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756 results for “immune genes”
Data from: Polymorphic tandem repeats shape single-cell gene expression across the immune landscape
<p>This dataset contains the association summary statistics (v0.1) for genome-wide tandem repeat (TR) expression quantitative trait (eQTL) analysis of TenK10K Phase 1 (https://doi.org/10.1101/2024.11.02.621562). </p> <p>Please access the README for a detailed description of file contents. </p> <p> </p>
Immune disease variants modulate gene expression in regulatory CD4+ T cells
<p>We mapped genetic regulation (QTL) of gene expression and chromatin activity in Tregs and we identified 133 colocalizing loci with immune disease variants.<br> For the time being, the preprint DOI: <a href="https://doi.org/10.1101/654632">10.1101/654632</a></p>
Data from: Differential gene expression during recall of behaviorally conditioned immune enhancement in rats: a pilot study
<p><strong>Background:</strong> Behaviorally conditioned immune functions are suggested to be regulated by bidirectional interactions between CNS and peripheral immune system <em>via</em> the hypothalamic-pituitary-adrenal (HPA) axis, sympathetic nervous system (SNS), and the parasympathetic nervous system (PNS). Since the current knowledge about biochemical pathways triggering conditioned immune enhancement is limited, the aim of this pilot study was gaining more insights into that.</p> <p><strong>Methods: </strong>Rats were conditioned with camphor smell and poly I:C injection, mimicking a viral infection. Following stimulus re-exposure, animals were sacrificed at different time points, and neural tissues along the HPA axis was analyzed with a rat genome array together with plasma protein using Luminex analysis.</p> <p><strong>Results:</strong> In the hypothalamus, we observed a strong upregulation of genes related to Wnt/β-catenin signaling (Otx2, Spp1, Fzd6, Zic1), monoaminergic transporter Slc18a2 and opioid-inhibitory G-protein Gpr88 as well as downregulation of dopaminergic receptors, vasoactive intestinal peptide Vip, and pro-melanin-concentrating hormone Pmch. In the pituitary, we recognized mostly upregulation of steroid synthesis in combination with GABAergic, cholinergic and opioid related neurotransmission, in adrenal glands, altered genes showed a pattern of activated metabolism plus upregulation of adrenoceptors Adrb3 and Adra1a. Data obtained from spleen showed a strong upregulation of immunomodulatory genes, chemo-/cytokines and glutamatergic/cholinergic neurotransmission related genes, as also confirmed by increased chemokine and ACTH levels in plasma.</p> <p><strong>Conclusions:</strong> Our data indicate that in addition to the classic HPA axis, there could be additional pathways as e.g. the cholinergic anti-inflammatory pathway (CAIP), connecting brain and immune system, modulating and finetuning communication between brain and immune system.</p>
Can immune gene silencing via dsRNA feeding promote pathogenic viruses to control the globally invasive Argentine ant?
<p><span>Pest control methods that can target pest species with limited environmental impacts are a conservation and economic priority. Species-specific pest control using RNA interference is a challenging but promising avenue in developing the next generation of pest management. We investigate the feasibility of manipulating a biological invader's immune system using double-stranded RNA (dsRNA) in order to increase susceptibility to naturally occurring pathogens. We used the invasive Argentine ant as a model, targeting the immunity-associated genes <em>Spaetzle</em> and <em>Dicer-1</em> with dsRNA. We show that feeding of <em>Spaetzle</em> dsRNA can result in partial target gene silencing for up to 28 days in the laboratory and five days in the field. <em>Dicer-1</em> dsRNA only resulted in partial gene knockdown after two days in the laboratory. Double-stranded RNA treatments were associated with significant gene expression disruptions across immune pathways in the laboratory and to a lower extent in the field. We observed occasional changes in viral loads in dsRNA-treated groups. However, immune pathways disruption did not result in consistent increase in microbial infections, nor did they alter ant abundance in the field. Our study explores the feasibility of lowering a pest's immunity as a control tool. We demonstate that it is possible to alter immune gene expression of pest species and pathogen loads, though in our system the affected pathogens did not appear to influence pest abundance. We provide advice on future directions for dsRNA-mediated immune disruption in pest species, including potential avenues to improve dsRNA delivery as well as the importance of the biology of the pest system and its pathogens.</span></p>
Can immune gene silencing via dsRNA feeding promote pathogenic viruses to control the globally invasive Argentine ant?
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Immune-associated orthologous genes across primates
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Data from: Single cell RNA-seq analysis reveals that prenatal arsenic exposure results in long-term, adverse effects on immune gene expression in response to Influenza A infection
<p>Arsenic exposure via drinking water is a serious environmental health concern. Epidemiological studies suggest a strong association between prenatal<i> </i>arsenic exposure and subsequent childhood respiratory infections, as well as morbidity from respiratory diseases in adulthood, long after systemic clearance of arsenic.<i> </i>We investigated the impact of exclusive prenatal arsenic exposure on the inflammatory immune response and respiratory health after an adult influenza A (IAV) lung infection. C57BL/6J mice were exposed to 100 ppb sodium arsenite<i> in utero,</i> and subsequently infected with IAV (H1N1) after maturation to adulthood. Assessment of lung tissue and bronchoalveolar lavage fluid (BALF) at various time points post IAV infection reveals greater lung damage and inflammation in arsenic exposed mice versus control mice. Single-cell RNA sequencing analysis of immune cells harvested from IAV infected lungs suggests that the enhanced inflammatory response is mediated by dysregulation of innate immune function of monocyte derived macrophages, neutrophils, NK cells, and alveolar macrophages. Our results suggest that prenatal arsenic exposure results in lasting effects on the adult host innate immune response to IAV infection, long after exposure to arsenic, leading to greater immunopathology. This study provides the first direct evidence that exclusive prenatal exposure to arsenic in drinking water causes predisposition to a hyperinflammatory response to IAV infection in adult mice, which is associated with significant lung damage.</p>
Gene expression remodelling and immune response during adaptive divergence in an African cichlid fish
<p><span>Variation in gene expression contributes to ecological speciation by facilitating population persistence in novel environments. Likewise, immune response can be a relevant factor in speciation driven by adaptation to different environments. Previous studies examining gene expression differences between recently diverged ecotypes often relied on only one pair of populations, targeted the expression of only a subset of genes, or used wild caught-individuals. Here, we investigated the contribution of habitat-specific parasites and symbionts and the underlying immunological capabilities of ecotype hosts to adaptive divergence in lake-river population pairs of the cichlid fish <i>Astatotilapia burtoni</i>. To shed light on the role of phenotypic plasticity in adaptive divergence, we compared parasite and microbiota communities, immune response, and gene expression patterns of fish from natural habitats and a lake-like pond setup. In all investigated population pairs, lake fish were more heavily parasitized than river fish, both in terms of parasite taxa composition and infection abundance. Innate immune response in the wild was higher in lake than in river populations and elevated in a river population exposed to lake parasites in the pond setup. Environmental differences between lake and river habitat and their distinct parasite communities shaped differential gene expression, involving genes functioning in osmoregulation and immune response. Most changes in gene expression between lake and river samples in the wild and in the pond setup were based on a plastic response. Finally, gene expression and bacterial communities of wild-caught individuals and individuals acclimated to lake-like pond conditions showed shifts underlying adaptive phenotypic plasticity.</span></p>
AhR Gene Expression in Immune cell subtypes
<p>Benjamin J. Schmiedel, Divya Singh, Ariel Madrigal, Alan G. Valdovino-Gonzalez, Brandie M. White, Jose Zapardiel-Gonzalo, Brendan Ha, Gokmen Altay, Jason A. Greenbaum, Graham McVicker, Grégory Seumois, Anjana Rao, Mitchell Kronenberg, Bjoern Peters, Pandurangan Vijayanand,<br> Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression,<br> Cell,<br> Volume 175, Issue 6,<br> 2018,<br> Pages 1701-1715.e16,<br> ISSN 0092-8674,<br> https://doi.org/10.1016/j.cell.2018.10.022.<br> (http://www.sciencedirect.com/science/article/pii/S009286741831331X)</p> <p><br> Abstract: Summary<br> While many genetic variants have been associated with risk for human diseases, how these variants affect gene expression in various cell types remains largely unknown. To address this gap, the DICE (database of immune cell expression, expression quantitative trait loci [eQTLs], and epigenomics) project was established. Considering all human immune cell types and conditions studied, we identified cis-eQTLs for a total of 12,254 unique genes, which represent 61% of all protein-coding genes expressed in these cell types. Strikingly, a large fraction (41%) of these genes showed a strong cis-association with genotype only in a single cell type. We also found that biological sex is associated with major differences in immune cell gene expression in a highly cell-specific manner. These datasets will help reveal the effects of disease risk-associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis (https://dice-database.org).<br> Keywords: DICE; immunology; GWAS; genetic variants; human immune cells; gene expression; eGenes; eQTLs; sex</p> <p>https://dice-database.org/genes/ahr#boxplot</p>
Data from: Microevolutionary selection dynamics acting on immune genes of the green veined white butterfly, Pieris napi
Insects rely on their innate immune system to successfully mediate complex interactions with their microbiota, as well as the microbes present in the environment. Previous work has shown that components of the canonical immune gene repertoire evolve rapidly and have evolutionary characteristics originating from interactions with fast-evolving microorganisms. Although these interactions are likely to vary among populations, there is a poor understanding of the microevolutionary dynamics of immune genes, especially in non-Dipteran insects. Here we use the full set of canonical insect immune genes to investigate microevolutionary dynamics acting on these genes between and among populations by comparing three allopatric populations of the Green Veined White butterfly, Pieris napi (Lepidoptera, Pieridae). Immune genes showed increased genetic diversity compared to genes from the rest of the genome and various functional categories exhibited different types of signatures of selection, at different evolutionary scales, presenting a complex pattern of selection dynamics. Signatures of balancing selection were identified in 10 genes, and 17 genes appear to be under positive selection. Genes involved with the cellular arm of the immune response as well as the Toll pathway appear to be enriched among our outlier loci, regardless of functional category. This suggests that the targets of selection might focus upon an entire pathway, more than on functional subsets across pathways. Our microevolutionary results are similar to previously observed macroevolutionary patterns from diverse taxa, suggesting that either the immune system is robust to dramatic differences in life history and microbial communities, or that diverse microbes exert similar selection pressures.
Autoimmunity-associated allele of tyrosine phosphatase gene PTPN22 enhances anti-viral immunity
<p>The 1858C>T allele of the tyrosine phosphatase <em>PTPN22</em> is present in 5-10% of the North American population and is strongly associated with numerous autoimmune diseases. Although research has been done to define how this allele potentiates autoimmunity, the influence <em>PTPN22</em> and its pro-autoimmune allele have in anti-viral immunity remains poorly defined. Here, we use single-cell RNA-sequencing and functional studies to interrogate the impact of this pro-autoimmune allele on anti-viral immunity during Lymphocytic Choriomeningitis Virus clone 13 (LCMV-cl13) infection. Mice homozygous for this allele (PEP-619WW) clear the LCMV-cl13 virus whereas wildtype (PEP-WT) mice cannot. This is associated with enhanced anti-viral CD4 T cell responses and a more immunostimulatory CD8a<sup>-</sup> cDC phenotype. Adoptive transfer studies demonstrated that PEP-619WW enhanced anti-viral CD4 T cell function through virus-specific CD4 T cell-intrinsic and extrinsic mechanisms. Taken together, our data show that the pro-autoimmune allele of <em>Ptpn22</em> drives a beneficial anti-viral immune response thereby preventing what is normally a chronic virus infection.</p>
Immune disease risk variants regulate gene expression dynamics during CD4+ T cell activation
<p>During activation, T cells undergo extensive changes in gene expression which shape the properties of cells to exert their effector function. Therefore, understanding the genetic regulation of gene expression during T cell activation provides essential insights into how genetic variants influence the response to infections and immune diseases. We generated a single-cell map of expression quantitative trait loci (eQTL) across a T cell activation time-course. We profiled 655,349 CD4+ naive and memory T cells, capturing transcriptional states of unstimulated cells and three time points of cell activation in 119 healthy individuals. We identified 38 cell clusters, including stable clusters such as central and effector memory T cells and transient clusters that were only present at individual time points of activation, such as interferon-responding cells. We mapped eQTLs using a T cell activation trajectory and identified 6,407 eQTL genes, of which a third (2,265 genes) were dynamically regulated during T cell activation. We integrated this information with GWAS variants for immune-mediated diseases and observed 127 colocalizations, with significant enrichment in dynamic eQTLs. Immune disease loci colocalized with genes that are involved in the regulation of T cell activation, and genes with similar functions tended to be perturbed in the same direction by disease risk alleles. Our results emphasize the importance of mapping context-specific gene expression regulation, provide insights into the mechanisms of genetic susceptibility of immune diseases, and help prioritize new therapeutic targets.</p> <p>This dataset comprises of summary stats for eQTLs identified in the study (parquet files) and the ones which passed significance threshold (tensor_out.tar.gz archive). Files are described by cell subset (CD4 Naive, CD 4 Memory, TEMRA, TCM, etc.), time since activation (16h, 4h, 5days) as described in the publication (preprint https://doi.org/10.1101/2021.12.06.470953)</p>
Data and code for "Multi-omics Reveals Microbiome, Host Gene Expression, and Immune Landscape in Gastric Carcinogenesis" by Park et al., iScience 2022
<p>This repository is a part of the supplementary document in Park et al., "Multi-omics Reveals Microbiome, Host Gene Expression, and Immune Landscape in Gastric Carcinogenesis" published in iScience 2022.</p> <p>Abstract: To date, there has been no multi-omic analysis characterizing the intricate relationships between the intragastric microbiome and gastric mucosal gene expression in gastric carcinogenesis. Using multi-omic approaches, we provide a comprehensive view of the connections between the microbiome and host gene expression in distinct stages of gastric carcinogenesis (i.e., healthy, gastritis, cancer). We uncover associations specific to disease states. For example, uniquely in gastritis, Helicobacteraceae is highly correlated with the expression of <em>FAM3D</em>, which has been previously implicated in gastrointestinal inflammation. Additionally, in gastric cancer but not in adjacent gastritis, Lachnospiraceae is highly correlated with the expression of <em>UBD</em>, which regulates mitosis and cell cycle time. Furthermore, lower abundances of B cells in gastric cancer compared to gastritis may suggest a previously unidentified immune evasion process in gastric carcinogenesis. Our integrative analysis provides the most comprehensive description of microbial, host transcriptomic, and immune cell factors of the gastric carcinogenesis pathway.</p>
Malignant pleural effusion LADC immunity 700 gene dataset
<p>MPE cytologic cell blocks of 83 LADC patients were analysed for the mRNA expression of 770 cancer-immune genes by the NanoString nCounter platform.</p>
An ssGSEA Based Immune-related Gene Prognostic Signature Combining Immune Infiltration and Immune Checkpoint for Breast Cancer Patients
<p>This is the gene expression and related clinical data of breast cancer patients obtained from TCGA. Original codes and data from GEO database could be found in GitHub via link "https://github.com/Grevilblois/R-codes-for-manuscript".</p>
Quit bugging me: Phorid fly parasitoids affect expression of an immune gene in foraging fire ant workers
<p>This data contains RT-qPCR and diet measurements for quantifying gene expression of red imported fire ant, <em>Solenopsis invicta </em>workers in the presence and absence of the parasitoid fire ant decapitating fly, <em>Pseudacteon curvatus</em>, and assessing the amount of food after exposure to <em>P. curvatus</em>, respectively. The genes investigated were the <em>Solenopsis invicta</em> <em>foraging gene</em> (<em>Sifor</em>), <em>odorant binding protein 11 </em>(<em>OBP-11</em>), <em>abaecin, defensin-2 </em>(<em>Def-2</em>),<em> cytochrome P450 4C1-like </em>(<em>CYP4C1-like</em>), and <em>hymenoptaecin </em>(<em>hym</em>)<em>. Ribosomal Protein 18</em> (<em>RPL18</em>) was used as the reference gene. These genes of <em>S. invicta</em> workers of unknown infection status in fire ant colonies exposed to decapitating flies and control colonies were observed over a 48-h period. Two diets were measured before and after in control and treatment colonies (i.e., colonies exposed to <em>P. curvatus</em>).</p>
Identification and Exploration of Immunity-Related Genes and Natural Products for Alzheimer's Disease Based on Bioinformatics, Molecular Docking and Molecular Dynamics
<p>Supplementary material to the article: Identification and Exploration of Immunity-Related Genes and Natural Products for Alzheimer’s Disease Based on Bioinformatics, Molecular Docking and Molecular Dynamics,These data are available to researchers.</p>
Modulation of gene expression in immune related organs by in-ovo stimulation with probiotics and prophybiotics in broiler chickens
<p><span>The current study was performed to further investigate the tissue specific immune modulation and metabolic gene regulation of these <em>in-ovo</em> stimulated chickens. Accordingly, the expression of immune related genes was determined in the secondary immune organs, cecal tonsils and the spleen as well as the liver which is an important organ for both the immune system and metabolism. Additionally, the expression of the genes related to metabolism was also analyzed in the liver.</span></p>
No evidence for single-copy immune-gene specific signals of selection in termites
<p>Selection pressures from pathogens appear to play an important role in shaping social evolution. Social behavior, in particular brood care, is associated with pathogen pressure in wood-dwelling "lower" termites. Yet, generally pathogen pressure is predicted to be low in wood-dwelling termite species that never leave the nest except for the mating flight. In comparison, pathogen pressure is predicted to be higher in species that leave the nest to forage, and thus constantly encounter a diversity of microbes from their environment. We hypothesized that such differences in predicted pathogen pressure are also reflected by differences in the intensity of natural selection on immune genes. We tested this hypothesis in a phylogenetic framework, analyzing rates of non-synonymous and synonymous substitutions on single-copy immune genes. Therefore, we leveraged recent genomic and transcriptomic data from eight termite species, representing wood-dwelling and foraging species as well as 14 additional species spanning the winged insects (Pterygota). Our results provide no evidence for a role of pathogen pressure in selection intensity on single-copy immune genes. Instead, we found evidence for a genome-wide pattern of relaxed selection in termites.</p>
Relationships between immune gene expression and circulating cytokine levels in wild house mice
<p>1. Quantitative PCR (qPCR) has been commonly used to measure gene expression in a number of research contexts, but the measured RNA concentrations do not always represent the concentrations of active proteins which they encode. This can be due to transcriptional regulation or post-translational modifications, or localisation of immune environments, as can occur during infection. However, in studies using free-living non-model species, such as in ecoimmunological research, qPCR may be the only available option to measure a parameter of interest, and so understanding the quantitative link between gene expression and associated effector protein levels is vital.</p> <p>2. Here we use qPCR to measure concentrations of RNA from mesenteric lymph node (MLN) and spleen tissue, and multiplex ELISA of blood serum to measure circulating cytokine concentrations in a wild population of a model species, Mus musculus domesticus.</p> <p>3. Few significant correlations were found between gene expression levels and circulating cytokines of the same immune genes or proteins, or related functional groups. Where significant correlations were observed, these were most frequently within the measured tissue (i.e. the expression levels of genes measured from spleen tissue were more likely to correlate with each other rather than with genes measured from MLN tissue, or with cytokine concentrations measured from blood).</p> <p>4. Potential reasons for discrepancies between measures, including differences in decay rates and transcriptional regulation networks are discussed. We highlight the relative usefulness of different measures under different research questions, and consider what might be inferred from immune assays.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
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