An interaction quantitative trait loci tool implicates epistatic functional variants in an apoptosis pathway in smallpox vaccine eQTL data.

Expression quantitative trait loci (eQTL) studies have functionalized nucleic acid variants through the regulation of gene expression. Although most eQTL studies only examine the effects of single variants on transcription, a more complex process of variant-variant interaction (epistasis) may regulate transcription. Herein, we describe a tool called interaction QTL (iQTL) designed to efficiently detect epistatic interactions that regulate gene expression. To maximize biological relevance and minimize the computational and hypothesis testing burden, iQTL restricts interactions such that one variant is within a user-defined proximity of the transcript (cis-regulatory). We apply iQTL to a data set of 183 smallpox vaccine study participants with genome-wide association study and gene expression data from unstimulated samples and samples stimulated by inactivated vaccinia virus. While computing only 0.15% of possible interactions, we identify 11 probe sets whose expression is regulated through a variant-variant interaction. We highlight the functional epistatic interactions among apoptosis-related genes, DIABLO, TRAPPC4 and FADD, in the context of smallpox vaccination. We also use an integrative network approach to characterize these iQTL interactions in a posterior network of known prior functional interactions. iQTL is an efficient, open-source tool to analyze variant interactions in eQTL studies, providing better understanding of the function of epistasis in immune response and other complex phenotypes.

Gene signatures associated with adaptive humoral immunity following seasonal influenza A/H1N1 vaccination.

This study aimed to identify gene expression markers shared between both influenza hemagglutination inhibition (HAI) and virus-neutralization antibody (VNA) responses. We enrolled 158 older subjects who received the 2010-2011 trivalent inactivated influenza vaccine. Influenza-specific HAI and VNA titers and mRNA-sequencing were performed using blood samples obtained at Days 0, 3 and 28 post vaccination. For antibody response at Day 28 versus Day 0, several gene sets were identified as significant in predictive models for HAI (n=7) and VNA (n=35) responses. Five gene sets (comprising the genes MAZ, TTF, GSTM, RABGGTA, SMS, CA, IFNG and DOPEY) were in common for both HAI and VNA. For response at Day 28 versus Day 3, many gene sets were identified in predictive models for HAI (n=13) and VNA (n=41). Ten gene sets (comprising biologically related genes, such as MAN1B1, POLL, CEBPG, FOXP3, IL12A, TLR3, TLR7 and others) were shared between HAI and VNA. These identified gene sets demonstrated a high degree of network interactions and likelihood for functional relationships. Influenza-specific HAI and VNA responses demonstrated a remarkable degree of similarity. Although unique gene set signatures were identified for each humoral outcome, several gene sets were determined to be in common with both HAI and VNA response to influenza vaccine.

Transcriptomic profiles of high and low antibody responders to smallpox vaccine.

Despite its eradication over 30 years ago, smallpox (as well as other orthopox viruses) remains a pathogen of interest both in terms of biodefense and for its use as a vector for vaccines and immunotherapies. Here we describe the application of mRNA-Seq transcriptome profiling to understanding immune responses in smallpox vaccine recipients. Contrary to other studies examining gene expression in virally infected cell lines, we utilized a mixed population of peripheral blood mononuclear cells in order to capture the essential intercellular interactions that occur in vivo, and would otherwise be lost, using single cell lines or isolated primary cell subsets. In this mixed cell population we were able to detect expression of all annotated vaccinia genes. On the host side, a number of genes encoding cytokines, chemokines, complement factors and intracellular signaling molecules were downregulated upon viral infection, whereas genes encoding histone proteins and the interferon response were upregulated. We also identified a small number of genes that exhibited significantly different expression profiles in subjects with robust humoral immunity compared with those with weaker humoral responses. Our results provide evidence that differential gene regulation patterns may be at work in individuals with robust humoral immunity compared with those with weaker humoral immune responses.

The role of HLA-DR-DQ haplotypes in variable antibody responses to anthrax vaccine adsorbed.

Host genetic variation, particularly within the human leukocyte antigen (HLA) loci, reportedly mediates heterogeneity in immune response to certain vaccines; however, no large study of genetic determinants of anthrax vaccine response has been described. We searched for associations between the immunoglobulin G antibody to protective antigen (AbPA) response to Anthrax Vaccine Adsorbed (AVA) in humans, and polymorphisms at HLA class I (HLA-A, -B, and -C) and class II (HLA-DRB1, -DQA1, -DQB1, -DPB1) loci. The study included 794 European-Americans and 200 African-Americans participating in a 43-month, double-blind and placebo-controlled clinical trial of AVA (clinicaltrials.gov identifier NCT00119067). Among European-Americans, genes from tightly linked HLA-DRB1, -DQA1, -DQB1 haplotypes displayed significant overall associations with longitudinal variation in AbPA levels at 4, 8, 26 and 30 weeks from baseline in response to vaccination with three or four doses of AVA (global P=6.53 × 10(-4)). In particular, carriage of the DRB1-DQA1-DQB1 haplotypes (*)1501-(*)0102-(*)0602 (P=1.17 × 10(-5)), (*)0101-(*)0101-(*)0501 (P=0.009) and (*)0102-(*)0101-(*)0501 (P=0.006) was associated with significantly lower AbPA levels. In carriers of two copies of these haplotypes, lower AbPA levels persisted following subsequent vaccinations. No significant associations were observed amongst African-Americans or for any HLA class I allele/haplotype. Further studies will be required to replicate these findings and to explore the role of host genetic variation outside of the HLA region.

An assessment of the association between childhood asthma and HLA DRB1*03 using extended haplotype analysis.

Ancestral haplotypes between human leukocyte antigen (HLA) class I and class II alleles are well-recognized in the literature. We previously published a positive association between the class II HLA allele DRB1*03 and the subsequent development of asthma in a retrospective cohort of 383 children. To refine this association, we investigated whether DRB1*03-specific haplotypes extending across the HLA are associated with asthma incidence. We found evidence of strong HLA DRB1*03-dependent linkage disequilibrium across the region, but no association between DRB1*03 ancestral haplotypes and childhood asthma. We did, however, observe a trend toward a positive association between HLA DRB1*03 and asthma by adding non-ancestral DRB1*03 positive haplotypes. Our results suggest that the role of the HLA DRB1*03 in asthma susceptibility is independent of ancestral-haplotype-mediated linkage disequilibrium.

Associations between cytokine/cytokine receptor single nucleotide polymorphisms and humoral immunity to measles, mumps and rubella in a Somali population.

We genotyped a Somali population (n = 85; age < or =30 years) for 617 cytokine and cytokine receptor single nucleotide polymorphisms (SNPs) using Illumina GoldenGate genotyping to determine associations with measles, mumps and rubella immunity. Overall, 61 significant associations (P < or = 0.01) were found between SNPs belonging to cytokine receptor genes regulating T helper (Th)1 (IL12RB2, IL2RA and B) and Th2 (IL4R and IL10RB) immunity, and cytokine (IL1B, TNFA, IL6 and IFNB1) and cytokine receptor (IL1RA, IFNAR2, IL18R1, TNFRSF1A and B) genes regulating innate immunity and variations in antibody levels to measles, mumps and/or rubella. SNPs within two major inflammatory cytokine genes, TNFA and interleukin (IL) 6, showed associations with measles-specific antibodies. Specifically, the minor allele variant of rs1799964 (TNFA -1211 C>T) was associated with primarily seronegative values (median enzyme immunoassay index values < or =0.87; P = 0.002; q = 0.23) in response to measles disease and/or vaccination. A heterozygous variant CT for rs2069849 (IL6 +4272C>T; Phe201Phe) was also associated with seronegative values and a lower median level of antibody response to measles disease and/or vaccination (P = 0.004; q = 0.36) or measles vaccination alone (P = 0.008). Several SNPs within the coding and regulatory regions of cytokine and cytokine receptor genes showed associations with mumps and rubella antibody levels but were less informative as strong linkage disequilibrium patterns and lower frequencies for minor alleles were observed among these SNPs. Our study identifies specific SNPs in innate immune response genes that may play a role in modulating antibody responses to measles vaccination and/or infection in Somali subjects.

Personalized vaccinology: A review.

At the current time, the field of vaccinology remains empirical in many respects. Vaccine development, vaccine immunogenicity, and vaccine efficacy have, for the most part, historically been driven by an empiric "isolate-inactivate-inject" paradigm. In turn, a population-level public health paradigm of "the same dose for everyone for every disease" model has been the normative thinking in regard to prevention of vaccine-preventable infectious diseases. In addition, up until recently, no vaccines had been designed specifically to overcome the immunosenescence of aging, consistent with a post-WWII mentality of developing vaccines and vaccine programs for children. It is now recognized that the current lack of knowledge concerning how immune responses to vaccines are generated is a critical barrier to understanding poor vaccine responses in the elderly and in immunoimmaturity, discovery of new correlates of vaccine immunogenicity (vaccine response biomarkers), and a directed approach to new vaccine development. The new fields of vaccinomics and adversomics provide models that permit global profiling of the innate, humoral, and cellular immune responses integrated at a systems biology level. This has advanced the science beyond that of reductionist scientific approaches by revealing novel interactions between and within the immune system and other biological systems (beyond transcriptional level), which are critical to developing "downstream" adaptive humoral and cellular responses to infectious pathogens and vaccines. Others have applied systems level approaches to the study of antibody responses (a.k.a. "systems serology"), [1] high-dimensional cell subset immunophenotyping through CyTOF, [2,3] and vaccine induced metabolic changes [4]. In turn, this knowledge is being utilized to better understand the following: identifying who is at risk for which infections; the level of risk that exists regarding poor immunogenicity and/or serious adverse events; and the type or dose of vaccine needed to fully protect an individual. In toto, such approaches allow for a personalized approach to the practice of vaccinology, analogous to the substantial inroads that individualized medicine is playing in other fields of human health and medicine. Herein we briefly review the field of vaccinomics, adversomics, and personalized vaccinology.

Knowledge gaps persist and hinder progress in eliminating mumps.

Mumps, a common childhood disease in the pre-vaccine era that causes swelling of the parotid salivary glands, can lead to orchitis, viral meningitis, and sensorineural deafness. While the incidence of disease decreased dramatically after the vaccine was added to standard vaccination schedules, the disease has made a substantial resurgence in recent years. As a result, it becomes critical to examine the factors involved in recurring outbreaks. Although low and incomplete vaccination coverage may be a key reason, it does not fully explain the issue due to the high rate of occurrence in populations with high vaccination coverage rates. Multiple studies suggest that waning immunity and secondary vaccine failure play a large role, the effects of which were previously masked by subclinical boosting. Significant knowledge gaps persist around the exact role and mechanism of waning immunity and demonstrate the need for more research in this area, as well as a reevaluation of mumps vaccine policy.

Low-resolution structure of the complex of human blood platelet factor 4 with heparin determined by small-angle neutron scattering.

Small-angle neutron scattering was used to confirm that human platelet factor 4 was a compact tetrameric globular protein of radius of gyration 1.74 nm and indistinguishable from a sphere. The same technique, when applied to the 1:1 mol/mol complex of platelet factor and heparin of Mr 14000, revealed that the radius of gyration of the particle varied, depending on the relative proportion of 2H2O to H2O in the solvent. Analysis of this variation by the method of Ibel and Stuhrmann (Ibel, K. and Stuhrmann, H.B. (1975) J. Mol. Biol. 93, 255-266) revealed that in the complex the material of greatest neutron-scattering length (the highly sulphated polysaccharide heparin) was furthest from the centre of the particle. This confirms the postulate of Luscombe and Holbrook (Luscombe, M. and Holbrook, J.J. (1983) in Glycoconjugates (Chester, A.M., Heinegård, D., Lundblad, A. and Svensson, S., eds.), pp. 818-819, Secretariat, Lund) that the exact 1:1 mole ratio of heparin (Mr greater than 10 000) to platelet factor in this stable complex arises from the heparin winding around the outside of a globular protein core.

Medical students as sources of rubella and measles outbreaks.

Medical students demonstrate a high degree of susceptibility to rubella and measles, and hence are at risk for infection and transmission of these viruses. The purpose of our study was to examine the role medical students play as sources or vectors in rubella and measles outbreaks. We conducted a survey of all US and Canadian public health departments to determine how often students were implicated in outbreaks (response rate, 88.7%). We also performed a literature search to identify any cases not reported to health departments, as well as examined the medical, social, and economic consequences of such outbreaks in the medical setting. Since 1981, 9% of health departments have recorded at least one outbreak of rubella or measles in which medical students were specifically implicated as sources or vectors. Increased morbidity, mortality, and adverse economic consequences resulted from these outbreaks. Our data confirm that medical students are important sources/vectors in rubella and measles outbreaks. We recommend that all medical students be immune to these viruses.

Failure to reach the goal of measles elimination. Apparent paradox of measles infections in immunized persons.

BACKGROUND: Measles is the most transmissible disease known to man. During the 1980s, the number of measles cases in the United States rose dramatically. Surprisingly, 20% to 40% of these cases occurred in persons who had been appropriately immunized against measles. In response, the United States adopted a two-dose universal measles immunization program. We critically examine the effect of vaccine failure in measles occurring in immunized persons. METHODS: We performed a computerized bibliographic literature search (National Library of Medicine) for all English-language articles dealing with measles outbreaks. We limited our search to reports of US and Canadian school-based outbreaks of measles, and we spoke with experts to get estimates of vaccine failure rates. In addition, we devised a hypothetical model of a school where measles immunization rates could be varied, vaccine failure rates could be calculated, and the percentage of measles cases occurring in immunized students could be determined. RESULTS: We found 18 reports of measles outbreaks in very highly immunized school populations where 71% to 99.8% of students were immunized against measles. Despite these high rates of immunization, 30% to 100% (mean, 77%) of all measles cases in these outbreaks occurred in previously immunized students. In our hypothetical school model, after more than 95% of schoolchildren are immunized against measles, the majority of measles cases occur in appropriately immunized children. CONCLUSIONS: The apparent paradox is that as measles immunization rates rise to high levels in a population, measles becomes a disease of immunized persons. Because of the failure rate of the vaccine and the unique transmissibility of the measles virus, the currently available measles vaccine, used in a single-dose strategy, is unlikely to completely eliminate measles. The long-term success of a two-dose strategy to eliminate measles remains to be determined.

Outbreak of parasitic gastroenteritis among travelers returning from Africa.

Eosinophilia and intestinal infections with a trematode parasite developed in 18 of the 20 American tourists who traveled to Kenya and Tanzania; the fact that the two other tourists also had eosinophilia suggested that they too had been infested. Because no adult flukes were recovered, a specific identification could not be made, but the eggs we observed resembled those of an Echinostoma. Several tour members had mild, nonspecific abdominal complaints, but ten had moderately severe abdominal cramps and loose or watery stools. Treatment with praziquantel was associated with rapid symptomatic improvement, and after treatment no parasitic eggs were recovered from patients' stools.

Isolation and rapid identification of an abundant self-peptide from class II HLA-DRB1*0401 alleles induced by measles vaccine virus infection.

Class II HLA-DR genes play an important role in the immune response to viral antigens. The effect of measles vaccine virus (MVV) infection on the induction of self-peptides presented by HLA-DR molecules during the immune response to viral infection is poorly known. Here, we describe a strategy for isolation and rapid sequence determination of an MVV-inducible class II bound peptide from a membrane protein (Leu-13). Peptides bound to HLA-DR4 (DRB1*0401 peptide complex) were eluted from immunoaffinity-purified HLA-DR4, peptides were differentially screened by MALDI-TOF-MS and subsequently sequenced by post source decay (PSD)-MALDI-TOF-MS. Human B-cells infected with MVV demonstrated an enhanced pattern of self-peptide production after MVV infection. This relatively simple analytical protocol provides a sensitive method for the direct identification of peptides associated with MHC class II DR molecules. More broadly, this same approach can be used to identify sequences of specific MVV processed peptides presented by any class II MHC DR molecule.

Marked atypical lymphocytosis, hepatitis, and skin rash in sulfasalazine drug allergy.

A 38-year-old man presented with a generalized pruritic maculopapular rash, fever, myalgias, and edema of the face and neck. Laboratory examination revealed eosinophilia, atypical lymphocytosis, and abnormal liver function results. The clinical course was characterized by rapid resolution after initiation of steroid therapy and withdrawal of sulfasalazine, which had been started three weeks earlier for abdominal cramping and diarrhea. This clinical picture suggests a drug-induced hypersensitivity reaction to a drug commonly used for inflammatory bowel disease, sulfasalazine.

Achieving the national health objective for influenza immunization: success of an institution-wide vaccination program.

PURPOSE: To enhance influenza vaccination rates for high-risk outpatients at the Department of Veterans Affairs Medical Center (VAMC) in Minneapolis, Minnesota, an institution-wide immunization program was implemented during 1987. PATIENTS AND METHODS: The program consisted of: (1) a hospital policy allowing nurses to vaccinate without a signed physician's order; (2) stamped reminders on all clinic progress notes; (3) a 2-week walk-in flu shot clinic; (4) influenza vaccination "stations" in the busiest clinic areas; and (5) a mailing to all outpatients. Risk characteristics and vaccination rates for patients were estimated from a validated self-administered postcard questionnaire mailed to 500 randomly selected outpatients. For comparison, 500 patients were surveyed from each of three other Midwestern VAMCs without similar programs. RESULTS: Overall, 70.6% of Minneapolis patients were high-risk and 58.3% of them were vaccinated. In contrast, 69.9% of patients at the comparison medical centers were high-risk, but only 29.9% of them were vaccinated. CONCLUSION: The Minneapolis VAMC influenza vaccination program was highly successful and may serve as a useful model for achieving the national health objective for influenza immunization.

Frequency of adverse reactions after influenza vaccination.

PURPOSE: Although concern about side effects constitutes a major deterrent to patient compliance with recommendations for influenza vaccination, there is a paucity of data about the frequency of adverse reactions to newer trivalent vaccines. Our aim was to determine the frequency of adverse reactions to influenza vaccine in older, chronically ill persons, many of whom are at high risk for influenza-related morbidity. PATIENTS AND METHODS: We conducted a telephone survey of 40% of the patients who were vaccinated at a walk-in flu shot clinic. The subjects were randomly assigned to two groups. To determine postvaccine symptom rates, Group I was interviewed seven days after vaccination. Group II was interviewed 21 days after vaccination in order to control for baseline symptom rates. Both groups were queried about fever, disability, and flu-like illness in the week preceding the interview. RESULTS: Of 816 patients selected, 650 (79.6%) completed the interview. The mean age of the subjects was 63, and more than two thirds were at risk for influenza-related morbidity. The frequencies of self-reported fever (5.3% versus 5.1%, p = 0.91) and disability (10.4% versus 9.3%, p = 0.65) were similar in the two groups. However, a significantly higher proportion of Group I subjects reported a flu-like illness compared to the Group II subjects (14.2% versus 8.7%, p = 0.03). Although Group I subjects were more likely to report flu-like illness within two days of vaccination compared to a similar time interval for Group II subjects, there was no corresponding clustering of disability after vaccination. CONCLUSION: We conclude that the overall frequency of symptoms in both groups was low; however, the absolute risk of a flu-like illness was 5.5% higher during the first week following influenza vaccination when compared with the third week after the injection. These symptoms did not result in a decreased ability to perform usual daily activities.