Operational tolerance research in liver transplantation: a bibliometric analysis using a new web resource.

Background: Operational tolerance in liver transplantation (OT-LT), defined as the graft survival with normal function in absence of immunosuppression, has been a field of intense research since the 1980s. Thereafter, tens of clinical trials and hundreds of articles have been published, making it challenging for researchers to assimilate all the information, more so outside of their disciplines. The aim of the present study was to analyze the research in OT-LT through a new web tool (https://tolerance.imib.es). Methods: We have developed a web resource that allowed the identification of the present trends and potential research avenues in OL-LT, an overview biomedical terms that were most often cited, including which journals published the most articles, and an advanced search engine that exploited all the information in these publications. Results: A total of 734 studies were analyzed until November 2023, with a mean of 15 articles published per year, a total sum of 3,751 impact factor points and a total of 26,542 citations. The analysis of citations allowed us to establish a ranking of the most prolific countries, authors, journals and institutions, in addition to the most influential publications in OT-LT. Likewise, keyword and co-occurrence analyses answered which themes involving OT-LT are the most popular, whereas cooperation analysis showed that principal authors in OT-LT form a network, although the lack of international cooperation, especially with regard to clinical trials, appears to be one of the main challenges. Conclusion: Despite its limitations, our web tool will allow both OT-LT expert and novel researchers to be able to draw a comprehensive picture of the past, present and future of OT-LT research.

Purinergic P2X7 receptor expression increases in leukocytes from intra-abdominal septic patients.

Inflammation is a tightly coordinated response of the host immune system to bacterial and viral infections, triggered by the production of inflammatory cytokines. Sepsis is defined as a systemic inflammatory response followed by immunosuppression of the host and organ dysfunction. This imbalance of the immune response increases the risk of mortality of patients with sepsis, making it a major problem for critical care units worldwide. The P2X7 receptor plays a crucial role in activating the immune system by inducing the activation of peripheral blood mononuclear cells. In this study, we analyzed a cohort of abdominal origin septic patients and found that the expression of the P2X7 receptor in the plasma membrane is elevated in the different subsets of lymphocytes. We observed a direct relationship between the percentage of P2X7-expressing lymphocytes and the early inflammatory response in sepsis. Additionally, in patients whose lymphocytes presented a higher percentage of P2X7 surface expression, the total lymphocytes populations proportionally decreased. Furthermore, we found a correlation between elevated soluble P2X7 receptors in plasma and inflammasome-dependent cytokine IL-18. In summary, our work demonstrates that P2X7 expression is highly induced in lymphocytes during sepsis, and this correlates with IL-18, along with other inflammatory mediators such as IL-6, IL-8, and procalcitonin.

Polyphenols as NLRP3 inflammasome modulators in cardiometabolic diseases: a review of in vivo studies.

The nucleotide-binding domain and leucine-rich repeat containing receptors (NLRs) are components of the innate immune system, important in coordinating the inflammatory response. Among them, NLRP3 can form inflammasomes, multiprotein complexes activating the inflammatory caspase-1 and leading, through a cell death-mediated signaling cascade, to the release of several proinflammatory cytokines. Dietary polyphenols, plant secondary metabolites, have been reported to exhibit anti-inflammatory properties, although studies have focused most on their effect on the expression of the final circulating cytokines rather than on the upstream signals activating the NLRP3 inflammasome. The present review explores current knowledge on the potential of dietary polyphenols to regulate the whole NLRP3 inflammasome pathway, in the context of cardiometabolic pathologies (obesity, cardiovascular diseases, type 2 diabetes and non-alcoholic fatty liver disease), based on in vivo studies. A clear tendency towards a decrease in the expression of the whole NLRP3 inflammasome signaling pathway when several animal models were supplemented with polyphenols was observed, commonly showing a dose-response effect; these modifications were concomitant with clinical improvements in the pathologies. Nevertheless, the diversity of doses used, the disparity in polyphenol structures tested and, particularly, the scarce clinical trials and exploration of mechanisms of action show the need to develop further research on the topic.

A New Functional Food Ingredient Obtained from Aloe ferox by Spray Drying.

Aloe mucilages of Aloe ferox (A. ferox) and Aloe vera (A. vera) were spray-dried (SD) at 150, 160 and 170 °C. Polysaccharide composition, total phenolic compounds (TPC), antioxidant capacity and functional properties (FP) were determined. A. ferox polysaccharides were comprised mainly of mannose, accounting for >70% of SD aloe mucilages; similar results were observed for A. vera. Further, an acetylated mannan with a degree of acetylation >90% was detected in A. ferox by 1H NMR and FTIR. SD increased the TPC as well as the antioxidant capacity of A. ferox measured by both ABTS and DPPH methods, in particular by ~30%, ~28% and ~35%, respectively, whereas in A. vera, the antioxidant capacity measured by ABTS was reduced (>20%) as a consequence of SD. Further, FP, such as swelling, increased around 25% when A. ferox was spray-dried at 160 °C, while water retention and fat adsorption capacities exhibited lower values when the drying temperature increased. The occurrence of an acetylated mannan with a high degree of acetylation, together with the enhanced antioxidant capacity, suggests that SD A. ferox could be a valuable alternative raw material for the development of new functional food ingredients based on Aloe plants.

Harnessing the Vnn1 pantetheinase pathway boosts short chain fatty acids production and mucosal protection in colitis.

OBJECTIVE: In the management of patients with IBD, there is a need to identify prognostic markers and druggable biological pathways to improve mucosal repair and probe the efficacy of tumour necrosis factor alpha biologics. Vnn1 is a pantetheinase that degrades pantetheine to pantothenate (vitamin B5, a precursor of coenzyme A (CoA) biosynthesis) and cysteamine. Vnn1 is overexpressed by inflamed colonocytes. We investigated its contribution to the tolerance of the intestinal mucosa to colitis-induced injury. DESIGN: We performed an RNA sequencing study on colon biopsy samples from patients with IBD stratified according to clinical severity and modalities of treatment. We generated the VIVA mouse transgenic model, which specifically overexpresses Vnn1 on intestinal epithelial cells and explored its susceptibility to colitis. We developed a pharmacological mimicry of Vnn1 overexpression by administration of Vnn1 derivatives. RESULTS: VNN1 overexpression on colonocytes correlates with IBD severity. VIVA mice are resistant to experimentally induced colitis. The pantetheinase activity of Vnn1 is cytoprotective in colon: it enhances CoA regeneration and metabolic adaptation of colonocytes; it favours microbiota-dependent production of short chain fatty acids and mostly butyrate, shown to regulate mucosal energetics and to be reduced in patients with IBD. This prohealing phenotype is recapitulated by treating control mice with the substrate (pantethine) or the products of pantetheinase activity prior to induction of colitis. In severe IBD, the protection conferred by the high induction of VNN1 might be compromised because its enzymatic activity may be limited by lack of available substrates. In addition, we identify the elevation of indoxyl sulfate in urine as a biomarker of Vnn1 overexpression, also detected in patients with IBD. CONCLUSION: The induction of Vnn1/VNN1 during colitis in mouse and human is a compensatory mechanism to reinforce the mucosal barrier. Therefore, enhancement of vitamin B5-driven metabolism should improve mucosal healing and might increase the efficacy of anti-inflammatory therapy.

High-Intensity Ultrasound Processing Enhances the Bioactive Compounds, Antioxidant Capacity and Microbiological Quality of Melon (Cucumis melo) Juice.

The bioactive compounds, antioxidant capacity and microbiological quality of melon juice processed by high-intensity ultrasound (HIUS) were studied. Melon juice was processed at two ultrasound intensities (27 and 52 W/cm2) for two different processing times (10 and 30 min) using two duty cycles (30 and 75%). Unprocessed juice was taken as a control. Total carotenoids and total phenolic compounds (TPC) were the bioactive compounds analyzed while the antioxidant capacity was determined by DPPH, ABTS and FRAP assays. The microbiological quality was tested by counting the aerobic and coliforms count as well as molds and yeasts. Total carotenoids increased by up to 42% while TPC decreased by 33% as a consequence of HIUS processing regarding control juice (carotenoids: 23 µg/g, TPC: 1.1 mg GAE/g), gallic acid and syringic acid being the only phenolic compounds identified. The antioxidant capacity of melon juice was enhanced by HIUS, achieving values of 45% and 20% of DPPH and ABTS inhibition, respectively, while >120 mg TE/100 g was determined by FRAP assay. Further, the microbial load of melon juice was significantly reduced by HIUS processing, coliforms and molds being the most sensitive. Thus, the HIUS could be an excellent alternative supportive the deep-processing of melon products.

Diurnal Interplay between Epithelium Physiology and Gut Microbiota as a Metronome for Orchestrating Immune and Metabolic Homeostasis.

The behavior and physiology of most organisms are temporally coordinated and aligned with geophysical time by a complex interplay between the master and peripheral clocks. Disruption of such rhythmic physiological activities that are hierarchically organized has been linked to a greater risk of developing diseases ranging from cancer to metabolic syndrome. Herein, we summarize the molecular clockwork that is employed by intestinal epithelial cells to anticipate environmental changes such as rhythmic food intake and potentially dangerous environmental stress. We also discuss recent discoveries contributing to our understanding of how a proper rhythm of intestinal stem cells may achieve coherence for the maintenance of tissue integrity. Emerging evidence indicates that the circadian oscillations in the composition of the microbiota may operate as an important metronome for the proper preservation of intestinal physiology and more. Furthermore, in this review, we outline how epigenetic clocks that are based on DNA methylation levels may extensively rewire the clock-controlled functions of the intestinal epithelium that are believed to become arrhythmic during aging.

Gene Regulatory Network Dynamical Logical Models for Plant Development.

Mathematical and computational approaches that integrate and model the concerted action of multiple genetic and nongenetic components holding highly nonlinear interactions are fundamental for the study of developmental processes. Among these, gene regulatory network (GRN) dynamical models are very useful to understand how diverse types of regulatory constraints restrict the multigene expression patterns that characterize different cell fates. In this chapter we present a hands-on approach to model GRN dynamics, taking as a working example a well-curated and experimentally grounded GRN developmental module proposed by our group: the flower organ specification gene regulatory network (FOS-GRN). We demonstrate how to build and analyze a GRN model according to the following steps: (1) integration of molecular genetic data and formulation of logical rules specifying the dynamic behavior of each gene; (2) determination of steady states (attractors) corresponding to each cell type; (3) validation of the GRN model; and (4) extension of the deterministic model with the inclusion of stochasticity in order to model cell-state transitions dependent on noise due to fluctuations of the involved gen products. The methodologies explained here in detail can be applied to any other developmental module.

CD14 release induced by P2X7 receptor restricts inflammation and increases survival during sepsis.

P2X7 receptor activation induces the release of different cellular proteins, such as CD14, a glycosylphosphatidylinositol (GPI)-anchored protein to the plasma membrane important for LPS signaling via TLR4. Circulating CD14 has been found at elevated levels in sepsis, but the exact mechanism of CD14 release in sepsis has not been established. Here, we show for first time that P2X7 receptor induces the release of CD14 in extracellular vesicles, resulting in a net reduction in macrophage plasma membrane CD14 that functionally affects LPS, but not monophosphoryl lipid A, pro-inflammatory cytokine production. Also, we found that during a murine model of sepsis, P2X7 receptor activity is important for maintaining elevated levels of CD14 in biological fluids and a decrease in its activity results in higher bacterial load and exacerbated organ damage, ultimately leading to premature deaths. Our data reveal that P2X7 is a key receptor for helping to clear sepsis because it maintains elevated concentrations of circulating CD14 during infection.

When the immune system detects an infection, it often launches an inflammatory response to fight off the disease. This defense mechanism is activated by a cascade of signaling molecules that can aggravate inflammation, causing it to damage the body's own tissues and organs. This life-threatening reaction is referred to as sepsis, and kills around 11 million people each year. New approaches are therefore needed to help alleviate the damage caused by this condition. The inflammatory response is often triggered by proteins called receptors, which sit on the surface of immune cells. When these receptors are activated, they induce cells to secrete proteins that travel around the body and activate immune cells that can eliminate the infection. In 2016, a group of researchers showed that a receptor called P2X7 stimulates the release of a signaling molecule called CD14. Patients with sepsis often have elevated amounts of CD14 in their bloodstream. Yet, it remained unclear what causes this rise in CD14 and what role this molecule plays in the development of sepsis. Now, Alarcón-Vila et al. ­ including some of the researchers involved in the 2016 study ­ have investigated the role of P2X7 in mice undergoing sepsis. This was done by puncturing the mice's intestines, causing bacteria to leak out and initiate an over-active immune response. Alarcón-Vila et al. found that mice lacking the P2X7 receptor had less CD14 and struggled to eliminate the bacterial infection from their system. This increase in bacteria caused excessive damage to the mice's organs, ultimately leading to premature death. These findings suggest that P2X7 plays an important role in preventing the onset of sepsis by helping maintain high levels of CD14 following infection. This result could help to identify new therapies that reduce the mortality rates of septic infections.

Multi-level gene regulatory network models to understand complex mechanisms underlying plant development.

Patterning in plant development is the emergent outcome of the feedback-based interplay between tissue-coupled intracellular regulatory networks and physicochemical fields. This interplay gives rise to dynamics that evolve on a wide spectrum of spatiotemporal scales. This imposes important challenges for computational approaches to model the dynamics of plant development. These challenges are being tackled in recent times by computational and mathematical advances that have made progress in the modelling of regulatory networks, as well as in approaches to couple the latter to physicochemical fields. Efforts in this direction are fundamental to identify the dynamical constraints that emerge from non-cellular autonomous activity in cell-fate decisions and patterning, and requires an understanding of how multi-level and multi-scale processes are coupled. Here, we discuss the use of multi-level modeling and simulation tools for the study of multicellular systems, with emphasis on plants. As illustrative examples, we discuss recent works elucidating the mechanisms that underlie patterning in the root meristem of Arabidopsis thaliana, and in plant responses to environmental conditions.

Severe Autoinflammatory Manifestations and Antibody Deficiency Due to Novel Hypermorphic PLCG2 Mutations.

Autoinflammatory diseases (AIDs) were first described as clinical disorders characterized by recurrent episodes of seemingly unprovoked sterile inflammation. In the past few years, the identification of novel AIDs expanded their phenotypes toward more complex clinical pictures associating vasculopathy, autoimmunity, or immunodeficiency. Herein, we describe two unrelated patients suffering since the neonatal period from a complex disease mainly characterized by severe sterile inflammation, recurrent bacterial infections, and marked humoral immunodeficiency. Whole-exome sequencing detected a novel, de novo heterozygous PLCG2 variant in each patient (p.Ala708Pro and p.Leu845_Leu848del). A clear enhanced PLCγ2 activity for both variants was demonstrated by both ex vivo calcium responses of the patient's B cells to IgM stimulation and in vitro assessment of PLC activity. These data supported the autoinflammation and PLCγ2-associated antibody deficiency and immune dysregulation (APLAID) diagnosis in both patients. Immunological evaluation revealed a severe decrease of immunoglobulins and B cells, especially class-switched memory B cells, with normal T and NK cell counts. Analysis of bone marrow of one patient revealed a reduced immature B cell fraction compared with controls. Additional investigations showed that both PLCG2 variants activate the NLRP3-inflammasome through the alternative pathway instead of the canonical pathway. Collectively, the evidences here shown expand APLAID diversity toward more severe phenotypes than previously reported including dominantly inherited agammaglobulinemia, add novel data about its genetic basis, and implicate the alternative NLRP3-inflammasome activation pathway in the basis of sterile inflammation.

Assessment of Cell Adhesion After Purinoceptor Activation.

Cell adhesion is a characteristic feature of phagocytic myeloid cells, which is important for several inflammatory processes, such as migration, invasion, and proliferation. Purinergic signaling in macrophages plays an important role in cell adhesion of this cell type to different extracellular substrates. This protocol describes the use of two different detection methods to quantify cell adhesion upon P2X7 receptor activation by extracellular ATP.

P2X7 receptor induces mitochondrial failure in monocytes and compromises NLRP3 inflammasome activation during sepsis.

Sepsis is characterized by a systemic inflammatory response followed by immunosuppression of the host. Metabolic defects and mitochondrial failure are common in immunocompromised patients with sepsis. The NLRP3 inflammasome is important for establishing an inflammatory response after activation by the purinergic P2X7 receptor. Here, we study a cohort of individuals with intra-abdominal origin sepsis and show that patient monocytes have impaired NLRP3 activation by the P2X7 receptor. Furthermore, most sepsis-related deaths are among patients whose NLRP3 activation is profoundly altered. In monocytes from sepsis patients, the P2X7 receptor is associated with mitochondrial dysfunction. Furthermore, activation of the P2X7 receptor results in mitochondrial damage, which in turn inhibits NLRP3 activation by HIF-1α. We show that mortality increases in a mouse model of sepsis when the P2X7 receptor is activated in vivo. These data reveal a molecular mechanism initiated by the P2X7 receptor that contributes to NLRP3 impairment during infection.

Modeling the Epigenetic Landscape in Plant Development.

Computational mechanistic models enable a systems-level understanding of plant development by integrating available molecular experimental data and simulating their collective dynamical behavior. Boolean gene regulatory network dynamical models have been extensively used as a qualitative modeling framework for such purpose. More recently, network modeling protocols have been extended to model the epigenetic landscape associated with gene regulatory networks. In addition to understanding the concerted action of interconnected genes, epigenetic landscape models aim to uncover the patterns of cell state transition events that emerge under diverse genetic and environmental background conditions. In this chapter we present simple protocols that naturally extend gene regulatory network modeling and demonstrate their use in modeling plant developmental processes under the epigenetic landscape framework. We focus on conceptual clarity and practical implementation, providing directions to the corresponding technical literature. The protocols presented here can be applied to any well-characterized gene regulatory network in plants, animals, or human disease.

Medical Systems Biology.

The aim of this volume is to encourage the use of systems-level methodologies to contribute to the improvement of human-health . We intend to motivate biomedical researchers to complement their current theoretical and empirical practice with up-to-date systems biology conceptual approaches. Our perspective is based on the deep understanding of the key biomolecular regulatory mechanisms that underlie health, as well as the emergence and progression of human-disease . We strongly believe that the contemporary systems biology perspective opens the door to the effective development of novel methodologies to the improvement of prevention . This requires a deeper and integrative understanding of the involved underlying systems-level mechanisms. In order to explain our proposal in a simple way, in this chapter we privilege the conceptual exposition of our chosen framework over formal considerations. The formal exposition of our proposal will be expanded and discussed later in the next chapters.

Modeling Procedures.

Being concerned by the understanding of the mechanism underlying chronic degenerative diseases , we presented in the previous chapter the medical systems biology conceptual framework that we present for that purpose in this volume. More specifically, we argued there the clear advantages offered by a state-space perspective when applied to the systems-level description of the biomolecular machinery that regulates complex degenerative diseases. We also discussed the importance of the dynamical interplay between the risk factors and the network of interdependencies that characterizes the biochemical, cellular, and tissue-level biomolecular reactions that underlie the physiological processes in health and disease. As we pointed out in the previous chapter, the understanding of this interplay (articulated around cellular phenotypic plasticity properties, regulated by specific kinds of gene regulatory networks) is necessary if prevention is chosen as the human-health improvement strategy (potentially involving the modulation of the patient's lifestyle). In this chapter we provide the medical systems biology mathematical and computational modeling tools required for this task.

Case Studies.

The aim of this chapter is to illustrate the modeling procedures discussed in the previous chapter via three well-chosen examples.

Lytic cell death induced by melittin bypasses pyroptosis but induces NLRP3 inflammasome activation and IL-1ß release.

The nucleotide-binding domain and leucine-rich repeat-containing receptor with a pyrin domain 3 (NLRP3) inflammasome is a sensor for different types of infections and alterations of homeostatic parameters, including abnormally high levels of the extracellular nucleotide ATP or crystallization of different metabolites. All NLRP3 activators trigger a similar intracellular pathway, where a decrease in intracellular K+ concentration and permeabilization of plasma membrane are key steps. Cationic amphipathic antimicrobial peptides and peptide toxins permeabilize the plasma membrane. In fact, some of them have been described to activate the NLRP3 inflammasome. Among them, the bee venom antimicrobial toxin peptide melittin is known to elicit an inflammatory reaction via the NLRP3 inflammasome in response to bee venom. Our study found that melittin induces canonical NLRP3 inflammasome activation by plasma membrane permeabilization and a reduction in the intracellular K+ concentration. Following melittin treatment, the apoptosis-associated speck-like protein, an adaptor protein with a caspase recruitment domain (ASC), was necessary to activate caspase-1 and induce IL-1ß release. However, cell death induced by melittin prevented the formation of large ASC aggregates, amplification of caspase-1 activation, IL-18 release and execution of pyroptosis. Therefore, melittin-induced activation of the NLRP3 inflammasome results in an attenuated inflammasome response that does not result in caspase-1 dependent cell death.

A novel Pyrin-Associated Autoinflammation with Neutrophilic Dermatosis mutation further defines 14-3-3 binding of pyrin and distinction to Familial Mediterranean Fever.

OBJECTIVE: Pyrin-Associated Autoinflammation with Neutrophilic Dermatosis (PAAND) is a recently described monogenic autoinflammatory disease. The causal p.S242R MEFV mutation disrupts a binding motif of the regulatory 14-3-3 proteins within pyrin. Here, we investigate a family with clinical features consistent with PAAND in whom the novel p.E244K MEFV mutation, located in the +2 site of the 14-3-3 binding motif in pyrin, has been found. METHODS: Multiplex cytokine analyses were performed on p.E244K patient and control serum. Peripheral blood mononuclear cells were stimulated ex vivo with lipopolysaccharide (LPS). In vitro, inflammasome complex formation was evaluated by flow cytometry of Apoptosis-associated Speck-like protein containing a Caspase recruitment domain (ASC) specks. Interleukin-1ß (IL-1ß) and IL-18 production was quantified by ELISA. The ability of the p.E244K pyrin mutation to interact with 14-3-3 was assessed by immunoprecipitation. RESULTS: PAAND p.E244K patient serum displayed a different cytokine profile compared with patients with Familial Mediterranean Fever (FMF). In overexpression models, p.E244K pyrin was associated with decreased 14-3-3 binding and increased ASC speck formation. THP-1 monocytes expressing PAAND pyrin mutations demonstrated spontaneous caspase-1-dependent IL-1ß and IL-18 secretion, as well as cell death, which were significantly greater than those of wild-type and the FMF-associated mutation p.M694V. CONCLUSION: In PAAND, disruption of the +2 position of a 14-3-3 binding motif in pyrin results in its constitutive activation, with spontaneous production of IL-1ß and IL-18, associated with inflammatory cell death. The altered serum cytokine profile may explain the different clinical features exhibited by PAAND patients compared with those with FMF.

Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation, and Prediction.

Mathematical models based on dynamical systems theory are well-suited tools for the integration of available molecular experimental data into coherent frameworks in order to propose hypotheses about the cooperative regulatory mechanisms driving developmental processes. Computational analysis of the proposed models using well-established methods enables testing the hypotheses by contrasting predictions with observations. Within such framework, Boolean gene regulatory network dynamical models have been extensively used in modeling plant development. Boolean models are simple and intuitively appealing, ideal tools for collaborative efforts between theorists and experimentalists. In this chapter we present protocols used in our group for the study of diverse plant developmental processes. We focus on conceptual clarity and practical implementation, providing directions to the corresponding technical literature.