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Genomics of Host-Pathogen Interactions
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Genomics of Host-Pathogen Interactions

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (10 September 2020) | Viewed by 14807

Special Issue Editors

Prof. Dr. Davide Roncarati

E-Mail Website
Guest Editor
Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy
Interests: human pathogens; virulence factors; comparative transcriptomics; ChIP-sequencing
Dr. Maria Letizia Di Martino

E-Mail Website
Guest Editor
Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden
Interests: host–pathogen interaction; enteropathogens; virulence gene regulation; Tn-Seq

Special Issue Information

Dear Colleagues,

Host–pathogen interactions can be seen as a battle between two competitors. On one side, the pathogen employs several virulence factors to exploit the host. On the other side, the host counteracts with immune defense responses to clear the pathogen or reduce its deleterious effects. A detailed comprehension of the events that take place during the different stages of infection is crucial for our understanding of infectious diseases, as well as for the identification of potential new targets for therapeutic intervention. The genomics revolution has profoundly changed our perspectives in the field of infection biology. The development of high-throughput sequencing approaches has switched host–pathogen interaction studies from the single gene to the genome-wide perspective. Now, fitness effects as well as gene expression can be analysed in thousands of genetic loci on both the pathogen and the host side. This emerging trend in infection biology provides us with a complex tool to understand host–pathogen interactions at a previously unattainable level.

This Special Issue of Genes will address the main advances in the field of host–pathogen interaction, with a particular emphasis on genomics approaches employed to shed light on the complex interactions of bacterial pathogens with their hosts and/or host cells.

Prof. Davide Roncarati
Dr. Maria Letizia Di Martino
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Host–pathogen interaction
  • Genome-wide approaches
  • Fitness effects
  • Gene expression
  • Regulation of virulence factors
  • Host responses
  • Tn-Seq
  • Dual-Seq
  • CRISPR/Cas9 screening

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Published Papers (2 papers)

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Research

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19 pages, 8806 KiB  
Article
Protein Coding and Long Noncoding RNA (lncRNA) Transcriptional Landscape in SARS-CoV-2 Infected Bronchial Epithelial Cells Highlight a Role for Interferon and Inflammatory Response
by Radhakrishnan Vishnubalaji, Hibah Shaath and Nehad M. Alajez
Genes 2020, 11(7), 760; https://doi.org/10.3390/genes11070760 - 7 Jul 2020
Cited by 98 | Viewed by 9431
Abstract
The global spread of COVID-19, caused by pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for an imminent response from medical research communities to better understand this rapidly spreading infection. Employing multiple bioinformatics and computational pipelines on transcriptome data from [...] Read more.
The global spread of COVID-19, caused by pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for an imminent response from medical research communities to better understand this rapidly spreading infection. Employing multiple bioinformatics and computational pipelines on transcriptome data from primary normal human bronchial epithelial cells (NHBE) during SARS-CoV-2 infection revealed activation of several mechanistic networks, including those involved in immunoglobulin G (IgG) and interferon lambda (IFNL) in host cells. Induction of acute inflammatory response and activation of tumor necrosis factor (TNF) was prominent in SARS-CoV-2 infected NHBE cells. Additionally, disease and functional analysis employing ingenuity pathway analysis (IPA) revealed activation of functional categories related to cell death, while those associated with viral infection and replication were suppressed. Several interferon (IFN) responsive gene targets (IRF9, IFIT1, IFIT2, IFIT3, IFITM1, MX1, OAS2, OAS3, IFI44 and IFI44L) were highly upregulated in SARS-CoV-2 infected NBHE cell, implying activation of antiviral IFN innate response. Gene ontology and functional annotation of differently expressed genes in patient lung tissues with COVID-19 revealed activation of antiviral response as the hallmark. Mechanistic network analysis in IPA identified 14 common activated, and 9 common suppressed networks in patient tissue, as well as in the NHBE cell model, suggesting a plausible role for these upstream regulator networks in the pathogenesis of COVID-19. Our data revealed expression of several viral proteins in vitro and in patient-derived tissue, while several host-derived long noncoding RNAs (lncRNAs) were identified. Our data highlights activation of IFN response as the main hallmark associated with SARS-CoV-2 infection in vitro and in human, and identified several differentially expressed lncRNAs during the course of infection, which could serve as disease biomarkers, while their precise role in the host response to SARS-CoV-2 remains to be investigated. Full article
(This article belongs to the Special Issue Genomics of Host-Pathogen Interactions)
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Review

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31 pages, 869 KiB  
Review
Interplay between Regulatory RNAs and Signal Transduction Systems during Bacterial Infection
by Emma Piattelli, Johann Peltier and Olga Soutourina
Genes 2020, 11(10), 1209; https://doi.org/10.3390/genes11101209 - 16 Oct 2020
Cited by 8 | Viewed by 4335
Abstract
The ability of pathogenic bacteria to stably infect the host depends on their capacity to respond and adapt to the host environment and on the efficiency of their defensive mechanisms. Bacterial envelope provides a physical barrier protecting against environmental threats. It also constitutes [...] Read more.
The ability of pathogenic bacteria to stably infect the host depends on their capacity to respond and adapt to the host environment and on the efficiency of their defensive mechanisms. Bacterial envelope provides a physical barrier protecting against environmental threats. It also constitutes an important sensory interface where numerous sensing systems are located. Signal transduction systems include Two-Component Systems (TCSs) and alternative sigma factors. These systems are able to sense and respond to the ever-changing environment inside the host, altering the bacterial transcriptome to mitigate the impact of the stress. The regulatory networks associated with signal transduction systems comprise small regulatory RNAs (sRNAs) that can be directly involved in the expression of virulence factors. The aim of this review is to describe the importance of TCS- and alternative sigma factor-associated sRNAs in human pathogens during infection. The currently available genome-wide approaches for studies of TCS-regulated sRNAs will be discussed. The differences in the signal transduction mediated by TCSs between bacteria and higher eukaryotes and the specificity of regulatory RNAs for their targets make them appealing targets for discovery of new strategies to fight against multi-resistant bacteria. Full article
(This article belongs to the Special Issue Genomics of Host-Pathogen Interactions)
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