Adenoviruses are common pathogens that have been engineered and used for medical purposes. While their recognition by innate immune cells such as macrophages and dendritic cells is well characterized, interactions with neutrophils remain poorly understood. Using cytometry,confocal and electron microscopy, we showed that neutrophils bind to antibody-coated adenoviruses and engulf them in a phagosome. Single-cell transcriptomic approach reveals that adenovirus phagocytosis activates a specific transcriptional program in neutrophils. It also triggers calcium entry, reactive oxygen species production in the phagosome and CXCL8 release. Moreover, 4 hours after adenovirus incubation, 50% of neutrophils undergo calcium- and RIPK3-dependent cell death, accompanied by Neutrophil Extracellular Trap emission. This rapid cell death impaired complete viral degradation after 3 hours, allowing residual adenoviruses to retain genomic expression potential in target cells Thus, our data suggest that, during adenoviral infection, the neutrophil response may promote a pro-inflammatory environment that could damage host tissues.

The endoplasmic reticulum (ER) is a highly dynamic intracellular organelle that forms close contact sites with other organelles and the plasma membrane. These membrane contact sites play essential roles in lipid exchange and calcium homeostasis. ER membrane proteins from the VAP, ORP, and ESYT families are key players in the formation and function of these contacts. Numerous interactions between these proteins are likely critical for their activity. We investigate the interactome between these protein families in live cells by analyzing two members from each family, using FRET between pairs of proteins labeled with fluorescent proteins. FRET is detected by Fluorescence Lifetime Imaging Microscopy. Our quantitative approach shows that all tested proteins clusterize and sometimes interact within their respective families and that their organization at the nano-meter scale can be disrupted by specific mutations or domain deletions. In particular, we show that the coiled-coil domains of ORP5 and ORP8 are required for the formation of both homomeric and heteromeric complexes. Moreover, we demonstrate that FRET-FLIM can detect intramolecular conformational changes in response to alterations in the cellular environment, such as variations in Ca2+concentra-tion, as observed for ESYT1. We also identify novel interfamily organization, including clustering between VAPB and ORP8, and between ESYT2 and ORP5/8. Finally, our approach highlights the broad interaction network (interactome) of VAPA/B and shows how various potential binding partners can influence FRET efficiency.

Fluorescence microscopy is commonly used to observe living cells and organisms, but it can induce phototoxicity, which may lead to erroneous interpretations. The primary cause of phototoxic cell damage is the production of reactive oxygen species (ROS), which can crosslink intracellular proteins and nucleic acids. Using profile microindentation and atomic force microscopy, we demonstrate that excitation of various fluorescent probes causes a rapid dose-dependent increase in cell stiffness across multiple cell types. This photostiffening effect explains why T cells loaded with the Fluo-4 calcium probe stop protruding within seconds after light excitation. We show that upon fluorophore excitation, ROS production is correlated with increased stiffness, and we reproduce the effect by incubating cells with H2O2 or the photosensitizer pheophorbide a. This study underscores the importance of controls and proposes photostiffening as a method for quantifying phototoxicity.

AlphaFold2 (AF2) and RoseTTaFold (RF) have revolutionized structural biology, serving as highly reliable and effective methods for predicting protein structures. This article explores their impact and limitations, focusing on their integration into experimental pipelines and their application in diverse protein classes, including membrane proteins, intrinsically disordered proteins (IDPs), and oligomers. In experimental pipelines, AF2 models help X-ray crystallography in resolving the phase problem, while complementarity with mass spectrometry and NMR data enhances structure determination and protein flexibility prediction. Predicting the structure of membrane proteins remains challenging for both AF2 and RF due to difficulties in capturing conformational ensembles and interactions with the membrane. Improvements in incorporating membrane-specific features and predicting the structural effect of mutations are crucial. For intrinsically disordered proteins, AF2's confidence score (pLDDT) serves as a competitive disorder predictor, but integrative approaches including molecular dynamics (MD) simulations or hydrophobic cluster analyses are advocated for accurate dynamics representation. AF2 and RF show promising results for oligomeric models, outperforming traditional docking methods, with AlphaFold-Multimer showing improved performance. However, some caveats remain in particular for membrane proteins. Real-life examples demonstrate AF2's predictive capabilities in unknown protein structures, but models should be evaluated for their agreement with experimental data. Furthermore, AF2 models can be used complementarily with MD simulations. In this Perspective, we propose a "wish list" for improving deep-learning-based protein folding prediction models, including using experimental data as constraints and modifying models with binding partners or post-translational modifications. Additionally, a meta-tool for ranking and suggesting composite models is suggested, driving future advancements in this rapidly evolving field.

The phagocyte NADPH oxidase (NOX2) is a key enzyme of the innate immune system generating superoxide anions (O2•-), precursors of reactive oxygen species. The NOX2 protein complex is composed of six subunits: two membrane proteins (gp91phox and p22phox) forming the catalytic core, three cytosolic proteins (p67phox, p47phox and p40phox) and a small GTPase Rac. The sophisticated activation mechanism of the NADPH oxidase relies on the assembly of cytosolic subunits with the membrane-bound components. A chimeric protein, called ‘Trimera’, composed of the essential domains of the cytosolic proteins p47phox (aa 1–286), p67phox (aa 1–212) and full-length Rac1Q61L, enables a constitutive and robust NOX2 activity in cells without the need of any stimulus. We employed Trimera as a single activating protein of the phagocyte NADPH oxidase in living cells and examined the consequences on the cell physiology of this continuous and long-term NOX activity. We showed that the sustained high level of NOX activity causes acidification of the intracellular pH, triggers apoptosis and leads to local peroxidation of lipids in the membrane. These local damages to the membrane correlate with the strong tendency of the Trimera to clusterize in the plasma membrane observed by FRET-FLIM microscopy.

Phagocytic cells form the first line of defense in an organism, engulfing microbial pathogens. Phagocytosis involves cell mechanical changes that are not yet well understood. Understanding these mechanical modifications promises to shed light on the immune processes that trigger pathological complications. Previous studies showed that phagocytes undergo a sequence of spreading events around their target followed by an increase in cell tension. Seemingly in contradiction, other studies observed an increase in cell tension concomitant with membrane expansion. Even though phagocytes are viscoelastic, few studies have quantified viscous changes during phagocytosis. It is also unclear whether cell lines behave mechanically similarly to primary neutrophils. We addressed the question of simultaneous versus sequential spreading and mechanical changes during phagocytosis by using immunoglobulin-G-coated 8- and 20-μm-diameter beads as targets. We used a micropipette-based single-cell rheometer to monitor viscoelastic properties during phagocytosis by both neutrophil-like PLB cells and primary human neutrophils. We show that the faster expansion of PLB cells on larger beads is a geometrical effect reflecting a constant advancing speed of the phagocytic cup. Cells become stiffer on 20- than on 8-μm beads, and the relative timing of spreading and stiffening of PLB cells depends on target size: on larger beads, stiffening starts before maximal spreading area is reached but ends after reaching maximal area. On smaller beads, the stiffness begins to increase after cells have engulfed the bead. Similar to PLB cells, primary cells become stiffer on larger beads but start spreading and stiffen faster, and the stiffening begins before the end of spreading on both bead sizes. Our results show that mechanical changes in phagocytes are not a direct consequence of cell spreading and that models of phagocytosis should be amended to account for causes of cell stiffening other than membrane expansion.

To accomplish their critical task of removing infected cells and fighting pathogens, leukocytes activate by forming specialized interfaces with other cells. The physics of this key immunological process are poorly understood, but it is important to understand them because leukocytes have been shown to react to their mechanical environment. Using an innovative micropipette rheometer, we show in three different types of leukocytes that, when stimulated by microbeads mimicking target cells, leukocytes become up to 10 times stiffer and more viscous. These mechanical changes start within seconds after contact and evolve rapidly over minutes. Remarkably, leukocyte elastic and viscous properties evolve in parallel, preserving a well-defined ratio that constitutes a mechanical signature specific to each cell type. Our results indicate that simultaneously tracking both elastic and viscous properties during an active cell process provides a new, to our knowledge, way to investigate cell mechanical processes. Our findings also suggest that dynamic immunomechanical measurements can help discriminate between leukocyte subtypes during activation.

Globularia alypum (GA), a plant of the Globulariacea family, has long been used as a traditional cure for inflammatory and metabolic illnesses. In addition to various in vitro model studies, the current work focuses on the antioxidant and anti-inflammatory properties of GA in human colon biopsies. The phenol components in GA aqueous extract (GAAE) were identified by Liquid Chromatography-Electrospray Ionization Mass Spectrometry. The antioxidant ability of GAAE was tested in vitro utilizing chemiluminescence and flow cytometry using fluorescent yeasts n conjunction with PLB-985-human myeloid leukemia cells. Experiments on human colon biopsies after a biopsy challenge with Escherichia coli-lipopolysaccharides aimed to see if GAAE had an anti-inflammatory impact on human colon inflammation. Western blotting was used to assess the expression of several inflammatory markers. According to the findings, GAAE had a significant influence on hydrogen peroxide and cellular reactive oxygen species. GAAE inhibited the activities of cyclooxygenase 2 and nuclear factor B in inflamed biopsies, indicating anti-inflammatory action. The present study is the first to show that GA has a beneficial effect on human colon inflammation, thanks to its significant antioxidant activity in vitro. According to these preliminary data, GA may be utilized to treat a range of human inflammatory illnesses.

Globularia alypum (GA), a plant of the Globulariacea family, has long been used as a traditional cure for inflammatory and metabolic illnesses. In addition to various in vitro model studies, the current work focuses on the antioxidant and anti-inflammatory properties of GA in human colon biopsies. The phenol components in GA aqueous extract (GAAE) were identified by Liquid Chromatography-Electrospray Ionization Mass Spectrometry. The antioxidant ability of GAAE was tested in vitro utilizing chemiluminescence and flow cytometry using fluorescent yeasts n conjunction with PLB-985-human myeloid leukemia cells. Experiments on human colon biopsies after a biopsy challenge with Escherichia coli-lipopolysaccharides aimed to see if GAAE had an anti-inflammatory impact on human colon inflammation. Western blotting was used to assess the expression of several inflammatory markers. According to the findings, GAAE had a significant influence on hydrogen peroxide and cellular reactive oxygen species. GAAE inhibited the activities of cyclooxygenase 2 and nuclear factor B in inflamed biopsies, indicating anti-inflammatory action. The present study is the first to show that GA has a beneficial effect on human colon inflammation, thanks to its significant antioxidant activity in vitro. According to these preliminary data, GA may be utilized to treat a range of human inflammatory illnesses.

Phagocytes, especially neutrophils, can produce reactive oxygen species (ROS), through the activation of the NADPH oxidase (NOX2). Although this enzyme is crucial for host-pathogen defense, ROS production by neutrophils can be harmful in several pathologies such as cardiovascular diseases or chronic pulmonary diseases. The ROS production by NOX2 involves the assembly of the cytosolic subunits (p67phox, p47phox, and p40phox) and Rac with the membrane subunits (gp91phox and p22phox). Many studies are devoted to the activation of NOX2. However, the mechanisms that cause NADPH oxidase deactivation and thus terminate ROS production are not well known. Here we investigated the ability of class I phosphoinositide 3-kinases (PI3Ks) to sustain NADPH oxidase activation. The NADPH oxidase activation was triggered by seeding neutrophil-like PLB-985 cells, or human neutrophils on immobilized fibrinogen. Adhesion of the neutrophils, mediated by β2 integrins, induced activation of the NADPH oxidase and translocation of the cytosolic subunits at the plasma membrane. Inhibition of class I PI3Ks, and especially PI3Kβ, terminated ROS production. This deactivation of NOX2 is due to the release of the cytosolic subunits, p67phox and p47phox from the plasma membrane. Overexpression of an active form of Rac 1 did not prevent the drop of ROS production upon inhibition of class I PI3Ks. Moreover, the phosphorylation of p47phox at S328, a potential target of kinases activated by the PI3K pathway, was unchanged. Our results indicate that the experimental downregulation of class I PI3K products triggers the plasma membrane NADPH oxidase deactivation. Release of p47phox from the plasma membrane may involve its PX domains that bind PI3K products.

Neutrophils are the first cells recruited at the site of infections, where they phagocytose the pathogens. Inside the phagosome, pathogens are killed by proteolytic enzymes that are delivered to the phagosome following granule fusion, and by reactive oxygen species (ROS) produced by the NADPH oxidase. The NADPH oxidase complex comprises membrane proteins (NOX2 and p22phox), cytoplasmic subunits (p67phox, p47phox, and p40phox) and the small GTPase Rac. These subunits assemble at the phagosomal membrane upon phagocytosis. In resting neutrophils the catalytic subunit NOX2 is mainly present at the plasma membrane and in the specific granules. We show here that NOX2 is also present in early and recycling endosomes in human neutrophils and in the neutrophil-like cell line PLB-985 expressing GFP-NOX2. In the latter cells, an increase in NOX2 at the phagosomal membrane was detected by live-imaging after phagosome closure, probably due to fusion of endosomes with the phagosome. Using super-resolution microscopy in PLB-985 WT cells, we observed that NOX2 forms discrete clusters in the plasma membrane. The number of clusters increased during frustrated phagocytosis. In PLB-985NCF1ΔGT cells that lack p47phox and do not assemble a functional NADPH oxidase, the number of clusters remained stable during phagocytosis. Our data suggest a role for p47phox and possibly ROS production in NOX2 recruitment at the phagosome.

The key purpose of phagocytosis is the destruction of pathogenic microorganisms. The phagocytes exert a wide array of killing mechanisms that allow mastering the vast majority of pathogens. One of these mechanisms consists in the production of reactive oxygen species inside the phagosome by a specific enzyme, the phagocyte NADPH oxidase. This enzyme is composed of 6 proteins that need to assemble to form a complex on the phagosomal membrane. Multiple signaling pathways tightly regulate the assembly. We briefly summarize key features of the enzyme and its regulation. We then focus on several related topics that address the activity of the NADPH oxidase during phagocytosis. Novel fluorescence microscopy techniques combined with fluorescent protein labeling of NADPH oxidase subunits opened the view on the structure and dynamics of these proteins in living cells. This combination revealed details of the role of anionic phospholipids in the control of phagosomal ROS production. It also added critical information to propose a 3D model of the complex between the cytosolic subunits prior to activation, in complement to other structural data on the oxidase.

Phagocyte NADPH oxidase produces superoxide anions, a precursor of reactive oxygen species (ROS) critical for host responses to microbial infections. However, uncontrolled ROS production contributes to inflammation, making NADPH oxidase a major drug target. It consists of two membranous (Nox2 and p22(phox)) and three cytosolic subunits (p40(phox), p47(phox), and p67(phox)) that undergo structural changes during enzyme activation. Unraveling the interactions between these subunits and the resulting conformation of the complex could shed light on NADPH oxidase regulation and help identify inhibition sites. However, the structures and the interactions of flexible proteins comprising several well-structured domains connected by intrinsically disordered protein segments are difficult to investigate by conventional techniques such as X-ray crystallography, NMR, or cryo-EM. Here, we developed an analytical strategy based on FRET-fluorescence lifetime imaging (FLIM) and fluorescence cross-correlation spectroscopy (FCCS) to structurally and quantitatively characterize NADPH oxidase in live cells. We characterized the inter- and intramolecular interactions of its cytosolic subunits by elucidating their conformation, stoichiometry, interacting fraction, and affinities in live cells. Our results revealed that the three subunits have a 1:1:1 stoichiometry and that nearly 100% of them are present in complexes in living cells. Furthermore, combining FRET data with small-angle X-ray scattering (SAXS) models and published crystal structures of isolated domains and subunits, we built a 3D model of the entire cytosolic complex. The model disclosed an elongated complex containing a flexible hinge separating two domains ideally positioned at one end of the complex and critical for oxidase activation and interactions with membrane components.

Redox biology has become a major issue in numerous areas of physiology. Reactive oxygen species (ROS) have a broad range of roles from signal transduction to growth control and cell death. To understand the nature of these roles, accurate measurement of the reactive compounds is required. An increasing number of tools for ROS detection is available; however, the specificity and sensitivity of these tools are often insufficient. Furthermore, their specificity has been rarely evaluated in complex physiological conditions. Many ROS probes are sensitive to environmental conditions in particular pH, which may interfere with ROS detection and cause misleading results. Accurate detection of ROS in physiology and pathophysiology faces additional challenges concerning the precise localization of the ROS and the timing of their production and disappearance. Certain ROS are membrane permeable, and certain ROS probes move across cells and organelles. Targetable ROS probes such as fluorescent protein-based biosensors are required for accurate localization. Here we analyze these challenges in more detail, provide indications on the strength and weakness of current tools for ROS detection, and point out developments that will provide improved ROS detection methods in the future. There is no universal method that fits all situations in physiology and cell biology. A detailed knowledge of the ROS probes is required to choose the appropriate method for a given biological problem. The knowledge of the shortcomings of these probes should also guide the development of new sensors.