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Antiviral adaptive immunity and tolerance in the mosquito Aedes aegyti

Mosquitoes spread pathogenic arboviruses while themselves tolerate infection. We here characterize an immunity pathway providing long-term antiviral protection and define how this pathway discriminates between self and non-self. Mosquitoes use viral RNAs to create viral derived cDNAs (vDNAs) central to the antiviral response. vDNA molecules are acquired through a process of reverse-transcription and recombination directed by endogenous retrotransposons. These vDNAs are thought to integrate in the host genome as endogenous viral elements (EVEs). Sequencing of pre-integrated vDNA revealed that the acquisition process exquisitely distinguishes viral from host RNA, providing one layer of self-nonself discrimination. Importantly, we show EVE-derived piRNAs have antiviral activity and are loaded onto Piwi4 to inhibit virus replication. In a second layer of self-non-self discrimination, Piwi4 preferentially loads EVE-derived piRNAs, discriminating against transposon-targeting piRNAs. Our findings define a fundamental virus-specific immunity pathway in mosquitoes that uses EVEs as a potent and specific antiviral transgenerational mechanism.

immunology

Bioorthogonal Antigens Allow The Study Of Intracellular Processing And Presentation Of Post-Translationally Modified Antigens

Proteolysis is fundamental to many biological processes. In the immune system, it underpins the activation of the adaptive immune response: degradation of antigenic material into short peptides and presentation thereof on major histocompatibility complexes, leads to activation of T-cells. This initiates the adaptive immune response against many pathogens.

immunology

Growth-factor like gene regulation is separable from survival and maturation in antibody secreting cells

Recurrent mutational activation of the MAP kinase pathway in plasma cell myeloma implicates growth factor-like signaling responses in the biology of antibody secreting cells (ASCs). Physiological ASCs survive in niche microenvironments, but how niche signals are propagated and integrated is poorly understood. Here we dissect such a response in human ASCs using an in vitro model. Applying time course expression data and parsimonious gene correlation networking analysis (PGCNA), we map expression changes that occur during the maturation of proliferating plasmablast to quiescent plasma cell under survival conditions including the potential niche signal TGFB3. This analysis demonstrates a convergent pattern of differentiation, linking UPR/ER stress to secretory optimization, co-ordinated with cell cycle exit. TGFB3 supports ASC survival while having a limited effect on gene expression including up-regulation of CXCR4. This is associated with a significant shift in response to SDF1 in ASCs with amplified ERK1/2 activation, growth factor-like immediate early gene regulation and EGR1 protein expression. Similarly, ASCs responding to survival conditions initially induce partially overlapping sets of immediate early genes, without sustaining the response. Thus, in human ASCs growth factor-like gene regulation is transiently imposed by niche signals but is not sustained during subsequent survival and maturation.

immunology

Antigen receptor locus dynamics is orchestrated near the sol-gel phase transition to enforce stepwise VDJ gene rearrangement

Diverse antibody repertoires are generated through remote genomic interactions involving immunoglobulin variable (VH), diversity (DH) and joining (JH) gene segments. How such interactions are orchestrated remains unknown. We developed a novel strategy to track VH-DHJH motion and interactions in live B-lymphocytes. We found that VH and DHJH segments were trapped in configurations that only allowed constrained local motion, such that spatially proximal VH and DHJH segments remained in proximity, whereas spatially remote segments explored their immediate neighborhood while remaining remote. Comparison of experimental and simulated data revealed that such a highly constrained motion was imposed by a network of cross-linked chromatin chains characteristic of a gel phase, yet it was poised near the sol phase, a solution of independent chromatin chains. We propose that epigenetically induced gel droplets and the proximity to the sol-gel phase transition constitute the mechanism that orchestrates ordered VDJ rearrangement.

immunology

Stochastic simulations show how passive immunization can influence the germinal centre reaction and optimize host humoral responses

Passive immunization with antigen-specific antibodies was shown recently to induce lasting improvements in endogenous antibody production, raising the prospect of using passive immunization as a tool to engineer host humoral responses. The mechanism with which administered antibodies alter endogenous antibody production remains unknown. B cells that produce antigen-specific antibodies evolve and get selected in germinal centres (GCs). This selection requires that B cells acquire antigen presented in GCs. We hypothesized that passive immunization biases this selection in favour of B cells with high affinities for antigen. Administered antibodies form immune complexes with antigen which only B cells with higher affinities than the administered antibodies for antigen can rupture and acquire antigen, thus increasing the selection stringency in GCs. With this mechanistic hypothesis, we constructed a stochastic simulation model of the GC reaction. The simulations recapitulated and synthesized several independent experimental observations, presenting strong evidence in support of our hypothesis. Further, the simulations revealed a quality-quantity trade-off constraining the GC response. As the selection stringency increased, surviving B cells had higher affinities for antigen but fewer B cells survived. Increasing antigen availability in the GC relaxed this constraint. The affinity of the administered antibodies and/or antigen availability could thus be tuned to maximize the GC output. Comprehensively spanning parameter space, we predict passive immunization protocols that exploit the quality-quantity trade-off and maximize the GC output. Our study thus presents a new conceptual understanding of the GC reaction and a computational framework for the rational optimization of passive immunization strategies.\n\nSignificance statementWhen natural antibody production is inadequate, passive immunization with external antibodies can alleviate disease. Remarkably, passive immunization induced lasting improvements in natural antibody production in recent studies, suggesting that it could be deployed to engineer natural antibody responses. However, how administered antibodies alter natural antibody production remains unknown. B cells that produce antibodies targeting specific antigen evolve in germinal centres (GCs). We hypothesized that administered antibodies form complexes with antigen, preferentially allowing B cells with higher affinities to acquire antigen and be selected, thus altering antibody production. With this mechanistic hypothesis, we performed stochastic simulations of the GC reaction, which recapitulated experiments, unravelled a quality-quantity trade-off constraining the GC response, and predicted passive immunization protocols that maximized the GC output.

immunology

Haematological parameters and plasma levels of 8-iso-prostaglandin F2α in malaria-sickle cell co-morbidity: A cross sectional study

IntroductionMalaria and sickle cell disease (SCD) co-morbidity have previously been reported in Ghana. However, there is paucity of data on haematological profiles and oxidative stress in comorbidity states. This study identified novel inflammatory biomarkers associated with malaria in SCD and analyzed the levels of 8-iso-prostaglandin F2 oxidative stress biomarker in malaria-SCD co-morbidity in Ghanaian patients.\n\nMethodsBlood (5ml) was collected from malaria patients into K3-EDTA tube. Malaria parasites speciation and quantification were then done according WHO guidelines. All eligible samples were assayed for haematological profile, sickle cell phenotyping, infectious markers (hepatitis B, hepatitis C, syphilis and HIV 1&2) and plasma levels of 8-epi-prostaglandin F2..\n\nResultsPrevalence of malaria in SCD (malaria-SCD) was 13.4% (45/335). Male: female ratio was 0.8:1 (X2=1.43, p=0.231). Mean ages for malaria in normal haemoglobin type (malaria-HbAA) and malaria-SCD were 12.79{+/-}4.91 and 11.56{+/-}3.65 years respectively (p=0.048). Geometric mean of parasite density was higher in malaria-HbAA (20394 parasites/l vs. 9990 parasites/l, p=0.001) whilst mean body temperature was higher in malaria-SCD (39.0{+/-}0.87{degrees}C vs. 37.9{+/-}1.15{degrees}C, p=0.001). Mean leukocytes, lymphocytes, eosinophils, monocytes, platelets and platelet indices values were significantly elevated in malaria-SCD. Significant reduction in RBC and RBC indices in malaria-SCD were also observed. Eosinophils-to-basophils ratio (EBR) and monocytes-to-basophils ratio (MBR) were novel cellular inflammatory biomarkers which could predict malaria in SCD. The sensitivities of cut-off values of EBR>14, MBR>22 and combined use of EBR>14 and MBR>22 were 79.55%, 84.09% and 91.11% respectively. Mean 8-iso-prostaglandin F2 was 338.1pg/ml in malaria-HbAA and 643.8pg/ml in malaria-SCD (p=0.001). 8-iso-prostaglandin F2 correlated with parasite density (r=0.787, p=0.001), temperature (r=0.566, p=0.001) and leucocytes (r=0.573, p=0.001) and negatively correlated with RBC (r=-0.476, p=0.003), haemoglobin (r=-0.851, p=0.001) and haematocrit (r=-0.735, p=0.001).\n\nConclusionPlasmodium falciparum parasitaemia increases oxidative damage and causes derangement haematological parameters. Cut of values of EBR>14 and MBR>22 could predict malaria in SCD.

immunology

PD-1 suppresses the maintenance of cell couples between cytotoxic T cells and tumor target cells within the tumor

CD8+ T cell killing of tumor cells is suppressed by the tumor microenvironment. Inhibitory receptors, prominently PD-1, are key mediators of this suppression. To discover cellular defects triggered by tumor exposure and associated PD-1 signaling, we have established an ex vivo imaging approach to investigate CD8+ tumor infiltrating lymphocytes (TILs) interacting with tumor targets. Whilst TIL:tumor cell couples formed effectively, couple stability deteriorated within 1-2 minutes. This was associated with excessive cofilin recruitment to the cellular interface, coincident deterioration of f-actin structures, increased TIL locomotion, and impaired tumor cell killing. Diminished engagement of PD-1 within the tumor, but not acute ex vivo blockade, partially restored cell couple maintenance and killing. PD-1 thus suppresses TIL function by inducing a polarization-impaired state.

immunology

Programmed Delayed Splicing: A Mechanism for Timed Inflammatory Gene Expression

Inflammation involves timed gene expression, suggesting that the fine-tuned onset, amplitude, and termination of expression of hundreds of genes is of critical importance to organismal homeostasis. Recent study of post-transcriptional regulation of inflammatory gene expression led to the suggestion of a regulatory role for pre-mRNA splicing. Here, using a hybrid capture approach to purify incompletely spliced, chromatin-associated pre-mRNAs, we use deep sequencing to study pre-mRNA splicing of the NF-B transcriptome. By freezing transcription and examining subsequent splicing of complete transcripts, we find many introns splice tens to hundreds of times slower than average. Investigating the basis of these delays, we focused on evolutionarily conserved introns with suboptimal splice donor sequences and found that strengthening these donor sites by as few as two nucleotides in minigene reporter assays markedly increased gene expression for several targets. This suggests that such sites can act as timing elements that both delay mRNA production and limit expression amplitude. To broaden this mechanistic view, we applied deep learning sequence-to-function models with feature attribution to identify additional regulatory sequences--both intronic and exonic--that may contribute to delayed splicing through mechanisms independent of donor site strength. This integrated approach revealed non-canonical motifs enriched in slow-splicing introns, pointing to a broader repertoire of cis-elements that can fine-tune transcript maturation during inflammation. Together, these findings support a model in which the temporal regulation of pre-mRNA splicing serves as a layer of control in inflammatory gene expression, and raise the possibility that similar timing mechanisms operate in other rapid-response transcriptional programs.

immunology

Crystal structure of m4-1BB/4-1BBL complex reveals an unusual dimeric ligand that undergoes structural changes upon receptor binding.

The interaction between the 4-1BB and its ligand 4-1BBL provides co-stimulatory signals for T cell activation and proliferation, but differences in the mouse and human molecules might result in differential engagement of this pathway. Here, we report the crystal structure of mouse 4-1BBL and of the mouse 4-1BB/4-1BBL complex, together provide insights into the molecular recognition of the cognate receptor by m4-1BBL. In contrast to all human or mouse TNF ligands that form non-covalent mostly trimeric assemblies, the m4-1BBL structure formed a novel disulfide linked dimeric assembly. The structure showed that certain differences in the amino acid composition along the intramolecular interface, together with two specific residues (Cys 246 and Ser 256) that are exclusively present in m4-1BBL, are responsible for unique dimerization. Unexpectedly, upon binding to m4-1BB, m4-1BBL undergoes structural changes within each protomer, in addition the individual m4-1BBL protomers rotate with respect to each other, leading to a different dimerization interface with more inter-subunit interactions. In the m4-1BB/4-1BBL complex, each receptor monomer binds exclusively to a single ligand subunit with contributions of cysteine-rich domain (CRD) 1, CRD2 and CRD3. Furthermore, structure-guided mutagenesis of the binding interface revealed that novel binding interactions with the GH loop, rather than the DE loop, are energetically critical and define the species based receptor selectivity for m4-1BBL. A comparison with the human 4-1BB/4-1BBL complex highlighted several differences between the ligand and receptor binding interfaces and provide an explanation for the absence of inter species cross-reactivity between human and mouse 4-1BB and 4-1BBL molecules.

immunology

Human IFNε: Spaciotemporal expression, hormone regulation and innate immunity in the female reproductive tract

Interferon epsilon (IFN{varepsilon}) plays an important role in regulating protective immunity in the female reproductive tract in mouse models; but the expression and regulation of this IFN{varepsilon} in the human FRT had not yet been characterised. Here we show that IFN{varepsilon} is selectively and highly expressed in the human FRT, a unique characteristic among the many types of IFN. IFN{varepsilon} has distinct expression patterns in upper compared with lower FRT where it is predominantly expressed in the basal layers of the stratified squamous epithelia. We demonstrate direct regulation of IFN{varepsilon} expression is suppressed by progesterone consistent with its inverse correlation with progesterone receptor expression, but only in the endometrium where its expression therefore fluctuates throughout the menstrual cycle. We show that IFN{varepsilon} regulates immunoregulatory IFN regulated genes (IRGs) in FRT epithelial cells. The characterisation of huIFN{varepsilon} expression in both the upper and the lower FRT epithelia and its protective properties make this IFN well placed to be an important player in mediating hormonal control of FRT immune response and susceptibility to FRT infection.\n\nSummaryBourke et al. characterise the novel type I interferon epsilon (IFN{varepsilon}), as the only IFN constitutively expressed throughout the human female reproductive tract (FRT), where it is hormonally regulated and modules IFN dependent FRT immunity.

immunology

IgA-deficient humans exhibit gut microbiota dysbiosis despite production of compensatory IgM

Immunoglobulin A is the dominant antibody isotype found in mucosal secretions and enforces host-microbiota symbiosis in mice, yet selective IgA-deficiency (sIgAd) is the most common primary immunodeficiency in humans and is often described as asymptomatic. Here, we determined the effects of IgA deficiency on human gut microbiota composition and evaluated the possibility that secretion of IgM can compensate for a lack of secretory IgA. We used 16S rRNA gene sequencing and bacterial cell sorting to evaluate gut microbiota composition and IgA or IgM coating of the gut microbiota in 15 sIgAd subjects and 15 matched controls. Although sIgAd subjects secreted a significant amount of IgM into the intestinal lumen, this was insufficient to fully compensate for the lack of secretory IgA. Indeed, sIgAd subjects displayed an altered gut microbiota composition as compared to healthy controls, which was characterized by a trend towards decreased overall microbial diversity and significant shifts in the relative abundances of specific microbial taxa. While IgA targets a defined subset of the microbiota via high-level coating, compensatory IgM binds a broader subset of the microbiota in a less targeted manner. We conclude that IgA plays a critical and non-redundant role in controlling gut microbiota composition in humans and that secretory IgA has evolved to maintain a diverse and stable gut microbial community that promotes human health, enhances resistance to infection, and is resilient to perturbation.

immunology

Conformational states control Lck switching between free and confined diffusion modes in T cells

T cell receptor (TCR) phosphorylation by Lck is an essential step in T cell activation. It is known the conformational states of Lck control enzymatic activity; however, the underlying principles of how Lck finds its substrate in the plasma membrane remain elusive. Here, single-particle tracking is paired with photoactivatable localization microscopy (sptPALM) to observe the diffusive modes of Lck in the plasma membrane. Individual Lck molecules switched between free and confined diffusion in resting and stimulated T cells. Conformational state, but not partitioning into membrane domains, caused Lck confinement as open conformation Lck was more confined than closed. Further confinement of kinase-dead versions of Lck suggests that Lck interacts with open active Lck to cause confinement, irrespectively of kinase activity. Our data supports a model that confined diffusion of open Lck results in high local phosphorylation rates and closed Lck diffuses freely to enable wide-range scanning of the plasma membrane.

immunology

Analysis of an HIV model with post-treatment control

Recent investigation indicated that latent reservoir and immune impairment are responsible for the post-treatment control of HIV infection. In this paper, we simplify the disease model with latent reservoir and immune impairment and perform a series of mathematical analysis. We obtain the basic infection reproductive number R0 to characterize the viral dynamics. We prove that when R0 < 1, the uninfected equilibrium of the proposed model is globally asymptotically stable. When R0 > 1, we obtain two thresholds, the post-treatment immune control threshold and the elite control threshold. The model has bistable behaviors in the interval between the two thresholds. If the proliferation rate of CTLs is less than the post-treatment immune control threshold, the model does not have positive equilibria. In this case, the immune free equilibrium is stable and the system will have virus rebound. On the other hand, when the proliferation rate of CTLs is greater than the elite control threshold, the system has stable positive immune equilibrium and unstable immune free equilibrium. Thus, the system is under elite control.\n\nAuthor summaryIn this article, we use mathematical model to investigate the combined effect of latent reservoir and immune impairment on the post-treatment control of HIV infection. By simplifying an HIV model with latent reservoir and immune impairment, and performing mathematical analysis, we obtain the post-treatment immune control threshold and the elite control threshold for the HIV dynamics when R0 > 1. The HIV model displays bistable behaviors in the interval between the two thresholds. We illustrate our results using both mathematical analysis and numerical simulation. Our result is consistent with recent medical experiment. We show that patient with low proliferation rate of CTLs may undergo virus rebound, and patient with high proliferation rate of CTLs may obtain elite control of HIV infection. We perform bifurcation analysis to illustrate the infection status of patient with the variation of proliferation rate of CTLs, which potentially explain the reason behind different outcomes among HIV patients.

immunology

Differential induction of interferon stimulated genes between type I and type III interferons is independent of interferon receptor abundance

It is currently believed that type I and III interferons (IFNs) have redundant functions. However, the preferential distribution of type III IFN receptor on epithelial cells suggests functional differences at epithelial surfaces. Here, using human intestinal epithelial cells we could show that although both type I and type III IFNs confer an antiviral state to the cells, they do so with distinct kinetics. Type I IFN signaling is characterized by an acute strong induction of interferon stimulated genes (ISGs) and confers fast antiviral protection. On the contrary, the slow acting type III IFN mediated antiviral protection is characterized by a weaker induction of ISGs in a delayed manner compared to type I IFN. Moreover, while transcript profiling revealed that both IFNs induced a similar set of ISGs, their temporal expression strictly depended on the IFNs, thereby leading to unique antiviral environments. Using a combination of data-driven mathematical modeling and experimental validation, we addressed the molecular reason for this differential kinetic of ISG expression. We could demonstrate that these kinetic differences are intrinsic to each signaling pathway and not due to different expression levels of the corresponding IFN receptors. We report that type III IFN is specifically tailored to act in specific cell types not only due to the restriction of its receptor but also by providing target cells with a distinct antiviral environment compared to type I IFN. We propose that this specific environment is key at surfaces that are often challenged with the extracellular environment.\n\nAuthor summaryThe human intestinal tract plays two important roles in the body: first it is responsible for nutrient absorption and second it is the primary barrier which protects the human body from the outside environment. This complex tissue is constantly exposed to commensal bacteria and is often exposed to both bacterial and viral pathogens. To protect itself, the gut produces, among others, secreted agents called interferons which help to fight against pathogen attacks. There are several varieties (type I, II, and III) of interferons and our work aims at understanding how type I and III interferon act to protect human intestinal epithelial cells (hIECs) during viral infection. In this study, we confirmed that both interferons can protect hIECs against viral infection but with different kinetics. We determined that type I confer an antiviral state to hIECs faster than type III interferons. We uncovered that these differences were intrinsic to each pathway and not the result of differential abundance of the respective interferon receptors. The results of this study suggest that type III interferon may provide a different antiviral environment to the epithelium target cells which is likely critical for maintaining gut homeostasis. Our findings will also help us to design therapies to aid in controlling and eliminating viral infections of the gut.

immunology

Cell type-specific role of lamin-B1 and its inflammation-driven reduction in organ building and aging

Cellular architectural proteins often participate in organ development and maintenance. Although functional decay of some of these proteins during aging is known, the cell-type specific developmental role and the cause and consequence of their subsequent decay remain to be established especially in mammals. By studying lamins, the nuclear structural proteins, we demonstrate that lamin-B1 functions specifically in the thymic epithelial cells (TECs) for proper thymus organogenesis. An upregulation of proinflammatory cytokines in the intra-thymic myeloid immune cells during aging accompanies a gradual reduction of adult TEC lamins-B1. These cytokines cause adult TEC senescence and lamin-B1 reduction. We identify 17 adult TEC subsets and show that TEC lamin-B1 maintains the composition of these TECs. Lamin-B1 supports the expression of TEC genes needed for maintaining adult thymic architecture and function. Thus, structural proteins involved in organ building and maintenance can undergo inflammation-driven decay which can in turn contribute to age-associated organ degeneration.

immunology

Sex differences in IL-17 determine chronicity in male versus female urinary tract infection

Sex-based differences influence incidence and outcome of infectious disease. Women have a significantly greater incidence of urinary tract infection (UTI) than men, yet, conversely, male UTI is more persistent with greater associated morbidity. Mechanisms underlying these sex-based differences are unknown, in part due to a lack of experimental models. We optimized a model to transurethrally infect male mice and directly compared UTI in both sexes. Although both sexes were initially equally colonized by uropathogenic E. coli, only male and testosterone-treated female mice remained chronically infected for up to 4 weeks. Female mice had more robust innate responses, including higher IL-17 expression, and increased {gamma}{delta} T and LTi-like cells in the bladder following infection. Accordingly, neutralizing IL-17 abolished resolution in female mice, identifying the cytokine pathway necessary for bacterial clearance. Our findings support the concept that sex-based responses to UTI contribute to impaired innate immunity in males and provide a rationale for non-antibiotic-based immune targeting to improve the response to UTI.\n\nOne Sentence SummaryWe investigated mechanisms underlying the clinical observation that while urinary tract infection is more prevalent in women, it is more severe in men, observing that in contrast to robust immune responses characterized by IL-17 in female animals, male mice develop chronic infection, following a failure to initiate innate immunity.

immunology

Aging Boosts Antiviral CD8+T Cell Memory Through Improved Engagement Of Diversified Recall Response Determinants

The determinants of protective CD8+ memory T cell (CD8+TM) immunity remain incompletely defined and may in fact constitute an evolving agency as aging CD8+TM progressively acquire enhanced rather than impaired recall capacities. Here, we show that old as compared to young antiviral CD8+TM more effectively harness disparate molecular processes (cytokine signaling, trafficking, effector functions, and co-stimulation/inhibition) that in concert confer greater secondary reactivity. The relative reliance on these pathways is contingent on the nature of the secondary challenge (greater for chronic than acute viral infections) and over time, aging CD8+TM re-establish a dependence on the same accessory signals required for effective priming of naive CD8+T cells in the first place. Thus, our findings are consistent with the recently proposed \"rebound model\" that stipulates a gradual alignment of naive and CD8+TM properties, and identify a diversified collection of potential targets that may be exploited for the therapeutic modulation of CD8+TM immunity.

immunology

Cellular polarity asymmetrically functionalizes pathogen recognition receptor-mediated intrinsic immune response in human intestinal epithelium cells

Intestinal epithelial cells (IECs) act as a physical barrier separating the commensal-containing intestinal tract from the sterile interior. These cells have found a complex balance allowing them to be prepared for pathogen attacks while still tolerating the presence of bacteria/viral stimuli present in the lumen of the gut. Using primary human IECs, we probed the mechanisms, which allow for such a tolerance. We discovered that viral infection emanating from the basolateral side of IECs elicited a stronger intrinsic immune response as compared to lumenal apical infection. We determined that this asymmetric immune response was driven by the clathrin-sorting adapter AP-1B which mediates the polarized sorting of Toll-like receptor 3 (TLR3) toward the basolateral side of IECs. Mice and human IECs lacking AP-1B showed an exacerbated immune response following apical stimulation. Together these results suggest a model where the cellular polarity program plays an integral role in the ability of IECs to partially tolerate apical commensals while remaining fully responsive against invasive basolateral pathogens.

immunology