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Peerboom C, de Kater S, Jonker N, Rieter MPJM, Wijne T, Wierenga CJ. Delaying the GABA Shift Indirectly Affects Membrane Properties in the Developing Hippocampus. J Neurosci 2023; 43:5483-5500. [PMID: 37438107 PMCID: PMC10376938 DOI: 10.1523/jneurosci.0251-23.2023] [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: 02/10/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/14/2023] Open
Abstract
During the first two postnatal weeks, intraneuronal chloride concentrations in rodents gradually decrease, causing a shift from depolarizing to hyperpolarizing GABA responses. The postnatal GABA shift is delayed in rodent models for neurodevelopmental disorders and in human patients, but the impact of a delayed GABA shift on the developing brain remains obscure. Here we examine the direct and indirect consequences of a delayed postnatal GABA shift on network development in organotypic hippocampal cultures made from 6- to 7-d-old mice by treating the cultures for 1 week with VU0463271, a specific inhibitor of the chloride exporter KCC2. We verified that VU treatment delayed the GABA shift and kept GABA signaling depolarizing until DIV9. We found that the structural and functional development of excitatory and inhibitory synapses at DIV9 was not affected after VU treatment. In line with previous studies, we observed that GABA signaling was already inhibitory in control and VU-treated postnatal slices. Surprisingly, 14 d after the VU treatment had ended (DIV21), we observed an increased frequency of spontaneous inhibitory postsynaptic currents in CA1 pyramidal cells, while excitatory currents were not changed. Synapse numbers and release probability were unaffected. We found that dendrite-targeting interneurons in the stratum radiatum had an elevated resting membrane potential, while pyramidal cells were less excitable compared with control slices. Our results show that depolarizing GABA signaling does not promote synapse formation after P7, and suggest that postnatal intracellular chloride levels indirectly affect membrane properties in a cell-specific manner.SIGNIFICANCE STATEMENT During brain development, the action of neurotransmitter GABA shifts from depolarizing to hyperpolarizing. This shift is a thought to play a critical role in synapse formation. A delayed shift is common in rodent models for neurodevelopmental disorders and in human patients, but its consequences for synaptic development remain obscure. Here, we delayed the GABA shift by 1 week in organotypic hippocampal cultures and carefully examined the consequences for circuit development. We find that delaying the shift has no direct effects on synaptic development, but instead leads to indirect, cell type-specific changes in membrane properties. Our data call for careful assessment of alterations in cellular excitability in neurodevelopmental disorders.
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Affiliation(s)
- Carlijn Peerboom
- Cell Biology, Neurobiology and Biophysics, Biology Department, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Sam de Kater
- Cell Biology, Neurobiology and Biophysics, Biology Department, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Nikki Jonker
- Cell Biology, Neurobiology and Biophysics, Biology Department, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Marijn P J M Rieter
- Cell Biology, Neurobiology and Biophysics, Biology Department, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Tessel Wijne
- Cell Biology, Neurobiology and Biophysics, Biology Department, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Corette J Wierenga
- Cell Biology, Neurobiology and Biophysics, Biology Department, Utrecht University, Utrecht, 3584 CH, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, 6525 AJ, The Netherlands
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Scheper J, Badenhausser I, Kantelhardt J, Kirchweger S, Bartomeus I, Bretagnolle V, Clough Y, Gross N, Raemakers I, Vilà M, Zaragoza-Trello C, Kleijn D. Biodiversity and pollination benefits trade off against profit in an intensive farming system. Proc Natl Acad Sci U S A 2023; 120:e2212124120. [PMID: 37399410 PMCID: PMC10334771 DOI: 10.1073/pnas.2212124120] [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: 07/15/2022] [Accepted: 05/17/2023] [Indexed: 07/05/2023] Open
Abstract
Agricultural expansion and intensification have boosted global food production but have come at the cost of environmental degradation and biodiversity loss. Biodiversity-friendly farming that boosts ecosystem services, such as pollination and natural pest control, is widely being advocated to maintain and improve agricultural productivity while safeguarding biodiversity. A vast body of evidence showing the agronomic benefits of enhanced ecosystem service delivery represent important incentives to adopt practices enhancing biodiversity. However, the costs of biodiversity-friendly management are rarely taken into account and may represent a major barrier impeding uptake by farmers. Whether and how biodiversity conservation, ecosystem service delivery, and farm profit can go hand in hand is unknown. Here, we quantify the ecological, agronomic, and net economic benefits of biodiversity-friendly farming in an intensive grassland-sunflower system in Southwest France. We found that reducing land-use intensity on agricultural grasslands drastically enhances flower availability and wild bee diversity, including rare species. Biodiversity-friendly management on grasslands furthermore resulted in an up to 17% higher revenue on neighboring sunflower fields through positive effects on pollination service delivery. However, the opportunity costs of reduced grassland forage yields consistently exceeded the economic benefits of enhanced sunflower pollination. Our results highlight that profitability is often a key constraint hampering adoption of biodiversity-based farming and uptake critically depends on society's willingness to pay for associated delivery of public goods such as biodiversity.
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Affiliation(s)
- Jeroen Scheper
- Plant Ecology and Nature Conservation Group, Wageningen University, 6700 AAWageningen, The Netherlands
| | - Isabelle Badenhausser
- Unité de Recherche Pluridisciplinaire Prairies Plantes Fourragères, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, F-86600Lusignan, France
| | - Jochen Kantelhardt
- Institute of Agricultural and Forestry Economics, Department of Economics and Social Sciences, University of Natural Resources and Life Sciences, Vienna, 1180Vienna, Austria
| | - Stefan Kirchweger
- Studienzentrum für Internationale Analysen–Schlierbach, Studienzentrum für Internationale Analysen, 4553Schlierbach, Austria
| | - Ignasi Bartomeus
- Estación Biológica de Doñana – Consejo Superior de Investigaciones Científicas, E-41092Sevilla, Spain
| | - Vincent Bretagnolle
- Centre d’Etudes Biologiques de Chizé, UMR7372, Centre national de la recherche scientifique & Université de La Rochelle, F-79360Villiers-en-Bois, France
- Long-Term Socio-Ecological Research platform « Zone Atelier Plaine & Val de Sèvre », 79360Villiers-en-Bois, France
| | - Yann Clough
- Centre for Environmental and Climate Science, Lund University, 22362Lund, Sweden
| | - Nicolas Gross
- Université Clermont Auvergne, l’Institut national de recherche pour l’agriculture, l’alimentation et l’environnement, VetAgro Sup, Unité Mixte de Recherche 212 Ecosystème Prairial, F-63000Clermont-Ferrand, France
| | - Ivo Raemakers
- Independent amateur entomologist, 6247CGGronsveld, The Netherlands
| | - Montserrat Vilà
- Estación Biológica de Doñana – Consejo Superior de Investigaciones Científicas, E-41092Sevilla, Spain
- Department of Plant Biology and Ecology, Facultad de Biología, University of Sevilla, 41012Sevilla, Spain
| | - Carlos Zaragoza-Trello
- Estación Biológica de Doñana – Consejo Superior de Investigaciones Científicas, E-41092Sevilla, Spain
| | - David Kleijn
- Plant Ecology and Nature Conservation Group, Wageningen University, 6700 AAWageningen, The Netherlands
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de Haas RJ, Tas RP, van den Broek D, Zheng C, Nguyen H, Kang A, Bera AK, King NP, Voets IK, de Vries R. De novo designed ice-binding proteins from twist-constrained helices. Proc Natl Acad Sci U S A 2023; 120:e2220380120. [PMID: 37364125 PMCID: PMC10319034 DOI: 10.1073/pnas.2220380120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/02/2023] [Indexed: 06/28/2023] Open
Abstract
Attaining molecular-level control over solidification processes is a crucial aspect of materials science. To control ice formation, organisms have evolved bewildering arrays of ice-binding proteins (IBPs), but these have poorly understood structure-activity relationships. We propose that reverse engineering using de novo computational protein design can shed light on structure-activity relationships of IBPs. We hypothesized that the model alpha-helical winter flounder antifreeze protein uses an unusual undertwisting of its alpha-helix to align its putative ice-binding threonine residues in exactly the same direction. We test this hypothesis by designing a series of straight three-helix bundles with an ice-binding helix projecting threonines and two supporting helices constraining the twist of the ice-binding helix. Our findings show that ice-recrystallization inhibition by the designed proteins increases with the degree of designed undertwisting, thus validating our hypothesis, and opening up avenues for the computational design of IBPs.
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Affiliation(s)
- Robbert J. de Haas
- Department of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen, WE6708, The Netherlands
| | - Roderick P. Tas
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, MB5600, The Netherlands
| | - Daniëlle van den Broek
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, MB5600, The Netherlands
| | - Chuanbao Zheng
- Department of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen, WE6708, The Netherlands
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Ilja K. Voets
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, MB5600, The Netherlands
| | - Renko de Vries
- Department of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen, WE6708, The Netherlands
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Carotti V, van Megen WH, Rigalli JP, Barros ER, Sommers V, Rutten L, Sommerdijk N, Peters DJM, van Asbeck-van der Wijst J, Hoenderop JGJ. Extracellular vesicles contribute to early cyst development in autosomal dominant polycystic kidney disease by cell-to-cell communication. FASEB J 2023; 37:e23006. [PMID: 37249915 DOI: 10.1096/fj.202300490r] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 05/31/2023]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is characterized by the formation of fluid-filled cysts within the kidney due to mutations in PKD1 or PKD2. Although the disease remains incompletely understood, one of the factors associated with ADPKD progression is the release of nucleotides (including ATP), which can initiate autocrine or paracrine purinergic signaling by binding to their receptors. Recently, we and others have shown that increased extracellular vesicle (EVs) release from PKD1 knockout cells can stimulate cyst growth through effects on recipient cells. Given that EVs are an important communicator between different nephron segments, we hypothesize that EVs released from PKD1 knockout distal convoluted tubule (DCT) cells can stimulate cyst growth in the downstream collecting duct (CD). Here, we show that administration of EVs derived from Pkd1-/- mouse distal convoluted tubule (mDCT15) cells result in a significant increase in extracellular ATP release from Pkd1-/- mouse inner medullary collecting duct (iMCD3) cells. In addition, exposure of Pkd1-/- iMCD3 cells to EVs derived from Pkd1-/- mDCT15 cells led to an increase in the phosphorylation of the serine/threonine-specific protein Akt, suggesting activation of proliferative pathways. Finally, the exposure of iMCD3 Pkd1-/- cells to mDCT15 Pkd1-/- EVs increased cyst size in Matrigel. These findings indicate that EVs could be involved in intersegmental communication between the distal convoluted tubule and the collecting duct and potentially stimulate cyst growth.
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Affiliation(s)
- Valentina Carotti
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Wouter H van Megen
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Juan P Rigalli
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Eric R Barros
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Vera Sommers
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Luco Rutten
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nico Sommerdijk
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Joost G J Hoenderop
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, the Netherlands
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55
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Kang S, Kim G, Choi M, Jeong M, van der Heden van Noort GJ, Roh SH, Shin D. Structural insights into ubiquitin chain cleavage by Legionella ovarian tumor deubiquitinases. Life Sci Alliance 2023; 6:e202201876. [PMID: 37100438 PMCID: PMC10133868 DOI: 10.26508/lsa.202201876] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/17/2023] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
Although ubiquitin is found only in eukaryotes, several pathogenic bacteria and viruses possess proteins that hinder the host ubiquitin system. Legionella, a gram-negative intracellular bacterium, possesses an ovarian tumor (OTU) family of deubiquitinases (Lot DUBs). Herein, we describe the molecular characteristics of Lot DUBs. We elucidated the structure of the LotA OTU1 domain and revealed that entire Lot DUBs possess a characteristic extended helical lobe that is not found in other OTU-DUBs. The structural topology of an extended helical lobe is the same throughout the Lot family, and it provides an S1' ubiquitin-binding site. Moreover, the catalytic triads of Lot DUBs resemble those of the A20-type OTU-DUBs. Furthermore, we revealed a unique mechanism by which LotA OTU domains cooperate together to distinguish the length of the chain and preferentially cleave longer K48-linked polyubiquitin chains. The LotA OTU1 domain itself cleaves K6-linked ubiquitin chains, whereas it is also essential for assisting the cleavage of longer K48-linked polyubiquitin chains by the OTU2 domain. Thus, this study provides novel insights into the structure and mechanism of action of Lot DUBs.
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Affiliation(s)
- Sangwoo Kang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Gyuhee Kim
- School of Biological Science, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Minhyeong Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Minwoo Jeong
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | | | - Soung-Hun Roh
- School of Biological Science, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Donghyuk Shin
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
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56
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Ouboter HT, Arshad A, Berger S, Saucedo Sanchez JG, Op den Camp HJM, Jetten MSM, Welte CU, Kurth JM. Acetate and Acetyl-CoA Metabolism of ANME-2 Anaerobic Archaeal Methanotrophs. Appl Environ Microbiol 2023; 89:e0036723. [PMID: 37272802 PMCID: PMC10304654 DOI: 10.1128/aem.00367-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 03/02/2023] [Accepted: 05/15/2023] [Indexed: 06/06/2023] Open
Abstract
Acetyl-CoA synthetase (ACS) and acetate ligase (ACD) are widespread among microorganisms, including archaea, and play an important role in their carbon metabolism, although only a few of these enzymes have been characterized. Anaerobic methanotrophs (ANMEs) have been reported to convert methane anaerobically into CO2, polyhydroxyalkanoate, and acetate. Furthermore, it has been suggested that they might be able to use acetate for anabolism or aceticlastic methanogenesis. To better understand the potential acetate metabolism of ANMEs, we characterized an ACS from ANME-2a as well as an ACS and an ACD from ANME-2d. The conversion of acetate into acetyl-CoA (Vmax of 8.4 μmol mg-1 min-1 and Km of 0.7 mM acetate) by the monomeric 73.8-kDa ACS enzyme from ANME-2a was more favorable than the formation of acetate from acetyl-CoA (Vmax of 0.4 μmol mg-1 min-1 and Km of 0.2 mM acetyl-CoA). The monomeric 73.4-kDa ACS enzyme from ANME-2d had similar Vmax values for both directions (Vmax,acetate of 0.9 μmol mg-1 min-1 versus Vmax,acetyl-CoA of 0.3 μmol mg-1 min-1). The heterotetrameric ACD enzyme from ANME-2d was active solely in the acetate-producing direction. Batch incubations of an enrichment culture dominated by ANME-2d fed with 13C2-labeled acetate produced 3 μmol of [13C]methane in 7 days, suggesting that this anaerobic methanotroph might have the potential to reverse its metabolism and perform aceticlastic methanogenesis using ACS to activate acetate albeit at low rates (2 nmol g [dry weight]-1 min-1). Together, these results show that ANMEs may have the potential to use acetate for assimilation as well as to use part of the surplus acetate for methane production. IMPORTANCE Acetyl-CoA plays a key role in carbon metabolism and is found at the junction of many anabolic and catabolic reactions. This work describes the biochemical properties of ACS and ACD enzymes from ANME-2 archaea. This adds to our knowledge of archaeal ACS and ACD enzymes, only a few of which have been characterized to date. Furthermore, we validated the in situ activity of ACS in ANME-2d, showing the conversion of acetate into methane by an enrichment culture dominated by ANME-2d.
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Affiliation(s)
- Heleen T. Ouboter
- Radboud Institute of Biological and Environmental Sciences, Microbiology Cluster, Radboud University, Nijmegen, Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
| | - Arslan Arshad
- Radboud Institute of Biological and Environmental Sciences, Microbiology Cluster, Radboud University, Nijmegen, Netherlands
| | - Stefanie Berger
- Radboud Institute of Biological and Environmental Sciences, Microbiology Cluster, Radboud University, Nijmegen, Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
| | - Jesus Gerardo Saucedo Sanchez
- Radboud Institute of Biological and Environmental Sciences, Microbiology Cluster, Radboud University, Nijmegen, Netherlands
| | - Huub J. M. Op den Camp
- Radboud Institute of Biological and Environmental Sciences, Microbiology Cluster, Radboud University, Nijmegen, Netherlands
| | - Mike S. M. Jetten
- Radboud Institute of Biological and Environmental Sciences, Microbiology Cluster, Radboud University, Nijmegen, Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
| | - Cornelia U. Welte
- Radboud Institute of Biological and Environmental Sciences, Microbiology Cluster, Radboud University, Nijmegen, Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
| | - Julia M. Kurth
- Radboud Institute of Biological and Environmental Sciences, Microbiology Cluster, Radboud University, Nijmegen, Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
- Microcosm Earth Center, Philipps-Universität Marburg and Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Slaats S, Weissbart H, Schoffelen JM, Meyer AS, Martin AE. Delta-Band Neural Responses to Individual Words Are Modulated by Sentence Processing. J Neurosci 2023; 43:4867-4883. [PMID: 37221093 PMCID: PMC10312058 DOI: 10.1523/jneurosci.0964-22.2023] [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: 05/06/2022] [Revised: 04/17/2023] [Accepted: 04/27/2023] [Indexed: 05/25/2023] Open
Abstract
To understand language, we need to recognize words and combine them into phrases and sentences. During this process, responses to the words themselves are changed. In a step toward understanding how the brain builds sentence structure, the present study concerns the neural readout of this adaptation. We ask whether low-frequency neural readouts associated with words change as a function of being in a sentence. To this end, we analyzed an MEG dataset by Schoffelen et al. (2019) of 102 human participants (51 women) listening to sentences and word lists, the latter lacking any syntactic structure and combinatorial meaning. Using temporal response functions and a cumulative model-fitting approach, we disentangled delta- and theta-band responses to lexical information (word frequency), from responses to sensory and distributional variables. The results suggest that delta-band responses to words are affected by sentence context in time and space, over and above entropy and surprisal. In both conditions, the word frequency response spanned left temporal and posterior frontal areas; however, the response appeared later in word lists than in sentences. In addition, sentence context determined whether inferior frontal areas were responsive to lexical information. In the theta band, the amplitude was larger in the word list condition ∼100 milliseconds in right frontal areas. We conclude that low-frequency responses to words are changed by sentential context. The results of this study show how the neural representation of words is affected by structural context and as such provide insight into how the brain instantiates compositionality in language.SIGNIFICANCE STATEMENT Human language is unprecedented in its combinatorial capacity: we are capable of producing and understanding sentences we have never heard before. Although the mechanisms underlying this capacity have been described in formal linguistics and cognitive science, how they are implemented in the brain remains to a large extent unknown. A large body of earlier work from the cognitive neuroscientific literature implies a role for delta-band neural activity in the representation of linguistic structure and meaning. In this work, we combine these insights and techniques with findings from psycholinguistics to show that meaning is more than the sum of its parts; the delta-band MEG signal differentially reflects lexical information inside and outside sentence structures.
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Affiliation(s)
- Sophie Slaats
- Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
- The International Max Planck Research School for Language Sciences, 6525 XD Nijmegen, The Netherlands
| | - Hugo Weissbart
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 EN Nijmegen, The Netherlands
| | - Jan-Mathijs Schoffelen
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 EN Nijmegen, The Netherlands
| | - Antje S Meyer
- Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 EN Nijmegen, The Netherlands
| | - Andrea E Martin
- Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 EN Nijmegen, The Netherlands
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Dekker M, Van der Giessen E, Onck PR. Phase separation of intrinsically disordered FG-Nups is driven by highly dynamic FG motifs. Proc Natl Acad Sci U S A 2023; 120:e2221804120. [PMID: 37307457 DOI: 10.1073/pnas.2221804120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 05/09/2023] [Indexed: 06/14/2023] Open
Abstract
The intrinsically disordered FG-Nups in the central channel of the nuclear pore complex (NPC) form a selective permeability barrier, allowing small molecules to traverse by passive diffusion, while large molecules can only translocate with the help of nuclear transport receptors. The exact phase state of the permeability barrier remains elusive. In vitro experiments have shown that some FG-Nups can undergo phase separation into condensates that display NPC-like permeability barrier properties. Here, we use molecular dynamics simulations at amino acid resolution to study the phase separation characteristics of each of the disordered FG-Nups of the yeast NPC. We find that GLFG-Nups undergo phase separation and reveal that the FG motifs act as highly dynamic hydrophobic stickers that are essential for the formation of FG-Nup condensates featuring droplet-spanning percolated networks. Additionally, we study phase separation in an FG-Nup mixture that resembles the NPC stoichiometry and observe that an NPC condensate is formed containing multiple GLFG-Nups. We find that the phase separation of this NPC condensate is also driven by FG-FG interactions, similar to the homotypic FG-Nup condensates. Based on the observed phase separation behavior, the different FG-Nups of the yeast NPC can be divided into two classes: The FG-Nups (mostly GLFG-type) located in the central channel of the NPC form a highly dynamic percolated network formed by many short-lived FG-FG interactions, while the peripheral FG-Nups (mostly FxFG-type) at the entry and exit of the NPC channel likely form an entropic brush.
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Affiliation(s)
- Maurice Dekker
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Erik Van der Giessen
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
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59
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Steins A, Carroll C, Choong FJ, George AJ, He JS, Parsons KM, Feng S, Man SM, Kam C, van Loon LM, Poh P, Ferreira R, Mann GJ, Gruen RL, Hannan KM, Hannan RD, Schulte KM. Cell death and barrier disruption by clinically used iodine concentrations. Life Sci Alliance 2023; 6:e202201875. [PMID: 36944419 PMCID: PMC10031031 DOI: 10.26508/lsa.202201875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/23/2023] Open
Abstract
Povidone-iodine (PVP-I) inactivates a broad range of pathogens. Despite its widespread use over decades, the safety of PVP-I remains controversial. Its extended use in the current SARS-CoV-2 virus pandemic urges the need to clarify safety features of PVP-I on a cellular level. Our investigation in epithelial, mesothelial, endothelial, and innate immune cells revealed that the toxicity of PVP-I is caused by diatomic iodine (I2), which is rapidly released from PVP-I to fuel organic halogenation with fast first-order kinetics. Eukaryotic toxicity manifests at below clinically used concentrations with a threshold of 0.1% PVP-I (wt/vol), equalling 1 mM of total available I2 Above this threshold, membrane disruption, loss of mitochondrial membrane potential, and abolition of oxidative phosphorylation induce a rapid form of cell death we propose to term iodoptosis. Furthermore, PVP-I attacks lipid rafts, leading to the failure of tight junctions and thereby compromising the barrier functions of surface-lining cells. Thus, the therapeutic window of PVP-I is considerably narrower than commonly believed. Our findings urge the reappraisal of PVP-I in clinical practice to avert unwarranted toxicity whilst safeguarding its benefits.
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Affiliation(s)
- Anne Steins
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, Australian National University, Acton, Australia
- College of Health and Medicine, Australian National University, Acton, Australia
| | - Christina Carroll
- College of Health and Medicine, Australian National University, Acton, Australia
| | - Fui Jiun Choong
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, Australian National University, Acton, Australia
| | - Amee J George
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, Australian National University, Acton, Australia
- ANU Centre for Therapeutic Discovery, Australian National University, Acton, Australia
| | - Jin-Shu He
- Division of Immunology and Infectious Disease, The John Curtin School of Medical Research, Australian National University, Acton, Australia
| | - Kate M Parsons
- Division of Immunology and Infectious Disease, The John Curtin School of Medical Research, Australian National University, Acton, Australia
| | - Shouya Feng
- Division of Immunology and Infectious Disease, The John Curtin School of Medical Research, Australian National University, Acton, Australia
| | - Si Ming Man
- Division of Immunology and Infectious Disease, The John Curtin School of Medical Research, Australian National University, Acton, Australia
| | - Cathelijne Kam
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, Australian National University, Acton, Australia
| | - Lex M van Loon
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, Australian National University, Acton, Australia
- College of Health and Medicine, Australian National University, Acton, Australia
| | - Perlita Poh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, Australian National University, Acton, Australia
| | - Rita Ferreira
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, Australian National University, Acton, Australia
| | - Graham J Mann
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, Australian National University, Acton, Australia
- College of Health and Medicine, Australian National University, Acton, Australia
| | - Russell L Gruen
- College of Health and Medicine, Australian National University, Acton, Australia
| | - Katherine M Hannan
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, Australian National University, Acton, Australia
- College of Health and Medicine, Australian National University, Acton, Australia
| | - Ross D Hannan
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, Australian National University, Acton, Australia
- College of Health and Medicine, Australian National University, Acton, Australia
| | - Klaus-Martin Schulte
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, Australian National University, Acton, Australia
- College of Health and Medicine, Australian National University, Acton, Australia
- Department of Endocrine Surgery, King's College Hospital NHS Foundation Trust, London, UK
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Rassi E, Lin WM, Zhang Y, Emmerzaal J, Haegens S. β Band Rhythms Influence Reaction Times. eNeuro 2023; 10:ENEURO.0473-22.2023. [PMID: 37364994 PMCID: PMC10312120 DOI: 10.1523/eneuro.0473-22.2023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 06/28/2023] Open
Abstract
Despite their involvement in many cognitive functions, β oscillations are among the least understood brain rhythms. Reports on whether the functional role of β is primarily inhibitory or excitatory have been contradictory. Our framework attempts to reconcile these findings and proposes that several β rhythms co-exist at different frequencies. β Frequency shifts and their potential influence on behavior have thus far received little attention. In this human magnetoencephalography (MEG) experiment, we asked whether changes in β power or frequency in auditory cortex and motor cortex influence behavior (reaction times) during an auditory sweep discrimination task. We found that in motor cortex, increased β power slowed down responses, while in auditory cortex, increased β frequency slowed down responses. We further characterized β as transient burst events with distinct spectro-temporal profiles influencing reaction times. Finally, we found that increased motor-to-auditory β connectivity also slowed down responses. In sum, β power, frequency, bursting properties, cortical focus, and connectivity profile all influenced behavioral outcomes. Our results imply that the study of β oscillations requires caution as β dynamics are multifaceted phenomena, and that several dynamics must be taken into account to reconcile mixed findings in the literature.
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Affiliation(s)
- Elie Rassi
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University, 6525 EN Nijmegen, The Netherlands
- Department of Psychology, Centre for Cognitive Neuroscience, Paris-Lodron-University of Salzburg, 5020 Salzburg, Austria
| | - Wy Ming Lin
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University, 6525 EN Nijmegen, The Netherlands
- Hector Research Institute for Education Sciences and Psychology, University of Tübingen, 72074 Tübingen, Germany
| | - Yi Zhang
- Department of Psychiatry, Columbia University, New York, NY 10032
| | - Jill Emmerzaal
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University, 6525 EN Nijmegen, The Netherlands
- Human Movement Biomechanics Research Group, Department of Movement Sciences, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium
- REVAL Rehabilitation Research Centre, Faculty of Rehabilitation Sciences, Hasselt University, 3500 Diepenbeek, Belgium
| | - Saskia Haegens
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University, 6525 EN Nijmegen, The Netherlands
- Department of Psychiatry, Columbia University, New York, NY 10032
- Division of Systems Neuroscience, New York State Psychiatric Institute, New York, NY 10032
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Mackenbach Y, Borst JGG. Somatic Integration of Incoherent Dendritic Inputs in the Gerbil Medial Superior Olive. J Neurosci 2023; 43:4093-4109. [PMID: 37130779 PMCID: PMC10255013 DOI: 10.1523/jneurosci.2215-22.2023] [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: 11/30/2022] [Revised: 04/11/2023] [Accepted: 04/14/2023] [Indexed: 05/04/2023] Open
Abstract
The medial superior olive (MSO) is a binaural nucleus that is specialized in detecting the relative arrival times of sounds at both ears. Excitatory inputs to its neurons originating from either ear are segregated to different dendrites. To study the integration of synaptic inputs both within and between dendrites, we made juxtacellular and whole-cell recordings from the MSO in anesthetized female gerbils, while presenting a "double zwuis" stimulus, in which each ear received its own set of tones, which were chosen in a way that all second-order distortion products (DP2s) could be uniquely identified. MSO neurons phase-locked to multiple tones within the multitone stimulus, and vector strength, a measure for spike phase-locking, generally depended linearly on the size of the average subthreshold response to a tone. Subthreshold responses to tones in one ear depended little on the presence of sound in the other ear, suggesting that inputs from different ears sum linearly without a substantial role for somatic inhibition. The "double zwuis" stimulus also evoked response components in the MSO neuron that were phase-locked to DP2s. Bidendritic subthreshold DP2s were quite rare compared with bidendritic suprathreshold DP2s. We observed that in a small subset of cells, the ability to trigger spikes differed substantially between both ears, which might be explained by a dendritic axonal origin. Some neurons that were driven monaurally by only one of the two ears nevertheless showed decent binaural tuning. We conclude that MSO neurons are remarkably good in finding binaural coincidences even among uncorrelated inputs.SIGNIFICANCE STATEMENT Neurons in the medial superior olive are essential for precisely localizing low-frequency sounds in the horizontal plane. From their soma, only two dendrites emerge, which are innervated by inputs originating from different ears. Using a new sound stimulus, we studied the integration of inputs both within and between these dendrites in unprecedented detail. We found evidence that inputs from different dendrites add linearly at the soma, but that small increases in somatic potentials could lead to large increases in the probability of generating a spike. This basic scheme allowed the MSO neurons to detect the relative arrival time of inputs at both dendrites remarkably efficient, although the relative size of these inputs could differ considerably.
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Affiliation(s)
- Yarmo Mackenbach
- Department of Neuroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA, The Netherlands
| | - J Gerard G Borst
- Department of Neuroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA, The Netherlands
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Rojek-Giffin M, Lebreton M, Daunizeau J, Fariña A, Gross J, De Dreu CKW. Learning rules of engagement for social exchange within and between groups. Proc Natl Acad Sci U S A 2023; 120:e2218443120. [PMID: 37126724 PMCID: PMC10175835 DOI: 10.1073/pnas.2218443120] [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: 11/07/2022] [Accepted: 03/29/2023] [Indexed: 05/03/2023] Open
Abstract
Globalizing economies and long-distance trade rely on individuals from different cultural groups to negotiate agreement on what to give and take. In such settings, individuals often lack insight into what interaction partners deem fair and appropriate, potentially seeding misunderstandings, frustration, and conflict. Here, we examine how individuals decipher distinct rules of engagement and adapt their behavior to reach agreements with partners from other cultural groups. Modeling individuals as Bayesian learners with inequality aversion reveals that individuals, in repeated ultimatum bargaining with responders sampled from different groups, can be more generous than needed. While this allows them to reach agreements, it also gives rise to biased beliefs about what is required to reach agreement with members from distinct groups. Preregistered behavioral (N = 420) and neuroimaging experiments (N = 49) support model predictions: Seeking equitable agreements can lead to overly generous behavior toward partners from different groups alongside incorrect beliefs about prevailing norms of what is appropriate in groups and cultures other than one's own.
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Affiliation(s)
- Michael Rojek-Giffin
- Institute for Psychology, Social, Economic and Organisational Psychology, Leiden University, 2333 AKLeiden, the Netherlands
| | - Maël Lebreton
- Paris-Jourdan Sciences Economiques UMR8545, Economics of Human Behavior Group, Paris School of Economics, 75014Paris, France
- Swiss Centre for Affective Sciences, Faculty of Psychology and Educational Sciences, Université de Genève, 1202Geneva, Switzerland
| | - Jean Daunizeau
- Sorbonne Université, Inserm Unite 1127, CNRS unite 7225, 75005Paris, France
- Paris Brain Institute (ICM), Motivation Brain & Behavior (MBB) Lab, Pitié-Salpêtrière Hospital, 75013Paris, France
| | - Andrea Fariña
- Institute for Psychology, Social, Economic and Organisational Psychology, Leiden University, 2333 AKLeiden, the Netherlands
| | - Jörg Gross
- Institute for Psychology, Social, Economic and Organisational Psychology, Leiden University, 2333 AKLeiden, the Netherlands
- Institute of Psychology, Social and Economic Psychology, University of Zurich, 8001Zurich, Switzerland
| | - Carsten K. W. De Dreu
- Institute for Psychology, Social, Economic and Organisational Psychology, Leiden University, 2333 AKLeiden, the Netherlands
- Amsterdam School of Economics, Center for Research in Experimental Economics and Political Decision Making, University of Amsterdam, 1018 WBAmsterdam, the Netherlands
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Koloko Ngassie ML, de Vries M, Borghuis T, Timens W, Sin DD, Nickle D, Joubert P, Horvatovich P, Marko-Varga G, Teske JJ, Vonk JM, Gosens R, Prakash YS, Burgess JK, Brandsma CA. Age-associated Differences in the Human Lung Extracellular Matrix. Am J Physiol Lung Cell Mol Physiol 2023; 324:L799-L814. [PMID: 37039368 DOI: 10.1152/ajplung.00334.2022] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
Extracellular matrix (ECM) remodeling has been associated with chronic lung diseases. However, information about specific age‑associated differences in lung ECM is currently limited. In this study we aimed to identify and localize age‑associated ECM differences in human lung using comprehensive transcriptomic, proteomic and immunohistochemical analyses. Our previously identified age-associated gene expression signature of the lung was re‑analyzed limiting it to an aging signature based on 270 control patients (37-80 years) and focused on the Matrisome core geneset using geneset enrichment analysis. To validate the age‑associated transcriptomic differences on protein level, we compared the age-associated ECM genes (FDR <0.05) with a profile of age‑associated proteins identified from a lung tissue proteomics dataset from 9 control patients (49-76 years) (FDR<0.05). Extensive immunohistochemical analysis was used to localize and semi-quantify the age-associated ECM differences in lung tissues from 62 control patients (18-82 years). Comparative analysis of transcriptomic and proteomic data identified 7 ECM proteins with higher expression with age at both gene and protein level: COL1A1, COL6A1, COL6A2, COL14A1, FBLN2, LTBP4 and LUM. With immunohistochemistry we demonstrated higher protein level with age for COL6A2 in whole tissue, parenchyma, airway wall and blood vessel, for COL14A1 and LUM in bronchial epithelium, and COL1A1 in lung parenchyma. Our study revealed that higher age is associated with lung ECM remodeling, with specific differences occurring in defined regions within the lung. These differences may affect lung structure and physiology with aging and as such may increase susceptibility for developing chronic lung diseases.
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Affiliation(s)
- Maunick Lefin Koloko Ngassie
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, Netherlands
| | - Maaike de Vries
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, Netherlands
- Department of Epidemiology, University Medical Center Groningen, Groningen, Netherlands
| | - Theo Borghuis
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, Netherlands
| | - Don D Sin
- Centre for Heart Lung Innovation at St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | | | - Philippe Joubert
- Pneumologie, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Canada
| | - Peter Horvatovich
- 7University of Groningen, Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, Groningen, Netherlands
| | - György Marko-Varga
- Center of Excellence in Biological and Medical Mass Spectrometry, Biomedical Center, Lund University, Sweden
| | - Jacob J Teske
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States
| | - Judith M Vonk
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, Netherlands
- Department of Epidemiology, University Medical Center Groningen, Groningen, Netherlands
| | - Reinoud Gosens
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, Netherlands
- Department of Molecular Pharmacology, University of Groningen, Groningen, Netherlands
| | - Y S Prakash
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States
| | - Janette K Burgess
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, Netherlands
| | - Corry-Anke Brandsma
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, Netherlands
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Hoefsmit EP, Völlmy F, Rozeman EA, Reijers IL, Versluis JM, Hoekman L, van Akkooi AC, Long GV, Schadendorf D, Dummer R, Altelaar M, Blank CU. Systemic LRG1 expression in melanoma is associated with disease progression and recurrence. Cancer Research Communications 2023; 3:672-683. [PMID: 37089863 PMCID: PMC10117404 DOI: 10.1158/2767-9764.crc-23-0015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/07/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
Abstract
The response rates upon neoadjuvant immune checkpoint blockade (ICB) in stage III melanoma are higher as compared to stage IV disease. Given that successful ICB depends on systemic immune response, we hypothesized that systemic immune suppression might be a mechanism responsible for lower response rates in late-stage disease, and also potentially with disease recurrence in early-stage disease. Plasma and serum samples of cohorts of melanoma patients were analyzed for circulating proteins using mass spectrometry proteomic profiling and Olink proteomic assay. A cohort of paired samples of patients with stage III that progressed to stage IV disease (n=64) was used to identify markers associated with higher tumor burden. Baseline patient samples from the OpACIN-neo study (n=83) and PRADO study (n=49; NCT02977052) were used as two independent cohorts to analyze whether the potential identified markers are also associated with disease recurrence after neoadjuvant ICB therapy. When comparing baseline proteins overlapping between patients with progressive disease and patients with recurrent disease, we found leucine-rich alpha-2-glycoprotein 1 (LRG1) to be associated with worse prognosis. Especially non-responder patients to neoadjuvant ICB (OpACIN-neo) with high LRG1 expression had a poor outcome with an estimated 36-month event-free survival of 14% as compared to 83% for non-responders with a low LRG1 expression (P = 0.014). This finding was validated in an independent cohort (P = 0.0021). LRG1 can be used as a biomarker to identify patients with high risk for disease progression and recurrence, and might be a target to be combined with neoadjuvant ICB.
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Affiliation(s)
- Esmee P. Hoefsmit
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Franziska Völlmy
- Biomolecular Mass Spectrometry and Proteomics, Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Elisa A. Rozeman
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Irene L.M. Reijers
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Judith M. Versluis
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Alexander C.J. van Akkooi
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Georgina V. Long
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Department of Medical Oncology, Royal North Shore and Mater Hospitals, Sydney, New South Wales, Australia
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen and Germany Cancer Consortium, Partner Site Essen, Essen, Germany
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zürich, University Zürich, Zürich, Switzerland
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
- Proteomics Facility, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Corresponding Authors: Christian U. Blank, The Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital (NKI-AVL), Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands. Phone: +312-0512-2960; E-mail: ; and Maarten Altelaar,
| | - Christian U. Blank
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
- Corresponding Authors: Christian U. Blank, The Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital (NKI-AVL), Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands. Phone: +312-0512-2960; E-mail: ; and Maarten Altelaar,
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Forbes PA, Kwan A, Mitchell DE, Blouin JS, Cullen KE. The Neural Basis for Biased Behavioral Responses Evoked by Galvanic Vestibular Stimulation in Primates. J Neurosci 2023; 43:1905-1919. [PMID: 36732070 PMCID: PMC10027042 DOI: 10.1523/jneurosci.0987-22.2023] [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: 05/23/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Noninvasive electrical stimulation of the vestibular system in humans has become an increasingly popular tool with a broad range of research and clinical applications. However, common assumptions regarding the neural mechanisms that underlie the activation of central vestibular pathways through such stimulation, known as galvanic vestibular stimulation (GVS), have not been directly tested. Here, we show that GVS is encoded by VIIIth nerve vestibular afferents with nonlinear dynamics that differ markedly from those predicted by current models. GVS produced asymmetric activation of both semicircular canal and otolith afferents to the onset versus offset and cathode versus anode of applied current, that in turn produced asymmetric eye movement responses in three awake-behaving male monkeys. Additionally, using computational methods, we demonstrate that the experimentally observed nonlinear neural response dynamics lead to an unexpected directional bias in the net population response when the information from both vestibular nerves is centrally integrated. Together our findings reveal the neural basis by which GVS activates the vestibular system, establish that neural response dynamics differ markedly from current predictions, and advance our mechanistic understanding of how asymmetric activation of the peripheral vestibular system alters vestibular function. We suggest that such nonlinear encoding is a general feature of neural processing that will be common across different noninvasive electrical stimulation approaches.SIGNIFICANCE STATEMENT Here, we show that the application of noninvasive electrical currents to the vestibular system (GVS) induces more complex responses than commonly assumed. We recorded vestibular afferent activity in macaque monkeys exposed to GVS using a setup analogous to human studies. GVS evoked notable asymmetries in irregular afferent responses to cathodal versus anodal currents. We developed a nonlinear model explaining these GVS-evoked afferent responses. Our model predicts that GVS induces directional biases in centrally integrated head motion signals and establishes electrical stimuli that recreate physiologically plausible sensations of motion. Altogether, our findings provide new insights into how GVS activates the vestibular system, which will be vital to advancing new clinical and biomedical applications.
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Affiliation(s)
- Patrick A Forbes
- Department of Neuroscience, Erasmus MC, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | | | | | - Jean-Sébastien Blouin
- School of Kinesiology, University of British Columbia, Vancouver, British Colombia V6T 1Z1, Canada
| | - Kathleen E Cullen
- Physiology, McGill University, Montréal, Québec H3G 1Y6, Canada
- Departments of Biomedical Engineering
- Otolaryngology-Head and Neck Surgery
- Neuroscience, Johns Hopkins University, Baltimore, Maryland 21205
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, Maryland 21205
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66
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van der Linden MN, Everts JC, van Roij R, van Blaaderen A. Realization of the Brazil-nut effect in charged colloids without external driving. Proc Natl Acad Sci U S A 2023; 120:e2213044120. [PMID: 36827263 PMCID: PMC9992820 DOI: 10.1073/pnas.2213044120] [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: 07/28/2022] [Accepted: 01/16/2023] [Indexed: 02/25/2023] Open
Abstract
Sedimentation is a ubiquitous phenomenon across many fields of science, such as geology, astrophysics, and soft matter. Sometimes, sedimentation leads to unusual phenomena, such as the Brazil-nut effect, where heavier (granular) particles reside on top of lighter particles after shaking. We show experimentally that a Brazil-nut effect can be realized in a binary colloidal system of long-range repulsive charged particles driven purely by Brownian motion and electrostatics without the need for activity. Using theory, we argue that not only the mass-per-charge for the heavier particles needs to be smaller than the mass-per-charge for the lighter particles but also that at high overall density, the system can be trapped in a long-lived metastable state, which prevents the occurrence of the equilibrium Brazil-nut effect. Therefore, we envision that our work provides valuable insights into the physics of strongly interacting systems, such as partially glassy and crystalline structures. Finally, our theory, which quantitatively agrees with the experimental data, predicts that the shapes of sedimentation density profiles of multicomponent charged colloids are greatly altered when the particles are charge-regulating with more than one ion species involved. Hence, we hypothesize that sedimentation experiments can aid in revealing the type of ion adsorption processes that determine the particle charge and possibly the value of the corresponding equilibrium constants.
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Affiliation(s)
| | - Jeffrey C. Everts
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw01-224, Poland
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Warsaw02-093, Poland
| | - René van Roij
- Institute for Theoretical Physics, Center for Extreme Matter and Emergent Phenomena, Utrecht University, Utrecht3584 CC, The Netherlands
| | - Alfons van Blaaderen
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht3584 CC, The Netherlands
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67
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Klink PC, Teeuwen RRM, Lorteije JAM, Roelfsema PR. Inversion of pop-out for a distracting feature dimension in monkey visual cortex. Proc Natl Acad Sci U S A 2023; 120:e2210839120. [PMID: 36812207 PMCID: PMC9992771 DOI: 10.1073/pnas.2210839120] [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: 06/27/2022] [Accepted: 01/25/2023] [Indexed: 02/24/2023] Open
Abstract
During visual search, it is important to reduce the interference of distracting objects in the scene. The neuronal responses elicited by the search target stimulus are typically enhanced. However, it is equally important to suppress the representations of distracting stimuli, especially if they are salient and capture attention. We trained monkeys to make an eye movement to a unique "pop-out" shape stimulus among an array of distracting stimuli. One of these distractors had a salient color that varied across trials and differed from the color of the other stimuli, causing it to also pop-out. The monkeys were able to select the pop-out shape target with high accuracy and actively avoided the pop-out color distractor. This behavioral pattern was reflected in the activity of neurons in area V4. Responses to the shape targets were enhanced, while the activity evoked by the pop-out color distractor was only briefly enhanced, directly followed by a sustained period of pronounced suppression. These behavioral and neuronal results demonstrate a cortical selection mechanism that rapidly inverts a pop-out signal to "pop-in" for an entire feature dimension thereby facilitating goal-directed visual search in the presence of salient distractors.
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Affiliation(s)
- P. Christiaan Klink
- Department of Vision and Cognition, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands
- Experimental Psychology, Helmholtz Institute, Utrecht University, 3584 CS, Utrecht, The Netherlands
- Laboratory of Visual Brain Therapy, Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Institut de la Vision, ParisF-75012, France
- Department of Integrative Neurophysiology, Centre for Neurogenomics and Cognitive Research, Vrije Universiteit, 1081 HV, Amsterdam, The Netherlands
| | - Rob R. M. Teeuwen
- Department of Vision and Cognition, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands
| | - Jeannette A. M. Lorteije
- Department of Vision and Cognition, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands
| | - Pieter R. Roelfsema
- Department of Vision and Cognition, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands
- Laboratory of Visual Brain Therapy, Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Institut de la Vision, ParisF-75012, France
- Department of Integrative Neurophysiology, Centre for Neurogenomics and Cognitive Research, Vrije Universiteit, 1081 HV, Amsterdam, The Netherlands
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
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Chen HA, Ho YJ, Mezzadra R, Adrover JM, Smolkin R, Zhu C, Woess K, Bernstein N, Schmitt G, Fong L, Luan W, Wuest A, Tian S, Li X, Broderick C, Hendrickson RC, Egeblad M, Chen Z, Alonso-Curbelo D, Lowe SW. Senescence Rewires Microenvironment Sensing to Facilitate Antitumor Immunity. Cancer Discov 2023; 13:432-453. [PMID: 36302222 PMCID: PMC9901536 DOI: 10.1158/2159-8290.cd-22-0528] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/16/2022] [Accepted: 10/24/2022] [Indexed: 02/07/2023]
Abstract
Cellular senescence involves a stable cell-cycle arrest coupled to a secretory program that, in some instances, stimulates the immune clearance of senescent cells. Using an immune-competent liver cancer model in which senescence triggers CD8 T cell-mediated tumor rejection, we show that senescence also remodels the cell-surface proteome to alter how tumor cells sense environmental factors, as exemplified by type II interferon (IFNγ). Compared with proliferating cells, senescent cells upregulate the IFNγ receptor, become hypersensitized to microenvironmental IFNγ, and more robustly induce the antigen-presenting machinery-effects also recapitulated in human tumor cells undergoing therapy-induced senescence. Disruption of IFNγ sensing in senescent cells blunts their immune-mediated clearance without disabling the senescence state or its characteristic secretory program. Our results demonstrate that senescent cells have an enhanced ability to both send and receive environmental signals and imply that each process is required for their effective immune surveillance. SIGNIFICANCE Our work uncovers an interplay between tissue remodeling and tissue-sensing programs that can be engaged by senescence in advanced cancers to render tumor cells more visible to the adaptive immune system. This new facet of senescence establishes reciprocal heterotypic signaling interactions that can be induced therapeutically to enhance antitumor immunity. See related article by Marin et al., p. 410. This article is highlighted in the In This Issue feature, p. 247.
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Affiliation(s)
- Hsuan-An Chen
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yu-Jui Ho
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Riccardo Mezzadra
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Ryan Smolkin
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Changyu Zhu
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Katharina Woess
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | | | - Linda Fong
- Calico Life Sciences, South San Francisco, California
| | - Wei Luan
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexandra Wuest
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sha Tian
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Xiang Li
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Caroline Broderick
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ronald C. Hendrickson
- Microchemistry and Proteomics Core Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mikala Egeblad
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Zhenghao Chen
- Calico Life Sciences, South San Francisco, California
| | - Direna Alonso-Curbelo
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Scott W. Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
- Howard Hughes Medical Institute, Chevy Chase, Maryland
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Slaats J, Wagena E, Smits D, Berends AA, Peters E, Bakker GJ, van Erp M, Weigelin B, Adema GJ, Friedl P. Adenosine A2a Receptor Antagonism Restores Additive Cytotoxicity by Cytotoxic T Cells in Metabolically Perturbed Tumors. Cancer Immunol Res 2022; 10:1462-1474. [PMID: 36162129 PMCID: PMC9716258 DOI: 10.1158/2326-6066.cir-22-0113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 07/30/2022] [Accepted: 09/21/2022] [Indexed: 01/10/2023]
Abstract
Cytotoxic T lymphocytes (CTL) are antigen-specific effector cells with the ability to eradicate cancer cells in a contact-dependent manner. Metabolic perturbation compromises the CTL effector response in tumor subregions, resulting in failed cancer cell elimination despite the infiltration of tumor-specific CTLs. Restoring the functionality of these tumor-infiltrating CTLs is key to improve immunotherapy. Extracellular adenosine is an immunosuppressive metabolite produced within the tumor microenvironment. Here, by applying single-cell reporter strategies in 3D collagen cocultures in vitro and progressing tumors in vivo, we show that adenosine weakens one-to-one pairing of activated effector CTLs with target cells, thereby dampening serial cytotoxic hit delivery and cumulative death induction. Adenosine also severely compromised CTL effector restimulation and expansion. Antagonization of adenosine A2a receptor (ADORA2a) signaling stabilized and prolonged CTL-target cell conjugation and accelerated lethal hit delivery by both individual contacts and CTL swarms. Because adenosine signaling is a near-constitutive confounding parameter in metabolically perturbed tumors, ADORA2a targeting represents an orthogonal adjuvant strategy to enhance immunotherapy efficacy.
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Affiliation(s)
- Jeroen Slaats
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Esther Wagena
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Daan Smits
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Annemarie A. Berends
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ella Peters
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Gert-Jan Bakker
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Merijn van Erp
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bettina Weigelin
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies,” University of Tübingen, Tübingen, Germany
| | - Gosse J. Adema
- Radiotherapy and Onco-Immunology Laboratory, Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Peter Friedl
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Genitourinary Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
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Bijlsma A, Omrani A, Spoelder M, Verharen JPH, Bauer L, Cornelis C, de Zwart B, van Dorland R, Vanderschuren LJMJ, Wierenga CJ. Social Play Behavior Is Critical for the Development of Prefrontal Inhibitory Synapses and Cognitive Flexibility in Rats. J Neurosci 2022; 42:8716-8728. [PMID: 36253083 PMCID: PMC9671579 DOI: 10.1523/jneurosci.0524-22.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 08/12/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022] Open
Abstract
Sensory driven activity during early life is critical for setting up the proper connectivity of the sensory cortices. We ask here whether social play behavior, a particular form of social interaction that is highly abundant during postweaning development, is equally important for setting up connections in the developing prefrontal cortex (PFC). Young male rats were deprived from social play with peers during the period in life when social play behavior normally peaks [postnatal day 21-42] (SPD rats), followed by resocialization until adulthood. We recorded synaptic currents in layer 5 cells in slices from medial PFC of adult SPD and control rats and observed that inhibitory synaptic currents were reduced in SPD slices, while excitatory synaptic currents were unaffected. This was associated with a decrease in perisomatic inhibitory synapses from parvalbumin-positive GABAergic cells. In parallel experiments, adult SPD rats achieved more reversals in a probabilistic reversal learning (PRL) task, which depends on the integrity of the PFC, by using a more simplified cognitive strategy than controls. Interestingly, we observed that one daily hour of play during SPD partially rescued the behavioral performance in the PRL, but did not prevent the decrease in PFC inhibitory synaptic inputs. Our data demonstrate the importance of unrestricted social play for the development of inhibitory synapses in the PFC and cognitive skills in adulthood and show that specific synaptic alterations in the PFC can result in a complex behavioral outcome.SIGNIFICANCE STATEMENT This study addressed the question whether social play behavior in juvenile rats contributes to functional development of the prefrontal cortex (PFC). We found that rats that had been deprived from juvenile social play (social play deprivation - SPD) showed a reduction in inhibitory synapses in the PFC and a simplified strategy to solve a complex behavioral task in adulthood. Providing one daily hour of play during SPD partially rescued the cognitive skills in these rats, but did not prevent the reduction in PFC inhibitory synapses. Our results demonstrate a key role for unrestricted juvenile social play in PFC development and emphasize the complex relation between PFC circuit connectivity and cognitive function.
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Affiliation(s)
- Ate Bijlsma
- Department of Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
- Department of Population Health Sciences, Section Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The Netherlands
| | - Azar Omrani
- Department of Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
- Department of Translational Neuroscience, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands
| | - Marcia Spoelder
- Department of Population Health Sciences, Section Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The Netherlands
| | - Jeroen P H Verharen
- Department of Population Health Sciences, Section Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The Netherlands
- Department of Translational Neuroscience, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands
| | - Lisa Bauer
- Department of Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Cosette Cornelis
- Department of Population Health Sciences, Section Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The Netherlands
| | - Beleke de Zwart
- Department of Population Health Sciences, Section Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The Netherlands
| | - René van Dorland
- Department of Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Louk J M J Vanderschuren
- Department of Population Health Sciences, Section Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The Netherlands
| | - Corette J Wierenga
- Department of Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
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71
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Onuki Y, Lakbila-Kamal O, Scheffer B, Van Someren EJW, Van der Werf YD. Selective Enhancement of Post-Sleep Visual Motion Perception by Repetitive Tactile Stimulation during Sleep. J Neurosci 2022; 42:7400-7411. [PMID: 35995563 PMCID: PMC9525164 DOI: 10.1523/jneurosci.1512-21.2022] [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: 07/23/2021] [Revised: 05/07/2022] [Accepted: 06/12/2022] [Indexed: 11/21/2022] Open
Abstract
Tactile sensations can bias visual perception in the awake state while visual sensitivity is known to be facilitated by sleep. It remains unknown, however, whether the tactile sensation during sleep can bias the visual improvement after sleep. Here, we performed nap experiments in human participants (n = 56, 18 males, 38 females) to demonstrate that repetitive tactile motion stimulation on the fingertip during slow wave sleep selectively enhanced subsequent visual motion detection. The visual improvement was associated with slow wave activity. The high activation at the high beta frequency was found in the occipital electrodes after the tactile motion stimulation during sleep, indicating a visual-tactile cross-modal interaction during sleep. Furthermore, a second experiment (n = 14, 14 females) to examine whether a hand- or head-centered coordination is dominant for the interpretation of tactile motion direction showed that the biasing effect on visual improvement occurs according to the hand-centered coordination. These results suggest that tactile information can be interpreted during sleep, and can induce the selective improvement of post-sleep visual motion detection.SIGNIFICANCE STATEMENT Tactile sensations can bias our visual perception as a form of cross-modal interaction. However, it was reported only in the awake state. Here we show that repetitive directional tactile motion stimulation on the fingertip during slow wave sleep selectively enhanced subsequent visual motion perception. Moreover, the visual improvement was positively associated with sleep slow wave activity. The tactile motion stimulation during slow wave activity increased the activation at the high beta frequency over the occipital electrodes. The visual improvement occurred in agreement with a hand-centered reference frame. These results suggest that our sleeping brain can interpret tactile information based on a hand-centered reference frame, which can cause the sleep-dependent improvement of visual motion detection.
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Affiliation(s)
- Yoshiyuki Onuki
- Department of Sleep and Cognition, Netherlands Institute for Neuroscience, an institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, 1105BA, The Netherlands
| | - Oti Lakbila-Kamal
- Department of Sleep and Cognition, Netherlands Institute for Neuroscience, an institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, 1105BA, The Netherlands
| | - Bo Scheffer
- Department of Sleep and Cognition, Netherlands Institute for Neuroscience, an institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, 1105BA, The Netherlands
| | - Eus J W Van Someren
- Department of Sleep and Cognition, Netherlands Institute for Neuroscience, an institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, 1105BA, The Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, 1081HV, The Netherlands
- Amsterdam UMC, Vrije Universiteit, Psychiatry, Amsterdam Neuroscience, Amsterdam, 1081HV, The Netherlands
| | - Ysbrand D Van der Werf
- Department of Anatomy and Neurosciences, Amsterdam UMC, location VU, University Medical Center, Amsterdam, 1081HZ, The Netherlands
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Rodriguez-Larios J, ElShafei A, Wiehe M, Haegens S. Visual working memory recruits two functionally distinct alpha rhythms in posterior cortex. eNeuro 2022; 9:ENEURO.0159-22.2022. [PMID: 36171059 PMCID: PMC9536853 DOI: 10.1523/eneuro.0159-22.2022] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/20/2022] [Accepted: 07/12/2022] [Indexed: 11/21/2022] Open
Abstract
Oscillatory activity in the human brain is dominated by posterior alpha oscillations (8-14 Hz), which have been shown to be functionally relevant in a wide variety of cognitive tasks. Although posterior alpha oscillations are commonly considered a single oscillator anchored at an individual alpha frequency (IAF; ∼10 Hz), previous work suggests that IAF reflects a spatial mixture of different brain rhythms. In this study, we assess whether Independent Component Analysis (ICA) can disentangle functionally distinct posterior alpha rhythms in the context of visual short-term memory retention. Magnetoencephalography (MEG) was recorded in 33 subjects while performing a visual working memory task. Group analysis at sensor level suggested the existence of a single posterior alpha oscillator that increases in power and decreases in frequency during memory retention. Conversely, single-subject analysis of independent components revealed the existence of two dissociable alpha rhythms: one that increases in power during memory retention (Alpha1) and another one that decreases in power (Alpha2). Alpha1 and Alpha2 rhythms were differentially modulated by the presence of visual distractors (Alpha1 increased in power while Alpha2 decreased) and had an opposite relationship with accuracy (positive for Alpha1 and negative for Alpha2). In addition, Alpha1 rhythms showed a lower peak frequency, a narrower peak width, a greater relative peak amplitude and a more central source than Alpha2 rhythms. Together, our results demonstrate that modulations in posterior alpha oscillations during short-term memory retention reflect the dynamics of at least two distinct brain rhythms with different functions and spatiospectral characteristics.Significance statementAlpha oscillations are the most prominent feature of the human brain's electrical activity, and consist of rhythmic neuronal activity in posterior parts of the cortex. Alpha is usually considered a single brain rhythm that changes in power and frequency to support cognitive operations. We here show that posterior alpha entails at least two dissociable rhythms with distinct functions and characteristics. These findings could solve previous inconsistencies in the literature regarding the direction of task-related alpha power/frequency modulations and their relation to cognitive performance. In addition, the existence of two distinct posterior alpha rhythms could have important consequences for the design of neurostimulation protocols aimed at modulating alpha oscillations and subsequently cognition.
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Affiliation(s)
- Julio Rodriguez-Larios
- Dept. of Psychiatry, Columbia University, New York, USA, NY 10032
- Div. of Systems Neuroscience, New York State Psychiatric Institute, New York, USA, NY 10032
| | - Alma ElShafei
- Donders Institute for Brain, Cognition & Behavior, Radboud University, Nijmegen, The Netherlands, 6525 EN
| | - Melanie Wiehe
- Donders Institute for Brain, Cognition & Behavior, Radboud University, Nijmegen, The Netherlands, 6525 EN
| | - Saskia Haegens
- Dept. of Psychiatry, Columbia University, New York, USA, NY 10032
- Div. of Systems Neuroscience, New York State Psychiatric Institute, New York, USA, NY 10032
- Donders Institute for Brain, Cognition & Behavior, Radboud University, Nijmegen, The Netherlands, 6525 EN
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Shitut S, Shen MJ, Claushuis B, Derks RJE, Giera M, Rozen D, Claessen D, Kros A. Generating Heterokaryotic Cells via Bacterial Cell-Cell Fusion. Microbiol Spectr 2022; 10:e0169322. [PMID: 35862998 PMCID: PMC9430406 DOI: 10.1128/spectrum.01693-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 05/15/2022] [Accepted: 06/22/2022] [Indexed: 11/20/2022] Open
Abstract
Fusion of cells is an important and common biological process that leads to the mixing of cellular contents and the formation of multinuclear cells. Cell fusion occurs when distinct membranes are brought into proximity of one another and merge to become one. Fusion holds promise for biotechnological innovations, for instance, for the discovery of urgently needed new antibiotics. Here, we used antibiotic-producing bacteria that can proliferate without their cell wall as a model to investigate cell-cell fusion. We found that fusion between genetically distinct cells yields heterokaryons that are viable, contain multiple selection markers, and show increased antimicrobial activity. The rate of fusion induced using physical and chemical methods was dependent on membrane fluidity, which is related to lipid composition as a function of cellular age. Finally, by using an innovative system of synthetic membrane-associated lipopeptides, we achieved targeted fusion between distinctly marked cells to further enhance fusion efficiency. These results provide a molecular handle to understand and control cell-cell fusion, which can be used in the future for the discovery of new drugs. IMPORTANCE Cell-cell fusion is instrumental in introducing different sets of genes in the same environment, which subsequently leads to diversity. There is need for new protocols to fuse cells of different types together for biotechnological applications like drug discovery. We present here wall-deficient cells as a platform for the same. We identify the fluidity of the membrane as an important characteristic for the process of fusion. We demonstrate a cell-specific approach for fusion using synthetically designed peptides yielding cells with modified antibiotic production profiles. Overall, wall-deficient cells can be a chassis for innovative metabolite production by providing an alternative method for cell-cell fusion.
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Affiliation(s)
- Shraddha Shitut
- Origins Centre, Groningen, the Netherlands
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Meng-Jie Shen
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Bart Claushuis
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Rico J. E. Derks
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Daniel Rozen
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Dennis Claessen
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Alexander Kros
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
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74
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van Bork R, Rhemtulla M, Sijtsma K, Borsboom D. A causal theory of error scores. Psychol Methods 2022:2022-83043-001. [PMID: 35878074 DOI: 10.1037/met0000521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In modern test theory, response variables are a function of a common latent variable that represents the measured attribute, and error variables that are unique to the response variables. While considerable thought goes into the interpretation of latent variables in these models (e.g., validity research), the interpretation of error variables is typically left implicit (e.g., describing error variables as residuals). Yet, many psychometric assumptions are essentially assumptions about error and thus being able to reason about psychometric models requires the ability to reason about errors. We propose a causal theory of error as a framework that enables researchers to reason about errors in terms of the data-generating mechanism. In this framework, the error variable reflects myriad causes that are specific to an item and, together with the latent variable, determine the scores on that item. We distinguish two types of item-specific causes: characteristic variables that differ between people (e.g., familiarity with words used in the item), and circumstance variables that vary over occasions in which the item is administered (e.g., a distracting noise). We show that different assumptions about these unique causes (a) imply different psychometric models; (b) have different implications for the chance experiment that makes these models probabilistic models; and (c) have different consequences for item bias, local homogeneity, and reliability coefficient α and the test-retest correlation. The ability to reason about the causes that produce error variance puts researchers in a better position to motivate modeling choices. (PsycInfo Database Record (c) 2022 APA, all rights reserved).
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Droogers WJ, Willems J, MacGillavry HD, de Jong APH. Duplex Labeling and Manipulation of Neuronal Proteins Using Sequential CRISPR/Cas9 Gene Editing. eNeuro 2022; 9:ENEURO.0056-22.2022. [PMID: 35851300 PMCID: PMC9333357 DOI: 10.1523/eneuro.0056-22.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 11/21/2022] Open
Abstract
CRISPR/Cas9-mediated knock-in methods enable the labeling of individual endogenous proteins to faithfully determine their spatiotemporal distribution in cells. However, reliable multiplexing of knock-in events in neurons remains challenging because of cross talk between editing events. To overcome this, we developed conditional activation of knock-in expression (CAKE), allowing efficient, flexible, and accurate multiplex genome editing in rat neurons. To diminish cross talk, CAKE is based on sequential, recombinase-driven guide RNA (gRNA) expression to control the timing of genomic integration of each donor sequence. We show that CAKE is broadly applicable to co-label various endogenous proteins, including cytoskeletal proteins, synaptic scaffolds, ion channels and neurotransmitter receptor subunits. To take full advantage of CAKE, we resolved the nanoscale co-distribution of endogenous synaptic proteins using super-resolution microscopy, demonstrating that their co-organization depends on synapse size. Finally, we introduced inducible dimerization modules, providing acute control over synaptic receptor dynamics in living neurons. These experiments highlight the potential of CAKE to reveal new biological insight. Altogether, CAKE is a versatile method for multiplex protein labeling that enables the detection, localization, and manipulation of endogenous proteins in neurons.Significance StatementAccurate localization and manipulation of endogenous proteins is essential to unravel neuronal function. While labeling of individual proteins is achievable with existing gene editing techniques, methods to label multiple proteins in neurons are limiting. We introduce a new CRISPR/Cas9 strategy, CAKE, achieving faithful duplex protein labeling using sequential editing of genes. We use CAKE to visualize the co-localization of essential neuronal proteins, including cytoskeleton components, ion channels and synaptic scaffolds. Using super-resolution microscopy, we demonstrate that the co-organization of synaptic scaffolds and neurotransmitter receptors scales with synapse size. Finally, we acutely modulate the dynamics of synaptic receptors using labeling with inducible dimerization domains. Thus, CAKE mediates accurate duplex endogenous protein labeling and manipulation to address biological questions in neurons.
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Affiliation(s)
- Wouter J Droogers
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Jelmer Willems
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Harold D MacGillavry
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Arthur P H de Jong
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
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Oude Lohuis MN, Marchesi P, Pennartz CMA, Olcese U. Functional (ir)Relevance of Posterior Parietal Cortex during Audiovisual Change Detection. J Neurosci 2022; 42:5229-5245. [PMID: 35641187 PMCID: PMC9236290 DOI: 10.1523/jneurosci.2150-21.2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 10/26/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 12/31/2022] Open
Abstract
The posterior parietal cortex (PPC) plays a key role in integrating sensory inputs from different modalities to support adaptive behavior. Neuronal activity in PPC reflects perceptual decision-making across behavioral tasks, but the mechanistic involvement of PPC is unclear. In an audiovisual change detection task, we tested the hypothesis that PPC is required to arbitrate between the noisy inputs from the two different modalities and help decide in which modality a sensory change occurred. In trained male mice, we found extensive single-neuron and population-level encoding of task-relevant visual and auditory stimuli, trial history, as well as upcoming behavioral responses. However, despite these rich neural correlates, which would theoretically be sufficient to solve the task, optogenetic inactivation of PPC did not affect visual or auditory performance. Thus, despite neural correlates faithfully tracking sensory variables and predicting behavioral responses, PPC was not relevant for audiovisual change detection. This functional dissociation questions the role of sensory- and task-related activity in parietal associative circuits during audiovisual change detection. Furthermore, our results highlight the necessity to dissociate functional correlates from mechanistic involvement when exploring the neural basis of perception and behavior.SIGNIFICANCE STATEMENT The posterior parietal cortex (PPC) is active during many daily tasks, but capturing its function has remained challenging. Specifically, it is proposed to function as an integration hub for multisensory inputs. Here, we tested the hypothesis that, rather than classical cue integration, mouse PPC is involved in the segregation and discrimination of sensory modalities. Surprisingly, although neural activity tracked current and past sensory stimuli and reflected the ongoing decision-making process, optogenetic inactivation did not affect task performance. Thus, we show an apparent redundancy of sensory and task-related activity in mouse PPC. These results narrow down the function of parietal circuits, as well as direct the search for those neural dynamics that causally drive perceptual decision-making.
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Affiliation(s)
- Matthijs N Oude Lohuis
- Cognitive and Systems Neuroscience Group, SILS, University of Amsterdam, Amsterdam 1098XH, The Netherlands
- Research Priority Area Brain and Cognition, University of Amsterdam, Amsterdam 1018WS, The Netherlands
| | - Pietro Marchesi
- Cognitive and Systems Neuroscience Group, SILS, University of Amsterdam, Amsterdam 1098XH, The Netherlands
- Research Priority Area Brain and Cognition, University of Amsterdam, Amsterdam 1018WS, The Netherlands
| | - Cyriel M A Pennartz
- Cognitive and Systems Neuroscience Group, SILS, University of Amsterdam, Amsterdam 1098XH, The Netherlands
- Research Priority Area Brain and Cognition, University of Amsterdam, Amsterdam 1018WS, The Netherlands
| | - Umberto Olcese
- Cognitive and Systems Neuroscience Group, SILS, University of Amsterdam, Amsterdam 1098XH, The Netherlands
- Research Priority Area Brain and Cognition, University of Amsterdam, Amsterdam 1018WS, The Netherlands
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Allen J, Rosendahl Huber A, Pleguezuelos-Manzano C, Puschhof J, Wu S, Wu X, Boot C, Saftien A, O’Hagan HM, Wang H, van Boxtel R, Clevers H, Sears CL. Colon Tumors in Enterotoxigenic Bacteroides fragilis (ETBF)-Colonized Mice Do Not Display a Unique Mutational Signature but Instead Possess Host-Dependent Alterations in the APC Gene. Microbiol Spectr 2022; 10:e0105522. [PMID: 35587635 PMCID: PMC9241831 DOI: 10.1128/spectrum.01055-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 03/27/2022] [Accepted: 03/31/2022] [Indexed: 12/13/2022] Open
Abstract
Enterotoxigenic Bacteroides fragilis (ETBF) is consistently found at higher frequency in individuals with sporadic and hereditary colorectal cancer (CRC) and induces tumorigenesis in several mouse models of CRC. However, whether specific mutations induced by ETBF lead to colon tumor formation has not been investigated. To determine if ETBF-induced mutations impact the Apc gene, and other tumor suppressors or proto-oncogenes, we performed whole-exome sequencing and whole-genome sequencing on tumors isolated after ETBF and sham colonization of Apcmin/+ and Apcmin/+Msh2fl/flVC mice, as well as whole-genome sequencing of organoids cocultured with ETBF. Our results indicate that ETBF-induced tumor formation results from loss of heterozygosity (LOH) of Apc, unless the mismatch repair system is disrupted, in which case, tumor formation results from new acquisition of protein-truncating mutations in Apc. In contrast to polyketide synthase-positive Escherichia coli (pks+ E. coli), ETBF does not produce a unique mutational signature; instead, ETBF-induced tumors arise from errors in DNA mismatch repair and homologous recombination DNA damage repair, established pathways of tumor formation in the colon, and the same genetic mechanism accounting for sham tumors in these mouse models. Our analysis informs how this procarcinogenic bacterium may promote tumor formation in individuals with inherited predispositions to CRC, such as Lynch syndrome or familial adenomatous polyposis (FAP). IMPORTANCE Many studies have shown that microbiome composition in both the mucosa and the stool differs in individuals with sporadic and hereditary colorectal cancer (CRC). Both human and mouse models have established a strong association between particular microbes and colon tumor induction. However, the genetic mechanisms underlying putative microbe-induced colon tumor formation are not well established. In this paper, we applied whole-exome sequencing and whole-genome sequencing to investigate the impact of ETBF-induced genetic changes on tumor formation. Additionally, we performed whole-genome sequencing of human colon organoids exposed to ETBF to validate the mutational patterns seen in our mouse models and begin to understand their relevance in human colon epithelial cells. The results of this study highlight the importance of ETBF colonization in the development of sporadic CRC and in individuals with hereditary tumor conditions, such as Lynch syndrome and familial adenomatous polyposis (FAP).
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Affiliation(s)
- Jawara Allen
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Axel Rosendahl Huber
- Oncode Institute, Utrecht, The Netherlands
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Cayetano Pleguezuelos-Manzano
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Jens Puschhof
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Shaoguang Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Xinqun Wu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Charelle Boot
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
| | - Aurelia Saftien
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
| | - Heather M. O’Hagan
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, Indiana, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana, USA
- Cell, Molecular and Cancer Biology Program, Indiana University School of Medicine, Bloomington, Indiana, USA
| | - Hao Wang
- Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine Institutions, Baltimore, Maryland, USA
| | - Ruben van Boxtel
- Oncode Institute, Utrecht, The Netherlands
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Cynthia L. Sears
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins Medicine Institutions, Baltimore, Maryland, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine Institutions, Baltimore, Maryland, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine Institutions, Baltimore, Maryland, USA
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78
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Scholtens LH, Pijnenburg R, de Lange SC, Huitinga I, van den Heuvel MP. Common Microscale and Macroscale Principles of Connectivity in the Human Brain. J Neurosci 2022; 42:4147-4163. [PMID: 35422441 PMCID: PMC9121834 DOI: 10.1523/jneurosci.1572-21.2022] [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: 07/30/2021] [Revised: 01/27/2022] [Accepted: 03/04/2022] [Indexed: 11/21/2022] Open
Abstract
The brain requires efficient information transfer between neurons and large-scale brain regions. Brain connectivity follows predictable organizational principles. At the cellular level, larger supragranular pyramidal neurons have larger, more branched dendritic trees, more synapses, and perform more complex computations; at the macroscale, region-to-region connections display a diverse architecture with highly connected hub areas facilitating complex information integration and computation. Here, we explore the hypothesis that the branching structure of large-scale region-to-region connectivity follows similar organizational principles as the neuronal scale. We examine microscale connectivity of basal dendritic trees of supragranular pyramidal neurons (300+) across 10 cortical areas in five human donor brains (1 male, 4 female). Dendritic complexity was quantified as the number of branch points, tree length, spine count, spine density, and overall branching complexity. High-resolution diffusion-weighted MRI was used to construct white matter trees of corticocortical wiring. Examining complexity of the resulting white matter trees using the same measures as for dendritic trees shows heteromodal association areas to have larger, more complex white matter trees than primary areas (p < 0.0001) and macroscale complexity to run in parallel with microscale measures, in terms of number of inputs (r = 0.677, p = 0.032), branch points (r = 0.797, p = 0.006), tree length (r = 0.664, p = 0.036), and branching complexity (r = 0.724, p = 0.018). Our findings support the integrative theory that brain connectivity follows similar principles of connectivity at neuronal and macroscale levels and provide a framework to study connectivity changes in brain conditions at multiple levels of organization.SIGNIFICANCE STATEMENT Within the human brain, cortical areas are involved in a wide range of processes, requiring different levels of information integration and local computation. At the cellular level, these regional differences reflect a predictable organizational principle with larger, more complexly branched supragranular pyramidal neurons in higher order regions. We hypothesized that the 3D branching structure of macroscale corticocortical connections follows the same organizational principles as the cellular scale. Comparing branching complexity of dendritic trees of supragranular pyramidal neurons and of MRI-based regional white matter trees of macroscale connectivity, we show that macroscale branching complexity is larger in higher order areas and that microscale and macroscale complexity go hand in hand. Our findings contribute to a multiscale integrative theory of brain connectivity.
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Affiliation(s)
- Lianne H Scholtens
- Complex Traits Genetics Department, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Rory Pijnenburg
- Complex Traits Genetics Department, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Siemon C de Lange
- Complex Traits Genetics Department, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Inge Huitinga
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, 1105 BA Amsterdam, The Netherlands
- Brain Plasticity Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Martijn P van den Heuvel
- Complex Traits Genetics Department, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Department of Child Psychiatry, Amsterdam Neuroscience, Amsterdam University Medical Center, 1081 HV Amsterdam, The Netherlands
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79
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De la O Becerra KI, Oosterheert W, van den Bos RM, Xenaki KT, Lorent JH, Ruyken M, Schouten A, Rooijakkers SHM, van Bergen En Henegouwen PMP, Gros P. Multifaceted Activities of Seven Nanobodies against Complement C4b. J I 2022; 208:2207-2219. [PMID: 35428691 PMCID: PMC9047069 DOI: 10.4049/jimmunol.2100647] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 02/14/2022] [Indexed: 11/20/2022]
Abstract
Cleavage of the mammalian plasma protein C4 into C4b initiates opsonization, lysis, and clearance of microbes and damaged host cells by the classical and lectin pathways of the complement system. Dysregulated activation of C4 and other initial components of the classical pathway may cause or aggravate pathologies, such as systemic lupus erythematosus, Alzheimer disease, and schizophrenia. Modulating the activity of C4b by small-molecule or protein-based inhibitors may represent a promising therapeutic approach for preventing excessive inflammation and damage to host cells and tissue. Here, we present seven nanobodies, derived from llama (Lama glama) immunization, that bind to human C4b (Homo sapiens) with high affinities ranging from 3.2 nM to 14 pM. The activity of the nanobodies varies from no to complete inhibition of the classical pathway. The inhibiting nanobodies affect different steps in complement activation, in line with blocking sites for proconvertase formation, C3 substrate binding to the convertase, and regulator-mediated inactivation of C4b. For four nanobodies, we determined single-particle cryo-electron microscopy structures in complex with C4b at 3.4–4 Å resolution. The structures rationalize the observed functional effects of the nanobodies and define their mode of action during complement activation. Thus, we characterized seven anti-C4b nanobodies with diverse effects on the classical pathway of complement activation that may be explored for imaging, diagnostic, or therapeutic applications. Diverse binding properties are revealed for seven nanobodies against C4b. Cryo-electron microscopy structures of C4b–nanobody complexes indicate nanobodies’ modes of action. Nanobodies have therapeutic potential and are useful for labeling studies.
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Affiliation(s)
- Karla I De la O Becerra
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Wout Oosterheert
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Ramon M van den Bos
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Katerina T Xenaki
- Cell Biology, Neurobiology & Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Joseph H Lorent
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands; and
| | - Maartje Ruyken
- Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Arie Schouten
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | | | | | - Piet Gros
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands;
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80
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Janssen JJE, Lagerwaard B, Porbahaie M, Nieuwenhuizen AG, Savelkoul HFJ, van Neerven RJJ, Keijer J, de Boer VCJ. Extracellular flux analyses reveal differences in mitochondrial PBMC metabolism between high-fit and low-fit females. Am J Physiol Endocrinol Metab 2022; 322:E141-E153. [PMID: 35001658 PMCID: PMC8897018 DOI: 10.1152/ajpendo.00365.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Analyzing metabolism of peripheral blood mononuclear cells (PBMCs) can possibly serve as a cellular metabolic read-out for lifestyle factors and lifestyle interventions. However, the impact of PBMC composition on PBMC metabolism is not yet clear, neither is the differential impact of a longer-term lifestyle factor versus a short-term lifestyle intervention. We investigated the effect of aerobic fitness level and a recent exercise bout on PBMC metabolism in females. PBMCs from 31 young female adults divided into a high-fit (V̇o2peak ≥ 47 mL/kg/min, n = 15) and low-fit (V̇o2peak ≤ 37 mL/kg/min, n = 16) groups were isolated at baseline and overnight after a single bout of exercise (60 min, 70% V̇o2peak). Oxygen consumption rate (OCR) and glycolytic rate (GR) were measured using extracellular flux (XF) assays and PBMC subsets were characterized using fluorescence-activated cell sorting (FACS). Basal OCR, FCCP-induced OCR, spare respiratory capacity, ATP-linked OCR, and proton leak were significantly higher in high-fit than in low-fit females (all P < 0.01), whereas no significant differences in glycolytic rate (GR) were found (all P > 0.05). A recent exercise bout did not significantly affect GR or OCR parameters (all P > 0.05). The overall PBMC composition was similar between high-fit and low-fit females. Mitochondrial PBMC function was significantly higher in PBMCs from high-fit than from low-fit females, which was unrelated to PBMC composition and not impacted by a recent bout of exercise. Our study reveals a link between PBMC metabolism and levels of aerobic fitness, increasing the relevance of PBMC metabolism as a marker to study the impact of lifestyle factors on human health.NEW & NOTEWORTHY Mitochondrial metabolism was significantly higher in PBMCs from high-fit than from low-fit females. This was unrelated to PBMC composition and not impacted by a recent bout of exercise. Our study reveals a link between PBMC metabolism and levels of aerobic fitness, increasing the relevance of PBMC metabolism as a marker to study the impact of lifestyle factors on human health.
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Affiliation(s)
- Joëlle J E Janssen
- Human and Animal Physiology, Wageningen University and Research, Wageningen, The Netherlands
- Cell Biology and Immunology, Wageningen University and Research, Wageningen, The Netherlands
| | - Bart Lagerwaard
- Human and Animal Physiology, Wageningen University and Research, Wageningen, The Netherlands
- TI Food and Nutrition, Wageningen, The Netherlands
| | - Mojtaba Porbahaie
- Cell Biology and Immunology, Wageningen University and Research, Wageningen, The Netherlands
| | - Arie G Nieuwenhuizen
- Human and Animal Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Huub F J Savelkoul
- Cell Biology and Immunology, Wageningen University and Research, Wageningen, The Netherlands
| | - R J Joost van Neerven
- Cell Biology and Immunology, Wageningen University and Research, Wageningen, The Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Vincent C J de Boer
- Human and Animal Physiology, Wageningen University and Research, Wageningen, The Netherlands
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Schorcht A, Cottrell CA, Pugach P, Ringe RP, Han AX, Allen JD, van den Kerkhof TLGM, Seabright GE, Schermer EE, Ketas TJ, Burger JA, van Schooten J, LaBranche CC, Ozorowski G, de Val N, Bader DLV, Schuitemaker H, Russell CA, Montefiori DC, van Gils MJ, Crispin M, Klasse PJ, Ward AB, Moore JP, Sanders RW. The Glycan Hole Area of HIV-1 Envelope Trimers Contributes Prominently to the Induction of Autologous Neutralization. J Virol 2022; 96:e0155221. [PMID: 34669426 PMCID: PMC8754230 DOI: 10.1128/jvi.01552-21] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/14/2021] [Indexed: 01/15/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) trimeric envelope glycoprotein (Env) is heavily glycosylated, creating a dense glycan shield that protects the underlying peptidic surface from antibody recognition. The absence of conserved glycans, due to missing potential N-linked glycosylation sites (PNGS), can result in strain-specific, autologous neutralizing antibody (NAb) responses. Here, we sought to gain a deeper understanding of the autologous neutralization by introducing holes in the otherwise dense glycan shields of the AMC011 and AMC016 SOSIP trimers. Specifically, when we knocked out the N130 and N289 glycans, which are absent from the well-characterized B41 SOSIP trimer, we observed stronger autologous NAb responses. We also analyzed the highly variable NAb responses induced in rabbits by diverse SOSIP trimers from subtypes A, B, and C. Statistical analysis, using linear regression, revealed that the cumulative area exposed on a trimer by glycan holes correlates with the magnitude of the autologous NAb response. IMPORTANCE Forty years after the first description of HIV-1, the search for a protective vaccine is still ongoing. The sole target for antibodies that can neutralize the virus are the trimeric envelope glycoproteins (Envs) located on the viral surface. The glycoprotein surface is covered with glycans that shield off the underlying protein components from recognition by the immune system. However, the Env trimers of some viral strains have holes in the glycan shield. Immunized animals developed antibodies against such glycan holes. These antibodies are generally strain specific. Here, we sought to gain a deeper understanding of what drives these specific immune responses. First, we show that strain-specific neutralizing antibody responses can be increased by creating artificial holes in the glycan shield. Second, when studying a diverse set of Env trimers with different characteristics, we found that the surface area of the glycan holes contributes prominently to the induction of strain-specific neutralizing antibodies.
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Affiliation(s)
- Anna Schorcht
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - Christopher A. Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Pavel Pugach
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Rajesh P. Ringe
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Alvin X. Han
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - Joel D. Allen
- Centre for Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton, England, United Kingdom
| | - Tom L. G. M. van den Kerkhof
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - Gemma E. Seabright
- Centre for Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton, England, United Kingdom
| | - Edith E. Schermer
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - Thomas J. Ketas
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Judith A. Burger
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - Jelle van Schooten
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - Celia C. LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Natalia de Val
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Daniel L. V. Bader
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - Colin A. Russell
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Marit J. van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
| | - Max Crispin
- Centre for Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton, England, United Kingdom
| | - P. J. Klasse
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - John P. Moore
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection & Immunity Institute (AI&AII), Amsterdam UMC, Location Meibergdreef, University of Amsterdam, Amsterdam, The Netherlands
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
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van Esveld SL, Meerstein‐Kessel L, Boshoven C, Baaij JF, Barylyuk K, Coolen JPM, van Strien J, Duim RAJ, Dutilh BE, Garza DR, Letterie M, Proellochs NI, de Ridder MN, Venkatasubramanian PB, de Vries LE, Waller RF, Kooij TWA, Huynen MA. A Prioritized and Validated Resource of Mitochondrial Proteins in Plasmodium Identifies Unique Biology. mSphere 2021; 6:e0061421. [PMID: 34494883 PMCID: PMC8550323 DOI: 10.1128/msphere.00614-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/23/2021] [Indexed: 11/20/2022] Open
Abstract
Plasmodium species have a single mitochondrion that is essential for their survival and has been successfully targeted by antimalarial drugs. Most mitochondrial proteins are imported into this organelle, and our picture of the Plasmodium mitochondrial proteome remains incomplete. Many data sources contain information about mitochondrial localization, including proteome and gene expression profiles, orthology to mitochondrial proteins from other species, coevolutionary relationships, and amino acid sequences, each with different coverage and reliability. To obtain a comprehensive, prioritized list of Plasmodium falciparum mitochondrial proteins, we rigorously analyzed and integrated eight data sets using Bayesian statistics into a predictive score per protein for mitochondrial localization. At a corrected false discovery rate of 25%, we identified 445 proteins with a sensitivity of 87% and a specificity of 97%. They include proteins that have not been identified as mitochondrial in other eukaryotes but have characterized homologs in bacteria that are involved in metabolism or translation. Mitochondrial localization of seven Plasmodium berghei orthologs was confirmed by epitope labeling and colocalization with a mitochondrial marker protein. One of these belongs to a newly identified apicomplexan mitochondrial protein family that in P. falciparum has four members. With the experimentally validated mitochondrial proteins and the complete ranked P. falciparum proteome, which we have named PlasmoMitoCarta, we present a resource to study unique proteins of Plasmodium mitochondria. IMPORTANCE The unique biology and medical relevance of the mitochondrion of the malaria parasite Plasmodium falciparum have made it the subject of many studies. However, we actually do not have a comprehensive assessment of which proteins reside in this organelle. Many omics data are available that are predictive of mitochondrial localization, such as proteomics data and expression data. Individual data sets are, however, rarely complete and can provide conflicting evidence. We integrated a wide variety of available omics data in a manner that exploits the relative strengths of the data sets. Our analysis gave a predictive score for the mitochondrial localization to each nuclear encoded P. falciparum protein and identified 445 likely mitochondrial proteins. We experimentally validated the mitochondrial localization of seven of the new mitochondrial proteins, confirming the quality of the complete list. These include proteins that have not been observed mitochondria before, adding unique mitochondrial functions to P. falciparum.
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Affiliation(s)
- Selma L. van Esveld
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
| | - Lisette Meerstein‐Kessel
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Radboud Institute for Health Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Cas Boshoven
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Jochem F. Baaij
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Konstantin Barylyuk
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Joeri van Strien
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Ronald A. J. Duim
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Bas E. Dutilh
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Daniel R. Garza
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Marijn Letterie
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Nicholas I. Proellochs
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Michelle N. de Ridder
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | | | - Laura E. de Vries
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Ross F. Waller
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Taco W. A. Kooij
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Martijn A. Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
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Pascal Andreu V, Augustijn HE, van den Berg K, van der Hooft JJJ, Fischbach MA, Medema MH. BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes. mSystems 2021; 6:e0093721. [PMID: 34581602 PMCID: PMC8547482 DOI: 10.1128/msystems.00937-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/24/2021] [Indexed: 12/28/2022] Open
Abstract
Microbial gene clusters encoding the biosynthesis of primary and secondary metabolites play key roles in shaping microbial ecosystems and driving microbiome-associated phenotypes. Although effective approaches exist to evaluate the metabolic potential of such bacteria through identification of these metabolic gene clusters in their genomes, no automated pipelines exist to profile the abundance and expression levels of such gene clusters in microbiome samples to generate hypotheses about their functional roles, and to find associations with phenotypes of interest. Here, we describe BiG-MAP, a bioinformatic tool to profile abundance and expression levels of gene clusters across metagenomic and metatranscriptomic data and evaluate their differential abundance and expression under different conditions. To illustrate its usefulness, we analyzed 96 metagenomic samples from healthy and caries-associated human oral microbiome samples and identified 252 gene clusters, including unreported ones, that were significantly more abundant in either phenotype. Among them, we found the muc operon, a gene cluster known to be associated with tooth decay. Additionally, we found a putative reuterin biosynthetic gene cluster from a Streptococcus strain to be enriched but not exclusively found in healthy samples; metabolomic data from the same samples showed masses with fragmentation patterns consistent with (poly)acrolein, which is known to spontaneously form from the products of the reuterin pathway and has been previously shown to inhibit pathogenic Streptococcus mutans strains. Thus, we show how BiG-MAP can be used to generate new hypotheses on potential drivers of microbiome-associated phenotypes and prioritize the experimental characterization of relevant gene clusters that may mediate them. IMPORTANCE Microbes play an increasingly recognized role in determining host-associated phenotypes by producing small molecules that interact with other microorganisms or host cells. The production of these molecules is often encoded in syntenic genomic regions, also known as gene clusters. With the increasing numbers of (multi)omics data sets that can help in understanding complex ecosystems at a much deeper level, there is a need to create tools that can automate the process of analyzing these gene clusters across omics data sets. This report presents a new software tool called BiG-MAP, which allows assessing gene cluster abundance and expression in microbiome samples using metagenomic and metatranscriptomic data. Here, we describe the tool and its functionalities, as well as its validation using a mock community. Finally, using an oral microbiome data set, we show how it can be used to generate hypotheses regarding the functional roles of gene clusters in mediating host phenotypes.
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Affiliation(s)
| | | | - Koen van den Berg
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | | | - Michael A. Fischbach
- Department of Bioengineering, Stanford University, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
- ChEM-H, Stanford University, Stanford, California, USA
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
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84
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Garrigues S, Kun RS, Peng M, Gruben BS, Benoit Gelber I, Mäkelä M, de Vries RP. The Cultivation Method Affects the Transcriptomic Response of Aspergillus niger to Growth on Sugar Beet Pulp. Microbiol Spectr 2021; 9:e0106421. [PMID: 34431718 PMCID: PMC8552599 DOI: 10.1128/spectrum.01064-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/20/2022] Open
Abstract
In nature, filamentous fungi are exposed to diverse nutritional sources and changes in substrate availability. Conversely, in submerged cultures, mycelia are continuously exposed to the existing substrates, which are depleted over time. Submerged cultures are the preferred choice for experimental setups in laboratory and industry and are often used for understanding the physiology of fungi. However, to what extent the cultivation method affects fungal physiology, with respect to utilization of natural substrates, has not been addressed in detail. Here, we compared the transcriptomic responses of Aspergillus niger grown in submerged culture and solid culture, both containing sugar beet pulp (SBP) as a carbon source. The results showed that expression of CAZy (Carbohydrate Active enZyme)-encoding and sugar catabolic genes in liquid SBP was time dependent. Moreover, additional components of SBP delayed the A. niger response to the degradation of pectin present in SBP. In addition, we demonstrated that liquid cultures induced wider transcriptome variability than solid cultures. Although there was a correlation regarding sugar metabolic gene expression patterns between liquid and solid cultures, it decreased in the case of CAZyme-encoding genes. In conclusion, the transcriptomic response of A. niger to SBP is influenced by the culturing method, limiting the value of liquid cultures for understanding the behavior of fungi in natural habitats. IMPORTANCE Understanding the interaction between filamentous fungi and their natural and biotechnological environments has been of great interest for the scientific community. Submerged cultures are preferred over solid cultures at a laboratory scale to study the natural response of fungi to different stimuli found in nature (e.g., carbon/nitrogen sources, pH). However, whether and to what extent submerged cultures introduce variation in the physiology of fungi during growth on plant biomass have not been studied in detail. In this study, we compared the transcriptomic responses of Aspergillus niger to growth on liquid and solid cultures containing sugar beet pulp (a by-product of the sugar industry) as a carbon source. We demonstrate that the transcriptomic response of A. niger was highly affected by the culture condition, since the transcriptomic response obtained in a liquid environment could not fully explain the behavior of the fungus in a solid environment. This could partially explain the differences often observed between the phenotypes on plates compared to liquid cultures.
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Affiliation(s)
- Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Roland S. Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Birgit S. Gruben
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
- Microbiology, Utrecht University, Utrecht, The Netherlands
| | - Isabelle Benoit Gelber
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
- Microbiology, Utrecht University, Utrecht, The Netherlands
| | - Miia Mäkelä
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
- Microbiology, Utrecht University, Utrecht, The Netherlands
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85
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Dijkstra N, van Gaal S, Geerligs L, Bosch SE, van Gerven MAJ. No Evidence for Neural Overlap between Unconsciously Processed and Imagined Stimuli. eNeuro 2021; 8:ENEURO.0228-21.2021. [PMID: 34593516 PMCID: PMC8577044 DOI: 10.1523/eneuro.0228-21.2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 11/23/2022] Open
Abstract
Visual representations can be generated via feedforward or feedback processes. The extent to which these processes result in overlapping representations remains unclear. Previous work has shown that imagined stimuli elicit similar representations as perceived stimuli throughout the visual cortex. However, while representations during imagery are indeed only caused by feedback processing, neural processing during perception is an interplay of both feedforward and feedback processing. This means that any representational overlap could be because of overlap in feedback processes. In the current study, we aimed to investigate this issue by characterizing the overlap between feedforward- and feedback-initiated category representations during imagined stimuli, conscious perception, and unconscious processing using fMRI in humans of either sex. While all three conditions elicited stimulus representations in left lateral occipital cortex (LOC), significant similarities were observed only between imagery and conscious perception in this area. Furthermore, connectivity analyses revealed stronger connectivity between frontal areas and left LOC during conscious perception and in imagery compared with unconscious processing. Together, these findings can be explained by the idea that long-range feedback modifies visual representations, thereby reducing representational overlap between purely feedforward- and feedback-initiated stimulus representations measured by fMRI. Neural representations influenced by feedback, either stimulus driven (perception) or purely internally driven (imagery), are, however, relatively similar.
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Affiliation(s)
- Nadine Dijkstra
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500 GL, Nijmegen, The Netherlands
- Wellcome Centre for Human Neuroimaging, University College London, London WC1N 3AR, United Kingdom
| | - Simon van Gaal
- Department of Psychology, Brain & Cognition, University of Amsterdam, 1000 GG, Amsterdam, The Netherlands
| | - Linda Geerligs
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500 GL, Nijmegen, The Netherlands
| | - Sander E Bosch
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500 GL, Nijmegen, The Netherlands
| | - Marcel A J van Gerven
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500 GL, Nijmegen, The Netherlands
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Balhuizen MD, van Dijk A, Jansen JWA, van de Lest CHA, Veldhuizen EJA, Haagsman HP. Outer Membrane Vesicles Protect Gram-Negative Bacteria against Host Defense Peptides. mSphere 2021; 6:e0052321. [PMID: 34232080 PMCID: PMC8386409 DOI: 10.1128/msphere.00523-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 01/11/2023] Open
Abstract
Host defense peptides (HDPs) are part of the innate immune system and constitute a first line of defense against invading pathogens. They possess antimicrobial activity against a broad spectrum of pathogens. However, pathogens have been known to adapt to hostile environments. Therefore, the bacterial response to treatment with HDPs was investigated. Previous observations suggested that sublethal concentrations of HDPs increase the release of outer membrane vesicles (OMVs) in Escherichia coli. First, the effects of sublethal treatment with HDPs CATH-2, PMAP-36, and LL-37 on OMV release of several Gram-negative bacteria were analyzed. Treatment with PMAP-36 and CATH-2 induced release of OMVs, but treatment with LL-37 did not. The OMVs were further characterized with respect to morphological properties. The HDP-induced OMVs often had disc-like shapes. The beneficial effect of bacterial OMV release was studied by determining the susceptibility of E. coli toward HDPs in the presence of OMVs. The minimal bactericidal concentration was increased in the presence of OMVs. It is concluded that OMV release is a means of bacteria to dispose of HDP-affected membrane. Furthermore, OMVs act as a decoy for HDPs and thereby protect the bacterium. IMPORTANCE Antibiotic resistance is a pressing problem and estimated to be a leading cause of mortality by 2050. Antimicrobial peptides, also known as host defense peptides (HDPs), and HDP-derived antimicrobials have potent antimicrobial activity and high potential as alternatives to antibiotics due to low resistance development. Some resistance mechanisms have developed in bacteria, and complete understanding of bacterial defense against HDPs will aid their use in the clinic. This study provides insight into outer membrane vesicles (OMVs) as potential defense mechanisms against HDPs, which will allow anticipation of unforeseen resistance to HDPs in clinical use and possibly prevention of bacterial resistance by the means of OMVs.
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Affiliation(s)
- Melanie D. Balhuizen
- Section of Molecular Host Defence, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Albert van Dijk
- Section of Molecular Host Defence, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jeroen W. A. Jansen
- Section of Cell Biology, Metabolism and Cancer, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Chris H. A. van de Lest
- Section of Cell Biology, Metabolism and Cancer, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Edwin J. A. Veldhuizen
- Section of Immunology, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Henk P. Haagsman
- Section of Molecular Host Defence, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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Fleury E, Trnková P, Spruijt K, Herault J, Lebbink F, Heufelder J, Hrbacek J, Horwacik T, Kajdrowicz T, Denker A, Gerard A, Hofverberg P, Mamalui M, Slopsema R, Pignol J, Hoogeman M. Characterization of the HollandPTC proton therapy beamline dedicated to uveal melanoma treatment and an interinstitutional comparison. Med Phys 2021; 48:4506-4522. [PMID: 34091930 PMCID: PMC8457201 DOI: 10.1002/mp.15024] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/08/2021] [Accepted: 05/25/2021] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Eye-dedicated proton therapy (PT) facilities are used to treat malignant intraocular lesions, especially uveal melanoma (UM). The first commercial ocular PT beamline from Varian was installed in the Netherlands. In this work, the conceptual design of the new eyeline is presented. In addition, a comprehensive comparison against five PT centers with dedicated ocular beamlines is performed, and the clinical impact of the identified differences is analyzed. MATERIAL/METHODS The HollandPTC eyeline was characterized. Four centers in Europe and one in the United States joined the study. All centers use a cyclotron for proton beam generation and an eye-dedicated nozzle. Differences among the chosen ocular beamlines were in the design of the nozzle, nominal energy, and energy spectrum. The following parameters were collected for all centers: technical characteristics and a set of distal, proximal, and lateral region measurements. The measurements were performed with detectors available in-house at each institution. The institutions followed the International Atomic Energy Agency (IAEA) Technical Report Series (TRS)-398 Code of Practice for absolute dose measurement, and the IAEA TRS-398 Code of Practice, its modified version or International Commission on Radiation Units and Measurements Report No. 78 for spread-out Bragg peak normalization. Energy spreads of the pristine Bragg peaks were obtained with Monte Carlo simulations using Geant4. Seven tumor-specific case scenarios were simulated to evaluate the clinical impact among centers: small, medium, and large UM, located either anteriorly, at the equator, or posteriorly within the eye. Differences in the depth dose distributions were calculated. RESULTS A pristine Bragg peak of HollandPTC eyeline corresponded to the constant energy of 75 MeV (maximal range 3.97 g/cm2 in water) with an energy spread of 1.10 MeV. The pristine Bragg peaks for the five participating centers varied from 62.50 to 104.50 MeV with an energy spread variation between 0.10 and 0.70 MeV. Differences in the average distal fall-offs and lateral penumbrae (LPs) (over the complete set of clinically available beam modulations) among all centers were up to 0.25 g/cm2 , and 0.80 mm, respectively. Average distal fall-offs of the HollandPTC eyeline were 0.20 g/cm2 , and LPs were between 1.50 and 2.15 mm from proximal to distal regions, respectively. Treatment time, around 60 s, was comparable among all centers. The virtual source-to-axis distance of 120 cm at HollandPTC was shorter than for the five participating centers (range: 165-350 cm). Simulated depth dose distributions demonstrated the impact of the different beamline characteristics among institutions. The largest difference was observed for a small UM located at the posterior pole, where a proximal dose between two extreme centers was up to 20%. CONCLUSIONS HollandPTC eyeline specifications are in accordance with five other ocular PT beamlines. Similar clinical concepts can be applied to expect the same high local tumor control. Dosimetrical properties among the six institutions induce most likely differences in ocular radiation-related toxicities. This interinstitutional comparison could support further research on ocular post-PT complications. Finally, the findings reported in this study could be used to define dosimetrical guidelines for ocular PT to unify the concepts among institutions.
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Affiliation(s)
- Emmanuelle Fleury
- Department of RadiotherapyErasmus MC Cancer Institute, University Medical Center RotterdamThe Netherlands
- Holland Proton Therapy CenterDelftThe Netherlands
| | - Petra Trnková
- Department of RadiotherapyErasmus MC Cancer Institute, University Medical Center RotterdamThe Netherlands
- Departement of Radiation OncologyMedical University of ViennaViennaAustria
| | - Kees Spruijt
- Holland Proton Therapy CenterDelftThe Netherlands
| | - Joël Herault
- Departement of Radiation OncologyCentre Antoine LacassagneNiceFrance
| | | | - Jens Heufelder
- Helmholtz‐Zentrum Berlin für Materialien und EnergieBerlinGermany
- Department of OphthalmologyCharité ‐ Universitätsmedizin BerlinBerlinGermany
| | - Jan Hrbacek
- Paul Scherrer Institute Center for Proton TherapyVilligenSwitzerland
| | - Tomasz Horwacik
- Institute of Nuclear PhysicsPolish Academy of SciencesKrakówPoland
| | | | - Andrea Denker
- Helmholtz‐Zentrum Berlin für Materialien und EnergieBerlinGermany
| | - Anaïs Gerard
- Departement of Radiation OncologyCentre Antoine LacassagneNiceFrance
| | - Petter Hofverberg
- Departement of Radiation OncologyCentre Antoine LacassagneNiceFrance
| | - Maria Mamalui
- Department of Radiation OncologyUniversity of FloridaGainesvilleFloridaUSA
| | - Roelf Slopsema
- Department of Radiation OncologyEmory Proton Therapy CenterAtlantaGeorgiaUSA
| | | | - Mischa Hoogeman
- Department of RadiotherapyErasmus MC Cancer Institute, University Medical Center RotterdamThe Netherlands
- Holland Proton Therapy CenterDelftThe Netherlands
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Dotlačil J. Parsing as a Cue-Based Retrieval Model. Cogn Sci 2021; 45:e13020. [PMID: 34379334 PMCID: PMC8459291 DOI: 10.1111/cogs.13020] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 06/09/2021] [Accepted: 06/26/2021] [Indexed: 12/01/2022]
Abstract
This paper develops a novel psycholinguistic parser and tests it against experimental and corpus reading data. The parser builds on the recent research into memory structures, which argues that memory retrieval is content-addressable and cue-based. It is shown that the theory of cue-based memory systems can be combined with transition-based parsing to produce a parser that, when combined with the cognitive architecture ACT-R, can model reading and predict online behavioral measures (reading times and regressions). The parser's modeling capacities are tested against self-paced reading experimental data (Grodner & Gibson, 2005), eye-tracking experimental data (Staub, 2011), and a self-paced reading corpus (Futrell et al., 2018).
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89
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Elings W, Chikunova A, van Zanten DB, Drenth R, Ahmad MUD, Blok AJ, Timmer M, Perrakis A, Ubbink M. Two β-Lactamase Variants with Reduced Clavulanic Acid Inhibition Display Different Millisecond Dynamics. Antimicrob Agents Chemother 2021; 65:e0262820. [PMID: 34031049 PMCID: PMC8284444 DOI: 10.1128/aac.02628-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 05/07/2021] [Indexed: 11/20/2022] Open
Abstract
The β-lactamase of Mycobacterium tuberculosis, BlaC, is susceptible to inhibition by clavulanic acid. The ability of this enzyme to escape inhibition through mutation was probed using error-prone PCR combined with functional screening in Escherichia coli. The variant that was found to confer the most inhibitor resistance, K234R, as well as variant G132N that was found previously were characterized using X-ray crystallography and nuclear magnetic resonance (NMR) relaxation experiments to probe structural and dynamic properties. The G132N mutant exists in solution in two almost equally populated conformations that exchange with a rate of ca. 88 s-1. The conformational change affects a broad region of the enzyme. The crystal structure reveals that the Asn132 side chain forces the peptide bond between Ser104 and Ile105 in a cis-conformation. The crystal structure suggests multiple conformations for several side chains (e.g., Ser104 and Ser130) and a short loop (positions 214 to 216). In the K234R mutant, the active-site dynamics are significantly diminished with respect to the wild-type enzyme. These results show that multiple evolutionary routes are available to increase inhibitor resistance in BlaC and that active-site dynamics on the millisecond time scale are not required for catalytic function.
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Affiliation(s)
- Wouter Elings
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | | | - Ralphe Drenth
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Misbha Ud Din Ahmad
- Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Anneloes J. Blok
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Monika Timmer
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Anastassis Perrakis
- Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
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90
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Vaes N, Schonkeren SL, Rademakers G, Holland AM, Koch A, Gijbels MJ, Keulers TG, de Wit M, Moonen L, Van der Meer JRM, van den Boezem E, Wolfs TGAM, Threadgill DW, Demmers J, Fijneman RJA, Jimenez CR, Vanden Berghe P, Smits KM, Rouschop KMA, Boesmans W, Hofstra RMW, Melotte V. Loss of enteric neuronal Ndrg4 promotes colorectal cancer via increased release of Nid1 and Fbln2. EMBO Rep 2021; 22:e51913. [PMID: 33890711 PMCID: PMC8183412 DOI: 10.15252/embr.202051913] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 10/16/2020] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/28/2022] Open
Abstract
The N-Myc Downstream-Regulated Gene 4 (NDRG4), a prominent biomarker for colorectal cancer (CRC), is specifically expressed by enteric neurons. Considering that nerves are important members of the tumor microenvironment, we here establish different Ndrg4 knockout (Ndrg4-/- ) CRC models and an indirect co-culture of primary enteric nervous system (ENS) cells and intestinal organoids to identify whether the ENS, via NDRG4, affects intestinal tumorigenesis. Linking immunostainings and gastrointestinal motility (GI) assays, we show that the absence of Ndrg4 does not trigger any functional or morphological GI abnormalities. However, combining in vivo, in vitro, and quantitative proteomics data, we uncover that Ndrg4 knockdown is associated with enlarged intestinal adenoma development and that organoid growth is boosted by the Ndrg4-/- ENS cell secretome, which is enriched for Nidogen-1 (Nid1) and Fibulin-2 (Fbln2). Moreover, NID1 and FBLN2 are expressed in enteric neurons, enhance migration capacities of CRC cells, and are enriched in human CRC secretomes. Hence, we provide evidence that the ENS, via loss of Ndrg4, is involved in colorectal pathogenesis and that ENS-derived Nidogen-1 and Fibulin-2 enhance colorectal carcinogenesis.
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Affiliation(s)
- Nathalie Vaes
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Simone L Schonkeren
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Glenn Rademakers
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Amy M Holland
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Alexander Koch
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Marion J Gijbels
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Department of Molecular GeneticsCardiovascular Research Institute Maastricht (CARIM)MaastrichtThe Netherlands
- Department of Medical BiochemistryAcademic Medical CenterAmsterdamThe Netherlands
| | - Tom G Keulers
- Department of RadiotherapyGROW‐School for Oncology and Developmental Biology and Comprehensive Cancer Center Maastricht MUMC+Maastricht UniversityMaastrichtThe Netherlands
| | - Meike de Wit
- Department of Medical Oncology and Oncoproteomics LaboratoryCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdam UMCAmsterdamThe Netherlands
- Department of PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Laura Moonen
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Jaleesa R M Van der Meer
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Edith van den Boezem
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Tim G A M Wolfs
- Department of PediatricsGROW‐School for Oncology and Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - David W Threadgill
- Department of Molecular and Cellular MedicineTexas A&M University Health Science CenterCollege StationTXUSA
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Jeroen Demmers
- Proteomics CenterErasmus University Medical CenterRotterdamThe Netherlands
| | | | - Connie R Jimenez
- Department of Medical Oncology and Oncoproteomics LaboratoryCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdam UMCAmsterdamThe Netherlands
| | - Pieter Vanden Berghe
- Laboratory for Enteric Neuroscience (LENS) and Translational Research Center for Gastrointestinal Disorders (TARGID)Department of Chronic Diseases, Metabolism and AgeingKU LeuvenLeuvenBelgium
| | - Kim M Smits
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Kasper M A Rouschop
- Department of RadiotherapyGROW‐School for Oncology and Developmental Biology and Comprehensive Cancer Center Maastricht MUMC+Maastricht UniversityMaastrichtThe Netherlands
| | - Werend Boesmans
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Biomedical Research Institute (BIOMED)Hasselt UniversityHasseltBelgium
| | - Robert M W Hofstra
- Department of Clinical GeneticsErasmus University Medical CenterRotterdamThe Netherlands
| | - Veerle Melotte
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Department of Clinical GeneticsErasmus University Medical CenterRotterdamThe Netherlands
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91
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Sterken MG, van Sluijs L, Wang YA, Ritmahan W, Gultom ML, Riksen JAG, Volkers RJM, Snoek LB, Pijlman GP, Kammenga JE. Punctuated Loci on Chromosome IV Determine Natural Variation in Orsay Virus Susceptibility of Caenorhabditis elegans Strains Bristol N2 and Hawaiian CB4856. J Virol 2021; 95:e02430-20. [PMID: 33827942 PMCID: PMC8315983 DOI: 10.1128/jvi.02430-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/29/2021] [Indexed: 01/06/2023] Open
Abstract
Host-pathogen interactions play a major role in evolutionary selection and shape natural genetic variation. The genetically distinct Caenorhabditis elegans strains, Bristol N2 and Hawaiian CB4856, are differentially susceptible to the Orsay virus (OrV). Here, we report the dissection of the genetic architecture of susceptibility to OrV infection. We compare OrV infection in the relatively resistant wild-type CB4856 strain to the more susceptible canonical N2 strain. To gain insight into the genetic architecture of viral susceptibility, 52 fully sequenced recombinant inbred lines (CB4856 × N2 RILs) were exposed to OrV. This led to the identification of two loci on chromosome IV associated with OrV resistance. To verify the two loci and gain additional insight into the genetic architecture controlling virus infection, introgression lines (ILs) that together cover chromosome IV, were exposed to OrV. Of the 27 ILs used, 17 had an CB4856 introgression in an N2 background, and 10 had an N2 introgression in a CB4856 background. Infection of the ILs confirmed and fine-mapped the locus underlying variation in OrV susceptibility, and we found that a single nucleotide polymorphism in cul-6 may contribute to the difference in OrV susceptibility between N2 and CB4856. An allele swap experiment showed the strain CB4856 became as susceptible as the N2 strain by having an N2 cul-6 allele, although having the CB4856 cul-6 allele did not increase resistance in N2. In addition, we found that multiple strains with nonoverlapping introgressions showed a distinct infection phenotype from the parental strain, indicating that there are punctuated locations on chromosome IV determining OrV susceptibility. Thus, our findings reveal the genetic complexity of OrV susceptibility in C. elegans and suggest that viral susceptibility is governed by multiple genes.IMPORTANCE Genetic variation determines the viral susceptibility of hosts. Yet, pinpointing which genetic variants determine viral susceptibility remains challenging. Here, we have exploited the genetic tractability of the model organism Caenorhabditis elegans to dissect the genetic architecture of Orsay virus infection. Our results provide novel insight into natural determinants of Orsay virus infection.
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Affiliation(s)
- Mark G Sterken
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Lisa van Sluijs
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Yiru A Wang
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Wannisa Ritmahan
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Mitra L Gultom
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Joost A G Riksen
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Rita J M Volkers
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - L Basten Snoek
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
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92
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Kusumawardhani H, Furtwängler B, Blommestijn M, Kaltenytė A, van der Poel J, Kolk J, Hosseini R, de Winde JH. Adaptive Laboratory Evolution Restores Solvent Tolerance in Plasmid-Cured Pseudomonas putida S12: a Molecular Analysis. Appl Environ Microbiol 2021; 87:e00041-21. [PMID: 33674430 PMCID: PMC8091024 DOI: 10.1128/aem.00041-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/24/2021] [Indexed: 11/23/2022] Open
Abstract
Pseudomonas putida S12 is inherently solvent tolerant and constitutes a promising platform for biobased production of aromatic compounds and biopolymers. The megaplasmid pTTS12 of P. putida S12 carries several gene clusters involved in solvent tolerance, and the removal of this megaplasmid caused a significant reduction in solvent tolerance. In this study, we succeeded in restoring solvent tolerance in plasmid-cured P. putida S12 using adaptive laboratory evolution (ALE), underscoring the innate solvent tolerance of this strain. Whole-genome sequencing identified several single nucleotide polymorphisms (SNPs) and a mobile element insertion enabling ALE-derived strains to survive and sustain growth in the presence of a high toluene concentration (10% [vol/vol]). We identified mutations in an RND efflux pump regulator, arpR, that resulted in constitutive upregulation of the multifunctional efflux pump ArpABC. SNPs were also found in the intergenic region and subunits of ATP synthase, RNA polymerase subunit β', a global two-component regulatory system (GacA/GacS), and a putative AraC family transcriptional regulator, Afr. Transcriptomic analysis further revealed a constitutive downregulation of energy-consuming activities in ALE-derived strains, such as flagellar assembly, FoF1 ATP synthase, and membrane transport proteins. In summary, constitutive expression of a solvent extrusion pump in combination with high metabolic flexibility enabled the restoration of the solvent tolerance trait in P. putida S12 lacking its megaplasmid.IMPORTANCE Sustainable production of high-value chemicals can be achieved by bacterial biocatalysis. However, bioproduction of biopolymers and aromatic compounds may exert stress on the microbial production host and limit the resulting yield. Having a solvent tolerance trait is highly advantageous for microbial hosts used in the biobased production of aromatics. The presence of a megaplasmid has been linked to the solvent tolerance trait of Pseudomonas putida; however, the extent of innate, intrinsic solvent tolerance in this bacterium remained unclear. Using adaptive laboratory evolution, we successfully adapted the plasmid-cured P. putida S12 strain to regain its solvent tolerance. Through these adapted strains, we began to clarify the causes, origins, limitations, and trade-offs of the intrinsic solvent tolerance in P. putida This work sheds light on the possible genetic engineering targets to enhance solvent tolerance in Pseudomonas putida as well as other bacteria.
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Affiliation(s)
| | | | | | - Adelė Kaltenytė
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Jaap van der Poel
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Jan Kolk
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Rohola Hosseini
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
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93
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Izquierdo Lafuente B, Ummels R, Kuijl C, Bitter W, Speer A. Mycobacterium tuberculosis Toxin CpnT Is an ESX-5 Substrate and Requires Three Type VII Secretion Systems for Intracellular Secretion. mBio 2021; 12:e02983-20. [PMID: 33653883 PMCID: PMC8092274 DOI: 10.1128/mbio.02983-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/25/2021] [Indexed: 11/20/2022] Open
Abstract
CpnT, a NAD+ glycohydrolase, is the only known toxin that is secreted by Mycobacterium tuberculosis CpnT is composed of two domains; the C-terminal domain is the toxin, whereas the N-terminal domain is required for secretion. CpnT shows characteristics of type VII secretion (T7S) substrates, including a predicted helix-turn-helix domain followed by a secretion motif (YxxxE). Disruption of this motif indeed abolished CpnT secretion. By analyzing different mutants, we established that CpnT is specifically secreted by the ESX-5 system in Mycobacterium marinum under axenic conditions and during macrophage infection. Surprisingly, intracellular secretion of CpnT was also dependent on both ESX-1 and ESX-4. These secretion defects could be partially rescued by coinfection with wild-type bacteria, indicating that secreted effectors are involved in this process. In summary, our data reveal that three different type VII secretion systems have to be functional in order to observe intracellular secretion of the toxin CpnT.IMPORTANCE For decades, it was believed that the intracellular pathogen M. tuberculosis does not possess toxins. Only fairly recently it was discovered that CpnT is a potent secreted toxin of M. tuberculosis, causing necrotic cell death in host cells. However, until now the secretion pathway remained unknown. In our study, we were able to identify CpnT as a substrate of the mycobacterial type VII secretion system. Pathogenic mycobacteria have up to five different type VII secretion systems, called ESX-1 to ESX-5, which play distinct roles for the pathogen during growth or infection. We were able to elucidate that CpnT is exclusively secreted by the ESX-5 system in bacterial culture. However, to our surprise we discovered that, during infection studies, CpnT secretion relies on intact ESX-1, ESX-4, and ESX-5 systems. We elucidate for the first time the intertwined interplay of three different and independent secretion systems to secrete one substrate during infection.
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Affiliation(s)
- B Izquierdo Lafuente
- Section of Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - R Ummels
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, Amsterdam, The Netherlands
| | - C Kuijl
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, Amsterdam, The Netherlands
| | - W Bitter
- Section of Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, Amsterdam, The Netherlands
| | - A Speer
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, Amsterdam, The Netherlands
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94
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van Gelder CAGH, Penning R, Veth TS, Catsburg LAE, Hoogenraad CC, MacGillavry HD, Altelaar M. Temporal Quantitative Proteomics of mGluR-induced Protein Translation and Phosphorylation in Neurons. Mol Cell Proteomics 2020; 19:1952-1968. [PMID: 32912969 PMCID: PMC7710149 DOI: 10.1074/mcp.ra120.002199] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 06/29/2020] [Revised: 09/04/2020] [Indexed: 01/12/2023] Open
Abstract
At neuronal synapses, activation of group I metabotropic glutamate receptors (mGluR1/5) triggers a form of long-term depression (mGluR-LTD) that relies on new protein synthesis and the internalization of AMPA-type glutamate receptors. Dysregulation of these processes has been implicated in the development of mental disorders such as autism spectrum disorders and therefore merit a better understanding on a molecular level. Here, to study mGluR-induced signaling pathways, we integrated quantitative phosphoproteomics with the analyses of newly synthesized proteins via bio-orthogonal amino acids (azidohomoalanine) in a pulsed labeling strategy in cultured hippocampal neurons stimulated with DHPG, a specific agonist for group I mGluRs. We identified several kinases with important roles in DHPG-induced mGluR activation, which we confirmed using small molecule kinase inhibitors. Furthermore, changes in the AMPA receptor endocytosis pathway in both protein synthesis and protein phosphorylation were identified, whereby Intersectin-1 was validated as a novel player in this pathway. This study revealed several new insights into the molecular pathways downstream of group I mGluR activation in hippocampal neurons, and provides a rich resource for further analyses.
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Affiliation(s)
- Charlotte A G H van Gelder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Renske Penning
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Tim S Veth
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Lisa A E Catsburg
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Casper C Hoogenraad
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Harold D MacGillavry
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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95
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Schorcht A, van den Kerkhof TLGM, Cottrell CA, Allen JD, Torres JL, Behrens AJ, Schermer EE, Burger JA, de Taeye SW, Torrents de la Peña A, Bontjer I, Gumbs S, Ozorowski G, LaBranche CC, de Val N, Yasmeen A, Klasse PJ, Montefiori DC, Moore JP, Schuitemaker H, Crispin M, van Gils MJ, Ward AB, Sanders RW. Neutralizing Antibody Responses Induced by HIV-1 Envelope Glycoprotein SOSIP Trimers Derived from Elite Neutralizers. J Virol 2020; 94:e01214-20. [PMID: 32999024 PMCID: PMC7925178 DOI: 10.1128/jvi.01214-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 06/16/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
The induction of broadly neutralizing antibodies (bNAbs) is a major goal in vaccine research. HIV-1-infected individuals that develop exceptionally strong bNAb responses, termed elite neutralizers, can inform vaccine design by providing blueprints for the induction of similar bNAb responses. We describe a new recombinant native-like envelope glycoprotein (Env) SOSIP trimer, termed AMC009, based on the viral founder sequences of an elite neutralizer. The subtype B AMC009 SOSIP protein formed stable native-like trimers that displayed multiple bNAb epitopes. Overall, its structure at 4.3-Å resolution was similar to that of BG505 SOSIP.664. The AMC009 trimer resembled one from a second elite neutralizer, AMC011, in having a dense and complete glycan shield. When tested as immunogens in rabbits, the AMC009 trimers did not induce autologous neutralizing antibody (NAb) responses efficiently while the AMC011 trimers did so very weakly, outcomes that may reflect the completeness of their glycan shields. The AMC011 trimer induced antibodies that occasionally cross-neutralized heterologous tier 2 viruses, sometimes at high titer. Cross-neutralizing antibodies were more frequently elicited by a trivalent combination of AMC008, AMC009, and AMC011 trimers, all derived from subtype B viruses. Each of these three individual trimers could deplete the NAb activity from the rabbit sera. Mapping the polyclonal sera by electron microscopy revealed that antibodies of multiple specificities could bind to sites on both autologous and heterologous trimers. These results advance our understanding of how to use Env trimers in multivalent vaccination regimens and the immunogenicity of trimers derived from elite neutralizers.IMPORTANCE Elite neutralizers, i.e., individuals who developed unusually broad and potent neutralizing antibody responses, might serve as blueprints for HIV-1 vaccine design. Here, we studied the immunogenicity of native-like recombinant envelope glycoprotein (Env) trimers based on viral sequences from elite neutralizers. While immunization with single trimers from elite neutralization did not recapitulate the breadth and potency of neutralization observed in these infected individuals, a combination of three subtype B Env trimers from elite neutralizers resulted in some neutralization breadth within subtype B viruses. These results should guide future efforts to design vaccines to induce broadly neutralizing antibodies.
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Affiliation(s)
- Anna Schorcht
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Tom L G M van den Kerkhof
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Joel D Allen
- School of Biological Science, University of Southampton, Southampton, United Kingdom
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Anna-Janina Behrens
- School of Biological Science, University of Southampton, Southampton, United Kingdom
| | - Edith E Schermer
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Judith A Burger
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Steven W de Taeye
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Alba Torrents de la Peña
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Ilja Bontjer
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Stephanie Gumbs
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Celia C LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Natalia de Val
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick National Laboratory, Leidos Biomedical Research Inc., Frederick, Maryland, USA
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, USA
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, USA
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, USA
| | | | - Max Crispin
- School of Biological Science, University of Southampton, Southampton, United Kingdom
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, USA
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96
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de Jonge PA, Smit Sibinga DJC, Boright OA, Costa AR, Nobrega FL, Brouns SJJ, Dutilh BE. Development of Styrene Maleic Acid Lipid Particles as a Tool for Studies of Phage-Host Interactions. J Virol 2020; 94:e01559-20. [PMID: 32938760 PMCID: PMC7654272 DOI: 10.1128/jvi.01559-20] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 01/08/2023] Open
Abstract
The infection of a bacterium by a phage starts with attachment to a receptor molecule on the host cell surface by the phage. Since receptor-phage interactions are crucial to successful infections, they are major determinants of phage host range and, by extension, of the broader effects that phages have on bacterial communities. Many receptor molecules, particularly membrane proteins, are difficult to isolate because their stability is supported by their native membrane environments. Styrene maleic acid lipid particles (SMALPs), a recent advance in membrane protein studies, are the result of membrane solubilizations by styrene maleic acid (SMA) copolymer chains. SMALPs thereby allow for isolation of membrane proteins while maintaining their native environment. Here, we explore SMALPs as a tool to isolate and study phage-receptor interactions. We show that SMALPs produced from taxonomically distant bacterial membranes allow for receptor-specific decrease of viable phage counts of several model phages that span the three largest phage families. After characterizing the effects of incubation time and SMALP concentration on the activity of three distinct phages, we present evidence that the interaction between two model phages and SMALPs is specific to bacterial species and the phage receptor molecule. These interactions additionally lead to DNA ejection by nearly all particles at high phage titers. We conclude that SMALPs are a potentially highly useful tool for phage-host interaction studies.IMPORTANCE Bacteriophages (viruses that infect bacteria or phages) impact every microbial community. All phage infections start with the binding of the viral particle to a specific receptor molecule on the host cell surface. Due to its importance in phage infections, this first step is of interest to many phage-related research and applications. However, many phage receptors are difficult to isolate. Styrene maleic acid lipid particles (SMALPs) are a recently developed approach to isolate membrane proteins in their native environment. In this study, we explore SMALPs as a tool to study phage-receptor interactions. We find that different phage species bind to SMALPs, while maintaining specificity to their receptor. We then characterize the time and concentration dependence of phage-SMALP interactions and furthermore show that they lead to genome ejection by the phage. The results presented here show that SMALPs are a useful tool for future studies of phage-receptor interactions.
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Affiliation(s)
- Patrick A de Jonge
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Dieuwke J C Smit Sibinga
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Oliver A Boright
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
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97
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Ogando NS, Zevenhoven-Dobbe JC, van der Meer Y, Bredenbeek PJ, Posthuma CC, Snijder EJ. The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. J Virol 2020; 94:e01246-20. [PMID: 32938769 PMCID: PMC7654266 DOI: 10.1128/jvi.01246-20] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/09/2020] [Indexed: 02/08/2023] Open
Abstract
Coronaviruses (CoVs) stand out for their large RNA genome and complex RNA-synthesizing machinery comprising 16 nonstructural proteins (nsps). The bifunctional nsp14 contains 3'-to-5' exoribonuclease (ExoN) and guanine-N7-methyltransferase (N7-MTase) domains. While the latter presumably supports mRNA capping, ExoN is thought to mediate proofreading during genome replication. In line with such a role, ExoN knockout mutants of mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) were previously reported to have crippled but viable hypermutation phenotypes. Remarkably, using reverse genetics, a large set of corresponding ExoN knockout mutations has now been found to be lethal for another betacoronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV). For 13 mutants, viral progeny could not be recovered, unless-as happened occasionally-reversion had first occurred. Only a single mutant was viable, likely because its E191D substitution is highly conservative. Remarkably, a SARS-CoV-2 ExoN knockout mutant was found to be unable to replicate, resembling observations previously made for alpha- and gammacoronaviruses, but starkly contrasting with the documented phenotype of ExoN knockout mutants of the closely related SARS-CoV. Subsequently, we established in vitro assays with purified recombinant MERS-CoV nsp14 to monitor its ExoN and N7-MTase activities. All ExoN knockout mutations that proved lethal in reverse genetics were found to severely decrease ExoN activity while not affecting N7-MTase activity. Our study strongly suggests that CoV nsp14 ExoN has an additional function, which apparently is critical for primary viral RNA synthesis and thus differs from the proofreading function that, based on previous MHV and SARS-CoV studies, was proposed to boost longer-term replication fidelity.IMPORTANCE The bifunctional nsp14 subunit of the coronavirus replicase contains 3'-to-5' exoribonuclease (ExoN) and guanine-N7-methyltransferase domains. For the betacoronaviruses MHV and SARS-CoV, ExoN was reported to promote the fidelity of genome replication, presumably by mediating a form of proofreading. For these viruses, ExoN knockout mutants are viable while displaying an increased mutation frequency. Strikingly, we have now established that the equivalent ExoN knockout mutants of two other betacoronaviruses, MERS-CoV and SARS-CoV-2, are nonviable, suggesting an additional and critical ExoN function in their replication. This is remarkable in light of the very limited genetic distance between SARS-CoV and SARS-CoV-2, which is highlighted, for example, by 95% amino acid sequence identity in their nsp14 sequences. For (recombinant) MERS-CoV nsp14, both its enzymatic activities were evaluated using newly developed in vitro assays that can be used to characterize these key replicative enzymes in more detail and explore their potential as target for antiviral drug development.
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Affiliation(s)
- Natacha S Ogando
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jessika C Zevenhoven-Dobbe
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Yvonne van der Meer
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter J Bredenbeek
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Clara C Posthuma
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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98
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Klemm T, Ebert G, Calleja DJ, Allison CC, Richardson LW, Bernardini JP, Lu BGC, Kuchel NW, Grohmann C, Shibata Y, Gan ZY, Cooney JP, Doerflinger M, Au AE, Blackmore TR, van der Heden van Noort GJ, Geurink PP, Ovaa H, Newman J, Riboldi‐Tunnicliffe A, Czabotar PE, Mitchell JP, Feltham R, Lechtenberg BC, Lowes KN, Dewson G, Pellegrini M, Lessene G, Komander D. Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2. EMBO J 2020; 39:e106275. [PMID: 32845033 PMCID: PMC7461020 DOI: 10.15252/embj.2020106275] [Citation(s) in RCA: 283] [Impact Index Per Article: 70.8] [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: 07/17/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/26/2022] Open
Abstract
The SARS-CoV-2 coronavirus encodes an essential papain-like protease domain as part of its non-structural protein (nsp)-3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin-like ISG15 protein modifications as well as, with lower activity, Lys48-linked polyubiquitin. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin-binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. To identify PLpro inhibitors in a repurposing approach, screening of 3,727 unique approved drugs and clinical compounds against SARS2 PLpro identified no compounds that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non-covalent small molecule SARS PLpro inhibitors also target SARS2 PLpro, prevent self-processing of nsp3 in cells and display high potency and excellent antiviral activity in a SARS-CoV-2 infection model.
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Affiliation(s)
- Theresa Klemm
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Gregor Ebert
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Dale J Calleja
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Cody C Allison
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Lachlan W Richardson
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Jonathan P Bernardini
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
- Department of Biochemistry and Molecular BiologyMichael Smith Laboratories University of British ColumbiaVancouverBCCanada
| | - Bernadine GC Lu
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Nathan W Kuchel
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Christoph Grohmann
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Yuri Shibata
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Zhong Yan Gan
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - James P Cooney
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Marcel Doerflinger
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Amanda E Au
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Timothy R Blackmore
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | | | - Paul P Geurink
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CentreLeidenThe Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CentreLeidenThe Netherlands
| | - Janet Newman
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)Biomedical ProgramParkvilleVic.Australia
| | | | - Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Jeffrey P Mitchell
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Rebecca Feltham
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Bernhard C Lechtenberg
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Kym N Lowes
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Grant Dewson
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Marc Pellegrini
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
| | - Guillaume Lessene
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
- Pharmacology and Therapeutics DepartmentUniversity of MelbourneMelbourneVic.Australia
| | - David Komander
- The Walter and Eliza Hall Institute of Medical Research and Department of Medical BiologyUniversity of MelbourneMelbourneVic.Australia
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99
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Spit M, Fenderico N, Jordens I, Radaszkiewicz T, Lindeboom RGH, Bugter JM, Cristobal A, Ootes L, van Osch M, Janssen E, Boonekamp KE, Hanakova K, Potesil D, Zdrahal Z, Boj SF, Medema JP, Bryja V, Koo B, Vermeulen M, Maurice MM. RNF43 truncations trap CK1 to drive niche-independent self-renewal in cancer. EMBO J 2020; 39:e103932. [PMID: 32965059 PMCID: PMC7503102 DOI: 10.15252/embj.2019103932] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 11/11/2019] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/26/2022] Open
Abstract
Wnt/β-catenin signaling is a primary pathway for stem cell maintenance during tissue renewal and a frequent target for mutations in cancer. Impaired Wnt receptor endocytosis due to loss of the ubiquitin ligase RNF43 gives rise to Wnt-hypersensitive tumors that are susceptible to anti-Wnt-based therapy. Contrary to this paradigm, we identify a class of RNF43 truncating cancer mutations that induce β-catenin-mediated transcription, despite exhibiting retained Wnt receptor downregulation. These mutations interfere with a ubiquitin-independent suppressor role of the RNF43 cytosolic tail that involves Casein kinase 1 (CK1) binding and phosphorylation. Mechanistically, truncated RNF43 variants trap CK1 at the plasma membrane, thereby preventing β-catenin turnover and propelling ligand-independent target gene transcription. Gene editing of human colon stem cells shows that RNF43 truncations cooperate with p53 loss to drive a niche-independent program for self-renewal and proliferation. Moreover, these RNF43 variants confer decreased sensitivity to anti-Wnt-based therapy. Our data demonstrate the relevance of studying patient-derived mutations for understanding disease mechanisms and improved applications of precision medicine.
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Affiliation(s)
- Maureen Spit
- Department of Cell Biology and Oncode InstituteCenter for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Nicola Fenderico
- Department of Cell Biology and Oncode InstituteCenter for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Ingrid Jordens
- Department of Cell Biology and Oncode InstituteCenter for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Tomasz Radaszkiewicz
- Department of Experimental BiologyFaculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Rik GH Lindeboom
- Department of Molecular Biology and Oncode InstituteFaculty of ScienceRadboud Institute for Molecular Life SciencesRadboud University NijmegenNijmegenThe Netherlands
| | - Jeroen M Bugter
- Department of Cell Biology and Oncode InstituteCenter for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Alba Cristobal
- Department of Cell Biology and Oncode InstituteCenter for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Lars Ootes
- Department of Cell Biology and Oncode InstituteCenter for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Max van Osch
- Department of Cell Biology and Oncode InstituteCenter for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Eline Janssen
- Department of Cell Biology and Oncode InstituteCenter for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Kim E Boonekamp
- Department of Cell Biology and Oncode InstituteCenter for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Katerina Hanakova
- Central European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - David Potesil
- Central European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - Zbynek Zdrahal
- Central European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - Sylvia F Boj
- Hubrecht Organoid TechnologyUtrechtThe Netherlands
| | - Jan Paul Medema
- Laboratory for Experimental Oncology and Radiobiology and Oncode InstituteCenter for Experimental and Molecular MedicineAmsterdam UMCCancer Center AmsterdamUniversity of AmsterdamAmsterdamThe Netherlands
| | - Vitezslav Bryja
- Department of Experimental BiologyFaculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Bon‐Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna BioCenter (VBC)ViennaAustria
| | - Michiel Vermeulen
- Department of Molecular Biology and Oncode InstituteFaculty of ScienceRadboud Institute for Molecular Life SciencesRadboud University NijmegenNijmegenThe Netherlands
| | - Madelon M Maurice
- Department of Cell Biology and Oncode InstituteCenter for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
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100
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Seidl MF, Kramer HM, Cook DE, Fiorin GL, van den Berg GCM, Faino L, Thomma BPHJ. Repetitive Elements Contribute to the Diversity and Evolution of Centromeres in the Fungal Genus Verticillium. mBio 2020; 11:e01714-20. [PMID: 32900804 PMCID: PMC7482064 DOI: 10.1128/mbio.01714-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023] Open
Abstract
Centromeres are chromosomal regions that are crucial for chromosome segregation during mitosis and meiosis, and failed centromere formation can contribute to chromosomal anomalies. Despite this conserved function, centromeres differ significantly between and even within species. Thus far, systematic studies into the organization and evolution of fungal centromeres remain scarce. In this study, we identified the centromeres in each of the 10 species of the fungal genus Verticillium and characterized their organization and evolution. Chromatin immunoprecipitation of the centromere-specific histone CenH3 (ChIP-seq) and chromatin conformation capture (Hi-C) followed by high-throughput sequencing identified eight conserved, large (∼150-kb), AT-, and repeat-rich regional centromeres that are embedded in heterochromatin in the plant pathogen Verticillium dahliae Using Hi-C, we similarly identified repeat-rich centromeres in the other Verticillium species. Strikingly, a single degenerated long terminal repeat (LTR) retrotransposon is strongly associated with centromeric regions in some but not all Verticillium species. Extensive chromosomal rearrangements occurred during Verticillium evolution, of which some could be linked to centromeres, suggesting that centromeres contributed to chromosomal evolution. The size and organization of centromeres differ considerably between species, and centromere size was found to correlate with the genome-wide repeat content. Overall, our study highlights the contribution of repetitive elements to the diversity and rapid evolution of centromeres within the fungal genus VerticilliumIMPORTANCE The genus Verticillium contains 10 species of plant-associated fungi, some of which are notorious pathogens. Verticillium species evolved by frequent chromosomal rearrangements that contribute to genome plasticity. Centromeres are instrumental for separation of chromosomes during mitosis and meiosis, and failed centromere functionality can lead to chromosomal anomalies. Here, we used a combination of experimental techniques to identify and characterize centromeres in each of the Verticillium species. Intriguingly, we could strongly associate a single repetitive element to the centromeres of some of the Verticillium species. The presence of this element in the centromeres coincides with increased centromere sizes and genome-wide repeat expansions. Collectively, our findings signify a role of repetitive elements in the function, organization, and rapid evolution of centromeres in a set of closely related fungal species.
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Affiliation(s)
- Michael F Seidl
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, the Netherlands
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
| | - H Martin Kramer
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
| | - David E Cook
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
- Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Gabriel L Fiorin
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
| | | | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
- Environmental Biology Department, Sapienza Università di Roma, Rome, Italy
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
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