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Resolving trained immunity with systems biology.
Koeken, VACM, van Crevel, R, Netea, MG, Li, Y
European journal of immunology. 2021;(4):773-784
Abstract
Trained immunity is characterized by long-term functional reprogramming of innate immune cells following challenge with pathogens or microbial ligands during infection or vaccination. This cellular reprogramming leads to increased responsiveness upon restimulation, and is mediated through epigenetic and metabolic modifications. In this review, we describe how molecular mechanisms underlying trained immunity, for example, induced by β-glucan or Bacille Calmette-Guérin (BCG) vaccination, can be investigated by using and integrating different layers of information including genome, epigenome, transcriptome, proteome, metabolome, microbiome, immune cell phenotyping, and function. We also describe the most commonly used experimental and computational techniques. Finally, we provide a number of examples of how a systems biology approach was applied to study trained immunity to understand interindividual variation or the complex interplay between molecular layers. In conclusion, trained immunity represents an opportunity for regulating innate immune function, and understanding the complex interplay of mechanisms that mediate trained immunity might enable us to employ it as a clinical tool in the future.
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Targeting extracellular nutrient dependencies of cancer cells.
Garcia-Bermudez, J, Williams, RT, Guarecuco, R, Birsoy, K
Molecular metabolism. 2020;:67-82
Abstract
BACKGROUND Cancer cells rewire their metabolism to meet the energetic and biosynthetic demands of their high proliferation rates and environment. Metabolic reprogramming of cancer cells may result in strong dependencies on nutrients that could be exploited for therapy. While these dependencies may be in part due to the nutrient environment of tumors, mutations or expression changes in metabolic genes also reprogram metabolic pathways and create addictions to extracellular nutrients. SCOPE OF REVIEW This review summarizes the major nutrient dependencies of cancer cells focusing on their discovery and potential mechanisms by which metabolites become limiting for tumor growth. We further detail available therapeutic interventions based on these metabolic features and highlight opportunities for restricting nutrient availability as an anti-cancer strategy. MAJOR CONCLUSIONS Strategies to limit nutrients required for tumor growth using dietary interventions or nutrient degrading enzymes have previously been suggested for cancer therapy. The best clinical example of exploiting cancer nutrient dependencies is the treatment of leukemia with l-asparaginase, a first-line chemotherapeutic that depletes serum asparagine. Despite the success of nutrient starvation in blood cancers, it remains unclear whether this approach could be extended to other solid tumors. Systematic studies to identify nutrient dependencies unique to individual tumor types have the potential to discover targets for therapy.
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Microbial Contribution to the Human Metabolome: Implications for Health and Disease.
Van Treuren, W, Dodd, D
Annual review of pathology. 2020;:345-369
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Abstract
The human gastrointestinal tract is home to an incredibly dense population of microbes. These microbes employ unique strategies to capture energy in this largely anaerobic environment. In the process of breaking down dietary- and host-derived substrates, the gut microbiota produce a broad range of metabolic products that accumulate to high levels in the gut. Increasingly, studies are revealing that these chemicals impact host biology, either by acting on cells within the gastrointestinal tract or entering circulation and exerting their effects at distal sites within the body. Given the high level of functional diversity in the gut microbiome and the varied diets that we consume, the repertoire of microbiota-derived molecules within our bodies varies dramatically across individuals. Thus, the microbes in our gut and the metabolic end products they produce represent a phenotypic lever that we can potentially control to develop new therapeutics for personalized medicine. Here, we review current understanding of how microbes in the gastrointestinal tract contribute to the molecules within our gut and those that circulate within our bodies. We also highlight examples of how these molecules affect host physiology and discuss potential strategies for controlling their production to promote human health and to treat disease.
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Metabolic phenotyping of malnutrition during the first 1000 days of life.
Mayneris-Perxachs, J, Swann, JR
European journal of nutrition. 2019;(3):909-930
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Abstract
Nutritional restrictions during the first 1000 days of life can impair or delay the physical and cognitive development of the individual and have long-term consequences for their health. Metabolic phenotyping (metabolomics/metabonomics) simultaneously measures a diverse range of low molecular weight metabolites in a sample providing a comprehensive assessment of the individual's biochemical status. There are a growing number of studies applying such approaches to characterize the metabolic derangements induced by various forms of early-life malnutrition. This includes acute and chronic undernutrition and specific micronutrient deficiencies. Collectively, these studies highlight the diverse and dynamic metabolic disruptions resulting from various forms of nutritional deficiencies. Perturbations were observed in many pathways including those involved in energy, amino acid, and bile acid metabolism, the metabolic interactions between the gut microbiota and the host, and changes in metabolites associated with gut health. The information gleaned from such studies provides novel insights into the mechanisms linking malnutrition with developmental impairments and assists in the elucidation of candidate biomarkers to identify individuals at risk of developmental shortfalls. As the metabolic profile represents a snapshot of the biochemical status of an individual at a given time, there is great potential to use this information to tailor interventional strategies specifically to the metabolic needs of the individual.
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Biomarkers of a Healthy Nordic Diet-From Dietary Exposure Biomarkers to Microbiota Signatures in the Metabolome.
Landberg, R, Hanhineva, K
Nutrients. 2019;(1)
Abstract
Whole diets and dietary patterns are increasingly highlighted in modern nutrition and health research instead of single food items or nutrients alone. The Healthy Nordic Diet is a dietary pattern typically associated with beneficial health outcomes in observational studies, but results from randomized controlled trials are mixed. Dietary assessment is one of the greatest challenges in observational studies and compliance is a major challenge in dietary interventions. During the last decade, research has shown the great importance of the gut microbiota in health and disease. Studies have have both shown that the Nordic diet affects the gut microbiota and that the gut microbiota predicts the effects of such a diet. Rapid technique developments in the area of high-throughput mass spectrometry have enabled the large-scale use of metabolomics both as an objective measurement of dietary intake as well as in providing the final readout of the endogenous metabolic processes and the impact of the gut microbiota. In this review, we give an update on the current status on biomarkers that reflect a Healthy Nordic Diet or individual components thereof (food intake biomarkers), biomarkers that show the effects of a Healthy Nordic Diet and biomarkers reflecting the role of a Healthy Nordic Diet on the gut microbiota as well as how the gut microbiota or derived molecules may be used to predict the effects of a Healthy Nordic Diet on different outcomes.
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Review: Synovial Cell Metabolism and Chronic Inflammation in Rheumatoid Arthritis.
Falconer, J, Murphy, AN, Young, SP, Clark, AR, Tiziani, S, Guma, M, Buckley, CD
Arthritis & rheumatology (Hoboken, N.J.). 2018;(7):984-999
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Metabolomic studies of body fluids show that immune-mediated inflammatory diseases such as rheumatoid arthritis (RA) are associated with metabolic disruption. This is likely to reflect the increased bioenergetic and biosynthetic demands of sustained inflammation and changes in nutrient and oxygen availability in damaged tissue. The synovial membrane lining layer is the principal site of inflammation in RA. Here, the resident cells are fibroblast-like synoviocytes (FLS) and synovial tissue macrophages, which are transformed toward overproduction of enzymes that degrade cartilage and bone and cytokines that promote immune cell infiltration. Recent studies have shown metabolic changes in both FLS and macrophages from RA patients, and these may be therapeutically targetable. However, because the origins and subset-specific functions of synoviocytes are poorly understood, and the signaling modules that control metabolic deviation in RA synovial cells are yet to be explored, significant additional research is needed to translate these findings to clinical application. Furthermore, in many inflamed tissues, different cell types can forge metabolic collaborations through solute carriers in their membranes to meet a high demand for energy or biomolecules. Such relationships are likely to exist in the synovium and have not been studied. Finally, it is not yet known whether metabolic change is a consequence of disease or whether primary changes to cellular metabolism might underlie or contribute to the pathogenesis of early-stage disease. In this review article, we collate what is known about metabolism in synovial tissue cells and highlight future directions of research in this area.
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Early Programming of Obesity Throughout the Life Course: A Metabolomics Perspective.
Rauschert, S, Kirchberg, FF, Marchioro, L, Koletzko, B, Hellmuth, C, Uhl, O
Annals of nutrition & metabolism. 2017;(3):201-209
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Abstract
BACKGROUND Over the last decades, research on early life risk factors for obesity and its comorbidities in early life has gained attention within the field of developmental origins of health and diseases. Metabolomics studies that are trying to find early life biomarker and intervention targets for the early development of obesity and associated cardiovascular diseases could help break the inter-generational cycle of obesity. SUMMARY Metabolomics studies in the field of early programming are scarce and causality is lacking at this stage, as most of the studies are cross-sectional. The main metabolites in the focus of obesity are branched-chain and aromatic amino acids, long-chain polyunsaturated fatty acids, lysophosphatidylcholines, and sphingomyelins. Sex and puberty have not been considered in most of the biomarker studies, but show differences in the metabolite associations to obesity. Key Messages: There is still a lot unknown about the associations between early programming exposures, metabolite concentrations, and the development of obesity. The few studies focusing on this topic find similar metabolite classes in the same age groups being associated with rapid early growth or obesity; but due to differences in the methodological and statistical approaches, the single species often differ. Therefore, more research, preferably with standardized approaches, is needed.
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Effects of testosterone therapy on BMI, blood pressure, and laboratory profile of transgender men: a systematic review.
Velho, I, Fighera, TM, Ziegelmann, PK, Spritzer, PM
Andrology. 2017;(5):881-888
Abstract
Testosterone is the main hormonal agent used for cross-sex hormone therapy in female-to-male transgender persons. Our aim was to systematically review the literature concerning the effects of testosterone on body mass index (BMI), blood pressure, hematocrit, hemoglobin, lipid profile, and liver enzymes in transgender men. PUBMED and EMBASE were searched for studies published until March 2017. Studies were included if they reported interventions with any dose of testosterone and comparison of variables before and during treatment. Of 455 potentially eligible articles, 13 were reviewed. Study duration ranged from 6 to 60 months, sample size ranged from 12 to 97 patients, and the most common treatment was parenteral testosterone undecanoate 1000 mg/12 weeks. Slight but significant increases in BMI were reported (from 1.3 to 11.4%). Three out of seven studies assessing the impact of different testosterone formulations on blood pressure detected modest increases or clinically irrelevant changes in this variable. In another study, however, two patients developed hypertension, which was resolved after cessation of testosterone therapy. Decreases in HDL-cholesterol and increases in LDL-cholesterol were consistently observed. Eight studies observed a relationship between testosterone and increased hemoglobin (range: 4.9-12.5%) and hematocrit (range: 4.4-17.6%), but discontinuation of androgen therapy was not necessary. In one study, two patients developed erythrocytosis (hematocrit >52%) after 9 and 12 months of treatment. One study analyzing testosterone formulations observed smaller increases in hemoglobin and hematocrit with testosterone gel. Six studies assessing liver function showed slight or no changes. Overall, the quality of evidence was low, given the lack of randomized clinical/controlled trials and the small sample sizes. In conclusion, exogenous testosterone administration to transgender men was associated with modest increases in BMI, hemoglobin/hematocrit, and LDL-cholesterol, and with decreases in HDL-cholesterol. Long-term studies are needed to assess the long-term risks of testosterone therapy, particularly as they relate to cardiometabolic risks such as diabetes, dyslipidemia and the metabolic syndrome.
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Food Fight: Role of Itaconate and Other Metabolites in Antimicrobial Defense.
Luan, HH, Medzhitov, R
Cell metabolism. 2016;(3):379-387
Abstract
Itaconate is a newly discovered mammalian metabolite bearing significant implications for our understanding of cellular immunometabolism and antimicrobial defense. Here, we explore recent findings regarding the role of itaconate in the innate immune response and highlight the emerging principle that metabolites can have distinct immunological functions independent of bioenergetics.
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Nutrimetabonomics: nutritional applications of metabolic profiling.
Swann, JR, Claus, SP
Science progress. 2014;(Pt 1):41-7
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Abstract
An individual's metabolic phenotype, and ultimately health, is significantly influenced by complex interactions between their genes and the diet. Studying these associations and their downstream biochemical consequences has proven extremely challenging using traditional hypothesis-led strategies. Metabonomics, a systems biology approach, allows the global metabolic response of biological systems to stimuli to be characterised. Through the application of this approach to nutritional-based research, nutrimetabonomics, the biochemical response to dietary inputs is being investigated at greater levels of resolution. This has allowed novel insights to be gained regarding intricate diet-gene interactions and their consequences for health and disease. In this review, we present some of the latest research exploring how nutrimetabonomics can assist in the elucidation of novel biomarkers of dietary behaviour and provide new perspectives on diet-health relationships. The use of this approach to study the metabolic interplay between the gut microbiota and the host is also explored.