Persistent complement dysregulation with signs of thromboinflammation in active Long Covid

Long Covid is a debilitating condition of unknown etiology. We performed multimodal proteomics analyses of blood serum from COVID-19 patients followed up to 12 months after confirmed severe acute respiratory syndrome coronavirus 2 infection. Analysis of >6500 proteins in 268 longitudinal samples revealed dysregulated activation of the complement system, an innate immune protection and homeostasis mechanism, in individuals experiencing Long Covid. Thus, active Long Covid was characterized by terminal complement system dysregulation and ongoing activation of the alternative and classical complement pathways, the latter associated with increased antibody titers against several herpesviruses possibly stimulating this pathway. Moreover, markers of hemolysis, tissue injury, platelet activation, and monocyte-platelet aggregates were increased in Long Covid. Machine learning confirmed complement and thromboinflammatory proteins as top biomarkers, warranting diagnostic and therapeutic interrogation of these systems.

Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy

Intratumoral immune cells are crucial for tumor control and antitumor responses during immunotherapy. Immune cell trafficking into tumors is mediated by binding of specific immune cell receptors to chemokines, a class of secreted chemotactic cytokines. To broadly characterize chemokine expression and function in melanoma, we used multiplexed mass cytometry-based imaging of protein markers and RNA transcripts to analyze the chemokine landscape and immune infiltration in metastatic melanoma samples. Tumors that lacked immune infiltration were devoid of most of the profiled chemokines and exhibited low levels of antigen presentation and markers of inflammation. Infiltrated tumors were characterized by expression of multiple chemokines. CXCL9 and CXCL10 were often localized in patches associated with dysfunctional T cells expressing the B lymphocyte chemoattractant CXCL13. In tumors with B cells but no B cell follicles, T cells were the sole source of CXCL13, suggesting that T cells play a role in B cell recruitment and potentially in B cell follicle formation. B cell patches and follicles were also enriched with TCF7⁺ naïve-like T cells, a cell type that is predictive of response to immune checkpoint blockade. Our data highlight the strength of targeted RNA and protein codetection to analyze tumor immune microenvironments based on chemokine expression and suggest that the formation of tertiary lymphoid structures may be accompanied by naïve and naïve-like T cell recruitment, which may contribute to antitumor activity.

Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data

Summary

Highly multiplexed imaging technologies enable spatial profiling of dozens of biomarkers in situ. Here, we describe cytomapper, a computational tool written in R, that enables visualization of pixel- and cell-level information obtained by multiplexed imaging. To illustrate its utility, we analysed 100 images obtained by imaging mass cytometry from a cohort of type 1 diabetes patients. In addition, cytomapper includes a Shiny application that allows hierarchical gating of cells based on marker expression and visualization of selected cells in corresponding images.

Availability and implementation

The cytomapper package can be installed via https://www.bioconductor.org/packages/release/bioc/html/cytomapper.html. Code for analysis and further instructions can be found at https://github.com/BodenmillerGroup/cytomapper_publication.

Supplementary information

Supplementary data are available at Bioinformatics online.

How mechanistic modelling supports decision making for the control of enzootic infectious diseases

Controlling enzootic diseases, which generate a large cumulative burden and are often unregulated, is needed for sustainable farming, competitive agri-food chains, and veterinary public health. We discuss the benefits and challenges of mechanistic epidemiological modelling for livestock enzootics, with particular emphasis on the need for interdisciplinary approaches. We focus on issues arising when modelling pathogen spread at various scales (from farm to the region) to better assess disease control and propose targeted options. We discuss in particular the inclusion of farmers' strategic decision-making, the integration of within-host scale to refine intervention targeting, and the need to ground models on data.

Identifying main drivers and testing control strategies for CCHFV spread

Crimean Congo Haemorrhagic Fever (CCHF) is an emerging zoonotic disease. The causative agent is a virus (CCHFV), mainly transmitted by ticks of the species Hyalomma marginatum in Eastern Europe and Turkey. In order to test potential scenarios for the control of pathogen spread, the basic reproduction number (R0) for CCHF was calculated. This calculation was based on a population dynamics model and parameter values from the literature for pathogen transmission. The tick population dynamics model takes into account the major processes involved and gives estimates for tick survival from one stage to the other and number of feeding ticks. It also considers the influence of abiotic (meteorological variables) and biotic factors (host densities) on model outputs, which were compared with data collected in Central Anatolia (Turkey). R0 computation was thereafter used to test control strategies and especially the effect of acaricide treatment. Simulation results indicate that such treatments could have valuable effects provided that the acaricide is applied regularly throughout the spring and summer, and over several years. Furthermore, a sensitivity analysis to abiotic and biotic factors showed that, even though temperature has a strong impact on model outputs, host (mainly hare) densities also play a role. The kind of model we have developed provides insight into the ability of different strategies to prevent and control disease spread and has proved its relevance when associated with field trials.

Snack food intake in ad libitum fed rats is triggered by the combination of fat and carbohydrates

Snack food like potato chips substantially contributes to energy intake in humans. In contrast to basic food, snacks are consumed additionally to other meals and may thereby lead to non-homeostatic energy intake. Snack food is also frequently associated with hedonic hyperphagia, a food intake independent from hunger. Analysis of brain activity patterns by manganese-enhanced MRI has previously revealed that the intake of potato chips in ad libitum fed rats strongly activates the reward system of the rat brain, which may lead to hedonic hyperphagia. The purpose of the present study was to develop a two-choice preference test to identify molecular determinants of snack food triggering extra food intake in ad libitum fed rats. Different kinds of test food were presented three times a day for 10 min each time. To minimize the influence of organoleptic properties, each test food was applied in a homogenous mixture with standard chow. Food intake as well as food intake-related locomotor activity were analyzed to evaluate the effects induced by the test foods in the two-choice preference test. In summary, fat (F), carbohydrates (CH), and a mixture of fat and carbohydrates (FCH) led to a higher food intake compared to standard chow. Notably, potato chip test food (PC) was highly significantly preferred over standard chow (STD) and also over their single main macronutrients F and CH. Only FCH induced an intake comparable to PC. Despite its low energy density, fat-free potato chip test food (ffPC) was also significantly preferred over STD and CH, but not over F, FCH, and PC. Thus, it can be concluded that the combination of fat and carbohydrates is a major molecular determinant of potato chips triggering hedonic hyperphagia. The applied two-choice preference test will facilitate future studies on stimulating and suppressive effects of other food components on non-homeostatic food intake.

Manganese-enhanced magnetic resonance imaging for mapping of whole brain activity patterns associated with the intake of snack food in ad libitum fed rats

Non-homeostatic hyperphagia, which is a major contributor to obesity-related hyperalimentation, is associated with the diet’s molecular composition influencing, for example, the energy content. Thus, specific food items such as snack food may induce food intake independent from the state of satiety. To elucidate mechanisms how snack food may induce non-homeostatic food intake, it was tested if manganese-enhanced magnetic resonance imaging (MEMRI) was suitable for mapping the whole brain activity related to standard and snack food intake under normal behavioral situation. Application of the MnCl₂ solution by osmotic pumps ensured that food intake was not significantly affected by the treatment. After z-score normalization and a non-affine three-dimensional registration to a rat brain atlas, significantly different grey values of 80 predefined brain structures were recorded in ad libitum fed rats after the intake of potato chips compared to standard chow at the group level. Ten of these areas had previously been connected to food intake, in particular to hyperphagia (e.g. dorsomedial hypothalamus or the anterior paraventricular thalamic nucleus) or to the satiety system (e.g. arcuate hypothalamic nucleus or solitary tract); 27 areas were related to reward/addiction including the core and shell of the nucleus accumbens, the ventral pallidum and the ventral striatum (caudate and putamen). Eleven areas associated to sleep displayed significantly reduced Mn²⁺-accumulation and six areas related to locomotor activity showed significantly increased Mn²⁺-accumulation after the intake of potato chips. The latter changes were associated with an observed significantly higher locomotor activity. Osmotic pump-assisted MEMRI proved to be a promising technique for functional mapping of whole brain activity patterns associated to nutritional intake under normal behavior.

Contingency contacting. Combining positive reinforcement and escape extinction procedures to treat persistent food refusal

Chronic food refusal has traditionally been treated with forced feeding and other physical prompting-based procedures when positive reinforcement procedures prove inadequate. Potential problems with such procedures, however, include exacerbation of feeding difficulties and health risks, as well as low parental approval and probability of implementation. Contingency contacting maximizes contact between oral acceptance and positive reinforcement, prevents escape functions of inappropriate behaviors, and requires minimal physical contact between feeder and child. Performances of two children exhibiting chronic food refusal were observed under baseline, positive reinforcement, and contingency contacting conditions. Positive reinforcement increased acceptance only slightly and did not change negative vocalization or interruption for one child. Contingency contacting rapidly increased acceptance and grams of food consumed, and decreased negative vocalization and interruption for both children. Withdrawal to positive reinforcement decreased acceptance for both children and grams consumed for one. Reinstituting contingency contacting rapidly increased acceptance and recovery of grams consumed for one child. Parental approval ratings and treatment and research implications are discussed.