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Petersen M, Hoffstaedter F, Nägele FL, Mayer C, Schell M, Rimmele DL, Zyriax BC, Zeller T, Kühn S, Gallinat J, Fiehler J, Twerenbold R, Omidvarnia A, Patil KR, Eickhoff SB, Thomalla G, Cheng B. A latent clinical-anatomical dimension relating metabolic syndrome to brain structure and cognition. eLife 2024; 12:RP93246. [PMID: 38512127 PMCID: PMC10957178 DOI: 10.7554/elife.93246] [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] [Indexed: 03/22/2024] Open
Abstract
The link between metabolic syndrome (MetS) and neurodegenerative as well as cerebrovascular conditions holds substantial implications for brain health in at-risk populations. This study elucidates the complex relationship between MetS and brain health by conducting a comprehensive examination of cardiometabolic risk factors, brain morphology, and cognitive function in 40,087 individuals. Multivariate, data-driven statistics identified a latent dimension linking more severe MetS to widespread brain morphological abnormalities, accounting for up to 71% of shared variance in the data. This dimension was replicable across sub-samples. In a mediation analysis, we could demonstrate that MetS-related brain morphological abnormalities mediated the link between MetS severity and cognitive performance in multiple domains. Employing imaging transcriptomics and connectomics, our results also suggest that MetS-related morphological abnormalities are linked to the regional cellular composition and macroscopic brain network organization. By leveraging extensive, multi-domain data combined with a dimensional stratification approach, our analysis provides profound insights into the association of MetS and brain health. These findings can inform effective therapeutic and risk mitigation strategies aimed at maintaining brain integrity.
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Affiliation(s)
- Marvin Petersen
- Department of Neurology, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Felix Hoffstaedter
- Institute for Systems Neuroscience, Medical Faculty, Heinrich-Heine University DüsseldorfDüsseldorfGermany
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM-7), Research Center JülichJülichGermany
| | - Felix L Nägele
- Department of Neurology, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Carola Mayer
- Department of Neurology, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Maximilian Schell
- Department of Neurology, University Medical Center Hamburg-EppendorfHamburgGermany
| | - D Leander Rimmele
- Department of Neurology, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Birgit-Christiane Zyriax
- Midwifery Science-Health Services Research and Prevention, Institute for Health Services Research in Dermatology and Nursing (IVDP), University Medical Center Hamburg-EppendorfHamburgGermany
| | - Tanja Zeller
- Department of Cardiology, University Heart and Vascular CenterHamburgGermany
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/LuebeckHamburgGermany
- University Center of Cardiovascular Science, University Heart and Vascular CenterHamburgGermany
| | - Simone Kühn
- Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Jürgen Gallinat
- Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Jens Fiehler
- Department of Diagnostic and Interventional Neuroradiology, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Raphael Twerenbold
- Department of Cardiology, University Heart and Vascular CenterHamburgGermany
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/LuebeckHamburgGermany
- University Center of Cardiovascular Science, University Heart and Vascular CenterHamburgGermany
- Epidemiological Study Center, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Amir Omidvarnia
- Institute for Systems Neuroscience, Medical Faculty, Heinrich-Heine University DüsseldorfDüsseldorfGermany
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM-7), Research Center JülichJülichGermany
| | - Kaustubh R Patil
- Institute for Systems Neuroscience, Medical Faculty, Heinrich-Heine University DüsseldorfDüsseldorfGermany
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM-7), Research Center JülichJülichGermany
| | - Simon B Eickhoff
- Institute for Systems Neuroscience, Medical Faculty, Heinrich-Heine University DüsseldorfDüsseldorfGermany
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM-7), Research Center JülichJülichGermany
| | - Goetz Thomalla
- Department of Neurology, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Bastian Cheng
- Department of Neurology, University Medical Center Hamburg-EppendorfHamburgGermany
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2
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Wohlwend M, Laurila PP, Goeminne LJE, Lima T, Daskalaki I, Li X, von Alvensleben G, Crisol B, Mangione R, Gallart-Ayala H, Burri O, Butler S, Morris J, Turner N, Ivanisevic J, Auwerx J. Inhibition of CERS1 in skeletal muscle exacerbates age-related muscle dysfunction. eLife 2024; 12:RP90522. [PMID: 38506902 PMCID: PMC10954306 DOI: 10.7554/elife.90522] [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] [Indexed: 03/21/2024] Open
Abstract
Age-related muscle wasting and dysfunction render the elderly population vulnerable and incapacitated, while underlying mechanisms are poorly understood. Here, we implicate the CERS1 enzyme of the de novo sphingolipid synthesis pathway in the pathogenesis of age-related skeletal muscle impairment. In humans, CERS1 abundance declines with aging in skeletal muscle cells and, correlates with biological pathways involved in muscle function and myogenesis. Furthermore, CERS1 is upregulated during myogenic differentiation. Pharmacological or genetic inhibition of CERS1 in aged mice blunts myogenesis and deteriorates aged skeletal muscle mass and function, which is associated with the occurrence of morphological features typical of inflammation and fibrosis. Ablation of the CERS1 orthologue lagr-1 in Caenorhabditis elegans similarly exacerbates the age-associated decline in muscle function and integrity. We discover genetic variants reducing CERS1 expression in human skeletal muscle and Mendelian randomization analysis in the UK biobank cohort shows that these variants reduce muscle grip strength and overall health. In summary, our findings link age-related impairments in muscle function to a reduction in CERS1, thereby underlining the importance of the sphingolipid biosynthesis pathway in age-related muscle homeostasis.
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Affiliation(s)
- Martin Wohlwend
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Pirkka-Pekka Laurila
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Ludger JE Goeminne
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Tanes Lima
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Ioanna Daskalaki
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Xiaoxu Li
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Giacomo von Alvensleben
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Barbara Crisol
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Renata Mangione
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Hector Gallart-Ayala
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne (UNIL)LausanneSwitzerland
| | - Olivier Burri
- Bioimaging and optics platform, École polytechnique fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Stephen Butler
- School of Chemistry, University of New South Wales SydneySydneyAustralia
| | - Jonathan Morris
- School of Chemistry, University of New South Wales SydneySydneyAustralia
| | - Nigel Turner
- Cellular Bioenergetics Laboratory, Victor Chang Cardiac Research InstituteDarlinghurstAustralia
- School of Biomedical Sciences, University of New South Wales SydneySydneyAustralia
| | - Julijana Ivanisevic
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne (UNIL)LausanneSwitzerland
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de LausanneLausanneSwitzerland
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3
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Hahn L, Eickhoff SB, Mueller K, Schilbach L, Barthel H, Fassbender K, Fliessbach K, Kornhuber J, Prudlo J, Synofzik M, Wiltfang J, Diehl-Schmid J, Otto M, Dukart J, Schroeter ML. Resting-state alterations in behavioral variant frontotemporal dementia are related to the distribution of monoamine and GABA neurotransmitter systems. eLife 2024; 13:e86085. [PMID: 38224473 PMCID: PMC10789488 DOI: 10.7554/elife.86085] [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: 01/10/2023] [Accepted: 12/14/2023] [Indexed: 01/16/2024] Open
Abstract
Background Aside to clinical changes, behavioral variant frontotemporal dementia (bvFTD) is characterized by progressive structural and functional alterations in frontal and temporal regions. We examined if there is a selective vulnerability of specific neurotransmitter systems in bvFTD by evaluating the link between disease-related functional alterations and the spatial distribution of specific neurotransmitter systems and their underlying gene expression levels. Methods Maps of fractional amplitude of low-frequency fluctuations (fALFF) were derived as a measure of local activity from resting-state functional magnetic resonance imaging for 52 bvFTD patients (mean age = 61.5 ± 10.0 years; 14 females) and 22 healthy controls (HC) (mean age = 63.6 ± 11.9 years; 13 females). We tested if alterations of fALFF in patients co-localize with the non-pathological distribution of specific neurotransmitter systems and their coding mRNA gene expression. Furthermore, we evaluated if the strength of co-localization is associated with the observed clinical symptoms. Results Patients displayed significantly reduced fALFF in frontotemporal and frontoparietal regions. These alterations co-localized with the distribution of serotonin (5-HT1b and 5-HT2a) and γ-aminobutyric acid type A (GABAa) receptors, the norepinephrine transporter (NET), and their encoding mRNA gene expression. The strength of co-localization with NET was associated with cognitive symptoms and disease severity of bvFTD. Conclusions Local brain functional activity reductions in bvFTD followed the distribution of specific neurotransmitter systems indicating a selective vulnerability. These findings provide novel insight into the disease mechanisms underlying functional alterations. Our data-driven method opens the road to generate new hypotheses for pharmacological interventions in neurodegenerative diseases even beyond bvFTD. Funding This study has been supported by the German Consortium for Frontotemporal Lobar Degeneration, funded by the German Federal Ministry of Education and Research (BMBF; grant no. FKZ01GI1007A).
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Affiliation(s)
- Lisa Hahn
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre JülichJülichGermany
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Simon B Eickhoff
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre JülichJülichGermany
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Karsten Mueller
- Max Planck Institute for Human Cognitive and Brain SciencesLeipzigGermany
| | - Leonhard Schilbach
- LVR-Klinikum DüsseldorfDüsseldorfGermany
- Medical Faculty, Ludwig-Maximilians-UniversitätMünchenGermany
| | - Henryk Barthel
- Department for Nuclear Medicine, University Hospital LeipzigLeipzigGermany
| | - Klaus Fassbender
- Department of Neurology, Saarland University HospitalHomburgGermany
| | - Klaus Fliessbach
- Department of Psychiatry and Psychotherapy, University Hospital BonnBonnGermany
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Johannes Kornhuber
- Department of Psychiatry and Psychotherapy, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-NurembergErlangenGermany
| | - Johannes Prudlo
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
- Department of Neurology, University Medicine RostockRostockGermany
| | - Matthis Synofzik
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain ResearchTübingenGermany
| | - Jens Wiltfang
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen (UMG), Medical University GöttingenGöttingenGermany
- Neurosciences and Signaling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of AveiroAveiroPortugal
| | - Janine Diehl-Schmid
- Department of Psychiatry and Psychotherapy, Technical University of MunichMunichGermany
- kbo-Inn-Salzach-Klinikum, Clinical Center for Psychiatry, Psychotherapy, Psychosomatic Medicine, Geriatrics and NeurologyWasserburg/InnGermany
| | | | - Markus Otto
- Department of Neurology, Ulm UniversityUlmGermany
- Department of Neurology, Martin-Luther-University Halle-WittenbergHalleGermany
| | - Juergen Dukart
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre JülichJülichGermany
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Matthias L Schroeter
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain SciencesLeipzigGermany
- Clinic for Cognitive Neurology, University Hospital LeipzigLeipzigGermany
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4
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Vitet H, Bruyère J, Xu H, Séris C, Brocard J, Abada YS, Delatour B, Scaramuzzino C, Venance L, Saudou F. Huntingtin recruits KIF1A to transport synaptic vesicle precursors along the mouse axon to support synaptic transmission and motor skill learning. eLife 2023; 12:e81011. [PMID: 37431882 PMCID: PMC10365837 DOI: 10.7554/elife.81011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/06/2023] [Indexed: 07/12/2023] Open
Abstract
Neurotransmitters are released at synapses by synaptic vesicles (SVs), which originate from SV precursors (SVPs) that have traveled along the axon. Because each synapse maintains a pool of SVs, only a small fraction of which are released, it has been thought that axonal transport of SVPs does not affect synaptic function. Here, studying the corticostriatal network both in microfluidic devices and in mice, we find that phosphorylation of the Huntingtin protein (HTT) increases axonal transport of SVPs and synaptic glutamate release by recruiting the kinesin motor KIF1A. In mice, constitutive HTT phosphorylation causes SV over-accumulation at synapses, increases the probability of SV release, and impairs motor skill learning on the rotating rod. Silencing KIF1A in these mice restored SV transport and motor skill learning to wild-type levels. Axonal SVP transport within the corticostriatal network thus influences synaptic plasticity and motor skill learning.
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Affiliation(s)
- Hélène Vitet
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut NeuroscienceGrenobleFrance
| | - Julie Bruyère
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut NeuroscienceGrenobleFrance
| | - Hao Xu
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSLParisFrance
| | - Claire Séris
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut NeuroscienceGrenobleFrance
| | - Jacques Brocard
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut NeuroscienceGrenobleFrance
| | - Yah-Sé Abada
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute, ICM, Inserm U1127, CNRS UMR7225ParisFrance
| | - Benoît Delatour
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute, ICM, Inserm U1127, CNRS UMR7225ParisFrance
| | - Chiara Scaramuzzino
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut NeuroscienceGrenobleFrance
| | - Laurent Venance
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSLParisFrance
| | - Frédéric Saudou
- Univ. Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Grenoble Institut NeuroscienceGrenobleFrance
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5
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Cumplido-Mayoral I, García-Prat M, Operto G, Falcon C, Shekari M, Cacciaglia R, Milà-Alomà M, Lorenzini L, Ingala S, Meije Wink A, Mutsaerts HJMM, Minguillón C, Fauria K, Molinuevo JL, Haller S, Chetelat G, Waldman A, Schwarz AJ, Barkhof F, Suridjan I, Kollmorgen G, Bayfield A, Zetterberg H, Blennow K, Suárez-Calvet M, Vilaplana V, Gispert JD. Biological brain age prediction using machine learning on structural neuroimaging data: Multi-cohort validation against biomarkers of Alzheimer's disease and neurodegeneration stratified by sex. eLife 2023; 12:e81067. [PMID: 37067031 PMCID: PMC10181824 DOI: 10.7554/elife.81067] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 04/10/2023] [Indexed: 04/18/2023] Open
Abstract
Brain-age can be inferred from structural neuroimaging and compared to chronological age (brain-age delta) as a marker of biological brain aging. Accelerated aging has been found in neurodegenerative disorders like Alzheimer's disease (AD), but its validation against markers of neurodegeneration and AD is lacking. Here, imaging-derived measures from the UK Biobank dataset (N=22,661) were used to predict brain-age in 2,314 cognitively unimpaired (CU) individuals at higher risk of AD and mild cognitive impaired (MCI) patients from four independent cohorts with available biomarker data: ALFA+, ADNI, EPAD, and OASIS. Brain-age delta was associated with abnormal amyloid-β, more advanced stages (AT) of AD pathology and APOE-ε4 status. Brain-age delta was positively associated with plasma neurofilament light, a marker of neurodegeneration, and sex differences in the brain effects of this marker were found. These results validate brain-age delta as a non-invasive marker of biological brain aging in non-demented individuals with abnormal levels of biomarkers of AD and axonal injury.
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Affiliation(s)
- Irene Cumplido-Mayoral
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- Universitat Pompeu FabraBarcelonaSpain
| | - Marina García-Prat
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
| | - Grégory Operto
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- CIBER Fragilidad y Envejecimiento Saludable (CIBERFES)MadridFrance
| | - Carles Falcon
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN)MadridSpain
| | - Mahnaz Shekari
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- Universitat Pompeu FabraBarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
| | - Raffaele Cacciaglia
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- CIBER Fragilidad y Envejecimiento Saludable (CIBERFES)MadridFrance
| | - Marta Milà-Alomà
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- Universitat Pompeu FabraBarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- CIBER Fragilidad y Envejecimiento Saludable (CIBERFES)MadridFrance
| | - Luigi Lorenzini
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit AmsterdamAmsterdamNetherlands
| | - Silvia Ingala
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit AmsterdamAmsterdamNetherlands
| | - Alle Meije Wink
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit AmsterdamAmsterdamNetherlands
| | - Henk JMM Mutsaerts
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit AmsterdamAmsterdamNetherlands
| | - Carolina Minguillón
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- CIBER Fragilidad y Envejecimiento Saludable (CIBERFES)MadridFrance
| | - Karine Fauria
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- CIBER Fragilidad y Envejecimiento Saludable (CIBERFES)MadridFrance
| | - José Luis Molinuevo
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
| | - Sven Haller
- CIRD Centre d'Imagerie Rive DroiteGenevaSwitzerland
| | - Gael Chetelat
- Normandie Univ, UNICAEN, INSERM, U1237, PhIND "Physiopathology and Imaging of Neurological Disorders", Institut Blood and BrainCyceronFrance
| | - Adam Waldman
- Centre for Dementia Prevention, Edinburgh Imaging, and UK Dementia Research Institute at The University of EdinburghEdinburghUnited Kingdom
| | | | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Amsterdam Neuroscience, Vrije Universiteit AmsterdamAmsterdamNetherlands
- Institutes of Neurology and Healthcare Engineering, University College LondonLondonUnited Kingdom
| | | | | | | | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, University of GothenburgMölndalSweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University HospitalMölndalSweden
- Department of Neurodegenerative Disease, UCL Queen Square Institute of NeurologyLondonUnited Kingdom
- Hong Kong Center for Neurodegenerative DiseasesHong KongChina
- UK Dementia Research Institute at UCLLondonUnited Kingdom
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, University of GothenburgMölndalSweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University HospitalMölndalSweden
| | - Marc Suárez-Calvet
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- CIBER Fragilidad y Envejecimiento Saludable (CIBERFES)MadridFrance
- Servei de Neurologia, Hospital del MarBarcelonaSpain
| | - Verónica Vilaplana
- Department of Signal Theory and Communications, Universitat Politècnica de CatalunyaBarcelonaSpain
| | - Juan Domingo Gispert
- Barcelonaβeta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
- IMIM (Hospital del Mar Medical Research Institute)BarcelonaSpain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN)MadridSpain
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6
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Aguinagalde Salazar L, den Boer MA, Castenmiller SM, Zwarthoff SA, de Haas C, Aerts PC, Beurskens FJ, Schuurman J, Heck AJR, van Kessel K, Rooijakkers SHM. Promoting Fc-Fc interactions between anti-capsular antibodies provides strong immune protection against Streptococcus pneumoniae. eLife 2023; 12:80669. [PMID: 36947116 PMCID: PMC10032657 DOI: 10.7554/elife.80669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 03/09/2023] [Indexed: 03/23/2023] Open
Abstract
Streptococcus pneumoniae is the leading cause of community-acquired pneumonia and an important cause of childhood mortality. Despite the introduction of successful vaccines, the global spread of both non-vaccine serotypes and antibiotic-resistant strains reinforces the development of alternative therapies against this pathogen. One possible route is the development of monoclonal antibodies (mAbs) that induce killing of bacteria via the immune system. Here, we investigate whether mAbs can be used to induce killing of pneumococcal serotypes for which the current vaccines show unsuccessful protection. Our study demonstrates that when human mAbs against pneumococcal capsule polysaccharides (CPS) have a poor capacity to induce complement activation, a critical process for immune protection against pneumococci, their activity can be strongly improved by hexamerization-enhancing mutations. Our data indicate that anti-capsular antibodies may have a low capacity to form higher-order oligomers (IgG hexamers) that are needed to recruit complement component C1. Indeed, specific point mutations in the IgG-Fc domain that strengthen hexamerization strongly enhance C1 recruitment and downstream complement activation on encapsulated pneumococci. Specifically, hexamerization-enhancing mutations E430G or E345K in CPS6-IgG strongly potentiate complement activation on S. pneumoniae strains that express capsular serotype 6 (CPS6), and the highly invasive serotype 19A strain. Furthermore, these mutations improve complement activation via mAbs recognizing CPS3 and CPS8 strains. Importantly, hexamer-enhancing mutations enable mAbs to induce strong opsonophagocytic killing by human neutrophils. Finally, passive immunization with CPS6-IgG1-E345K protected mice from developing severe pneumonia. Altogether, this work provides an important proof of concept for future optimization of antibody therapies against encapsulated bacteria.
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Affiliation(s)
| | - Maurits A den Boer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
- Netherlands Proteomics Center, Utrecht, Netherlands
| | - Suzanne M Castenmiller
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Seline A Zwarthoff
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Carla de Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Piet C Aerts
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | | | | | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
- Netherlands Proteomics Center, Utrecht, Netherlands
| | - Kok van Kessel
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Suzan H M Rooijakkers
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
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7
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Haenelt D, Trampel R, Nasr S, Polimeni JR, Tootell RBH, Sereno MI, Pine KJ, Edwards LJ, Helbling S, Weiskopf N. High-resolution quantitative and functional MRI indicate lower myelination of thin and thick stripes in human secondary visual cortex. eLife 2023; 12:e78756. [PMID: 36888685 PMCID: PMC9995117 DOI: 10.7554/elife.78756] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 02/08/2023] [Indexed: 03/09/2023] Open
Abstract
The characterization of cortical myelination is essential for the study of structure-function relationships in the human brain. However, knowledge about cortical myelination is largely based on post-mortem histology, which generally renders direct comparison to function impossible. The repeating pattern of pale-thin-pale-thick stripes of cytochrome oxidase (CO) activity in the primate secondary visual cortex (V2) is a prominent columnar system, in which histology also indicates different myelination of thin/thick versus pale stripes. We used quantitative magnetic resonance imaging (qMRI) in conjunction with functional magnetic resonance imaging (fMRI) at ultra-high field strength (7 T) to localize and study myelination of stripes in four human participants at sub-millimeter resolution in vivo. Thin and thick stripes were functionally localized by exploiting their sensitivity to color and binocular disparity, respectively. Resulting functional activation maps showed robust stripe patterns in V2 which enabled further comparison of quantitative relaxation parameters between stripe types. Thereby, we found lower longitudinal relaxation rates (R1) of thin and thick stripes compared to surrounding gray matter in the order of 1-2%, indicating higher myelination of pale stripes. No consistent differences were found for effective transverse relaxation rates (R2*). The study demonstrates the feasibility to investigate structure-function relationships in living humans within one cortical area at the level of columnar systems using qMRI.
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Affiliation(s)
- Daniel Haenelt
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain SciencesLeipzigGermany
- International Max Planck Research School on Neuroscience of Communication: Function, Structure, and PlasticityLeipzigGermany
| | - Robert Trampel
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain SciencesLeipzigGermany
| | - Shahin Nasr
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General HospitalCharlestownUnited States
- Department of Radiology, Harvard Medical SchoolBostonUnited States
| | - Jonathan R Polimeni
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General HospitalCharlestownUnited States
- Department of Radiology, Harvard Medical SchoolBostonUnited States
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Roger BH Tootell
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General HospitalCharlestownUnited States
- Department of Radiology, Harvard Medical SchoolBostonUnited States
| | - Martin I Sereno
- Department of Psychology, College of Sciences, San Diego State UniversitySan DiegoUnited States
| | - Kerrin J Pine
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain SciencesLeipzigGermany
| | - Luke J Edwards
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain SciencesLeipzigGermany
| | - Saskia Helbling
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain SciencesLeipzigGermany
- Poeppel Lab, Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck SocietyFrankfurt am MainGermany
| | - Nikolaus Weiskopf
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain SciencesLeipzigGermany
- Felix Bloch Institute for Solid State Physics, Faculty of Physics and Earth Sciences, Leipzig UniversityLeipzigGermany
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8
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Jimenez-Vazquez EN, Arad M, Macías Á, Vera-Pedrosa ML, Cruz FM, Gutierrez LK, Cuttitta AJ, Monteiro da Rocha A, Herron TJ, Ponce-Balbuena D, Guerrero-Serna G, Binah O, Michele DE, Jalife J. SNTA1 gene rescues ion channel function and is antiarrhythmic in cardiomyocytes derived from induced pluripotent stem cells from muscular dystrophy patients. eLife 2022; 11:e76576. [PMID: 35762211 PMCID: PMC9239678 DOI: 10.7554/elife.76576] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/07/2022] [Indexed: 01/10/2023] Open
Abstract
Background Patients with cardiomyopathy of Duchenne Muscular Dystrophy (DMD) are at risk of developing life-threatening arrhythmias, but the mechanisms are unknown. We aimed to determine the role of ion channels controlling cardiac excitability in the mechanisms of arrhythmias in DMD patients. Methods To test whether dystrophin mutations lead to defective cardiac NaV1.5-Kir2.1 channelosomes and arrhythmias, we generated iPSC-CMs from two hemizygous DMD males, a heterozygous female, and two unrelated control males. We conducted studies including confocal microscopy, protein expression analysis, patch-clamping, non-viral piggy-bac gene expression, optical mapping and contractility assays. Results Two patients had abnormal ECGs with frequent runs of ventricular tachycardia. iPSC-CMs from all DMD patients showed abnormal action potential profiles, slowed conduction velocities, and reduced sodium (INa) and inward rectifier potassium (IK1) currents. Membrane NaV1.5 and Kir2.1 protein levels were reduced in hemizygous DMD iPSC-CMs but not in heterozygous iPSC-CMs. Remarkably, transfecting just one component of the dystrophin protein complex (α1-syntrophin) in hemizygous iPSC-CMs from one patient restored channelosome function, INa and IK1 densities, and action potential profile in single cells. In addition, α1-syntrophin expression restored impulse conduction and contractility and prevented reentrant arrhythmias in hiPSC-CM monolayers. Conclusions We provide the first demonstration that iPSC-CMs reprogrammed from skin fibroblasts of DMD patients with cardiomyopathy have a dysfunction of the NaV1.5-Kir2.1 channelosome, with consequent reduction of cardiac excitability and conduction. Altogether, iPSC-CMs from patients with DMD cardiomyopathy have a NaV1.5-Kir2.1 channelosome dysfunction, which can be rescued by the scaffolding protein α1-syntrophin to restore excitability and prevent arrhythmias. Funding Supported by National Institutes of Health R01 HL122352 grant; 'la Caixa' Banking Foundation (HR18-00304); Fundación La Marató TV3: Ayudas a la investigación en enfermedades raras 2020 (LA MARATO-2020); Instituto de Salud Carlos III/FEDER/FSE; Horizon 2020 - Research and Innovation Framework Programme GA-965286 to JJ; the CNIC is supported by the Instituto de Salud Carlos III (ISCIII), the Ministerio de Ciencia e Innovación (MCIN) and the Pro CNIC Foundation), and is a Severo Ochoa Center of Excellence (grant CEX2020-001041-S funded by MICIN/AEI/10.13039/501100011033). American Heart Association postdoctoral fellowship 19POST34380706s to JVEN. Israel Science Foundation to OB and MA [824/19]. Rappaport grant [01012020RI]; and Niedersachsen Foundation [ZN3452] to OB; US-Israel Binational Science Foundation (BSF) to OB and TH [2019039]; Dr. Bernard Lublin Donation to OB; and The Duchenne Parent Project Netherlands (DPPNL 2029771) to OB. National Institutes of Health R01 AR068428 to DM and US-Israel Binational Science Foundation Grant [2013032] to DM and OB.
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Affiliation(s)
- Eric N Jimenez-Vazquez
- Department of Internal Medicine and Molecular and Integrative Physiology, Center for Arrhythmia Research, University of MichiganAnn ArborUnited States
| | - Michael Arad
- Leviev Heart Center, Sheba Medical Center, Tel Hashomer, and Tel Aviv UniversityTel AvivIsrael
| | - Álvaro Macías
- Centro Nacional de Investigaciones Cardiovasculares (CNIC) Carlos III, Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV)MadridSpain
| | - Maria L Vera-Pedrosa
- Centro Nacional de Investigaciones Cardiovasculares (CNIC) Carlos III, Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV)MadridSpain
| | - Francisco Miguel Cruz
- Centro Nacional de Investigaciones Cardiovasculares (CNIC) Carlos III, Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV)MadridSpain
| | - Lilian K Gutierrez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC) Carlos III, Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV)MadridSpain
| | - Ashley J Cuttitta
- Department of Molecular and Integrative Physiology, University of Michigan Medical SchoolAnn ArborUnited States
| | - André Monteiro da Rocha
- Department of Internal Medicine and Molecular and Integrative Physiology, Center for Arrhythmia Research, University of MichiganAnn ArborUnited States
| | - Todd J Herron
- Department of Internal Medicine and Molecular and Integrative Physiology, Center for Arrhythmia Research, University of MichiganAnn ArborUnited States
| | - Daniela Ponce-Balbuena
- Department of Internal Medicine and Molecular and Integrative Physiology, Center for Arrhythmia Research, University of MichiganAnn ArborUnited States
| | - Guadalupe Guerrero-Serna
- Department of Internal Medicine and Molecular and Integrative Physiology, Center for Arrhythmia Research, University of MichiganAnn ArborUnited States
| | - Ofer Binah
- Department of Physiology, Biophysics and Systems Biology, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of TechnologyHaifaIsrael
| | - Daniel E Michele
- Department of Molecular and Integrative Physiology, University of Michigan Medical SchoolAnn ArborUnited States
| | - José Jalife
- Department of Internal Medicine and Molecular and Integrative Physiology, Center for Arrhythmia Research, University of MichiganAnn ArborUnited States
- Centro Nacional de Investigaciones Cardiovasculares (CNIC) Carlos III, Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV)MadridSpain
- Department of Molecular and Integrative Physiology, University of Michigan Medical SchoolAnn ArborUnited States
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9
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Chen Y, Li F, Nielsen J. Genome-scale modeling of yeast metabolism: retrospectives and perspectives. FEMS Yeast Res 2022; 22:foac003. [PMID: 35094064 PMCID: PMC8862083 DOI: 10.1093/femsyr/foac003] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/06/2022] [Accepted: 01/27/2022] [Indexed: 11/30/2022] Open
Abstract
Yeasts have been widely used for production of bread, beer and wine, as well as for production of bioethanol, but they have also been designed as cell factories to produce various chemicals, advanced biofuels and recombinant proteins. To systematically understand and rationally engineer yeast metabolism, genome-scale metabolic models (GEMs) have been reconstructed for the model yeast Saccharomyces cerevisiae and nonconventional yeasts. Here, we review the historical development of yeast GEMs together with their recent applications, including metabolic flux prediction, cell factory design, culture condition optimization and multi-yeast comparative analysis. Furthermore, we present an emerging effort, namely the integration of proteome constraints into yeast GEMs, resulting in models with improved performance. At last, we discuss challenges and perspectives on the development of yeast GEMs and the integration of proteome constraints.
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Affiliation(s)
- Yu Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Feiran Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- BioInnovation Institute, DK2200 Copenhagen N, Denmark
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10
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Kalidindi HT, Cross KP, Lillicrap TP, Omrani M, Falotico E, Sabes PN, Scott SH. Rotational dynamics in motor cortex are consistent with a feedback controller. eLife 2021; 10:e67256. [PMID: 34730516 PMCID: PMC8691841 DOI: 10.7554/elife.67256] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
Recent studies have identified rotational dynamics in motor cortex (MC), which many assume arise from intrinsic connections in MC. However, behavioral and neurophysiological studies suggest that MC behaves like a feedback controller where continuous sensory feedback and interactions with other brain areas contribute substantially to MC processing. We investigated these apparently conflicting theories by building recurrent neural networks that controlled a model arm and received sensory feedback from the limb. Networks were trained to counteract perturbations to the limb and to reach toward spatial targets. Network activities and sensory feedback signals to the network exhibited rotational structure even when the recurrent connections were removed. Furthermore, neural recordings in monkeys performing similar tasks also exhibited rotational structure not only in MC but also in somatosensory cortex. Our results argue that rotational structure may also reflect dynamics throughout the voluntary motor system involved in online control of motor actions.
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Affiliation(s)
| | - Kevin P Cross
- Centre for Neuroscience Studies, Queen's UniversityKingstonCanada
| | - Timothy P Lillicrap
- Centre for Computation, Mathematics and Physics, University College LondonLondonUnited Kingdom
| | - Mohsen Omrani
- Centre for Neuroscience Studies, Queen's UniversityKingstonCanada
| | - Egidio Falotico
- The BioRobotics Institute, Scuola Superiore Sant'AnnaPisaItaly
| | - Philip N Sabes
- Department of Physiology, University of California, San FranciscoSan FranciscoUnited States
| | - Stephen H Scott
- Centre for Neuroscience Studies, Queen's UniversityKingstonCanada
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11
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Lemke SM, Ramanathan DS, Darevksy D, Egert D, Berke JD, Ganguly K. Coupling between motor cortex and striatum increases during sleep over long-term skill learning. eLife 2021; 10:e64303. [PMID: 34505576 PMCID: PMC8439654 DOI: 10.7554/elife.64303] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 08/09/2021] [Indexed: 01/02/2023] Open
Abstract
The strength of cortical connectivity to the striatum influences the balance between behavioral variability and stability. Learning to consistently produce a skilled action requires plasticity in corticostriatal connectivity associated with repeated training of the action. However, it remains unknown whether such corticostriatal plasticity occurs during training itself or 'offline' during time away from training, such as sleep. Here, we monitor the corticostriatal network throughout long-term skill learning in rats and find that non-rapid-eye-movement (NREM) sleep is a relevant period for corticostriatal plasticity. We first show that the offline activation of striatal NMDA receptors is required for skill learning. We then show that corticostriatal functional connectivity increases offline, coupled to emerging consistent skilled movements, and coupled cross-area neural dynamics. We then identify NREM sleep spindles as uniquely poised to mediate corticostriatal plasticity, through interactions with slow oscillations. Our results provide evidence that sleep shapes cross-area coupling required for skill learning.
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Affiliation(s)
- Stefan M Lemke
- Neuroscience Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Neurology Service, San Francisco Veterans Affairs Medical CenterSan FranciscoUnited States
- Department of Neurology, University of California, San FranciscoSan FranciscoUnited States
- Istituto Italiano di TecnologiaRoveretoItaly
| | | | - David Darevksy
- Neurology Service, San Francisco Veterans Affairs Medical CenterSan FranciscoUnited States
- Department of Neurology, University of California, San FranciscoSan FranciscoUnited States
| | - Daniel Egert
- Department of Neurology, University of California, San FranciscoSan FranciscoUnited States
| | - Joshua D Berke
- Department of Neurology, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences and Kavli Institute for Fundamental Neuroscience, University of California, San FranciscoSan FranciscoUnited States
| | - Karunesh Ganguly
- Neurology Service, San Francisco Veterans Affairs Medical CenterSan FranciscoUnited States
- Department of Neurology, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences and Kavli Institute for Fundamental Neuroscience, University of California, San FranciscoSan FranciscoUnited States
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12
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Kim BY, Wang JR, Miller DE, Barmina O, Delaney E, Thompson A, Comeault AA, Peede D, D'Agostino ERR, Pelaez J, Aguilar JM, Haji D, Matsunaga T, Armstrong EE, Zych M, Ogawa Y, Stamenković-Radak M, Jelić M, Veselinović MS, Tanasković M, Erić P, Gao JJ, Katoh TK, Toda MJ, Watabe H, Watada M, Davis JS, Moyle LC, Manoli G, Bertolini E, Košťál V, Hawley RS, Takahashi A, Jones CD, Price DK, Whiteman N, Kopp A, Matute DR, Petrov DA. Highly contiguous assemblies of 101 drosophilid genomes. eLife 2021; 10:e66405. [PMID: 34279216 PMCID: PMC8337076 DOI: 10.7554/elife.66405] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/16/2021] [Indexed: 12/13/2022] Open
Abstract
Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.
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Affiliation(s)
- Bernard Y Kim
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Jeremy R Wang
- Department of Genetics, University of North CarolinaChapel HillUnited States
| | - Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children’s HospitalSeattleUnited States
| | - Olga Barmina
- Department of Evolution and Ecology, University of California DavisDavisUnited States
| | - Emily Delaney
- Department of Evolution and Ecology, University of California DavisDavisUnited States
| | - Ammon Thompson
- Department of Evolution and Ecology, University of California DavisDavisUnited States
| | - Aaron A Comeault
- School of Natural Sciences, Bangor UniversityBangorUnited Kingdom
| | - David Peede
- Biology Department, University of North CarolinaChapel HillUnited States
| | | | - Julianne Pelaez
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Jessica M Aguilar
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Diler Haji
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Teruyuki Matsunaga
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | | | - Molly Zych
- Molecular and Cellular Biology Program, University of WashingtonSeattleUnited States
| | - Yoshitaka Ogawa
- Department of Biological Sciences, Tokyo Metropolitan UniversityHachiojiJapan
| | | | - Mihailo Jelić
- Faculty of Biology, University of BelgradeBelgradeSerbia
| | | | - Marija Tanasković
- University of Belgrade, Institute for Biological Research "Siniša Stanković", National Institute of Republic of SerbiaBelgradeSerbia
| | - Pavle Erić
- University of Belgrade, Institute for Biological Research "Siniša Stanković", National Institute of Republic of SerbiaBelgradeSerbia
| | - Jian-Jun Gao
- School of Ecology and Environmental Science, Yunnan UniversityKunmingChina
| | - Takehiro K Katoh
- School of Ecology and Environmental Science, Yunnan UniversityKunmingChina
| | | | - Hideaki Watabe
- Biological Laboratory, Sapporo College, Hokkaido University of EducationSapporoJapan
| | - Masayoshi Watada
- Graduate School of Science and Engineering, Ehime UniversityMatsuyamaJapan
| | - Jeremy S Davis
- Department of Biology, University of KentuckyLexingtonUnited States
| | - Leonie C Moyle
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Giulia Manoli
- Neurobiology and Genetics, Theodor Boveri Institute, Biocentre, University of WürzburgWürzburgGermany
| | - Enrico Bertolini
- Neurobiology and Genetics, Theodor Boveri Institute, Biocentre, University of WürzburgWürzburgGermany
| | - Vladimír Košťál
- Institute of Entomology, Biology Centre, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - R Scott Hawley
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Stowers Institute for Medical ResearchKansas CityUnited States
| | - Aya Takahashi
- Department of Biological Sciences, Tokyo Metropolitan UniversityHachiojiJapan
| | - Corbin D Jones
- Biology Department, University of North CarolinaChapel HillUnited States
| | - Donald K Price
- School of Life Science, University of NevadaLas VegasUnited States
| | - Noah Whiteman
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California DavisDavisUnited States
| | - Daniel R Matute
- Biology Department, University of North CarolinaChapel HillUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
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13
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Cura Costa E, Otsuki L, Rodrigo Albors A, Tanaka EM, Chara O. Spatiotemporal control of cell cycle acceleration during axolotl spinal cord regeneration. eLife 2021; 10:e55665. [PMID: 33988504 PMCID: PMC8205487 DOI: 10.7554/elife.55665] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/13/2021] [Indexed: 01/05/2023] Open
Abstract
Axolotls are uniquely able to resolve spinal cord injuries, but little is known about the mechanisms underlying spinal cord regeneration. We previously found that tail amputation leads to reactivation of a developmental-like program in spinal cord ependymal cells (Rodrigo Albors et al., 2015), characterized by a high-proliferation zone emerging 4 days post-amputation (Rost et al., 2016). What underlies this spatiotemporal pattern of cell proliferation, however, remained unknown. Here, we use modeling, tightly linked to experimental data, to demonstrate that this regenerative response is consistent with a signal that recruits ependymal cells during ~85 hours after amputation within ~830 μm of the injury. We adapted Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) technology to axolotls (AxFUCCI) to visualize cell cycles in vivo. AxFUCCI axolotls confirmed the predicted appearance time and size of the injury-induced recruitment zone and revealed cell cycle synchrony between ependymal cells. Our modeling and imaging move us closer to understanding bona fide spinal cord regeneration.
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Affiliation(s)
- Emanuel Cura Costa
- Systems Biology Group (SysBio), Institute of Physics of Liquids and Biological Systems (IFLySIB), National Scientific and Technical Research Council (CONICET) and University of La Plata (UNLP)La PlataArgentina
| | - Leo Otsuki
- The Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Aida Rodrigo Albors
- Division of Cell and Developmental Biology, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Elly M Tanaka
- The Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC)ViennaAustria
| | - Osvaldo Chara
- Systems Biology Group (SysBio), Institute of Physics of Liquids and Biological Systems (IFLySIB), National Scientific and Technical Research Council (CONICET) and University of La Plata (UNLP)La PlataArgentina
- Center for Information Services and High Performance Computing, Technische Universität DresdenDresdenGermany
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14
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Wang D, Hensman J, Kutkaite G, Toh TS, Galhoz A, Dry JR, Saez-Rodriguez J, Garnett MJ, Menden MP, Dondelinger F. A statistical framework for assessing pharmacological responses and biomarkers using uncertainty estimates. eLife 2020; 9:e60352. [PMID: 33274713 PMCID: PMC7746236 DOI: 10.7554/elife.60352] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/04/2020] [Indexed: 12/16/2022] Open
Abstract
High-throughput testing of drugs across molecular-characterised cell lines can identify candidate treatments and discover biomarkers. However, the cells' response to a drug is typically quantified by a summary statistic from a best-fit dose-response curve, whilst neglecting the uncertainty of the curve fit and the potential variability in the raw readouts. Here, we model the experimental variance using Gaussian Processes, and subsequently, leverage uncertainty estimates to identify associated biomarkers with a new Bayesian framework. Applied to in vitro screening data on 265 compounds across 1074 cancer cell lines, our models identified 24 clinically established drug-response biomarkers, and provided evidence for six novel biomarkers by accounting for association with low uncertainty. We validated our uncertainty estimates with an additional drug screen of 26 drugs, 10 cell lines with 8 to 9 replicates. Our method is applicable to any dose-response data without replicates, and improves biomarker discovery for precision medicine.
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Affiliation(s)
- Dennis Wang
- Sheffield Institute for Translational Neuroscience, University of SheffieldSheffieldUnited Kingdom
- Department of Computer Science, University of SheffieldSheffieldUnited Kingdom
| | | | - Ginte Kutkaite
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental HealthNeuherbergGermany
- Department of Biology, Ludwig-Maximilians University MunichMartinsriedGermany
| | - Tzen S Toh
- The Medical School, University of SheffieldSheffieldUnited Kingdom
| | - Ana Galhoz
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental HealthNeuherbergGermany
- Department of Biology, Ludwig-Maximilians University MunichMartinsriedGermany
| | - Jonathan R Dry
- Research and Early Development, Oncology R&D, AstraZenecaBostonUnited States
| | - Julio Saez-Rodriguez
- Institute of Computational Biomedicine,Faculty of Medicine,Heidelberg Universityand Heidelberg University Hospital, BioquantHeidelbergGermany
| | | | - Michael P Menden
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental HealthNeuherbergGermany
- Department of Biology, Ludwig-Maximilians University MunichMartinsriedGermany
- German Center for Diabetes Research (DZD e.V.)NeuherbergGermany
| | - Frank Dondelinger
- Centre for Health Informatics, Computation and Statistics, Lancaster Medical School, Lancaster UniversityLancasterUnited Kingdom
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15
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Ashraf U, Benoit-Pilven C, Navratil V, Ligneau C, Fournier G, Munier S, Sismeiro O, Coppée JY, Lacroix V, Naffakh N. Influenza virus infection induces widespread alterations of host cell splicing. NAR Genom Bioinform 2020; 2:lqaa095. [PMID: 33575639 PMCID: PMC7680258 DOI: 10.1093/nargab/lqaa095] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/24/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022] Open
Abstract
Influenza A viruses (IAVs) use diverse mechanisms to interfere with cellular gene expression. Although many RNA-seq studies have documented IAV-induced changes in host mRNA abundance, few were designed to allow an accurate quantification of changes in host mRNA splicing. Here, we show that IAV infection of human lung cells induces widespread alterations of cellular splicing, with an overall increase in exon inclusion and decrease in intron retention. Over half of the mRNAs that show differential splicing undergo no significant changes in abundance or in their 3' end termination site, suggesting that IAVs can specifically manipulate cellular splicing. Among a randomly selected subset of 21 IAV-sensitive alternative splicing events, most are specific to IAV infection as they are not observed upon infection with VSV, induction of interferon expression or induction of an osmotic stress. Finally, the analysis of splicing changes in RED-depleted cells reveals a limited but significant overlap with the splicing changes in IAV-infected cells. This observation suggests that hijacking of RED by IAVs to promote splicing of the abundant viral NS1 mRNAs could partially divert RED from its target mRNAs. All our RNA-seq datasets and analyses are made accessible for browsing through a user-friendly Shiny interface (http://virhostnet.prabi.fr:3838/shinyapps/flu-splicing or https://github.com/cbenoitp/flu-splicing).
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Affiliation(s)
- Usama Ashraf
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 75013 Paris, France
| | - Clara Benoit-Pilven
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR5292, 69675 Bron, France
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, Université Lyon 1, 69622 Villeurbanne, France
- EPI ERABLE, INRIA Grenoble Rhône-Alpes, 38330 Montbonnot-Saint-Martin France
| | - Vincent Navratil
- PRABI, Rhône-Alpes Bioinformatics Center, Université Lyon 1, 69622 Villeurbanne, France
- European Virus Bioinformatics Center, 07743 Jena, Germany
- Institut Français de Bioinformatique, IFB-core, UMS 3601, 91057 Évry, France
| | - Cécile Ligneau
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
| | - Guillaume Fournier
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
| | - Sandie Munier
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
| | - Odile Sismeiro
- Institut Pasteur, Pôle BIOMICS, Plateforme Transcriptome et Epigenome, 75015 Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Pôle BIOMICS, Plateforme Transcriptome et Epigenome, 75015 Paris, France
| | - Vincent Lacroix
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, Université Lyon 1, 69622 Villeurbanne, France
- EPI ERABLE, INRIA Grenoble Rhône-Alpes, 38330 Montbonnot-Saint-Martin France
| | - Nadia Naffakh
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR3569, Université de Paris, 75015 Paris, France
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16
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Cleary CM, Moreira TS, Takakura AC, Nelson MT, Longden TA, Mulkey DK. Vascular control of the CO 2/H +-dependent drive to breathe. eLife 2020; 9:e59499. [PMID: 32924935 PMCID: PMC7521922 DOI: 10.7554/elife.59499] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/14/2020] [Indexed: 12/17/2022] Open
Abstract
Respiratory chemoreceptors regulate breathing in response to changes in tissue CO2/H+. Blood flow is a fundamental determinant of tissue CO2/H+, yet little is known regarding how regulation of vascular tone in chemoreceptor regions contributes to respiratory behavior. Previously, we showed in rat that CO2/H+-vasoconstriction in the retrotrapezoid nucleus (RTN) supports chemoreception by a purinergic-dependent mechanism (Hawkins et al., 2017). Here, we show in mice that CO2/H+ dilates arterioles in other chemoreceptor regions, thus demonstrating CO2/H+ vascular reactivity in the RTN is unique. We also identify P2Y2 receptors in RTN smooth muscle cells as the substrate responsible for this response. Specifically, pharmacological blockade or genetic deletion of P2Y2 from smooth muscle cells blunted the ventilatory response to CO2, and re-expression of P2Y2 receptors only in RTN smooth muscle cells fully rescued the CO2/H+ chemoreflex. These results identify P2Y2 receptors in RTN smooth muscle cells as requisite determinants of respiratory chemoreception.
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MESH Headings
- Animals
- Carbon Dioxide/metabolism
- Chemoreceptor Cells/metabolism
- Hydrogen/metabolism
- Medulla Oblongata/physiology
- Mice
- Mice, Knockout
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/physiology
- Receptors, Purinergic P2Y2/genetics
- Receptors, Purinergic P2Y2/metabolism
- Receptors, Purinergic P2Y2/physiology
- Respiration
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Affiliation(s)
- Colin M Cleary
- Department of Physiology and Neurobiology, University of ConnecticutStorrsUnited States
| | - Thiago S Moreira
- Department of Physiology and Biophysics, University of São PauloSão PauloBrazil
| | - Ana C Takakura
- Department of Pharmacology, University of São PauloSão PauloBrazil
| | - Mark T Nelson
- Department of Pharmacology, University of VermontBurlingtonUnited States
- Institute of Cardiovascular SciencesManchesterUnited Kingdom
| | - Thomas A Longden
- Department of Physiology, University of MarylandBaltimoreUnited States
| | - Daniel K Mulkey
- Department of Physiology and Neurobiology, University of ConnecticutStorrsUnited States
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17
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Takemura H, Palomero-Gallagher N, Axer M, Gräßel D, Jorgensen MJ, Woods R, Zilles K. Anatomy of nerve fiber bundles at micrometer-resolution in the vervet monkey visual system. eLife 2020; 9:e55444. [PMID: 32844747 PMCID: PMC7532002 DOI: 10.7554/elife.55444] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 08/22/2020] [Indexed: 12/11/2022] Open
Abstract
Although the primate visual system has been extensively studied, detailed spatial organization of white matter fiber tracts carrying visual information between areas has not been fully established. This is mainly due to the large gap between tracer studies and diffusion-weighted MRI studies, which focus on specific axonal connections and macroscale organization of fiber tracts, respectively. Here we used 3D polarization light imaging (3D-PLI), which enables direct visualization of fiber tracts at micrometer resolution, to identify and visualize fiber tracts of the visual system, such as stratum sagittale, inferior longitudinal fascicle, vertical occipital fascicle, tapetum and dorsal occipital bundle in vervet monkey brains. Moreover, 3D-PLI data provide detailed information on cortical projections of these tracts, distinction between neighboring tracts, and novel short-range pathways. This work provides essential information for interpretation of functional and diffusion-weighted MRI data, as well as revision of wiring diagrams based upon observations in the vervet visual system.
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Affiliation(s)
- Hiromasa Takemura
- Center for Information and Neural Networks (CiNet), National Institute of Information and Communications Technology, and Osaka UniversityOsakaJapan
- Graduate School of Frontier Biosciences, Osaka UniversityOsakaJapan
| | - Nicola Palomero-Gallagher
- Institute of Neuroscience and Medicine INM-1, Research Centre JülichJülichGermany
- Department of Psychiatry, Psychotherapy and Psychosomatics, Medical Faculty, RWTH AachenAachenGermany
- C. & O. Vogt Institute for Brain Research, Heinrich-Heine-UniversityDüsseldorfGermany
| | - Markus Axer
- Institute of Neuroscience and Medicine INM-1, Research Centre JülichJülichGermany
| | - David Gräßel
- Institute of Neuroscience and Medicine INM-1, Research Centre JülichJülichGermany
| | - Matthew J Jorgensen
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of MedicineWinston-SalemUnited States
| | - Roger Woods
- Ahmanson-Lovelace Brain Mapping Center, Departments of Neurology and of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLALos AngelesUnited States
| | - Karl Zilles
- Institute of Neuroscience and Medicine INM-1, Research Centre JülichJülichGermany
- JARA - Translational Brain MedicineAachenGermany
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18
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Humphrey J, Birsa N, Milioto C, McLaughlin M, Ule AM, Robaldo D, Eberle AB, Kräuchi R, Bentham M, Brown AL, Jarvis S, Bodo C, Garone M, Devoy A, Soraru G, Rosa A, Bozzoni I, Fisher EMC, Mühlemann O, Schiavo G, Ruepp MD, Isaacs AM, Plagnol V, Fratta P. FUS ALS-causative mutations impair FUS autoregulation and splicing factor networks through intron retention. Nucleic Acids Res 2020; 48:6889-6905. [PMID: 32479602 PMCID: PMC7337901 DOI: 10.1093/nar/gkaa410] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 04/21/2020] [Accepted: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
Mutations in the RNA-binding protein FUS cause amyotrophic lateral sclerosis (ALS), a devastating neurodegenerative disease. FUS plays a role in numerous aspects of RNA metabolism, including mRNA splicing. However, the impact of ALS-causative mutations on splicing has not been fully characterized, as most disease models have been based on overexpressing mutant FUS, which will alter RNA processing due to FUS autoregulation. We and others have recently created knockin models that overcome the overexpression problem, and have generated high depth RNA-sequencing on FUS mutants in parallel to FUS knockout, allowing us to compare mutation-induced changes to genuine loss of function. We find that FUS-ALS mutations induce a widespread loss of function on expression and splicing. Specifically, we find that mutant FUS directly alters intron retention levels in RNA-binding proteins. Moreover, we identify an intron retention event in FUS itself that is associated with its autoregulation. Altered FUS levels have been linked to disease, and we show here that this novel autoregulation mechanism is altered by FUS mutations. Crucially, we also observe this phenomenon in other genetic forms of ALS, including those caused by TDP-43, VCP and SOD1 mutations, supporting the concept that multiple ALS genes interact in a regulatory network.
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Affiliation(s)
- Jack Humphrey
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- UK Dementia Research Institute
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Nicol Birsa
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- UK Dementia Research Institute
| | - Carmelo Milioto
- UK Dementia Research Institute
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Martha McLaughlin
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Agnieszka M Ule
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - David Robaldo
- UK Dementia Research Institute
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Andrea B Eberle
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern 3012, Switzerland
| | - Rahel Kräuchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern 3012, Switzerland
| | - Matthew Bentham
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Anna-Leigh Brown
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Seth Jarvis
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- UK Dementia Research Institute
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Cristian Bodo
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | | | - Anny Devoy
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- UK Dementia Research Institute
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, London SE5 9RT, UK
| | - Gianni Soraru
- Department of Neurosciences, Università degli Studi di Padova, Padova 35121, Italy
| | - Alessandro Rosa
- Sapienza University of Rome, Rome 00185, Italy
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Rome 00161, Italy
| | - Irene Bozzoni
- Sapienza University of Rome, Rome 00185, Italy
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Rome 00161, Italy
| | - Elizabeth M C Fisher
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern 3012, Switzerland
| | - Giampietro Schiavo
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- UK Dementia Research Institute
- Discoveries Centre for Regenerative and Precision Medicine, University College London Campus, London WC1N 3BG, UK
| | - Marc-David Ruepp
- UK Dementia Research Institute
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, London SE5 9RT, UK
| | - Adrian M Isaacs
- UK Dementia Research Institute
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Vincent Plagnol
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
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19
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Rugani R, Vallortigara G, Priftis K, Regolin L. Numerical magnitude, rather than individual bias, explains spatial numerical association in newborn chicks. eLife 2020; 9:e54662. [PMID: 32584257 PMCID: PMC7316507 DOI: 10.7554/elife.54662] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 05/31/2020] [Indexed: 11/29/2022] Open
Abstract
We associate small numbers with the left and large numbers with the right side of space. Recent evidence from human newborns and non-human animals has challenged the primary role assigned to culture, in determining this spatial numerical association (SNA). Nevertheless, the effect of individual spatial biases has not been considered in previous research. Here, we tested the effect of numerical magnitude in SNA and we controlled for itablendividual biases. We trained 3-day-old chicks (Gallus gallus) on a given numerical magnitude (5). Then chicks could choose between two identical, left or right, stimuli both representing either 2, 8, or 5 elements. We computed the percentage of Left-sided Choice (LC). Numerical magnitude, but not individual lateral bias, explained LC: LC2 vs. 2>LC5 vs. 5>LC8 vs. 8. These findings suggest that SNA originates from pre-linguistic precursors, and pave the way to the investigation of the neural correlates of the number space association.
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Affiliation(s)
- Rosa Rugani
- Department of General Psychology, University of PadovaPadovaItaly
- Department of Psychology, University of PennsylvaniaPhiladelphiaUnited States
| | | | | | - Lucia Regolin
- Department of General Psychology, University of PadovaPadovaItaly
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20
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Reichmann J, Dobie K, Lister LM, Crichton JH, Best D, MacLennan M, Read D, Raymond ES, Hung CC, Boyle S, Shirahige K, Cooke HJ, Herbert M, Adams IR. Tex19.1 inhibits the N-end rule pathway and maintains acetylated SMC3 cohesin and sister chromatid cohesion in oocytes. J Cell Biol 2020; 219:e201702123. [PMID: 32232464 PMCID: PMC7199850 DOI: 10.1083/jcb.201702123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 12/31/2019] [Accepted: 02/11/2020] [Indexed: 12/14/2022] Open
Abstract
Age-dependent oocyte aneuploidy, a major cause of Down syndrome, is associated with declining sister chromatid cohesion in postnatal oocytes. Here we show that cohesion in postnatal mouse oocytes is regulated by Tex19.1. We show Tex19.1-/- oocytes have defects maintaining chiasmata, missegregate their chromosomes during meiosis, and transmit aneuploidies to the next generation. Furthermore, we show that mouse Tex19.1 inhibits N-end rule protein degradation mediated by its interacting partner UBR2, and that Ubr2 itself has a previously undescribed role in negatively regulating the acetylated SMC3 subpopulation of cohesin in mitotic somatic cells. Lastly, we show that acetylated SMC3 is associated with meiotic chromosome axes in mouse oocytes, and that this population of cohesin is specifically depleted in the absence of Tex19.1. These findings indicate that Tex19.1 regulates UBR protein activity to maintain acetylated SMC3 and sister chromatid cohesion in postnatal oocytes and prevent aneuploidy from arising in the female germline.
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Affiliation(s)
- Judith Reichmann
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Karen Dobie
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Lisa M. Lister
- Institute for Genetic Medicine, Newcastle University, Biomedicine West Wing, Centre for Life, Newcastle upon Tyne, UK
| | - James H. Crichton
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Diana Best
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Marie MacLennan
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - David Read
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Eleanor S. Raymond
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Chao-Chun Hung
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Shelagh Boyle
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Katsuhiko Shirahige
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Howard J. Cooke
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Mary Herbert
- Institute for Genetic Medicine, Newcastle University, Biomedicine West Wing, Centre for Life, Newcastle upon Tyne, UK
- Newcastle Fertility Centre, Biomedicine West Wing, Centre for Life, Newcastle upon Tyne, UK
| | - Ian R. Adams
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
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21
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Weis S, Patil KR, Hoffstaedter F, Nostro A, Yeo BTT, Eickhoff SB. Sex Classification by Resting State Brain Connectivity. Cereb Cortex 2020; 30:824-835. [PMID: 31251328 PMCID: PMC7444737 DOI: 10.1093/cercor/bhz129] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 05/03/2019] [Accepted: 05/28/2019] [Indexed: 12/15/2022] Open
Abstract
A large amount of brain imaging research has focused on group studies delineating differences between males and females with respect to both cognitive performance as well as structural and functional brain organization. To supplement existing findings, the present study employed a machine learning approach to assess how accurately participants' sex can be classified based on spatially specific resting state (RS) brain connectivity, using 2 samples from the Human Connectome Project (n1 = 434, n2 = 310) and 1 fully independent sample from the 1000BRAINS study (n = 941). The classifier, which was trained on 1 sample and tested on the other 2, was able to reliably classify sex, both within sample and across independent samples, differing both with respect to imaging parameters and sample characteristics. Brain regions displaying highest sex classification accuracies were mainly located along the cingulate cortex, medial and lateral frontal cortex, temporoparietal regions, insula, and precuneus. These areas were stable across samples and match well with previously described sex differences in functional brain organization. While our data show a clear link between sex and regionally specific brain connectivity, they do not support a clear-cut dimorphism in functional brain organization that is driven by sex alone.
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Affiliation(s)
- Susanne Weis
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich, Germany
| | - Kaustubh R Patil
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich, Germany
| | - Felix Hoffstaedter
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich, Germany
| | - Alessandra Nostro
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Art and Sciences (KNAW), Amsterdam, the Netherlands
| | - B T Thomas Yeo
- ECE, CIRC, N.1, MNP and NGS, National University of Singapore, Singapore
| | - Simon B Eickhoff
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich, Germany
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22
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Xiong Z, Dankova G, Howe LJ, Lee MK, Hysi PG, de Jong MA, Zhu G, Adhikari K, Li D, Li Y, Pan B, Feingold E, Marazita ML, Shaffer JR, McAloney K, Xu SH, Jin L, Wang S, de Vrij FMS, Lendemeijer B, Richmond S, Zhurov A, Lewis S, Sharp GC, Paternoster L, Thompson H, Gonzalez-Jose R, Bortolini MC, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Uitterlinden AG, Ikram MA, Wolvius E, Kushner SA, Nijsten TEC, Palstra RJTS, Boehringer S, Medland SE, Tang K, Ruiz-Linares A, Martin NG, Spector TD, Stergiakouli E, Weinberg SM, Liu F, Kayser M. Novel genetic loci affecting facial shape variation in humans. eLife 2019; 8:e49898. [PMID: 31763980 PMCID: PMC6905649 DOI: 10.7554/elife.49898] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 07/03/2019] [Accepted: 11/22/2019] [Indexed: 12/14/2022] Open
Abstract
The human face represents a combined set of highly heritable phenotypes, but knowledge on its genetic architecture remains limited, despite the relevance for various fields. A series of genome-wide association studies on 78 facial shape phenotypes quantified from 3-dimensional facial images of 10,115 Europeans identified 24 genetic loci reaching study-wide suggestive association (p < 5 × 10-8), among which 17 were previously unreported. A follow-up multi-ethnic study in additional 7917 individuals confirmed 10 loci including six unreported ones (padjusted < 2.1 × 10-3). A global map of derived polygenic face scores assembled facial features in major continental groups consistent with anthropological knowledge. Analyses of epigenomic datasets from cranial neural crest cells revealed abundant cis-regulatory activities at the face-associated genetic loci. Luciferase reporter assays in neural crest progenitor cells highlighted enhancer activities of several face-associated DNA variants. These results substantially advance our understanding of the genetic basis underlying human facial variation and provide candidates for future in-vivo functional studies.
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Affiliation(s)
- Ziyi Xiong
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Gabriela Dankova
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Laurence J Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
| | - Pirro G Hysi
- Department of Twin Research and Genetic EpidemiologyKing’s College LondonLondonUnited Kingdom
| | - Markus A de Jong
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Oral & Maxillofacial Surgery, Special Dental Care, and OrthodonticsErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenNetherlands
| | - Gu Zhu
- QIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Kaustubh Adhikari
- Department of Genetics, Evolution, and EnvironmentUniversity College LondonLondonUnited Kingdom
| | - Dan Li
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
| | - Yi Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Bo Pan
- Department of Auricular ReconstructionPlastic Surgery HospitalBeijingChina
| | - Eleanor Feingold
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
| | - John R Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
| | | | - Shu-Hua Xu
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Li Jin
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life SciencesFudan UniversityShanghaiChina
| | - Sijia Wang
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Femke MS de Vrij
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Bas Lendemeijer
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Stephen Richmond
- Applied Clinical Research and Public Health, University Dental SchoolCardiff UniversityCardiffUnited Kingdom
| | - Alexei Zhurov
- Applied Clinical Research and Public Health, University Dental SchoolCardiff UniversityCardiffUnited Kingdom
| | - Sarah Lewis
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Gemma C Sharp
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
- School of Oral and Dental SciencesUniversity of BristolBristolUnited Kingdom
| | - Lavinia Paternoster
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Holly Thompson
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Rolando Gonzalez-Jose
- Instituto Patagonico de Ciencias Sociales y Humanas, CENPAT-CONICETPuerto MadrynArgentina
| | | | - Samuel Canizales-Quinteros
- UNAM-Instituto Nacional de Medicina Genomica, Facultad de QuımicaUnidad de Genomica de Poblaciones Aplicada a la SaludMexico CityMexico
| | - Carla Gallo
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y FilosofıaUniversidad Peruana Cayetano HerediaLimaPeru
| | - Giovanni Poletti
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y FilosofıaUniversidad Peruana Cayetano HerediaLimaPeru
| | - Gabriel Bedoya
- GENMOL (Genetica Molecular)Universidad de AntioquiaMedellınColombia
| | | | - André G Uitterlinden
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Internal MedicineErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - M Arfan Ikram
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Eppo Wolvius
- Department of Oral & Maxillofacial Surgery, Special Dental Care, and OrthodonticsErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Steven A Kushner
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Tamar EC Nijsten
- Department of DermatologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Robert-Jan TS Palstra
- Department of BiochemistryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Stefan Boehringer
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenNetherlands
| | | | - Kun Tang
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
| | - Andres Ruiz-Linares
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life SciencesFudan UniversityShanghaiChina
- Aix-Marseille Université, CNRS, EFS, ADESMarseilleFrance
| | | | - Timothy D Spector
- Department of Twin Research and Genetic EpidemiologyKing’s College LondonLondonUnited Kingdom
| | - Evie Stergiakouli
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
- School of Oral and Dental SciencesUniversity of BristolBristolUnited Kingdom
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
- Department of AnthropologyUniversity of PittsburghPittsburghUnited States
| | - Fan Liu
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Manfred Kayser
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
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