Associations between extended class I HLA-LTA-TNF-LST1-class II HLA haplotypes and class I-class II HLA-only haplotypes, and rubella-specific cytokine responses.

<p>Only haplotypes with estimated frequencies ≥0.01 and <i>p</i>-values ≤0.15 are presented.</p>a<p>Haplotype effects estimated using a haplotype t-statistic that assesses associations of cytokine levels across haplotypes. Allele <i>p</i>-value compares the haplotype of interest to all other haplotypes combined. Statistically significant findings (<i>p</i><0.05) are shown in bold. Analyses adjust for age at blood draw, gender, race, age at first rubella vaccine, age at second rubella vaccine, and cohort status.</p>b<p>Common SNPs from the LTA gene: [rs2857602 (A>G), rs2857708 (G>A), rs915654 (T>A), rs2844482 (G>A), rs1041981 (C>A), rs1799964 (A>G), rs1799724 (G>A)]; TNF gene: rs1800629 (G>A); LST1 gene: [rs2256965 (G>A), and rs2256974 (C>A)].</p

Associations between extended class I-HLA-LTA-TNF-LST1 haplotypes and class I HLA-only haplotypes, and rubella-specific cytokine responses.

<p>Only haplotypes with estimated frequencies ≥0.01 and <i>p</i>-values ≤0.15 are presented.</p>a<p>Haplotype effects estimated using a haplotype t-statistic that assesses associations of cytokine levels across haplotypes. Allele <i>p</i>-value compares the haplotype of interest to all other haplotypes combined. Statistically significant findings (<i>p</i><0.05) are shown in bold. Analyses adjust for age at blood draw, gender, race, age at first rubella vaccine, age at second rubella vaccine, and cohort status.</p>b<p>Common SNPs from the LTA gene: [rs2857602 (A>G), rs2857708 (G>A), rs915654 (T>A), rs2844482 (G>A), rs1041981 (C>A), rs1799964 (A>G), rs1799724 (G>A)]; TNF gene: rs1800629 (G>A); LST1 gene: [rs2256965 (G>A), and rs2256974 (C>A)].</p

Demographic characteristics of the study population (n = 714).

<p>Demographic characteristics of the study population (n = 714).</p

Associations between extended haplotypes and HLA-only haplotypes, and rubella virus-specific antibody responses.

<p>Only haplotypes with estimated frequencies ≥0.01 and <i>p</i>-values ≤0.15 are presented.</p>a<p>Haplotype effects estimated using a haplotype t-statistic that assesses associations of antibody levels across haplotypes. Allele <i>p</i>-value compares the haplotype of interest to all other haplotypes combined. Statistically significant findings (<i>p</i><0.05) are shown in bold. Analyses adjust for age at blood draw, gender, race, age at first rubella vaccine, age at second rubella vaccine, and cohort status.</p>b<p>Common SNPs from the LTA gene: [rs2857602 (A>G), rs2857708 (G>A), rs915654 (T>A), rs2844482 (G>A), rs1041981 (C>A), rs1799964 (A>G), rs1799724 (G>A)]; TNF gene: rs1800629 (G>A); LST1 gene: [rs2256965 (G>A), and rs2256974 (C>A)].</p

A schematic overview of the extended human leukocyte antigen (HLA) complex, encompassing the lymphotoxin alpha (LTA), tumor necrosis factor (TNF) and leukocyte specific transcript -1 (LST1) genes on chromosome 6 (6p21.3).

<p>A 3,145 kb segment of the extended HLA gene region is shown. The LTA, TNF, and LST1 loci encoded in the class III region of the HLA complex in relation to HLA-B and HLA-DRB1 loci. The positions of single nucleotide polymorphisms (SNPs) selected from LTA [rs2857602 (31641357), rs2857708 (31641585), rs915654 (31646476), rs2844482 (31647746), rs1041981 (31648763), rs1799964 (31650287), rs1799724 (31650461)], TNF [rs1800629 (31651010)], and LST1 [rs2256965 (31663109), rs2256974 (31663371)] gene families and used for haplotype estimation are shown. Targeted sets of extended haplotypes used in this study: (1) haplotypes containing the three class I HLA loci (A-C-B) and the set of ten-SNP haplotypes, (2) haplotypes containing ten-SNP haplotypes and the class II HLA loci (DRB1-DQA1-DQB1-DPA1-DPB1), and (3) haplotypes containing class I HLA loci (A-C-B), the set of ten-SNP haplotypes, and alleles of class II HLA loci (DRB1-DQA1-DQB1-DPA1-DPB1). Note: the figure is not to scale.</p

Genome-Wide Characterization of Transcriptional Patterns in High and Low Antibody Responders to Rubella Vaccination

<div><p></p><p>Immune responses to current rubella vaccines demonstrate significant inter-individual variability. We performed mRNA-Seq profiling on PBMCs from high and low antibody responders to rubella vaccination to delineate transcriptional differences upon viral stimulation. Generalized linear models were used to assess the per gene fold change (FC) for stimulated versus unstimulated samples or the interaction between outcome and stimulation. Model results were evaluated by both FC and p-value. Pathway analysis and self-contained gene set tests were performed for assessment of gene group effects.</p><p>Of 17,566 detected genes, we identified 1,080 highly significant differentially expressed genes upon viral stimulation (p<1.00E⁻¹⁵, FDR<1.00E⁻¹⁴), including various immune function and inflammation-related genes, genes involved in cell signaling, cell regulation and transcription, and genes with unknown function. Analysis by immune outcome and stimulation status identified 27 genes (p≤0.0006 and FDR≤0.30) that responded differently to viral stimulation in high vs. low antibody responders, including major histocompatibility complex (MHC) class I genes (<i>HLA-A</i>, <i>HLA-B</i> and <i>B2M</i> with p = 0.0001, p = 0.0005 and p = 0.0002, respectively), and two genes related to innate immunity and inflammation (<i>EMR3</i> and <i>MEFV</i> with p = 1.46E⁻⁰⁸ and p = 0.0004, respectively). Pathway and gene set analysis also revealed transcriptional differences in antigen presentation and innate/inflammatory gene sets and pathways between high and low responders. Using mRNA-Seq genome-wide transcriptional profiling, we identified antigen presentation and innate/inflammatory genes that may assist in explaining rubella vaccine-induced immune response variations. Such information may provide new scientific insights into vaccine-induced immunity useful in rational vaccine development and immune response monitoring.</p></div

Dotplots of mRNA-Seq gene expression counts for A (EMR3, EGF-like module containing, mucin-like, gene) and B (MEFV, Mediterranean fever, gene), demonstrating differences in gene expression in high antibody responders compared to low antibody responders to rubella vaccination.

<p>Lines indicate the mean value of the counts within groups. Vertical axis is log₂(gene counts). HU-gene counts for unstimulated PBMCs of high responders; HS-gene counts for rubella virus-stimulated PBMCs of high responders; LU-gene counts for unstimulated PBMCs of low responders; LS-gene counts for rubella virus-stimulated PBMCs of low responders.</p

Analysis of mRNA-Seq reads/transcripts, mapping to Rubella virus genome.

<p>Quantification of viral transcripts in the high and low antibody responder groups was done using the Bowtie alignment tool, with alignment of reads to the Rubella virus strain Wistar RA 27/3, complete genome GenBank: FJ211588.1. <b>A</b> Mapping of rubella virus (RV)-specific reads in high antibody responders compared to low antibody responders to rubella vaccination; <b>B</b> Mapping of RV-specific reads across different rubella virus proteins. Bars represent mean ± SD.</p

Overall response to rubella virus stimulation in PBMC samples of vaccines.

a<p>Gene symbol and gene description are provided for gene identification, information on immune function-related genes is provided in italic font.</p>b<p>Fold change for overall response to stimulation analysis (all stimulated samples vs. all unstimulated samples; Stim/Unstim, S/U).</p>c<p>P-value and false discovery rate (FDR) for the overall analysis.</p>d<p>Fold change for High responders, stimulated vs. unstimulated samples (HS/HU).</p>e<p>Fold change for Low responders, stimulated vs. unstimulated samples (LS/LU).</p

Differential response to rubella virus stimulation in high vs. low antibody responders to rubella vaccination.

a<p>Gene symbol and gene description are provided for gene identification.</p>b<p>Fold change for the interaction (HS/HU)/(LS/LU).</p>c<p>P-value and false discovery rate for the interaction.</p>d<p>Fold change in High responders, stimulated vs. unstimulated samples (HS/HU).</p>e<p>Fold change in Low responders, stimulated vs. unstimulated samples (LS/LU).</p