scholarly journals Localized skin inflammation during cutaneous leishmaniasis drives a chronic, systemic IFN-γ signature

2021 ◽  
Vol 15 (4) ◽  
pp. e0009321
Author(s):  
Camila Farias Amorim ◽  
Fernanda O. Novais ◽  
Ba T. Nguyen ◽  
Mauricio T. Nascimento ◽  
Jamile Lago ◽  
...  
Keyword(s):  
Cutaneous Leishmaniasis ◽  
Elevated Serum ◽  
Functional Enrichment ◽  
Transcriptional Analysis ◽  
Marker Genes ◽  
Specific Marker ◽  
Phagocytic Cells ◽  
Systemic Spread ◽  
Dominant Feature ◽  
Ifn Γ

Cutaneous leishmaniasis is a localized infection controlled by CD4+ T cells that produce IFN-γ within lesions. Phagocytic cells recruited to lesions, such as monocytes, are then exposed to IFN-γ which triggers their ability to kill the intracellular parasites. Consistent with this, transcriptional analysis of patient lesions identified an interferon stimulated gene (ISG) signature. To determine whether localized L. braziliensis infection triggers a systemic immune response that may influence the disease, we performed RNA sequencing (RNA-seq) on the blood of L. braziliensis-infected patients and healthy controls. Functional enrichment analysis identified an ISG signature as the dominant transcriptional response in the blood of patients. This ISG signature was associated with an increase in monocyte- and macrophage-specific marker genes in the blood and elevated serum levels IFN-γ. A cytotoxicity signature, which is a dominant feature in the lesions, was also observed in the blood and correlated with an increased abundance of cytolytic cells. Thus, two transcriptional signatures present in lesions were found systemically, although with a substantially reduced number of differentially expressed genes (DEGs). Finally, we found that the number of DEGs and ISGs in leishmaniasis was similar to tuberculosis–another localized infection–but significantly less than observed in malaria. In contrast, the cytolytic signature and increased cytolytic cell abundance was not found in tuberculosis or malaria. Our results indicate that systemic signatures can reflect what is occurring in leishmanial lesions. Furthermore, the presence of an ISG signature in blood monocytes and macrophages suggests a mechanism to limit systemic spread of the parasite, as well as enhance parasite control by pre-activating cells prior to lesion entry.

scholarly journals Localized skin inflammation during cutaneous leishmaniasis drives a chronic, systemic IFN-γ signature

2020 ◽  
Author(s):  
Camila Farias Amorim ◽  
Fernanda O. Novais ◽  
Ba T. Nguyen ◽  
Mauricio T. Nascimento ◽  
Jamile Lago ◽  
...  
Keyword(s):  
Cutaneous Leishmaniasis ◽  
Functional Enrichment ◽  
Transcriptional Analysis ◽  
Rna Seq ◽  
Parasite Control ◽  
Cutaneous Lesions ◽  
Systemic Spread ◽  
Dominant Feature ◽  
Monocytes And Macrophages ◽  
Ifn Γ

AbstractCutaneous leishmaniasis is a localized infection controlled by CD4+ T cells that produce IFN-γ within lesions. Phagocytic cells recruited to lesions, such as monocytes, are then exposed to IFN-γ which triggers their ability to kill the intracellular parasites. Consistent with this, a transcriptional analysis of lesions from patients identified the presence of a strong interferon stimulated gene (ISG) signature. To determine what systemic responses are occurring that might influence the disease, we performed RNA sequencing (RNA-seq) on the blood of L. braziliensis-infected patients, as well as healthy controls. Functional enrichment analysis identified a transcriptional ISG signature as the dominant response in the blood of patients. An increase in monocytes and macrophages in the blood, estimated from our RNA-seq dataset, was positively correlated with this ISG signature. Consistent with this result, patients had circulating IFN-γ in their serum. A cytotoxicity signature, which is a dominant feature in the lesions, was also found in the blood and correlated with an increased abundance of cytolytic cells. Thus, two transcriptional signatures present in lesions were found systemically, although with a substantially reduced number of differentially expressed genes (DEGs). Finally, we found that the number of DEGs and ISGs in leishmaniasis was similar to tuberculosis – another localized infection – but significantly less than observed in malaria. In contrast, the cytolytic signature and increased cytolytic cell abundance was not found in tuberculosis or malaria. Our results indicate that systemic signatures can reflect what is occurring in leishmanial lesions. Furthermore, the presence of an ISG signature in blood monocytes and macrophages suggests a mechanism to limit systemic spread of the parasite, as well as enhance parasite control by pre-activating cells prior to lesion entry.Author summaryCutaneous leishmaniasis caused by the protozoan Leishmania braziliensis exhibits two dominant inflammatory responses in cutaneous lesions: Interferon-γ (IFN-γ)-mediated signaling, which promotes parasite control, and cytolysis mediated by cytotoxic CD8+ T and NK cells, which promotes increased pathology. To determine if these responses were limited to cutaneous lesions, we performed RNA-seq on the blood of cutaneous leishmaniasis (CL) patients, and detected both transcriptional signatures in the peripheral blood. The presence of interferon stimulated genes, as well as circulating IFN-γ, suggests that protective immune responses are not limited to the lesion site, but are occurring systemically. This may be one mechanism to ensure optimal control of the parasites, both by limiting their systemic spread and by pre-activating cells to kill the parasites prior to entry into the lesions. The cytolytic transcriptional signature was uniquely detectable in the blood of L. braziliensis patients when compared to the blood of patients with tuberculosis (TB) or malaria, further emphasizing the importance of this pathway in cutaneous leishmaniasis. Taken together, these data suggest that this localized infection has a systemic component that may have an impact the development of the disease.

scholarly journals PU.1 Regulates Cathepsin S Expression in Large Yellow Croaker (Larimichthys crocea) Macrophages

2022 ◽  
Vol 12 ◽  
Author(s):  
Xiang-Yang Zhang ◽  
Xinyue Zhuo ◽  
Jie Cheng ◽  
Xiaohong Wang ◽  
Kexin Liang ◽  
...  
Keyword(s):  
Head Kidney ◽  
Cathepsin S ◽  
Marker Genes ◽  
Large Yellow Croaker ◽  
Specific Marker ◽  
Oxygen Species ◽  
Larimichthys Crocea ◽  
Macrophage Cell ◽  
Ifn Γ ◽  
Bactericidal Activities

Different morphologies have been detected in teleost macrophages. In this study, two macrophage cell lines were sub-cloned from a large yellow croaker head kidney cell line, LYCK. One type of sub-cloned cells was fusiform but the other was round, named LYC-FM and LYC-RM cells respectively, based on their morphologies. Both types showed the characteristics of macrophages, including expression of macrophage-specific marker genes, possession of phagocytic and bactericidal activities, and production of reactive oxygen species (ROS) and nitric oxide (NO). The transcription factor PU.1, crucial for the development of macrophages in mammals, was found to exist in two transcripts, PU.1a and PU.1b, in large yellow croaker, and constitutively expressed in LYC-FM and LYC-RM cells. The expression levels of PU.1a and PU.1b could be upregulated by recombinant large yellow croaker IFN-γ protein (rLcIFN-γ). Further studies showed that both PU.1a and PU.1b increased the expression of cathepsin S (CTSS) by binding to different E26−transformation−specific (Ets) motifs of the CTSS promoter. Additionally, we demonstrated that all three domains of PU.1a and PU.1b were essential for initiating CTSS expression by truncated mutation experiments. Our results therefore provide the first evidence that teleost PU.1 has a role in regulating the expression of CTSS.

scholarly journals scSorter: assigning cells to known cell types according to marker genes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Hongyu Guo ◽  
Jun Li
Keyword(s):  
Real Data ◽  
Cell Types ◽  
Exact Expression ◽  
Marker Genes ◽  
Specific Marker ◽  
Sequencing Data ◽  
Reference Dataset ◽  
Over Expression ◽  
Higher Power ◽  
Cell Type Specific

AbstractOn single-cell RNA-sequencing data, we consider the problem of assigning cells to known cell types, assuming that the identities of cell-type-specific marker genes are given but their exact expression levels are unavailable, that is, without using a reference dataset. Based on an observation that the expected over-expression of marker genes is often absent in a nonnegligible proportion of cells, we develop a method called scSorter. scSorter allows marker genes to express at a low level and borrows information from the expression of non-marker genes. On both simulated and real data, scSorter shows much higher power compared to existing methods.

scholarly journals Identification of cell-type-specific marker genes from co-expression patterns in tissue samples

2021 ◽  
Author(s):  
Yixuan Qiu ◽  
Jiebiao Wang ◽  
Jing Lei ◽  
Kathryn Roeder
Keyword(s):  
Single Cell ◽  
Expression Patterns ◽  
R Package ◽  
Supplementary Information ◽  
Marker Genes ◽  
Specific Marker ◽  
Cell Type ◽  
Correlation Pattern ◽  
Tissue Samples ◽  
Bulk Data

Abstract Motivation Marker genes, defined as genes that are expressed primarily in a single cell type, can be identified from the single cell transcriptome; however, such data are not always available for the many uses of marker genes, such as deconvolution of bulk tissue. Marker genes for a cell type, however, are highly correlated in bulk data, because their expression levels depend primarily on the proportion of that cell type in the samples. Therefore, when many tissue samples are analyzed, it is possible to identify these marker genes from the correlation pattern. Results To capitalize on this pattern, we develop a new algorithm to detect marker genes by combining published information about likely marker genes with bulk transcriptome data in the form of a semi-supervised algorithm. The algorithm then exploits the correlation structure of the bulk data to refine the published marker genes by adding or removing genes from the list. Availability and implementation We implement this method as an R package markerpen, hosted on CRAN (https://CRAN.R-project.org/package=markerpen). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals JIND: Joint Integration and Discrimination for Automated Single-Cell Annotation

2020 ◽  
Author(s):  
Mohit Goyal ◽  
Guillermo Serrano ◽  
Ilan Shomorony ◽  
Mikel Hernaez ◽  
Idoia Ochoa
Keyword(s):  
Single Cell ◽  
Cell Types ◽  
Marker Genes ◽  
Specific Marker ◽  
Rna Seq ◽  
Batch Effects ◽  
Cell Type ◽  
Latent Space ◽  
Cell Type Specific ◽  
Low Dimensional

AbstractSingle-cell RNA-seq is a powerful tool in the study of the cellular composition of different tissues and organisms. A key step in the analysis pipeline is the annotation of cell-types based on the expression of specific marker genes. Since manual annotation is labor-intensive and does not scale to large datasets, several methods for automated cell-type annotation have been proposed based on supervised learning. However, these methods generally require feature extraction and batch alignment prior to classification, and their performance may become unreliable in the presence of cell-types with very similar transcriptomic profiles, such as differentiating cells. We propose JIND, a framework for automated cell-type identification based on neural networks that directly learns a low-dimensional representation (latent code) in which cell-types can be reliably determined. To account for batch effects, JIND performs a novel asymmetric alignment in which the transcriptomic profile of unseen cells is mapped onto the previously learned latent space, hence avoiding the need of retraining the model whenever a new dataset becomes available. JIND also learns cell-type-specific confidence thresholds to identify and reject cells that cannot be reliably classified. We show on datasets with and without batch effects that JIND classifies cells more accurately than previously proposed methods while rejecting only a small proportion of cells. Moreover, JIND batch alignment is parallelizable, being more than five or six times faster than Seurat integration. Availability: https://github.com/mohit1997/JIND.

scholarly journals Revealing immune responses in the Mycobacterium avium subsp. paratuberculosis-infected THP-1 cells using single cell RNA-sequencing

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254194
Author(s):  
Hong-Tae Park ◽  
Woo Bin Park ◽  
Suji Kim ◽  
Jong-Sung Lim ◽  
Gyoungju Nah ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Single Cell ◽  
Mycobacterium Avium ◽  
Expression Patterns ◽  
Cell Types ◽  
Marker Genes ◽  
Specific Marker ◽  
Cell Type ◽  
Cytokines And Chemokines

Mycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic and debilitating disease in ruminants. MAP is also considered to be a possible cause of Crohn’s disease in humans. However, few studies have focused on the interactions between MAP and human macrophages to elucidate the pathogenesis of Crohn’s disease. We sought to determine the initial responses of human THP-1 cells against MAP infection using single-cell RNA-seq analysis. Clustering analysis showed that THP-1 cells were divided into seven different clusters in response to phorbol-12-myristate-13-acetate (PMA) treatment. The characteristics of each cluster were investigated by identifying cluster-specific marker genes. From the results, we found that classically differentiated cells express CD14, CD36, and TLR2, and that this cell type showed the most active responses against MAP infection. The responses included the expression of proinflammatory cytokines and chemokines such as CCL4, CCL3, IL1B, IL8, and CCL20. In addition, the Mreg cell type, a novel cell type differentiated from THP-1 cells, was discovered. Thus, it is suggested that different cell types arise even when the same cell line is treated under the same conditions. Overall, analyzing gene expression patterns via scRNA-seq classification allows a more detailed observation of the response to infection by each cell type.

scholarly journals Metagenomic profiling of host-associated bacteria from 8 datasets of the red alga Porphyra purpurea, with MetaPhlAn 3.0

2020 ◽  
Author(s):  
Orestis Nousias ◽  
Federica Montesanto
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
Reference Database ◽  
Marker Genes ◽  
Specific Marker ◽  
Bacterial Genomes ◽  
Associated Bacteria ◽  
Pan Genome ◽  
Nucleotide Database ◽  
Porphyra Purpurea

AbstractMicrobial communities play a fundamental role in the association with marine algae, in fact they are recognized to be actively involved in growth and morphogenesis.Porphyra purpurea is a red algae commonly found in the intertidal zone with an high economical value, indeed several species belonging to the genus Porphyra are intensely cultivated in the Eastern Asian countries. Moreover, P. purpurea is widely used as model species in different fields, mainly due to its peculiar life cycle. Despite of that, little is known about the microbial community associated to this species. Here we report the microbial-associated diversity of P. purpurea in four different localities (Ireland, Italy United Kingdom and USA) through the analysis of eight metagenomic datasets obtained from the publicly available metagenomic nucleotide database (https://www.ebi.ac.uk/ena/). The metagenomic datasets were quality controlled with FastQC version 0.11.8, pre-processed with Trimmomatic version 0.39 and analysed with Methaplan 3.0, with a reference database containing clade specific marker genes from ~ 99.500 bacterial genomes, following the pan-genome approach, in order to identify the putative bacterial taxonomies and their relative abundances. Furthermore, we compared the results to the 16S rRNA metagenomic analysis pipeline of MGnify database to evaluate the effectiveness of the two methods. Out of the 43 bacterial species identified with MetaPhlAn 3.0 only 5 were common with the MGnify results and from the 21 genera, only 9 were common. This approach highlighted the different taxonomical resolution of a 16S rRNA OTU-based method in contrast to the pan-genome approach deployed by MetaPhlAn 3.0.

scholarly journals Protective and Pathogenic Immune Responses to Cutaneous Leishmaniasis

2021 ◽  
Author(s):  
Elina Panahi ◽  
Danielle I. Stanisic ◽  
Christopher S. Peacock ◽  
Lara J. Herrero
Keyword(s):  
Immune Response ◽  
Immune Responses ◽  
Cutaneous Leishmaniasis ◽  
Adaptive Immune Response ◽  
Leishmania Parasite ◽  
Host Immune System ◽  
Phagocytic Cells ◽  
Host Immune Responses ◽  
Outcome Severity ◽  
Common Clinical Presentation

Leishmania (Kinetoplastida: Trypanosomatidae) parasites are known to cause a broad spectrum of clinical diseases in humans, collectively known as the leishmaniases. Cutaneous leishmaniasis is the most common clinical presentation with varying degrees of severity largely driven by host immune responses, specifically the interplay between innate and adaptive immune response. The establishment of a T lymphocyte driven cell-mediated immune response, leading to activated phagocytic cells, leading to Leishmania parasite killing and control of infection. Alternatively, the Leishmania parasite manipulates the host immune system, enabling parasite proliferation and clinical disease. Here we review how the cumulative interactions of different aspects of the host immune response determines disease outcome, severity, and immunity to re-infection.

scholarly journals Nanoemulsified Butenafine for Enhanced Performance against Experimental Cutaneous Leishmaniasis

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Adriana Bezerra-Souza ◽  
Jéssica A. de Jesus ◽  
Márcia D. Laurenti ◽  
Aikaterini Lalatsa ◽  
Dolores R. Serrano ◽  
...  
Keyword(s):  
Cutaneous Leishmaniasis ◽  
Colloidal Stability ◽  
Therapeutic Potential ◽  
Similar Efficacy ◽  
Delivery Systems ◽  
Free Form ◽  
Standard Drug ◽  
Inflammatory Reactions ◽  
Ifn Γ ◽  
Dermal Lesions

The production of ergosterol lipid involves the activity of different enzymes and is a crucial event for the Leishmania membrane homeostasis. Such enzymes can be blocked by azoles and allylamines drugs, such as the antifungal butenafine chloride. This drug was active on parasites that cause cutaneous and visceral leishmaniasis. Based on the leishmanicidal activity of butenafine chloride and considering the absence of reports about the therapeutic potential of this drug in cutaneous leishmaniasis, the present work is aimed at analyzing the efficacy of butenafine formulated in two different topical delivery systems, the self-nanoemulsifying drug delivery systems (BUT-SNEDDS) and in a SNEDDS-based nanogel (BUT-SNEDDS gel) as well as in the free form in experimental cutaneous leishmaniasis. Physical studies showed that both formulations were below 300 nm with low polydispersity (<0.5) good colloidal stability (around -25 mV). Increased steady-state flux was reported for nanoenabled butenafine formulations with reduced lag time in Franz cell diffusion assays across Strat-M membranes. No toxic or inflammatory reactions were detected in animals treated with BUT-SNEDDS, BUT-SNEDDS gel, or butenafine. Animals topically treated with butenafine (free or nanoformulated) showed small dermal lesions and low tissue parasitism. Furthermore, BUT-SNEDD gel and butenafine presented similar efficacy than the standard drug Glucantime given by the intralesional route. Increased levels of IFN-γ were observed in animals treated with BUT-SNEDDS gel or butenafine. Based on these data, the antifungal drug butenafine chloride can be considered an interesting repurposed drug for the treatment of cutaneous leishmaniasis.

scholarly journals Synergy of arbuscular mycorrhizal symbiosis and exogenous Ca2+ benefits peanut (Arachis hypogaea L.) growth through the shared hormone and flavonoid pathway

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Li Cui ◽  
Feng Guo ◽  
Jialei Zhang ◽  
Sha Yang ◽  
JingJing Meng ◽  
...  
Keyword(s):  
Arachis Hypogaea ◽  
Mycorrhizal Fungi ◽  
Differentially Expressed Gene ◽  
Sufficient Conditions ◽  
Arbuscular Mycorrhizal ◽  
Mycorrhizal Symbiosis ◽  
Marker Genes ◽  
Specific Marker ◽  
Flavonoid Pathway ◽  
Am Symbiosis

Abstract Peanut yield is severely affected by exchangeable calcium ion (Ca2+) deficiency in the soil. Arbuscular mycorrhizal (AM) symbiosis increases the absorption of Ca2+ for host plants. Here, we analyzed the physiological and transcriptional changes in the roots of Arachis hypogaea L. colonized by Funneliformismosseae under Ca2+-deficient and -sufficient conditions. The results showed that exogenous Ca2+ application increased arbuscular mycorrhizal fungi (AMF) colonization, plant dry weight, and Ca content of AM plants. Simultaneously, transcriptome analysis showed that Ca2+ application further induced 74.5% of differentially expressed gene transcripts in roots of AM peanut seedlings. These genes are involved in AM symbiosis development, hormone biosynthesis and signal transduction, and carotenoid and flavonoid biosynthesis. The transcripts of AM-specific marker genes in AM plants with Ca2+ deprivation were further up-regulated by Ca2+ application. Gibberellic acid (GA3) and flavonoid contents were higher in roots of AM- and Ca2+-treated plants, but salicylic acid (SA) and carotenoid contents specifically increased in roots of the AM plants. Thus, these results suggest that the synergy of AM symbiosis and Ca2+ improves plant growth due to the shared GA- and flavonoid-mediated pathway, whereas SA and carotenoid biosynthesis in peanut roots are specific to AM symbiosis.

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