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      Lytic bacteriophages induce the secretion of antiviral and proinflammatory cytokines from human respiratory epithelial cells

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          Abstract

          Phage therapy is a therapeutic approach to treat multidrug-resistant (MDR) infections that employs lytic bacteriophages (phages) to eliminate bacteria. Despite the abundant evidence for its success as an antimicrobial in Eastern Europe, there is scarce data regarding its effects on the human host. Here, we aimed to understand how lytic phages interact with cells of the airway epithelium, the tissue site that is colonized by bacterial biofilms in numerous chronic respiratory disorders. Using a panel of Pseudomonas aeruginosa phages and human airway epithelial cells (AECs) derived from a person with cystic fibrosis (CF), we determined that interactions between phages and epithelial cells depend on specific phage properties as well as physiochemical features of the microenvironment. Although poor at internalizing phages, the airway epithelium responds to phage exposure by changing its transcriptional profile and secreting antiviral and proinflammatory cytokines that correlate with specific phage families. Overall, our findings indicate that mammalian responses to phages are heterogenous and could potentially alter the way that respiratory local defenses aid in bacterial clearance during phage therapy. Thus, besides phage receptor specificity in a particular bacterial isolate, the criteria to select lytic phages for therapy should be expanded to include mammalian cell responses.

          Abstract

          Phage therapy is being explored to treat multidrug-resistant bacterial infections, but the possible direct effects of phages on the human host are less well understood. This study shows that therapeutic phages can be detected by epithelial cells of the human respiratory tract, eliciting proinflammatory responses that depend on specific phage properties and the airway microenvironment.

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          Most cited references92

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            STAR: ultrafast universal RNA-seq aligner.

            Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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              edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

              Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. Availability: The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org). Contact: mrobinson@wehi.edu.au
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: VisualizationRole: Writing – review & editing
                Role: InvestigationRole: Methodology
                Role: MethodologyRole: ResourcesRole: Writing – review & editing
                Role: MethodologyRole: ResourcesRole: Writing – review & editing
                Role: MethodologyRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: MethodologyRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Biol
                PLoS Biol
                plos
                PLOS Biology
                Public Library of Science (San Francisco, CA USA )
                1544-9173
                1545-7885
                23 April 2024
                April 2024
                23 April 2024
                : 22
                : 4
                : e3002566
                Affiliations
                [1 ] Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, New Hampshire, United States of America
                [2 ] Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
                [3 ] Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
                [4 ] Center for Biological Imaging, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
                [5 ] Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
                [6 ] Center for Phage Biology and Therapy, Yale University, New Haven, Connecticut, United States of America
                [7 ] Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
                [8 ] Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, United States of America
                [9 ] Quantitative Biology Institute, Yale University, New Haven, Connecticut, United States of America
                [10 ] Department of Medicine, Yale University, New Haven, Connecticut, United States of America
                Monash University, AUSTRALIA
                Author notes

                PET is cofounder of Felix Biotechnology, Inc., a company that seeks to develop phages for human therapy. Yale University has an institutional conflict of interest related to this project (PET & JLK). Yale may receive financial benefit related to the therapy used in this protocol.

                Author information
                https://orcid.org/0000-0002-5246-4718
                https://orcid.org/0000-0003-4767-6238
                Article
                PBIOLOGY-D-23-02532
                10.1371/journal.pbio.3002566
                11037538
                38652717
                4eb182c7-3380-4bc5-9990-1f93c22c0fa4
                © 2024 Zamora et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 29 September 2023
                : 27 February 2024
                Page count
                Figures: 8, Tables: 0, Pages: 30
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000897, Cystic Fibrosis Foundation;
                Award ID: ZAMORA20F0
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000060, National Institute of Allergy and Infectious Diseases;
                Award ID: T32AI060525
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000897, Cystic Fibrosis Foundation;
                Award ID: ARMBRU19F0
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000897, Cystic Fibrosis Foundation;
                Award ID: ARMBRU22F5
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000050, National Heart, Lung, and Blood Institute;
                Award ID: T32HL129949
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000897, Cystic Fibrosis Foundation;
                Award ID: BOMBER21P0
                Award Recipient :
                This work was supported by a Cystic Fibrosis Foundation (CFF, www.cff.org) Postdoctoral Fellowship ZAMORA20F0 and National Institute of Health (NIH, www.nih.org) grant T32AI060525 to P.F.Z.; CFF grants ARMBRU19F0 and ARMBRU22F5 and NIH grant T32HL129949 to C.R.A; and CFF grant BOMBER21P0 to J.M.B. The funders of this work did not play a role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Organisms
                Viruses
                Bacteriophages
                Biology and Life Sciences
                Anatomy
                Biological Tissue
                Epithelium
                Medicine and Health Sciences
                Anatomy
                Biological Tissue
                Epithelium
                Biology and Life Sciences
                Physiology
                Immune Physiology
                Cytokines
                Biology and Life Sciences
                Immunology
                Immune System
                Innate Immune System
                Cytokines
                Medicine and Health Sciences
                Immunology
                Immune System
                Innate Immune System
                Cytokines
                Biology and Life Sciences
                Developmental Biology
                Molecular Development
                Cytokines
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Bacterial Pathogens
                Pseudomonas Aeruginosa
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogens
                Microbial Pathogens
                Bacterial Pathogens
                Pseudomonas Aeruginosa
                Biology and Life Sciences
                Organisms
                Bacteria
                Pseudomonas
                Pseudomonas Aeruginosa
                Medicine and Health Sciences
                Oncology
                Cancer Treatment
                Cytokine Therapy
                Biology and Life Sciences
                Cell Biology
                Cellular Types
                Animal Cells
                Epithelial Cells
                Biology and Life Sciences
                Anatomy
                Biological Tissue
                Epithelium
                Epithelial Cells
                Medicine and Health Sciences
                Anatomy
                Biological Tissue
                Epithelium
                Epithelial Cells
                Biology and Life Sciences
                Immunology
                Vaccination and Immunization
                Antiviral Therapy
                Medicine and Health Sciences
                Immunology
                Vaccination and Immunization
                Antiviral Therapy
                Medicine and Health Sciences
                Public and Occupational Health
                Preventive Medicine
                Vaccination and Immunization
                Antiviral Therapy
                Biology and Life Sciences
                Physiology
                Physiological Processes
                Secretion
                Custom metadata
                Relevant data are within the paper and its Supporting Information files. RNA sequencing FASTQ files are available from the NCBI SRA database (BioProject PRJNA1075455). A raw counts table and associated metadata are available at NCBI GEO under the accession number GSE255619. The code for this analysis can be found in https://github.com/Bomberger-Lab/ and https://zenodo.org/doi/10.5281/zenodo.10723798. Phage sequences are available from NCBI GenBank (PSA04 MZ089728, PSA34 MZ089739, OMKO1 ON631220, and LPS-5 PP203294).

                Life sciences
                Life sciences

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