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Privitera M, von Ziegler LM, Floriou-Servou A, Duss SN, Zhang R, Waag R, Leimbacher S, Sturman O, Roessler FK, Heylen A, Vermeiren Y, Van Dam D, De Deyn PP, Germain PL, Bohacek J. Noradrenaline release from the locus coeruleus shapes stress-induced hippocampal gene expression. eLife 2024; 12:RP88559. [PMID: 38477670 DOI: 10.7554/elife.88559] [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] [Indexed: 03/14/2024] Open
Abstract
Exposure to an acute stressor triggers a complex cascade of neurochemical events in the brain. However, deciphering their individual impact on stress-induced molecular changes remains a major challenge. Here, we combine RNA sequencing with selective pharmacological, chemogenetic, and optogenetic manipulations to isolate the contribution of the locus coeruleus-noradrenaline (LC-NA) system to the acute stress response in mice. We reveal that NA release during stress exposure regulates a large and reproducible set of genes in the dorsal and ventral hippocampus via β-adrenergic receptors. For a smaller subset of these genes, we show that NA release triggered by LC stimulation is sufficient to mimic the stress-induced transcriptional response. We observe these effects in both sexes, and independent of the pattern and frequency of LC activation. Using a retrograde optogenetic approach, we demonstrate that hippocampus-projecting LC neurons directly regulate hippocampal gene expression. Overall, a highly selective set of astrocyte-enriched genes emerges as key targets of LC-NA activation, most prominently several subunits of protein phosphatase 1 (Ppp1r3c, Ppp1r3d, Ppp1r3g) and type II iodothyronine deiodinase (Dio2). These results highlight the importance of astrocytic energy metabolism and thyroid hormone signaling in LC-mediated hippocampal function and offer new molecular targets for understanding how NA impacts brain function in health and disease.
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Affiliation(s)
- Mattia Privitera
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland, Zurich, Switzerland
| | - Lukas M von Ziegler
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland, Zurich, Switzerland
| | - Amalia Floriou-Servou
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland, Zurich, Switzerland
| | - Sian N Duss
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland, Zurich, Switzerland
| | - Runzhong Zhang
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Rebecca Waag
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland, Zurich, Switzerland
| | - Sebastian Leimbacher
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Oliver Sturman
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland, Zurich, Switzerland
| | - Fabienne K Roessler
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Annelies Heylen
- Laboratory of Neurochemistry and Behavior, Experimental Neurobiology Unit, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Yannick Vermeiren
- Laboratory of Neurochemistry and Behavior, Experimental Neurobiology Unit, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Division of Human Nutrition and Health, Chair Group of Nutritional Biology, Wageningen University & Research (WUR), Wageningen, Netherlands
| | - Debby Van Dam
- Laboratory of Neurochemistry and Behavior, Experimental Neurobiology Unit, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Alzheimer Center, University of Groningen and University Medical Center Groningen (UMCG), Groningen, Netherlands
| | - Peter P De Deyn
- Laboratory of Neurochemistry and Behavior, Experimental Neurobiology Unit, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Alzheimer Center, University of Groningen and University Medical Center Groningen (UMCG), Groningen, Netherlands
- Department of Neurology, Memory Clinic of Hospital Network Antwerp (ZNA) Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Pierre-Luc Germain
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland, Zurich, Switzerland
- Computational Neurogenomics, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
- Laboratory of Statistical Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Johannes Bohacek
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland, Zurich, Switzerland
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Gerbaldo F, Sonder E, Fischer V, Frei S, Wang J, Gapp K, Robinson MD, Germain PL. On the identification of differentially-active transcription factors from ATAC-seq data. bioRxiv 2024:2024.03.06.583825. [PMID: 38496482 PMCID: PMC10942475 DOI: 10.1101/2024.03.06.583825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
ATAC-seq has emerged as a rich epigenome profiling technique, and is commonly used to identify Transcription Factors (TFs) underlying given phenomena. A number of methods can be used to identify differentially-active TFs through the accessibility of their DNA-binding motif, however little is known on the best approaches for doing so. Here we benchmark several such methods using a combination of curated datasets with various forms of short-term perturbations on known TFs, as well as semi-simulations. We include both methods specifically designed for this type of data as well as some that can be repurposed for it. We also investigate variations to these methods, and identify three particularly promising approaches (chromVAR-limma with critical adjustments, monaLisa and a combination of GC smooth quantile normalization and multivariate modeling). We further investigate the specific use of nucleosome-free fragments, the combination of top methods, and the impact of technical variation. Finally, we illustrate the use of the top methods on a novel dataset to characterize the impact on DNA accessibility of TRAnscription Factor TArgeting Chimeras (TRAFTAC), which can deplete TFs - in our case NFkB - at the protein level.
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Affiliation(s)
- Felix Gerbaldo
- Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Systems Neuroscience, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Emanuel Sonder
- Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Systems Neuroscience, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland
| | - Vincent Fischer
- Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Selina Frei
- Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Jiayi Wang
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Katharina Gapp
- Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland
| | - Pierre-Luc Germain
- Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland
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3
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Gazorpak M, Hugentobler KM, Paul D, Germain PL, Kretschmer M, Ivanova I, Frei S, Mathis K, Rudolf R, Mompart Barrenechea S, Fischer V, Xue X, Ptaszek AL, Holzinger J, Privitera M, Hierlemann A, Meijer OC, Konrat R, Carreira EM, Bohacek J, Gapp K. Harnessing PROTAC technology to combat stress hormone receptor activation. Nat Commun 2023; 14:8177. [PMID: 38071198 PMCID: PMC10710461 DOI: 10.1038/s41467-023-44031-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Counteracting the overactivation of glucocorticoid receptors (GR) is an important therapeutic goal in stress-related psychiatry and beyond. The only clinically approved GR antagonist lacks selectivity and induces unwanted side effects. To complement existing tools of small-molecule-based inhibitors, we present a highly potent, catalytically-driven GR degrader, KH-103, based on proteolysis-targeting chimera technology. This selective degrader enables immediate and reversible GR depletion that is independent of genetic manipulation and circumvents transcriptional adaptations to inhibition. KH-103 achieves passive inhibition, preventing agonistic induction of gene expression, and significantly averts the GR's genomic effects compared to two currently available inhibitors. Application in primary-neuron cultures revealed the dependency of a glucocorticoid-induced increase in spontaneous calcium activity on GR. Finally, we present a proof of concept for application in vivo. KH-103 opens opportunities for a more lucid interpretation of GR functions with translational potential.
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Affiliation(s)
- Mahshid Gazorpak
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland
- Neuroscience Center Zürich, ETH Zürich and University of Zürich, 8057, Zürich, Switzerland
| | - Karina M Hugentobler
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Dominique Paul
- Lab of Statistical Bioinformatics, University of Zürich, 8057, Zürich, Switzerland
| | - Pierre-Luc Germain
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland
- Lab of Statistical Bioinformatics, University of Zürich, 8057, Zürich, Switzerland
- Computational Neurogenomics, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland
| | - Miriam Kretschmer
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland
- Neuroscience Center Zürich, ETH Zürich and University of Zürich, 8057, Zürich, Switzerland
| | - Iryna Ivanova
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland
| | - Selina Frei
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland
| | - Kei Mathis
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland
| | - Remo Rudolf
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland
| | - Sergio Mompart Barrenechea
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland
| | - Vincent Fischer
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland
- Neuroscience Center Zürich, ETH Zürich and University of Zürich, 8057, Zürich, Switzerland
| | - Xiaohan Xue
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, 4056, Basel, Switzerland
| | - Aleksandra L Ptaszek
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Max Perutz Laboratories, Department of Structural and Computational Biology, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Julian Holzinger
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Max Perutz Laboratories, Department of Structural and Computational Biology, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Mattia Privitera
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland
| | - Andreas Hierlemann
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, 4056, Basel, Switzerland
| | - Onno C Meijer
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, 2300, RA, Leiden, the Netherlands
| | - Robert Konrat
- Department of Structural and Computational Biology, University of Vienna, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Erick M Carreira
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
| | - Johannes Bohacek
- Neuroscience Center Zürich, ETH Zürich and University of Zürich, 8057, Zürich, Switzerland
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland
| | - Katharina Gapp
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Science and Technology, ETH Zürich, 8057, Zürich, Switzerland.
- Neuroscience Center Zürich, ETH Zürich and University of Zürich, 8057, Zürich, Switzerland.
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4
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Fischer V, Kretschmer M, Germain PL, Kaur J, Mompart-Barrenechea S, Pelczar P, Schürmann D, Schär P, Gapp K. Sperm chromatin accessibility's involvement in the intergenerational effects of stress hormone receptor activation. Transl Psychiatry 2023; 13:378. [PMID: 38065942 PMCID: PMC10709351 DOI: 10.1038/s41398-023-02684-z] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Dexamethasone is a stress hormone receptor agonist used widely in clinics. We and others previously showed that paternal administration of dexamethasone in mice affects the phenotype of their offspring. The substrate of intergenerational transmission of environmentally induced effects often involves changes in sperm RNA, yet other epigenetic modifications in the germline can be affected and are also plausible candidates. First, we tested the involvement of altered sperm RNAs in the transmission of dexamethasone induced phenotypes across generations. We did this by injecting sperm RNA into naïve fertilized oocytes, before performing metabolic and behavioral phenotyping of the offspring. We observed phenotypic changes in discordance with those found in offspring generated by in vitro fertilization using sperm from dexamethasone exposed males. Second, we investigated the effect of dexamethasone on chromatin accessibility using ATAC sequencing and found significant changes at specific genomic features and gene regulatory loci. Employing q-RT-PCR, we show altered expression of a gene in the tissue of offspring affected by accessibility changes in sperm. Third, we establish a correlation between specific DNA modifications and stress hormone receptor activity as a likely contributing factor influencing sperm accessibility. Finally, we independently investigated this dependency by genetically reducing thymine-DNA glycosylase levels and observing concomitant changes at the level of chromatin accessibility and stress hormone receptor activity.
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Affiliation(s)
- Vincent Fischer
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, Zürich, Switzerland
| | - Miriam Kretschmer
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, Zürich, Switzerland
| | - Pierre-Luc Germain
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Zürich, Switzerland
- Computational Neurogenomics, Institute for Neuroscience, Department of Health Science and Technology, Zürich, Switzerland
- Laboratory of Statistical Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Jasmine Kaur
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Sergio Mompart-Barrenechea
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Pawel Pelczar
- Center for Transgenic Models, University of Basel, Basel, Switzerland
| | - David Schürmann
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Primo Schär
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Katharina Gapp
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland.
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, Zürich, Switzerland.
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5
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Pradeu T, Daignan-Fornier B, Ewald A, Germain PL, Okasha S, Plutynski A, Benzekry S, Bertolaso M, Bissell M, Brown JS, Chin-Yee B, Chin-Yee I, Clevers H, Cognet L, Darrason M, Farge E, Feunteun J, Galon J, Giroux E, Green S, Gross F, Jaulin F, Knight R, Laconi E, Larmonier N, Maley C, Mantovani A, Moreau V, Nassoy P, Rondeau E, Santamaria D, Sawai CM, Seluanov A, Sepich-Poore GD, Sisirak V, Solary E, Yvonnet S, Laplane L. Reuniting philosophy and science to advance cancer research. Biol Rev Camb Philos Soc 2023; 98:1668-1686. [PMID: 37157910 PMCID: PMC10869205 DOI: 10.1111/brv.12971] [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: 09/22/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/10/2023]
Abstract
Cancers rely on multiple, heterogeneous processes at different scales, pertaining to many biomedical fields. Therefore, understanding cancer is necessarily an interdisciplinary task that requires placing specialised experimental and clinical research into a broader conceptual, theoretical, and methodological framework. Without such a framework, oncology will collect piecemeal results, with scant dialogue between the different scientific communities studying cancer. We argue that one important way forward in service of a more successful dialogue is through greater integration of applied sciences (experimental and clinical) with conceptual and theoretical approaches, informed by philosophical methods. By way of illustration, we explore six central themes: (i) the role of mutations in cancer; (ii) the clonal evolution of cancer cells; (iii) the relationship between cancer and multicellularity; (iv) the tumour microenvironment; (v) the immune system; and (vi) stem cells. In each case, we examine open questions in the scientific literature through a philosophical methodology and show the benefit of such a synergy for the scientific and medical understanding of cancer.
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Affiliation(s)
- Thomas Pradeu
- CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux 33076, France
- CNRS UMR8590, Institut d’Histoire et Philosophie des Sciences et des Technique, University Paris I Panthéon-Sorbonne, 13 rue du Four, Paris 75006, France
| | - Bertrand Daignan-Fornier
- CNRS UMR 5095 Institut de Biochimie et Génétique Cellulaires, University of Bordeaux, 1 rue Camille St Saens, Bordeaux 33077, France
| | - Andrew Ewald
- Departments of Cell Biology and Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Pierre-Luc Germain
- Department of Health Sciences and Technology, Institute for Neurosciences, Eidgenössische Technische Hochschule (ETH) Zürich, Universitätstrasse 2, Zürich 8092, Switzerland
- Department of Molecular Life Sciences, Laboratory of Statistical Bioinformatics, Universität Zürich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Samir Okasha
- Department of Philosophy, University of Bristol, Cotham House, Bristol, BS6 6JL, UK
| | - Anya Plutynski
- Department of Philosophy, Washington University in St. Louis, and Associate with Division of Biology and Biomedical Sciences, St. Louis, MO 63105, USA
| | - Sébastien Benzekry
- Computational Pharmacology and Clinical Oncology (COMPO) Unit, Inria Sophia Antipolis-Méditerranée, Cancer Research Center of Marseille, Inserm UMR1068, CNRS UMR7258, Aix Marseille University UM105, 27, bd Jean Moulin, Marseille 13005, France
| | - Marta Bertolaso
- Research Unit of Philosophy of Science and Human Development, Università Campus Bio-Medico di Roma, Via Àlvaro del Portillo, 21-00128, Rome, Italy
- Centre for Cancer Biomarkers, University of Bergen, Bergen 5007, Norway
| | - Mina Bissell
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Joel S. Brown
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Benjamin Chin-Yee
- Division of Hematology, Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 800 Commissioners Rd E, London, ON, Canada
- Rotman Institute of Philosophy, Western University, 1151 Richmond Street North, London, ON, Canada
| | - Ian Chin-Yee
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, 800 Commissioners Rd E, London, ON, Canada
| | - Hans Clevers
- Pharma, Research and Early Development (pRED) of F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, Basel 4070, Switzerland
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, Utrecht 3584 CT, The Netherlands
| | - Laurent Cognet
- CNRS UMR 5298, Laboratoire Photonique Numérique et Nanosciences, University of Bordeaux, Rue François Mitterrand, Talence 33400, France
| | - Marie Darrason
- Department of Pneumology and Thoracic Oncology, University Hospital of Lyon, 165 Chem. du Grand Revoyet, 69310 Pierre Bénite, Lyon, France
- Lyon Institute of Philosophical Research, Lyon 3 Jean Moulin University, 1 Av. des Frères Lumière, Lyon 69007, France
| | - Emmanuel Farge
- Mechanics and Genetics of Embryonic and Tumor Development group, Institut Curie, CNRS, UMR168, Inserm, Centre Origines et conditions d’apparition de la vie (OCAV) Paris Sciences Lettres Research University, Sorbonne University, Institut Curie, 11 rue Pierre et Marie Curie, Paris 75005, France
| | - Jean Feunteun
- INSERM U981, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
| | - Jérôme Galon
- INSERM UMRS1138, Integrative Cancer Immunology, Cordelier Research Center, Sorbonne Université, Université Paris Cité, 15 rue de l’École de Médecine, Paris 75006, France
| | - Elodie Giroux
- Lyon Institute of Philosophical Research, Lyon 3 Jean Moulin University, 1 Av. des Frères Lumière, Lyon 69007, France
| | - Sara Green
- Section for History and Philosophy of Science, Department of Science Education, University of Copenhagen, Rådmandsgade 64, Copenhagen 2200, Denmark
| | - Fridolin Gross
- CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux 33076, France
| | - Fanny Jaulin
- INSERM U1279, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, 3223 Voigt Dr, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Ezio Laconi
- Department of Biomedical Sciences, School of Medicine, University of Cagliari, Via Università 40, Cagliari 09124, Italy
| | - Nicolas Larmonier
- CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux 33076, France
| | - Carlo Maley
- Arizona Cancer Evolution Center, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85287, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85287, USA
- Center for Evolution and Medicine, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Alberto Mantovani
- Department of Biomedical Sciences, Humanitas University, 4 Via Rita Levi Montalcini, 20090 Pieve Emanuele, Milan, Italy
- Department of Immunology and Inflammation, Istituto Clinico Humanitas Humanitas Cancer Center (IRCCS) Humanitas Research Hospital, Via Manzoni 56, Rozzano, Milan 20089, Italy
- The William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Violaine Moreau
- INSERM UMR1312, Bordeaux Institute of Oncology (BRIC), University of Bordeaux, 146 Rue Léo Saignat, Bordeaux 33076, France
| | - Pierre Nassoy
- CNRS UMR 5298, Laboratoire Photonique Numérique et Nanosciences, University of Bordeaux, Rue François Mitterrand, Talence 33400, France
| | - Elena Rondeau
- INSERM U1111, ENS Lyon and Centre International de Recherche en Infectionlogie (CIRI), 46 Allée d’Italie, Lyon 69007, France
| | - David Santamaria
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca 37007, Spain
| | - Catherine M. Sawai
- INSERM UMR1312, Bordeaux Institute of Oncology (BRIC), University of Bordeaux, 146 Rue Léo Saignat, Bordeaux 33076, France
| | - Andrei Seluanov
- Department of Biology and Medicine, University of Rochester, Rochester, NY 14627, USA
| | | | - Vanja Sisirak
- CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux 33076, France
| | - Eric Solary
- INSERM U1287, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
- Département d’hématologie, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
- Université Paris-Saclay, Faculté de Médecine, 63 Rue Gabriel Péri, Le Kremlin-Bicêtre 94270, France
| | - Sarah Yvonnet
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark
| | - Lucie Laplane
- CNRS UMR8590, Institut d’Histoire et Philosophie des Sciences et des Technique, University Paris I Panthéon-Sorbonne, 13 rue du Four, Paris 75006, France
- INSERM U1287, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
- Center for Biology and Society, College of Liberal Arts and Sciences, Arizona State University, 1100 S McAllister Ave, Tempe, AZ 85281, USA
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6
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Fan Z, Ardicoglu R, Batavia AA, Rust R, von Ziegler L, Waag R, Zhang J, Desgeorges T, Sturman O, Dang H, Weber R, Roszkowski M, Moor AE, Schwab ME, Germain PL, Bohacek J, De Bock K. The vascular gene Apold1 is dispensable for normal development but controls angiogenesis under pathological conditions. Angiogenesis 2023; 26:385-407. [PMID: 36933174 PMCID: PMC10328887 DOI: 10.1007/s10456-023-09870-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/06/2023] [Indexed: 03/19/2023]
Abstract
The molecular mechanisms of angiogenesis have been intensely studied, but many genes that control endothelial behavior and fate still need to be described. Here, we characterize the role of Apold1 (Apolipoprotein L domain containing 1) in angiogenesis in vivo and in vitro. Single-cell analyses reveal that - across tissues - the expression of Apold1 is restricted to the vasculature and that Apold1 expression in endothelial cells (ECs) is highly sensitive to environmental factors. Using Apold1-/- mice, we find that Apold1 is dispensable for development and does not affect postnatal retinal angiogenesis nor alters the vascular network in adult brain and muscle. However, when exposed to ischemic conditions following photothrombotic stroke as well as femoral artery ligation, Apold1-/- mice display dramatic impairments in recovery and revascularization. We also find that human tumor endothelial cells express strikingly higher levels of Apold1 and that Apold1 deletion in mice stunts the growth of subcutaneous B16 melanoma tumors, which have smaller and poorly perfused vessels. Mechanistically, Apold1 is activated in ECs upon growth factor stimulation as well as in hypoxia, and Apold1 intrinsically controls EC proliferation but not migration. Our data demonstrate that Apold1 is a key regulator of angiogenesis in pathological settings, whereas it does not affect developmental angiogenesis, thus making it a promising candidate for clinical investigation.
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Affiliation(s)
- Zheng Fan
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland
- Institute of Anatomy, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Raphaela Ardicoglu
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
| | - Aashil A Batavia
- Department of Pathology and Molecular Pathology, University and University Hospital Zürich, Zurich, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Ruslan Rust
- Department of Health Sciences and Technology, Institute for Regenerative Medicine, University of Zürich, ETH Zürich, Zurich, Switzerland
| | - Lukas von Ziegler
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
| | - Rebecca Waag
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
| | - Jing Zhang
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland
| | - Thibaut Desgeorges
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland
| | - Oliver Sturman
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
| | - Hairuo Dang
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland
- DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
| | - Rebecca Weber
- Department of Health Sciences and Technology, Institute for Regenerative Medicine, University of Zürich, ETH Zürich, Zurich, Switzerland
| | - Martin Roszkowski
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Martin E Schwab
- Department of Health Sciences and Technology, Institute for Regenerative Medicine, University of Zürich, ETH Zürich, Zurich, Switzerland
| | - Pierre-Luc Germain
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
- Department of Health Sciences and Technology, Computational Neurogenomics, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Department for Molecular Life Sciences, Laboratory of Statistical Bioinformatics, University of Zürich, Zurich, Switzerland
| | - Johannes Bohacek
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland.
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland.
| | - Katrien De Bock
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland.
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7
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Sonrel A, Luetge A, Soneson C, Mallona I, Germain PL, Knyazev S, Gilis J, Gerber R, Seurinck R, Paul D, Sonder E, Crowell HL, Fanaswala I, Al-Ajami A, Heidari E, Schmeing S, Milosavljevic S, Saeys Y, Mangul S, Robinson MD. Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability. Genome Biol 2023; 24:119. [PMID: 37198712 DOI: 10.1186/s13059-023-02962-5] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 05/06/2023] [Indexed: 05/19/2023] Open
Abstract
Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but with a focus here on computational methods, benchmarking is critical to dissect important steps of analysis pipelines, formally assess performance across common situations as well as edge cases, and ultimately guide users on what tools to use. Benchmarking can also be important for community building and advancing methods in a principled way. We conducted a meta-analysis of recent single-cell benchmarks to summarize the scope, extensibility, and neutrality, as well as technical features and whether best practices in open data and reproducible research were followed. The results highlight that while benchmarks often make code available and are in principle reproducible, they remain difficult to extend, for example, as new methods and new ways to assess methods emerge. In addition, embracing containerization and workflow systems would enhance reusability of intermediate benchmarking results, thus also driving wider adoption.
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Affiliation(s)
- Anthony Sonrel
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Almut Luetge
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Charlotte Soneson
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Izaskun Mallona
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Pierre-Luc Germain
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
- D-HEST Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
| | - Sergey Knyazev
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Jeroen Gilis
- Department of Applied Mathematics, Computer Science & Statistics, Ghent University, Ghent, Belgium
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Reto Gerber
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Ruth Seurinck
- Department of Applied Mathematics, Computer Science & Statistics, Ghent University, Ghent, Belgium
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
| | - Dominique Paul
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Emanuel Sonder
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
- D-HEST Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
| | - Helena L Crowell
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Imran Fanaswala
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Ahmad Al-Ajami
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Elyas Heidari
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Stephan Schmeing
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Stefan Milosavljevic
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Yvan Saeys
- Department of Applied Mathematics, Computer Science & Statistics, Ghent University, Ghent, Belgium
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland.
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8
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Soutschek M, Germade T, Germain PL, Schratt G. enrichMiR predicts functionally relevant microRNAs based on target collections. Nucleic Acids Res 2022; 50:W280-W289. [PMID: 35609985 PMCID: PMC9252831 DOI: 10.1093/nar/gkac395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/25/2022] [Accepted: 05/05/2022] [Indexed: 11/12/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are among the main post-transcriptional regulators of gene expression. A number of data collections and prediction tools have gathered putative or confirmed targets of these regulators. It is often useful, for discovery and validation, to harness such collections to perform target enrichment analysis in given transcriptional signatures or gene-sets in order to predict involved miRNAs. While several methods have been proposed to this end, a flexible and user-friendly interface for such analyses using various approaches and collections is lacking. enrichMiR (https://ethz-ins.org/enrichMiR/) addresses this gap by enabling users to perform a series of enrichment tests, based on several target collections, to rank miRNAs according to their likely involvement in the control of a given transcriptional signature or gene-set. enrichMiR results can furthermore be visualised through interactive and publication-ready plots. To guide the choice of the appropriate analysis method, we benchmarked various tests across a panel of experiments involving the perturbation of known miRNAs. Finally, we showcase enrichMiR functionalities in a pair of use cases.
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Affiliation(s)
- Michael Soutschek
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland
| | - Tomás Germade
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich, Switzerland
| | - Pierre-Luc Germain
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich, Switzerland.,Lab of Statistical Bioinformatics, DMLS, University of Zürich, Switzerland.,Swiss Institute of Bioinformatics, Switzerland
| | - Gerhard Schratt
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland
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9
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Abstract
Doublets are prevalent in single-cell sequencing data and can lead to artifactual findings. A number of strategies have therefore been proposed to detect them. Building on the strengths of existing approaches, we developed
scDblFinder, a fast, flexible and accurate Bioconductor-based doublet detection method. Here we present the method, justify its design choices, demonstrate its performance on both single-cell RNA and accessibility (ATAC) sequencing data, and provide some observations on doublet formation, detection, and enrichment analysis. Even in complex datasets,
scDblFinder can accurately identify most heterotypic doublets, and was already found by an independent benchmark to outcompete alternatives.
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Affiliation(s)
- Pierre-Luc Germain
- DMLS Lab of Statistical Bioinformatics, University of Zürich, Zürich, 805, Switzerland
- D-HEST Institute for Neuroscience, ETH Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Aaron Lun
- Genentech Inc., South San Francisco, CA, USA
| | | | - Will Macnair
- Pharma Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases, F. Hoffmann-LaRoche Ltd, Basel, Switzerland
| | - Mark D. Robinson
- DMLS Lab of Statistical Bioinformatics, University of Zürich, Zürich, 805, Switzerland
- Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
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10
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von Ziegler LM, Floriou-Servou A, Waag R, Das Gupta RR, Sturman O, Gapp K, Maat CA, Kockmann T, Lin HY, Duss SN, Privitera M, Hinte L, von Meyenn F, Zeilhofer HU, Germain PL, Bohacek J. Multiomic profiling of the acute stress response in the mouse hippocampus. Nat Commun 2022; 13:1824. [PMID: 35383160 PMCID: PMC8983670 DOI: 10.1038/s41467-022-29367-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 03/11/2022] [Indexed: 12/26/2022] Open
Abstract
The acute stress response mobilizes energy to meet situational demands and re-establish homeostasis. However, the underlying molecular cascades are unclear. Here, we use a brief swim exposure to trigger an acute stress response in mice, which transiently increases anxiety, without leading to lasting maladaptive changes. Using multiomic profiling, such as proteomics, phospho-proteomics, bulk mRNA-, single-nuclei mRNA-, small RNA-, and TRAP-sequencing, we characterize the acute stress-induced molecular events in the mouse hippocampus over time. Our results show the complexity and specificity of the response to acute stress, highlighting both the widespread changes in protein phosphorylation and gene transcription, and tightly regulated protein translation. The observed molecular events resolve efficiently within four hours after initiation of stress. We include an interactive app to explore the data, providing a molecular resource that can help us understand how acute stress impacts brain function in response to stress. Acute stress can help individuals to respond to challenging events, although chronic stress leads to maladaptive changes. Here, the authors present a multi omic analysis profiling acute stress-induced changes in the mouse hippocampus, providing a resource for the scientific community.
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Affiliation(s)
- Lukas M von Ziegler
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Amalia Floriou-Servou
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Rebecca Waag
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Rebecca R Das Gupta
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.,Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Oliver Sturman
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Katharina Gapp
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Christina A Maat
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Tobias Kockmann
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Han-Yu Lin
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Sian N Duss
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Mattia Privitera
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Laura Hinte
- Laboratory of Nutrition and Metabolic Epigenetics, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Ferdinand von Meyenn
- Laboratory of Nutrition and Metabolic Epigenetics, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Hanns U Zeilhofer
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.,Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Pierre-Luc Germain
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland.,Computational Neurogenomics, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland.,Laboratory of Statistical Bioinformatics, Department for Molecular Life Sciences, University of Zürich, Zurich, Switzerland
| | - Johannes Bohacek
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland. .,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland.
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11
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Daswani R, Gilardi C, Soutschek M, Nanda P, Weiss K, Bicker S, Fiore R, Dieterich C, Germain PL, Winterer J, Schratt G. microRNA-138 controls hippocampal interneuron function and short-term memory in mice. eLife 2022; 11:74056. [PMID: 35290180 PMCID: PMC8963876 DOI: 10.7554/elife.74056] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 03/13/2022] [Indexed: 11/21/2022] Open
Abstract
The proper development and function of neuronal circuits rely on a tightly regulated balance between excitatory and inhibitory (E/I) synaptic transmission, and disrupting this balance can cause neurodevelopmental disorders, for example, schizophrenia. MicroRNA-dependent gene regulation in pyramidal neurons is important for excitatory synaptic function and cognition, but its role in inhibitory interneurons is poorly understood. Here, we identify miR138-5p as a regulator of short-term memory and inhibitory synaptic transmission in the mouse hippocampus. Sponge-mediated miR138-5p inactivation specifically in mouse parvalbumin (PV)-expressing interneurons impairs spatial recognition memory and enhances GABAergic synaptic input onto pyramidal neurons. Cellular and behavioral phenotypes associated with miR138-5p inactivation are paralleled by an upregulation of the schizophrenia (SCZ)-associated Erbb4, which we validated as a direct miR138-5p target gene. Our findings suggest that miR138-5p is a critical regulator of PV interneuron function in mice, with implications for cognition and SCZ. More generally, they provide evidence that microRNAs orchestrate neural circuit development by fine-tuning both excitatory and inhibitory synaptic transmission.
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Affiliation(s)
- Reetu Daswani
- Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Carlotta Gilardi
- Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Michael Soutschek
- Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Pakruti Nanda
- Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Kerstin Weiss
- Institute for Physiological Chemistry, Philipp University of Marburg, Marberg, Germany
| | - Silvia Bicker
- Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Roberto Fiore
- Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Christoph Dieterich
- Department of Internal Medicine III, Heidelberg University, Heidelberg, Germany
| | - Pierre-Luc Germain
- Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Jochen Winterer
- Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Gerhard Schratt
- Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
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12
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Soutschek M, Gross F, Schratt G, Germain PL. scanMiR: a biochemically-based toolkit for versatile and efficient microRNA target prediction. Bioinformatics 2022; 38:2466-2473. [PMID: 35188178 DOI: 10.1093/bioinformatics/btac110] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/22/2022] [Accepted: 02/17/2022] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION microRNAs are important post-transcriptional regulators of gene expression, but the identification of functionally relevant targets is still challenging. Recent research has shown improved prediction of microRNA-mediated repression using a biochemical model combined with empirically-derived k-mer affinity predictions, however these findings are not easily applicable. RESULTS We translate this approach into a flexible and user-friendly bioconductor package, scanMiR, also available through a web interface. Using lightweight linear models, scanMiR efficiently scans for binding sites, estimates their affinity, and predicts aggregated transcript repression. Moreover, flexible 3'-supplementary alignment enables the prediction of unconventional interactions, such as bindings potentially leading to target-directed microRNA degradation or slicing. We showcase scanMiR through a systematic scan for such unconventional sites on neuronal transcripts, including lncRNAs and circRNAs. Finally, in addition to the main bioconductor package implementing these functions, we provide a user-friendly web application enabling the scanning of sequences, the visualization of predicted bindings, and the browsing of predicted target repression. AVAILABILITY scanMiR and companion packages are implemented in R, released under the GPL-3 and accessible on Bioconductor (https://bioconductor.org/packages/release/bioc/html/scanMiR.html) as well as through a shiny web server (https://ethz-ins.org/scanMiR/). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Michael Soutschek
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland
| | - Fridolin Gross
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich, Switzerland
| | - Gerhard Schratt
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland
| | - Pierre-Luc Germain
- Lab of Statistical Bioinformatics, IMLS, University of Zürich, Switzerland.,Swiss Institute of Bioinformatics, Switzerland
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13
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Caporale N, Leemans M, Birgersson L, Germain PL, Cheroni C, Borbély G, Engdahl E, Lindh C, Bressan RB, Cavallo F, Chorev NE, D'Agostino GA, Pollard SM, Rigoli MT, Tenderini E, Tobon AL, Trattaro S, Troglio F, Zanella M, Bergman Å, Damdimopoulou P, Jönsson M, Kiess W, Kitraki E, Kiviranta H, Nånberg E, Öberg M, Rantakokko P, Rudén C, Söder O, Bornehag CG, Demeneix B, Fini JB, Gennings C, Rüegg J, Sturve J, Testa G. From cohorts to molecules: Adverse impacts of endocrine disrupting mixtures. Science 2022; 375:eabe8244. [PMID: 35175820 DOI: 10.1126/science.abe8244] [Citation(s) in RCA: 100] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Convergent evidence associates exposure to endocrine disrupting chemicals (EDCs) with major human diseases, even at regulation-compliant concentrations. This might be because humans are exposed to EDC mixtures, whereas chemical regulation is based on a risk assessment of individual compounds. Here, we developed a mixture-centered risk assessment strategy that integrates epidemiological and experimental evidence. We identified that exposure to an EDC mixture in early pregnancy is associated with language delay in offspring. At human-relevant concentrations, this mixture disrupted hormone-regulated and disease-relevant regulatory networks in human brain organoids and in the model organisms Xenopus leavis and Danio rerio, as well as behavioral responses. Reinterrogating epidemiological data, we found that up to 54% of the children had prenatal exposures above experimentally derived levels of concern, reaching, for the upper decile compared with the lowest decile of exposure, a 3.3 times higher risk of language delay.
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Affiliation(s)
- Nicolò Caporale
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy.,Human Technopole, V.le Rita Levi-Montalcini, 1, 20157 Milan, Italy
| | - Michelle Leemans
- UMR 7221, Phyma, CNRS-Muséum National d'Histoire Naturelle, Sorbonne Université, 75005 Paris, France
| | - Lina Birgersson
- Department of Biological and Environmental Sciences, University of Gothenburg, 41463 Gothenburg, Sweden
| | - Pierre-Luc Germain
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Cristina Cheroni
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy.,Human Technopole, V.le Rita Levi-Montalcini, 1, 20157 Milan, Italy
| | - Gábor Borbély
- Swedish Toxicology Sciences Research Center (SWETOX), Södertälje, Sweden
| | - Elin Engdahl
- Swedish Toxicology Sciences Research Center (SWETOX), Södertälje, Sweden.,Department of Organismal Biology, Environmental Toxicology, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Christian Lindh
- Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, SE-221 85 Lund, Sweden
| | - Raul Bardini Bressan
- Medical Research Council Centre for Regenerative Medicine and Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, UK
| | - Francesca Cavallo
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Nadav Even Chorev
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Giuseppe Alessandro D'Agostino
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Steven M Pollard
- Medical Research Council Centre for Regenerative Medicine and Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, UK
| | - Marco Tullio Rigoli
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy
| | - Erika Tenderini
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Alejandro Lopez Tobon
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Sebastiano Trattaro
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy
| | - Flavia Troglio
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Matteo Zanella
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Åke Bergman
- Swedish Toxicology Sciences Research Center (SWETOX), Södertälje, Sweden.,Department of Environmental Science, Stockholm University, SE-10691 Stockholm, Sweden.,School of Science and Technology, Örebro University, SE-70182 Örebro, Sweden
| | - Pauliina Damdimopoulou
- Swedish Toxicology Sciences Research Center (SWETOX), Södertälje, Sweden.,Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Maria Jönsson
- Department of Organismal Biology, Environmental Toxicology, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Wieland Kiess
- Hospital for Children and Adolescents, Department of Women and Child Health, University Hospital, University of Leipzig, 04103 Leipzig, Germany
| | - Efthymia Kitraki
- Lab of Basic Sciences, Faculty of Dentistry, National and Kapodistrian University of Athens, 152 72 Athens, Greece
| | - Hannu Kiviranta
- Department of Health Security, Finnish Institute for Health and Welfare (THL), Kuopio 70210, Finland
| | - Eewa Nånberg
- School of Health Sciences, Örebro University, SE-70182 Örebro, Sweden
| | - Mattias Öberg
- Swedish Toxicology Sciences Research Center (SWETOX), Södertälje, Sweden.,Institute of Environmental Medicine, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Panu Rantakokko
- Department of Health Security, Finnish Institute for Health and Welfare (THL), Kuopio 70210, Finland
| | - Christina Rudén
- Department of Environmental Science, Stockholm University, SE-10691 Stockholm, Sweden
| | - Olle Söder
- Department of Women's and Children's Health, Pediatric Endocrinology Division, Karolinska Institutet and University Hospital, SE-17176 Stockholm, Sweden
| | - Carl-Gustaf Bornehag
- Faculty of Health, Science and Technology, Department of Health Sciences, Karlstad University, SE- 651 88 Karlstad, Sweden.,Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Barbara Demeneix
- UMR 7221, Phyma, CNRS-Muséum National d'Histoire Naturelle, Sorbonne Université, 75005 Paris, France
| | - Jean-Baptiste Fini
- UMR 7221, Phyma, CNRS-Muséum National d'Histoire Naturelle, Sorbonne Université, 75005 Paris, France
| | - Chris Gennings
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joëlle Rüegg
- Swedish Toxicology Sciences Research Center (SWETOX), Södertälje, Sweden.,Department of Organismal Biology, Environmental Toxicology, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Joachim Sturve
- Department of Biological and Environmental Sciences, University of Gothenburg, 41463 Gothenburg, Sweden
| | - Giuseppe Testa
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy.,Human Technopole, V.le Rita Levi-Montalcini, 1, 20157 Milan, Italy
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14
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Abstract
Doublets are prevalent in single-cell sequencing data and can lead to artifactual findings. A number of strategies have therefore been proposed to detect them. Building on the strengths of existing approaches, we developed scDblFinder, a fast, flexible and accurate Bioconductor-based doublet detection method. Here we present the method, justify its design choices, demonstrate its performance on both single-cell RNA and accessibility (ATAC) sequencing data, and provide some observations on doublet formation, detection, and enrichment analysis. Even in complex datasets, scDblFinder can accurately identify most heterotypic doublets, and was already found by an independent benchmark to outcompete alternatives.
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Affiliation(s)
- Pierre-Luc Germain
- DMLS Lab of Statistical Bioinformatics, University of Zürich, Zürich, 805, Switzerland
- D-HEST Institute for Neuroscience, ETH Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Aaron Lun
- Genentech Inc., South San Francisco, CA, USA
| | | | - Will Macnair
- Pharma Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases, F. Hoffmann-LaRoche Ltd, Basel, Switzerland
| | - Mark D. Robinson
- DMLS Lab of Statistical Bioinformatics, University of Zürich, Zürich, 805, Switzerland
- Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
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15
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Colameo D, Rajman M, Soutschek M, Bicker S, von Ziegler L, Bohacek J, Winterer J, Germain PL, Dieterich C, Schratt G. Pervasive compartment-specific regulation of gene expression during homeostatic synaptic scaling. EMBO Rep 2021; 22:e52094. [PMID: 34396684 PMCID: PMC8490987 DOI: 10.15252/embr.202052094] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 07/12/2021] [Accepted: 07/20/2021] [Indexed: 12/13/2022] Open
Abstract
Synaptic scaling is a form of homeostatic plasticity which allows neurons to adjust their action potential firing rate in response to chronic alterations in neural activity. Synaptic scaling requires profound changes in gene expression, but the relative contribution of local and cell‐wide mechanisms is controversial. Here we perform a comprehensive multi‐omics characterization of the somatic and process compartments of primary rat hippocampal neurons during synaptic scaling. We uncover both highly compartment‐specific and correlating changes in the neuronal transcriptome and proteome. Whereas downregulation of crucial regulators of neuronal excitability occurs primarily in the somatic compartment, structural components of excitatory postsynapses are mostly downregulated in processes. Local inhibition of protein synthesis in processes during scaling is confirmed for candidate synaptic proteins. Motif analysis further suggests an important role for trans‐acting post‐transcriptional regulators, including RNA‐binding proteins and microRNAs, in the local regulation of the corresponding mRNAs. Altogether, our study indicates that, during synaptic scaling, compartmentalized gene expression changes might co‐exist with neuron‐wide mechanisms to allow synaptic computation and homeostasis.
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Affiliation(s)
- David Colameo
- Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Marek Rajman
- Institute for Physiological Chemistry, Biochemical-Pharmacological Center Marburg, Philipps-University of Marburg, Marburg, Germany
| | - Michael Soutschek
- Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Silvia Bicker
- Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Lukas von Ziegler
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland.,Laboratory of Behavioural and Molecular Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
| | - Johannes Bohacek
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland.,Laboratory of Behavioural and Molecular Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
| | - Jochen Winterer
- Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Pierre-Luc Germain
- Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, Zurich, Switzerland.,Laboratory of Statistical Bioinformatics, Department of Molecular Life Sciences, University of Zürich, Zurich, Switzerland
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Heidelberg, Germany
| | - Gerhard Schratt
- Laboratory of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
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16
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Floriou-Servou A, von Ziegler L, Waag R, Schläppi C, Germain PL, Bohacek J. The Acute Stress Response in the Multiomic Era. Biol Psychiatry 2021; 89:1116-1126. [PMID: 33722387 DOI: 10.1016/j.biopsych.2020.12.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/13/2020] [Accepted: 12/30/2020] [Indexed: 12/18/2022]
Abstract
Studying the stress response is a major pillar of neuroscience research not only because stress is a daily reality but also because the exquisitely fine-tuned bodily changes triggered by stress are a neuroendocrinological marvel. While the genome-wide changes induced by chronic stress have been extensively studied, we know surprisingly little about the complex molecular cascades triggered by acute stressors, the building blocks of chronic stress. The acute stress (or fight-or-flight) response mobilizes organismal energy resources to meet situational demands. However, successful stress coping also requires the efficient termination of the stress response. Maladaptive coping-particularly in response to severe or repeated stressors-can lead to allostatic (over)load, causing wear and tear on tissues, exhaustion, and disease. We propose that deep molecular profiling of the changes triggered by acute stressors could provide molecular correlates for allostatic load and predict healthy or maladaptive stress responses. We present a theoretical framework to interpret multiomic data in light of energy homeostasis and activity-dependent gene regulation, and we review the signaling cascades and molecular changes rapidly induced by acute stress in different cell types in the brain. In addition, we review and reanalyze recent data from multiomic screens conducted mainly in the rodent hippocampus and amygdala after acute psychophysical stressors. We identify challenges surrounding experimental design and data analysis, and we highlight promising new research directions to better understand the stress response on a multiomic level.
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Affiliation(s)
- Amalia Floriou-Servou
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Switzerland; Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zürich, Switzerland
| | - Lukas von Ziegler
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Switzerland; Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zürich, Switzerland
| | - Rebecca Waag
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Switzerland; Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zürich, Switzerland
| | - Christa Schläppi
- Computational Neurogenomics, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Switzerland; Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zürich, Switzerland
| | - Pierre-Luc Germain
- Computational Neurogenomics, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Switzerland; Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zürich, Switzerland; Laboratory of Statistical Bioinformatics, Department for Molecular Life Sciences, University of Zürich, Zürich, Switzerland.
| | - Johannes Bohacek
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Switzerland; Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zürich, Switzerland.
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17
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Huang R, Soneson C, Germain PL, Schmidt TSB, Mering CV, Robinson MD. treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses. Genome Biol 2021; 22:157. [PMID: 34001188 PMCID: PMC8127214 DOI: 10.1186/s13059-021-02368-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 04/28/2021] [Indexed: 12/13/2022] Open
Abstract
treeclimbR is for analyzing hierarchical trees of entities, such as phylogenies or cell types, at different resolutions. It proposes multiple candidates that capture the latent signal and pinpoints branches or leaves that contain features of interest, in a data-driven way. It outperforms currently available methods on synthetic data, and we highlight the approach on various applications, including microbiome and microRNA surveys as well as single-cell cytometry and RNA-seq datasets. With the emergence of various multi-resolution genomic datasets, treeclimbR provides a thorough inspection on entities across resolutions and gives additional flexibility to uncover biological associations.
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Affiliation(s)
- Ruizhu Huang
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, 8057, Switzerland
| | - Charlotte Soneson
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, 8057, Switzerland
- Present Address: Friedrich Miescher Institute for Biomedical Research and SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland
| | - Pierre-Luc Germain
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, 8057, Switzerland
- D-HEST Institute for Neuroscience, Swiss Federal Institute of Technology, Zurich, 8057, Switzerland
| | - Thomas S B Schmidt
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, 8057, Switzerland
- Present Address: European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, 69117, Germany
| | - Christian Von Mering
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, 8057, Switzerland
| | - Mark D Robinson
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, 8057, Switzerland.
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18
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Gerber S, Schratt G, Germain PL. Streamlining differential exon and 3' UTR usage with diffUTR. BMC Bioinformatics 2021; 22:189. [PMID: 33849458 PMCID: PMC8045333 DOI: 10.1186/s12859-021-04114-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/30/2021] [Indexed: 12/13/2022] Open
Abstract
Background Despite the importance of alternative poly-adenylation and 3′ UTR length for a variety of biological phenomena, there are limited means of detecting UTR changes from standard transcriptomic data. Results We present the diffUTR Bioconductor package which streamlines and improves upon differential exon usage (DEU) analyses, and leverages existing DEU tools and alternative poly-adenylation site databases to enable differential 3′ UTR usage analysis. We demonstrate the diffUTR features and show that it is more flexible and more accurate than state-of-the-art alternatives, both in simulations and in real data. Conclusions diffUTR enables differential 3′ UTR analysis and more generally facilitates DEU and the exploration of their results. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04114-7.
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Affiliation(s)
- Stefan Gerber
- Group of Computational Neurogenomics, D-HEST Institute for Neurosciences, ETH Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Lab of Systems Neuroscience, D-HEST Institute for Neurosciences, ETH Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Gerhard Schratt
- Lab of Systems Neuroscience, D-HEST Institute for Neurosciences, ETH Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Pierre-Luc Germain
- Group of Computational Neurogenomics, D-HEST Institute for Neurosciences, ETH Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. .,Lab of Statistical Bioinformatics, DMLS, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. .,SIB Swiss Institute of Bioinformatics, Zurich, Switzerland.
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19
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Salovska B, Zhu H, Gandhi T, Frank M, Li W, Rosenberger G, Wu C, Germain PL, Zhou H, Hodny Z, Reiter L, Liu Y. Isoform-resolved correlation analysis between mRNA abundance regulation and protein level degradation. Mol Syst Biol 2021; 16:e9170. [PMID: 32175694 PMCID: PMC7073818 DOI: 10.15252/msb.20199170] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 02/06/2020] [Accepted: 02/12/2020] [Indexed: 12/15/2022] Open
Abstract
Profiling of biological relationships between different molecular layers dissects regulatory mechanisms that ultimately determine cellular function. To thoroughly assess the role of protein post‐translational turnover, we devised a strategy combining pulse stable isotope‐labeled amino acids in cells (pSILAC), data‐independent acquisition mass spectrometry (DIA‐MS), and a novel data analysis framework that resolves protein degradation rate on the level of mRNA alternative splicing isoforms and isoform groups. We demonstrated our approach by the genome‐wide correlation analysis between mRNA amounts and protein degradation across different strains of HeLa cells that harbor a high grade of gene dosage variation. The dataset revealed that specific biological processes, cellular organelles, spatial compartments of organelles, and individual protein isoforms of the same genes could have distinctive degradation rate. The protein degradation diversity thus dissects the corresponding buffering or concerting protein turnover control across cancer cell lines. The data further indicate that specific mRNA splicing events such as intron retention significantly impact the protein abundance levels. Our findings support the tight association between transcriptome variability and proteostasis and provide a methodological foundation for studying functional protein degradation.
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Affiliation(s)
- Barbora Salovska
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA.,Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hongwen Zhu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | | | - Max Frank
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | | | - Chongde Wu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Pierre-Luc Germain
- Institute for Neuroscience, D-HEST, ETH Zurich, Zurich, Switzerland.,Statistical Bioinformatics Lab, DMLS, University of Zürich, Zurich, Switzerland
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zdenek Hodny
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA.,Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
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20
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Privitera M, Ferrari KD, von Ziegler LM, Sturman O, Duss SN, Floriou-Servou A, Germain PL, Vermeiren Y, Wyss MT, De Deyn PP, Weber B, Bohacek J. Author Correction: A complete pupillometry toolbox for real-time monitoring of locus coeruleus activity in rodents. Nat Protoc 2021; 16:4108. [PMID: 33446938 DOI: 10.1038/s41596-021-00493-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mattia Privitera
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Kim David Ferrari
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland.,Experimental Imaging and Neuroenergetics, Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Lukas M von Ziegler
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Oliver Sturman
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Sian N Duss
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Amalia Floriou-Servou
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Pierre-Luc Germain
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Yannick Vermeiren
- Department of Biomedical Sciences, Laboratory of Neurochemistry and Behavior, Institute Born-Bunge, University of Antwerp, Wilrijk (Antwerp), Antwerpen, Belgium.,Department of Neurology and Alzheimer Center, University of Groningen and University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Matthias T Wyss
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland.,Experimental Imaging and Neuroenergetics, Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Peter P De Deyn
- Department of Biomedical Sciences, Laboratory of Neurochemistry and Behavior, Institute Born-Bunge, University of Antwerp, Wilrijk (Antwerp), Antwerpen, Belgium.,Department of Neurology and Alzheimer Center, University of Groningen and University Medical Center Groningen (UMCG), Groningen, the Netherlands.,Department of Neurology, Memory Clinic of Hospital Network Antwerp (ZNA) Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Bruno Weber
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland. .,Experimental Imaging and Neuroenergetics, Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.
| | - Johannes Bohacek
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland. .,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland.
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21
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Crowell HL, Soneson C, Germain PL, Calini D, Collin L, Raposo C, Malhotra D, Robinson MD. muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data. Nat Commun 2020; 11:6077. [PMID: 33257685 PMCID: PMC7705760 DOI: 10.1038/s41467-020-19894-4] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [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: 06/23/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has become an empowering technology to profile the transcriptomes of individual cells on a large scale. Early analyses of differential expression have aimed at identifying differences between subpopulations to identify subpopulation markers. More generally, such methods compare expression levels across sets of cells, thus leading to cross-condition analyses. Given the emergence of replicated multi-condition scRNA-seq datasets, an area of increasing focus is making sample-level inferences, termed here as differential state analysis; however, it is not clear which statistical framework best handles this situation. Here, we surveyed methods to perform cross-condition differential state analyses, including cell-level mixed models and methods based on aggregated pseudobulk data. To evaluate method performance, we developed a flexible simulation that mimics multi-sample scRNA-seq data. We analyzed scRNA-seq data from mouse cortex cells to uncover subpopulation-specific responses to lipopolysaccharide treatment, and provide robust tools for multi-condition analysis within the muscat R package.
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Affiliation(s)
- Helena L Crowell
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Charlotte Soneson
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
- Friedrich Miescher Institute for Biomedical Research and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Pierre-Luc Germain
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- D-HEST Institute for Neuroscience, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Daniela Calini
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases, Roche Innovation Center Basel, Basel, Switzerland
| | - Ludovic Collin
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases, Roche Innovation Center Basel, Basel, Switzerland
| | - Catarina Raposo
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases, Roche Innovation Center Basel, Basel, Switzerland
| | - Dheeraj Malhotra
- F. Hoffmann-La Roche Ltd., Pharma Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases, Roche Innovation Center Basel, Basel, Switzerland
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
- SIB Swiss Institute of Bioinformatics, Zurich, Switzerland.
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22
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Gapp K, van Steenwyk G, Germain PL, Matsushima W, Rudolph KLM, Manuella F, Roszkowski M, Vernaz G, Ghosh T, Pelczar P, Mansuy IM, Miska EA. Alterations in sperm long RNA contribute to the epigenetic inheritance of the effects of postnatal trauma. Mol Psychiatry 2020; 25:2162-2174. [PMID: 30374190 PMCID: PMC7473836 DOI: 10.1038/s41380-018-0271-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/11/2018] [Indexed: 12/22/2022]
Abstract
Psychiatric diseases have a strong heritable component known to not be restricted to DNA sequence-based genetic inheritance alone but to also involve epigenetic factors in germ cells. Initial evidence suggested that sperm RNA is causally linked to the transmission of symptoms induced by traumatic experiences. Here, we show that alterations in long RNA in sperm contribute to the inheritance of specific trauma symptoms. Injection of long RNA fraction from sperm of males exposed to postnatal trauma recapitulates the effects on food intake, glucose response to insulin and risk-taking in adulthood whereas the small RNA fraction alters body weight and behavioural despair. Alterations in long RNA are maintained after fertilization, suggesting a direct link between sperm and embryo RNA.
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Affiliation(s)
- K Gapp
- Gurdon Institute, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QN, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - G van Steenwyk
- Laboratory of Neuroepigenetics, University of Zürich and Swiss Federal Institute of Technology, Brain Research Institute, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - P L Germain
- Laboratory of Neuroepigenetics, University of Zürich and Swiss Federal Institute of Technology, Brain Research Institute, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - W Matsushima
- Gurdon Institute, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QN, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - K L M Rudolph
- Gurdon Institute, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QN, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - F Manuella
- Laboratory of Neuroepigenetics, University of Zürich and Swiss Federal Institute of Technology, Brain Research Institute, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - M Roszkowski
- Laboratory of Neuroepigenetics, University of Zürich and Swiss Federal Institute of Technology, Brain Research Institute, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - G Vernaz
- Gurdon Institute, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QN, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - T Ghosh
- Gurdon Institute, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QN, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - P Pelczar
- Center for Transgenic Models, University of Basel, Mattenstrasse 22, CH-4002, Basel, Switzerland
| | - I M Mansuy
- Laboratory of Neuroepigenetics, University of Zürich and Swiss Federal Institute of Technology, Brain Research Institute, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.
| | - E A Miska
- Gurdon Institute, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QN, UK.
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
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23
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Germain PL, Sonrel A, Robinson MD. pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools. Genome Biol 2020; 21:227. [PMID: 32873325 PMCID: PMC7465801 DOI: 10.1186/s13059-020-02136-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/06/2020] [Indexed: 11/13/2022] Open
Abstract
We present pipeComp ( https://github.com/plger/pipeComp ), a flexible R framework for pipeline comparison handling interactions between analysis steps and relying on multi-level evaluation metrics. We apply it to the benchmark of single-cell RNA-sequencing analysis pipelines using simulated and real datasets with known cell identities, covering common methods of filtering, doublet detection, normalization, feature selection, denoising, dimensionality reduction, and clustering. pipeComp can easily integrate any other step, tool, or evaluation metric, allowing extensible benchmarks and easy applications to other fields, as we demonstrate through a study of the impact of removal of unwanted variation on differential expression analysis.
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Affiliation(s)
- Pierre-Luc Germain
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, Zürich, 8057 Switzerland
- SIB Swiss Institute of Bioinformatics, Zürich, Switzerland
- D-HEST Institute for Neurosciences, ETH Zürich, Winterthurerstrasse 190, Zürich, 8057 Switzerland
| | - Anthony Sonrel
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, Zürich, 8057 Switzerland
- SIB Swiss Institute of Bioinformatics, Zürich, Switzerland
| | - Mark D. Robinson
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, Zürich, 8057 Switzerland
- SIB Swiss Institute of Bioinformatics, Zürich, Switzerland
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24
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Privitera M, Ferrari KD, von Ziegler LM, Sturman O, Duss SN, Floriou-Servou A, Germain PL, Vermeiren Y, Wyss MT, De Deyn PP, Weber B, Bohacek J. A complete pupillometry toolbox for real-time monitoring of locus coeruleus activity in rodents. Nat Protoc 2020; 15:2301-2320. [PMID: 32632319 DOI: 10.1038/s41596-020-0324-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/01/2020] [Indexed: 01/20/2023]
Abstract
The locus coeruleus (LC) is a region in the brainstem that produces noradrenaline and is involved in both normal and pathological brain function. Pupillometry, the measurement of pupil diameter, provides a powerful readout of LC activity in rodents, primates and humans. The protocol detailed here describes a miniaturized setup that can screen LC activity in rodents in real-time and can be established within 1-2 d. Using low-cost Raspberry Pi computers and cameras, the complete custom-built system costs only ~300 euros, is compatible with stereotaxic surgery frames and seamlessly integrates into complex experimental setups. Tools for pupil tracking and a user-friendly Pupillometry App allow quantification, analysis and visualization of pupil size. Pupillometry can discriminate between different, physiologically relevant firing patterns of the LC and can accurately report LC activation as measured by noradrenaline turnover. Pupillometry provides a rapid, non-invasive readout that can be used to verify accurate placement of electrodes/fibers in vivo, thus allowing decisions about the inclusion/exclusion of individual animals before experiments begin.
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Affiliation(s)
- Mattia Privitera
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Kim David Ferrari
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland.,Experimental Imaging and Neuroenergetics, Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Lukas M von Ziegler
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Oliver Sturman
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Sian N Duss
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Amalia Floriou-Servou
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Pierre-Luc Germain
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Yannick Vermeiren
- Department of Biomedical Sciences, Laboratory of Neurochemistry and Behavior, Institute Born-Bunge, University of Antwerp, Wilrijk (Antwerp), Antwerpen, Belgium.,Department of Neurology and Alzheimer Center, University of Groningen and University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Matthias T Wyss
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland.,Experimental Imaging and Neuroenergetics, Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Peter P De Deyn
- Department of Biomedical Sciences, Laboratory of Neurochemistry and Behavior, Institute Born-Bunge, University of Antwerp, Wilrijk (Antwerp), Antwerpen, Belgium.,Department of Neurology and Alzheimer Center, University of Groningen and University Medical Center Groningen (UMCG), Groningen, the Netherlands.,Department of Neurology, Memory Clinic of Hospital Network Antwerp (ZNA) Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Bruno Weber
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland. .,Experimental Imaging and Neuroenergetics, Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.
| | - Johannes Bohacek
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland. .,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland.
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25
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Zanella M, Vitriolo A, Andirko A, Martins PT, Sturm S, O’Rourke T, Laugsch M, Malerba N, Skaros A, Trattaro S, Germain PL, Mihailovic M, Merla G, Rada-Iglesias A, Boeckx C, Testa G. Dosage analysis of the 7q11.23 Williams region identifies BAZ1B as a major human gene patterning the modern human face and underlying self-domestication. Sci Adv 2019; 5:eaaw7908. [PMID: 31840056 PMCID: PMC6892627 DOI: 10.1126/sciadv.aaw7908] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 09/26/2019] [Indexed: 05/10/2023]
Abstract
We undertook a functional dissection of chromatin remodeler BAZ1B in neural crest (NC) stem cells (NCSCs) from a uniquely informative cohort of typical and atypical patients harboring 7q11.23 copy number variants. Our results reveal a key contribution of BAZ1B to NCSC in vitro induction and migration, coupled with a crucial involvement in NC-specific transcriptional circuits and distal regulation. By intersecting our experimental data with new paleogenetic analyses comparing modern and archaic humans, we found a modern-specific enrichment for regulatory changes both in BAZ1B and its experimentally defined downstream targets, thereby providing the first empirical validation of the human self-domestication hypothesis and positioning BAZ1B as a master regulator of the modern human face. In so doing, we provide experimental evidence that the craniofacial and cognitive/behavioral phenotypes caused by alterations of the Williams-Beuren syndrome critical region can serve as a powerful entry point into the evolution of the modern human face and prosociality.
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Affiliation(s)
- Matteo Zanella
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Alessandro Vitriolo
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Alejandro Andirko
- University of Barcelona, Barcelona, Spain
- University of Barcelona Institute of Complex Systems (UBICS), Barcelona, Spain
| | - Pedro Tiago Martins
- University of Barcelona, Barcelona, Spain
- University of Barcelona Institute of Complex Systems (UBICS), Barcelona, Spain
| | - Stefanie Sturm
- University of Barcelona, Barcelona, Spain
- University of Barcelona Institute of Complex Systems (UBICS), Barcelona, Spain
| | - Thomas O’Rourke
- University of Barcelona, Barcelona, Spain
- University of Barcelona Institute of Complex Systems (UBICS), Barcelona, Spain
| | - Magdalena Laugsch
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Human Genetics, University Hospital Cologne, Cologne, Germany
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Natascia Malerba
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Adrianos Skaros
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Sebastiano Trattaro
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Pierre-Luc Germain
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy
- D-HEST Institute for Neuroscience, ETH Zürich, Switzerland
| | - Marija Mihailovic
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Giuseppe Merla
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
- Institute of Biomedicine and Biotechnology of Cantabria, University of Cantabria, Cantabria, Spain
| | - Cedric Boeckx
- University of Barcelona, Barcelona, Spain
- University of Barcelona Institute of Complex Systems (UBICS), Barcelona, Spain
- Catalan Institute for Advanced Studies and Research (ICREA), Barcelona, Spain
| | - Giuseppe Testa
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Laboratory of Stem Cell Epigenetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy
- Human Technopole, Center for Neurogenomics, Via Cristina Belgioioso 171, Milan, Italy
- Corresponding author. , ,
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26
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Barbagiovanni G, Germain PL, Zech M, Atashpaz S, Lo Riso P, D'Antonio-Chronowska A, Tenderini E, Caiazzo M, Boesch S, Jech R, Haslinger B, Broccoli V, Stewart AF, Winkelmann J, Testa G. KMT2B Is Selectively Required for Neuronal Transdifferentiation, and Its Loss Exposes Dystonia Candidate Genes. Cell Rep 2019; 25:988-1001. [PMID: 30355503 PMCID: PMC6218204 DOI: 10.1016/j.celrep.2018.09.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 08/01/2018] [Accepted: 09/19/2018] [Indexed: 12/11/2022] Open
Abstract
Transdifferentiation of fibroblasts into induced neuronal cells (iNs) by the neuron-specific transcription factors Brn2, Myt1l, and Ascl1 is a paradigmatic example of inter-lineage conversion across epigenetically distant cells. Despite tremendous progress regarding the transcriptional hierarchy underlying transdifferentiation, the enablers of the concomitant epigenome resetting remain to be elucidated. Here, we investigated the role of KMT2A and KMT2B, two histone H3 lysine 4 methylases with cardinal roles in development, through individual and combined inactivation. We found that Kmt2b, whose human homolog's mutations cause dystonia, is selectively required for iN conversion through suppression of the alternative myocyte program and induction of neuronal maturation genes. The identification of KMT2B-vulnerable targets allowed us, in turn, to expose, in a cohort of 225 patients, 45 unique variants in 39 KMT2B targets, which represent promising candidates to dissect the molecular bases of dystonia.
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Affiliation(s)
- Giulia Barbagiovanni
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Pierre-Luc Germain
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Michael Zech
- Institut für Neurogenomik, Helmholtz Zentrum München, 85764 Munich, Germany; Klinik und Poliklinik für Neurologie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Sina Atashpaz
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Pietro Lo Riso
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | | | - Erika Tenderini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | | | - Sylvia Boesch
- Department of Neurology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Robert Jech
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General Faculty Hospital, 12821 Prague, Czech Republic
| | - Bernhard Haslinger
- Klinik und Poliklinik für Neurologie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Vania Broccoli
- San Raffaele Scientific Institute, 20132 Milan, Italy; National Research Council (CNR), Institute of Neuroscience, 20129 Milan, Italy
| | - Adrian Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01069 Dresden, Germany
| | - Juliane Winkelmann
- Institut für Neurogenomik, Helmholtz Zentrum München, 85764 Munich, Germany; Lehrstuhl für Neurogenetik und Institut für Humangenetik, Technische Universität München, 81675 Munich, Germany; Munich Cluster for Systems Neurology, SyNergy, 81829 Munich, Germany
| | - Giuseppe Testa
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy.
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27
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Liu Y, Mi Y, Mueller T, Kreibich S, Williams EG, Van Drogen A, Borel C, Frank M, Germain PL, Bludau I, Mehnert M, Seifert M, Emmenlauer M, Sorg I, Bezrukov F, Bena FS, Zhou H, Dehio C, Testa G, Saez-Rodriguez J, Antonarakis SE, Hardt WD, Aebersold R. Multi-omic measurements of heterogeneity in HeLa cells across laboratories. Nat Biotechnol 2019; 37:314-322. [PMID: 30778230 DOI: 10.1038/s41587-019-0037-y] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 11/21/2018] [Indexed: 11/09/2022]
Abstract
Reproducibility in research can be compromised by both biological and technical variation, but most of the focus is on removing the latter. Here we investigate the effects of biological variation in HeLa cell lines using a systems-wide approach. We determine the degree of molecular and phenotypic variability across 14 stock HeLa samples from 13 international laboratories. We cultured cells in uniform conditions and profiled genome-wide copy numbers, mRNAs, proteins and protein turnover rates in each cell line. We discovered substantial heterogeneity between HeLa variants, especially between lines of the CCL2 and Kyoto varieties, and observed progressive divergence within a specific cell line over 50 successive passages. Genomic variability has a complex, nonlinear effect on transcriptome, proteome and protein turnover profiles, and proteotype patterns explain the varying phenotypic response of different cell lines to Salmonella infection. These findings have implications for the interpretation and reproducibility of research results obtained from human cultured cells.
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Affiliation(s)
- Yansheng Liu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA. .,Yale Cancer Biology Institute, Yale University, West Haven, CT, USA.
| | - Yang Mi
- Heidelberg University, Faculty of Biosciences, Heidelberg, Germany.,Joint Research Center for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Torsten Mueller
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | - Evan G Williams
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Audrey Van Drogen
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical School, and University Hospitals of Geneva, Geneva, Switzerland
| | - Max Frank
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | - Isabell Bludau
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Martin Mehnert
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Michael Seifert
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases, Dresden, Germany
| | | | - Isabel Sorg
- Biozentrum, University of Basel, Basel, Switzerland
| | - Fedor Bezrukov
- Department of Genetic Medicine and Development, University of Geneva Medical School, and University Hospitals of Geneva, Geneva, Switzerland
| | | | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | | | - Giuseppe Testa
- IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Julio Saez-Rodriguez
- Joint Research Center for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, Aachen, Germany.,Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Bioquant Heidelberg, Germany
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, and University Hospitals of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
| | | | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. .,Faculty of Science, University of Zurich, Zurich, Switzerland.
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28
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Abstract
Stressful experiences are linked to anxiety disorders in humans. Similar effects are observed in rodent models, where anxiety is often measured in classic conflict tests such as the open-field test. Spontaneous rearing behavior, in which rodents stand on their hind legs to explore, can also be observed in this test yet is often ignored. We define two forms of rearing, supported rearing (in which the animal rears against the walls of the arena) and unsupported rearing (in which the animal rears without contacting the walls of the arena). Using an automated open-field test, we show that both rearing behaviors appear to be strongly context dependent and show clear sex differences, with females rearing less than males. We show that unsupported rearing is sensitive to acute stress, and is reduced under more averse testing conditions. Repeated testing and handling procedures lead to changes in several parameters over varying test sessions, yet unsupported rearing appears to be rather stable within a given animal. Rearing behaviors could therefore provide an additional measure of anxiety in rodents relevant for behavioral studies, as they appear to be highly sensitive to context and may be used in repeated testing designs.
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Affiliation(s)
- Oliver Sturman
- a Department of Health Sciences and Technology, Lab of Molecular and Behavioral Neuroscience , ETH Zurich , Zurich , Switzerland
| | - Pierre-Luc Germain
- b Brain Research Institute , University of Zurich , Zurich , Switzerland
| | - Johannes Bohacek
- a Department of Health Sciences and Technology, Lab of Molecular and Behavioral Neuroscience , ETH Zurich , Zurich , Switzerland
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29
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Bohacek J, Engmann O, Germain PL, Schelbert S, Mansuy IM. Transgenerational epigenetic inheritance: from biology to society-Summary Latsis Symposium Aug 28-30, 2017, Zürich, Switzerland. Environ Epigenet 2018; 4:dvy012. [PMID: 30034821 PMCID: PMC6049026 DOI: 10.1093/eep/dvy012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Johannes Bohacek
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zürich and Department of Health Science and Technology of the ETH Zürich, Zürich, Switzerland
| | - Olivia Engmann
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zürich and Department of Health Science and Technology of the ETH Zürich, Zürich, Switzerland
| | - Pierre-Luc Germain
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zürich and Department of Health Science and Technology of the ETH Zürich, Zürich, Switzerland
| | - Silvia Schelbert
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zürich and Department of Health Science and Technology of the ETH Zürich, Zürich, Switzerland
| | - Isabelle M Mansuy
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zürich and Department of Health Science and Technology of the ETH Zürich, Zürich, Switzerland
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30
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Germain PL, Chiapperino L, Testa G. The European politics of animal experimentation: From Victorian Britain to 'Stop Vivisection'. Stud Hist Philos Biol Biomed Sci 2017; 64:75-87. [PMID: 28689133 DOI: 10.1016/j.shpsc.2017.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 06/05/2017] [Accepted: 06/08/2017] [Indexed: 06/07/2023]
Abstract
This paper identifies a common political struggle behind debates on the validity and permissibility of animal experimentation, through an analysis of two recent European case studies: the Italian implementation of the European Directive 2010/63/EC regulating the use of animals in science, and the recent European Citizens' Initiative (ECI) 'Stop Vivisection'. Drawing from a historical parallel with Victorian antivivisectionism, we highlight important threads in our case studies that mark the often neglected specificities of debates on animal experimentation. From the representation of the sadistic scientist in the XIX century, to his/her claimed capture by vested interests and evasion of public scrutiny in the contemporary cases, we show that animals are not simply the focus of the debate, but also a privileged locus at which much broader issues are being raised about science, its authority, accountability and potential misalignment with public interest. By highlighting this common socio-political conflict underlying public controversies around animal experimentation, our work prompts the exploration of modes of authority and argumentation that, in establishing the usefulness of animals in science, avoid reenacting the traditional divide between epistemic and political fora.
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Affiliation(s)
- Pierre-Luc Germain
- Department of Experimental Oncology, Istituto Europeo di Oncologia (IEO), IFOM-IEO Campus, via Adamello 16, 20139 Milano, Italy; Brain Research Institute, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Luca Chiapperino
- Faculty of Social and Political Sciences, University of Lausanne, Bâtiment Géopolis, CH 1015 Lausanne, Switzerland.
| | - Giuseppe Testa
- Department of Experimental Oncology, Istituto Europeo di Oncologia (IEO), IFOM-IEO Campus, via Adamello 16, 20139 Milano, Italy; Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Via Santa Sofia 9, 20122 Milano, Italy.
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31
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Gabriele M, Vulto-van Silfhout AT, Germain PL, Vitriolo A, Kumar R, Douglas E, Haan E, Kosaki K, Takenouchi T, Rauch A, Steindl K, Frengen E, Misceo D, Pedurupillay CRJ, Stromme P, Rosenfeld JA, Shao Y, Craigen WJ, Schaaf CP, Rodriguez-Buritica D, Farach L, Friedman J, Thulin P, McLean SD, Nugent KM, Morton J, Nicholl J, Andrieux J, Stray-Pedersen A, Chambon P, Patrier S, Lynch SA, Kjaergaard S, Tørring PM, Brasch-Andersen C, Ronan A, van Haeringen A, Anderson PJ, Powis Z, Brunner HG, Pfundt R, Schuurs-Hoeijmakers JHM, van Bon BWM, Lelieveld S, Gilissen C, Nillesen WM, Vissers LELM, Gecz J, Koolen DA, Testa G, de Vries BBA. YY1 Haploinsufficiency Causes an Intellectual Disability Syndrome Featuring Transcriptional and Chromatin Dysfunction. Am J Hum Genet 2017; 100:907-925. [PMID: 28575647 DOI: 10.1016/j.ajhg.2017.05.006] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/04/2017] [Indexed: 01/06/2023] Open
Abstract
Yin and yang 1 (YY1) is a well-known zinc-finger transcription factor with crucial roles in normal development and malignancy. YY1 acts both as a repressor and as an activator of gene expression. We have identified 23 individuals with de novo mutations or deletions of YY1 and phenotypic features that define a syndrome of cognitive impairment, behavioral alterations, intrauterine growth restriction, feeding problems, and various congenital malformations. Our combined clinical and molecular data define "YY1 syndrome" as a haploinsufficiency syndrome. Through immunoprecipitation of YY1-bound chromatin from affected individuals' cells with antibodies recognizing both ends of the protein, we show that YY1 deletions and missense mutations lead to a global loss of YY1 binding with a preferential retention at high-occupancy sites. Finally, we uncover a widespread loss of H3K27 acetylation in particular on the YY1-bound enhancers, underscoring a crucial role for YY1 in enhancer regulation. Collectively, these results define a clinical syndrome caused by haploinsufficiency of YY1 through dysregulation of key transcriptional regulators.
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Affiliation(s)
- Michele Gabriele
- Laboratory of Stem Cell Epigenetics, Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | | | - Pierre-Luc Germain
- Laboratory of Stem Cell Epigenetics, Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Alessandro Vitriolo
- Laboratory of Stem Cell Epigenetics, Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Raman Kumar
- School of Medicine and Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Evelyn Douglas
- SA Clinical Genetics Service, SA Pathology, Adelaide, SA 5000, Australia; School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - Eric Haan
- SA Clinical Genetics Service, SA Pathology, Adelaide, SA 5000, Australia; School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, 160-8582 Tokyo, Japan
| | - Toshiki Takenouchi
- Center for Medical Genetics, Keio University School of Medicine, 160-8582 Tokyo, Japan
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Eirik Frengen
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0315 Oslo, Norway
| | - Doriana Misceo
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0315 Oslo, Norway
| | | | - Petter Stromme
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital and University of Oslo, 0313 Oslo, Norway
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yunru Shao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - William J Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Rodriguez-Buritica
- Division of Genetics, Department of Pediatrics, University of Texas Health, Houston, TX 77030, USA
| | - Laura Farach
- Division of Genetics, Department of Pediatrics, University of Texas Health, Houston, TX 77030, USA
| | - Jennifer Friedman
- Departments of Neurosciences and Pediatrics, University of California, San Diego, and Rady Children's Hospital, San Diego, CA 92123, USA
| | - Perla Thulin
- Department of Neurology, University of Utah, San Diego, CA 92123, USA
| | - Scott D McLean
- Clinical Genetics Section, Children's Hospital of San Antonio, San Antonio, TX 78207, USA
| | - Kimberly M Nugent
- Clinical Genetics Section, Children's Hospital of San Antonio, San Antonio, TX 78207, USA
| | - Jenny Morton
- Birmingham Women's Hospital, B15 2TG Birmingham, UK
| | - Jillian Nicholl
- SA Clinical Genetics Service, SA Pathology, Adelaide, SA 5000, Australia; School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - Joris Andrieux
- Institut de Génétique Médicale, Hopital Jeanne de Flandre, 59000 Lille, France
| | | | - Pascal Chambon
- Laboratory of Cytogenetics, Rouen University Hospital, 76031 Rouen, France
| | - Sophie Patrier
- Service d'Anatomie Pathologique, Rouen University Hospital, 76031 Rouen, France
| | - Sally A Lynch
- National Centre for Medical Genetics, Our Lady's Children's Hospital, D12 V004 Dublin, Ireland
| | - Susanne Kjaergaard
- Department of Clinical Genetics, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Pernille M Tørring
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | | | - Anne Ronan
- Hunter Genetics, Waratah, NSW 2298, Australia
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Peter J Anderson
- Australian Craniofacial Unit, Women's and Children's Hospital, North Adelaide, SA 5006, Australia
| | - Zöe Powis
- Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | | | - Bregje W M van Bon
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Stefan Lelieveld
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Willy M Nillesen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Jozef Gecz
- School of Medicine and Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia; South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - David A Koolen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Giuseppe Testa
- Laboratory of Stem Cell Epigenetics, Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy; Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy.
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
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Germain PL, Vitriolo A, Adamo A, Laise P, Das V, Testa G. RNAontheBENCH: computational and empirical resources for benchmarking RNAseq quantification and differential expression methods. Nucleic Acids Res 2016; 44:5054-67. [PMID: 27190234 PMCID: PMC4914128 DOI: 10.1093/nar/gkw448] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/09/2016] [Indexed: 11/13/2022] Open
Abstract
RNA sequencing (RNAseq) has become the method of choice for transcriptome analysis, yet no consensus exists as to the most appropriate pipeline for its analysis, with current benchmarks suffering important limitations. Here, we address these challenges through a rich benchmarking resource harnessing (i) two RNAseq datasets including ERCC ExFold spike-ins; (ii) Nanostring measurements of a panel of 150 genes on the same samples; (iii) a set of internal, genetically-determined controls; (iv) a reanalysis of the SEQC dataset; and (v) a focus on relative quantification (i.e. across-samples). We use this resource to compare different approaches to each step of RNAseq analysis, from alignment to differential expression testing. We show that methods providing the best absolute quantification do not necessarily provide good relative quantification across samples, that count-based methods are superior for gene-level relative quantification, and that the new generation of pseudo-alignment-based software performs as well as established methods, at a fraction of the computing time. We also assess the impact of library type and size on quantification and differential expression analysis. Finally, we have created a R package and a web platform to enable the simple and streamlined application of this resource to the benchmarking of future methods.
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Affiliation(s)
- Pierre-Luc Germain
- European Institute of Oncology, Department of Experimental Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Alessandro Vitriolo
- European Institute of Oncology, Department of Experimental Oncology, Via Adamello 16, 20139 Milano, Italy University of Milan, Department of Oncology and Hemato-Oncology, Via Festa del Perdono 7, 20122 Milano, Italy
| | - Antonio Adamo
- European Institute of Oncology, Department of Experimental Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Pasquale Laise
- European Institute of Oncology, Department of Experimental Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Vivek Das
- European Institute of Oncology, Department of Experimental Oncology, Via Adamello 16, 20139 Milano, Italy University of Milan, Department of Oncology and Hemato-Oncology, Via Festa del Perdono 7, 20122 Milano, Italy
| | - Giuseppe Testa
- European Institute of Oncology, Department of Experimental Oncology, Via Adamello 16, 20139 Milano, Italy University of Milan, Department of Oncology and Hemato-Oncology, Via Festa del Perdono 7, 20122 Milano, Italy
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Germain PL. From replica to instruments: animal models in biomedical research. Hist Philos Life Sci 2014; 36:114-28. [PMID: 25515266 DOI: 10.1007/s40656-014-0007-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/16/2014] [Indexed: 05/09/2023]
Abstract
The ways in which other animal species can be informative about human biology are not exhausted by the traditional picture of the animal model. In this paper, I propose to distinguish two roles which laboratory organisms can have in biomedical research. In the more traditional case, organisms act as surrogates for human beings, and as such are expected to be more manageable replicas of humans. However, animal models can inform us about human biology in a much less straightforward way, by being used as measuring devices-what I call their instrumental role. I first characterize this role and provide criteria for it, before illustrating it with some examples from biomedical research, especially cancer research. In such an instrumental role, phenotypes are not expected to phenocopy human phenomena, but instead have the purely instrumental value of detecting or measuring differences. I argue that the instrumental role is more prevalent than might first be suspected, and that some characteristics of contemporary biomedical research are increasingly shifting the use of laboratory organisms to the instrumental role. Finally, in light of the distinction proposed, I discuss the meaning of the expression "animal model".
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Affiliation(s)
- Pierre-Luc Germain
- Università degli Studi di Milano and European Institute of Oncology (IEO), Campus IFOM-IEO, Via Adamello, 16, 20139, Milan, Italy,
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Caganova M, Carrisi C, Varano G, Mainoldi F, Zanardi F, Germain PL, George L, Alberghini F, Ferrarini L, Talukder AK, Ponzoni M, Testa G, Nojima T, Doglioni C, Kitamura D, Toellner KM, Su IH, Casola S. Germinal center dysregulation by histone methyltransferase EZH2 promotes lymphomagenesis. J Clin Invest 2014. [DOI: 10.1172/jci75675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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35
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Caganova M, Carrisi C, Varano G, Mainoldi F, Zanardi F, Germain PL, George L, Alberghini F, Ferrarini L, Talukder AK, Ponzoni M, Testa G, Nojima T, Doglioni C, Kitamura D, Toellner KM, Su IH, Casola S. Germinal center dysregulation by histone methyltransferase EZH2 promotes lymphomagenesis. J Clin Invest 2013; 123:5009-22. [PMID: 24200695 PMCID: PMC3859423 DOI: 10.1172/jci70626] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 09/03/2013] [Indexed: 01/13/2023] Open
Abstract
Protection against deadly pathogens requires the production of high-affinity antibodies by B cells, which are generated in germinal centers (GCs). Alteration of the GC developmental program is common in many B cell malignancies. Identification of regulators of the GC response is crucial to develop targeted therapies for GC B cell dysfunctions, including lymphomas. The histone H3 lysine 27 methyltransferase enhancer of zeste homolog 2 (EZH2) is highly expressed in GC B cells and is often constitutively activated in GC-derived non-Hodgkin lymphomas (NHLs). The function of EZH2 in GC B cells remains largely unknown. Herein, we show that Ezh2 inactivation in mouse GC B cells caused profound impairment of GC responses, memory B cell formation, and humoral immunity. EZH2 protected GC B cells against activation-induced cytidine deaminase (AID) mutagenesis, facilitated cell cycle progression, and silenced plasma cell determinant and tumor suppressor B-lymphocyte-induced maturation protein 1 (BLIMP1). EZH2 inhibition in NHL cells induced BLIMP1, which impaired tumor growth. In conclusion, EZH2 sustains AID function and prevents terminal differentiation of GC B cells, which allows antibody diversification and affinity maturation. Dysregulation of the GC reaction by constitutively active EZH2 facilitates lymphomagenesis and identifies EZH2 as a possible therapeutic target in NHL and other GC-derived B cell diseases.
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MESH Headings
- Animals
- Apoptosis
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- Cell Cycle
- Cytidine Deaminase/deficiency
- Cytidine Deaminase/genetics
- Cytidine Deaminase/physiology
- DNA Damage
- Enhancer of Zeste Homolog 2 Protein
- Enzyme Activation
- Gene Expression Regulation, Neoplastic
- Gene Rearrangement, B-Lymphocyte, Heavy Chain
- Gene Silencing
- Germinal Center/enzymology
- Germinal Center/immunology
- Germinal Center/pathology
- Immunity, Humoral
- Immunologic Memory
- Lymphoma, Non-Hodgkin/enzymology
- Lymphoma, Non-Hodgkin/etiology
- Lymphoma, Non-Hodgkin/genetics
- Lymphoma, Non-Hodgkin/pathology
- Lymphopoiesis
- Methylation
- Mice
- Mice, Transgenic
- Polycomb Repressive Complex 2/deficiency
- Polycomb Repressive Complex 2/genetics
- Polycomb Repressive Complex 2/physiology
- Positive Regulatory Domain I-Binding Factor 1
- Protein Processing, Post-Translational
- Transcription Factors/physiology
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Affiliation(s)
- Marieta Caganova
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Chiara Carrisi
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Gabriele Varano
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Federica Mainoldi
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Federica Zanardi
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Pierre-Luc Germain
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Laura George
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Federica Alberghini
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Luca Ferrarini
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Asoke K. Talukder
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Maurilio Ponzoni
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Giuseppe Testa
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Takuya Nojima
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Claudio Doglioni
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Daisuke Kitamura
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Kai-M. Toellner
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - I-hsin Su
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Stefano Casola
- The Institute of Molecular Oncology (IFOM) of the Italian Foundation for Cancer Research (FIRC), Milan, Italy.
European Institute of Oncology, Milan, Italy.
Medical Research Council Centre for Immune Regulation, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom.
InterpretOmics India, Bangalore, India.
Unit of Lymphoid Malignancies, Department of Onco-Haematology, San Raffaele Scientific Institute, Milan, Italy.
Division of Molecular Biology, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba, Japan.
Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore
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36
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Blasimme A, Maugeri P, Germain PL. What mechanisms can't do: explanatory frameworks and the function of the p53 gene in molecular oncology. Stud Hist Philos Biol Biomed Sci 2013; 44:374-84. [PMID: 23478029 DOI: 10.1016/j.shpsc.2013.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 02/08/2013] [Indexed: 05/21/2023]
Abstract
What has been called the new mechanistic philosophy conceives of mechanisms as the main providers of biological explanation. We draw on the characterization of the p53 gene in molecular oncology, to show that explaining a biological phenomenon (cancer, in our case) implies instead a dynamic interaction between the mechanistic level-rendered at the appropriate degree of ontological resolution-and far more general explanatory tools that perform a fundamental epistemic role in the provision of biological explanations. We call such tools "explanatory frameworks". They are called frameworks to stress their higher level of generality with respect to bare mechanisms; on the other hand, they are called explanatory because, as we show in this paper, their importance in explaining biological phenomena is not secondary with respect to mechanisms. We illustrate how explanatory frameworks establish selective and local criteria of causal relevance that drive the search for, characterisation and usage of biological mechanisms. Furthermore, we show that explanatory frameworks allow for changes of scientific perspective on the causal relevance of mechanisms going beyond the account provided by the new mechanistic philosophy.
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Affiliation(s)
- Alessandro Blasimme
- INSERM UMR 1027, Université Paul Sabatier, Département d'épidémiologie et de santé publique, Faculté de Médecine, 37 allées Jules Guesde F-31000 Toulouse, France.
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Fragola G, Germain PL, Laise P, Cuomo A, Blasimme A, Gross F, Signaroldi E, Bucci G, Sommer C, Pruneri G, Mazzarol G, Bonaldi T, Mostoslavsky G, Casola S, Testa G. Cell reprogramming requires silencing of a core subset of polycomb targets. PLoS Genet 2013; 9:e1003292. [PMID: 23468641 PMCID: PMC3585017 DOI: 10.1371/journal.pgen.1003292] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 12/16/2012] [Indexed: 01/16/2023] Open
Abstract
Transcription factor (TF)–induced reprogramming of somatic cells into induced pluripotent stem cells (iPSC) is associated with genome-wide changes in chromatin modifications. Polycomb-mediated histone H3 lysine-27 trimethylation (H3K27me3) has been proposed as a defining mark that distinguishes the somatic from the iPSC epigenome. Here, we dissected the functional role of H3K27me3 in TF–induced reprogramming through the inactivation of the H3K27 methylase EZH2 at the onset of reprogramming. Our results demonstrate that surprisingly the establishment of functional iPSC proceeds despite global loss of H3K27me3. iPSC lacking EZH2 efficiently silenced the somatic transcriptome and differentiated into tissues derived from the three germ layers. Remarkably, the genome-wide analysis of H3K27me3 in Ezh2 mutant iPSC cells revealed the retention of this mark on a highly selected group of Polycomb targets enriched for developmental regulators controlling the expression of lineage specific genes. Erasure of H3K27me3 from these targets led to a striking impairment in TF–induced reprogramming. These results indicate that PRC2-mediated H3K27 trimethylation is required on a highly selective core of Polycomb targets whose repression enables TF–dependent cell reprogramming. Multicellular organisms are composed of a variety of cell types. Over the last years we have learned that cell differentiation is fully reversible and that it takes few specific transcription factors (proteins that bind to DNA and regulate gene expression) to convert one cell type into another. The most dramatic example is the reprogramming of somatic cells into stem cells that reacquire the potential to give rise to all cell types of the body. This process entails the resetting of the gene expression program of the somatic cells necessary to acquire a pluripotent state but remains poorly understood. Here, we defined the role in cell reprogramming of the Polycomb axis, one of the key effectors of gene silencing that operates through a specific chemical modification of histones (the trimethylation of lysine-27 on histone H3) that is stably inherited from one cell generation to the next. Surprisingly, we uncovered a selective requirement for Polycomb silencing during somatic cell reprogramming. Upon inactivation of the essential Polycomb protein EZH2, histones trimethylated on lysine-27 were retained on a selected subset of physiological Polycomb target genes whose products control normal development, and erasure of the histone mark from these critical genes abolished reprogramming.
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Affiliation(s)
- Giulia Fragola
- European Institute of Oncology, IFOM-IEO Campus, Milan, Italy
- IFOM Foundation, FIRC Institute of Molecular Oncology Foundation, IFOM-IEO Campus, Milan, Italy
| | | | - Pasquale Laise
- European Institute of Oncology, IFOM-IEO Campus, Milan, Italy
| | | | | | - Fridolin Gross
- European Institute of Oncology, IFOM-IEO Campus, Milan, Italy
| | | | - Gabriele Bucci
- European Institute of Oncology, IFOM-IEO Campus, Milan, Italy
| | - Cesar Sommer
- Boston University School of Medicine, Boston, Massachusetts, United States of America
| | | | | | - Tiziana Bonaldi
- European Institute of Oncology, IFOM-IEO Campus, Milan, Italy
| | - Gustavo Mostoslavsky
- Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Stefano Casola
- IFOM Foundation, FIRC Institute of Molecular Oncology Foundation, IFOM-IEO Campus, Milan, Italy
- * E-mail: (S Casola); (G Testa)
| | - Giuseppe Testa
- European Institute of Oncology, IFOM-IEO Campus, Milan, Italy
- * E-mail: (S Casola); (G Testa)
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