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Results for “Immunology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 181 records · Page 10Linked to original sources

bioRxiv2014

Ontogenic, phenotypic, and functional characterization of XCR1+ dendritic cells leads to a consistent classification of intestinal dendritic cells based on the expression of XCR1 and SIRPα

In the past, lack of lineage markers confounded the classification of dendritic cells (DC) in the intestine and impeded a full understanding of their location and function. We have recently shown that the chemokine receptor XCR1 is a lineage marker for cross-presenting DC in the spleen. Now we provide evidence that intestinal XCR1+ DC largely, but not fully, overlap with CD103+ CD11b- DC, the hypothesized correlate of \"cross-presenting DC\" in the intestine, and are selectively dependent in their development on the transcription factor Batf3. XCR1+ DC are located in the villi and epithelial crypts of the lamina propria of the small intestine, the T cell zones of Peyers Patches, and in the T cell zones and sinuses of the draining mesenteric lymph node. Functionally, we could demonstrate for the first time that XCR1+ / CD103+ CD11b- DC excel in the cross-presentation of orally applied antigen. Together, our data show that XCR1 is a lineage marker for cross-presenting DC also in the intestinal immune system. Further, extensive phenotypic analyses reveal that expression of the integrin SIRP consistently demarcates the XCR1- DC population. We propose a simplified and consistent classification system for intestinal DC based on the expression of XCR1 and SIRP.

Immunology↗

bioRxiv2014

Regulatory vs. helper CD4+ T-cell ratios and the progression of HIV/AIDS disease

The causes of individual variability in the length of time between human immunodeficiency virus (HIV) infection and the development of AIDS are incompletely understood. Here, we present a novel hypothesis: that the relative magnitude of responses to HIV mediated by CD4+ T regulatory (Treg) cells vs. CD4+ T effector (Teff) cells is a critical determinant of variability in AIDS progression rates. We use a simple mathematical model to show that this hypothesis can plausibly explain three qualitatively different outcomes of HIV infection - fast or slow progression to AIDS, and long-term non-progression to AIDS - based on individual variation in underlying T-cell response. This hypothesis also provides a unifying explanation for various other empirical observations, suggesting in particular that both aging and certain dual infections increase the rate of AIDS progression because they increase the strength of the Treg cell response. We discuss potential therapeutic implications of our results.

Immunology↗

bioRxiv2014

V genes in primates from whole genome shotgun data

The adaptive immune system uses V genes for antigen recognition. The evolutionary diversification and selection processes within and across species and orders are poorly understood. Here, we studied the amino acid (AA) sequences obtained of translated in-frame V exons of immunoglobulins (IG) and T cell receptors (TR) from 16 primate species whose genomes have been sequenced. Multi-species comparative analysis supports the hypothesis that V genes in the IG loci undergo birth/death processes, thereby permitting rapid adaptability over evolutionary time. We also show that multiple cladistic groupings exist in the TRA (35 clades) and TRB (25 clades) V gene loci and that each primate species typically contributes at least one V gene to each of these clade. The results demonstrate that IG V genes and TR V genes have quite different evolutionary pathways; multiple duplications can explain the IG loci results, while co-evolutionary pressures can explain the phylogenetic results, as seen in genes of the TR loci. We describe how each of the 35 V genes clades of the TRA locus and 25 clades of the TRB locus must have specific and necessary roles for the viability of the species.

Immunology↗

bioRxiv2014

V genes in rodents from whole genome sequencing data

We studied the V exons of 14 rodent species obtained from whole genome sequencing (WGS) datasets. Compared to other mammals, we found an increase in the number of immunoglobulin (IG) V genes in the heavy (IGH) and kappa chain (IGK) loci. We provide evidence for a reduction genes in lambda chain (IGL) locus, disappearing entirely in one of the species(Dipodomys ordii). We show relationships amongst the V genes of the T-cell receptors (TR) found in primates, possessing ortholog sequences between them. As compared with other mammals, there is an increase in the number of TRAV genes within rodents. Such an increase within this locus is caused by duplication events involving a few putative V genes. This duplication phenomenon does not occur in the TRBV locus. In those species that underwent an expansion of TRAV genes, we found that they also have a correspondingly larger number of MHC Class I genes. The results suggest that selective pressures have conditioned the expansion of V genomic repertoire the TRA, IGK and IGH loci during the diversification process of rodents.

Immunology↗

bioRxiv2014

Mouse conventional dendritic cells can be universally classified based on the mutually exclusive expression of XCR1 and SIRPα

Since the identification of mouse dendritic cells (DC) in the early 70s, all attempts to consistently classify the identified functional DC subpopulations according to their surface molecule expression failed. In the absence of DC lineage markers, a great variety of non-congruent surface molecules were used instead. Recent advances in the understanding of the involvement of transcription factors in the differentiation of DC subpopulations, together with the identification of a lineage marker for cross-presenting DC, have now allowed to establish a consistent and unified DC classification in the mouse. We demonstrate in the present article that all conventional DC in the mouse can be universally subdivided into either XCR1+ cross-presenting DC or SIRP+ DC, irrespective of their activation status. This advancement will greatly facilitate future work on the biology of mouse DC. We discuss this new classification in view of current DC classification systems in the mouse and the human.

Immunology↗

bioRxiv2015

On The Organization Of Human T Cell Receptor Loci.

The human T cell repertoire is complex and is generated by the rearrangement of variable (V), diversity (D) and joining (J) segments on the T cell receptor (TCR) loci. The T cell repertoire demonstrates selfsimilarity in terms clonal frequencies when defined by V, D and J gene segment usage; therefore to determine whether the structural ordering of these gene segments on the TCR loci contributes to the observed clonal frequencies, the TCR loci were examined for self-similarity and periodicity in terms of gene segment organization. Logarithmic transformation of numeric sequence order demonstrated that the V and J gene segments for both T cell receptor (TRA) and {beta} (TRB) loci were arranged in a selfsimilar manner when the spacing between the adjacent segments was considered as a function of the size of the neighboring gene segment, with an average fractal dimension of 1.5. The ratio of genomic distance between either the J (in TRA) or D (in TRB) segments and successive V segments on these loci declined logarithmically with a slope of similar magnitude. Accounting for the gene segments occurring on helical DNA molecules in a logarithmic distribution, sine and cosine functions of the log transformed angular coordinates of the start and stop nucleotides of successive TCR gene segments showed an ordered progression from the 5 to the 3 end of the locus, supporting a log-periodic organization. T cell clonal frequencies, based on V and J segment usage, from three normal stem cell donors were plotted against the V and J segment on TRB locus and demonstrated a periodic distribution. We hypothesize that this quasi-periodic variation in gene-segment representation in the T cell clonal repertoire may be influenced by the location of the gene segments on the periodic-logarithmically scaled TCR loci. Interactions between the two strands of DNA in the double helix may influence the probability of gene segment usage by means of either constructive or destructive interference resulting from the superposition of the two helices.

Immunology↗

bioRxiv2015

Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription

Macrophages differentiated from human induced pluripotent stem cells (IPSDMs) are a potentially valuable new tool for linking genotype to phenotype in functional studies. However, at a genome-wide level these cells have remained largely uncharacterised. Here, we compared the transcriptomes of naive and lipopolysaccharide (LPS) stimulated monocyte-derived macrophages (MDMs) and IPSDMs using RNA-Seq. The IPSDM and MDM transcriptomes were broadly similar and exhibited a highly conserved response to LPS. However, there were also significant differences in the expression of genes associated with antigen presentation and tissue remodelling. Furthermore, genes coding for multiple chemokines involved in neutrophil recruitment were more highly expressed in IPSDMs upon LPS stimulation. Additionally, analysing individual transcript expression identified hundreds of genes undergoing alternative promoter and 3' untranslated region usage following LPS treatment representing a previously under-appreciated level of regulation in the LPS response.

Immunology↗

bioRxiv2015

Inferring processes underlying B-cell repertoire diversity.

We quantify the VDJ recombination and somatic hypermutation processes in human B-cells using probabilistic inference methods on high-throughput DNA sequence repertoires of human B-cell receptor heavy chains. Our analysis captures the statistical properties of the naive repertoire, first after its initial generation via VDJ recombination and then after selection for functionality. We also infer statistical properties of the somatic hypermutation machinery (exclusive of subsequent effects of selection). Our main results are the following: the B-cell repertoire is substantially more diverse than T-cell repertoires, due to longer junctional insertions; sequences that pass initial selection are distinguished by having a higher probability of being generated in a VDJ recombination event; somatic hypermutations have a non-uniform distribution along the V gene that is well explained by an independent site model for the sequence context around the hypermutation site.

Immunology↗

bioRxiv2015

Novel APC-like properties of human NK cells directly regulate T cell activation

Initiation of the adaptive immune response is dependent on the priming of naive T cells by APCs. Proteomic analysis of unactivated and activated human NK cell membrane-enriched fractions demonstrated that activated NK cells can efficiently stimulate T cells, since they upregulate MHC class II molecules and multiple ligands for TCR costimulatory molecules. Furthermore, by manipulating antigen administration, we show that NK cells possess multiple independent unique pathways for antigen uptake. These results highlight NK cell-mediated cytotoxicity and specific ligand recognition by cell surface-activating receptors on NK cells as unique mechanisms for antigen capturing and presentation. In addition, we analyzed the T cell-activating potential of human NK cells derived from different clinical conditions, such as inflamed tonsils and noninfected and CMV-infected uterine decidual samples, and from transporter-associated processing antigen 2-deficient patients. This in vivo analysis revealed that proinflammatory, but not immune-suppressive, microenvironmental requirements can selectively dictate upregulation of T cell-activating molecules on NK cells. Taken together, these observations offer new and unexpected insights into the direct interactions between NK and T cells and suggest novel APC-like activating functions for human NK cells.\n\nNonstandard abbreviations used

Immunology↗

bioRxiv2015

The NADPH oxidase and microbial killing by neutrophils, with a particular emphasis on the proposed antimicrobial role of myeloperoxidase within the phagocytic vacuole

This review is devoted to a consideration of the way in which the NADPH oxidase of neutrophils, NOX2, functions to enable the efficient killing of bacteria and fungi. It includes a critical examination of the current dogma that its primary purpose is the generation of hydrogen peroxide as substrate for myeloperoxide catalysed generation of hypochlorite. Instead it is demonstrated that NADPH oxidase functions to optimise the ionic and pH conditions within the vacuole for the solubilisation and optimal activity of the proteins released into this compartment from the cytoplasmic granules, which kill and digest the microbes. The general role of other NOX systems as electrochemical generators to alter the pH and ionic composition in compartments on either side of a membrane in plants and animals will also be examined.

Immunology↗

bioRxiv2015

Ex vivo mycobacterial growth inhibition assay (MGIA) for tuberculosis vaccine testing - a protocol for mouse splenocytes

The testing of vaccines for tuberculosis is costly and time-consuming, and dependent on preclinical animal challenge models and clinical trials. We have recently developed a mycobacterial growth inhibition assay (MGIA) to test vaccine efficacy ex vivo. This assay measures the summative effect of the host immune response and may serve as a novel tool to facilitate vaccine testing. It has generated much interest recently, and to facilitate technology transfer and reproducibility between laboratories, we here describe a detailed protocol for an ex vivo MGIA in mouse splenocytes.

Immunology↗

bioRxiv2015

Fluctuating fitness shapes the clone size distribution of immune repertoires

The adaptive immune system relies on the diversity of receptors expressed on the surface of B and T-cells to protect the organism from a vast amount of pathogenic threats. The proliferation and degradation dynamics of different cell types (B cells, T cells, naive, memory) is governed by a variety of antigenic and environmental signals, yet the observed clone sizes follow a universal power law distribution. Guided by this reproducibility we propose effective models of somatic evolution where cell fate depends on an effective fitness. This fitness is determined by growth factors acting either on clones of cells with the same receptor responding to specific antigens, or directly on single cells with no regards for clones. We identify fluctuations in the fitness acting specifically on clones as the essential ingredient leading to the observed distributions. Combining our models with experiments we characterize the scale of fluctuations in antigenic environments and we provide tools to identify the relevant growth signals in different tissues and organisms. Our results generalize to any evolving population in a fluctuating environment.

Immunology↗

bioRxiv2015

Incomplete protection against dengue virus type 2 re-infection in Peru

Background. Nearly half of the worlds population is at risk for dengue, yet no licensed vaccine or anti-viral drug is currently available. Dengue is caused by any of four dengue virus serotypes (DENV-1 through DENV-4), and infection by a DENV serotype is assumed to provide life-long protection against re-infection by that serotype. We investigated the validity of this fundamental assumption during a large dengue epidemic caused by DENV-2 in Iquitos, Peru, in 2010-2011, 15 years after the first outbreak of DENV-2 in the region. Methodology/Principal Findings. We estimated the age-dependent prevalence of serotype-specific DENV antibodies from longitudinal cohort studies conducted between 1993 and 2010. During the 2010-2011 epidemic, active dengue cases were identified through active community- and clinic-based febrile surveillance studies, and acute inapparent DENV infections were identified through contact tracing studies. Based on the age-specific prevalence of DENV-2 neutralizing antibodies, the age distribution of DENV-2 cases was markedly older than expected. Homologous protection was estimated at 35.1% (95% confidence interval: 0% -- 65.2%). At the individual level, pre-existing DENV-2 antibodies were associated with an incomplete reduction in the frequency of symptoms. Among dengue cases, 43% (26/66) exhibited elevated DENV-2 neutralizing antibody titers for years prior to infection, compared with 76% (13/17) of inapparent infections (age-adjusted odds ratio: 4.2; 95% confidence interval: 1.1 - 17.7). Conclusions/Significance. Our data indicate that protection from homologous DENV re-infection may be incomplete in some circumstances, which provides context for the limited vaccine efficacy against DENV-2 in recent trials. Further studies are warranted to confirm this phenomenon and to evaluate the potential role of incomplete homologous protection in DENV transmission dynamics. Author SummaryHomotypic immunity against DENV infection has been assumed to be complete and lifelong, and to our knowledge, instances of homologous DENV re-infection have not been rigorously documented. However, few long-term studies have been conducted in such a way that homologous re-infection could be observed, if it did in fact occur. Our study provides evidence that homologous re-infection may occur in certain circumstances. We draw from data collected during a 2010-2011 DENV-2 epidemic in northeastern Peru, 15 years after the initial DENV-2 outbreak in the region. This finding has significant implications for our understanding of dengue epidemiology and for dengue vaccine formulation, which may need to consider multiple genotypes of each serotype. Data from other long-term dengue epidemiology studies should be analyzed to determine of homologous re-infection is a more widespread phenomenon.

Immunology↗

bioRxiv2015

Dynamical System Modeling to Simulate Donor T Cell Response to Whole Exome Sequencing-Derived Recipient Peptides Demonstrates Different Alloreactivity Potential In HLA-Matched and Mismatched Donor-Recipient Pairs

Abstract.Immune reconstitution kinetics and subsequent clinical outcomes in HLA matched recipients of allogeneic stem cell transplantation (SCT) are variable and difficult to predict. Considering SCT as a dynamical system, may allow sequence differences across the exomes of the transplant donors and recipients to be used to simulate an alloreactive T cell response, which may allow better clinical outcome prediction. To accomplish this, whole exome sequencing was performed on 34 HLA matched SCT donor-recipient pairs (DRP), and the nucleotide sequence differences translated to peptides. The binding affinity of the peptides to the relevant HLA in each DRP was determined. The resulting array of peptide-HLA binding affinity values in each patient was considered as an operator modifying a hypothetical T cell repertoire vector, in which each T cell clone proliferates in accordance to the logistic equation of growth. Using an iterating system of matrices, each simulated T cell clones growth was calculated with the steady state population being proportional to the magnitude of the binding affinity of the driving HLA-peptide complex. Incorporating competition between T cell clones responding to different HLA-peptide complexes reproduces a number of features of clinically observed T cell clonal repertoire in the simulated repertoire. These include, sigmoidal growth kinetics of individual T cell clones and overall repertoire, Power Law clonal frequency distribution, increase in repertoire complexity over time with increasing clonal diversity and finally, alteration of clonal dominance when a different antigen array is encountered, such as in stem cell transplantation. The simulated, alloreactive T cell repertoire was markedly different in HLA matched DRP. The patterns were differentiated by rate of growth, and steady state magnitude of the simulated T cell repertoire and demonstrate a possible correlation with survival. In conclusion, exome wide sequence differences in DRP may allow simulation of donor alloreactive T cell response to recipient antigens and may provide a quantitative basis for refining donor selection and titration of immunosuppression following SCT.

Immunology↗

bioRxiv2015

Small Heat Shock Proteins and Eicosanoid Pathways Modulate Caspase-1 Activity in the Fat Bodies of Antheraea pernyi

After heat shock injury, a group of proteins that regulate protein-folding processes are synthesised to prevent damage. Caspase is an enzyme responsible for the execution ostress-induced apoptosis. Heat shock proteins (Hsp) are capable of modulating caspase activity. In addition to changes in protein synthesis, heat shock causes the release of arachidonic acid (AA) from plasma membranes and the subsequent synthesis of eicosanoids, i.e., activation of the AA pathways. The development of cytoprotective strategies might depend on whether caspase-1 activity is affected by heat shock preconditioning and the associated pharmacological modulations after heat shock injury. Therefore, we studied the effects of heat shock preconditioning and modulations of the eicosanoid pathways on Ap-sHSP20.8 and on the final apoptotic effector enzyme caspase-1 to clarify whether these effects were modulated in the fat bodies of Antheraea pernyi injured by heat shock. We concluded that eicosanoid biosynthesis inhibitors might be utilised to simultaneously decrease Hsp 20.8 synthesis and to increase caspase-1 activity. Modifications of the eicosanoid pathways might also be used to mediate caspase-1 activity under hyperthermic conditions, suggesting a novel mechanism for regulation of caspase-1 in the fat bodies of A. pernyi

Immunology↗

bioRxiv2015

Glucose modulates Drosophila longevity and immunity independent of the microbiota.

The acquisition of nutrients is essential for maintenance of metabolic processes in all organisms. Nutritional imbalance contributes to myriad metabolic disorders that include malnutrition, diabetes, and even cancer. Recently, the importance of macronutrient ratio of food has emerged as a critical factor to determine health outcomes. Here we show that individual modifications to a completely defined diet markedly impact multiple aspects of organism wellbeing in Drosophila melanogaster. Through a longitudinal survey of several diets we demonstrate that increased levels of dietary glucose significantly improve longevity and immunity in adult Drosophila. Our metagenomic studies, show that relative macronutrient levels not only influence the host, but also have a profound impact on microbiota composition. However, we found that elevated dietary glucose extended the lifespan of adult flies even when raised in a germ-free environment. Furthermore, when challenged with a chronic enteric infection, flies fed a diet with added glucose had increased survival times even in the absence of an intact microbiota. Thus, in contrast to known links between the microbiota and animal health, our findings uncover a novel microbiota-independent response to diet that impacts host wellbeing. As dietary responses are highly conserved in animals, we believe our results offer a general understanding of the association between glucose metabolism and animal health.

Immunology↗

bioRxiv2015

High efficiency transfection of thymic epithelial cell lines and primary thymic epithelial cells by Nucleofection.

Thymic epithelial cells (TECs) are required for the development and differentiation of T cells and are sufficient for the positive and negative selection of developing T cells. Although TECs play a critical role in T cell biology, simple, efficient and readily scalable methods for the transfection of TEC lines and primary TECs have not been described. We tested the efficiency of Nucleofection for the transfection of 4 different mouse thymic epithelial cell lines that had been derived from cortical or medullary epithelium. We also tested primary mouse thymic epithelial cells isolated from fetal and postnatal stages. We found that Nucleofection was highly efficient for the transfection of thymic epithelial cells, with transfection efficiencies of 30-70% for the cell lines and 15-35% for primary TECs with low amounts of cell death. Efficient transfection by Nucleofection can be performed with established cortical and medullary thymic epithelial cell lines as well as primary TECs isolated from E15.5 day fetal thymus or postnatal day 3 or 30 thymus tissue. The high efficiency of Nucleofection for TEC transfection will enable the use of TEC lines in high throughput transfection studies and simplifies the transfection of primary TECs for in vitro or in vivo analysis.

Immunology↗

bioRxiv2015

Conjecture: Some auto-immune diseases are caused by the tissue, not a problem with the immune system

Applying highly sensitive modern immune profiling techniques to the blood or inflamed tissue of auto-immune patients with one of the common T-cell mediated diseases fails to detect large clonal expansions or other signs of a dysregulated immune system. Additionally, these new methods have shown that self-reactive T-cells are found in the periphery (and are not completely negatively selected in the thymus as previously believed). Combining these new data with well-established studies in auto-immunity leads to the conjecture that certain auto-immune diseases are likely to be caused by defects in tissue, not by dysregulation of the adaptive immune system. In particular, one hypothesis is that specific tissues up-regulate HLA class 2 genes, presenting epitopes that are bound by CD4+ helper T cells, which facilitates an immune response against the tissue specific cells.

Immunology↗