Proteolytic Vesicles Derived from Salmonella enterica Serovar Typhimurium-Infected Macrophages: Enhancing MMP-9-Mediated Invasion and EV Accumulation

Proteolysis of the extracellular matrix (ECM) by matrix metalloproteinases (MMPs) plays a crucial role in the immune response to bacterial infections. Here we report the secretion of MMPs associated with proteolytic extracellular vesicles (EVs) released by macrophages in response to Salmonella enterica serovar Typhimurium infection. Specifically, we used global proteomics, in vitro, and in vivo approaches to investigate the composition and function of these proteolytic EVs. Using a model of S. Typhimurium infection in murine macrophages, we isolated and characterized a population of small EVs. Bulk proteomics analysis revealed significant changes in protein cargo of naïve and S. Typhimurium-infected macrophage-derived EVs, including the upregulation of MMP-9. The increased levels of MMP-9 observed in immune cells exposed to S. Typhimurium were found to be regulated by the toll-like receptor 4 (TLR-4)-mediated response to bacterial lipopolysaccharide. Macrophage-derived EV-associated MMP-9 enhanced the macrophage invasion through Matrigel as selective inhibition of MMP-9 reduced macrophage invasion. Systemic administration of fluorescently labeled EVs into immunocompromised mice demonstrated that EV-associated MMP activity facilitated increased accumulation of EVs in spleen and liver tissues. This study suggests that macrophages secrete proteolytic EVs to enhance invasion and ECM remodeling during bacterial infections, shedding light on an essential aspect of the immune response.

Genetically Engineered MRI-Trackable Extracellular Vesicles as SARS-CoV-2 Mimetics for Mapping ACE2 Binding In Vivo

The elucidation of viral-receptor interactions and an understanding of virus-spreading mechanisms are of great importance, particularly in the era of a pandemic. Indeed, advances in computational chemistry, synthetic biology, and protein engineering have allowed precise prediction and characterization of such interactions. Nevertheless, the hazards of the infectiousness of viruses, their rapid mutagenesis, and the need to study viral-receptor interactions in a complex in vivo setup call for further developments. Here, we show the development of biocompatible genetically engineered extracellular vesicles (EVs) that display the receptor binding domain (RBD) of SARS-CoV-2 on their surface as coronavirus mimetics (EVsRBD). Loading EVsRBD with iron oxide nanoparticles makes them MRI-visible and, thus, allows mapping of the binding of RBD to ACE2 receptors noninvasively in live subjects. Moreover, we show that EVsRBD can be modified to display mutants of the RBD of SARS-CoV-2, allowing rapid screening of currently raised or predicted variants of the virus. The proposed platform thus shows relevance and cruciality in the examination of quickly evolving pathogenic viruses in an adjustable, fast, and safe manner. Relying on MRI for visualization, the presented approach could be considered in the future to map ligand-receptor binding events in deep tissues, which are not accessible to luminescence-based imaging.

Malaria parasites release vesicle subpopulations with signatures of different destinations

Malaria is the most serious mosquito-borne parasitic disease, caused mainly by the intracellular parasite Plasmodium falciparum. The parasite invades human red blood cells and releases extracellular vesicles (EVs) to alter its host responses. It becomes clear that EVs are generally composed of sub-populations. Seeking to identify EV subpopulations, we subject malaria-derived EVs to size-separation analysis, using asymmetric flow field-flow fractionation. Multi-technique analysis reveals surprising characteristics: we identify two distinct EV subpopulations differing in size and protein content. Small EVs are enriched in complement-system proteins and large EVs in proteasome subunits. We then measure the membrane fusion abilities of each subpopulation with three types of host cellular membranes: plasma, late and early endosome. Remarkably, small EVs fuse to early endosome liposomes at significantly greater levels than large EVs. Atomic force microscope imaging combined with machine-learning methods further emphasizes the difference in biophysical properties between the two subpopulations. These results shed light on the sophisticated mechanism by which malaria parasites utilize EV subpopulations as a communication tool to target different cellular destinations or host systems.

Bacterial infection disrupts established germinal center reactions through monocyte recruitment and impaired metabolic adaptation

Consecutive exposures to different pathogens are highly prevalent and often alter the host immune response. However, it remains unknown how a secondary bacterial infection affects an ongoing adaptive immune response elicited against primary invading pathogens. We demonstrated that recruitment of Sca-1⁺ monocytes into lymphoid organs during Salmonella Typhimurium (STm) infection disrupted pre-existing germinal center (GC) reactions. GC responses induced by influenza, plasmodium, or commensals deteriorated following STm infection. GC disruption was independent of the direct bacterial interactions with B cells and instead was induced through recruitment of CCR2-dependent Sca-1⁺ monocytes into the lymphoid organs. GC collapse was associated with impaired cellular respiration and was dependent on TNFα and IFNγ, the latter of which was essential for Sca-1⁺ monocyte differentiation. Monocyte recruitment and GC disruption also occurred during LPS-supplemented vaccination and Listeria monocytogenes infection. Thus, systemic activation of the innate immune response upon severe bacterial infection is induced at the expense of antibody-mediated immunity.

Monitoring Distribution Dynamics of EV RNA Cargo Within Recipient Monocytes and Macrophages

Extracellular vesicles (EVs) are produced by across almost all the living kingdoms and play a crucial role in cell-cell communication processes. EVs are especially important for pathogens, as Plasmodium falciparum (Pf) parasite, the leading causing species in human malaria. Malaria parasites are able to modulate the host immune response from a distance via delivering diverse cargo components inside the EVs, such as proteins and nucleic acids. We have previously shown that imaging flow cytometry (IFC) can be effectively used to monitor the uptake of different cargo components of malaria derived EVs by host human monocytes. Here, we take this approach one step further and demonstrate that we can directly investigate the dynamics of the cargo distribution pattern over time by monitoring its distribution within two different recipient cells of the immune system, monocytes vs macrophages. By staining the RNA cargo of the vesicles and monitor the signal we were able to evaluate the kinetics of its delivery and measure different parameters of the cargo’s distribution post internalization. Interestingly, we found that while the level of the EV uptake is similar, the pattern of the signal for RNA cargo distribution is significantly different between these two recipient immune cells. Our results demonstrate that this method can be applied to study the distribution dynamics of the vesicle cargo post uptake to different types of cells. This can benefit significantly to our understanding of the fate of cargo components post vesicle internalization in the complex interface between pathogen-derived vesicles and their host recipient cells.

Imaging of Extracellular Vesicles Derived from Plasmodium falciparum-Infected Red Blood Cells Using Atomic Force Microscopy

Malaria is one the most devastating infectious diseases in the world: of the five malaria-associated parasites, Plasmodium falciparum and P. vivax are the most pathogenic and widespread, respectively. P. falciparum invades human red blood cells (RBCs), releasing extracellular vesicles (Pf-EV) carrying DNA, RNA and protein cargo components involved in host-pathogen communications in the course of the disease. Different strategies have been used to analyze Pf-EV biophysically and chemically. Atomic force microscopy (AFM) stands out as a powerful tool for rendering high quality images of extracellular vesicles. In this technique, a sharp tip attached to a cantilever reconstructs the topographic surface of the extracellular vesicles and probes their nano-mechanical properties based on force-distance curves. Here, we describe a method to separate Pf-EV using differential ultracentrifugation, followed by nanoparticle tracking analysis (NTA) to quantify and estimate the size distribution. Finally, the AFM imaging procedure on Pf-EV adsorbed on a Mg²⁺-modified mica surface is detailed.

Malaria parasites both repress host CXCL10 and use it as a cue for growth acceleration

Pathogens are thought to use host molecular cues to control when to initiate life-cycle transitions, but these signals are mostly unknown, particularly for the parasitic disease malaria caused by Plasmodium falciparum. The chemokine CXCL10 is present at high levels in fatal cases of cerebral malaria patients, but is reduced in patients who survive and do not have complications. Here we show a Pf 'decision-sensing-system' controlled by CXCL10 concentration. High CXCL10 expression prompts P. falciparum to initiate a survival strategy via growth acceleration. Remarkably, P. falciparum inhibits CXCL10 synthesis in monocytes by disrupting the association of host ribosomes with CXCL10 transcripts. The underlying inhibition cascade involves RNA cargo delivery into monocytes that triggers RIG-I, which leads to HUR1 binding to an AU-rich domain of the CXCL10 3'UTR. These data indicate that when the parasite can no longer keep CXCL10 at low levels, it can exploit the chemokine as a cue to shift tactics and escape.

Antibody-Free Labeling of Malaria-Derived Extracellular Vesicles Using Flow Cytometry

Extracellular vesicles (EVs) are cell-derived membrane-bound structures that are believed to play a major role in intercellular communication by allowing cells to exchange proteins and genetic cargo between them. In particular, pathogens, such as the malaria parasite Plasmodium (P.) falciparum, utilize EVs to promote their growth and to alter their host's response. Thus, better characterization of these secreted organelles will enhance our understanding of the cellular processes that govern EVs' biology and pathological functions. Here we present a method that utilizes a high-end flow cytometer system to characterize small EVs, i.e., with a diameter less than 200 nm. Using this method, we could evaluate different parasite-derived EV populations according to their distinct cargo by using antibody-free labeling. It further allows to closely monitor a sub-population of vesicles carrying parasitic DNA cargo. This ability paves the way to conducting a more 'educated' analysis of the various EV cargo components.

Tuberculosis's cargoman: bacteria load RNA into host extracellular vesicles

Tuberculosis remains one of the deadliest infectious diseases worldwide. Mycobacterium tuberculosis (M.tb) has developed various mechanisms to manipulate the human host, in particular by disrupting the host phagosome and the immune response. It is becoming evident that secreted extracellular vesicles (EVs) are involved in the dynamic crosstalk between M.tb and the host cells. These vesicles shuttle different cargo components, such as RNA , lipids, and proteins, between cells. In this issue of EMBO Reports , Cheng and Schorey 1 describe a previously unknown EV‐mediated process, regulating M.tb RNA loading into EVs and their internalization by naïve macrophages. They identify the mycobacterial Sec2 secretion system as involved in RNA loading into EVs and show that secreted vesicles contain bacterial RNA that not only promotes IFN ‐β production upon entry into target cells, but also leads to M.tb clearance via the activation of the host's RIG ‐I/MAVS signaling pathway. Importantly, combined treatment with secreted EVs and antibiotics decreases bacterial load in a mouse model, improving lung pathology compared to treatment with antibiotics alone.

Monitoring Extracellular Vesicle Cargo Active Uptake by Imaging Flow Cytometry

Extracellular vesicles are essential for long distance cell–cell communication. They function as carriers of different compounds, including proteins, lipids and nucleic acids. Pathogens, like malaria parasites (Plasmodium falciparum, Pf), excel in employing vesicle release to mediate cell communication in diverse processes, particularly in manipulating the host response. Establishing research tools to study the interface between pathogen-derived vesicles and their host recipient cells will greatly benefit the scientific community. Here, we present an imaging flow cytometry (IFC) method for monitoring the uptake of malaria-derived vesicles by host immune cells. By staining different cargo components, we were able to directly track the cargo’s internalization over time and measure the kinetics of its delivery. Impressively, we demonstrate that this method can be used to specifically monitor the translocation of a specific protein within the cellular milieu upon internalization of parasitic cargo; namely, we were able to visually observe how uptaken parasitic Pf-DNA cargo leads to translocation of transcription factor IRF3 from the cytosol to the nucleus within the recipient immune cell. Our findings demonstrate that our method can be used to study cellular dynamics upon vesicle uptake in different host–pathogen and pathogen–pathogen systems.

Quantitative identification of senescent cells in aging and disease

Senescent cells are present in premalignant lesions and sites of tissue damage and accumulate in tissues with age. In vivo identification, quantification and characterization of senescent cells are challenging tasks that limit our understanding of the role of senescent cells in diseases and aging. Here, we present a new way to precisely quantify and identify senescent cells in tissues on a single‐cell basis. The method combines a senescence‐associated beta‐galactosidase assay with staining of molecular markers for cellular senescence and of cellular identity. By utilizing technology that combines flow cytometry with high‐content image analysis, we were able to quantify senescent cells in tumors, fibrotic tissues, and tissues of aged mice. Our approach also yielded the finding that senescent cells in tissues of aged mice are larger than nonsenescent cells. Thus, this method provides a basis for quantitative assessment of senescent cells and it offers proof of principle for combination of different markers of senescence. It paves the way for screening of senescent cells for identification of new senescence biomarkers, genes that bypass senescence or senolytic compounds that eliminate senescent cells, thus enabling a deeper understanding of the senescent state in vivo.

Very high background radiation areas of Ramsar, Iran: preliminary biological studies

People in some areas of Ramsar, a city in northern Iran, receive an annual radiation absorbed dose from background radiation that is up to 260 mSv y(-1), substantially higher than the 20 mSv y(-1) that is permitted for radiation workers. Inhabitants of Ramsar have lived for many generations in these high background areas. Cytogenetic studies show no significant differences between people in the high background compared to people in normal background areas. An in vitro challenge dose of 1.5 Gy of gamma rays was administered to the lymphocytes, which showed significantly reduced frequency for chromosome aberrations of people living in high background compared to those in normal background areas in and near Ramsar. Specifically, inhabitants of high background radiation areas had about 56% the average number of induced chromosomal abnormalities of normal background radiation area inhabitants following this exposure. This suggests that adaptive response might be induced by chronic exposure to natural background radiation as opposed to acute exposure to higher (tens of mGy) levels of radiation in the laboratory. There were no differences in laboratory tests of the immune systems, and no noted differences in hematological alterations between these two groups of people.

The effects of changing atmospheric oxygen concentrations and background radiation levels on radiogenic DNA damage rates

Both background radiation levels and atmospheric oxygen concentrations have changed dramatically over the history of life on earth. Because oxygen has a strong modifying influence on radiogenic mutation rates, these factors must be considered jointly to determine changes in radiogenic mutation rates over time. Using accepted models that describe how both of these parameters have changed through time, we find that radiogenic mutation rates in organisms have fluctuated between about 1.5 to 2.5 times current levels through most of the history of life. The results of this study have interesting implications that may impact our understanding of how modern organisms respond to radiation damage and of models that use molecular clocks to date species divergence times. It is also possible that changing oxygen levels have served to buffer mutation rate changes that result from changes in background radiation levels over time.

Radiation safety at the University of Rochester's Laser Fusion Research Facility

The fusion research conducted at the Laboratory for Laser Energetics requires large amounts of tritium and generates brief but very high, neutron fluxes. This raises a number of radiological concerns that have been satisfactorily addressed via a combination of engineering controls, training, and administrative controls. These problems encountered and our solutions to them are described in this paper.

Radiation safety considerations for large, multi-user laboratories

Many research institutions are adding new laboratory space in the form of large, multi-user rooms with an open architecture. Unfortunately, many of the features that make such rooms attractive to researchers make them difficult to manage from a radiation safety perspective. In particular, coping with radiological incidents and enforcing radiation safety standards are difficult when several research teams share a common room. This paper discusses the problems noted in such laboratories at the University of Rochester and Yale University and describes the manner in which some of these problems have been addressed.

Conducting subsurface soil and groundwater radiological investigations: a case study from the University of Rochester

The University of Rochester performed subsurface soil and groundwater radiological assessments in the vicinity of a research building to investigate for contamination from possible past releases of licensed radioactive materials. During the course of this investigation, our contractors developed candidate well drilling and sampling plans. The University of Rochester selected one of these plans, which was subsequently modified due to unexpected costs associated with the local geology. This paper describes the factors that were considered during the development and implementation of the drilling and sampling plan, as well as other considerations and concepts that are inherent in many environmental investigations.

University of Rochester laboratory inspection checklist

In early 1999, the University of Rochester significantly revised our laboratory inspection program. As part of this revision, we developed a new checklist to be used during laboratory inspections to help promote consistency between inspections and between inspectors.

Determining and reporting fetal radiation exposure from diagnostic radiation

Pregnant women are sometimes exposed to diagnostic ionizing radiation for any number of legitimate medical reasons. When this occurs, it is important to perform an accurate fetal dose estimate using standard methodologies as quickly as possible and to convey this information to the woman's physician, along with a summary of appropriate published medical guidelines. This will provide the physician and the patient with the information necessary to make an informed decision regarding the potential impact of this radiation exposure on the pregnancy. At the same time, it is important to recognize that not all pregnancies end well, and there is a finite chance that legal action could ensue because of this, even if radiation exposure was negligible. For this reason, it is also important to make sure that standard, accepted protocols are followed in calculating radiation exposure and the health physicist provide advice only in his or her areas of competence.

Apparent high tritium intake by a radiation worker at the University of Rochester

On 20 September 1999, a urine sample submitted by a University of Rochester radiation worker was noted to have a count rate of about 759,500 disintegrations per minute (dpm) per milliliter as analyzed on the Radiation Safety Unit (RSU) Packard liquid sintillation counter. The sample was recounted that day with variable results but each time indicating several hundred thousand dpm of activity present. Calculations indicated this corresponded to a whole-body uptake of about 518 MBq (14 nmCi) and a whole-body dose of about 10 msv (1 rem). An investigation indicated it was unlikely for these analytical results to indicate an actual uptake of tritium and suggested the results were most likely due to chemical luminescence in the sample. Accordingly, no dose was assigned to this worker from the exposure.

Calculations of background beta-gamma radiation dose through geologic time

Life on earth is exposed to a background level of ionizing radiation from a number of sources, including beta and gamma radiation from geologic and biologic materials. Radiation dose from geologic emitters has changed because of the chemical evolution of the continental crust, changes in the relative abundances of 235U and 238U, and the radioactive decay of uranium, thorium, and 40K with time. The radiation dose from internal 40K has decreased by a factor of about eight because of changes in the activity concentration of 40K in potassium over the past 4 billion years. Radiation exposure from geologic materials has decreased from about 1.6 mGy y(-1) to 0.66 mGy y(-1) over the past 4 billion years, and radiation exposure to an organism with a potassium concentration of 250 mmol L(-1) has decreased from about 5.5 to about 0.70 mGy y(-1). Accordingly, background radiation exposure from these two sources has dropped from about 7.0 to 1.35 mGy y(-1) during the time life has existed on Earth. The conservative nature of mutation repair mechanisms in modern organisms suggest that these mechanisms may have evolved in the distant past and that organisms may retain some of the capability of efficiently repairing damage from higher radiation levels than exist at present.