Megaproject will chart human immune diversity.

Human Immunome Project's survey aims to improve drugs and vaccines.

A Comprehensive View on the Human Antibody Repertoire Against Staphylococcus aureus Antigens in the General Population.

Our goal was to provide a comprehensive overview of the antibody response to Staphylococcus aureus antigens in the general population as a basis for defining disease-specific profiles and diagnostic signatures. We tested the specific IgG and IgA responses to 79 staphylococcal antigens in 996 individuals from the population-based Study of Health in Pomerania. Using a dilution-based multiplex suspension array, we extended the dynamic range of specific antibody detection to seven orders of magnitude, allowing the precise quantification of high and low abundant antibody specificities in the same sample. The observed IgG and IgA antibody responses were highly heterogeneous with differences between individuals as well as between bacterial antigens that spanned several orders of magnitude. Some antigens elicited significantly more IgG than IgA and vice versa. We confirmed a strong influence of colonization on the antibody response and quantified the influence of sex, smoking, age, body mass index, and serum glucose on anti-staphylococcal IgG and IgA. However, all host parameters tested explain only a small part of the extensive variability in individual response to the different antigens of S. aureus.

Interindividual Variability in Lymphocyte Stimulation and Transcriptomic Response Predicts Mycophenolic Acid Sensitivity in Healthy Volunteers.

Mycophenolic acid (MPA) is an immunosuppressant commonly used to prevent renal transplant rejection and treat glomerulonephritis. MPA inhibits IMPDH2 within stimulated lymphocytes, reducing guanosine synthesis. Despite the widespread use of MPA, interindividual variability in response remains with rates of allograft rejection up to 15% and approximately half of individuals fail to achieve complete remission to lupus nephritis. We sought to identify contributors to interindividual variability in MPA response, hypothesizing that the HPRT1 salvage guanosine synthesis contributes to variability. MPA sensitivity was measured in 40 healthy individuals using an ex vivo lymphocyte viability assay. Measurement of candidate gene expression (n ± 40) and single-cell RNA-sequencing (n ± 6) in lymphocytes was performed at baseline, poststimulation, and post-MPA treatment. After stimulation, HPRT1 expression was 2.1-fold higher in resistant individuals compared with sensitive individuals (P ± 0.049). Knockdown of HPRT1 increased MPA sensitivity (12%; P ± 0.003), consistent with higher expression levels in resistant individuals. Sensitive individuals had higher IMPDH2 expression and 132% greater stimulation. In lymphocyte subpopulations, differentially expressed genes between sensitive and resistant individuals included KLF2 and LTB. Knockdown of KLF2 and LTB aligned with the predicted direction of effect on proliferation. In sensitive individuals, more frequent receptor-ligand interactions were observed after stimulation (P ± 0.0004), but fewer interactions remained after MPA treatment (P ± 0.0014). These data identify a polygenic transcriptomic signature in lymphocyte subpopulations predictive of MPA response. The degree of lymphocyte stimulation, HPRT1, KLF2, and LTB expression may serve as markers of MPA efficacy.

Anti-tumor immune response varies among individuals: A gene expression profiling of mouse melanoma.

Melanoma is amongst the most aggressive malignant tumors. The purpose of this study is to detect the tumor microenvironment systematically using multi-omics analyses and to propose strategies for precision medicine. Multiple factors of tumor microenvironment contribute to the drug resistance and immune surveillance failure. Here we analyzed genome mutations and characterized the immune state of tumor microenvironments in mouse melanoma by whole exome sequencing (WES) and RNA sequencing (RNA-Seq) approaches. Somatic mutation analysis revealed 35.1% novel mutations in mouse tumors when compared with B16F10 cell line, provided a basis for multi-site sequencing for accurate neoantigen selection. Mutation cluster, gene expression comparison, and gene ontology (GO) analyses by R packages proved DNA repair damage, inflammation, slower cell division, and metabolic change in tumor microenvironment. Further analyses of T-cell receptor (TCR) sequences, immune signaling pathway activation, tumor infiltrated immune cells and chemokine expression revealed extensive difference of antitumor immune response among individuals. Our study revealed the characteristics of tumor microenvironment with mouse melanoma model, suggested the need of comprehensive genome mutations and personal immune state analyses for cancer precision medicine.

Unveiling Interindividual Variability of Human Fibroblast Innate Immune Response Using Robust Cell-Based Protocols.

The LabEx Milieu Interieur (MI) project is a clinical study centered on the detailed characterization of the baseline and induced immune responses in blood samples from 1,000 healthy donors. Analyses of these samples has lay ground for seminal studies on the genetic and environmental determinants of immunologic variance in a healthy cohort population. In the current study we developed in vitro methods enabling standardized quantification of MI-cohort-derived primary fibroblasts responses. Our results show that in vitro human donor cohort fibroblast responses to stimulation by different MAMPs analogs allows to characterize individual donor immune-phenotype variability. The results provide proof-of-concept foundation to a new experimental framework for such studies. A bio-bank of primary fibroblast lines was generated from 323 out of 1,000 healthy individuals selected from the MI-study cohort. To study inter-donor variability of innate immune response in primary human dermal fibroblasts we chose to measure the TLR3 and TLR4 response pathways, both receptors being expressed and previously studied in fibroblasts. We established high-throughput automation compatible methods for standardized primary fibroblast cell activation, using purified MAMPS analogs, poly I:C and LPS that stimulate TLR3 and TLR4 pathways respectively. These results were in turn compared with a stimulation method using infection by HSV-1 virus. Our "Add-only" protocol minimizes high-throughput automation system variability facilitating whole process automation from cell plating through stimulation to recovery of cell supernatants, and fluorescent labeling. Images were acquired automatically by high-throughput acquisition on an automated high-content imaging microscope. Under these methodological conditions standardized image acquisition provided for quantification of cellular responses allowing biological variability to be measured with low system noise and high biological signal fidelity. Optimal for automated analysis of immuno-phenotype of primary human cell responses our method and experimental framework as reported here is highly compatible to high-throughput screening protocols like those necessary for chemo-genomic screening. In context of primary fibroblasts derived from donors enrolled to the MI-clinical-study our results open the way to assert the utility of studying immune-phenotype characteristics relevant to a human clinical cohort.

Fast and fierce versus slow and smooth: Heterogeneity in immune responses to Plasmodium in the controlled human malaria infection model.

Controlled human malaria infection (CHMI) is an established model in clinical malaria research. Upon exposure to Plasmodium falciparum parasites, malaria-naive volunteers differ in dynamics and composition of their immune profiles and subsequent capacity to generate protective immunity. CHMI volunteers are either inflammatory responders who have prominent cellular IFN-γ production primarily driven by adaptive T cells, or tempered responders who skew toward antibody-mediated humoral immunity. When exposed to consecutive CHMIs under antimalarial chemoprophylaxis, individuals who can control parasitemia after a single immunization (fast responders) are more likely to be protected against a subsequent challenge infection. Fast responders tend to be inflammatory responders who can rapidly induce long-lived IFN-γ+ T cell responses. Slow responders or even non-responders can also be protected, but via a more diverse range of responses that take a longer time to reach full protective efficacy, in part due to their tempered phenotype. The latter group can be identified at baseline before CHMI by higher expression of inhibitory ligands CTLA-4 and TIM-3 on CD4+ T cells. Delineating heterogeneity in human immune responses to P. falciparum will facilitate rational design and strategy towards effective malaria vaccines.

Whole parasite vaccines for the asexual blood stages of Plasmodium.

After many decades of research, an effective vaccine for malaria is still not available. Most research efforts have focused on identifying a key target antigen and then using powerful adjuvants to generate specific antibodies that can block parasites from entering host cells (hepatocytes, red blood cells). However, the inability to generate sufficiently potent antibody responses has led to significant disappointment with current vaccine programs. An additional challenge for sub-unit vaccines is that key vaccine antigens are highly polymorphic. These challenges have spurred radically different approaches to malaria vaccine development. Many of these involve the use of "whole parasites"-either extracted from mosquitoes or cultured. With these, every parasite molecule for that particular strain is included in the vaccine. This strategy is showing great promise following several clinical trials with irradiated sporozoites. However, a whole-parasite approach to a blood stage vaccine has not advanced as quickly. This article outlines the history, the different approaches that are being taken and the challenges associated with whole parasite blood stage vaccines and discusses recent exciting developments as these vaccines now move into the clinic.

Longitudinal Intra- and Inter-individual variation in T-cell subsets of HIV-infected and uninfected men participating in the LA Multi-Center AIDS Cohort Study.

To assess the intra-individual and inter-individuals biological variation and the effect of aging on lymphocyte T-cells subsets.We assessed lymphocyte phenotypes (CD3, CD4, and CD8 T-cells) in 89 HIV-1-infected and 88 uninfected white non-Hispanic men every 6 months, to examine the biological variation for those measurements, and the average change in lymphocyte phenotype over 34 years.The markers showed significant intra-individuality in HIV-infected and uninfected individuals with index of individuality of <1.4. No mean changes were seen over the 34 years, with the exception of percentage CD4T-cells in HIV-uninfected individuals.In the pre-HAART era, HIV-infected individuals experienced an increase in mean absolute CD3 T-cell numbers (11.21 cells/µL, P = 0.02) and absolute CD8 T-cell numbers (34.57 cell/µl, P < .001), and in the percentage of CD8 T-cells (1.45%, P < .001) per year and a significant decrease in mean absolute CD4 T-cell numbers (23.68 cells/µl, P < .001) and in the percentage of CD4 T-cells (1.49%, P < .001) per year.In the post-HAART era, no changes in mean levels were observed in absolute CD3 T-cell count (P = .15) or percentage (P = .99). Significant decreases were seen in mean count (8.56 cells/µl, P < .001) and percentage (0.59%, P < .001) of CD8 T-cells, and increases in mean absolute count (10.72 cells/µl, P < .001) and percentage (0.47%, P < .001) of CD4 T-cells.With the exception of CD4 (%), no average changes per year were seen in lymphocyte phenotype of HIV-uninfected men. The results of coefficients of variation of intra and inter-individuals of this study can be useful for HIV-1 infection monitoring and in addition the observation could be a useful guide for intra- and inter-individual coefficient variations, and establishing quality goal studies of different blood biomarkers in healthy and other diseases.

[Milieu Interieur: defining a healthy immune response for a better understanding of diseases]. / Milieu Intérieur : définir les limites d'une réponse immunitaire saine pour mieux comprendre la maladie.

What all individuals have in common is that they are all different. Some of the greatest differences between any two individuals may be related to their immune responses. These differences may result in variable outcome to infection, disease severity and response to medical therapies. Differences in immune responses are partly resulting from evolutionary forces acting at the level of host genetics and may also be due to differences encountered through environment and lifestyle. Despite these well-known inter-individual differences, this inherent variability is rarely included in clinical approaches or drug development. The LabEx Milieu Interieur consortium was established in 2011 to better define these immune differences in a healthy population and identify their genetic and environmental determinants. Such an understanding is crucial to achieve the promise of precision medicine that will take into account an individual specific immune response to ensure that public health strategies capitalize on recent scientific progress.

Race-related differences in functional antibody response to pneumococcal vaccination in HIV-infected individuals.

BACKGROUND: Both HIV positivity and African American (AA) ethnicity are associated with increased incidence of invasive pneumococcal disease (IPD). Poor immune response to pneumococcal polysaccharide-based vaccines may contribute to the race related increased frequency of IPD in African American HIV positive individuals. METHODS: Caucasian and AA HIV-infected (HIV+) individuals 40-65 years old with CD4+ T cells/µl (CD4) >200 on antiretroviral therapy (ART) received either the 13-valent pneumococcal conjugate vaccine (PCV) followed by the 23-valent pneumococcal polysaccharide vaccine (PPV) or PPV only. Serum IgG, IgM and opsonophagocytic antibody responses to serotypes 14 and 23F as well as serum IgG and opsonophagocytic antibody responses to serotype 19A were measured pre- and post-vaccination. We measured serum markers of inflammation in all participants and performed single cell gene expression profiling at the baseline by HD Biomark in Caucasians and African Americans. RESULTS: There were no significant differences in pre-immunization inflammatory markers or post-vaccination IgG and IgM concentrations between Caucasian and African American participants. However, we found significantly lower opsonophagocytic activity in response to serotypes 14 and 19A in the AA group compared to the Caucasian group. There was no association between inflammatory markers and immune response to vaccination, however we found extensive biomodal variation in gene expression levels in single IgM+ memory B cells. Differentially expressed genes may be related to differences in the immune response between ethnic groups. CONCLUSIONS: Distinct racial differences were found in the functional immune response following either PPV and/or PCV/PPV immunization in HIV-positive adults, although these differences were serotype dependent. Decreased ability to respond to vaccination may in part explain racial disparities in pneumococcal disease epidemiology. ClinicalTrials.gov ID: NCT03039491.

Spectrum of susceptibility to air quality and weather in individual children with atopic dermatitis.

BACKGROUND: Exposure to air pollution aggravates symptoms of atopic dermatitis (AD) in children in the population studies. Variability in individual patient's response from individual susceptibility is needed to be explored. OBJECTIVE: This study aimed to investigate spectrum of individual variability in the associations between AD symptoms and air quality. METHODS: We enrolled 89 children aged 0-6 years with AD (22 890 person-days). Daily manifestation of symptoms was recorded for an average of 257 days (range 100-499). Both an individual analysis using logistic regression models and an overall analysis using a generalized estimating equation were performed. RESULTS: The odds ratios of an individual ranged 0.24-8.11 for particulate matter <10 µm in diameter (PM10 ), 0.09-101.92 for nitrogen oxide (NO2 ), 0.03-44.00 for ozone (O3 ), 0.11-58.30 for sulfur dioxide (SO2 ), 0.00-15.83 for carbon monoxide (CO), 0.00-39 446.94 for temperature, and 0.03-5.18 for relative humidity, demonstrating a wide individual variability. In the overall analysis, PM10 , NO2 , SO2 , and CO had a significantly positive association, whereas temperature and relative humidity were negatively associated with AD symptoms. Air pollution was responsible for aggravation of symptoms from 24.7% (O3 ) to 39.3% (SO2 ) of AD children. Overall, 71.9% of the AD children responded to at least one or more air pollution and weather variable. CONCLUSION: Responses of AD children to air pollution and weather variable were considerably variable among individuals. An individualized model would be useful to forecast and manage AD symptoms in patients.

Benralizumab: a new approach for the treatment of severe eosinophilic asthma

Eosinophilic asthma is the most common phenotype of severe asthma. It is characterized by abnormal production and release of type 2 cytokines from T helper type 2 (TH2) lymphocytes and type 2 innate lymphoid cells, such as IL-5. This leads to a persistent increase and activation of eosinophils in blood and the airways despite treatment with high-dose inhaled corticosteroids. Eosinophil differentiation, survival, and activation are preferentially regulated by IL-5, a cytokine that binds to the IL-5 receptor (IL-5R), which is located on the surface of eosinophils or basophils and plays a critical role in the pathogenesis and severity of asthma. Benralizumab is a monoclonal antibody that binds to IL-5R via its Fab domain, blocking the binding of IL-5 to its receptor and resulting in inhibition of eosinophil differentiation and maturation in bone marrow. In addition, this antibody is able to bind through its afucosylated Fc domain to the RIIIa region of the Fcgamma receptor on NK cells, macrophages, and neutrophils, thus strongly inducing antibody-dependent, cell-mediated cytotoxicity in both circulating and tissue-resident eosinophils. This double function of benralizumab induces almost complete fast and maintained depletion of eosinophils that is much greater than that induced by other monoclonal antibodies targeting the IL-5 pathway, such as mepolizumab and reslizumab. This review focuses on benralizumab as an alternative to other agents targeting the IL-5 pathway in the treatment of eosinophilic asthma

El asma eosinofílica es el fenotipo más común del asma grave. Se caracteriza por una producción y liberación anómala de citocinas de tipo 2, como la IL-5, por los linfocitos T colaboradores de tipo 2 (Th2) y las células linfoides innatas de tipo 2 (ILC-2). Con ello se activan los eosinófilos y se incrementa su número en sangre y vías respiratorias, a pesar del tratamiento con dosis altas de corticosteroides inhalados. La diferenciación, supervivencia y activación de los eosinófilos está regulada principalmente por la IL-5, una citocina que se une a su receptor (IL-5R), situado en la superficie de eosinófilos y basófilos, y que desempeña un papel fundamental en la patogénesis y gravedad del asma. El benralizumab es un anticuerpo monoclonal que se une al IL-5R a través de su dominio Fab, bloqueando la unión de la IL-5 a su receptor, lo que provoca una inhibición de la diferenciación y maduración de los eosinófilos en la médula ósea. Además, este anticuerpo es capaz de unirse a través de su dominio Fc afucosilado a la región RIIIa del receptor Fcgamma situado en células NK, macrófagos y neutrófilos, induciendo así una intensa citotoxicidad mediada por células dependiente de anticuerpos (ADCC), tanto de los eosinófilos circulantes como de los residentes en tejidos. Esta doble función del benralizumab induce una disminución casi completa de los eosinófilos de una forma rápida y mantenida, mucho mayor a la inducida por otros anticuerpos monoclonales dirigidos contra la IL-5, como el mepolizumab o el reslizumab. Esta revisión se centra en describir el uso del benralizumab en el tratamiento del asma eosinofílica como una alternativa a otros agentes que actúan directamente sobre la IL-5

Autoimmune diseases and asthma

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Absolute CD4+ T cell count overstate immune recovery assessed by CD4+/CD8+ ratio in HIV-infected patients on treatment.

OBJECTIVES: To analyse the correlation and concordance between aCD4, CD4%, CD4/CD8, their intra-patient variability, and to compare the immune recovery (IR) rates based on the three parameters in HIV-infected patients after starting antiretroviral therapy. METHODS: From a prospectively followed cohort, patients who maintained HIV-RNA suppression in ≥95% of the determinations throughout the follow-up were selected. IR was defined as aCD4 >650/µl, CD4% ≥38% or CD4/CD8 ≥1. RESULTS: A total of 1164 patients with a median follow-up of 5 years were analysed. The increases in aCD4, CD4% and CD4/CD8 were highest during the first year and considerably lower thereafter regardless of baseline aCD4. The annual increases in aCD4 showed poor correlations with those of CD4% (r = 0.143-0.250) and CD4/CD8 (r = 0.101-0.192) but were high between CD4% and CD4/CD8 (r = 0.765-0.844; p<0.001). The median intra-annual coefficients of variation for aCD4, CD4/CD8 and CD4% were 12.5, 8.5 and 6.6, respectively. After five years, 66.7%, 41.6% and 42.1% of the patients reached aCD4 >650/µl, CD4% ≥38%, and CD4/CD8 ≥1, respectively, while only 31% achieved both aCD4 and CD4/CD8 target values. CONCLUSIONS: The increases in aCD4 poorly correlate with those of CD4% and CD4/CD8. IR rates based on aCD4 significantly overstate those obtained by CD4% and CD4/CD8. CD4% and CD4/CD8 are more stable markers than aCD4 and should be taken into account to monitor the IR after treatment initiation.

Sex-specific patterns of gene expression following influenza vaccination.

Sex-based variations in the immune response to the influenza vaccines was reported, however, the genetic basis responsible for the sex variations in the immune response toward the influenza vaccines remains unclear. Here, the genes responsible for sex-specific responses after vaccination with trivalent inactivated influenza virus were identified. These genes were enriched in virus response pathways, especially interferon signaling. A list of genes showing different responses to the vaccine between females and males were obtained next. Our results demonstrated that females generate stronger immune responses to seasonal influenza vaccines within 24 hours than males. However, most of these genes with variability between sexes had the opposite expression levels after three days, suggesting that males retained the immune responses longer than female. To summary, our study identified genes responsible for the sex variations toward influenza vaccination. Our findings might provide insights into the development of the sex-dependent influenza vaccines.

The potential role of pharmacogenomics and biotransformation in hypersensitivity reactions to paracetamol.

PURPOSE OF REVIEW: The aim of the present review is to discuss recent advances supporting a role of paracetamol metabolism in hypersensitivity reactions to this drug. RECENT FINDINGS: Recent developments in the identification of novel paracetamol metabolites, as well as in allele frequencies and functional effects of genetic variation leading to the bioavailablity of reactive paracetamol metabolites, have led to the identification of potential pharmacogenomic and metabolomic targets in studies seeking mechanisms involved in hypersensitivity reactions caused by this drug. Particularly relevant are identification of araquidonate metabolites, identification of specific-binding sequences for reactive paracetamol metabolite-protein adducts, and studies on the frequencies and the functional impact of duplication or multiduplication of genes involved in the formation of reactive metabolites, as well as complete gene deletion or deleterious mutations in genes involved in the detoxification of paracetamol reactive metabolites. In addition, recent evidence points to sex, ethnic origin and age as relevant factors in the production of reactive paracetamol metabolites. SUMMARY: High inter-individual variability in the production of reactive paracetamol metabolites exists, and factors leading to increased bioavailability of reactive paracetamol metabolites are being uncovered. Additional research is required to link these factors to paracetamol-induced hypersensitivity reactions.

The ecology of immune state in a wild mammal, Mus musculus domesticus.

The immune state of wild animals is largely unknown. Knowing this and what affects it is important in understanding how infection and disease affects wild animals. The immune state of wild animals is also important in understanding the biology of their pathogens, which is directly relevant to explaining pathogen spillover among species, including to humans. The paucity of knowledge about wild animals' immune state is in stark contrast to our exquisitely detailed understanding of the immunobiology of laboratory animals. Making an immune response is costly, and many factors (such as age, sex, infection status, and body condition) have individually been shown to constrain or promote immune responses. But, whether or not these factors affect immune responses and immune state in wild animals, their relative importance, and how they interact (or do not) are unknown. Here, we have investigated the immune ecology of wild house mice-the same species as the laboratory mouse-as an example of a wild mammal, characterising their adaptive humoral, adaptive cellular, and innate immune state. Firstly, we show how immune variation is structured among mouse populations, finding that there can be extensive immune discordance among neighbouring populations. Secondly, we identify the principal factors that underlie the immunological differences among mice, showing that body condition promotes and age constrains individuals' immune state, while factors such as microparasite infection and season are comparatively unimportant. By applying a multifactorial analysis to an immune system-wide analysis, our results bring a new and unified understanding of the immunobiology of a wild mammal.