Analyzing bacterial extracellular vesicles in human body fluids by orthogonal biophysical separation and biochemical characterization

Tulkens, Joeri; Wever, Olivier De; Hendrix, An

doi:10.1038/s41596-019-0236-5

Cited by 158 publications

(209 citation statements)

References 44 publications

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“…In some EV preparations, 75% of the total RNA reads originate exogenously (Wang et al, 2012 ; Fritz et al, 2016 ; Galvanin et al, 2019 ). Tulkens et al outlined a newly-developed combinatorial strategy including ultrafiltration, chromatography, and density gradient ultracentrifugation to fractionate bacterial- and host-derived EVs and other contaminating particles (Tulkens et al, 2020 ). This and other new experimental approaches we have reviewed, when carefully implemented, will help us gain a greater understanding of the mutualistic human-microbe relationship.…”

Section: Extracellular Vesicle Physiology and Biomedical Relevancementioning

confidence: 99%

Characterizing Extracellular Vesicles and Their Diverse RNA Contents

2020

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Cells release nanometer-scale, lipid bilayer-enclosed biomolecular packages (extracellular vesicles; EVs) into their surrounding environment. EVs are hypothesized to be intercellular communication agents that regulate physiological states by transporting biomolecules between near and distant cells. The research community has consistently advocated for the importance of RNA contents in EVs by demonstrating that: (1) EV-related RNA contents can be detected in a liquid biopsy, (2) disease states significantly alter EV-related RNA contents, and (3) sensitive and specific liquid biopsies can be implemented in precision medicine settings by measuring EV-derived RNA contents. Furthermore, EVs have medical potential beyond diagnostics. Both natural and engineered EVs are being investigated for therapeutic applications such as regenerative medicine and as drug delivery agents. This review focuses specifically on EV characterization, analysis of their RNA content, and their functional implications. The NIH extracellular RNA communication (ERC) program has catapulted human EV research from an RNA profiling standpoint by standardizing the pipeline for working with EV transcriptomics data, and creating a centralized database for the scientific community. There are currently thousands of RNA-sequencing profiles hosted on the Extracellular RNA Atlas alone (Murillo et al., 2019 ), encompassing a variety of human biofluid types and health conditions. While a number of significant discoveries have been made through these studies individually, integrative analyses of these data have thus far been limited. A primary focus of the ERC program over the next five years is to bring higher resolution tools to the EV research community so that investigators can isolate and analyze EV sub-populations, and ultimately single EVs sourced from discrete cell types, tissues, and complex biofluids. Higher resolution techniques will be essential for evaluating the roles of circulating EVs at a level which impacts clinical decision making. We expect that advances in microfluidic technologies will drive near-term innovation and discoveries about the diverse RNA contents of EVs. Long-term translation of EV-based RNA profiling into a mainstay medical diagnostic tool will depend upon identifying robust patterns of circulating genetic material that correlate with a change in health status.

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Section: Extracellular Vesicle Physiology and Biomedical Relevancementioning

confidence: 99%

Characterizing Extracellular Vesicles and Their Diverse RNA Contents

2020

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“…Bacterial cells communicate with their host and other bacteria through direct contacts and secretion of soluble products, such as metabolites (e.g., short-chain fatty acids), lipoglycans, quorum sensing peptides, nucleic acids, proteins, and membrane vesicles, also known as bacterial extracellular vesicles (BEVs) [25,26].…”

Section: Bacterial Extracellular Vesicles (Bevs): Biogenesis and Cargmentioning

confidence: 99%

“…Gram-negative bacteria follow two main pathways for vesicle formation. The first formation route involves blebbing of the outer membrane of the bacterial envelope, generating outer-membrane vesicles (OMVs); and the second pathway entails explosive cell lysis forming outer-inner membrane vesicles (OIMVs) and explosive outer-membrane vesicles (EOMVs) [8,26]. Gram-positive bacteria produce cytoplasmic membrane vesicles (CMVs) through endolysin-triggered bubbling cell death [8,29].…”

Section: Bacterial Extracellular Vesicles (Bevs): Biogenesis and Cargmentioning

confidence: 99%

“…There exists a growing consensus that BEVs from the resident microbiota can enter the systemic circulation [26,[52][53][54][55][56][57]. BEVs released by bacteria in the gut lumen can cross the epithelial barrier to gain access into the underlying submucosa enabling them to interact with various resident immune cell populations (dendritic cells, neutrophils and macrophages) as well as potentially disseminate more widely around the body via the systemic or lymphatic circulation to reach distant tissues and organs or even the brain (Fig.…”

Section: Microbiota-derived Bevs Can Enter the Systemic Circulation Amentioning

confidence: 99%

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Emerging role of bacterial extracellular vesicles in cancer

2020

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Shedding of microbial extracellular vesicles constitutes a universal mechanism for inter-kingdom and intra-kingdom communication that is conserved among prokaryotic and eukaryotic microbes. In this review we delineate fundamental aspects of bacterial extracellular vesicles (BEVs) including their biogenesis, cargo composition, and interactions with host cells. We critically examine the evidence that BEVs from the host gut microbiome can enter the circulatory system to disseminate to distant organs and tissues. The potential involvement of BEVs in carcinogenesis is evaluated and future research ideas explored. We further discuss the potential of BEVs in microbiome-based liquid biopsies for cancer diagnostics and bioengineering strategies for cancer therapy.

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“…Blood microbial EVs are usually detectable in humans; however, studies about urine microbial EVs are still lacking. 8 Only one recent study identified dysbiosis in the asthma group using microbe-derived EVs in children. 9 Two papers published in this issue of the Allergy, Asthma & Immunology Research have shown the significance of urine microbial EVs in allergic diseases, which for the first time are the studies show the presence of urine microbial EVs in allergic airway disease.…”

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confidence: 99%