Influenza vaccine format mediates distinct cellular and antibody responses in human immune organoids

Highly effective vaccines elicit specific, robust, and durable adaptive immune responses. To advance informed vaccine design, it is critical that we understand the cellular dynamics underlying responses to different antigen formats. Here, we sought to understand how antigen-specific B and T cells were activated and participated in adaptive immune responses within the mucosal site. Using a human tonsil organoid model, we tracked the differentiation and kinetics of the adaptive immune response to influenza vaccine and virus modalities. Each antigen format elicited distinct B and T cell responses, including differences in their magnitude, diversity, phenotype, function, and breadth. These differences culminated in substantial changes in the corresponding antibody response. A major source of antigen format-related variability was the ability to recruit naive vs. memory B and T cells to the response. These findings have important implications for vaccine design and the generation of protective immune responses in the upper respiratory tract

Transcript-indexed ATAC-seq for precision immune profiling.

T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy

Clinical quantitative traits controlling MOG-EAE in female and male B6-Chr#^PWD/PhJ strains.

<p>(A-B) day of onset (DO), (C-D) days affected (DA), (E-F) cumulative disease score (CDS), (G-H) severity index (SI), and (I-J) peak score (PS). Females in left column (pink) and males in right column (blue). The significance of the observed differences in clinical trait variables among female and male strains was determined using the Mann-Whitney U test of each strain against the mean trait variable for all strains by sex. *, p<0.05; * p<0.01; ***, p<0.001; ****, p<0.0001.</p

Clinical quantitative traits controlling MOG-EAE in female and male B6-Chr#^PWD/PhJ strains.

<p>(A-B) day of onset (DO), (C-D) days affected (DA), (E-F) cumulative disease score (CDS), (G-H) severity index (SI), and (I-J) peak score (PS). Females in left column (pink) and males in right column (blue). The significance of the observed differences in clinical trait variables among female and male strains was determined using the Mann-Whitney U test of each strain against the mean trait variable for all strains by sex. *, p<0.05; * p<0.01; ***, p<0.001; ****, p<0.0001.</p

Influence of sex hormone-dependent signaling pathways on genetic control of the EAE sexual dimorphism.

<p>Gene lists were generated using the polymorphic MS-GWAS orthologues residing within EAE-QTL/BTL that were either male-specific, female-specific, or non-sex-specific. These lists were used to identify the top associated functional gene networks using the core analysis feature in IPA (<b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117993#pone.0117993.t001" target="_blank">Table 1</a></b>). GWAS candidates are dark shaded. Within these networks, we identified genes that were predicted to be regulated by estrogens and/or androgens using the connect tool in IPA’s Pathway Designer. These genes included <i>Rac</i>, <i>Erk</i>, <i>Pkc</i>, <i>Il-1</i>, <i>Akt</i>, <i>Pi3k</i>, and members of the MAPK family, including p38 MAPK. These genes were pulled out from the main non-sex-specific module and displayed at the bottom of the figure to more easily observe their connections to the male- and female-specific modules.</p

Activation of p38 MAPK in CD4 T cells controls IL-17 production and autoimmune encephalomyelitis

Although several transcription factors have been shown to be critical for the induction and maintenance of IL-17 expression by CD4 Th cells, less is known about the role of nontranscriptional mechanisms. Here we show that the p38 MAPK signaling pathway is essential for in vitro and in vivo IL-17 production by regulating IL-17 synthesis in CD4 T cells through the activation of the eukaryotic translation initiation factor 4E/MAPK-interacting kinase (eIF-4E/MNK) pathway. We also show that p38 MAPK activation is required for the development and progression of both chronic and relapsing-remitting forms of experimental allergic encephalomyelitis (EAE), the principal autoimmune model of multiple sclerosis. Furthermore, we show that regulation of p38 MAPK activity specifically in T cells is sufficient to modulate EAE severity. Thus, mechanisms other than the regulation of gene expression also contribute to Th17 cell effector functions and, potentially, to the pathogenesis of other Th17 cell-mediated diseases

Clinical disease course of MOG-EAE in consomic strains is sexually dimorphic.

<p>A composite female and male clinical disease course for all consomic strains (N≥149 per sex, N≥5 per strain) studied was generated using the mean daily clinical scores. The significance of the observed differences in disease course severity was determined by two-way ANOVA followed by Bonferroni multiple comparison test. A significant effect of sex (p<0.0001), days post-immunization (p<0.0001), and sex-by-days post-immunization interaction term (p<0.0001) were detected with * p<0.05; ** p<0.01; *** p<0.001; **** p<0.0001.</p

Physical mapping of QTL controlling MOG-EAE in female and male B6-Chr#^PWD/PhJ strains of mice.

<p>Cohorts of (<b>A</b>) female and (<b>B</b>) male mice were immunized for the induction of EAE using the 2×MOG_35–55+CFA protocol. The significance of the observed differences in disease course severity among the strains was determined by two-way ANOVA with post hoc multiple comparisons tests of female and male strains against the composite disease course (<b>C</b>) for all female and male strains respectively. The significance of observed differences in disease course, cumulative disease score (CDS), days affected (DA), severity index (SI), peak score (PS), incidence (I), and day of onset (DO) was determined using the Mann-Whitney U test of female and male strain against the corresponding quantitative trait variables for all female and male strains studied, respectively. Arrows indicate the direction of the change in disease course severity; red symbols for female-specific QTL, blue symbols for male-specific QTL, and black symbols for non-sex-specific QTL are shown.</p