Leishmania parasites alternate between extracellular promastigote stages in the insect vector and an obligate intracellular amastigote stage that proliferates within the phagolysosomal compartment of macrophages in the mammalian host. Most enzymes involved in Leishmania central carbon metabolism are constitutively expressed and stage-specific changes in energy metabolism remain poorly defined. Using 13C-stable isotope resolved metabolomics and 2H2O labelling, we show that amastigote differentiation is associated with reduction in growth rate and induction of a distinct stringent metabolic state. This state is characterized by a global decrease in the uptake and utilization of glucose and amino acids, a reduced secretion of organic acids and increased fatty acid β-oxidation. Isotopomer analysis showed that catabolism of hexose and fatty acids provide C4 dicarboxylic acids (succinate/malate) and acetyl-CoA for the synthesis of glutamate via a compartmentalized mitochondrial tricarboxylic acid (TCA) cycle. In vitro cultivated and intracellular amastigotes are acutely sensitive to inhibitors of mitochondrial aconitase and glutamine synthetase, indicating that these anabolic pathways are essential for intracellular growth and virulence. Lesion-derived amastigotes exhibit a similar metabolism to in vitro differentiated amastigotes, indicating that this stringent response is coupled to differentiation signals rather than exogenous nutrient levels. Induction of a stringent metabolic response may facilitate amastigote survival in a nutrient-poor intracellular niche and underlie the increased dependence of this stage on hexose and mitochondrial metabolism.
Background: The commercially available 10x Genomics protocol to generate droplet-based single cell RNA-seq (scRNA-seq) data is enjoying growing popularity among researchers. Fundamental to the analysis of such scRNA-seq data is the ability to cluster similar or same cells into non-overlapping groups. Many competing methods have been proposed for this task, but there is currently little guidance with regards to which method to use. Methods: Here we use one gold standard 10x Genomics dataset, generated from the mixture of three cell lines, as well as multiple silver standard 10x Genomics datasets generated from peripheral blood mononuclear cells to examine not only the accuracy but also running time and robustness of a dozen methods. Results: We found that Seurat outperformed other methods, although performance seems to be dependent on many factors, including the complexity of the studied system. Furthermore, we found that solutions produced by different methods have little in common with each other. Conclusions: In light of this we conclude that the choice of clustering tool crucially determines interpretation of scRNA-seq data generated by 10x Genomics. Hence practitioners and consumers should remain vigilant about the outcome of 10x Genomics scRNA-seq analysis.
Leishmania parasites proliferate within nutritionally complex niches in their sandfly vector and mammalian hosts. However, the extent to which these parasites utilize different carbon sources remains poorly defined. In this study, we have followed the incorporation of various 13 C-labeled carbon sources into the intracellular and secreted metabolites of Leishmania mexicana promastigotes using gas chromatography-mass spectrometry and C]alanine uptake and catabolism. TCA cycle anaplerosis is apparently needed to sustain glutamate production under standard culture conditions. Specifically, inhibition of mitochondrial aconitase with sodium fluoroacetate resulted in the rapid depletion of intracellular glutamate pools and growth arrest. Addition of high concentrations of exogenous glutamate alleviated this growth arrest. These findings suggest that glycosomal and mitochondrial metabolism in Leishmania promastigotes is tightly coupled and that, in contrast to the situation in some other trypanosomatid parasites, the TCA cycle has crucial anabolic functions.Leishmania spp. are parasitic protozoa that cause a spectrum of disease in humans, ranging from self-limiting cutaneous infections to disseminating infections (mucocutaneous and visceral leishmaniasis) that can lead to severe morbidity and death (1). Approximately 12 million people are infected worldwide, resulting in more than 50,000 deaths each year (2). There are no vaccines against any of these diseases, and current drug therapies are both limited and, in many cases, are being undermined by widespread resistance (2). Although the genomes of several Leishmania species have now been sequenced and key aspects of metabolism intensively studied, major gaps exist in our understanding of central carbon metabolism in these divergent eukaryotes (3, 4). Given the importance of intermediary metabolism for parasite growth and protection against host microbicidal processes, detailed dissection of Leishmania carbon metabolism may reveal new therapeutic targets (4 -6).Leishmania develop as extracellular flagellated promastigote stages within the digestive tract of the sandfly vector. This stage is transmitted to the mammalian host when the female sandfly host takes a blood meal and is rapidly phagocytosed by neutrophils and macrophages (1). Promastigotes internalized into the phagolysosome compartment of macrophages differentiate into the obligate intracellular amastigote stage that perpetuates infection in the mammalian host. Promastigote stages are readily cultivated in vitro and have been the focus of most metabolic studies. Like the intensively studied insect (procyclic) stage of the related trypanosomatid, Trypanosoma brucei (7,8), Leishmania promastigotes are thought to catabolize glucose via glycolysis, with the initial enzymes in this pathway being largely or exclusively compartmentalized in modified peroxisomes, termed glycosomes (9, 10). The glycosomal catabolism of glucose to 1,3-bisphosphoglycerate requires an investment of both ATP and NAD ϩ , and the rate at whic...
MotivationGene set enrichment (GSE) analysis allows researchers to efficiently extract biological insight from long lists of differentially expressed genes by interrogating them at a systems level. In recent years, there has been a proliferation of GSE analysis methods and hence it has become increasingly difficult for researchers to select an optimal GSE tool based on their particular dataset. Moreover, the majority of GSE analysis methods do not allow researchers to simultaneously compare gene set level results between multiple experimental conditions.ResultsThe ensemble of genes set enrichment analyses (EGSEA) is a method developed for RNA-sequencing data that combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets. EGSEA’s gene set database contains around 25 000 gene sets from sixteen collections. It has multiple visualization capabilities that allow researchers to view gene sets at various levels of granularity. EGSEA has been tested on simulated data and on a number of human and mouse datasets and, based on biologists’ feedback, consistently outperforms the individual tools that have been combined. Our evaluation demonstrates the superiority of the ensemble approach for GSE analysis, and its utility to effectively and efficiently extrapolate biological functions and potential involvement in disease processes from lists of differentially regulated genes.Availability and ImplementationEGSEA is available as an R package at http://www.bioconductor.org/packages/EGSEA/. The gene sets collections are available in the R package EGSEAdata from http://www.bioconductor.org/packages/EGSEAdata/.Supplementary information Supplementary data are available at Bioinformatics online.
G-CSF is a hemopoietic growth factor that has a role in steady state granulopoiesis, as well as in mature neutrophil activation and function. G-CSF- and G-CSF receptor-deficient mice are profoundly protected in several models of rheumatoid arthritis, and Ab blockade of G-CSF also protects against disease. To further investigate the actions of blocking G-CSF/G-CSF receptor signaling in inflammatory disease, and as a prelude to human studies of the same approach, we developed a neutralizing mAb to the murine G-CSF receptor, which potently antagonizes binding of murine G-CSF and thereby inhibits STAT3 phosphorylation and G-CSF receptor signaling. Anti-G-CSF receptor rapidly halted the progression of established disease in collagen Ab-induced arthritis in mice. Neutrophil accumulation in joints was inhibited, without rendering animals neutropenic, suggesting an effect of G-CSF receptor blockade on neutrophil homing to inflammatory sites. Consistent with this, neutrophils in the blood and arthritic joints of anti-G-CSF receptor-treated mice showed alterations in cell adhesion receptors, with reduced CXCR2 and increased CD62L expression. Furthermore, blocking neutrophil trafficking with anti-G-CSF receptor suppressed local production of proinflammatory cytokines (IL-1β, IL-6) and chemokines (KC, MCP-1) known to drive tissue damage. Differential gene expression analysis of joint neutrophils showed a switch away from an inflammatory phenotype following anti-G-CSF receptor therapy in collagen Ab-induced arthritis. Importantly, G-CSF receptor blockade did not adversely affect viral clearance during influenza infection in mice. To our knowledge, we describe for the first time the effect of G-CSF receptor blockade in a therapeutic model of inflammatory joint disease and provide support for pursuing this therapeutic approach in treating neutrophil-associated inflammatory diseases.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.