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Deschildre J, Vandemoortele B, Loers JU, De Preter K, Vermeirssen V. Evaluation of single-sample network inference methods for precision oncology. NPJ Syst Biol Appl 2024; 10:18. [PMID: 38360881 PMCID: PMC10869342 DOI: 10.1038/s41540-024-00340-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024] Open
Abstract
A major challenge in precision oncology is to detect targetable cancer vulnerabilities in individual patients. Modeling high-throughput omics data in biological networks allows identifying key molecules and processes of tumorigenesis. Traditionally, network inference methods rely on many samples to contain sufficient information for learning, resulting in aggregate networks. However, to implement patient-tailored approaches in precision oncology, we need to interpret omics data at the level of individual patients. Several single-sample network inference methods have been developed that infer biological networks for an individual sample from bulk RNA-seq data. However, only a limited comparison of these methods has been made and many methods rely on 'normal tissue' samples as reference, which are not always available. Here, we conducted an evaluation of the single-sample network inference methods SSN, LIONESS, SWEET, iENA, CSN and SSPGI using transcriptomic profiles of lung and brain cancer cell lines from the CCLE database. The methods constructed functional gene networks with distinct network characteristics. Hub gene analyses revealed different degrees of subtype-specificity across methods. Single-sample networks were able to distinguish between tumor subtypes, as exemplified by node strength clustering, enrichment of known subtype-specific driver genes among hubs and differential node strength. We also showed that single-sample networks correlated better to other omics data from the same cell line as compared to aggregate networks. We conclude that single-sample network inference methods can reflect sample-specific biology when 'normal tissue' samples are absent and we point out peculiarities of each method.
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Affiliation(s)
- Joke Deschildre
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Boris Vandemoortele
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jens Uwe Loers
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Lab of Translational Onco-genomics and Bio-informatics, Center for Medical Biotechnology (VIB-UGent), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Vanessa Vermeirssen
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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2
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Delanote J, Correa Rojo A, Wells PM, Steves CJ, Ertaylan G. Systematic identification of the role of gut microbiota in mental disorders: a TwinsUK cohort study. Sci Rep 2024; 14:3626. [PMID: 38351227 PMCID: PMC10864280 DOI: 10.1038/s41598-024-53929-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
Mental disorders are complex disorders influenced by multiple genetic, environmental, and biological factors. Specific microbiota imbalances seem to affect mental health status. However, the mechanisms by which microbiota disturbances impact the presence of depression, stress, anxiety, and eating disorders remain poorly understood. Currently, there are no robust biomarkers identified. We proposed a novel pyramid-layer design to accurately identify microbial/metabolomic signatures underlying mental disorders in the TwinsUK registry. Monozygotic and dizygotic twins discordant for mental disorders were screened, in a pairwise manner, for differentially abundant bacterial genera and circulating metabolites. In addition, multivariate analyses were performed, accounting for individual-level confounders. Our pyramid-layer study design allowed us to overcome the limitations of cross-sectional study designs with significant confounder effects and resulted in an association of the abundance of genus Parabacteroides with the diagnosis of mental disorders. Future research should explore the potential role of Parabacteroides as a mediator of mental health status. Our results indicate the potential role of the microbiome as a modifier in mental disorders that might contribute to the development of novel methodologies to assess personal risk and intervention strategies.
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Affiliation(s)
- Julie Delanote
- Sustainable Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Alejandro Correa Rojo
- Sustainable Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium
| | - Philippa M Wells
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, 3-4th Floor South Wing Block D, Westminster Bridge Road, London, SE1 7EH, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, 3-4th Floor South Wing Block D, Westminster Bridge Road, London, SE1 7EH, UK
- Department of Ageing and Health, St Thomas' Hospital, 9th floor, North Wing, Westminster Bridge Road, London, SE1 7EH, UK
| | - Gökhan Ertaylan
- Sustainable Health, Flemish Institute for Technological Research (VITO), Mol, Belgium.
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3
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Vandenhole M, Mermans C, De Beer B, Xue W, Zhao Y, Ozoe Y, Liu G, Dermauw W, Van Leeuwen T. A glutamate-gated chloride channel as the mite-specific target-site of dicofol and other diphenylcarbinol acaricides. Commun Biol 2023; 6:1160. [PMID: 37957415 PMCID: PMC10643420 DOI: 10.1038/s42003-023-05488-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
Dicofol has been widely used to control phytophagous mites. Although dicofol is chemically related to DDT, its mode of action has remained elusive. Here, we mapped dicofol resistance in the spider mite Tetranychus urticae to two genomic regions. Each region harbored a glutamate-gated chloride channel (GluCl) gene that contained a mutation-G314D or G326E-known to confer resistance against the unrelated acaricide abamectin. Using electrophysiology assays we showed that dicofol and other diphenylcarbinol acaricides-bromopropylate and chlorobenzilate-induce persistent currents in Xenopus oocytes expressing wild-type T. urticae GluCl3 receptors and potentiate glutamate responses. In contrast, the G326E substitution abolished the agonistic activity of all three compounds. Assays with the wild-type Drosophila GluClα revealed that this receptor was unresponsive to dicofol. Homology modeling combined with ligand-docking confirmed the specificity of electrophysiology assays. Altogether, this work elucidates the mode of action of diphenylcarbinols as mite-specific agonists of GluCl.
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Affiliation(s)
- Marilou Vandenhole
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, Belgium
| | - Catherine Mermans
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, Belgium
| | - Berdien De Beer
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, Belgium
| | - Wenxin Xue
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, Belgium
| | - Yilan Zhao
- School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 693 Xiongchu Blvd, Wuhan, China
| | - Yoshihisa Ozoe
- Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
| | - Genyan Liu
- School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 693 Xiongchu Blvd, Wuhan, China
| | - Wannes Dermauw
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, Belgium.
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Burgemeester Van Gansberghelaan 96, Merelbeke, Belgium.
| | - Thomas Van Leeuwen
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, Belgium.
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Candry P, Chadwick GL, Caravajal-Arroyo JM, Lacoere T, Winkler MKH, Ganigué R, Orphan VJ, Rabaey K. Trophic interactions shape the spatial organization of medium-chain carboxylic acid producing granular biofilm communities. ISME J 2023; 17:2014-2022. [PMID: 37715042 PMCID: PMC10579388 DOI: 10.1038/s41396-023-01508-8] [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] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/17/2023]
Abstract
Granular biofilms producing medium-chain carboxylic acids (MCCA) from carbohydrate-rich industrial feedstocks harbor highly streamlined communities converting sugars to MCCA either directly or via lactic acid as intermediate. We investigated the spatial organization and growth activity patterns of MCCA producing granular biofilms grown on an industrial side stream to test (i) whether key functional guilds (lactic acid producing Olsenella and MCCA producing Oscillospiraceae) stratified in the biofilm based on substrate usage, and (ii) whether spatial patterns of growth activity shaped the unique, lenticular morphology of these biofilms. First, three novel isolates (one Olsenella and two Oscillospiraceae species) representing over half of the granular biofilm community were obtained and used to develop FISH probes, revealing that key functional guilds were not stratified. Instead, the outer 150-500 µm of the granular biofilm consisted of a well-mixed community of Olsenella and Oscillospiraceae, while deeper layers were made up of other bacteria with lower activities. Second, nanoSIMS analysis of 15N incorporation in biofilms grown in normal and lactic acid amended conditions suggested Oscillospiraceae switched from sugars to lactic acid as substrate. This suggests competitive-cooperative interactions may govern the spatial organization of these biofilms, and suggests that optimizing biofilm size may be a suitable process engineering strategy. Third, growth activities were similar in the polar and equatorial biofilm peripheries, leaving the mechanism behind the lenticular biofilm morphology unexplained. Physical processes (e.g., shear hydrodynamics, biofilm life cycles) may have contributed to lenticular biofilm development. Together, this study develops an ecological framework of MCCA-producing granular biofilms that informs bioprocess development.
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Affiliation(s)
- Pieter Candry
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA
| | - Grayson L Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - José Maria Caravajal-Arroyo
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Tim Lacoere
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | | | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Center for Advanced Processes and Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, 9000, Ghent, Belgium
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
- Center for Advanced Processes and Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, 9000, Ghent, Belgium.
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Schuermans N, El Chehadeh S, Hemelsoet D, Gautheron J, Vantyghem MC, Nouioua S, Tazir M, Vigouroux C, Auclair M, Bogaert E, Dufour S, Okawa F, Hilbert P, Van Doninck N, Taquet MC, Rosseel T, De Clercq G, Debackere E, Van Haverbeke C, Cherif FR, Urtizberea JA, Chanson JB, Funalot B, Authier FJ, Kaya S, Terryn W, Callens S, Depypere B, Van Dorpe J, Poppe B, Impens F, Mizushima N, Depienne C, Jéru I, Dermaut B. Loss of phospholipase PLAAT3 causes a mixed lipodystrophic and neurological syndrome due to impaired PPARγ signaling. Nat Genet 2023; 55:1929-1940. [PMID: 37919452 DOI: 10.1038/s41588-023-01535-3] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 09/16/2023] [Indexed: 11/04/2023]
Abstract
Phospholipase A/acyltransferase 3 (PLAAT3) is a phospholipid-modifying enzyme predominantly expressed in neural and white adipose tissue (WAT). It is a potential drug target for metabolic syndrome, as Plaat3 deficiency in mice protects against diet-induced obesity. We identified seven patients from four unrelated consanguineous families, with homozygous loss-of-function variants in PLAAT3, who presented with a lipodystrophy syndrome with loss of fat varying from partial to generalized and associated with metabolic complications, as well as variable neurological features including demyelinating neuropathy and intellectual disability. Multi-omics analysis of mouse Plaat3-/- and patient-derived WAT showed enrichment of arachidonic acid-containing membrane phospholipids and a strong decrease in the signaling of peroxisome proliferator-activated receptor gamma (PPARγ), the master regulator of adipocyte differentiation. Accordingly, CRISPR-Cas9-mediated PLAAT3 inactivation in human adipose stem cells induced insulin resistance, altered adipocyte differentiation with decreased lipid droplet formation and reduced the expression of adipogenic and mature adipocyte markers, including PPARγ. These findings establish PLAAT3 deficiency as a hereditary lipodystrophy syndrome with neurological manifestations, caused by a PPARγ-dependent defect in WAT differentiation and function.
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Affiliation(s)
- Nika Schuermans
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Salima El Chehadeh
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Strasbourg, France
- Laboratoire de Génétique Médicale, UMRS_1112, Institut de Génétique Médicale d'Alsace (IGMA), Université de Strasbourg et INSERM, Strasbourg, France
| | | | - Jérémie Gautheron
- Sorbonne Université, INSERM UMRS_938, Centre de Recherche Saint-Antoine (CRSA), Paris, France
| | - Marie-Christine Vantyghem
- Endocrinology, Diabetology, Metabolism Department, National Competence Centre for Rare Diseases of Insulin Secretion and Insulin Sensitivity (PRISIS), Lille University Hospital, Lille, France
- University of Lille, INSERM U1190, European Genomic Institute for Diabetes, Lille, France
| | - Sonia Nouioua
- Department of Neurology of the EHS of Cherchell, University Centre of Blida, Tipaza, Algeria
- NeuroSciences Research Laboratory, University of Algiers Benyoucef Benkhedda, Algiers, Algeria
| | - Meriem Tazir
- NeuroSciences Research Laboratory, University of Algiers Benyoucef Benkhedda, Algiers, Algeria
- Department of Neurology, CHU Algiers (Mustapha Pacha Hospital), Algiers, Algeria
| | - Corinne Vigouroux
- Sorbonne Université, INSERM UMRS_938, Centre de Recherche Saint-Antoine (CRSA), Paris, France
- Assistance Publique-Hôpitaux de Paris, Saint-Antoine University Hospital, National Reference Center for Rare Diseases of Insulin Secretion and Insulin Sensitivity (PRISIS), Department of Endocrinology, Diabetology and Reproductive Endocrinology, and Department of Molecular Biology and Genetics, Paris, France
| | - Martine Auclair
- Sorbonne Université, INSERM UMRS_938, Centre de Recherche Saint-Antoine (CRSA), Paris, France
- Assistance Publique-Hôpitaux de Paris, Saint-Antoine University Hospital, National Reference Center for Rare Diseases of Insulin Secretion and Insulin Sensitivity (PRISIS), Department of Endocrinology, Diabetology and Reproductive Endocrinology, and Department of Molecular Biology and Genetics, Paris, France
| | - Elke Bogaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Sara Dufour
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- VIB Proteomics Core, VIB, Ghent, Belgium
| | - Fumiya Okawa
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Bunkyo, Japan
| | - Pascale Hilbert
- Department of Molecular and Cellular Biology, Institute of Pathology and Genetics, Charleroi, Belgium
| | - Nike Van Doninck
- Department of Endocrinology and Diabetology, General Hospital VITAZ, Sint-Niklaas, Belgium
| | - Marie-Caroline Taquet
- Department of Internal Medicine and Nutrition, Hopitaux Universitaires Strasbourg, Strasbourg, France
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Griet De Clercq
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Elke Debackere
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | | | - Ferroudja Ramdane Cherif
- Department of Neurology of the EHS of Cherchell, University Centre of Blida, Tipaza, Algeria
- NeuroSciences Research Laboratory, University of Algiers Benyoucef Benkhedda, Algiers, Algeria
| | | | - Jean-Baptiste Chanson
- Service de Neurologie et Centre de Référence Neuromusculaire Nord/Est/Ile de France, Hôpital de Hautepierre, Strasbourg, France
| | - Benoit Funalot
- Department of Medical Genetics, Hôpital Henri Mondor, Université Paris-Est-Créteil, Créteil, France
- INSERM UMR955, Team Relaix, Faculty of Medicine, Créteil, France
| | - François-Jérôme Authier
- INSERM UMR955, Team Relaix, Faculty of Medicine, Créteil, France
- Centre Expert de Pathologie Neuromusculaire/Histologie, Département de Pathologie, Hôpital Henri Mondor, Université Paris-Est-Créteil, Créteil, France
| | - Sabine Kaya
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - Wim Terryn
- Department of Nephrology, Jan Yperman Hospital, Ieper, Belgium
| | - Steven Callens
- Department of General Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Bernard Depypere
- Department of Plastic and Reconstructive Surgery, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Francis Impens
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- VIB Proteomics Core, VIB, Ghent, Belgium
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Bunkyo, Japan
| | - Christel Depienne
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Strasbourg, France
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - Isabelle Jéru
- Sorbonne Université, INSERM UMRS_938, Centre de Recherche Saint-Antoine (CRSA), Paris, France
- Department of Medical Genetics, DMU BioGeM, Sorbonne Université, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Bart Dermaut
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
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6
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Sneyers F, Kerkhofs M, Speelman-Rooms F, Welkenhuyzen K, La Rovere R, Shemy A, Voet A, Eelen G, Dewerchin M, Tait SWG, Ghesquière B, Bootman MD, Bultynck G. Intracellular BAPTA directly inhibits PFKFB3, thereby impeding mTORC1-driven Mcl-1 translation and killing MCL-1-addicted cancer cells. Cell Death Dis 2023; 14:600. [PMID: 37684238 PMCID: PMC10491774 DOI: 10.1038/s41419-023-06120-4] [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: 11/18/2022] [Revised: 08/10/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
Intracellular Ca2+ signals control several physiological and pathophysiological processes. The main tool to chelate intracellular Ca2+ is intracellular BAPTA (BAPTAi), usually introduced into cells as a membrane-permeant acetoxymethyl ester (BAPTA-AM). Previously, we demonstrated that BAPTAi enhanced apoptosis induced by venetoclax, a BCL-2 antagonist, in diffuse large B-cell lymphoma (DLBCL). This finding implied a novel interplay between intracellular Ca2+ signaling and anti-apoptotic BCL-2 function. Hence, we set out to identify the underlying mechanisms by which BAPTAi enhances cell death in B-cell cancers. In this study, we discovered that BAPTAi alone induced apoptosis in hematological cancer cell lines that were highly sensitive to S63845, an MCL-1 antagonist. BAPTAi provoked a rapid decline in MCL-1-protein levels by inhibiting mTORC1-driven Mcl-1 translation. These events were not a consequence of cell death, as BAX/BAK-deficient cancer cells exhibited similar downregulation of mTORC1 activity and MCL-1-protein levels. Next, we investigated how BAPTAi diminished mTORC1 activity and identified its ability to impair glycolysis by directly inhibiting 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3) activity, a previously unknown effect of BAPTAi. Notably, these effects were also induced by a BAPTAi analog with low affinity for Ca2+. Consequently, our findings uncover PFKFB3 inhibition as an Ca2+-independent mechanism through which BAPTAi impairs cellular metabolism and ultimately compromises the survival of MCL-1-dependent cancer cells. These findings hold two important implications. Firstly, the direct inhibition of PFKFB3 emerges as a key regulator of mTORC1 activity and a promising target in MCL-1-dependent cancers. Secondly, cellular effects caused by BAPTAi are not necessarily related to Ca2+ signaling. Our data support the need for a reassessment of the role of Ca2+ in cellular processes when findings were based on the use of BAPTAi.
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Affiliation(s)
- Flore Sneyers
- KU Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, Campus Gasthuisberg O&N I, Herestraat 49 box 802, 3000, Leuven, Belgium
| | - Martijn Kerkhofs
- KU Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, Campus Gasthuisberg O&N I, Herestraat 49 box 802, 3000, Leuven, Belgium
| | - Femke Speelman-Rooms
- KU Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, Campus Gasthuisberg O&N I, Herestraat 49 box 802, 3000, Leuven, Belgium
- KU Leuven, Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, Campus Gasthuisberg O&N I bis, Herestraat 49 box 901, 3000, Leuven, Belgium
| | - Kirsten Welkenhuyzen
- KU Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, Campus Gasthuisberg O&N I, Herestraat 49 box 802, 3000, Leuven, Belgium
| | - Rita La Rovere
- KU Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, Campus Gasthuisberg O&N I, Herestraat 49 box 802, 3000, Leuven, Belgium
| | - Ahmed Shemy
- KU Leuven, Laboratory for Biomolecular Modelling and Design, Department of Chemistry, Celestijnenlaan 200G, 3001, Heverlee, Belgium
| | - Arnout Voet
- KU Leuven, Laboratory for Biomolecular Modelling and Design, Department of Chemistry, Celestijnenlaan 200G, 3001, Heverlee, Belgium
| | - Guy Eelen
- KU Leuven, Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, Leuven Cancer Institute, Campus Gasthuisberg O&N4, Herestraat 49 box 912, Leuven, Belgium
- VIB-KU Leuven, Center for Cancer Biology, Laboratory of Angiogenesis and Vascular Metabolism, Campus Gasthuisberg O&N4, Herestraat 49 box 912, 3000, Leuven, Belgium
| | - Mieke Dewerchin
- KU Leuven, Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, Leuven Cancer Institute, Campus Gasthuisberg O&N4, Herestraat 49 box 912, Leuven, Belgium
- VIB-KU Leuven, Center for Cancer Biology, Laboratory of Angiogenesis and Vascular Metabolism, Campus Gasthuisberg O&N4, Herestraat 49 box 912, 3000, Leuven, Belgium
| | - Stephen W G Tait
- Cancer Research UK Beatson Institute, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Bart Ghesquière
- KU Leuven, Laboratory of Applied Mass Spectrometry, Department of Cellular and Molecular Medicine, Leuven, Belgium - VIB, Metabolomics Core Facility Leuven, Center for Cancer Biology, Leuven, Belgium, Herestraat 49 box 912, 3000, Leuven, Belgium
| | - Martin D Bootman
- School of Life, Health and Chemical Sciences, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Walton Hall, Milton Keynes, MK7 6AA, UK.
| | - Geert Bultynck
- KU Leuven, Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, Campus Gasthuisberg O&N I, Herestraat 49 box 802, 3000, Leuven, Belgium.
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7
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Eeckhout E, Hamerlinck L, Jonckheere V, Van Damme P, van Loo G, Wullaert A. Gasdermin D independent canonical inflammasome responses cooperate with caspase-8 to establish host defense against gastrointestinal Citrobacter rodentium infection. Cell Death Dis 2023; 14:282. [PMID: 37080966 PMCID: PMC10119323 DOI: 10.1038/s41419-023-05801-4] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/22/2023]
Abstract
Citrobacter rodentium is an enteropathogen that causes intestinal inflammatory responses in mice reminiscent of the pathology provoked by enteropathogenic and enterohemorrhagic Escherichia coli infections in humans. C. rodentium expresses various virulence factors that target specific signaling proteins involved in executing apoptotic, necroptotic and pyroptotic cell death, suggesting that each of these distinct cell death modes performs essential host defense functions that the pathogen aims to disturb. However, the relative contributions of apoptosis, necroptosis and pyroptosis in protecting the host against C. rodentium have not been elucidated. Here we used mice with single or combined deficiencies in essential signaling proteins controlling apoptotic, necroptotic or pyroptotic cell death to reveal the roles of these cell death modes in host defense against C. rodentium. Gastrointestinal C. rodentium infections in mice lacking GSDMD and/or MLKL showed that both pyroptosis and necroptosis were dispensable for pathogen clearance. In contrast, while RIPK3-deficient mice showed normal C. rodentium clearance, mice with combined caspase-8 and RIPK3 deficiencies failed to clear intestinal pathogen loads. Although this demonstrated a crucial role for caspase-8 signaling in establishing intestinal host defense, Casp8-/-Ripk3-/- mice remained capable of preventing systemic pathogen persistence. This systemic host defense relied on inflammasome signaling, as Casp8-/-Ripk3-/- mice with combined caspase-1 and -11 deletion succumbed to C. rodentium infection. Interestingly, although it is known that C. rodentium can activate the non-canonical caspase-11 inflammasome, selectively disabling canonical inflammasome signaling by single caspase-1 deletion sufficed to render Casp8-/-Ripk3-/- mice vulnerable to C. rodentium-induced lethality. Moreover, Casp8-/-Ripk3-/- mice lacking GSDMD survived a C. rodentium infection, suggesting that pyroptosis was not crucial for the protective functions of canonical inflammasomes in these mice. Taken together, our mouse genetic experiments revealed an essential cooperation between caspase-8 signaling and GSDMD-independent canonical inflammasome signaling to establish intestinal and systemic host defense against gastrointestinal C. rodentium infection.
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Affiliation(s)
- Elien Eeckhout
- Department of Internal Medicine and Paediatrics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium
| | - Lisa Hamerlinck
- Department of Internal Medicine and Paediatrics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium
| | - Veronique Jonckheere
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Geert van Loo
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Andy Wullaert
- Department of Internal Medicine and Paediatrics, Ghent University, Ghent, Belgium.
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium.
- Laboratory of Proteinscience, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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8
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Meyer P, Van de Poel B, De Coninck B. UV-B light and its application potential to reduce disease and pest incidence in crops. Hortic Res 2021; 8:194. [PMID: 34465753 PMCID: PMC8408258 DOI: 10.1038/s41438-021-00629-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 05/03/2023]
Abstract
Ultraviolet-B radiation (280-315 nm), perceived by the plant photoreceptor UVR8, is a key environmental signal that influences plant growth and development and can reduce disease and pest incidence. The positive effect of UV-B on disease resistance and incidence in various plant species supports the implementation of supplemental UV-B radiation in sustainable crop production. However, despite many studies focusing on UV-B light, there is no consensus on the best mode of application. This review aims to analyze, evaluate, and organize the different application strategies of UV-B radiation in crop production with a focus on disease resistance. We summarize the physiological effects of UV-B light on plants and discuss how plants perceive and transduce UV-B light by the UVR8 photoreceptor as well as how this perception alters plant specialized metabolite production. Next, we bring together conclusions of various studies with respect to different UV-B application methods to improve plant resistance. In general, supplemental UV-B light has a positive effect on disease resistance in many plant-pathogen combinations, mainly through the induction of the production of specialized metabolites. However, many variables (UV-B light source, plant species, dose and intensity, timing during the day, duration, background light, etc.) make it difficult to compare and draw general conclusions. We compiled the information of recent studies on UV-B light applications, including e.g., details on the UV-B light source, experimental set-up, calculated UV-B light dose, intensity, and duration. This review provides practical insights and facilitates future research on UV-B radiation as a promising tool to reduce disease and pest incidence.
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Affiliation(s)
- Prisca Meyer
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
| | - Bram Van de Poel
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
| | - Barbara De Coninck
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium.
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9
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Martens S, Bridelance J, Roelandt R, Vandenabeele P, Takahashi N. MLKL in cancer: more than a necroptosis regulator. Cell Death Differ 2021; 28:1757-1772. [PMID: 33953348 PMCID: PMC8184805 DOI: 10.1038/s41418-021-00785-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [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: 12/30/2020] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 02/03/2023] Open
Abstract
Mixed lineage kinase domain-like protein (MLKL) emerged as executioner of necroptosis, a RIPK3-dependent form of regulated necrosis. Cell death evasion is one of the hallmarks of cancer. Besides apoptosis, some cancers suppress necroptosis-associated mechanisms by for example epigenetic silencing of RIPK3 expression. Conversely, necroptosis-elicited inflammation by cancer cells can fuel tumor growth. Recently, necroptosis-independent functions of MLKL were unraveled in receptor internalization, ligand-receptor degradation, endosomal trafficking, extracellular vesicle formation, autophagy, nuclear functions, axon repair, neutrophil extracellular trap (NET) formation, and inflammasome regulation. Little is known about the precise role of MLKL in cancer and whether some of these functions are involved in cancer development and metastasis. Here, we discuss current knowledge and controversies on MLKL, its structure, necroptosis-independent functions, expression, mutations, and its potential role as a pro- or anti-cancerous factor. Analysis of MLKL expression patterns reveals that MLKL is upregulated by type I/II interferon, conditions of inflammation, and tissue injury. Overall, MLKL may affect cancer development and metastasis through necroptosis-dependent and -independent functions.
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Affiliation(s)
- Sofie Martens
- Cell Death and Inflammation Lab, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jolien Bridelance
- Cell Death and Inflammation Lab, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Ria Roelandt
- Cell Death and Inflammation Lab, VIB Center for Inflammation Research, Ghent, Belgium
| | - Peter Vandenabeele
- Cell Death and Inflammation Lab, VIB Center for Inflammation Research, Ghent, Belgium.
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
| | - Nozomi Takahashi
- Cell Death and Inflammation Lab, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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10
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D'Cruz N, Vervoort G, Chalavi S, Dijkstra BW, Gilat M, Nieuwboer A. Thalamic morphology predicts the onset of freezing of gait in Parkinson's disease. NPJ Parkinsons Dis 2021; 7:20. [PMID: 33654103 PMCID: PMC7925565 DOI: 10.1038/s41531-021-00163-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/14/2021] [Indexed: 11/08/2022] Open
Abstract
The onset of freezing of gait (FOG) in Parkinson's disease (PD) is a critical milestone, marked by a higher risk of falls and reduced quality of life. FOG is associated with alterations in subcortical neural circuits, yet no study has assessed whether subcortical morphology can predict the onset of clinical FOG. In this prospective multimodal neuroimaging cohort study, we performed vertex-based analysis of grey matter morphology in fifty-seven individuals with PD at study entry and two years later. We also explored the behavioral correlates and resting-state functional connectivity related to these local volume differences. At study entry, we found that freezers (N = 12) and persons who developed FOG during the course of the study (converters) (N = 9) showed local inflations in bilateral thalamus in contrast to persons who did not (non-converters) (N = 36). Longitudinally, converters (N = 7) also showed local inflation in the left thalamus, as compared to non-converters (N = 36). A model including sex, daily levodopa equivalent dose, and local thalamic inflation predicted conversion with good accuracy (AUC: 0.87, sensitivity: 88.9%, specificity: 77.8%). Exploratory analyses showed that local thalamic inflations were associated with larger medial thalamic sub-nuclei volumes and better cognitive performance. Resting-state analyses further revealed that converters had stronger thalamo-cortical coupling with limbic and cognitive regions pre-conversion, with a marked reduction in coupling over the two years. Finally, validation using the PPMI cohort suggested FOG-specific non-linear evolution of thalamic local volume. These findings provide markers of, and deeper insights into conversion to FOG, which may foster earlier intervention and better mobility for persons with PD.
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Affiliation(s)
- Nicholas D'Cruz
- KU Leuven, Department of Rehabilitation Sciences, Neurorehabilitation Research Group, B-3000, Leuven, Belgium.
| | - Griet Vervoort
- KU Leuven, Department of Rehabilitation Sciences, Neurorehabilitation Research Group, B-3000, Leuven, Belgium
| | - Sima Chalavi
- KU Leuven, Department of Movement Sciences, Movement Control & Neuroplasticity Research Group, B-3000, Leuven, Belgium
| | - Bauke W Dijkstra
- KU Leuven, Department of Rehabilitation Sciences, Neurorehabilitation Research Group, B-3000, Leuven, Belgium
| | - Moran Gilat
- KU Leuven, Department of Rehabilitation Sciences, Neurorehabilitation Research Group, B-3000, Leuven, Belgium
| | - Alice Nieuwboer
- KU Leuven, Department of Rehabilitation Sciences, Neurorehabilitation Research Group, B-3000, Leuven, Belgium
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11
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Van Brempt M, Clauwaert J, Mey F, Stock M, Maertens J, Waegeman W, De Mey M. Predictive design of sigma factor-specific promoters. Nat Commun 2020; 11:5822. [PMID: 33199691 PMCID: PMC7670410 DOI: 10.1038/s41467-020-19446-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
To engineer synthetic gene circuits, molecular building blocks are developed which can modulate gene expression without interference, mutually or with the host's cell machinery. As the complexity of gene circuits increases, automated design tools and tailored building blocks to ensure perfect tuning of all components in the network are required. Despite the efforts to develop prediction tools that allow forward engineering of promoter transcription initiation frequency (TIF), such a tool is still lacking. Here, we use promoter libraries of E. coli sigma factor 70 (σ70)- and B. subtilis σB-, σF- and σW-dependent promoters to construct prediction models, capable of both predicting promoter TIF and orthogonality of the σ-specific promoters. This is achieved by training a convolutional neural network with high-throughput DNA sequencing data from fluorescence-activated cell sorted promoter libraries. This model functions as the base of the online promoter design tool (ProD), providing tailored promoters for tailored genetic systems.
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Affiliation(s)
- Maarten Van Brempt
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Jim Clauwaert
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, 9000, Ghent, Belgium
| | - Friederike Mey
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Michiel Stock
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, 9000, Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Willem Waegeman
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, 9000, Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000, Ghent, Belgium.
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12
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Eggermont M, Cornillie P, Dierick M, Adriaens D, Nevejan N, Bossier P, Van den Broeck W, Sorgeloos P, Defoirdt T, Declercq AM. The blue mussel inside: 3D visualization and description of the vascular-related anatomy of Mytilus edulis to unravel hemolymph extraction. Sci Rep 2020; 10:6773. [PMID: 32317671 PMCID: PMC7174403 DOI: 10.1038/s41598-020-62933-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/19/2020] [Indexed: 12/28/2022] Open
Abstract
The blue mussel Mytilus edulis is an intensely studied bivalve in biomonitoring programs worldwide. The lack of detailed descriptions of hemolymph-withdrawal protocols, particularly with regard to the place from where hemolymph could be perfused from, raises questions regarding the exact composition of aspirated hemolymph and does not exclude the possibility of contamination with other body-fluids. This study demonstrates the use of high resolution X-ray computed tomography and histology combined with 3D-reconstruction using AMIRA-software to visualize some important vascular-related anatomic structures of Mytilus edulis. Based on these images, different hemolymph extraction sites used in bivalve research were visualized and described, leading to new insights into hemolymph collection. Results show that hemolymph withdrawn from the posterior adductor muscle could be extracted from small spaces and fissures between the muscle fibers that are connected to at least one hemolymph supplying artery, more specifically the left posterior gastro-intestinal artery. Furthermore, 3D-reconstructions indicate that puncturing hemolymph from the pericard, anterior aorta, atria and ventricle in a non-invasive way should be possible. Hemolymph withdrawal from the heart is less straightforward and more prone to contamination from the pallial cavity. This study resulted simultaneously in a detailed description and visualization of the vascular-related anatomy of Mytilus edulis.
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Affiliation(s)
- Mieke Eggermont
- Laboratory of Aquaculture and Artemia Reference Center, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Pieter Cornillie
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Manuel Dierick
- Centre for X-ray Tomography (UGCT), Department Physics and Astronomy, Proeftuinstraat 86/N12, 9000, Gent, Belgium
- XRE nv. Bollebergen 2B box 1, 9052, Ghent, Belgium
| | - Dominique Adriaens
- Research Group Evolutionary Morphology of Vertebrates, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Nancy Nevejan
- Laboratory of Aquaculture and Artemia Reference Center, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Peter Bossier
- Laboratory of Aquaculture and Artemia Reference Center, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Wim Van den Broeck
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Patrick Sorgeloos
- Laboratory of Aquaculture and Artemia Reference Center, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Tom Defoirdt
- Laboratory of Aquaculture and Artemia Reference Center, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Annelies Maria Declercq
- Laboratory of Aquaculture and Artemia Reference Center, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium.
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium.
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13
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White JD, Ortega-Castrillon A, Virgo C, Indencleef K, Hoskens H, Shriver MD, Claes P. Sources of variation in the 3dMDface and Vectra H1 3D facial imaging systems. Sci Rep 2020; 10:4443. [PMID: 32157192 PMCID: PMC7064576 DOI: 10.1038/s41598-020-61333-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/17/2020] [Indexed: 12/21/2022] Open
Abstract
As technology advances and collaborations grow, our ability to finely quantify and explore morphological variation in 3D structures can enable important discoveries and insights into clinical, evolutionary, and genetic questions. However, it is critical to explore and understand the relative contribution of potential sources of error to the structures under study. In this study, we isolated the level of error in 3D facial images attributable to four sources, using the 3dMDface and Vectra H1 camera systems. When the two camera systems are used separately to image human participants, this analysis finds an upper bound of error potentially introduced by the use of the 3dMDface or Vectra H1 camera systems, in conjunction with the MeshMonk registration toolbox, at 0.44 mm and 0.40 mm, respectively. For studies using both camera systems, this upper bound increases to 0.85 mm, on average, and there are systematic differences in the representation of the eyelids, nostrils, and mouth by the two camera systems. Our results highlight the need for careful assessment of potential sources of error in 3D images, both in terms of magnitude and position, especially when dealing with very small measurements or performing many tests.
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Affiliation(s)
- Julie D White
- Department of Anthropology, The Pennsylvania State University, University Park, PA, United States.
| | - Alejandra Ortega-Castrillon
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
| | - Ciara Virgo
- Department of Anthropology, The Pennsylvania State University, University Park, PA, United States
| | - Karlijne Indencleef
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
| | - Hanne Hoskens
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Mark D Shriver
- Department of Anthropology, The Pennsylvania State University, University Park, PA, United States
| | - Peter Claes
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium.
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium.
- Murdoch Childrens Research Institute, Melbourne, Victoria, Australia.
- Department of Biomedical Engineering, University of Oxford, Oxford, United Kingdom.
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14
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Cornelis S, Tytgat O, Fauvart M, Gansemans Y, Vander Plaetsen AS, Wiederkehr RS, Deforce D, Van Nieuwerburgh F, Stakenborg T. Silicon µPCR Chip for Forensic STR Profiling with Hybeacon Probe Melting Curves. Sci Rep 2019; 9:7341. [PMID: 31089203 PMCID: PMC6517373 DOI: 10.1038/s41598-019-43946-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/01/2019] [Indexed: 11/09/2022] Open
Abstract
The demand to perform forensic DNA profiling outside of centralized laboratories and on the crime scene is increasing. Several criminal investigations would benefit tremendously from having DNA based information available in the first hours rather than days or weeks. However, due to the complexity and time-consuming nature of standard DNA fingerprinting methods, rapid and automated analyses are hard to achieve. We here demonstrate the implementation of an alternative DNA fingerprinting method in a single microchip. By combining PCR amplification and HyBeacon melting assays in a silicon Lab-on-a-chip (LoC), a significant step towards rapid on-site DNA fingerprinting is taken. The small form factor of a LoC reduces reagent consumption and increases portability. Additional miniaturization is achieved through an integrated heating element covering 24 parallel micro-reactors with a reaction volume of 0.14 µl each. The high level of parallelization allows the simultaneous analysis of 4 short tandem repeat (STR) loci and the amelogenin gender marker commonly included in forensic DNA analysis. A reference and crime scene sample can be analyzed simultaneously for direct comparison. Importantly, by using industry-standard semiconductor manufacturing processes, mass manufacturability can be guaranteed. Following assay design and optimization, complete 5-loci profiles could be robustly generated on-chip that are on par with those obtained using conventional benchtop real-time PCR thermal cyclers. Together, our results are an important step towards the development of commercial, mass-produced, portable devices for on-site testing in forensic DNA analysis.
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Affiliation(s)
- Senne Cornelis
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Olivier Tytgat
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Maarten Fauvart
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
| | | | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium.
| | | | - Tim Stakenborg
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
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15
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Van Cleemput J, Poelaert KCK, Laval K, Impens F, Van den Broeck W, Gevaert K, Nauwynck HJ. Pollens destroy respiratory epithelial cell anchors and drive alphaherpesvirus infection. Sci Rep 2019; 9:4787. [PMID: 30886217 PMCID: PMC6423322 DOI: 10.1038/s41598-019-41305-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 11/23/2018] [Accepted: 03/06/2019] [Indexed: 12/22/2022] Open
Abstract
Pollens are well-known triggers of respiratory allergies and asthma. The pollen burden in today's ambient air is constantly increasing due to rising climate change and air pollution. How pollens interact with the respiratory mucosa remains largely unknown due to a lack of representative model systems. We here demonstrate how pollen proteases of Kentucky bluegrass, white birch and hazel selectively destroy integrity and anchorage of columnar respiratory epithelial cells, but not of basal cells, in both ex vivo respiratory mucosal explants and in vitro primary equine respiratory epithelial cells (EREC). In turn, this pollen protease-induced damage to respiratory epithelial cell anchorage resulted in increased infection by the host-specific and ancestral alphaherpesvirus equine herpesvirus type 1 (EHV1). Pollen proteases of all three plant species were characterized by zymography and those of white birch were fully identified for the first time as serine proteases of the subtilase family and meiotic prophase aminopeptidase 1 using mass spectrometry-based proteomics. Together, our findings demonstrate that pollen proteases selectively and irreversibly damage integrity and anchorage of columnar respiratory epithelial cells. In turn, alphaherpesviruses benefit from this partial loss-of-barrier function, resulting in increased infection of the respiratory epithelium.
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Affiliation(s)
- Jolien Van Cleemput
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
- Department of Molecular Biology, Princeton University, 119 Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey, 08544, USA
| | - Katrien C K Poelaert
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Kathlyn Laval
- Department of Molecular Biology, Princeton University, 119 Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey, 08544, USA
| | - Francis Impens
- VIB Center for Medical Biotechnology, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
- VIB Proteomics Core, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Wim Van den Broeck
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Hans J Nauwynck
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium.
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