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Dong MS, Rokicki J, Dwyer D, Papiol S, Streit F, Rietschel M, Wobrock T, Müller-Myhsok B, Falkai P, Westlye LT, Andreassen OA, Palaniyappan L, Schneider-Axmann T, Hasan A, Schwarz E, Koutsouleris N. Multimodal workflows optimally predict response to repetitive transcranial magnetic stimulation in patients with schizophrenia: a multisite machine learning analysis. Transl Psychiatry 2024; 14:196. [PMID: 38664377 PMCID: PMC11045783 DOI: 10.1038/s41398-024-02903-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
The response variability to repetitive transcranial magnetic stimulation (rTMS) challenges the effective use of this treatment option in patients with schizophrenia. This variability may be deciphered by leveraging predictive information in structural MRI, clinical, sociodemographic, and genetic data using artificial intelligence. We developed and cross-validated rTMS response prediction models in patients with schizophrenia drawn from the multisite RESIS trial. The models incorporated pre-treatment sMRI, clinical, sociodemographic, and polygenic risk score (PRS) data. Patients were randomly assigned to receive active (N = 45) or sham (N = 47) rTMS treatment. The prediction target was individual response, defined as ≥20% reduction in pre-treatment negative symptom sum scores of the Positive and Negative Syndrome Scale. Our multimodal sequential prediction workflow achieved a balanced accuracy (BAC) of 94% (non-responders: 92%, responders: 95%) in the active-treated group and 50% in the sham-treated group. The clinical, clinical + PRS, and sMRI-based classifiers yielded BACs of 65%, 76%, and 80%, respectively. Apparent sadness, inability to feel, educational attainment PRS, and unemployment were most predictive of non-response in the clinical + PRS model, while grey matter density reductions in the default mode, limbic networks, and the cerebellum were most predictive in the sMRI model. Our sequential modelling approach provided superior predictive performance while minimising the diagnostic burden in the clinical setting. Predictive patterns suggest that rTMS responders may have higher levels of brain grey matter in the default mode and salience networks which increases their likelihood of profiting from plasticity-inducing brain stimulation methods, such as rTMS. The future clinical implementation of our models requires findings to be replicated at the international scale using stratified clinical trial designs.
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Grants
- FA-210/1 Deutsche Forschungsgemeinschaft (German Research Foundation)
- SCHW 1768/1-1 Deutsche Forschungsgemeinschaft (German Research Foundation)
- FA-210/1 Deutsche Forschungsgemeinschaft (German Research Foundation)
- SCHW 1768/1-1 Deutsche Forschungsgemeinschaft (German Research Foundation)
- FA-210/1 Deutsche Forschungsgemeinschaft (German Research Foundation)
- SCHW 1768/1-1 Deutsche Forschungsgemeinschaft (German Research Foundation)
- FA-210/1 Deutsche Forschungsgemeinschaft (German Research Foundation)
- 01ZX1904A Bundesministerium für Bildung, Wissenschaft, Forschung und Technologie (Federal Ministry for Education, Science, Research and Technology)
- 01KU1905A Bundesministerium für Bildung, Wissenschaft, Forschung und Technologie (Federal Ministry for Education, Science, Research and Technology)
- 01ZX1904A Bundesministerium für Bildung, Wissenschaft, Forschung und Technologie (Federal Ministry for Education, Science, Research and Technology)
- 01KU1905A Bundesministerium für Bildung, Wissenschaft, Forschung und Technologie (Federal Ministry for Education, Science, Research and Technology)
- 01ZX1904A Bundesministerium für Bildung, Wissenschaft und Kultur (Federal Ministry of Education, Science and Culture)
- ENP-161423 Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)
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Affiliation(s)
- Mark Sen Dong
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilian-University of Munich, Munich, Germany
- Max Planck Institute of Psychiatry, Munich, Germany
| | - Jaroslav Rokicki
- Centre of Research and Education in Forensic Psychiatry, Oslo Univerisity Hospital, Oslo, Norway
| | - Dominic Dwyer
- The University of Melbourne, Melbourne, VIC, Australia
| | - Sergi Papiol
- Max Planck Institute of Psychiatry, Munich, Germany
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
| | - Fabian Streit
- Department for Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Hector Institute for Artificial Intelligence in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Marcella Rietschel
- Department for Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Wobrock
- Centre for Mental Health, Darmstadt-Dieburg District Clinic, Gross-Umstadt, Germany
| | | | - Peter Falkai
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilian-University of Munich, Munich, Germany
- Max Planck Institute of Psychiatry, Munich, Germany
- Partner site Munich-Augsburg, DZPG (German Centre for Mental Health), Munich / Augsburg, Germany
| | | | - Ole A Andreassen
- Centre for Precision Psychiatry, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Lena Palaniyappan
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, QC, Canada
- Robarts Research Institute, Western University, London Ontario, Canada
| | - Thomas Schneider-Axmann
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Alkomiet Hasan
- Partner site Munich-Augsburg, DZPG (German Centre for Mental Health), Munich / Augsburg, Germany
- Department of Psychiatry, Psychotherapy and Psychosomatics, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Emanuel Schwarz
- Department for Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Hector Institute for Artificial Intelligence in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Nikolaos Koutsouleris
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilian-University of Munich, Munich, Germany.
- Max Planck Institute of Psychiatry, Munich, Germany.
- Partner site Munich-Augsburg, DZPG (German Centre for Mental Health), Munich / Augsburg, Germany.
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
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2
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Rauber S, Mohammadian H, Schmidkonz C, Atzinger A, Soare A, Treutlein C, Kemble S, Mahony CB, Geisthoff M, Angeli MR, Raimondo MG, Xu C, Yang KT, Lu L, Labinsky H, Saad MSA, Gwellem CA, Chang J, Huang K, Kampylafka E, Knitza J, Bilyy R, Distler JHW, Hanlon MM, Fearon U, Veale DJ, Roemer FW, Bäuerle T, Maric HM, Maschauer S, Ekici AB, Buckley CD, Croft AP, Kuwert T, Prante O, Cañete JD, Schett G, Ramming A. CD200 + fibroblasts form a pro-resolving mesenchymal network in arthritis. Nat Immunol 2024; 25:682-692. [PMID: 38396288 DOI: 10.1038/s41590-024-01774-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 01/30/2024] [Indexed: 02/25/2024]
Abstract
Fibroblasts are important regulators of inflammation, but whether fibroblasts change phenotype during resolution of inflammation is not clear. Here we use positron emission tomography to detect fibroblast activation protein (FAP) as a means to visualize fibroblast activation in vivo during inflammation in humans. While tracer accumulation is high in active arthritis, it decreases after tumor necrosis factor and interleukin-17A inhibition. Biopsy-based single-cell RNA-sequencing analyses in experimental arthritis show that FAP signal reduction reflects a phenotypic switch from pro-inflammatory MMP3+/IL6+ fibroblasts (high FAP internalization) to pro-resolving CD200+DKK3+ fibroblasts (low FAP internalization). Spatial transcriptomics of human joints indicates that pro-resolving niches of CD200+DKK3+ fibroblasts cluster with type 2 innate lymphoid cells, whereas MMP3+/IL6+ fibroblasts colocalize with inflammatory immune cells. CD200+DKK3+ fibroblasts stabilized the type 2 innate lymphoid cell phenotype and induced resolution of arthritis via CD200-CD200R1 signaling. Taken together, these data suggest a dynamic molecular regulation of the mesenchymal compartment during resolution of inflammation.
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Affiliation(s)
- Simon Rauber
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Hashem Mohammadian
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Christian Schmidkonz
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Department of Industrial Engineering and Health, Technical University Amberg-Weiden, Institute of Medical Engineering, Weiden, Germany
| | - Armin Atzinger
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Alina Soare
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Christoph Treutlein
- Institute of Radiology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Samuel Kemble
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Christopher B Mahony
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Manuel Geisthoff
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Mario R Angeli
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Maria G Raimondo
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Cong Xu
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Kai-Ting Yang
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Le Lu
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Hannah Labinsky
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Mina S A Saad
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Charles A Gwellem
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Jiyang Chang
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Kaiyue Huang
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Eleni Kampylafka
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Johannes Knitza
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Rostyslav Bilyy
- Department of Histology, Cytology, Embryology, Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
- Institute of Cellular Biology and Pathology 'Nicolae Simionescu', Bucharest, Romania
| | - Jörg H W Distler
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Clinic for Rheumatology, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Hiller Research Center, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Megan M Hanlon
- Molecular Rheumatology, School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Ursula Fearon
- Molecular Rheumatology, School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Douglas J Veale
- EULAR Centre for Arthritis & Rheumatic Diseases, St. Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Frank W Roemer
- Institute of Radiology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Tobias Bäuerle
- Institute of Radiology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Hans M Maric
- Rudolf-Virchow-Center for Integrative and Translational Imaging, University of Würzburg, Würzburg, Germany
| | - Simone Maschauer
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | | | - Adam P Croft
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Torsten Kuwert
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Olaf Prante
- Department of Nuclear Medicine, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | | | - Georg Schett
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Andreas Ramming
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany.
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany.
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3
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Tayebi Arasteh S, Ziller A, Kuhl C, Makowski M, Nebelung S, Braren R, Rueckert D, Truhn D, Kaissis G. Preserving fairness and diagnostic accuracy in private large-scale AI models for medical imaging. Commun Med (Lond) 2024; 4:46. [PMID: 38486100 PMCID: PMC10940659 DOI: 10.1038/s43856-024-00462-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 02/16/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Artificial intelligence (AI) models are increasingly used in the medical domain. However, as medical data is highly sensitive, special precautions to ensure its protection are required. The gold standard for privacy preservation is the introduction of differential privacy (DP) to model training. Prior work indicates that DP has negative implications on model accuracy and fairness, which are unacceptable in medicine and represent a main barrier to the widespread use of privacy-preserving techniques. In this work, we evaluated the effect of privacy-preserving training of AI models regarding accuracy and fairness compared to non-private training. METHODS We used two datasets: (1) A large dataset (N = 193,311) of high quality clinical chest radiographs, and (2) a dataset (N = 1625) of 3D abdominal computed tomography (CT) images, with the task of classifying the presence of pancreatic ductal adenocarcinoma (PDAC). Both were retrospectively collected and manually labeled by experienced radiologists. We then compared non-private deep convolutional neural networks (CNNs) and privacy-preserving (DP) models with respect to privacy-utility trade-offs measured as area under the receiver operating characteristic curve (AUROC), and privacy-fairness trade-offs, measured as Pearson's r or Statistical Parity Difference. RESULTS We find that, while the privacy-preserving training yields lower accuracy, it largely does not amplify discrimination against age, sex or co-morbidity. However, we find an indication that difficult diagnoses and subgroups suffer stronger performance hits in private training. CONCLUSIONS Our study shows that - under the challenging realistic circumstances of a real-life clinical dataset - the privacy-preserving training of diagnostic deep learning models is possible with excellent diagnostic accuracy and fairness.
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Affiliation(s)
- Soroosh Tayebi Arasteh
- Department of Diagnostic and Interventional Radiology, University Hospital RWTH Aachen, Aachen, Germany.
| | - Alexander Ziller
- Institute of Diagnostic and Interventional Radiology, Technical University of Munich, Munich, Germany.
- Artificial Intelligence in Healthcare and Medicine, Technical University of Munich, Munich, Germany.
| | - Christiane Kuhl
- Department of Diagnostic and Interventional Radiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Marcus Makowski
- Institute of Diagnostic and Interventional Radiology, Technical University of Munich, Munich, Germany
| | - Sven Nebelung
- Department of Diagnostic and Interventional Radiology, University Hospital RWTH Aachen, Aachen, Germany
| | - Rickmer Braren
- Institute of Diagnostic and Interventional Radiology, Technical University of Munich, Munich, Germany
| | - Daniel Rueckert
- Artificial Intelligence in Healthcare and Medicine, Technical University of Munich, Munich, Germany
| | - Daniel Truhn
- Department of Diagnostic and Interventional Radiology, University Hospital RWTH Aachen, Aachen, Germany.
| | - Georgios Kaissis
- Institute of Diagnostic and Interventional Radiology, Technical University of Munich, Munich, Germany.
- Artificial Intelligence in Healthcare and Medicine, Technical University of Munich, Munich, Germany.
- Department of Computing, Imperial College London, London, United Kingdom.
- Institute for Machine Learning in Biomedical Imaging, Helmholtz Munich, Neuherberg, Germany.
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4
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Boes M, Falter-Braun P. Long-COVID-19: the persisting imprint of SARS-CoV-2 infections on the innate immune system. Signal Transduct Target Ther 2023; 8:460. [PMID: 38097574 PMCID: PMC10721820 DOI: 10.1038/s41392-023-01717-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/02/2023] [Accepted: 11/19/2023] [Indexed: 12/17/2023] Open
Affiliation(s)
- Marianne Boes
- Center for Translational Immunology and Department of Pediatric Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Pascal Falter-Braun
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Munich, Neuherberg, Germany.
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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5
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Segets D, Andronescu C, Apfel UP. Accelerating CO 2 electrochemical conversion towards industrial implementation. Nat Commun 2023; 14:7950. [PMID: 38040758 PMCID: PMC10692087 DOI: 10.1038/s41467-023-43762-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 11/20/2023] [Indexed: 12/03/2023] Open
Abstract
Despite significant progress in CO2 conversion field, there remains a significant gap between fundamental research and the industrial demands. This Comment discusses key performance parameters for industrial applications and outlines current limitations in the field.
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Affiliation(s)
- Doris Segets
- Institute for Energy and Materials Processes-Particle Science and Technology, University of Duisburg-Essen, Carl-Benz-Str. 199, 47057, Duisburg, Germany
- Center for Nanointegration Duisburg-Essen (CENIDE), Carl-Benz-Str. 199, 47057, Duisburg, Germany
| | - Corina Andronescu
- Center for Nanointegration Duisburg-Essen (CENIDE), Carl-Benz-Str. 199, 47057, Duisburg, Germany
- Chemical Technology III, Faculty of Chemistry University of Duisburg-Essen, Carl-Benz-Straße 199, 47057, Duisburg, Germany
| | - Ulf-Peter Apfel
- Fraunhofer Institute for Environmental, Safety and Energy Technology UMSICHT, Osterfelderstraße 3, 46047, Oberhausen, Germany.
- Inorganic Chemistry I-Technical Electrochemistry, Ruhr University Bochum, Universitätsstraße 150, 44780, Bochum, Germany.
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6
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Liebers N, Bruch PM, Terzer T, Hernandez-Hernandez M, Paramasivam N, Fitzgerald D, Altmann H, Roider T, Kolb C, Knoll M, Lenze A, Platzbecker U, Röllig C, Baldus C, Serve H, Bornhäuser M, Hübschmann D, Müller-Tidow C, Stölzel F, Huber W, Benner A, Zenz T, Lu J, Dietrich S. Ex vivo drug response profiling for response and outcome prediction in hematologic malignancies: the prospective non-interventional SMARTrial. Nat Cancer 2023; 4:1648-1659. [PMID: 37783805 PMCID: PMC10733146 DOI: 10.1038/s43018-023-00645-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/31/2023] [Indexed: 10/04/2023]
Abstract
Ex vivo drug response profiling is a powerful tool to study genotype-drug response associations and is being explored as a tool set for precision medicine in cancer. Here we conducted a prospective non-interventional trial to investigate feasibility of ex vivo drug response profiling for treatment guidance in hematologic malignancies (SMARTrial, NCT03488641 ). The primary endpoint to provide drug response profiling reports within 7 d was met in 91% of all study participants (N = 80). Secondary endpoint analysis revealed that ex vivo resistance to chemotherapeutic drugs predicted chemotherapy treatment failure in vivo. We confirmed the predictive value of ex vivo response to chemotherapy in a validation cohort of 95 individuals with acute myeloid leukemia treated with daunorubicin and cytarabine. Ex vivo drug response profiles improved ELN-22 risk stratification in individuals with adverse risk. We conclude that ex vivo drug response profiling is clinically feasible and has the potential to predict chemotherapy response in individuals with hematologic malignancies beyond clinically established genetic markers.
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Affiliation(s)
- Nora Liebers
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIO ABCD), Aachen Bonn Cologne Düsseldorf, Germany
| | - Peter-Martin Bruch
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIO ABCD), Aachen Bonn Cologne Düsseldorf, Germany
| | - Tobias Terzer
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Nagarajan Paramasivam
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Donnacha Fitzgerald
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Tobias Roider
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Carolin Kolb
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Mareike Knoll
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Angela Lenze
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | | | | | - Claudia Baldus
- Department of Internal Medicine II, University Hospital of Kiel, Kiel, Germany
| | - Hubert Serve
- Department of Internal Medicine II, University Hospital of Frankfurt Main, Frankfurt am Main, Germany
| | | | - Daniel Hübschmann
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Friedrich Stölzel
- Department of Internal Medicine II, University Hospital of Kiel, Kiel, Germany
| | - Wolfgang Huber
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thorsten Zenz
- Department of Medical Oncology and Hematology, Universitätsspital & Universität Zürich, Zürich, Switzerland
- The LOOP Zürich-Medical Research Center, Zürich, Switzerland
| | - Junyan Lu
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Sascha Dietrich
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany.
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIO ABCD), Aachen Bonn Cologne Düsseldorf, Germany.
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany.
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7
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Nasretdinov A, Vinokurova D, Lemale CL, Burkhanova-Zakirova G, Chernova K, Makarova J, Herreras O, Dreier JP, Khazipov R. Diversity of cortical activity changes beyond depression during Spreading Depolarizations. Nat Commun 2023; 14:7729. [PMID: 38007508 PMCID: PMC10676372 DOI: 10.1038/s41467-023-43509-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/10/2023] [Indexed: 11/27/2023] Open
Abstract
Spreading depolarizations (SDs) are classically thought to be associated with spreading depression of cortical activity. Here, we found that SDs in patients with subarachnoid hemorrhage produce variable, ranging from depression to booming, changes in electrocorticographic activity, especially in the delta frequency band. In rats, depression of activity was characteristic of high-potassium-induced full SDs, whereas partial superficial SDs caused either little change or a boom of activity at the cortical vertex, supported by volume conduction of signals from spared delta generators in the deep cortical layers. Partial SDs also caused moderate neuronal depolarization and sustained excitation, organized in gamma oscillations in a narrow sub-SD zone. Thus, our study challenges the concept of homology between spreading depolarization and spreading depression by showing that SDs produce variable, from depression to booming, changes in activity at the cortical surface and in different cortical layers depending on the depth of SD penetration.
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Affiliation(s)
- Azat Nasretdinov
- Laboratory of Neurobiology, Kazan Federal University, Kazan, 420008, Russia
| | - Daria Vinokurova
- Laboratory of Neurobiology, Kazan Federal University, Kazan, 420008, Russia
- INMED-INSERM, Aix-Marseille University, Marseille, 13273, France
| | - Coline L Lemale
- Centre for Stroke Research Berlin, Department of Experimental Neurology and Department of Neurology, Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, D-10117, Berlin, Germany
| | | | - Ksenia Chernova
- Laboratory of Neurobiology, Kazan Federal University, Kazan, 420008, Russia
| | - Julia Makarova
- Department of Translational Neuroscience, Cajal Institute-CSIC, Madrid, Spain
| | - Oscar Herreras
- Department of Translational Neuroscience, Cajal Institute-CSIC, Madrid, Spain
| | - Jens P Dreier
- Centre for Stroke Research Berlin, Department of Experimental Neurology and Department of Neurology, Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, D-10117, Berlin, Germany
- Bernstein Centre for Computational Neuroscience Berlin, D-10115, Berlin, Germany
- Einstein Centre for Neurosciences Berlin, D-10117, Berlin, Germany
| | - Roustem Khazipov
- Laboratory of Neurobiology, Kazan Federal University, Kazan, 420008, Russia.
- INMED-INSERM, Aix-Marseille University, Marseille, 13273, France.
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8
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Dahl MJ, Bachman SL, Dutt S, Düzel S, Bodammer NC, Lindenberger U, Kühn S, Werkle-Bergner M, Mather M. The integrity of dopaminergic and noradrenergic brain regions is associated with different aspects of late-life memory performance. Nat Aging 2023; 3:1128-1143. [PMID: 37653256 PMCID: PMC10501910 DOI: 10.1038/s43587-023-00469-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 07/14/2023] [Indexed: 09/02/2023]
Abstract
Changes in dopaminergic neuromodulation play a key role in adult memory decline. Recent research has also implicated noradrenaline in shaping late-life memory. However, it is unclear whether these two neuromodulators have distinct roles in age-related cognitive changes. Here, combining longitudinal MRI of the dopaminergic substantia nigra-ventral tegmental area (SN-VTA) and noradrenergic locus coeruleus (LC) in younger (n = 69) and older (n = 251) adults, we found that dopaminergic and noradrenergic integrity are differentially associated with memory performance. While LC integrity was related to better episodic memory across several tasks, SN-VTA integrity was linked to working memory. Longitudinally, we found that older age was associated with more negative change in SN-VTA and LC integrity. Notably, changes in LC integrity reliably predicted future episodic memory. These differential associations of dopaminergic and noradrenergic nuclei with late-life cognitive decline have potential clinical utility, given their degeneration in several age-associated diseases.
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Affiliation(s)
- Martin J Dahl
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany.
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
| | - Shelby L Bachman
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Shubir Dutt
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Department of Psychology, University of Southern California, Los Angeles, CA, USA
| | - Sandra Düzel
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany
| | - Nils C Bodammer
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany
| | - Ulman Lindenberger
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany
- Max Planck UCL Centre for Computational Psychiatry and Ageing Research, London, UK
- Max Planck UCL Centre for Computational Psychiatry and Ageing Research, Berlin, Germany
| | - Simone Kühn
- Lise Meitner Group for Environmental Neuroscience, Max Planck Institute for Human Development, Berlin, Germany
- Department of Psychiatry and Psychotherapy, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Werkle-Bergner
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany
| | - Mara Mather
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Department of Psychology, University of Southern California, Los Angeles, CA, USA
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
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9
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Grosch M, Schraft L, Chan A, Küchenhoff L, Rapti K, Ferreira AM, Kornienko J, Li S, Radke MH, Krämer C, Clauder-Münster S, Perlas E, Backs J, Gotthardt M, Dieterich C, van den Hoogenhof MMG, Grimm D, Steinmetz LM. Striated muscle-specific base editing enables correction of mutations causing dilated cardiomyopathy. Nat Commun 2023; 14:3714. [PMID: 37349314 PMCID: PMC10287752 DOI: 10.1038/s41467-023-39352-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/08/2023] [Indexed: 06/24/2023] Open
Abstract
Dilated cardiomyopathy is the second most common cause for heart failure with no cure except a high-risk heart transplantation. Approximately 30% of patients harbor heritable mutations which are amenable to CRISPR-based gene therapy. However, challenges related to delivery of the editing complex and off-target concerns hamper the broad applicability of CRISPR agents in the heart. We employ a combination of the viral vector AAVMYO with superior targeting specificity of heart muscle tissue and CRISPR base editors to repair patient mutations in the cardiac splice factor Rbm20, which cause aggressive dilated cardiomyopathy. Using optimized conditions, we repair >70% of cardiomyocytes in two Rbm20 knock-in mouse models that we have generated to serve as an in vivo platform of our editing strategy. Treatment of juvenile mice restores the localization defect of RBM20 in 75% of cells and splicing of RBM20 targets including TTN. Three months after injection, cardiac dilation and ejection fraction reach wild-type levels. Single-nuclei RNA sequencing uncovers restoration of the transcriptional profile across all major cardiac cell types and whole-genome sequencing reveals no evidence for aberrant off-target editing. Our study highlights the potential of base editors combined with AAVMYO to achieve gene repair for treatment of hereditary cardiac diseases.
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Affiliation(s)
- Markus Grosch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Laura Schraft
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Adrian Chan
- Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Leonie Küchenhoff
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Kleopatra Rapti
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, BioQuant, University of Heidelberg, Heidelberg, Germany
| | - Anne-Maud Ferreira
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Kornienko
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Shengdi Li
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Michael H Radke
- Translational Cardiology and Functional Genomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Chiara Krämer
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, BioQuant, University of Heidelberg, Heidelberg, Germany
| | | | - Emerald Perlas
- Epigenetics and Neurobiology Unit, EMBL Rome, Monterotondo, Italy
| | - Johannes Backs
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Institute of Experimental Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Gotthardt
- Translational Cardiology and Functional Genomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Dieterich
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Maarten M G van den Hoogenhof
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Institute of Experimental Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Dirk Grimm
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, BioQuant, University of Heidelberg, Heidelberg, Germany
- German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany.
- Stanford Genome Technology Center, Palo Alto, CA, USA.
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10
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Mbani B, Greinert J. Analysis-ready optical underwater images of Manganese-nodule covered seafloor of the Clarion-Clipperton Zone. Sci Data 2023; 10:316. [PMID: 37231017 DOI: 10.1038/s41597-023-02245-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
We provide a sequence of analysis-ready optical underwater images from the Clarion-Clipperton Zone (CCZ) of the Pacific Ocean. The images were originally recorded using a towed camera sledge that photographed a seabed covered with polymetallic manganese-nodules, at an average water depth of 4,250 meters. The original degradation in visual quality and inconsistent scale among individual raw images due to different altitude implies that they are not scientifically comparable in their original form. Here, we present analysis-ready images that have already been pre-processed to account for this degradation. We also provide accompanying metadata for each image, which includes their geographic coordinates, depth of the seafloor, absolute scale (cm/pixel), and seafloor habitat class obtained from a previous study. The provided images are thus directly usable by the marine scientific community e.g., to train machine learning models for seafloor substrate classification and megafauna detection.
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Affiliation(s)
- Benson Mbani
- DeepSea Monitoring Group, GEOMAR Helmholtz Center for Ocean Research Kiel, Wischhofstraße 1-3, 24148, Kiel, Germany.
| | - Jens Greinert
- DeepSea Monitoring Group, GEOMAR Helmholtz Center for Ocean Research Kiel, Wischhofstraße 1-3, 24148, Kiel, Germany
- Institute of Geosciences, Kiel University, Ludewig-Meyn-Str. 10-12, 24118, Kiel, Germany
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11
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Pelz S, Chinichian N, Neyrand C, Blechinger P. Electricity supply quality and use among rural and peri-urban households and small firms in Nigeria. Sci Data 2023; 10:273. [PMID: 37173320 PMCID: PMC10181988 DOI: 10.1038/s41597-023-02185-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
We present a household and enterprise energy survey dataset collected within the framework of the PeopleSuN project in Nigeria in 2021. Across three Nigerian geopolitical zones, a total of 3,599 households and 1,122 small and medium-sized enterprises were surveyed. The sample is designed to be representative of rural and peri-urban grid-electrified regions of each zone. Our surveys collect data on demographic and socioeconomic characteristics, energy access and supply quality, electrical appliance ownership and usage time, cooking solutions, energy related capabilities, and supply preferences. We encourage academic use of the data presented and suggest three avenues of further research: (1) modelling appliance ownership likelihoods, electricity consumption levels and energy service needs in un-electrified regions; (2) identifying supply-side and demand-side solutions to address high usage of diesel generators; (3) exploring broader issues of multi-dimensional energy access, access to decent living standards and climate vulnerability.
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Grants
- FKZ 03SF0606A Bundesministerium für Bildung, Wissenschaft, Forschung und Technologie (Federal Ministry for Education, Science, Research and Technology)
- FKZ 03SF0606A Bundesministerium für Bildung, Wissenschaft, Forschung und Technologie (Federal Ministry for Education, Science, Research and Technology)
- FKZ 03SF0606A Bundesministerium für Bildung, Wissenschaft, Forschung und Technologie (Federal Ministry for Education, Science, Research and Technology)
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Affiliation(s)
- Setu Pelz
- International Institute for Applied Systems Analysis, Laxenburg, Austria.
- Off-Grid Systems, Reiner Lemoine Institut (RLI), Berlin, Germany.
| | - Narges Chinichian
- Off-Grid Systems, Reiner Lemoine Institut (RLI), Berlin, Germany
- Institute for Theoretical Physics, Technical University of Berlin, Berlin, Germany
| | - Clara Neyrand
- Off-Grid Systems, Reiner Lemoine Institut (RLI), Berlin, Germany
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12
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Wiedmann L, De Angelis Rigotti F, Vaquero-Siguero N, Donato E, Espinet E, Moll I, Alsina-Sanchis E, Bohnenberger H, Fernandez-Florido E, Mülfarth R, Vacca M, Gerwing J, Conradi LC, Ströbel P, Trumpp A, Mogler C, Fischer A, Rodriguez-Vita J. HAPLN1 potentiates peritoneal metastasis in pancreatic cancer. Nat Commun 2023; 14:2353. [PMID: 37095087 PMCID: PMC10126109 DOI: 10.1038/s41467-023-38064-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) frequently metastasizes into the peritoneum, which contributes to poor prognosis. Metastatic spreading is promoted by cancer cell plasticity, yet its regulation by the microenvironment is incompletely understood. Here, we show that the presence of hyaluronan and proteoglycan link protein-1 (HAPLN1) in the extracellular matrix enhances tumor cell plasticity and PDAC metastasis. Bioinformatic analysis showed that HAPLN1 expression is enriched in the basal PDAC subtype and associated with worse overall patient survival. In a mouse model for peritoneal carcinomatosis, HAPLN1-induced immunomodulation favors a more permissive microenvironment, which accelerates the peritoneal spread of tumor cells. Mechanistically, HAPLN1, via upregulation of tumor necrosis factor receptor 2 (TNFR2), promotes TNF-mediated upregulation of Hyaluronan (HA) production, facilitating EMT, stemness, invasion and immunomodulation. Extracellular HAPLN1 modifies cancer cells and fibroblasts, rendering them more immunomodulatory. As such, we identify HAPLN1 as a prognostic marker and as a driver for peritoneal metastasis in PDAC.
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Affiliation(s)
- Lena Wiedmann
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, 69120, Heidelberg, Germany
| | - Francesca De Angelis Rigotti
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Tumor-Stroma Communication Laboratory, Centro de Investigación Príncipe Felipe, 46012, Valencia, Spain
| | - Nuria Vaquero-Siguero
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Elisa Donato
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- HI-STEM - Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, 69120, Heidelberg, Germany
| | - Elisa Espinet
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- HI-STEM - Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, 69120, Heidelberg, Germany
- Department of Pathology and Experimental Therapy, School of Medicine, University of Barcelona (UB), L'Hospitalet de Llobregat, Barcelona, Spain
- Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, 08908, Spain
| | - Iris Moll
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Elisenda Alsina-Sanchis
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Institute for Clinical Chemistry, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Hanibal Bohnenberger
- Institute of Pathology, University Medical Center Göttingen, Georg-August-University, 37075, Göttingen, Germany
| | - Elena Fernandez-Florido
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Ronja Mülfarth
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, 69120, Heidelberg, Germany
| | - Margherita Vacca
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Jennifer Gerwing
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Lena-Christin Conradi
- Clinic of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Robert-Koch-Straβe 40, 37075, Göttingen, Germany
| | - Philipp Ströbel
- Institute of Pathology, University Medical Center Göttingen, Georg-August-University, 37075, Göttingen, Germany
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- HI-STEM - Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH, 69120, Heidelberg, Germany
| | - Carolin Mogler
- Institute of Pathology, Technical University of Munich, 81675, Munich, Germany
| | - Andreas Fischer
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
- Institute for Clinical Chemistry, University Medical Center Göttingen, 37075, Göttingen, Germany.
- German Center for Cardiovascular Research (DZHK), partner site Göttingen, Germany.
| | - Juan Rodriguez-Vita
- Division Vascular Signaling and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
- Tumor-Stroma Communication Laboratory, Centro de Investigación Príncipe Felipe, 46012, Valencia, Spain.
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13
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Kamrad S, Correia-Melo C, Szyrwiel L, Aulakh SK, Bähler J, Demichev V, Mülleder M, Ralser M. Metabolic heterogeneity and cross-feeding within isogenic yeast populations captured by DILAC. Nat Microbiol 2023; 8:441-454. [PMID: 36797484 PMCID: PMC9981460 DOI: 10.1038/s41564-022-01304-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/13/2022] [Indexed: 02/18/2023]
Abstract
Genetically identical cells are known to differ in many physiological parameters such as growth rate and drug tolerance. Metabolic specialization is believed to be a cause of such phenotypic heterogeneity, but detection of metabolically divergent subpopulations remains technically challenging. We developed a proteomics-based technology, termed differential isotope labelling by amino acids (DILAC), that can detect producer and consumer subpopulations of a particular amino acid within an isogenic cell population by monitoring peptides with multiple occurrences of the amino acid. We reveal that young, morphologically undifferentiated yeast colonies contain subpopulations of lysine producers and consumers that emerge due to nutrient gradients. Deconvoluting their proteomes using DILAC, we find evidence for in situ cross-feeding where rapidly growing cells ferment and provide the more slowly growing, respiring cells with ethanol. Finally, by combining DILAC with fluorescence-activated cell sorting, we show that the metabolic subpopulations diverge phenotypically, as exemplified by a different tolerance to the antifungal drug amphotericin B. Overall, DILAC captures previously unnoticed metabolic heterogeneity and provides experimental evidence for the role of metabolic specialization and cross-feeding interactions as a source of phenotypic heterogeneity in isogenic cell populations.
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Affiliation(s)
- Stephan Kamrad
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Clara Correia-Melo
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Lukasz Szyrwiel
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Simran Kaur Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Jürg Bähler
- Institute of Healthy Ageing and Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Vadim Demichev
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Michael Mülleder
- Core Facility-High-Throughput Mass Spectrometry, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Ralser
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany.
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
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14
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Li Z, Kuppe C, Ziegler S, Cheng M, Kabgani N, Menzel S, Zenke M, Kramann R, Costa IG. Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen. Nat Commun 2021; 12:6386. [PMID: 34737275 PMCID: PMC8568974 DOI: 10.1038/s41467-021-26530-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/04/2021] [Indexed: 12/18/2022] Open
Abstract
A major drawback of single-cell ATAC-seq (scATAC-seq) is its sparsity, i.e., open chromatin regions with no reads due to loss of DNA material during the scATAC-seq protocol. Here, we propose scOpen, a computational method based on regularized non-negative matrix factorization for imputing and quantifying the open chromatin status of regulatory regions from sparse scATAC-seq experiments. We show that scOpen improves crucial downstream analysis steps of scATAC-seq data as clustering, visualization, cis-regulatory DNA interactions, and delineation of regulatory features. We demonstrate the power of scOpen to dissect regulatory changes in the development of fibrosis in the kidney. This identifies a role of Runx1 and target genes by promoting fibroblast to myofibroblast differentiation driving kidney fibrosis.
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Affiliation(s)
- Zhijian Li
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, 52074, Aachen, Germany
| | - Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University Medical School, 52074, Aachen, Germany
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, 52074, Aachen, Germany
| | - Susanne Ziegler
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University Medical School, 52074, Aachen, Germany
| | - Mingbo Cheng
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, 52074, Aachen, Germany
| | - Nazanin Kabgani
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University Medical School, 52074, Aachen, Germany
| | - Sylvia Menzel
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University Medical School, 52074, Aachen, Germany
| | - Martin Zenke
- Department of Cell Biology, Institute of Biomedical Engineering, RWTH Aachen University Medical School, 52074, Aachen, Germany
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University Medical School, 52074, Aachen, Germany.
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, 52074, Aachen, Germany.
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, 3015GD, Rotterdam, The Netherlands.
| | - Ivan G Costa
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, 52074, Aachen, Germany.
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15
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Xu Y, Rothe R, Voigt D, Hauser S, Cui M, Miyagawa T, Patino Gaillez M, Kurth T, Bornhäuser M, Pietzsch J, Zhang Y. Convergent synthesis of diversified reversible network leads to liquid metal-containing conductive hydrogel adhesives. Nat Commun 2021; 12:2407. [PMID: 33893308 PMCID: PMC8065207 DOI: 10.1038/s41467-021-22675-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 03/12/2021] [Indexed: 02/02/2023] Open
Abstract
Many features of extracellular matrices, e.g., self-healing, adhesiveness, viscoelasticity, and conductivity, are associated with the intricate networks composed of many different covalent and non-covalent chemical bonds. Whereas a reductionism approach would have the limitation to fully recapitulate various biological properties with simple chemical structures, mimicking such sophisticated networks by incorporating many different functional groups in a macromolecular system is synthetically challenging. Herein, we propose a strategy of convergent synthesis of complex polymer networks to produce biomimetic electroconductive liquid metal hydrogels. Four precursors could be individually synthesized in one to two reaction steps and characterized, then assembled to form hydrogel adhesives. The convergent synthesis allows us to combine materials of different natures to generate matrices with high adhesive strength, enhanced electroconductivity, good cytocompatibility in vitro and high biocompatibility in vivo. The reversible networks exhibit self-healing and shear-thinning properties, thus allowing for 3D printing and minimally invasive injection for in vivo experiments.
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Affiliation(s)
- Yong Xu
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, Dresden, Germany
| | - Rebecca Rothe
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Institute of Radiopharmaceutical Cancer Research Department of Radiopharmaceutical and Chemical Biology, Dresden, Germany
- Technische Universität Dresden, School of Science, Faculty of Chemistry and Food Chemistry, Dresden, Germany
| | - Dagmar Voigt
- Technische Universität Dresden, Institute for Botany, Faculty of Biology, Dresden, Germany
| | - Sandra Hauser
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Institute of Radiopharmaceutical Cancer Research Department of Radiopharmaceutical and Chemical Biology, Dresden, Germany
| | - Meiying Cui
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, Dresden, Germany
| | - Takuya Miyagawa
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, Dresden, Germany
| | - Michelle Patino Gaillez
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, Dresden, Germany
| | - Thomas Kurth
- Technische Universität Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Technology Platform, EM Facilty, Dresden, Germany
| | - Martin Bornhäuser
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
- University Hospital Carl Gustav Carus der Technischen Universität Dresden, Medizinische Klinik und Poliklinik I, Dresden, Germany
| | - Jens Pietzsch
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Institute of Radiopharmaceutical Cancer Research Department of Radiopharmaceutical and Chemical Biology, Dresden, Germany.
- Technische Universität Dresden, School of Science, Faculty of Chemistry and Food Chemistry, Dresden, Germany.
| | - Yixin Zhang
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, Dresden, Germany.
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany.
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16
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Dittmann J, Haydn T, Metzger P, Ward GA, Boerries M, Vogler M, Fulda S. Next-generation hypomethylating agent SGI-110 primes acute myeloid leukemia cells to IAP antagonist by activating extrinsic and intrinsic apoptosis pathways. Cell Death Differ 2020; 27:1878-1895. [PMID: 31831875 PMCID: PMC7244748 DOI: 10.1038/s41418-019-0465-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 12/16/2022] Open
Abstract
Therapeutic efficacy of first-generation hypomethylating agents (HMAs) is limited in elderly acute myeloid leukemia (AML) patients. Therefore, combination strategies with targeted therapies are urgently needed. Here, we discover that priming with SGI-110 (guadecitabine), a next-generation HMA, sensitizes AML cells to ASTX660, a novel antagonist of cellular inhibitor of apoptosis protein 1 and 2 (cIAP1/2) and X-linked IAP (XIAP). Importantly, SGI-110 and ASTX660 synergistically induced cell death in a panel of AML cell lines as well as in primary AML samples while largely sparing normal CD34+ human progenitor cells, underlining the translational relevance of this combination. Unbiased transcriptome analysis revealed that SGI-110 alone or in combination with ASTX660 upregulated the expression of key regulators of both extrinsic and intrinsic apoptosis signaling pathways such as TNFRSF10B (DR5), FAS, and BAX. Individual knockdown of the death receptors TNFR1, DR5, and FAS significantly reduced SGI-110/ASTX660-mediated cell death, whereas blocking antibodies for tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) or FAS ligand (FASLG) failed to provide protection. Also, TNFα-blocking antibody Enbrel had little protective effect on SGI-110/ASTX660-induced cell death. Further, SGI-110 and ASTX660 acted in concert to promote cleavage of caspase-8 and BID, thereby providing a link between extrinsic and intrinsic apoptotic pathways. Consistently, sequential treatment with SGI-110 and ASTX660-triggered loss of mitochondrial membrane potential (MMP) and BAX activation which contributes to cell death, as BAX silencing significantly protected from SGI-110/ASTX660-mediated apoptosis. Together, these events culminated in the activation of caspases-3/-7, nuclear fragmentation, and cell death. In conclusion, SGI-110 and ASTX660 cooperatively induced apoptosis in AML cells by engaging extrinsic and intrinsic apoptosis pathways, highlighting the therapeutic potential of this combination for AML.
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Affiliation(s)
- Jessica Dittmann
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Tinka Haydn
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Patrick Metzger
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center, Faculty of Medicine, University Freiburg, Freiburg im Breisgau, Germany
- Institute of Molecular Medicine and Cell Research (IMMZ), Albert Ludwigs-University Freiburg, Freiburg im Breisgau, Germany
- Faculty of Biology, University Freiburg, Freiburg im Breisgau, Germany
| | | | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center, Faculty of Medicine, University Freiburg, Freiburg im Breisgau, Germany
- Institute of Molecular Medicine and Cell Research (IMMZ), Albert Ludwigs-University Freiburg, Freiburg im Breisgau, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg im Breisgau, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Meike Vogler
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Simone Fulda
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Frankfurt am Main, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Partner Site Frankfurt, Frankfurt am Main, Germany.
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17
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Brachem C, Winkler A, Tebrügge S, Weimar C, Erbel R, Jöckel KH, Stang A, Dragano N, Moebus S, Kowall B, Jokisch M. Associations between self-reported sleep characteristics and incident mild cognitive impairment: The Heinz Nixdorf Recall Cohort Study. Sci Rep 2020; 10:6542. [PMID: 32300149 PMCID: PMC7162850 DOI: 10.1038/s41598-020-63511-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/27/2020] [Indexed: 01/13/2023] Open
Abstract
Associations of sleep characteristics with mild cognitive impairment (MCI) have been examined in cross-sectional, but rarely in longitudinal studies. Incident MCI and sleep characteristics were assessed in 1,890 participants of the first and second follow-up of the Heinz Nixdorf Recall study, a population-based cohort study in Germany (age at first follow-up 50-80 years, mean follow-up 5.2 years). MCI was assessed with extensive cognitive tests. Sleep questionnaires including PSQI (Pittsburgh Sleep Quality Index) were used to assess sleep quality, sleep disturbances, time asleep, and time in bed. Relative risks (RR) of developing MCI when exposed to sleep characteristics were assessed in regression models adjusted for sociodemographic and cardiovascular risk factors. Poor sleep quality (PSQI > 5) (RR = 1.43, 95% CI: 1.12-1.82, fully adjusted, reference: PSQI ≤ 5) and difficulties initiating sleep (almost nightly versus never) (RR = 1.40, 0.94-2.08) were associated with incident MCI. For time in bed, the risk of MCI was increased for ≤ 5 hours (RR = 2.86, 1.24─6.60, reference:7 to <8 hours). In this longitudinal study with older participants, MCI risk was increased in persons with poor sleep quality, difficulties initiating sleep, and short time in bed.
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Affiliation(s)
- Christian Brachem
- Nutritional Epidemiology, Department of Nutrition and Food Science, Rheinische Friedrich-Wilhelms-University Bonn, Bonn, Germany
| | - Angela Winkler
- Department of Neurology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Sarah Tebrügge
- Department of Neurology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Christian Weimar
- Department of Neurology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Raimund Erbel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Andreas Stang
- Center of Clinical Epidemiology, Institute for Medical Informatics, Biometry and Epidemiology, Medical Faculty, University Duisburg-Essen, Essen, Germany
- School of Public Health, Department of Epidemiology Boston University, 715 Albany Street, Talbot Building, Boston, MA, 02118, USA
| | - Nico Dragano
- Institute of Medical Sociology, Medical Faculty, University of Duesseldorf, Duesseldorf, Germany
| | - Susanne Moebus
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Bernd Kowall
- Center of Clinical Epidemiology, Institute for Medical Informatics, Biometry and Epidemiology, Medical Faculty, University Duisburg-Essen, Essen, Germany.
| | - Martha Jokisch
- Department of Neurology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
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18
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Höfling L, Oesterle J, Berens P, Zeck G. Probing and predicting ganglion cell responses to smooth electrical stimulation in healthy and blind mouse retina. Sci Rep 2020; 10:5248. [PMID: 32251331 PMCID: PMC7090015 DOI: 10.1038/s41598-020-61899-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 02/19/2020] [Indexed: 11/14/2022] Open
Abstract
Retinal implants are used to replace lost photoreceptors in blind patients suffering from retinopathies such as retinitis pigmentosa. Patients wearing implants regain some rudimentary visual function. However, it is severely limited compared to normal vision because non-physiological stimulation strategies fail to selectively activate different retinal pathways at sufficient spatial and temporal resolution. The development of improved stimulation strategies is rendered difficult by the large space of potential stimuli. Here we systematically explore a subspace of potential stimuli by electrically stimulating healthy and blind mouse retina in epiretinal configuration using smooth Gaussian white noise delivered by a high-density CMOS-based microelectrode array. We identify linear filters of retinal ganglion cells (RGCs) by fitting a linear-nonlinear-Poisson (LNP) model. Our stimulus evokes spatially and temporally confined spiking responses in RGC which are accurately predicted by the LNP model. Furthermore, we find diverse shapes of linear filters in the linear stage of the model, suggesting diverse preferred electrical stimuli of RGCs. The linear filter base identified by our approach could provide a starting point of a model-guided search for improved stimuli for retinal prosthetics.
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Affiliation(s)
- Larissa Höfling
- Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
- Graduate Training Centre of Neuroscience, University of Tübingen, Tübingen, Germany
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
- Centre for Integrative Neuroscience, University of Tübingen, Tübingen, Germany
| | - Jonathan Oesterle
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Philipp Berens
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
- Bernstein Center for Computational Neuroscience, University of Tübingen, Tübingen, Germany
- Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Günther Zeck
- Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany.
- Bernstein Center for Computational Neuroscience, University of Tübingen, Tübingen, Germany.
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19
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Zareian B, Maboudi K, Daliri MR, Abrishami Moghaddam H, Treue S, Esghaei M. Attention strengthens across-trial pre-stimulus phase coherence in visual cortex, enhancing stimulus processing. Sci Rep 2020; 10:4837. [PMID: 32179777 PMCID: PMC7076023 DOI: 10.1038/s41598-020-61359-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 02/21/2020] [Indexed: 12/19/2022] Open
Abstract
Attention selectively routes the most behaviorally relevant information from the stream of sensory inputs through the hierarchy of cortical areas. Previous studies have shown that visual attention depends on the phase of oscillatory brain activities. These studies mainly focused on the stimulus presentation period, rather than the pre-stimulus period. Here, we hypothesize that selective attention controls the phase of oscillatory neural activities to efficiently process relevant information. We document an attentional modulation of pre-stimulus inter-trial phase coherence (a measure of deviation between instantaneous phases of trials) of low frequency local field potentials (LFP) in visual area MT of macaque monkeys. Our data reveal that phase coherence increases following a spatial cue deploying attention towards the receptive field of the recorded neural population. We further show that the attentional enhancement of phase coherence is positively correlated with the modulation of the stimulus-induced firing rate, and importantly, a higher phase coherence is associated with a faster behavioral response. These results suggest a functional utilization of intrinsic neural oscillatory activities for an enhanced processing of upcoming stimuli.
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Affiliation(s)
- Behzad Zareian
- Department of Psychology, University of California Riverside, Riverside, USA
| | - Kourosh Maboudi
- Department of Psychology, University of Wisconsin-Milwaukee, Milwaukee, USA
- School of Cognitive Sciences, Institute for Research in Fundamental Sciences, Tehran, Iran
| | - Mohammad Reza Daliri
- School of Cognitive Sciences, Institute for Research in Fundamental Sciences, Tehran, Iran
- Neuroscience and Neuroengineering Research Laboratory, Biomedical Engineering Department, School of Electrical Engineering, Iran University of Science and Technology, 16846-13114, Tehran, Iran
| | - Hamid Abrishami Moghaddam
- Faculty of Electrical and Computer Engineering, Khajeh Nasir Toosi University of Technology, Tehran, Iran
| | - Stefan Treue
- Cognitive Neuroscience Laboratory, German Primate Center - Leibniz Institute for Primate Research, Goettingen, Germany
- Faculty of Biology and Psychology, University of Goettingen, Goettingen, Germany
- Bernstein Center for Computational Neuroscience, Goettingen, Germany
- Leibniz-ScienceCampus Primate Cognition, Goettingen, Germany
| | - Moein Esghaei
- School of Cognitive Sciences, Institute for Research in Fundamental Sciences, Tehran, Iran.
- Cognitive Neuroscience Laboratory, German Primate Center - Leibniz Institute for Primate Research, Goettingen, Germany.
- Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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20
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Mousavi S, Escher U, Thunhorst E, Kittler S, Kehrenberg C, Bereswill S, Heimesaat MM. Vitamin C alleviates acute enterocolitis in Campylobacter jejuni infected mice. Sci Rep 2020; 10:2921. [PMID: 32076081 PMCID: PMC7031283 DOI: 10.1038/s41598-020-59890-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 02/03/2020] [Indexed: 11/12/2022] Open
Abstract
Human foodborne infections with the zoonotic pathogen Campylobacter jejuni are on the rise and constitute a significant socioeconomic burden worldwide. The health-beneficial, particularly anti-inflammatory effects of vitamin C (ascorbate) are well known. In our preclinical intervention study, we assessed potential anti-pathogenic and immunomodulatory effects of ascorbate in C. jejuni-infected secondary abiotic IL-10-/- mice developing acute campylobacteriosis similar to humans. Starting 4 days prior peroral C. jejuni-infection, mice received synthetic ascorbate via the drinking water until the end of the experiment. At day 6 post-infection, ascorbate-treated mice harbored slightly lower colonic pathogen loads and suffered from less severe C. jejuni-induced enterocolitis as compared to placebo control animals. Ascorbate treatment did not only alleviate macroscopic sequelae of infection, but also dampened apoptotic and inflammatory immune cell responses in the intestines that were accompanied by less pronounced pro-inflammatory cytokine secretion. Remarkably, the anti-inflammatory effects of ascorbate pretreatment in C. jejuni-infected mice were not restricted to the intestinal tract but could also be observed in extra-intestinal compartments including liver, kidneys and lungs. In conclusion, due to the potent anti-inflammatory effects observed in the clinical murine C. jejuni-infection model, ascorbate constitutes a promising novel option for prophylaxis and treatment of acute campylobacteriosis.
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Affiliation(s)
- Soraya Mousavi
- Institute for Microbiology, Infectious Diseases and Immunology, Gastrointestinal Microbiology Research Group, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ulrike Escher
- Institute for Microbiology, Infectious Diseases and Immunology, Gastrointestinal Microbiology Research Group, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Elisa Thunhorst
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Sophie Kittler
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Corinna Kehrenberg
- Institute for Veterinary Food Science, Justus-Liebig-University, Giessen, Germany
| | - Stefan Bereswill
- Institute for Microbiology, Infectious Diseases and Immunology, Gastrointestinal Microbiology Research Group, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Markus M Heimesaat
- Institute for Microbiology, Infectious Diseases and Immunology, Gastrointestinal Microbiology Research Group, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
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21
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Heimesaat MM, Mrazek K, Bereswill S. Murine fecal microbiota transplantation lowers gastrointestinal pathogen loads and dampens pro-inflammatory immune responses in Campylobacter jejuni infected secondary abiotic mice. Sci Rep 2019; 9:19797. [PMID: 31875037 PMCID: PMC6930309 DOI: 10.1038/s41598-019-56442-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 12/07/2019] [Indexed: 12/29/2022] Open
Abstract
Conventional mice are protected from Campylobacter jejuni infection by the murine host-specific gut microbiota composition. We here addressed whether peroral fecal microbiota transplantation (FMT) might be an antibiotics-independent option to lower even high gastrointestinal C. jejuni loads in the infected vertebrate host. To address this, secondary abiotic mice were generated by broad-spectrum antibiotic treatment and perorally infected with C. jejuni by gavage. One week later, mice were stably colonized with more than 109 C. jejuni and subjected to peroral FMT from murine donors on three consecutive days. Two weeks post-intervention, gastrointestinal C. jejuni loads were up to 7.5 orders of magnitude lower following murine FMT versus mock challenge. Remarkably, FMT reversed C. jejuni induced colonic epithelial apoptosis, but enhanced proliferative and regenerative responses in the colon thereby counteracting pathogenic cell damage. Furthermore, FMT dampened both, innate and adaptive immune cell responses in the large intestines upon C. jejuni infection that were accompanied by less C. jejuni-induced colonic nitric oxide secretion. Our study provides strong evidence that novel probiotic formulations developed as alternative option to FMT in severe intestinal inflammatory morbidities including Clostridoides difficile infection might be effective to treat campylobacteriosis and lower pathogen loads in colonized vertebrates including farm animals.
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Affiliation(s)
- Markus M Heimesaat
- Institute of Microbiology, Infectious Diseases and Immunology, Gastrointestinal Microbiology Research Group, Charité - University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
| | - Katharina Mrazek
- Institute of Microbiology, Infectious Diseases and Immunology, Gastrointestinal Microbiology Research Group, Charité - University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Stefan Bereswill
- Institute of Microbiology, Infectious Diseases and Immunology, Gastrointestinal Microbiology Research Group, Charité - University Medicine Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
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22
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Tenedini FM, Sáez González M, Hu C, Pedersen LH, Petruzzi MM, Spitzweck B, Wang D, Richter M, Petersen M, Szpotowicz E, Schweizer M, Sigrist SJ, Calderon de Anda F, Soba P. Maintenance of cell type-specific connectivity and circuit function requires Tao kinase. Nat Commun 2019; 10:3506. [PMID: 31383864 PMCID: PMC6683158 DOI: 10.1038/s41467-019-11408-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 07/13/2019] [Indexed: 01/05/2023] Open
Abstract
Sensory circuits are typically established during early development, yet how circuit specificity and function are maintained during organismal growth has not been elucidated. To gain insight we quantitatively investigated synaptic growth and connectivity in the Drosophila nociceptive network during larval development. We show that connectivity between primary nociceptors and their downstream neurons scales with animal size. We further identified the conserved Ste20-like kinase Tao as a negative regulator of synaptic growth required for maintenance of circuit specificity and connectivity. Loss of Tao kinase resulted in exuberant postsynaptic specializations and aberrant connectivity during larval growth. Using functional imaging and behavioral analysis we show that loss of Tao-induced ectopic synapses with inappropriate partner neurons are functional and alter behavioral responses in a connection-specific manner. Our data show that fine-tuning of synaptic growth by Tao kinase is required for maintaining specificity and behavioral output of the neuronal network during animal growth.
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Affiliation(s)
- Federico Marcello Tenedini
- Neuronal Patterning and Connectivity laboratory, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Maria Sáez González
- Neuronal Patterning and Connectivity laboratory, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Chun Hu
- Neuronal Patterning and Connectivity laboratory, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Lisa Hedegaard Pedersen
- Neuronal Patterning and Connectivity laboratory, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Mabel Matamala Petruzzi
- Neuronal Patterning and Connectivity laboratory, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Bettina Spitzweck
- Neuronal Patterning and Connectivity laboratory, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Denan Wang
- Neuronal Patterning and Connectivity laboratory, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Melanie Richter
- Neuronal Development laboratory, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Meike Petersen
- Neuronal Patterning and Connectivity laboratory, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Emanuela Szpotowicz
- Electron microscopy unit, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Michaela Schweizer
- Electron microscopy unit, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Stephan J Sigrist
- Institute of Biology, Free University Berlin, Takustr. 6, 14195, Berlin, Germany
| | - Froylan Calderon de Anda
- Neuronal Development laboratory, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany
| | - Peter Soba
- Neuronal Patterning and Connectivity laboratory, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251, Hamburg, Germany.
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