scholarly journals Dual RNA-Seq Enables Full-Genome Assembly of Measles Virus and Characterization of Host–Pathogen Interactions

2021 ◽  
Vol 9 (7) ◽  
pp. 1538
Author(s):  
Timokratis Karamitros ◽  
Vasiliki Pogka ◽  
Gethsimani Papadopoulou ◽  
Ourania Tsitsilonis ◽  
Maria Evangelidou ◽  
...  
Keyword(s):  
Immune Responses ◽  
Viral Infection ◽  
Peripheral Blood ◽  
Measles Virus ◽  
Full Genome ◽  
Rna Seq ◽  
Host Pathogen Interactions ◽  
Dnase Treatment ◽  
Host Pathogen

Measles virus (MeV) has a negative-sense 15 kb long RNA genome, which is generally conserved. Recent advances in high-throughput sequencing (HTS) and Dual RNA-seq allow the analysis of viral RNA genomes and the discovery of viral infection biomarkers, via the simultaneous characterization of the host transcriptome. However, these host–pathogen interactions remain largely unexplored in MeV infections. We performed untargeted Dual RNA-seq in 6 pharyngeal and 6 peripheral blood mononuclear cell (PBMCs) specimens from patients with MeV infection, as confirmed via routine real-time PCR testing. Following optimised DNase treatment of total nucleic acids, we used the pharyngeal samples to build poly-A-enriched NGS libraries. We reconstructed the viral genomes using the pharyngeal datasets and we further conducted differential expression, gene-ontology and pathways enrichment analysis to compare both the pharyngeal and the peripheral blood transcriptomes of the MeV-infected patients vs. control groups of healthy individuals. We obtained 6 MeV genotype-B3 full-genome sequences. We minutely analyzed the transcriptome of the MeV-infected pharyngeal epithelium, detecting all known viral infection biomarkers, but also revealing a functional cluster of local antiviral and inflammatory immune responses, which differ substantially from those observed in the PBMCs transcriptome. The application of Dual RNA-seq technologies in MeV-infected patients can potentially provide valuable information on the virus genome structure and the cellular innate immune responses and drive the discovery of new targets for antiviral therapy.

scholarly journals RNA-Sequencing Analyses of Small Bacterial RNAs and their Emergence as Virulence Factors in Host-Pathogen Interactions

2020 ◽  
Vol 21 (5) ◽  
pp. 1627 ◽  
Author(s):  
Idrissa Diallo ◽  
Patrick Provost
Keyword(s):  
Rna Sequencing ◽  
Virulence Factors ◽  
Membrane Vesicles ◽  
Outer Membrane Vesicles ◽  
Rna Seq ◽  
Host Pathogen Interactions ◽  
Bioinformatics Analyses ◽  
Additional Layer ◽  
Host Pathogen

Proteins have long been considered to be the most prominent factors regulating so-called invasive genes involved in host-pathogen interactions. The possible role of small non-coding RNAs (sRNAs), either intracellular, secreted or packaged in outer membrane vesicles (OMVs), remained unclear until recently. The advent of high-throughput RNA-sequencing (RNA-seq) techniques has accelerated sRNA discovery. RNA-seq radically changed the paradigm on bacterial virulence and pathogenicity to the point that sRNAs are emerging as an important, distinct class of virulence factors in both gram-positive and gram-negative bacteria. The potential of OMVs, as protectors and carriers of these functional, gene regulatory sRNAs between cells, has also provided an additional layer of complexity to the dynamic host-pathogen relationship. Using a non-exhaustive approach and through examples, this review aims to discuss the involvement of sRNAs, either free or loaded in OMVs, in the mechanisms of virulence and pathogenicity during bacterial infection. We provide a brief overview of sRNA origin and importance and describe the classical and more recent methods of identification that have enabled their discovery, with an emphasis on the theoretical lower limit of RNA sizes considered for RNA sequencing and bioinformatics analyses.

scholarly journals Next-generation technologies for studying host–pathogen interactions: a focus on dual transcriptomics, CRISPR/Cas9 screening and organs-on-chips

2019 ◽  
Vol 77 (6) ◽  
Author(s):  
Buket Baddal
Keyword(s):  
Infectious Disease ◽  
Drug Targets ◽  
Genome Mining ◽  
Three Dimensional ◽  
Local Environment ◽  
Rna Seq ◽  
Host Pathogen Interactions ◽  
Host Pathogen ◽  
On Chip ◽  
Organ Models

ABSTRACT Pathogens constantly interact with their hosts and the environment, and therefore have evolved unique virulence mechanisms to target and breach host defense barriers and manipulate host immune response to establish an infection. Advances in technologies that allow genome mining, gene editing such as CRISPR/Cas9, genomic, epigenomic and transcriptomic studies such as dual RNA-seq, coupled with bioinformatics, have accelerated the field of host–pathogen interactions within a broad range of infection models. Underpinning of the molecular changes that accompany invasion of eukaryotic cells with pathogenic microorganisms at the intersection of host, pathogen and their local environment has provided a better understanding of infectious disease mechanisms and antimicrobial strategies. The recent evolution of physiologically relevant three-dimensional (3-D) tissue/organ models and microfluidic organ-on-chip devices also provided a window to a more predictive framework of infectious disease processes. These approaches combined hold the potential to highly impact discovery of novel drug targets and vaccine candidates of the future. Here, we review three of the available and emerging technologies—dual RNA-seq, CRISPR/Cas9 screening and organs-on-chips, applicable to the high throughput study and deciphering of interaction networks between pathogens and their hosts that are critical for the development of novel therapeutics.

scholarly journals Resolving host–pathogen interactions by dual RNA-seq

2017 ◽  
Vol 13 (2) ◽  
pp. e1006033 ◽  
Author(s):  
Alexander J. Westermann ◽  
Lars Barquist ◽  
Jörg Vogel
Keyword(s):  
Rna Seq ◽  
Host Pathogen Interactions ◽  
Host Pathogen

scholarly journals Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs

2020 ◽  
Author(s):  
Bo Lu ◽  
Yi Yan ◽  
Liting Dong ◽  
Lingling Han ◽  
Yawei Liu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Severe Acute Respiratory Syndrome ◽  
Host Response ◽  
Comprehensive Analysis ◽  
Clinical Samples ◽  
Full Genome ◽  
Rna Seq ◽  
Sequencing Data ◽  
Genome Information

AbstractThe ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, poses a severe threat to humanity. Rapid and comprehensive analysis of both pathogen and host sequencing data is critical to track infection and inform therapies. In this study, we performed unbiased metatranscriptomic analysis of clinical samples from COVID-19 patients using a newly-developed RNA-seq library construction method (TRACE-seq), which utilizes tagmentation activity of Tn5 on RNA/DNA hybrids. This approach avoids the laborious and time-consuming steps in traditional RNA-seq procedure, and hence is fast, sensitive and convenient. We demonstrated that TRACE-seq allowed integrated characterization of full genome information of SARS-CoV-2, putative pathogens causing coinfection, antibiotic resistance and host response from single throat swabs. We believe that the integrated information will deepen our understanding of pathogenesis and improve diagnostic accuracy for infectious diseases.

scholarly journals Characterization of Porphyromonas gingivalis sialidase and disruption of its role in host–pathogen interactions

Microbiology ◽  
2019 ◽  
Vol 165 (11) ◽  
pp. 1181-1197 ◽  
Author(s):  
Andrew M. Frey ◽  
Marianne J. Satur ◽  
Chatchawal Phansopa ◽  
Kiyonobu Honma ◽  
Paulina A. Urbanowicz ◽  
...  
Keyword(s):  
Porphyromonas Gingivalis ◽  
Host Pathogen Interactions ◽  
Host Pathogen

scholarly journals Dual RNA-Seq of Mtb-Infected Macrophages In Vivo Reveals Ontologically Distinct Host-Pathogen Interactions

Cell Reports ◽  
2020 ◽  
Vol 30 (2) ◽  
pp. 335-350.e4 ◽  
Author(s):  
Davide Pisu ◽  
Lu Huang ◽  
Jennifer K. Grenier ◽  
David G. Russell
Keyword(s):  
Rna Seq ◽  
Host Pathogen Interactions ◽  
Host Pathogen
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