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Tyagi R, Rosa BA, Swain A, Artyomov MN, Jasmer DP, Mitreva M. Intestinal cell diversity and treatment responses in a parasitic nematode at single cell resolution. BMC Genomics 2024; 25:341. [PMID: 38575858 PMCID: PMC10996262 DOI: 10.1186/s12864-024-10203-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/08/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Parasitic nematodes, significant pathogens for humans, animals, and plants, depend on diverse organ systems for intra-host survival. Understanding the cellular diversity and molecular variations underlying these functions holds promise for developing novel therapeutics, with specific emphasis on the neuromuscular system's functional diversity. The nematode intestine, crucial for anthelmintic therapies, exhibits diverse cellular phenotypes, and unraveling this diversity at the single-cell level is essential for advancing knowledge in anthelmintic research across various organ systems. RESULTS Here, using novel single-cell transcriptomics datasets, we delineate cellular diversity within the intestine of adult female Ascaris suum, a parasitic nematode species that infects animals and people. Gene transcripts expressed in individual nuclei of untreated intestinal cells resolved three phenotypic clusters, while lower stringency resolved additional subclusters and more potential diversity. Clusters 1 and 3 phenotypes displayed variable congruence with scRNA phenotypes of C. elegans intestinal cells, whereas the A. suum cluster 2 phenotype was markedly unique. Distinct functional pathway enrichment characterized each A. suum intestinal cell cluster. Cluster 2 was distinctly enriched for Clade III-associated genes, suggesting it evolved within clade III nematodes. Clusters also demonstrated differential transcriptional responsiveness to nematode intestinal toxic treatments, with Cluster 2 displaying the least responses to short-term intra-pseudocoelomic nematode intestinal toxin treatments. CONCLUSIONS This investigation presents advances in knowledge related to biological differences among major cell populations of adult A. suum intestinal cells. For the first time, diverse nematode intestinal cell populations were characterized, and associated biological markers of these cells were identified to support tracking of constituent cells under experimental conditions. These advances will promote better understanding of this and other parasitic nematodes of global importance, and will help to guide future anthelmintic treatments.
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Affiliation(s)
- Rahul Tyagi
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, 63110, St. Louis, MO, USA
| | - Bruce A Rosa
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, 63110, St. Louis, MO, USA
| | - Amanda Swain
- Department of Pathology and Immunology, Washington University School of Medicine, 63110, Saint Louis, MO, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, 63110, Saint Louis, MO, USA
| | - Douglas P Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, 99164, Pullman, WA, USA.
| | - Makedonka Mitreva
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, 63110, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, 63110, St. Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, 63110, St Louis, MO, USA.
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2
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Wu S, Song R, Liu T, Li C. Antifungal therapy: Novel drug delivery strategies driven by new targets. Adv Drug Deliv Rev 2023; 199:114967. [PMID: 37336246 DOI: 10.1016/j.addr.2023.114967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/22/2023] [Accepted: 06/14/2023] [Indexed: 06/21/2023]
Abstract
In patients with compromised immunity, invasive fungal infections represent a significant cause of mortality. Given the limited availability and drawbacks of existing first-line antifungal drugs, there is a growing interest in exploring novel targets that could facilitate the development of new antifungal agents or enhance the effectiveness of conventional ones. While previous studies have extensively summarized new antifungal targets inherent in fungi for drug development purposes, the exploration of potential targets for novel antifungal drug delivery strategies has received less attention. In this review, we provide an overview of recent advancements in new antifungal drug delivery strategies that leverage novel targets, including those located in the physio-pathological barrier at the site of infection, the infection microenvironment, fungal-host interactions, and the fungal pathogen itself. The objective is to enhance therapeutic efficacy and mitigate toxic effects in fungal infections, particularly in challenging cases such as refractory, recurrent, and drug-resistant invasive fungal infections. We also discuss the current challenges and future prospects associated with target-driven antifungal drug delivery strategies, offering important insights into the clinical implementation of these innovative approaches.
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Affiliation(s)
- Shuang Wu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing 400716, PR China
| | - Ruiqi Song
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing 400716, PR China
| | - Tongbao Liu
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing 400716, PR China.
| | - Chong Li
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, Chongqing 400716, PR China; College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China.
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3
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Cao Y, Lin Y, Patrick E, Yang P, Yang JYH. scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction. Bioinformatics 2022; 38:4745-4753. [PMID: 36040148 PMCID: PMC9563679 DOI: 10.1093/bioinformatics/btac590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/21/2022] [Accepted: 08/28/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION With the recent surge of large-cohort scale single cell research, it is of critical importance that analytical methods can fully utilize the comprehensive characterization of cellular systems that single cell technologies produce to provide insights into samples from individuals. Currently, there is little consensus on the best ways to compress information from the complex data structures of these technologies to summary statistics that represent each sample (e.g. individuals). RESULTS Here, we present scFeatures, an approach that creates interpretable cellular and molecular representations of single-cell and spatial data at the sample level. We demonstrate that summarising a broad collection of features at the sample level is both important for understanding underlying disease mechanisms in different experimental studies and for accurately classifying disease status of individuals. AVAILABILITY scFeatures is publicly available as an R package at https://github.com/SydneyBioX/scFeatures. All data used in this study are publicly available with accession ID reported in the Methods section. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yue Cao
- Charles Perkins Centre, The University of Sydney, Sydney, Australia.,School of Mathematics and Statistics, The University of Sydney, Sydney, Australia
| | - Yingxin Lin
- Charles Perkins Centre, The University of Sydney, Sydney, Australia.,School of Mathematics and Statistics, The University of Sydney, Sydney, Australia
| | - Ellis Patrick
- Charles Perkins Centre, The University of Sydney, Sydney, Australia.,School of Mathematics and Statistics, The University of Sydney, Sydney, Australia.,Computational Systems Biology Group, Children's Medical Research Institute, Westmead, NSW, Australia
| | - Pengyi Yang
- Charles Perkins Centre, The University of Sydney, Sydney, Australia.,School of Mathematics and Statistics, The University of Sydney, Sydney, Australia.,Computational Systems Biology Group, Children's Medical Research Institute, Westmead, NSW, Australia
| | - Jean Yee Hwa Yang
- Charles Perkins Centre, The University of Sydney, Sydney, Australia.,School of Mathematics and Statistics, The University of Sydney, Sydney, Australia.,Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
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4
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Liu Y, Chen L, Yu J, Ye L, Hu H, Wang J, Wu B. Advances in Single-Cell Toxicogenomics in Environmental Toxicology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11132-11145. [PMID: 35881918 DOI: 10.1021/acs.est.2c01098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The toxicity evaluation system of environmental pollutants has undergone numerous changes due to the application of new technologies. Single-cell toxicogenomics is rapidly changing our view on environmental toxicology by increasing the resolution of our analysis to the level of a single cell. Applications of this technology in environmental toxicology have begun to emerge and are rapidly expanding the portfolio of existing technologies and applications. Here, we first summarized different methods involved in single-cell isolation and amplification in single-cell sequencing process, compared the advantages and disadvantages of different methods, and analyzed their development trends. Then, we reviewed the main advances of single-cell toxicogenomics in environmental toxicology, emphatically analyzed the application prospects of this technology in identifying the target cells of pollutants in early embryos, clarifying the heterogeneous response of cell subtypes to pollutants, and finding pathogenic bacteria in unknown microbes, and highlighted the unique characteristics of this approach with high resolution, high throughput, and high specificity by examples. We also offered a prediction of the further application of this technology and the revolution it brings in environmental toxicology. Overall, these advances will provide practical solutions for controlling or mitigating exogenous toxicological effects that threaten human and ecosystem health, contribute to improving our understanding of the physiological processes affected by pollutants, and lead to the emergence of new methods of pollution control.
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Affiliation(s)
- Yuxuan Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Ling Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Jing Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Haidong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Jinfeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
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5
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Sunita, Singh Y, Beamer G, Sun X, Shukla P. Recent developments in systems biology and genetic engineering toward design of vaccines for TB. Crit Rev Biotechnol 2022; 42:532-547. [PMID: 34641752 PMCID: PMC11208086 DOI: 10.1080/07388551.2021.1951649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
Abstract
Tuberculosis (TB) is one of the most prevalent diseases worldwide. The currently available Bacillus Calmette-Guérin vaccine is not sufficient in protecting against pulmonary TB. Although many vaccines have been evaluated in clinical trials, but none of them yet has proven to be more successful. Thus, new strategies are urgently needed to design more effective TB vaccines. The emergence of new technologies will undoubtedly accelerate the process of vaccine development. This review summarizes the potential and validated applications of emerging technologies, including: systems biology (genomics, proteomics, and transcriptomics), genetic engineering, and other computational tools to discover and develop novel vaccines against TB. It also discussed that the significant implementation of these approaches will play crucial roles in the development of novel vaccines to cure and control TB.
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Affiliation(s)
- Sunita
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Yogendra Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Gillian Beamer
- Department of Infectious Disease and Global Health, Tufts University, North Grafton, MA, USA
| | - Xingmin Sun
- Department of Molecular Medicine, College of Medicine (COM), University of South Florida, Tampa, FL, USA
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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6
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Nicolas A, Deplanche M, Commere PH, Diot A, Genthon C, Marques da Silva W, Azevedo V, Germon P, Jamme H, Guédon E, Le Loir Y, Laurent F, Bierne H, Berkova N. Transcriptome Architecture of Osteoblastic Cells Infected With Staphylococcus aureus Reveals Strong Inflammatory Responses and Signatures of Metabolic and Epigenetic Dysregulation. Front Cell Infect Microbiol 2022; 12:854242. [PMID: 35531332 PMCID: PMC9067450 DOI: 10.3389/fcimb.2022.854242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/03/2022] [Indexed: 11/21/2022] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen that causes a range of devastating diseases including chronic osteomyelitis, which partially relies on the internalization and persistence of S. aureus in osteoblasts. The identification of the mechanisms of the osteoblast response to intracellular S. aureus is thus crucial to improve the knowledge of this infectious pathology. Since the signal from specifically infected bacteria-bearing cells is diluted and the results are confounded by bystander effects of uninfected cells, we developed a novel model of long-term infection. Using a flow cytometric approach we isolated only S. aureus-bearing cells from mixed populations that allows to identify signals specific to intracellular infection. Here we present an in-depth analysis of the effect of long-term S. aureus infection on the transcriptional program of human osteoblast-like cells. After RNA-seq and KEGG and Reactome pathway enrichment analysis, the remodeled transcriptomic profile of infected cells revealed exacerbated immune and inflammatory responses, as well as metabolic dysregulations that likely influence the intracellular life of bacteria. Numerous genes encoding epigenetic regulators were downregulated. The later included genes coding for components of chromatin-repressive complexes (e.g., NuRD, BAHD1 and PRC1) and epifactors involved in DNA methylation. Sets of genes encoding proteins of cell adhesion or neurotransmission were also deregulated. Our results suggest that intracellular S. aureus infection has a long-term impact on the genome and epigenome of host cells, which may exert patho-physiological dysfunctions additionally to the defense response during the infection process. Overall, these results not only improve our conceptual understanding of biological processes involved in the long-term S. aureus infections of osteoblast-like cells, but also provide an atlas of deregulated host genes and biological pathways and identify novel markers and potential candidates for prophylactic and therapeutic approaches.
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Affiliation(s)
- Aurélie Nicolas
- Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Institut Agro, Science et Technologie du Lait et de l’OEuf (STLO), Rennes, France
| | - Martine Deplanche
- Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Institut Agro, Science et Technologie du Lait et de l’OEuf (STLO), Rennes, France
| | - Pierre-Henri Commere
- Cytometry and Biomarkers Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, Paris, France
| | - Alan Diot
- Centre International de Recherche en Infectiologie, CIRI, Inserm U1111, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche 5308 (UMR5308), Ecole Normale Supérieure (ENS) de Lyon, Universit´ Claude Bernard Lyon 1 (UCBL1), Lyon, France
- Hospices Civils de Lyon, French National Reference Centre for Staphylococci, Lyon, France
| | - Clemence Genthon
- Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Unité Service 1426 (US1426), Transcriptome Plateforme Technologique (GeT-PlaGe), Genotoul, Castanet-Tolosan, France
| | - Wanderson Marques da Silva
- Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Institut Agro, Science et Technologie du Lait et de l’OEuf (STLO), Rennes, France
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Vasco Azevedo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Pierre Germon
- Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Université François Rabelais, Infectiologie et Santé Publique (ISP), Tours, France
| | - Hélène Jamme
- Université Paris-Saclay, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Biologie de la Reproduction, Environnement, Epigénétique et Développement (BREED), Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, Biologie de la Reproduction, Environnement, Epigénétique et Développement (BREED), Maisons-Alfort, France
| | - Eric Guédon
- Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Institut Agro, Science et Technologie du Lait et de l’OEuf (STLO), Rennes, France
| | - Yves Le Loir
- Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Institut Agro, Science et Technologie du Lait et de l’OEuf (STLO), Rennes, France
| | - Fréderic Laurent
- Centre International de Recherche en Infectiologie, CIRI, Inserm U1111, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche 5308 (UMR5308), Ecole Normale Supérieure (ENS) de Lyon, Universit´ Claude Bernard Lyon 1 (UCBL1), Lyon, France
- Hospices Civils de Lyon, French National Reference Centre for Staphylococci, Lyon, France
| | - Hélène Bierne
- Université Paris-Saclay, Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Nadia Berkova
- Institut National de Recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Institut Agro, Science et Technologie du Lait et de l’OEuf (STLO), Rennes, France
- *Correspondence: Nadia Berkova,
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7
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Duraj T, Carrión-Navarro J, Seyfried TN, García-Romero N, Ayuso-Sacido A. Metabolic therapy and bioenergetic analysis: The missing piece of the puzzle. Mol Metab 2021; 54:101389. [PMID: 34749013 PMCID: PMC8637646 DOI: 10.1016/j.molmet.2021.101389] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Aberrant metabolism is recognized as a hallmark of cancer, a pillar necessary for cellular proliferation. Regarding bioenergetics (ATP generation), most cancers display a preference not only toward aerobic glycolysis ("Warburg effect") and glutaminolysis (mitochondrial substrate level-phosphorylation) but also toward other metabolites such as lactate, pyruvate, and fat-derived sources. These secondary metabolites can assist in proliferation but cannot fully cover ATP demands. SCOPE OF REVIEW The concept of a static metabolic profile is challenged by instances of heterogeneity and flexibility to meet fuel/anaplerotic demands. Although metabolic therapies are a promising tool to improve therapeutic outcomes, either via pharmacological targets or press-pulse interventions, metabolic plasticity is rarely considered. Lack of bioenergetic analysis in vitro and patient-derived models is hindering translational potential. Here, we review the bioenergetics of cancer and propose a simple analysis of major metabolic pathways, encompassing both affordable and advanced techniques. A comprehensive compendium of Seahorse XF bioenergetic measurements is presented for the first time. MAJOR CONCLUSIONS Standardization of principal readouts might help researchers to collect a complete metabolic picture of cancer using the most appropriate methods depending on the sample of interest.
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Affiliation(s)
- Tomás Duraj
- Faculty of Medicine, Institute for Applied Molecular Medicine (IMMA), CEU San Pablo University, 28668, Madrid, Spain.
| | - Josefa Carrión-Navarro
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223, Madrid, Spain; Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043, Madrid, Spain.
| | - Thomas N Seyfried
- Biology Department, Boston College, 140 Commonwealth Ave, Chestnut Hill, MA, 02467, USA.
| | - Noemí García-Romero
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223, Madrid, Spain; Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043, Madrid, Spain.
| | - Angel Ayuso-Sacido
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223, Madrid, Spain; Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043, Madrid, Spain; Faculty of Medicine, Universidad Francisco de Vitoria, 28223, Madrid, Spain.
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8
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Pedrioli A, Oxenius A. Single B cell technologies for monoclonal antibody discovery. Trends Immunol 2021; 42:1143-1158. [PMID: 34743921 DOI: 10.1016/j.it.2021.10.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 11/18/2022]
Abstract
Monoclonal antibodies (mAbs) are often selected from antigen-specific single B cells derived from different hosts, which are notably short-lived in ex vivo culture conditions and hence, arduous to interrogate. The development of several new techniques and protocols has facilitated the isolation and retrieval of antibody-coding sequences of antigen-specific B cells by also leveraging miniaturization of reaction volumes. Alternatively, mAbs can be generated independently of antigen-specific B cells, comprising display technologies and, more recently, artificial intelligence-driven algorithms. Consequently, a considerable variety of techniques are used, raising the demand for better consolidation. In this review, we present and discuss the major techniques available to interrogate antigen-specific single B cells to isolate antigen-specific mAbs, including their main advantages and disadvantages.
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Affiliation(s)
- Alessandro Pedrioli
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Annette Oxenius
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland.
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9
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Mallikarjunappa S, Brito LF, Pant SD, Schenkel FS, Meade KG, Karrow NA. Johne's Disease in Dairy Cattle: An Immunogenetic Perspective. Front Vet Sci 2021; 8:718987. [PMID: 34513975 PMCID: PMC8426623 DOI: 10.3389/fvets.2021.718987] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/19/2021] [Indexed: 12/25/2022] Open
Abstract
Johne's disease (JD), also known as paratuberculosis, is a severe production-limiting disease with significant economic and welfare implications for the global cattle industry. Caused by infection with Mycobacterium avium subspecies paratuberculosis (MAP), JD manifests as chronic enteritis in infected cattle. In addition to the economic losses and animal welfare issues associated with JD, MAP has attracted public health concerns with potential association with Crohn's disease, a human inflammatory bowel disease. The lack of effective treatment options, such as a vaccine, has hampered JD control resulting in its increasing global prevalence. The disease was first reported in 1895, but in recognition of its growing economic impact, extensive recent research facilitated by a revolution in technological approaches has led to significantly enhanced understanding of the immunological, genetic, and pathogen factors influencing disease pathogenesis. This knowledge has been derived from a variety of diverse models to elucidate host-pathogen interactions including in vivo and in vitro experimental infection models, studies measuring immune parameters in naturally-infected animals, and by studies conducted at the population level to enable the estimation of genetic parameters, and the identification of genetic markers and quantitative trait loci (QTL) putatively associated with susceptibility or resistance to JD. The main objectives of this review are to summarize these recent developments from an immunogenetics perspective and attempt to extract the principal and common findings emerging from this wealth of recent information. Based on these analyses, and in light of emerging technologies such as gene-editing, we conclude by discussing potential future avenues for effectively mitigating JD in cattle.
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Affiliation(s)
- Sanjay Mallikarjunappa
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Sameer D Pant
- Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Flavio S Schenkel
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Kieran G Meade
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Niel A Karrow
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
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10
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Wang X, Xia H, Liu S, Cao L, You F. Epigenetic regulation in antiviral innate immunity. Eur J Immunol 2021; 51:1641-1651. [PMID: 33964027 DOI: 10.1002/eji.202048975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/03/2021] [Indexed: 12/24/2022]
Abstract
Emerging life-threatening viruses have posed great challenges to public health. It is now increasingly clear that epigenetics plays a role in shaping host-virus interactions and there is a great need for a more thorough understanding of these intricate interactions through the epigenetic lens, which may represent potential therapeutic opportunities in the clinic. In this review, we highlight the current understanding of the roles of key epigenetic regulators - chromatin remodeling and histone modification - in modulating chromatin openness during host defense against virus. We also discuss how the RNA modification m6A (N6-methyladenosine) affects fundamental aspects of host-virus interactions. We conclude with future directions for uncovering more detailed functions that epigenetic regulation exerts on both host cells and viruses during infection.
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Affiliation(s)
- Xiao Wang
- Department of Immunology, Institute of Systems Biomedicine, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, P. R. China
| | - Huawei Xia
- Department of Immunology, Institute of Systems Biomedicine, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, P. R. China
| | - Shengde Liu
- Department of Gastrointestinal Oncology, Key laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital and Institute, Beijing, P. R. China
| | - Lili Cao
- Department of Immunology, Institute of Systems Biomedicine, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, P. R. China
| | - Fuping You
- Department of Immunology, Institute of Systems Biomedicine, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, P. R. China
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11
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Kaya HO, Cetin AE, Azimzadeh M, Topkaya SN. Pathogen detection with electrochemical biosensors: Advantages, challenges and future perspectives. J Electroanal Chem (Lausanne) 2021; 882:114989. [PMID: 33456428 PMCID: PMC7794054 DOI: 10.1016/j.jelechem.2021.114989] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/27/2020] [Accepted: 01/06/2021] [Indexed: 12/29/2022]
Abstract
Detection of pathogens, e.g., bacteria and viruses, is still a big challenge in analytical medicine due to their vast number and variety. Developing strategies for rapid, inexpensive, specific, and sensitive detection of the pathogens using nanomaterials, integrating with microfluidics devices, amplification methods, or even combining these strategies have received significant attention. Especially, after the health-threatening COVID-19 outbreak, rapid and sensitive detection of pathogens became very critical. Detection of pathogens could be realized with electrochemical, optical, mass sensitive, or thermal methods. Among them, electrochemical methods are very promising by bringing different advantages, i.e., they exhibit more versatile detection schemes and real-time quantification as well as label-free measurements, which provides a broader application perspective. In this review, we discuss the recent advances for the detection of bacteria and viruses using electrochemical biosensors. Moreover, electrochemical biosensors for pathogen detection were broadly reviewed in terms of analyte, bio-recognition and transduction elements. Different fabrication techniques, detection principles, and applications of various pathogens with the electrochemical biosensors were also discussed.
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Affiliation(s)
- Hüseyin Oğuzhan Kaya
- Department of Analytical Chemistry, Faculty of Pharmacy, Izmir Katip Celebi University, 35620, Izmir, Turkey
| | - Arif E Cetin
- Izmir Biomedicine and Genome Center, Balcova 35340, Izmir, Turkey
| | - Mostafa Azimzadeh
- Medical Nanotechnology & Tissue Engineering Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, 89195-999 Yazd, Iran
- Stem Cell Biology Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, 89195-999 Yazd, Iran
- Department of Advanced Medical Sciences and Technologies, School of Paramedicine, Shahid Sadoughi University of Medical Sciences, 8916188635 Yazd, Iran
| | - Seda Nur Topkaya
- Department of Analytical Chemistry, Faculty of Pharmacy, Izmir Katip Celebi University, 35620, Izmir, Turkey
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Fun(gi)omics: Advanced and Diverse Technologies to Explore Emerging Fungal Pathogens and Define Mechanisms of Antifungal Resistance. mBio 2020; 11:mBio.01020-20. [PMID: 33024032 PMCID: PMC7542357 DOI: 10.1128/mbio.01020-20] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The landscape of infectious fungal agents includes previously unidentified or rare pathogens with the potential to cause unprecedented casualties in biodiversity, food security, and human health. The influences of human activity, including the crisis of climate change, along with globalized transport, are underlying factors shaping fungal adaptation to increased temperature and expanded geographical regions. Furthermore, the emergence of novel antifungal-resistant strains linked to excessive use of antifungals (in the clinic) and fungicides (in the field) offers an additional challenge to protect major crop staples and control dangerous fungal outbreaks. The landscape of infectious fungal agents includes previously unidentified or rare pathogens with the potential to cause unprecedented casualties in biodiversity, food security, and human health. The influences of human activity, including the crisis of climate change, along with globalized transport, are underlying factors shaping fungal adaptation to increased temperature and expanded geographical regions. Furthermore, the emergence of novel antifungal-resistant strains linked to excessive use of antifungals (in the clinic) and fungicides (in the field) offers an additional challenge to protect major crop staples and control dangerous fungal outbreaks. Hence, the alarming frequency of fungal infections in medical and agricultural settings requires effective research to understand the virulent nature of fungal pathogens and improve the outcome of infection in susceptible hosts. Mycology-driven research has benefited from a contemporary and unified approach of omics technology, deepening the biological, biochemical, and biophysical understanding of these emerging fungal pathogens. Here, we review the current state-of-the-art multi-omics technologies, explore the power of data integration strategies, and highlight discovery-based revelations of globally important and taxonomically diverse fungal pathogens. This information provides new insight for emerging pathogens through an in-depth understanding of well-characterized fungi and provides alternative therapeutic strategies defined through novel findings of virulence, adaptation, and resistance.
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Abstract
Cells are known to be the most fundamental building block of life[...].
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Affiliation(s)
- Tuhin Subhra Santra
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India
| | - Fan-Gang Tseng
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu 30013, Taiwan;
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