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Özkan M, Eskiocak YC, Wingender G. Macrophage and dendritic cell subset composition can distinguish endotypes in adjuvant-induced asthma mouse models. PLoS One 2021; 16:e0250533. [PMID: 34061861 PMCID: PMC8168852 DOI: 10.1371/journal.pone.0250533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/01/2021] [Accepted: 05/18/2021] [Indexed: 12/27/2022] Open
Abstract
Asthma is a heterogeneous disease with neutrophilic and eosinophilic asthma as the main endotypes that are distinguished according to the cells recruited to the airways and the related pathology. Eosinophilic asthma is the treatment-responsive endotype, which is mainly associated with allergic asthma. Neutrophilic asthma is a treatment-resistant endotype, affecting 5-10% of asthmatics. Although eosinophilic asthma is well-studied, a clear understanding of the endotypes is essential to devise effective diagnosis and treatment approaches for neutrophilic asthma. To this end, we directly compared adjuvant-induced mouse models of neutrophilic (CFA/OVA) and eosinophilic (Alum/OVA) asthma side-by-side. The immune response in the inflamed lung was analyzed by multi-parametric flow cytometry and immunofluorescence. We found that eosinophilic asthma was characterized by a preferential recruitment of interstitial macrophages and myeloid dendritic cells, whereas in neutrophilic asthma plasmacytoid dendritic cells, exudate macrophages, and GL7+ activated B cells predominated. This differential distribution of macrophage and dendritic cell subsets reveals important aspects of the pathophysiology of asthma and holds the promise to be used as biomarkers to diagnose asthma endotypes.
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Affiliation(s)
- Müge Özkan
- Department of Genome Sciences and Molecular Biotechnology, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Balcova/Izmir, Turkey
| | | | - Gerhard Wingender
- Izmir Biomedicine and Genome Center (IBG), Balcova/Izmir, Turkey
- Department of Biomedicine and Health Technologies, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Balcova/Izmir, Turkey
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2
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Abstract
Mycobacterial pathogens can be categorized into three broad groups: Mycobacterium tuberculosis complex causing tuberculosis, M. leprae and M. lepromatosis causing leprosy, and atypical mycobacteria, or non-tuberculous mycobacteria (NTM), responsible for a wide range of diseases. Among the NTMs, M. ulcerans is responsible for the neglected tropical skin disease Buruli ulcer (BU). Most pathogenic mycobacteria, including M. leprae, evade effector mechanisms of the humoral immune system by hiding and replicating inside host cells and are furthermore excellent modulators of host immune responses. In contrast, M. ulcerans replicates predominantly extracellularly, sheltered from host immune responses through the cytotoxic and immunosuppressive effects of mycolactone, a macrolide produced by the bacteria. In the year 2018, 208,613 new cases of leprosy and 2713 new cases of BU were reported to WHO, figures which are notoriously skewed by vast underreporting of these diseases.
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Affiliation(s)
- Katharina Röltgen
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Gerd Pluschke
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
| | - John Stewart Spencer
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Patrick Joseph Brennan
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Charlotte Avanzi
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
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3
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Negrini F, O’Grady K, Hyvönen M, Folta KM, Baraldi E. Genomic structure and transcript analysis of the Rapid Alkalinization Factor (RALF) gene family during host-pathogen crosstalk in Fragaria vesca and Fragaria x ananassa strawberry. PLoS One 2020; 15:e0226448. [PMID: 32214345 PMCID: PMC7098601 DOI: 10.1371/journal.pone.0226448] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 11/25/2019] [Accepted: 03/01/2020] [Indexed: 11/19/2022] Open
Abstract
Rapid Alkalinization Factors (RALFs) are cysteine-rich peptides ubiquitous within plant kingdom. They play multiple roles as hormonal signals in diverse processes, including root elongation, cell growth, pollen tube development, and fertilization. Their involvement in host-pathogen crosstalk as negative regulators of immunity in Arabidopsis has also been recognized. In addition, peptides homologous to RALF are secreted by different fungal pathogens as effectors during early stages of infection. Previous studies have identified nine RALF genes in the diploid strawberry (Fragaria vesca) genome. This work describes the genomic organization of the RALF gene families in commercial octoploid strawberry (Fragaria × ananassa) and the re-annotated genome of F. vesca, and then compares findings with orthologs in Arabidopsis thaliana. We reveal the presence of 15 RALF genes in F. vesca genotype Hawaii 4 and 50 in Fragaria x ananassa cv. Camarosa, showing a non-homogenous localization of genes among the different Fragaria x ananassa subgenomes. Expression analysis of Fragaria x ananassa RALF genes upon infection with Colletotrichum acutatum or Botrytis cinerea showed that FanRALF3-1 was the only fruit RALF gene upregulated after fungal infection. In silico analysis was used to identify distinct pathogen inducible elements upstream of the FanRALF3-1 gene. Agroinfiltration of strawberry fruit with deletion constructs of the FanRALF3-1 promoter identified a 5' region required for FanRALF3-1 expression in fruit, but failed to identify a region responsible for fungal induced expression.
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Affiliation(s)
- Francesca Negrini
- Laboratory of Plant Pathology and Biotechnology, DISTAL, University of Bologna, Bologna Italy
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, United States of America
| | - Kevin O’Grady
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, United States of America
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Kevin M. Folta
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, United States of America
| | - Elena Baraldi
- Laboratory of Plant Pathology and Biotechnology, DISTAL, University of Bologna, Bologna Italy
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de Almeida BP, Vieira AF, Paredes J, Bettencourt-Dias M, Barbosa-Morais NL. Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome. PLoS Comput Biol 2019; 15:e1006832. [PMID: 30856170 PMCID: PMC6411098 DOI: 10.1371/journal.pcbi.1006832] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 08/30/2018] [Accepted: 01/25/2019] [Indexed: 02/05/2023] Open
Abstract
Centrosome amplification (CA) is a common feature of human tumours and a promising target for cancer therapy. However, CA's pan-cancer prevalence, molecular role in tumourigenesis and therapeutic value in the clinical setting are still largely unexplored. Here, we used a transcriptomic signature (CA20) to characterise the landscape of CA-associated gene expression in 9,721 tumours from The Cancer Genome Atlas (TCGA). CA20 is upregulated in cancer and associated with distinct clinical and molecular features of breast cancer, consistently with our experimental CA quantification in patient samples. Moreover, we show that CA20 upregulation is positively associated with genomic instability, alteration of specific chromosomal arms and C>T mutations, and we propose novel molecular players associated with CA in cancer. Finally, high CA20 is associated with poor prognosis and, by integrating drug sensitivity with drug perturbation profiles in cell lines, we identify candidate compounds for selectively targeting cancer cells exhibiting transcriptomic evidence for CA.
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Affiliation(s)
- Bernardo P. de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - André F. Vieira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP - Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - Joana Paredes
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP - Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | | | - Nuno L. Barbosa-Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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Taylor DL, Knowles DA, Scott LJ, Ramirez AH, Casale FP, Wolford BN, Guan L, Varshney A, Albanus RD, Parker SCJ, Narisu N, Chines PS, Erdos MR, Welch RP, Kinnunen L, Saramies J, Sundvall J, Lakka TA, Laakso M, Tuomilehto J, Koistinen HA, Stegle O, Boehnke M, Birney E, Collins FS. Interactions between genetic variation and cellular environment in skeletal muscle gene expression. PLoS One 2018; 13:e0195788. [PMID: 29659628 PMCID: PMC5901994 DOI: 10.1371/journal.pone.0195788] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 03/29/2018] [Indexed: 12/18/2022] Open
Abstract
From whole organisms to individual cells, responses to environmental conditions are influenced by genetic makeup, where the effect of genetic variation on a trait depends on the environmental context. RNA-sequencing quantifies gene expression as a molecular trait, and is capable of capturing both genetic and environmental effects. In this study, we explore opportunities of using allele-specific expression (ASE) to discover cis-acting genotype-environment interactions (GxE)—genetic effects on gene expression that depend on an environmental condition. Treating 17 common, clinical traits as approximations of the cellular environment of 267 skeletal muscle biopsies, we identify 10 candidate environmental response expression quantitative trait loci (reQTLs) across 6 traits (12 unique gene-environment trait pairs; 10% FDR per trait) including sex, systolic blood pressure, and low-density lipoprotein cholesterol. Although using ASE is in principle a promising approach to detect GxE effects, replication of such signals can be challenging as validation requires harmonization of environmental traits across cohorts and a sufficient sampling of heterozygotes for a transcribed SNP. Comprehensive discovery and replication will require large human transcriptome datasets, or the integration of multiple transcribed SNPs, coupled with standardized clinical phenotyping.
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Affiliation(s)
- D. Leland Taylor
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - David A. Knowles
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - Laura J. Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrea H. Ramirez
- Department of Medicine, Vanderbilt University Medical Center, Tennessee, United States of America
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Brooke N. Wolford
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Li Guan
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Arushi Varshney
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ricardo D’Oliveira Albanus
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Stephen C. J. Parker
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Narisu Narisu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Peter S. Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Michael R. Erdos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Ryan P. Welch
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Leena Kinnunen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Jouko Saramies
- South Karelia Social and Health Care District, Lappeenranta, Finland
| | - Jouko Sundvall
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Timo A. Lakka
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, University of Eastern Finland, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Jaakko Tuomilehto
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Neurosciences and Preventive Medicine, Danube University Krems, Krems, Austria
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
- Dasman Diabetes Institute, Dasman, Kuwait
| | - Heikki A. Koistinen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Medicine and Abdominal Center: Endocrinology, University of Helsinki and Helsinki University Central Hospital, Haartmaninkatu 4, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum 2U, Tukholmankatu 8, Helsinki, Finland
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- * E-mail: (EB); (FSC)
| | - Francis S. Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
- * E-mail: (EB); (FSC)
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Baud A, Mulligan MK, Casale FP, Ingels JF, Bohl CJ, Callebert J, Launay JM, Krohn J, Legarra A, Williams RW, Stegle O. Genetic Variation in the Social Environment Contributes to Health and Disease. PLoS Genet 2017; 13:e1006498. [PMID: 28121987 PMCID: PMC5266220 DOI: 10.1371/journal.pgen.1006498] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [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: 03/02/2016] [Accepted: 11/21/2016] [Indexed: 11/29/2022] Open
Abstract
Assessing the impact of the social environment on health and disease is challenging. As social effects are in part determined by the genetic makeup of social partners, they can be studied from associations between genotypes of one individual and phenotype of another (social genetic effects, SGE, also called indirect genetic effects). For the first time we quantified the contribution of SGE to more than 100 organismal phenotypes and genome-wide gene expression measured in laboratory mice. We find that genetic variation in cage mates (i.e. SGE) contributes to variation in organismal and molecular measures related to anxiety, wound healing, immune function, and body weight. Social genetic effects explained up to 29% of phenotypic variance, and for several traits their contribution exceeded that of direct genetic effects (effects of an individual's genotypes on its own phenotype). Importantly, we show that ignoring SGE can severely bias estimates of direct genetic effects (heritability). Thus SGE may be an important source of "missing heritability" in studies of complex traits in human populations. In summary, our study uncovers an important contribution of the social environment to phenotypic variation, sets the basis for using SGE to dissect social effects, and identifies an opportunity to improve studies of direct genetic effects.
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Affiliation(s)
- Amelie Baud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Megan K. Mulligan
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Jesse F. Ingels
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Casey J. Bohl
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Jacques Callebert
- AP-HP, Hôpital Lariboisière, Department of Biochemistry, INSERM U942, Paris, France
| | - Jean-Marie Launay
- AP-HP, Hôpital Lariboisière, Department of Biochemistry, INSERM U942, Paris, France
| | - Jon Krohn
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | | | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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Thampi SP, Doostmohammadi A, Shendruk TN, Golestanian R, Yeomans JM. Active micromachines: Microfluidics powered by mesoscale turbulence. Sci Adv 2016; 2:e1501854. [PMID: 27419229 PMCID: PMC4942321 DOI: 10.1126/sciadv.1501854] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 12/19/2015] [Accepted: 06/14/2016] [Indexed: 05/06/2023]
Abstract
Dense active matter, from bacterial suspensions and microtubule bundles driven by motor proteins to cellular monolayers and synthetic Janus particles, is characterized by mesoscale turbulence, which is the emergence of chaotic flow structures. By immersing an ordered array of symmetric rotors in an active fluid, we introduce a microfluidic system that exploits spontaneous symmetry breaking in mesoscale turbulence to generate work. The lattice of rotors self-organizes into a spin state where neighboring discs continuously rotate in permanent alternating directions due to combined hydrodynamic and elastic effects. Our virtual prototype demonstrates a new research direction for the design of micromachines powered by the nematohydrodynamic properties of active turbulence.
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Affiliation(s)
- Sumesh P. Thampi
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai 600036, India
- Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, UK
| | - Amin Doostmohammadi
- Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, UK
| | - Tyler N. Shendruk
- Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, UK
| | - Ramin Golestanian
- Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, UK
| | - Julia M. Yeomans
- Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, UK
- Corresponding author.
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