, Deák F, Paunovic I, Bakuli A, Saathoff E, von Meyer A, Markgraf A, Falk P, Reich J, Riess F, Girl P, Müller K, Radon K, Guggenbuehl Noller JM, Wölfel R, Hoelscher M, Kroidl I, Wieser A, Olbrich L, Alamoudi E, Anderson J, Baumann M, Behlen M, Beyerl J, Böhnlein R, Brauer A, Britz V, Bruger J, Caroli F, Contento L, Diekmannshemke J, Do A, Dobler G, Eberle U, Eckstein J, Frese J, Forster F, Frahnow T, Fröschl G, Geisenberger O, Gillig K, Heiber A, Hinske C, Hoefflin J, Hofberger T, Höfinger M, Hofmann L, Horn S, Huber K, Janke C, Kappl U, Kiani C, Kroidl A, Laxy M, Leidl R, Lindner F, Mayrhofer R, Mekota AM, Müller H, Metaxa D, Pattard L, Pletschette M, Prückner S, Pusl K, Raimúndez E, Rothe C, Schäfer N, Schandelmaier P, Schneider L, Schultz S, Schunk M, Schwettmann L, Seibold H, Sothmann P, Stapor P, Theis F, Thiel V, Thiesbrummel S, Thur N, Waibel J, Wallrauch C, Winter S, Wolff J, Wullinger P, Yaqine H, Zange S, Zeggini E, Zimmermann T, Zielke A, Ibraheem M, Ahmed M, Becker M, Diepers P, Schälte Y, Garí M, Pütz P, Pritsch M, Fingerle V, Le Gleut R, Gilberg L, Brand I, Diefenbach M, Eser T, Weinauer F, Martin S, Quenzel EM, Durner J, Girl P, Müller K, Radon K, Fuchs C, Hasenauer J. The interplay of viral loads, clinical presentation, and serological responses in SARS-CoV-2 – Results from a prospective cohort of outpatient COVID-19 cases. Virology 2022; 569:37-43. [PMID: 35245784 PMCID: PMC8855229 DOI: 10.1016/j.virol.2022.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 11/24/2022]
Abstract
Risk factors for disease progression and severity of SARS-CoV-2 infections require an understanding of acute and long-term virological and immunological dynamics. Fifty-one RT-PCR positive COVID-19 outpatients were recruited between May and December 2020 in Munich, Germany, and followed up at multiple defined timepoints for up to one year. RT-PCR and viral culture were performed and seroresponses measured. Participants were classified applying the WHO clinical progression scale. Short symptom to test time (median 5.0 days; p = 0.0016) and high viral loads (VL; median maximum VL: 3∙108 copies/mL; p = 0.0015) were indicative for viral culture positivity. Participants with WHO grade 3 at baseline had significantly higher VLs compared to those with WHO 1 and 2 (p = 0.01). VLs dropped fast within 1 week of symptom onset. Maximum VLs were positively correlated with the magnitude of Ro-N-Ig seroresponse (p = 0.022). Our results describe the dynamics of VLs and antibodies to SARS-CoV-2 in mild to moderate cases that can support public health measures during the ongoing global pandemic.
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14
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Way GP, Spitzer H, Burnham P, Raj A, Theis F, Singh S, Carpenter AE. Image-based profiling: a powerful and challenging new data type. Pac Symp Biocomput 2022; 27:407-411. [PMID: 34890168] [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] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Software has provided cell biologists the power to quantify specific cellular features in cell images at scale. Before long, these biologists also recognized the potential to extract much more biological information from the same images. From here, the field of image-based profiling, the process of extracting unbiased representations that capture morphological cell state, was born. We are still in the early days of image-based profiling, and it is clear that the many opportunities to interrogate biological systems come with significant challenges. These challenges include building expressive and biologically-relevant representations, adjusting for technical noise, writing generalizable software infrastructure, continuing to foster a culture of open science, and promoting FAIR (findable, accessible, interoperable, and reusable) data. We present a workshop at the Pacific Symposium on Biocomputing 2022 to introduce the field of image-based profiling to the broader computational biology community. In the following document, we introduce image-based profiling, discuss current state-of-the-art methods and limitations, and provide rationale for why now is the perfect time for the field to expand. We also introduce our invited speakers and agenda, which together provide an introduction to the field complemented by in-depth application areas in industry and academia. We also include five lightning talks to complement the invited speakers on various methodological and discovery advances.
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Affiliation(s)
- Gregory P Way
- Center for Health Artificial Intelligence, University of Colorado Anschutz Medical School, 1890 N Revere Ct. Aurora CO 80045, USA,
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15
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Nguyen P, Ohnmacht AJ, Galhoz A, Büttner M, Theis F, Menden MP. Künstliche Intelligenz und maschinelles Lernen in der Diabetesforschung. Diabetologe 2021. [DOI: 10.1007/s11428-021-00817-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Warnat-Herresthal S, Schultze H, Shastry KL, Manamohan S, Mukherjee S, Garg V, Sarveswara R, Händler K, Pickkers P, Aziz NA, Ktena S, Tran F, Bitzer M, Ossowski S, Casadei N, Herr C, Petersheim D, Behrends U, Kern F, Fehlmann T, Schommers P, Lehmann C, Augustin M, Rybniker J, Altmüller J, Mishra N, Bernardes JP, Krämer B, Bonaguro L, Schulte-Schrepping J, De Domenico E, Siever C, Kraut M, Desai M, Monnet B, Saridaki M, Siegel CM, Drews A, Nuesch-Germano M, Theis H, Heyckendorf J, Schreiber S, Kim-Hellmuth S, Nattermann J, Skowasch D, Kurth I, Keller A, Bals R, Nürnberg P, Rieß O, Rosenstiel P, Netea MG, Theis F, Mukherjee S, Backes M, Aschenbrenner AC, Ulas T, Breteler MMB, Giamarellos-Bourboulis EJ, Kox M, Becker M, Cheran S, Woodacre MS, Goh EL, Schultze JL. Swarm Learning for decentralized and confidential clinical machine learning. Nature 2021; 594:265-270. [PMID: 34040261 PMCID: PMC8189907 DOI: 10.1038/s41586-021-03583-3] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [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: 07/03/2020] [Accepted: 04/26/2021] [Indexed: 01/08/2023]
Abstract
Fast and reliable detection of patients with severe and heterogeneous illnesses is a major goal of precision medicine1,2. Patients with leukaemia can be identified using machine learning on the basis of their blood transcriptomes3. However, there is an increasing divide between what is technically possible and what is allowed, because of privacy legislation4,5. Here, to facilitate the integration of any medical data from any data owner worldwide without violating privacy laws, we introduce Swarm Learning—a decentralized machine-learning approach that unites edge computing, blockchain-based peer-to-peer networking and coordination while maintaining confidentiality without the need for a central coordinator, thereby going beyond federated learning. To illustrate the feasibility of using Swarm Learning to develop disease classifiers using distributed data, we chose four use cases of heterogeneous diseases (COVID-19, tuberculosis, leukaemia and lung pathologies). With more than 16,400 blood transcriptomes derived from 127 clinical studies with non-uniform distributions of cases and controls and substantial study biases, as well as more than 95,000 chest X-ray images, we show that Swarm Learning classifiers outperform those developed at individual sites. In addition, Swarm Learning completely fulfils local confidentiality regulations by design. We believe that this approach will notably accelerate the introduction of precision medicine. Swarm Learning is a decentralized machine learning approach that outperforms classifiers developed at individual sites for COVID-19 and other diseases while preserving confidentiality and privacy.
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Affiliation(s)
- Stefanie Warnat-Herresthal
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | | | | | | | | | - Vishesh Garg
- Hewlett Packard Enterprise, Houston, TX, USA.,Mesh Dynamics, Bangalore, India
| | | | - Kristian Händler
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany
| | - Peter Pickkers
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - N Ahmad Aziz
- Population Health Sciences, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Department of Neurology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Sofia Ktena
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Florian Tran
- Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany.,Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Michael Bitzer
- Department of Internal Medicine I, University Hospital, University of Tübingen, Tübingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,NGS Competence Center Tübingen, Tübingen, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,NGS Competence Center Tübingen, Tübingen, Germany
| | - Christian Herr
- Department of Internal Medicine V, Saarland University Hospital, Homburg, Germany
| | - Daniel Petersheim
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital LMU Munich, Munich, Germany
| | - Uta Behrends
- Children's Hospital, Medical Faculty, Technical University Munich, Munich, Germany
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Philipp Schommers
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Clara Lehmann
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Max Augustin
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Jan Rybniker
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, West German Genome Center, University of Cologne, Cologne, Germany
| | - Neha Mishra
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Joana P Bernardes
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Benjamin Krämer
- Clinical Infectious Diseases, Research Center Borstel and German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jonas Schulte-Schrepping
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Elena De Domenico
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany
| | | | - Michael Kraut
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany
| | | | | | - Maria Saridaki
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | | | - Anna Drews
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany
| | - Melanie Nuesch-Germano
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Heidi Theis
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany
| | - Jan Heyckendorf
- Clinical Infectious Diseases, Research Center Borstel and German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Sarah Kim-Hellmuth
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital LMU Munich, Munich, Germany
| | | | - Jacob Nattermann
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Dirk Skowasch
- Department of Internal Medicine II - Cardiology/Pneumology, University of Bonn, Bonn, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert Bals
- Department of Internal Medicine V, Saarland University Hospital, Homburg, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, West German Genome Center, University of Cologne, Cologne, Germany
| | - Olaf Rieß
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,NGS Competence Center Tübingen, Tübingen, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands.,Immunology & Metabolism, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Center Munich (HMGU), Neuherberg, Germany
| | - Sach Mukherjee
- Statistics and Machine Learning, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Michael Backes
- CISPA Helmholtz Center for Information Security, Saarbrücken, Germany
| | - Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | | | - Monique M B Breteler
- Population Health Sciences, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | | | - Matthijs Kox
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Matthias Becker
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany
| | | | | | - Eng Lim Goh
- Hewlett Packard Enterprise, Houston, TX, USA
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany. .,Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany. .,PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany.
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17
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Türei D, Valdeolivas A, Gul L, Palacio‐Escat N, Klein M, Ivanova O, Ölbei M, Gábor A, Theis F, Módos D, Korcsmáros T, Saez‐Rodriguez J. Integrated intra- and intercellular signaling knowledge for multicellular omics analysis. Mol Syst Biol 2021; 17:e9923. [PMID: 33749993 PMCID: PMC7983032 DOI: 10.15252/msb.20209923] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [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: 08/14/2020] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular knowledge of biological processes is a cornerstone in omics data analysis. Applied to single-cell data, such analyses provide mechanistic insights into individual cells and their interactions. However, knowledge of intercellular communication is scarce, scattered across resources, and not linked to intracellular processes. To address this gap, we combined over 100 resources covering interactions and roles of proteins in inter- and intracellular signaling, as well as transcriptional and post-transcriptional regulation. We added protein complex information and annotations on function, localization, and role in diseases for each protein. The resource is available for human, and via homology translation for mouse and rat. The data are accessible via OmniPath's web service (https://omnipathdb.org/), a Cytoscape plug-in, and packages in R/Bioconductor and Python, providing access options for computational and experimental scientists. We created workflows with tutorials to facilitate the analysis of cell-cell interactions and affected downstream intracellular signaling processes. OmniPath provides a single access point to knowledge spanning intra- and intercellular processes for data analysis, as we demonstrate in applications studying SARS-CoV-2 infection and ulcerative colitis.
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Affiliation(s)
- Dénes Türei
- Faculty of Medicine and Heidelberg University HospitalInstitute of Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | - Alberto Valdeolivas
- Faculty of Medicine and Heidelberg University HospitalInstitute of Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | | | - Nicolàs Palacio‐Escat
- Faculty of Medicine and Heidelberg University HospitalInstitute of Computational BiomedicineHeidelberg UniversityHeidelbergGermany
- Faculty of MedicineJoint Research Centre for Computational Biomedicine (JRC‐COMBINE)RWTH Aachen UniversityAachenGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
| | - Michal Klein
- Institute of Computational BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Olga Ivanova
- Faculty of Medicine and Heidelberg University HospitalInstitute of Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | - Márton Ölbei
- Earlham InstituteNorwichUK
- Quadram Institute BioscienceNorwichUK
| | - Attila Gábor
- Faculty of Medicine and Heidelberg University HospitalInstitute of Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | - Fabian Theis
- Institute of Computational BiologyHelmholtz Zentrum MünchenNeuherbergGermany
- Department of MathematicsTechnical University of MunichGarchingGermany
| | - Dezső Módos
- Earlham InstituteNorwichUK
- Quadram Institute BioscienceNorwichUK
| | | | - Julio Saez‐Rodriguez
- Faculty of Medicine and Heidelberg University HospitalInstitute of Computational BiomedicineHeidelberg UniversityHeidelbergGermany
- Faculty of MedicineJoint Research Centre for Computational Biomedicine (JRC‐COMBINE)RWTH Aachen UniversityAachenGermany
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18
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Kunze S, Cecil A, Prehn C, Möller G, Ohlmann A, Wildner G, Thurau S, Unger K, Rößler U, Hölter SM, Tapio S, Wagner F, Beyerlein A, Theis F, Zitzelsberger H, Kulka U, Adamski J, Graw J, Dalke C. Posterior subcapsular cataracts are a late effect after acute exposure to 0.5 Gy ionizing radiation in mice. Int J Radiat Biol 2021; 97:529-540. [PMID: 33464160 DOI: 10.1080/09553002.2021.1876951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 10/22/2022]
Abstract
PURPOSE The long-term effect of low and moderate doses of ionizing radiation on the lens is still a matter of debate and needs to be evaluated in more detail. MATERIAL AND METHODS We conducted a detailed histological analysis of eyes from B6C3F1 mice cohorts after acute gamma irradiation (60Co source; 0.063 Gy/min) at young adult age of 10 weeks with doses of 0.063, 0.125, and 0.5 Gy. Sham irradiated (0 Gy) mice were used as controls. To test for genetic susceptibility heterozygous Ercc2 mutant mice were used and compared to wild-type mice of the same strain background. Mice of both sexes were included in all cohorts. Eyes were collected 4 h, 12, 18 and 24 months after irradiation. For a better understanding of the underlying mechanisms, metabolomics analyses were performed in lenses and plasma samples of the same mouse cohorts at 4 and 12 h as well as 12, 18 and 24 months after irradiation. For this purpose, a targeted analysis was chosen. RESULTS This analysis revealed histological changes particularly in the posterior part of the lens that rarely can be observed by using Scheimpflug imaging, as we reported previously. We detected a significant increase of posterior subcapsular cataracts (PSCs) 18 and 24 months after irradiation with 0.5 Gy (odds ratio 9.3; 95% confidence interval 2.1-41.3) independent of sex and genotype. Doses below 0.5 Gy (i.e. 0.063 and 0.125 Gy) did not significantly increase the frequency of PSCs at any time point. In lenses, we observed a clear effect of sex and aging but not of irradiation or genotype. While metabolomics analyses of plasma from the same mice showed only a sex effect. CONCLUSIONS This article demonstrates a significant radiation-induced increase in the incidence of PSCs, which could not be identified using Scheimpflug imaging as the only diagnostic tool.
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Affiliation(s)
- Sarah Kunze
- Institute of Developmental Genetics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Neuherberg, Germany
| | - Alexander Cecil
- Research Unit Molecular Endocrinology and Metabolism, Genome Analysis Center, Helmholtz Center Munich German Research Center for Environmental Health, Neuherberg, Germany
| | - Cornelia Prehn
- Research Unit Molecular Endocrinology and Metabolism, Genome Analysis Center, Helmholtz Center Munich German Research Center for Environmental Health, Neuherberg, Germany
| | - Gabriele Möller
- Research Unit Molecular Endocrinology and Metabolism, Genome Analysis Center, Helmholtz Center Munich German Research Center for Environmental Health, Neuherberg, Germany
| | - Andreas Ohlmann
- Department of Ophthalmology, University Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Gerhild Wildner
- Department of Ophthalmology, University Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Stephan Thurau
- Department of Ophthalmology, University Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich German Research Center for Environmental Health, Neuherberg, Germany
| | - Ute Rößler
- Department Radiation Protection and Health, Federal Office of Radiation Protection, Oberschleissheim, Germany
| | - Sabine M Hölter
- Institute of Developmental Genetics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Neuherberg, Germany
| | - Soile Tapio
- Institute of Radiation Biology, Helmholtz Center Munich German Research Center for Environmental Health, Neuherberg, Germany.,School of Medicine, Technical University of Munich, Munich, Germany
| | - Florian Wagner
- Institute of Radiation Medicine, Helmholtz Center Munich German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Fabian Theis
- Institute of Computational Biology, Neuherberg, Germany
| | - Horst Zitzelsberger
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich German Research Center for Environmental Health, Neuherberg, Germany
| | - Ulrike Kulka
- Department Radiation Protection and Health, Federal Office of Radiation Protection, Oberschleissheim, Germany
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Genome Analysis Center, Helmholtz Center Munich German Research Center for Environmental Health, Neuherberg, Germany.,Lehrstuhl für Experimentelle Genetik, Technical University of Munich, Freising-Weihenstephan, Germany.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jochen Graw
- Institute of Developmental Genetics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Neuherberg, Germany
| | - Claudia Dalke
- Institute of Developmental Genetics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Neuherberg, Germany
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19
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Krautenbacher N, Kabesch M, Horak E, Braun-Fahrländer C, Genuneit J, Boznanski A, von Mutius E, Theis F, Fuchs C, Ege MJ. Asthma in farm children is more determined by genetic polymorphisms and in non-farm children by environmental factors. Pediatr Allergy Immunol 2021; 32:295-304. [PMID: 32997854 DOI: 10.1111/pai.13385] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 05/27/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND The asthma syndrome is influenced by hereditary and environmental factors. With the example of farm exposure, we study whether genetic and environmental factors interact for asthma. METHODS Statistical learning approaches based on penalized regression and decision trees were used to predict asthma in the GABRIELA study with 850 cases (9% farm children) and 857 controls (14% farm children). Single-nucleotide polymorphisms (SNPs) were selected from a genome-wide dataset based on a literature search or by statistical selection techniques. Prediction was assessed by receiver operating characteristics (ROC) curves and validated in the PASTURE cohort. RESULTS Prediction by family history of asthma and atopy yielded an area under the ROC curve (AUC) of 0.62 [0.57-0.66] in the random forest machine learning approach. By adding information on demographics (sex and age) and 26 environmental exposure variables, the quality of prediction significantly improved (AUC = 0.65 [0.61-0.70]). In farm children, however, environmental variables did not improve prediction quality. Rather SNPs related to IL33 and RAD50 contributed significantly to the prediction of asthma (AUC = 0.70 [0.62-0.78]). CONCLUSIONS Asthma in farm children is more likely predicted by other factors as compared to non-farm children though in both forms, family history may integrate environmental exposure, genotype and degree of penetrance.
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Affiliation(s)
- Norbert Krautenbacher
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Garching, Germany
| | - Michael Kabesch
- University Children's Hospital Regensburg (KUNO), Regensburg, Germany.,Clinic for Pediatric Pneumology and Neonatology, Hannover Medical School, Hannover, Germany.,The German Center for Lung Research (DZL), Germany
| | - Elisabeth Horak
- Department of Pediatrics and Adolescents, Innsbruck Medical University, Innsbruck, Austria
| | - Charlotte Braun-Fahrländer
- Swiss Tropical and Public Health Institute Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Jon Genuneit
- Institute of Epidemiology and Medical Biometry, Ulm University, Ulm, Germany.,Pediatric Epidemiology, Department of Pediatrics, Medical Faculty, Leipzig University, Leipzig, Germany
| | | | - Erika von Mutius
- The German Center for Lung Research (DZL), Germany.,Dr von Hauner Children's Hospital, LMU Munich, Munich, Germany.,Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Asthma and Allergy Prevention, Neuherberg, Germany
| | - Fabian Theis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Garching, Germany
| | - Christiane Fuchs
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Garching, Germany.,Department of Business Administration and Economics, Bielefeld University, Bielefeld, Germany
| | - Markus J Ege
- The German Center for Lung Research (DZL), Germany.,Dr von Hauner Children's Hospital, LMU Munich, Munich, Germany
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20
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Thomas J, Wang R, Batra R, Böhner A, Garzorz-Stark N, Eberlein B, Theis F, Biedermann T, Schmidt-Weber C, Zink A, Eyerich K, Eyerich S. CD23 Levels on B Cells Determine Long-Term Therapeutic Response in Patients with Atopic Eczema Treated with Selective IgE Immune Apheresis. J Invest Dermatol 2020; 141:681-685.e6. [PMID: 32949565 DOI: 10.1016/j.jid.2020.05.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/11/2020] [Accepted: 05/27/2020] [Indexed: 11/19/2022]
Affiliation(s)
- Jenny Thomas
- ZAUM-Center of Allergy and Environment, Technical University and Helmholtz Center Munich, Munich, Germany
| | - Rosi Wang
- Department of Dermatology and Allergy, Technical University of Munich, Munich, Germany.
| | - Richa Batra
- Institute of Computational Biology, Helmholtz Center Munich, Neuherberg, Germany
| | - Alexander Böhner
- Department of Dermatology and Allergy, Technical University of Munich, Munich, Germany
| | - Natalie Garzorz-Stark
- Department of Dermatology and Allergy, Technical University of Munich, Munich, Germany
| | - Bernadette Eberlein
- Department of Dermatology and Allergy, Technical University of Munich, Munich, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Center Munich, Neuherberg, Germany; Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Tilo Biedermann
- Department of Dermatology and Allergy, Technical University of Munich, Munich, Germany
| | - Carsten Schmidt-Weber
- ZAUM-Center of Allergy and Environment, Technical University and Helmholtz Center Munich, Munich, Germany
| | - Alexander Zink
- Department of Dermatology and Allergy, Technical University of Munich, Munich, Germany
| | - Kilian Eyerich
- Department of Dermatology and Allergy, Technical University of Munich, Munich, Germany; Unit of Dermatology and Venerology, Department of Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Stefanie Eyerich
- ZAUM-Center of Allergy and Environment, Technical University and Helmholtz Center Munich, Munich, Germany
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21
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Radon K, Saathoff E, Pritsch M, Guggenbühl Noller JM, Kroidl I, Olbrich L, Thiel V, Diefenbach M, Riess F, Forster F, Theis F, Wieser A, Hoelscher M. Publisher Correction to: Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19). BMC Public Health 2020; 20:1335. [PMID: 32873261 PMCID: PMC7461750 DOI: 10.1186/s12889-020-09394-x] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Katja Radon
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität (LMU) University Hospital Munich, Ziemssenstr. 1, 80336, Munich, Germany. .,Center for International Health, LMU University Hospital, Munich, Germany.
| | - Elmar Saathoff
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Michael Pritsch
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802, Munich, Germany
| | - Jessica Michelle Guggenbühl Noller
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802, Munich, Germany
| | - Inge Kroidl
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Laura Olbrich
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802, Munich, Germany
| | - Verena Thiel
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802, Munich, Germany
| | - Max Diefenbach
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802, Munich, Germany
| | - Friedrich Riess
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802, Munich, Germany
| | - Felix Forster
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität (LMU) University Hospital Munich, Ziemssenstr. 1, 80336, Munich, Germany
| | - Fabian Theis
- Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.,Departments of Mathematics and Life Sciences, Technical University of Munich, Munich, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802, Munich, Germany.,Max von Pettenkofer Institute, Faculty of Medicine, LMU of Munich, Munich, Germany
| | - Michael Hoelscher
- Center for International Health, LMU University Hospital, Munich, Germany.,Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
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22
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Radon K, Saathoff E, Pritsch M, Guggenbühl Noller JM, Kroidl I, Olbrich L, Thiel V, Diefenbach M, Riess F, Forster F, Theis F, Wieser A, Hoelscher M. Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19). BMC Public Health 2020; 20:1036. [PMID: 32605549 PMCID: PMC7324773 DOI: 10.1186/s12889-020-09164-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 06/23/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Due to the SARS-CoV-2 pandemic, public health interventions have been introduced globally in order to prevent the spread of the virus and avoid the overload of health care systems, especially for the most severely affected patients. Scientific studies to date have focused primarily on describing the clinical course of patients, identifying treatment options and developing vaccines. In Germany, as in many other regions, current tests for SARS-CoV2 are not conducted on a representative basis and in a longitudinal design. Furthermore, knowledge about the immune status of the population is lacking. Nonetheless, these data are needed to understand the dynamics of the pandemic and hence to appropriately design and evaluate interventions. For this purpose, we recently started a prospective population-based cohort in Munich, Germany, with the aim to develop a better understanding of the state and dynamics of the pandemic. METHODS In 100 out of 755 randomly selected constituencies, 3000 Munich households are identified via random route and offered enrollment into the study. All household members are asked to complete a baseline questionnaire and subjects ≥14 years of age are asked to provide a venous blood sample of ≤3 ml for the determination of SARS-CoV-2 IgG/IgA status. The residual plasma and the blood pellet are preserved for later genetic and molecular biological investigations. For twelve months, each household member is asked to keep a diary of daily symptoms, whereabouts and contacts via WebApp. If symptoms suggestive for COVID-19 are reported, family members, including children < 14 years, are offered a pharyngeal swab taken at the Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, for molecular testing for SARS-CoV-2. In case of severe symptoms, participants will be transferred to a Munich hospital. For one year, the study teams re-visits the households for blood sampling every six weeks. DISCUSSION With the planned study we will establish a reliable epidemiological tool to improve the understanding of the spread of SARS-CoV-2 and to better assess the effectiveness of public health measures as well as their socio-economic effects. This will support policy makers in managing the epidemic based on scientific evidence.
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Affiliation(s)
- Katja Radon
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität (LMU) University Hospital Munich, Ziemssenstr. 1, 80336 Munich, Germany
- Center for International Health, LMU University Hospital, Munich, Germany
| | - Elmar Saathoff
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802 Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Michael Pritsch
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802 Munich, Germany
| | | | - Inge Kroidl
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802 Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Laura Olbrich
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802 Munich, Germany
| | - Verena Thiel
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802 Munich, Germany
| | - Max Diefenbach
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802 Munich, Germany
| | - Friedrich Riess
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802 Munich, Germany
| | - Felix Forster
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität (LMU) University Hospital Munich, Ziemssenstr. 1, 80336 Munich, Germany
| | - Fabian Theis
- Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Departments of Mathematics and Life Sciences, Technical University of Munich, Munich, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802 Munich, Germany
- Max von Pettenkofer Institute, Faculty of Medicine, LMU of Munich, Munich, Germany
| | - Michael Hoelscher
- Center for International Health, LMU University Hospital, Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany, Leopoldstrasse 5, 80802 Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
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23
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Förster K, Ertl-Wagner B, Ehrhardt H, Busen H, Sass S, Pomschar A, Naehrlich L, Schulze A, Flemmer AW, Hübener C, Eickelberg O, Theis F, Dietrich O, Hilgendorff A. Altered relaxation times in MRI indicate bronchopulmonary dysplasia. Thorax 2019; 75:184-187. [PMID: 31048507 DOI: 10.1136/thoraxjnl-2018-212384] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 07/20/2018] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 11/04/2022]
Abstract
We developed a MRI protocol using transverse (T2) and longitudinal (T1) mapping sequences to characterise lung structural changes in preterm infants with bronchopulmonary dysplasia (BPD). We prospectively enrolled 61 infants to perform 3-Tesla MRI of the lung in quiet sleep. Statistical analysis was performed using logistic Group Lasso regression and logistic regression. Increased lung T2 relaxation time and decreased lung T1 relaxation time indicated BPD yielding an area under the curve (AUC) of 0.80. Results were confirmed in an independent study cohort (AUC 0.75) and mirrored by lung function testing, indicating the high potential for MRI in future BPD diagnostics. TRIAL REGISTRATION: DRKS00004600.
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Affiliation(s)
- Kai Förster
- Department of Neonatology, Perinatal Center Grosshadern, Dr von Hauner Children's Hospital, Ludwig Maximilian University of Munich, Munich, Germany.,Comprehensive Pneumology Center, German Lung Research Center (DZL), Helmholtz Zentrum München, Munich, Germany
| | - Birgit Ertl-Wagner
- Department of Radiology, German Lung Research Center (DZL), University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Harald Ehrhardt
- Department of General Pediatrics and Neonatology, German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Hannah Busen
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Steffen Sass
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Andreas Pomschar
- Department of Radiology, German Lung Research Center (DZL), University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Lutz Naehrlich
- Department of General Pediatrics and Neonatology, German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Andreas Schulze
- Department of Neonatology, Perinatal Center Grosshadern, Dr von Hauner Children's Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Andreas W Flemmer
- Department of Neonatology, Perinatal Center Grosshadern, Dr von Hauner Children's Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Christoph Hübener
- Department of Obstetrics and Gynecology, Perinatal Center Grosshadern, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Oliver Eickelberg
- Comprehensive Pneumology Center, German Lung Research Center (DZL), Helmholtz Zentrum München, Munich, Germany.,Division of Respiratory Sciences and Critical Care Medicine, University of Colorado at Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany.,Department of Mathematics, Technical University of Munich, Munich, Germany
| | - Olaf Dietrich
- Department of Radiology, German Lung Research Center (DZL), University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Anne Hilgendorff
- Department of Neonatology, Perinatal Center Grosshadern, Dr von Hauner Children's Hospital, Ludwig Maximilian University of Munich, Munich, Germany .,Comprehensive Pneumology Center, German Lung Research Center (DZL), Helmholtz Zentrum München, Munich, Germany
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24
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Kaderali L, Theis F, Ganusov VV, Ciupe SM, Mehr R, Ribeiro RM, Hernandez-Vargas EA. Editorial: Integrative Computational Systems Biology Approaches in Immunology and Medicine. Front Microbiol 2019; 9:3338. [PMID: 30728819 PMCID: PMC6351460 DOI: 10.3389/fmicb.2018.03338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/24/2018] [Indexed: 11/29/2022] Open
Affiliation(s)
- Lars Kaderali
- Institute of Bioinformatics, Universitätsmedizin Greifswald, Greifswald, Germany
| | | | - Vitaly V. Ganusov
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Stanca M. Ciupe
- Department of Mathematics, Virginia Tech, Blacksburg, VA, United States
| | - Ramit Mehr
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Ruy M. Ribeiro
- Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Esteban A. Hernandez-Vargas
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
- *Correspondence: Esteban A. Hernandez-Vargas
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Tischler J, Gruhn WH, Reid J, Allgeyer E, Buettner F, Marr C, Theis F, Simons BD, Wernisch L, Surani MA. Metabolic regulation of pluripotency and germ cell fate through α-ketoglutarate. EMBO J 2019; 38:embj.201899518. [PMID: 30257965 PMCID: PMC6315289 DOI: 10.15252/embj.201899518] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [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: 03/27/2018] [Revised: 08/24/2018] [Accepted: 08/27/2018] [Indexed: 12/16/2022] Open
Abstract
An intricate link is becoming apparent between metabolism and cellular identities. Here, we explore the basis for such a link in an in vitro model for early mouse embryonic development: from naïve pluripotency to the specification of primordial germ cells (PGCs). Using single-cell RNA-seq with statistical modelling and modulation of energy metabolism, we demonstrate a functional role for oxidative mitochondrial metabolism in naïve pluripotency. We link mitochondrial tricarboxylic acid cycle activity to IDH2-mediated production of alpha-ketoglutarate and through it, the activity of key epigenetic regulators. Accordingly, this metabolite has a role in the maintenance of naïve pluripotency as well as in PGC differentiation, likely through preserving a particular histone methylation status underlying the transient state of developmental competence for the PGC fate. We reveal a link between energy metabolism and epigenetic control of cell state transitions during a developmental trajectory towards germ cell specification, and establish a paradigm for stabilizing fleeting cellular states through metabolic modulation.
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Affiliation(s)
- Julia Tischler
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Wolfram H Gruhn
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - John Reid
- MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,The Alan Turing Institute, British Library, London, UK
| | - Edward Allgeyer
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Florian Buettner
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Carsten Marr
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Department of Mathematics, Chair of Mathematical Modeling of Biological Systems Technische Universität München, Garching, Germany
| | - Ben D Simons
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Lorenz Wernisch
- MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - M Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
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26
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Bastidas-Ponce A, Tritschler S, Dony L, Scheibner K, Tarquis-Medina M, Salinno C, Schirge S, Burtscher I, Böttcher A, Theis F, Lickert H, Bakhti M. Massive single-cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis. Development 2019; 146:dev.173849. [DOI: 10.1242/dev.173849] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 05/21/2019] [Indexed: 12/21/2022]
Abstract
Deciphering mechanisms of endocrine cell induction, specification and lineage allocation in vivo will provide valuable insights into how the islets of Langerhans are generated. Currently, it is ill defined how endocrine progenitors segregate into different endocrine subtypes during development. Here, we generated a novel Neurogenin3 (Ngn3)-Venus fusion (NVF) reporter mouse line, that closely mirrors the transient endogenous Ngn3 protein expression. To define an in vivo roadmap of endocrinogenesis, we performed single-cell RNA-sequencing of 36,351 pancreatic epithelial and NVF+ cells during secondary transition. This allowed to time-resolve and distinguish Ngn3low endocrine progenitors, Ngn3high endocrine precursors, Fev+ endocrine lineage and hormone+ endocrine subtypes and delineate molecular programs during the stepwise lineage restriction steps. Strikingly, we identified 58 novel signature genes that show the same transient expression dynamics as Ngn3 in the 7,260 profiled Ngn3-expressing cells. The differential expression of these genes in endocrine precursors associated with their cell-fate allocation towards distinct endocrine cell types. Thus, the generation of an accurately regulated NVF reporter allowed us to temporally resolve endocrine lineage development to provide a fine-grained single-cell molecular profile of endocrinogenesis in vivo.
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Affiliation(s)
- Aimée Bastidas-Ponce
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Technical University of Munich, School of Medicine, Munich, Germany
| | - Sophie Tritschler
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Technical University of Munich, School of Life Sciences Weihenstephan, Freising, Germany
| | - Leander Dony
- Institute of Computational Biology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804 Munich, Germany
| | - Katharina Scheibner
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Technical University of Munich, School of Medicine, Munich, Germany
| | - Marta Tarquis-Medina
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Technical University of Munich, School of Medicine, Munich, Germany
| | - Ciro Salinno
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Technical University of Munich, School of Medicine, Munich, Germany
| | - Silvia Schirge
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Anika Böttcher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Technical University of Munich, Department of Mathematics, Munich, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Technical University of Munich, School of Medicine, Munich, Germany
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
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Dalke C, Neff F, Bains SK, Bright S, Lord D, Reitmeir P, Rößler U, Samaga D, Unger K, Braselmann H, Wagner F, Greiter M, Gomolka M, Hornhardt S, Kunze S, Kempf SJ, Garrett L, Hölter SM, Wurst W, Rosemann M, Azimzadeh O, Tapio S, Aubele M, Theis F, Hoeschen C, Slijepcevic P, Kadhim M, Atkinson M, Zitzelsberger H, Kulka U, Graw J. Lifetime study in mice after acute low-dose ionizing radiation: a multifactorial study with special focus on cataract risk. Radiat Environ Biophys 2018; 57:99-113. [PMID: 29327260 PMCID: PMC5902533 DOI: 10.1007/s00411-017-0728-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/21/2017] [Indexed: 05/28/2023]
Abstract
Because of the increasing application of ionizing radiation in medicine, quantitative data on effects of low-dose radiation are needed to optimize radiation protection, particularly with respect to cataract development. Using mice as mammalian animal model, we applied a single dose of 0, 0.063, 0.125 and 0.5 Gy at 10 weeks of age, determined lens opacities for up to 2 years and compared it with overall survival, cytogenetic alterations and cancer development. The highest dose was significantly associated with increased body weight and reduced survival rate. Chromosomal aberrations in bone marrow cells showed a dose-dependent increase 12 months after irradiation. Pathological screening indicated a dose-dependent risk for several types of tumors. Scheimpflug imaging of the lens revealed a significant dose-dependent effect of 1% of lens opacity. Comparison of different biological end points demonstrated long-term effects of low-dose irradiation for several biological end points.
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Affiliation(s)
- Claudia Dalke
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, 85764 Neuherberg, Germany
| | - Frauke Neff
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Pathology, Neuherberg, Germany
- Present Address: Municipal Clinical Center Munich, Munich, Germany
| | - Savneet Kaur Bains
- Department of Life Sciences, Brunel University London, Uxbridge, UK
- Present Address: Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Scott Bright
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Present Address: University of Texas, MD Anderson, Houston, TX USA
| | - Deborah Lord
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Peter Reitmeir
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Health Economics and Health Care Management, Neuherberg, Germany
| | - Ute Rößler
- Department Radiation Protection and Health, Federal Office for Radiation Protection, Oberschleissheim, Germany
| | - Daniel Samaga
- Department Radiation Protection and Health, Federal Office for Radiation Protection, Oberschleissheim, Germany
- Present Address: Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit of Radiation Cytogenetics, Neuherberg, Germany
| | - Kristian Unger
- Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit of Radiation Cytogenetics, Neuherberg, Germany
| | - Herbert Braselmann
- Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit of Radiation Cytogenetics, Neuherberg, Germany
| | - Florian Wagner
- Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit Medical Radiation Physics and Diagnostics, Neuherberg, Germany
- Present Address: Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Radiation Protection, Neuherberg, Germany
| | - Matthias Greiter
- Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit Medical Radiation Physics and Diagnostics, Neuherberg, Germany
- Present Address: Helmholtz Center Munich, German Research Center for Environmental Health, Individual Monitoring Service, Neuherberg, Germany
| | - Maria Gomolka
- Department Radiation Protection and Health, Federal Office for Radiation Protection, Oberschleissheim, Germany
| | - Sabine Hornhardt
- Department Radiation Protection and Health, Federal Office for Radiation Protection, Oberschleissheim, Germany
| | - Sarah Kunze
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, 85764 Neuherberg, Germany
| | - Stefan J. Kempf
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Radiation Biology, Neuherberg, Germany
- Present Address: Department of Bioanalytical Sciences, CSL Behring GmbH, Marburg, Germany
| | - Lillian Garrett
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, 85764 Neuherberg, Germany
| | - Sabine M. Hölter
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, 85764 Neuherberg, Germany
| | - Wolfgang Wurst
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, 85764 Neuherberg, Germany
| | - Michael Rosemann
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Radiation Biology, Neuherberg, Germany
| | - Omid Azimzadeh
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Radiation Biology, Neuherberg, Germany
| | - Soile Tapio
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Radiation Biology, Neuherberg, Germany
| | - Michaela Aubele
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Pathology, Neuherberg, Germany
| | - Fabian Theis
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - Christoph Hoeschen
- Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit Medical Radiation Physics and Diagnostics, Neuherberg, Germany
- Present Address: Chair of Medical Systems Technology, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | | | - Munira Kadhim
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Michael Atkinson
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Radiation Biology, Neuherberg, Germany
| | - Horst Zitzelsberger
- Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit of Radiation Cytogenetics, Neuherberg, Germany
| | - Ulrike Kulka
- Department Radiation Protection and Health, Federal Office for Radiation Protection, Oberschleissheim, Germany
| | - Jochen Graw
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Developmental Genetics, 85764 Neuherberg, Germany
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28
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Garzorz-Stark N, Lauffer F, Krause L, Groß O, Traidl-Hoffmann C, Theis F, Schmidt-Weber C, Biedermann T, Eyerich S, Eyerich K. 489 TLR7/8 agonists stimulate plasmacytoid dendritic cells to initiate a Th17-deviated acute contact dermatitis in humans. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.07.685] [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: 11/29/2022]
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29
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Schneider MA, Christopoulos P, Muley T, Warth A, Klingmueller U, Thomas M, Herth FJF, Dienemann H, Mueller NS, Theis F, Meister M. AURKA, DLGAP5, TPX2, KIF11 and CKAP5: Five specific mitosis-associated genes correlate with poor prognosis for non-small cell lung cancer patients. Int J Oncol 2017; 50:365-372. [PMID: 28101582 PMCID: PMC5238780 DOI: 10.3892/ijo.2017.3834] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [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: 10/26/2016] [Accepted: 12/05/2016] [Indexed: 11/08/2022] Open
Abstract
The growth of a tumor depends to a certain extent on an increase in mitotic events. Key steps during mitosis are the regulated assembly of the spindle apparatus and the separation of the sister chromatids. The microtubule-associated protein Aurora kinase A phosphorylates DLGAP5 in order to correctly segregate the chromatids. Its activity and recruitment to the spindle apparatus is regulated by TPX2. KIF11 and CKAP5 control the correct arrangement of the microtubules and prevent their degradation. In the present study, we investigated the role of these five molecules in non-small cell lung cancer (NSCLC). We analyzed the expression of the five genes in a large cohort of NSCLC patients (n=362) by quantitative real-time PCR. Each of the genes was highly overexpressed in the tumor tissues compared to corresponding normal lung tissue. The correlation of the expression of the individual genes depended on the histology. An increased expression of AURKA, DLGAP5, TPX2, KIF11 and CKAP5 was associated with poor overall survival (P=0.001–0.065). AURKA was a significant prognostic marker using multivariate analyses (P=0.006). Immunofluorescence studies demonstrated that the five mitosis-associated proteins co-localized with the spindle apparatus during cell division. Taken together, our data demonstrate that the expression of the mitosis-associated genes AURKA, DLGAP5, TPX2, KIF11 and CKAP5 is associated with the prognosis of NSCLC patients.
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Affiliation(s)
- Marc A Schneider
- Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Petros Christopoulos
- Department of Thoracic Oncology, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Muley
- Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Arne Warth
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Ursula Klingmueller
- Systems Biology of Signal Transduction, German Cancer Research Center, Heidelberg, Germany
| | - Michael Thomas
- Department of Thoracic Oncology, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Felix J F Herth
- Department of Pneumology and Critical Care Medicine, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Hendrik Dienemann
- Department of Surgery, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Nikola S Mueller
- Cellular Dynamics and Cell Patterning, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Fabian Theis
- Cellular Dynamics and Cell Patterning, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Michael Meister
- Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
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30
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Luber B, Keller S, Zwingenberger G, Ebert K, Maier D, Geier B, Theis F, Hasenauer J, Hug S, Meyer-Hermann M, Dehghany J, Walch A, Aichler M, Lordick F, Haffner I. Identification of predictive response and resistance factors to targeted therapy in gastric cancer using a systems medicine approach. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)33002-7] [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: 11/17/2022]
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31
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Much D, Beyerlein A, Kindt A, Krumsiek J, Stückler F, Rossbauer M, Hofelich A, Wiesenäcker D, Hivner S, Herbst M, Römisch-Margl W, Prehn C, Adamski J, Kastenmüller G, Theis F, Ziegler AG, Hummel S. Lactation is associated with altered metabolomic signatures in women with gestational diabetes. Diabetologia 2016; 59:2193-202. [PMID: 27423999 DOI: 10.1007/s00125-016-4055-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/20/2016] [Indexed: 01/11/2023]
Abstract
AIMS/HYPOTHESIS Lactation for >3 months in women with gestational diabetes is associated with a reduced risk of type 2 diabetes that persists for up to 15 years postpartum. However, the underlying mechanisms are unknown. We examined whether in women with gestational diabetes lactation for >3 months is associated with altered metabolomic signatures postpartum. METHODS We enrolled 197 women with gestational diabetes at a median of 3.6 years (interquartile range 0.7-6.5 years) after delivery. Targeted metabolomics profiles (including 156 metabolites) were obtained during a glucose challenge test. Comparisons of metabolite concentrations and ratios between women who lactated for >3 months and women who lactated for ≤3 months or not at all were performed using linear regression with adjustment for age and BMI at the postpartum visit, time since delivery, and maternal education level, and correction for multiple testing. Gaussian graphical modelling was used to generate metabolite networks. RESULTS Lactation for >3 months was associated with a higher total lysophosphatidylcholine/total phosphatidylcholine ratio; in women with short-term follow-up, it was also associated with lower leucine concentrations and a lower total branched-chain amino acid concentration. Gaussian graphical modelling identified subgroups of closely linked metabolites within phosphatidylcholines and branched-chain amino acids that were affected by lactation for >3 months and have been linked to the pathophysiology of type 2 diabetes in previous studies. CONCLUSIONS/INTERPRETATION Lactation for >3 months in women with gestational diabetes is associated with changes in the metabolomics profile that have been linked to the early pathogenesis of type 2 diabetes.
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Affiliation(s)
- Daniela Much
- Institute of Diabetes Research, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
- Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Forschergruppe Diabetes e.V., Neuherberg, Germany
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Andreas Beyerlein
- Institute of Diabetes Research, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Alida Kindt
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jan Krumsiek
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ferdinand Stückler
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michaela Rossbauer
- Institute of Diabetes Research, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
- Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Forschergruppe Diabetes e.V., Neuherberg, Germany
| | - Anna Hofelich
- Institute of Diabetes Research, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - David Wiesenäcker
- Institute of Diabetes Research, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
- Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Pediatrics, Kinderklinik München Schwabing, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Susanne Hivner
- Institute of Diabetes Research, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
- Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Forschergruppe Diabetes e.V., Neuherberg, Germany
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Melanie Herbst
- Institute of Diabetes Research, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
- Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Forschergruppe Diabetes e.V., Neuherberg, Germany
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Werner Römisch-Margl
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Cornelia Prehn
- Genome Analysis Center, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jerzy Adamski
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
- Genome Analysis Center, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany
| | - Gabi Kastenmüller
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Fabian Theis
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
- Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Forschergruppe Diabetes e.V., Neuherberg, Germany
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Sandra Hummel
- Institute of Diabetes Research, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany.
- Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.
- Forschergruppe Diabetes e.V., Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany.
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Küpper M, Thomas J, Garzorz-Stark N, Krause L, Müller N, Biedermann T, Theis F, Schmidt-Weber C, Eyerich K, Eyerich S. 330 Characterization of multiple B cell subsets in peripheral blood of psoriasis patients identifies a correlation of regulatory B cells and disease severity. J Invest Dermatol 2016. [DOI: 10.1016/j.jid.2016.06.350] [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: 11/30/2022]
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Abstract
microRNAs and microRNA-independent RNA-binding proteins are 2 classes of post-transcriptional regulators that have been shown to cooperate in gene-expression regulation. We compared the genome-wide target sets of microRNAs and RBPs identified by recent CLIP-Seq technologies, finding that RBPs have distinct target sets and favor gene interaction network hubs. To identify microRNAs and RBPs with a similar functional context, we developed simiRa, a tool that compares enriched functional categories such as pathways and GO terms. We applied simiRa to the known functional cooperation between Pumilio family proteins and miR-221/222 in the regulation of tumor supressor gene p27 and show that the cooperation is reflected by similar enriched categories but not by target genes. SimiRa also predicts possible cooperation of microRNAs and RBPs beyond direct interaction on the target mRNA for the nuclear RBP TAF15. To further facilitate research into cooperation of microRNAs and RBPs, we made simiRa available as a web tool that displays the functional neighborhood and similarity of microRNAs and RBPs: http://vsicb-simira.helmholtz-muenchen.de.
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Affiliation(s)
- Martin Preusse
- a Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Computational Biology ; Neuherberg , Germany.,b Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Diabetes and Regeneration Research ; Neuherberg , Germany
| | - Carsten Marr
- a Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Computational Biology ; Neuherberg , Germany
| | - Sita Saunders
- c Bioinformatics; Department of Computer Science; University of Freiburg ; Freiburg , Germany
| | - Daniel Maticzka
- c Bioinformatics; Department of Computer Science; University of Freiburg ; Freiburg , Germany
| | - Heiko Lickert
- b Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Diabetes and Regeneration Research ; Neuherberg , Germany.,d Medical Faculty; Technische Universität München ; Munich , Germany
| | - Rolf Backofen
- c Bioinformatics; Department of Computer Science; University of Freiburg ; Freiburg , Germany.,e BIOSS Center for Biological Signaling Studies; Cluster of Excellence; University of Freiburg ; Freiburg , Germany
| | - Fabian Theis
- b Helmholtz Zentrum München - German Research Center for Environmental Health; Institute of Diabetes and Regeneration Research ; Neuherberg , Germany.,f Technische Universität München; Center for Mathematics; Chair of Mathematical Modeling of Biological Systems ; Garching , Germany
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Much D, Beyerlein A, Kindt A, Krumsiek J, Stückler F, Rossbauer M, Hofelich A, Wiesenäcker D, Hivner S, Herbst M, Römisch-Margl W, Prehn C, Adamski J, Kastenmüller G, Theis F, Ziegler AG, Hummel S. Lactation is associated with altered metabolomic signatures in women with gestational diabetes. DIABETOL STOFFWECHS 2016. [DOI: 10.1055/s-0036-1580927] [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: 10/21/2022]
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35
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Huypens P, Sass S, Wu M, Dyckhoff D, Tschöp M, Theis F, Marschall S, Hrabě de Angelis M, Beckers J. Epigenetic germline inheritance of diet-induced obesity and insulin resistance. Nat Genet 2016; 48:497-9. [PMID: 26974008 DOI: 10.1038/ng.3527] [Citation(s) in RCA: 217] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/12/2016] [Indexed: 12/15/2022]
Abstract
There is considerable controversy regarding epigenetic inheritance in mammalian gametes. Using in vitro fertilization to ensure exclusive inheritance via the gametes, we show that a parental high-fat diet renders offspring more susceptible to developing obesity and diabetes in a sex- and parent of origin-specific mode. The epigenetic inheritance of acquired metabolic disorders may contribute to the current obesity and diabetes pandemic.
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Affiliation(s)
- Peter Huypens
- Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Steffen Sass
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Moya Wu
- Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany
| | - Daniela Dyckhoff
- Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Matthias Tschöp
- German Center for Diabetes Research (DZD), Neuherberg, Germany.,Institute of Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany.,Division of Metabolic Diseases, Department of Medicine, Technische Universität München, Munich, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Mathematics, Technische Universität München, Garching, Germany
| | - Susan Marschall
- Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany.,Chair of Experimental Genetics, Technische Universität München, Freising, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany.,Chair of Experimental Genetics, Technische Universität München, Freising, Germany
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36
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Jung B, Padula D, Burtscher I, Landerer C, Lutter D, Theis F, Messias AC, Geerlof A, Sattler M, Kremmer E, Boldt K, Ueffing M, Lickert H. Pitchfork and Gprasp2 Target Smoothened to the Primary Cilium for Hedgehog Pathway Activation. PLoS One 2016; 11:e0149477. [PMID: 26901434 PMCID: PMC4763541 DOI: 10.1371/journal.pone.0149477] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 01/31/2016] [Indexed: 01/14/2023] Open
Abstract
The seven-transmembrane receptor Smoothened (Smo) activates all Hedgehog (Hh) signaling by translocation into the primary cilia (PC), but how this is regulated is not well understood. Here we show that Pitchfork (Pifo) and the G protein-coupled receptor associated sorting protein 2 (Gprasp2) are essential components of an Hh induced ciliary targeting complex able to regulate Smo translocation to the PC. Depletion of Pifo or Gprasp2 leads to failure of Smo translocation to the PC and lack of Hh target gene activation. Together, our results identify a novel protein complex that is regulated by Hh signaling and required for Smo ciliary trafficking and Hh pathway activation.
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Affiliation(s)
- Bomi Jung
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, München-Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, München-Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
| | - Daniela Padula
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, München-Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, München-Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, München-Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, München-Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
| | - Cedric Landerer
- Institute of Computational Biology, Helmholtz Zentrum München, München-Neuherberg, Germany
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville TN 37996, United States of America
| | - Dominik Lutter
- Institute of Computational Biology, Helmholtz Zentrum München, München-Neuherberg, Germany
- Institute of Diabetes and Adipositas, Helmholtz Zentrum München, München-Neuherberg, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Zentrum München, München-Neuherberg, Germany
| | - Ana C. Messias
- Institute of Structural Biology, Helmholtz Zentrum München, München-Neuherberg, Germany
- Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Arie Geerlof
- Institute of Structural Biology, Helmholtz Zentrum München, München-Neuherberg, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, München-Neuherberg, Germany
- Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Elisabeth Kremmer
- Institute of Molecular Immunology, Helmholtz Zentrum München, München-Neuherberg, Germany
| | - Karsten Boldt
- Department of Protein Science, Helmholtz Zentrum München, München-Neuherberg, Germany
- Centre of Ophthalmology, Institute for Ophthalmology Research, University of Tuebingen, 72076 Tuebingen, Germany
| | - Marius Ueffing
- Department of Protein Science, Helmholtz Zentrum München, München-Neuherberg, Germany
- Centre of Ophthalmology, Institute for Ophthalmology Research, University of Tuebingen, 72076 Tuebingen, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, München-Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, München-Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
- * E-mail:
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Rolle-Kampczyk UE, Krumsiek J, Otto W, Röder SW, Kohajda T, Borte M, Theis F, Lehmann I, von Bergen M. Metabolomics reveals effects of maternal smoking on endogenous metabolites from lipid metabolism in cord blood of newborns. Metabolomics 2016; 12:76. [PMID: 27065762 PMCID: PMC4783445 DOI: 10.1007/s11306-016-0983-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 12/17/2015] [Indexed: 01/13/2023]
Abstract
INTRODUCTION A general detrimental effect of smoking during pregnancy on the health of newborn children is well-documented, but the detailed mechanisms remain elusive. OBJECTIVES Beside the specific influence of environmental tobacco smoke derived toxicants on developmental regulation the impact on the metabolism of newborn children is of particular interest, first as a general marker of foetal development and second due to its potential predictive value for the later occurrence of metabolic diseases. METHODS Tobacco smoke exposure information from a questionnaire was confirmed by measuring the smoking related metabolites S-Phenyl mercapturic acid, S-Benzyl mercapturic acid and cotinine in maternal urine by LC-MS/MS. The impact of smoking on maternal endogenous serum metabolome and children's cord blood metabolome was assessed in a targeted analysis of 163 metabolites by an LC-MS/MS based assay. The anti-oxidative status of maternal serum samples was analysed by chemoluminiscence based method. RESULTS Here we present for the first time results of a metabolomic assessment of the cordblood of 40 children and their mothers. Several analytes from the group of phosphatidylcholines, namely PCaaC28:1, PCaaC32:3, PCaeC30:1, PCaeC32:2, PCaeC40:1, and sphingomyelin SM C26:0, differed significantly in mothers and children's sera depending on smoking status. In serum of smoking mothers the antioxidative capacity of water soluble compounds was not significantly changed while there was a significant decrease in the lipid fraction. CONCLUSION Our data give evidence that smoking during pregnancy alters both the maternal and children's metabolome. Whether the different pattern found in adults compared to newborn children could be related to different disease outcomes should be in the focus of future studies.
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Affiliation(s)
- Ulrike E. Rolle-Kampczyk
- Department of Metabolomics, Helmholtz Centre for Environmental Research – UFZ Leipzig, Leipzig, Germany
| | - Jan Krumsiek
- Institute of Computational Biology, Helmholtz Centre Munich & Mathematics, Oberschleißheim, Germany
| | - Wolfgang Otto
- Department of Proteomics, Helmholtz Centre for Environmental Research – UFZ Leipzig, Leipzig, Germany
| | - Stefan W. Röder
- Core Facility Studies, Helmholtz Centre for Environmental Research – UFZ Leipzig, Leipzig, Germany
| | - Tibor Kohajda
- Department of Metabolomics, Helmholtz Centre for Environmental Research – UFZ Leipzig, Leipzig, Germany
| | - Michael Borte
- Hospital “St. Georg” GmbH Leipzig, Academic Teaching Hospital of the University of Leipzig, Delitzscher Straße 141, 04129 Leipzig, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Centre Munich & Mathematics, Oberschleißheim, Germany
- TU Munich, Munich, Germany
| | - Irina Lehmann
- Core Facility Studies, Helmholtz Centre for Environmental Research – UFZ Leipzig, Leipzig, Germany
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research – UFZ Leipzig, Leipzig, Germany
| | - M. von Bergen
- Department of Metabolomics, Helmholtz Centre for Environmental Research – UFZ Leipzig, Leipzig, Germany
- Department of Proteomics, Helmholtz Centre for Environmental Research – UFZ Leipzig, Leipzig, Germany
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research – UFZ Leipzig, Leipzig, Germany
- Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, Universität Leipzig, Leipzig, Germany
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
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Waldera-Lupa DM, Kalfalah F, Florea AM, Sass S, Kruse F, Rieder V, Tigges J, Fritsche E, Krutmann J, Busch H, Boerries M, Meyer HE, Boege F, Theis F, Reifenberger G, Stühler K. Proteome-wide analysis reveals an age-associated cellular phenotype of in situ aged human fibroblasts. Aging (Albany NY) 2015; 6:856-78. [PMID: 25411231 PMCID: PMC4247387 DOI: 10.18632/aging.100698] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [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] [Indexed: 12/14/2022]
Abstract
We analyzed an ex vivo model of in situ aged human dermal fibroblasts, obtained from 15 adult healthy donors from three different age groups using an unbiased quantitative proteome-wide approach applying label-free mass spectrometry. Thereby, we identified 2409 proteins, including 43 proteins with an age-associated abundance change. Most of the differentially abundant proteins have not been described in the context of fibroblasts’ aging before, but the deduced biological processes confirmed known hallmarks of aging and led to a consistent picture of eight biological categories involved in fibroblast aging, namely proteostasis, cell cycle and proliferation, development and differentiation, cell death, cell organization and cytoskeleton, response to stress, cell communication and signal transduction, as well as RNA metabolism and translation. The exhaustive analysis of protein and mRNA data revealed that 77% of the age-associated proteins were not linked to expression changes of the corresponding transcripts. This is in line with an associated miRNA study and led us to the conclusion that most of the age-associated alterations detected at the proteome level are likely caused post-transcriptionally rather than by differential gene expression. In summary, our findings led to the characterization of novel proteins potentially associated with fibroblast aging and revealed that primary cultures of in situ aged fibroblasts are characterized by moderate age-related proteomic changes comprising the multifactorial process of aging.
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Affiliation(s)
- Daniel M Waldera-Lupa
- Institute for Molecular Medicine, Heinrich-Heine-University, Düsseldorf, Germany. Molecular Proteomics Laboratory, Biomedical Research Centre (BMFZ), Heinrich-Heine-University, Düsseldorf, Germany
| | - Faiza Kalfalah
- Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany
| | - Ana-Maria Florea
- Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Sass
- Institute of Computational Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Fabian Kruse
- Institute for Molecular Medicine, Heinrich-Heine-University, Düsseldorf, Germany. Molecular Proteomics Laboratory, Biomedical Research Centre (BMFZ), Heinrich-Heine-University, Düsseldorf, Germany
| | - Vera Rieder
- Institute for Molecular Medicine, Heinrich-Heine-University, Düsseldorf, Germany. Molecular Proteomics Laboratory, Biomedical Research Centre (BMFZ), Heinrich-Heine-University, Düsseldorf, Germany
| | - Julia Tigges
- Leibniz Research Institute for Environmental Medicine (IUF), Düsseldorf, Germany
| | - Ellen Fritsche
- Leibniz Research Institute for Environmental Medicine (IUF), Düsseldorf, Germany
| | - Jean Krutmann
- Leibniz Research Institute for Environmental Medicine (IUF), Düsseldorf, Germany
| | - Hauke Busch
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany. German Cancer Consortium (DKTK), Freiburg, Germany. German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
| | - Melanie Boerries
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany. German Cancer Consortium (DKTK), Freiburg, Germany. German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany
| | - Helmut E Meyer
- Department of Biomedical Research, Leibniz-Institute for Analytical Science - ISAS, Dortmund, Germany
| | - Fritz Boege
- Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany
| | - Fabian Theis
- Department of Mathematics, Technical University Munich, Garching, Germany
| | - Guido Reifenberger
- Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kai Stühler
- Institute for Molecular Medicine, Heinrich-Heine-University, Düsseldorf, Germany. Molecular Proteomics Laboratory, Biomedical Research Centre (BMFZ), Heinrich-Heine-University, Düsseldorf, Germany
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Raue A, Steiert B, Schelker M, Kreutz C, Maiwald T, Hass H, Vanlier J, Tönsing C, Adlung L, Engesser R, Mader W, Heinemann T, Hasenauer J, Schilling M, Höfer T, Klipp E, Theis F, Klingmüller U, Schöberl B, Timmer J. Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. Bioinformatics 2015; 31:3558-60. [PMID: 26142188 DOI: 10.1093/bioinformatics/btv405] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/28/2015] [Indexed: 02/02/2023] Open
Abstract
UNLABELLED Modeling of dynamical systems using ordinary differential equations is a popular approach in the field of systems biology. Two of the most critical steps in this approach are to construct dynamical models of biochemical reaction networks for large datasets and complex experimental conditions and to perform efficient and reliable parameter estimation for model fitting. We present a modeling environment for MATLAB that pioneers these challenges. The numerically expensive parts of the calculations such as the solving of the differential equations and of the associated sensitivity system are parallelized and automatically compiled into efficient C code. A variety of parameter estimation algorithms as well as frequentist and Bayesian methods for uncertainty analysis have been implemented and used on a range of applications that lead to publications. AVAILABILITY AND IMPLEMENTATION The Data2Dynamics modeling environment is MATLAB based, open source and freely available at http://www.data2dynamics.org. CONTACT andreas.raue@fdm.uni-freiburg.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- A Raue
- Merrimack Pharmaceuticals Inc., Discovery Devision, Cambridge, MA 02139, USA
| | - B Steiert
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany
| | - M Schelker
- Humboldt-Universität zu Berlin, Theoretical Biophysics, 10115 Berlin, Germany
| | - C Kreutz
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany
| | - T Maiwald
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany
| | - H Hass
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany
| | - J Vanlier
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany
| | - C Tönsing
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany
| | - L Adlung
- Systems Biology of Signal Transduction and
| | - R Engesser
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany
| | - W Mader
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany
| | - T Heinemann
- Divison of Theoretical Systems Biology, German Cancer Research Center, 69120 Heidelberg, Germany, BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - J Hasenauer
- Helmholtz Center Munich, Institute of Computational Biology, 85764 Neuherberg, Germany, Technische Universität München, Department of Mathematics, 85748 Garching, Germany and
| | | | - T Höfer
- Divison of Theoretical Systems Biology, German Cancer Research Center, 69120 Heidelberg, Germany, BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - E Klipp
- Humboldt-Universität zu Berlin, Theoretical Biophysics, 10115 Berlin, Germany
| | - F Theis
- Helmholtz Center Munich, Institute of Computational Biology, 85764 Neuherberg, Germany, Technische Universität München, Department of Mathematics, 85748 Garching, Germany and
| | | | - B Schöberl
- Merrimack Pharmaceuticals Inc., Discovery Devision, Cambridge, MA 02139, USA
| | - J Timmer
- University of Freiburg, Institute for Physics, 79104 Freiburg, Germany, BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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Calzolari F, Michel J, Baumgart EV, Theis F, Götz M, Ninkovic J. Fast clonal expansion and limited neural stem cell self-renewal in the adult subependymal zone. Nat Neurosci 2015; 18:490-2. [PMID: 25730673 DOI: 10.1038/nn.3963] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/27/2015] [Indexed: 12/15/2022]
Abstract
We analyzed the progeny of individual neural stem cells (NSCs) of the mouse adult subependymal zone (SEZ) in vivo and found a markedly fast lineage amplification, as well as limited NSC self-renewal and exhaustion in a few weeks. We further unraveled the mechanisms of neuronal subtype generation, finding that a higher proportion of NSCs were dedicated to generate deep granule cells in the olfactory bulb and that larger clones were produced by these NSCs.
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Affiliation(s)
- Filippo Calzolari
- 1] Institute of Stem Cell Research, Helmholtz Center, Munich, Germany. [2] Biomedical Center, University of Munich, Munich, Germany
| | - Julia Michel
- Institute of Stem Cell Research, Helmholtz Center, Munich, Germany
| | | | - Fabian Theis
- 1] Institute of Computational Biology, Helmholtz Center, Munich, Germany. [2] Institute for Mathematical Sciences, Technical University Munich, Garching, Germany
| | - Magdalena Götz
- 1] Institute of Stem Cell Research, Helmholtz Center, Munich, Germany. [2] Biomedical Center, University of Munich, Munich, Germany. [3] Munich cluster for Systems Neurology (SYNERGY), Ludwig-Maximilians-Universität, München, Germany
| | - Jovica Ninkovic
- 1] Institute of Stem Cell Research, Helmholtz Center, Munich, Germany. [2] Biomedical Center, University of Munich, Munich, Germany. [3] Munich cluster for Systems Neurology (SYNERGY), Ludwig-Maximilians-Universität, München, Germany
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Schmidt JM, Panzilius E, Bartsch HS, Irmler M, Beckers J, Kari V, Linnemann JR, Dragoi D, Hirschi B, Kloos UJ, Sass S, Theis F, Kahlert S, Johnsen SA, Sotlar K, Scheel CH. Stem-cell-like properties and epithelial plasticity arise as stable traits after transient Twist1 activation. Cell Rep 2015; 10:131-9. [PMID: 25578726 DOI: 10.1016/j.celrep.2014.12.032] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 12/01/2014] [Accepted: 12/15/2014] [Indexed: 11/18/2022] Open
Abstract
Master regulators of the epithelial-mesenchymal transition such as Twist1 and Snail1 have been implicated in invasiveness and the generation of cancer stem cells, but their persistent activity inhibits stem-cell-like properties and the outgrowth of disseminated cancer cells into macroscopic metastases. Here, we show that Twist1 activation primes a subset of mammary epithelial cells for stem-cell-like properties, which only emerge and stably persist following Twist1 deactivation. Consequently, when cells undergo a mesenchymal-epithelial transition (MET), they do not return to their original epithelial cell state, evidenced by acquisition of invasive growth behavior and a distinct gene expression profile. These data provide an explanation for how transient Twist1 activation may promote all steps of the metastatic cascade; i.e., invasion, dissemination, and metastatic outgrowth at distant sites.
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Affiliation(s)
- Johanna M Schmidt
- Institute of Stem Cell Research, Helmholtz Center for Health and Environmental Research Munich, 85764 Neuherberg, Germany
| | - Elena Panzilius
- Institute of Stem Cell Research, Helmholtz Center for Health and Environmental Research Munich, 85764 Neuherberg, Germany
| | - Harald S Bartsch
- Institute of Pathology, Medical School, Ludwig Maximilian University, 80337 Munich, Germany
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Center Munich, 85764 Neuherberg, Germany; Department of Experimental Genetics, Technical University Munich, 85354 Freising, Germany
| | - Vijayalakshmi Kari
- Department of General, Visceral and Pediatric Surgery, University Medical Center, 37075 Göttingen, Germany
| | - Jelena R Linnemann
- Institute of Stem Cell Research, Helmholtz Center for Health and Environmental Research Munich, 85764 Neuherberg, Germany
| | - Diana Dragoi
- Institute of Stem Cell Research, Helmholtz Center for Health and Environmental Research Munich, 85764 Neuherberg, Germany
| | - Benjamin Hirschi
- Institute of Stem Cell Research, Helmholtz Center for Health and Environmental Research Munich, 85764 Neuherberg, Germany
| | - Uwe J Kloos
- Institute of Stem Cell Research, Helmholtz Center for Health and Environmental Research Munich, 85764 Neuherberg, Germany
| | - Steffen Sass
- Institute of Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Department of Mathematics, Technical University Munich, 85747 Garching, Germany
| | - Steffen Kahlert
- Department of Obstetrics and Gynecology, Medical School, Ludwig Maximilian University, 80337 Munich, Germany
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, University Medical Center, 37075 Göttingen, Germany
| | - Karl Sotlar
- Institute of Pathology, Medical School, Ludwig Maximilian University, 80337 Munich, Germany
| | - Christina H Scheel
- Institute of Stem Cell Research, Helmholtz Center for Health and Environmental Research Munich, 85764 Neuherberg, Germany.
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Matthes M, Preusse M, Zhang J, Schechter J, Mayer D, Lentes B, Theis F, Prakash N, Wurst W, Trümbach D. Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain. Database (Oxford) 2014; 2014:bau083. [PMID: 25145340 PMCID: PMC4139671 DOI: 10.1093/database/bau083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The study of developmental processes in the mouse and other vertebrates includes the understanding of patterning along the anterior–posterior, dorsal–ventral and medial– lateral axis. Specifically, neural development is also of great clinical relevance because several human neuropsychiatric disorders such as schizophrenia, autism disorders or drug addiction and also brain malformations are thought to have neurodevelopmental origins, i.e. pathogenesis initiates during childhood and adolescence. Impacts during early neurodevelopment might also predispose to late-onset neurodegenerative disorders, such as Parkinson’s disease. The neural tube develops from its precursor tissue, the neural plate, in a patterning process that is determined by compartmentalization into morphogenetic units, the action of local signaling centers and a well-defined and locally restricted expression of genes and their interactions. While public databases provide gene expression data with spatio-temporal resolution, they usually neglect the genetic interactions that govern neural development. Here, we introduce Mouse IDGenes, a reference database for genetic interactions in the developing mouse brain. The database is highly curated and offers detailed information about gene expressions and the genetic interactions at the developing mid-/hindbrain boundary. To showcase the predictive power of interaction data, we infer new Wnt/β-catenin target genes by machine learning and validate one of them experimentally. The database is updated regularly. Moreover, it can easily be extended by the research community. Mouse IDGenes will contribute as an important resource to the research on mouse brain development, not exclusively by offering data retrieval, but also by allowing data input. Database URL:http://mouseidgenes.helmholtz-muenchen.de.
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Affiliation(s)
- Michaela Matthes
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Genetik, Emil-Ramannstr. 8, 85354 Freising, Germany, Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München, Zentrum Mathematik, Boltzmannstr. 3, 85747 Garching, Germany, Max-Planck-Institute of Psychiatry, Kraepelinstr. 2-10, 80804 München, Germany, Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), Standort München, Schillerstr. 44, 80336 München, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Entwicklungsgenetik, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Schillerstr. 44, 80336 München, Germany Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Genetik, Emil-Ramannstr. 8, 85354 Freising, Germany, Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München, Zentrum Mathematik, Boltzmannstr. 3, 85747 Garching, Germany, Max-Planck-In
| | - Martin Preusse
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Genetik, Emil-Ramannstr. 8, 85354 Freising, Germany, Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München, Zentrum Mathematik, Boltzmannstr. 3, 85747 Garching, Germany, Max-Planck-Institute of Psychiatry, Kraepelinstr. 2-10, 80804 München, Germany, Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), Standort München, Schillerstr. 44, 80336 München, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Entwicklungsgenetik, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Schillerstr. 44, 80336 München, Germany Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Genetik, Emil-Ramannstr. 8, 85354 Freising, Germany, Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München, Zentrum Mathematik, Boltzmannstr. 3, 85747 Garching, Germany, Max-Planck-In
| | - Jingzhong Zhang
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Genetik, Emil-Ramannstr. 8, 85354 Freising, Germany, Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München, Zentrum Mathematik, Boltzmannstr. 3, 85747 Garching, Germany, Max-Planck-Institute of Psychiatry, Kraepelinstr. 2-10, 80804 München, Germany, Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), Standort München, Schillerstr. 44, 80336 München, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Entwicklungsgenetik, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Schillerstr. 44, 80336 München, Germany
| | - Julia Schechter
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Genetik, Emil-Ramannstr. 8, 85354 Freising, Germany, Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München, Zentrum Mathematik, Boltzmannstr. 3, 85747 Garching, Germany, Max-Planck-Institute of Psychiatry, Kraepelinstr. 2-10, 80804 München, Germany, Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), Standort München, Schillerstr. 44, 80336 München, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Entwicklungsgenetik, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Schillerstr. 44, 80336 München, Germany
| | - Daniela Mayer
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Genetik, Emil-Ramannstr. 8, 85354 Freising, Germany, Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München, Zentrum Mathematik, Boltzmannstr. 3, 85747 Garching, Germany, Max-Planck-Institute of Psychiatry, Kraepelinstr. 2-10, 80804 München, Germany, Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), Standort München, Schillerstr. 44, 80336 München, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Entwicklungsgenetik, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Schillerstr. 44, 80336 München, Germany
| | - Bernd Lentes
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Genetik, Emil-Ramannstr. 8, 85354 Freising, Germany, Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München, Zentrum Mathematik, Boltzmannstr. 3, 85747 Garching, Germany, Max-Planck-Institute of Psychiatry, Kraepelinstr. 2-10, 80804 München, Germany, Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), Standort München, Schillerstr. 44, 80336 München, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Entwicklungsgenetik, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Schillerstr. 44, 80336 München, Germany
| | - Fabian Theis
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Genetik, Emil-Ramannstr. 8, 85354 Freising, Germany, Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München, Zentrum Mathematik, Boltzmannstr. 3, 85747 Garching, Germany, Max-Planck-Institute of Psychiatry, Kraepelinstr. 2-10, 80804 München, Germany, Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), Standort München, Schillerstr. 44, 80336 München, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Entwicklungsgenetik, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Schillerstr. 44, 80336 München, Germany Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Genetik, Emil-Ramannstr. 8, 85354 Freising, Germany, Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München, Zentrum Mathematik, Boltzmannstr. 3, 85747 Garching, Germany, Max-Planck-In
| | - Nilima Prakash
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Genetik, Emil-Ramannstr. 8, 85354 Freising, Germany, Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München, Zentrum Mathematik, Boltzmannstr. 3, 85747 Garching, Germany, Max-Planck-Institute of Psychiatry, Kraepelinstr. 2-10, 80804 München, Germany, Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), Standort München, Schillerstr. 44, 80336 München, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Entwicklungsgenetik, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Schillerstr. 44, 80336 München, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Genetik, Emil-Ramannstr. 8, 85354 Freising, Germany, Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München, Zentrum Mathematik, Boltzmannstr. 3, 85747 Garching, Germany, Max-Planck-Institute of Psychiatry, Kraepelinstr. 2-10, 80804 München, Germany, Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), Standort München, Schillerstr. 44, 80336 München, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Entwicklungsgenetik, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Schillerstr. 44, 80336 München, Germany Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Genetik, Emil-Ramannstr. 8, 85354 Freising, Germany, Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München, Zentrum Mathematik, Boltzmannstr. 3, 85747 Garching, Germany, Max-Planck-In
| | - Dietrich Trümbach
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Genetik, Emil-Ramannstr. 8, 85354 Freising, Germany, Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München, Zentrum Mathematik, Boltzmannstr. 3, 85747 Garching, Germany, Max-Planck-Institute of Psychiatry, Kraepelinstr. 2-10, 80804 München, Germany, Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), Standort München, Schillerstr. 44, 80336 München, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Entwicklungsgenetik, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany and Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Schillerstr. 44, 80336 München, Germany Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München-Weihenstephan, Lehrstuhl für Genetik, Emil-Ramannstr. 8, 85354 Freising, Germany, Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany, Technische Universität München, Zentrum Mathematik, Boltzmannstr. 3, 85747 Garching, Germany, Max-Planck-In
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Moignard V, Woodhouse S, Haghverdi L, Lilly J, Tanaka Y, Wilkinson A, Buettner F, Nishikawa SI, Piterman N, Kouskoff V, Theis F, Fisher J, Gottgens B. Decoding the transcriptional program for blood development from whole tissue single-cell gene expression measurements. Exp Hematol 2014. [DOI: 10.1016/j.exphem.2014.07.195] [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: 10/25/2022]
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Thalheimer F, Wingert S, De Giacomo P, Haetscher N, Brill B, Theis F, Hennighausen L, Schroeder T, Rieger M. Cytokine-regulated GADD45G induces differentiation and lineage selection in hematopoietic stem cells. Exp Hematol 2014. [DOI: 10.1016/j.exphem.2014.07.215] [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: 10/25/2022]
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Altmaier E, Emeny RT, Krumsiek J, Lacruz ME, Lukaschek K, Häfner S, Kastenmüller G, Römisch-Margl W, Prehn C, Mohney RP, Evans AM, Milburn MV, Illig T, Adamski J, Theis F, Suhre K, Ladwig KH. Metabolomic profiles in individuals with negative affectivity and social inhibition: a population-based study of Type D personality. Psychoneuroendocrinology 2013; 38:1299-309. [PMID: 23237813 DOI: 10.1016/j.psyneuen.2012.11.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 11/09/2012] [Accepted: 11/10/2012] [Indexed: 12/27/2022]
Abstract
BACKGROUND Individuals with negative affectivity who are inhibited in social situations are characterized as distressed, or Type D, and have an increased risk of cardiovascular disease (CVD). The underlying biomechanisms that link this psychological affect to a pathological state are not well understood. This study applied a metabolomic approach to explore biochemical pathways that may contribute to the Type D personality. METHODS Type D personality was determined by the Type D Scale-14. Small molecule biochemicals were measured using two complementary mass-spectrometry based metabolomics platforms. Metabolic profiles of Type D and non-Type D participants within a population-based study in Southern Germany were compared in cross-sectional regression analyses. The PHQ-9 and GAD-7 instruments were also used to assess symptoms of depression and anxiety, respectively, within this metabolomic study. RESULTS 668 metabolites were identified in the serum of 1502 participants (age 32-77); 386 of these individuals were classified as Type D. While demographic and biomedical characteristics were equally distributed between the groups, a higher level of depression and anxiety was observed in Type D individuals. Significantly lower levels of the tryptophan metabolite kynurenine were associated with Type D (p-value corrected for multiple testing=0.042), while no significant associations could be found for depression and anxiety. A Gaussian graphical model analysis enabled the identification of four potentially interesting metabolite networks that are enriched in metabolites (androsterone sulfate, tyrosine, indoxyl sulfate or caffeine) that associate nominally with Type D personality. CONCLUSIONS This study identified novel biochemical pathways associated with Type D personality and demonstrates that the application of metabolomic approaches in population studies can reveal mechanisms that may contribute to psychological health and disease.
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Affiliation(s)
- Elisabeth Altmaier
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
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Hoppe P, Schwarzfischer M, Nerlov C, Theis F, Schroeder T. Myeloid lineage choice is not controlled by the PU.1 - Gata1 switch. Exp Hematol 2013. [DOI: 10.1016/j.exphem.2013.05.270] [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: 11/26/2022]
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Haetscher N, Feuermann Y, Wingert S, Thalheimer F, Weiser C, Kowarsch A, Theis F, Schroeder T, Rieger M, Hennighausen L. The cytokine-induced microrna193b modulates ckit expression and STAT5 signaling. Exp Hematol 2013. [DOI: 10.1016/j.exphem.2013.05.178] [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: 11/25/2022]
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Thalheimer F, Wingert S, De Giacomo P, Kowarsch A, Theis F, Hennighausen L, Schroeder T, Rieger M. Extrinsically regulated Gadd45γ balances hematopoietic stem cell self-renewal and differentiation. Exp Hematol 2013. [DOI: 10.1016/j.exphem.2013.05.162] [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: 10/26/2022]
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Xu T, Holzapfel C, Dong X, Bader E, Yu Z, Prehn C, Perstorfer K, Jaremek M, Roemisch-Margl W, Rathmann W, Li Y, Wichmann HE, Wallaschofski H, Ladwig KH, Theis F, Suhre K, Adamski J, Illig T, Peters A, Wang-Sattler R. Effects of smoking and smoking cessation on human serum metabolite profile: results from the KORA cohort study. BMC Med 2013; 11:60. [PMID: 23497222 PMCID: PMC3653729 DOI: 10.1186/1741-7015-11-60] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 03/04/2013] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Metabolomics helps to identify links between environmental exposures and intermediate biomarkers of disturbed pathways. We previously reported variations in phosphatidylcholines in male smokers compared with non-smokers in a cross-sectional pilot study with a small sample size, but knowledge of the reversibility of smoking effects on metabolite profiles is limited. Here, we extend our metabolomics study with a large prospective study including female smokers and quitters. METHODS Using targeted metabolomics approach, we quantified 140 metabolite concentrations for 1,241 fasting serum samples in the population-based Cooperative Health Research in the Region of Augsburg (KORA) human cohort at two time points: baseline survey conducted between 1999 and 2001 and follow-up after seven years. Metabolite profiles were compared among groups of current smokers, former smokers and never smokers, and were further assessed for their reversibility after smoking cessation. Changes in metabolite concentrations from baseline to the follow-up were investigated in a longitudinal analysis comparing current smokers, never smokers and smoking quitters, who were current smokers at baseline but former smokers by the time of follow-up. In addition, we constructed protein-metabolite networks with smoking-related genes and metabolites. RESULTS We identified 21 smoking-related metabolites in the baseline investigation (18 in men and six in women, with three overlaps) enriched in amino acid and lipid pathways, which were significantly different between current smokers and never smokers. Moreover, 19 out of the 21 metabolites were found to be reversible in former smokers. In the follow-up study, 13 reversible metabolites in men were measured, of which 10 were confirmed to be reversible in male quitters. Protein-metabolite networks are proposed to explain the consistent reversibility of smoking effects on metabolites. CONCLUSIONS We showed that smoking-related changes in human serum metabolites are reversible after smoking cessation, consistent with the known cardiovascular risk reduction. The metabolites identified may serve as potential biomarkers to evaluate the status of smoking cessation and characterize smoking-related diseases.
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Affiliation(s)
- Tao Xu
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg 85764, Germany
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Köttgen A, Albrecht E, Teumer A, Vitart V, Krumsiek J, Hundertmark C, Pistis G, Ruggiero D, O'Seaghdha CM, Haller T, Yang Q, Tanaka T, Johnson AD, Kutalik Z, Smith AV, Shi J, Struchalin M, Middelberg RPS, Brown MJ, Gaffo AL, Pirastu N, Li G, Hayward C, Zemunik T, Huffman J, Yengo L, Zhao JH, Demirkan A, Feitosa MF, Liu X, Malerba G, Lopez LM, van der Harst P, Li X, Kleber ME, Hicks AA, Nolte IM, Johansson A, Murgia F, Wild SH, Bakker SJL, Peden JF, Dehghan A, Steri M, Tenesa A, Lagou V, Salo P, Mangino M, Rose LM, Lehtimäki T, Woodward OM, Okada Y, Tin A, Müller C, Oldmeadow C, Putku M, Czamara D, Kraft P, Frogheri L, Thun GA, Grotevendt A, Gislason GK, Harris TB, Launer LJ, McArdle P, Shuldiner AR, Boerwinkle E, Coresh J, Schmidt H, Schallert M, Martin NG, Montgomery GW, Kubo M, Nakamura Y, Tanaka T, Munroe PB, Samani NJ, Jacobs DR, Liu K, D'Adamo P, Ulivi S, Rotter JI, Psaty BM, Vollenweider P, Waeber G, Campbell S, Devuyst O, Navarro P, Kolcic I, Hastie N, Balkau B, Froguel P, Esko T, Salumets A, Khaw KT, Langenberg C, Wareham NJ, Isaacs A, Kraja A, Zhang Q, Wild PS, Scott RJ, Holliday EG, Org E, Viigimaa M, Bandinelli S, Metter JE, Lupo A, Trabetti E, Sorice R, Döring A, Lattka E, Strauch K, Theis F, Waldenberger M, Wichmann HE, Davies G, Gow AJ, Bruinenberg M, Stolk RP, Kooner JS, Zhang W, Winkelmann BR, Boehm BO, Lucae S, Penninx BW, Smit JH, Curhan G, Mudgal P, Plenge RM, Portas L, Persico I, Kirin M, Wilson JF, Mateo Leach I, van Gilst WH, Goel A, Ongen H, Hofman A, Rivadeneira F, Uitterlinden AG, Imboden M, von Eckardstein A, Cucca F, Nagaraja R, Piras MG, Nauck M, Schurmann C, Budde K, Ernst F, Farrington SM, Theodoratou E, Prokopenko I, Stumvoll M, Jula A, Perola M, Salomaa V, Shin SY, Spector TD, Sala C, Ridker PM, Kähönen M, Viikari J, Hengstenberg C, Nelson CP, Meschia JF, Nalls MA, Sharma P, Singleton AB, Kamatani N, Zeller T, Burnier M, Attia J, Laan M, Klopp N, Hillege HL, Kloiber S, Choi H, Pirastu M, Tore S, Probst-Hensch NM, Völzke H, Gudnason V, Parsa A, Schmidt R, Whitfield JB, Fornage M, Gasparini P, Siscovick DS, Polašek O, Campbell H, Rudan I, Bouatia-Naji N, Metspalu A, Loos RJF, van Duijn CM, Borecki IB, Ferrucci L, Gambaro G, Deary IJ, Wolffenbuttel BHR, Chambers JC, März W, Pramstaller PP, Snieder H, Gyllensten U, Wright AF, Navis G, Watkins H, Witteman JCM, Sanna S, Schipf S, Dunlop MG, Tönjes A, Ripatti S, Soranzo N, Toniolo D, Chasman DI, Raitakari O, Kao WHL, Ciullo M, Fox CS, Caulfield M, Bochud M, Gieger C. Genome-wide association analyses identify 18 new loci associated with serum urate concentrations. Nat Genet 2012; 45:145-54. [PMID: 23263486 DOI: 10.1038/ng.2500] [Citation(s) in RCA: 574] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 11/27/2012] [Indexed: 12/13/2022]
Abstract
Elevated serum urate concentrations can cause gout, a prevalent and painful inflammatory arthritis. By combining data from >140,000 individuals of European ancestry within the Global Urate Genetics Consortium (GUGC), we identified and replicated 28 genome-wide significant loci in association with serum urate concentrations (18 new regions in or near TRIM46, INHBB, SFMBT1, TMEM171, VEGFA, BAZ1B, PRKAG2, STC1, HNF4G, A1CF, ATXN2, UBE2Q2, IGF1R, NFAT5, MAF, HLF, ACVR1B-ACVRL1 and B3GNT4). Associations for many of the loci were of similar magnitude in individuals of non-European ancestry. We further characterized these loci for associations with gout, transcript expression and the fractional excretion of urate. Network analyses implicate the inhibins-activins signaling pathways and glucose metabolism in systemic urate control. New candidate genes for serum urate concentration highlight the importance of metabolic control of urate production and excretion, which may have implications for the treatment and prevention of gout.
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Affiliation(s)
- Anna Köttgen
- Renal Division, Freiburg University Hospital, Freiburg, Germany.
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