Use of high-throughput mass spectrometry to elucidate host–pathogen interactions inSalmonella

Abstract Background During infection by intracellular pathogens, a highly complex interplay occurs between the infected cell trying to degrade the invader and the pathogen which actively manipulates the host cell to enable survival and proliferation. Many intracellular pathogens pose important threats to human health and major efforts have been undertaken to better understand the host-pathogen interactions that eventually determine the outcome of the infection. Over the last decades, the unicellular eukaryote Dictyostelium discoideum has become an established infection model, serving as a surrogate macrophage that can be infected with a wide range of intracellular pathogens. In this study, we use high-throughput RNA-sequencing to analyze the transcriptional response of D. discoideum when infected with Mycobacterium marinum and Legionella pneumophila. The results were compared to available data from human macrophages. Results The majority of the transcriptional regulation triggered by the two pathogens was found to be unique for each bacterial challenge. Hallmark transcriptional signatures were identified for each infection, e.g. induction of endosomal sorting complexes required for transport (ESCRT) and autophagy genes in response to M. marinum and inhibition of genes associated with the translation machinery and energy metabolism in response to L. pneumophila. However, a common response to the pathogenic bacteria was also identified, which was not induced by non-pathogenic food bacteria. Finally, comparison with available data sets of regulation in human monocyte derived macrophages shows that the elicited response in D. discoideum is in many aspects similar to what has been observed in human immune cells in response to Mycobacterium tuberculosis and L. pneumophila. Conclusions Our study presents high-throughput characterization of D. discoideum transcriptional response to intracellular pathogens using RNA-seq. We demonstrate that the transcriptional response is in essence distinct to each pathogen and that in many cases, the corresponding regulation is recapitulated in human macrophages after infection by mycobacteria and L. pneumophila. This indicates that host-pathogen interactions are evolutionary conserved, derived from the early interactions between free-living phagocytic cells and bacteria. Taken together, our results strengthen the use of D. discoideum as a general infection model.

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Uncovering complex molecular networks in host–pathogen interactions using systems biology

Emerging Topics in Life Sciences ◽

10.1042/etls20180174 ◽

2019 ◽

Vol 3 (4) ◽

pp. 371-378

Author(s):

Joshua M. Peters ◽

Sydney L. Solomon ◽

Christopher Y. Itoh ◽

Bryan D. Bryson

Keyword(s):

Systems Biology ◽

High Throughput ◽

Cell Biology ◽

Molecular Networks ◽

Host Pathogen Interactions ◽

Exciting Field ◽

Specific Host ◽

Biomolecular Network ◽

Host Pathogen ◽

Analytical Frameworks

Abstract Interactions between pathogens and their hosts can induce complex changes in both host and pathogen states to privilege pathogen survival or host clearance of the pathogen. To determine the consequences of specific host–pathogen interactions, a variety of techniques in microbiology, cell biology, and immunology are available to researchers. Systems biology that enables unbiased measurements of transcriptomes, proteomes, and other biomolecules has become increasingly common in the study of host–pathogen interactions. These approaches can be used to generate novel hypotheses or to characterize the effects of particular perturbations across an entire biomolecular network. With proper experimental design and complementary data analysis tools, high-throughput omics techniques can provide novel insights into the mechanisms that underlie processes from phagocytosis to pathogen immune evasion. Here, we provide an overview of the suite of biochemical approaches for high-throughput analyses of host–pathogen interactions, analytical frameworks for understanding the resulting datasets, and a vision for the future of this exciting field.

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A Sensitive High-Throughput Assay for Evaluating Host-Pathogen Interactions in Cryptococcus neoformans Infection

PLoS ONE ◽

10.1371/journal.pone.0022773 ◽

2011 ◽

Vol 6 (7) ◽

pp. e22773 ◽

Cited By ~ 17

Author(s):

Deepa Srikanta ◽

Meng Yang ◽

Matthew Williams ◽

Tamara L. Doering

Keyword(s):

Cryptococcus Neoformans ◽

High Throughput ◽

Host Pathogen Interactions ◽

Host Pathogen ◽

High Throughput Assay

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The Application of High Throughput siRNA Screening Technology to Study Host-Pathogen Interactions

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/138620712799361834 ◽

2012 ◽

Vol 15 (4) ◽

pp. 299-305 ◽

Cited By ~ 2

Author(s):

Li Ou ◽

Dan Duan ◽

Jinhua Wu ◽

Edouard Nice ◽

Canhua Huang

Keyword(s):

High Throughput ◽

Host Pathogen Interactions ◽

Host Pathogen ◽

Screening Technology ◽

Sirna Screening

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Contributions of Mass Spectrometry-Based Proteomics to Understanding Salmonella-Host Interactions

Pathogens ◽

10.3390/pathogens9070581 ◽

2020 ◽

Vol 9 (7) ◽

pp. 581

Author(s):

Buyu Zhang ◽

Bohao Liu ◽

Yinglin Zhou ◽

Xinxiang Zhang ◽

Qinghua Zou ◽

...

Keyword(s):

Mass Spectrometry ◽

Affinity Purification ◽

Host Cells ◽

Secretion Systems ◽

Host Pathogen Interactions ◽

Host Interactions ◽

Functional Studies ◽

Type Iii Secretion Systems ◽

Host Pathogen ◽

Technological Platform

As a model pathogen, Salmonella invades both phagocytic and non-phagocytic host cells and adopts an intracellular lifestyle in a membrane-bound compartment during infection. Therefore, a systemic overview of Salmonella adaptations to distinct host cells together with host remodeling will assist us in charting the landscape of host-pathogen interactions. Central to the Salmonella-host interplay are bacterial virulence factors (effectors) that are injected into host cells by type III secretion systems (T3SSs). Despite great progress, functional studies of bacterial effectors have experienced daunting challenges as well. In the last decade, mass spectrometry-based proteomics has evolved into a powerful technological platform that can quantitatively measure thousands of proteins in terms of their expression as well as post-translational modifications. Here, we will review the applications of high-throughput proteomic technologies in understanding the dynamic reprogramming of both Salmonella and host proteomes during the course of infection. Furthermore, we will summarize the progress in utilizing affinity purification-mass spectrometry to screen for host substrates of Salmonella T3SS effectors. Finally, we will critically discuss some limitations/challenges with current proteomic platforms in the context of host-pathogen interactions and highlight some emerging technologies that may offer the promise of tackling these problems.

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High-Throughput Microfluidic Method To Study Biofilm Formation and Host-Pathogen Interactions in Pathogenic Escherichia coli

Applied and Environmental Microbiology ◽

10.1128/aem.04208-14 ◽

2015 ◽

Vol 81 (8) ◽

pp. 2827-2840 ◽

Cited By ~ 16

Author(s):

Yannick D. N. Tremblay ◽

Philippe Vogeleer ◽

Mario Jacques ◽

Josée Harel

Keyword(s):

Escherichia Coli ◽

High Throughput ◽

Biofilm Formation ◽

Cell Biology ◽

Shear Force ◽

Host Pathogen Interactions ◽

Content Type ◽

E Coli ◽

Rpmi Medium ◽

Host Pathogen

ABSTRACTBiofilm formation and host-pathogen interactions are frequently studied using multiwell plates; however, these closed systems lack shear force, which is present at several sites in the host, such as the intestinal and urinary tracts. Recently, microfluidic systems that incorporate shear force and very small volumes have been developed to provide cell biology models that resemblein vivoconditions. Therefore, the objective of this study was to determine if the BioFlux 200 microfluidic system could be used to study host-pathogen interactions and biofilm formation by pathogenicEscherichia coli. Strains of various pathotypes were selected to establish the growth conditions for the formation of biofilms in the BioFlux 200 system on abiotic (glass) or biotic (eukaryotic-cell) surfaces. Biofilm formation on glass was observed for the majority of strains when they were grown in M9 medium at 30°C but not in RPMI medium at 37°C. In contrast, HRT-18 cell monolayers enhanced binding and, in most cases, biofilm formation by pathogenicE. coliin RPMI medium at 37°C. As a proof of principle, the biofilm-forming ability of a diffusely adherentE. colimutant strain lacking AIDA-I, a known mediator of attachment, was assessed in our models. In contrast to the parental strain, which formed a strong biofilm, the mutant formed a thin biofilm on glass or isolated clusters on HRT-18 monolayers. In conclusion, we describe a microfluidic method for high-throughput screening that could be used to identify novel factors involved inE. colibiofilm formation and host-pathogen interactions under shear force.

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Pathogen-Host Interaction Repertoire at Proteome and Posttranslational Modification Levels During Fungal Infections

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.774340 ◽

2021 ◽

Vol 11 ◽

Author(s):

Yanjian Li ◽

Hailong Li ◽

Tianshu Sun ◽

Chen Ding

Keyword(s):

Mass Spectrometry ◽

Posttranslational Modification ◽

Antifungal Agents ◽

Fungal Infections ◽

Multidrug Resistant ◽

Fungal Diseases ◽

Host Pathogen Interactions ◽

Fungal Virulence ◽

Mortality And Morbidity ◽

Host Pathogen

Prevalence of fungal diseases has increased globally in recent years, which often associated with increased immunocompromised patients, aging populations, and the novel Coronavirus pandemic. Furthermore, due to the limitation of available antifungal agents mortality and morbidity rates of invasion fungal disease remain stubbornly high, and the emergence of multidrug-resistant fungi exacerbates the problem. Fungal pathogenicity and interactions between fungi and host have been the focus of many studies, as a result, lots of pathogenic mechanisms and fungal virulence factors have been identified. Mass spectrometry (MS)-based proteomics is a novel approach to better understand fungal pathogenicities and host–pathogen interactions at protein and protein posttranslational modification (PTM) levels. The approach has successfully elucidated interactions between pathogens and hosts by examining, for example, samples of fungal cells under different conditions, body fluids from infected patients, and exosomes. Many studies conclude that protein and PTM levels in both pathogens and hosts play important roles in progression of fungal diseases. This review summarizes mass spectrometry studies of protein and PTM levels from perspectives of both pathogens and hosts and provides an integrative conceptual outlook on fungal pathogenesis, antifungal agents development, and host–pathogen interactions.

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High throughput Raman spectroscopy for host-pathogen interactions (Conference Presentation)

Light-Based Diagnosis and Treatment of Infectious Diseases ◽

10.1117/12.2290047 ◽

2018 ◽

Author(s):

Anuradha Ramoji ◽

Natalie Toepfer ◽

Jan Rueger ◽

Abdullah S. Mondol ◽

Iwan W. Schie ◽

...

Keyword(s):

Raman Spectroscopy ◽

High Throughput ◽

Host Pathogen Interactions ◽

Host Pathogen

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Development and Characterization of High-Throughput Caenorhabditis elegans – Enterococcus faecium Infection Model

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.667327 ◽

2021 ◽

Vol 11 ◽

Author(s):

Alexey V. Revtovich ◽

Elissa Tjahjono ◽

Kavindra V. Singh ◽

Blake M. Hanson ◽

Barbara E. Murray ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Virulence Factors ◽

High Throughput ◽

World Health ◽

Infection Model ◽

Virulence Determinants ◽

Host Pathogen Interactions ◽

C Elegans ◽

Host Pathogen ◽

Host Death

The genus Enterococcus includes two Gram-positive pathogens of particular clinical relevance: E. faecalis and E. faecium. Infections with each of these pathogens are becoming more frequent, particularly in the case of hospital-acquired infections. Like most other bacterial species of clinical importance, antimicrobial resistance (and, specifically, multi-drug resistance) is an increasing threat, with both species considered to be of particular importance by the World Health Organization and the US Centers for Disease Control. The threat of antimicrobial resistance is exacerbated by the staggering difference in the speeds of development for the discovery and development of the antimicrobials versus resistance mechanisms. In the search for alternative strategies, modulation of host-pathogen interactions in general, and virulence inhibition in particular, have drawn substantial attention. Unfortunately, these approaches require a fairly comprehensive understanding of virulence determinants. This requirement is complicated by the fact that enterococcal infection models generally require vertebrates, making them slow, expensive, and ethically problematic, particularly when considering the thousands of animals that would be needed for the early stages of experimentation. To address this problem, we developed the first high-throughput C. elegans–E. faecium infection model involving host death. Importantly, this model recapitulates many key aspects of murine peritonitis models, including utilizing similar virulence determinants. Additionally, host death is independent of peroxide production, unlike other E. faecium–C. elegans virulence models, which allows the assessment of other virulence factors. Using this system, we analyzed a panel of lab strains with deletions of targeted virulence factors. Although removal of certain virulence factors (e.g., Δfms15) was sufficient to affect virulence, multiple deletions were generally required to affect pathogenesis, suggesting that host-pathogen interactions are multifactorial. These data were corroborated by genomic analysis of selected isolates with high and low levels of virulence. We anticipate that this platform will be useful for identifying new treatments for E. faecium infection.

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