Deimmunizing substitutions in Pseudomonas exotoxin domain III perturb antigen processing without eliminating T-cell epitopes

© 2019 Moss et al. Effective adaptive immune responses depend on activation of CD4 T cells via the presentation of antigen peptides in the context of major histocompatibility complex (MHC) class II. The structure of an antigen strongly influences its processing within the endolysosome and potentially controls the identity of peptides that are presented to T cells. A recombinant immunotoxin, comprising exotoxin A domain III (PE-III) from Pseudomonas aeruginosa and a cancer-specific antibody fragment, has been developed to manage cancer, but its effectiveness is limited by the induction of neutralizing antibodies. Here, we observed that this immunogenicity is substantially reduced by substituting six residues within PE-III. Although these substitutions targeted T-cell epitopes, we demonstrate that reduced conformational stability and protease resistance were responsible for the reduced antibody titer. Analysis of mouse T-cell responses coupled with biophysical studies on single-substitution versions of PE-III suggested that modest but comprehensible changes in T-cell priming can dramatically perturb antibody production. The most strongly responsive PE-III epitope was well-predicted by a structure-based algorithm. In summary, single-residue substitutions can drastically alter the processing and immunogenicity of PE-III but have only modest effects on CD4 T-cell priming in mice. Our findings highlight the importance of structure-based processing constraints for accurate epitope prediction

Advancing precision public health using human genomics: examples from the field and future research opportunities

Precision public health is a relatively new field that integrates components of precision medicine, such as human genomics research, with public health concepts to help improve population health. Despite interest in advancing precision public health initiatives using human genomics research, current and future opportunities in this emerging field remain largely undescribed. To that end, we provide examples of promising opportunities and current applications of genomics research within precision public health and outline future directions within five major domains of public health: biostatistics, environmental health, epidemiology, health policy and health services, and social and behavioral science. To further extend applications of genomics within precision public health research, three key cross-cutting challenges will need to be addressed: developing policies that implement precision public health initiatives at multiple levels, improving data integration and developing more rigorous methodologies, and incorporating initiatives that address health equity. Realizing the potential to better integrate human genomics within precision public health will require transdisciplinary efforts that leverage the strengths of both precision medicine and public health

Three dimensional structure directs T-cell epitope dominance associated with allergy

<p>Abstract</p> <p>Background</p> <p>CD4+ T-cell epitope immunodominance is not adequately explained by peptide selectivity in class II major histocompatibility proteins, but it has been correlated with adjacent segments of conformational flexibility in several antigens.</p> <p>Methods</p> <p>The published T-cell responses to two venom allergens and two aeroallergens were used to construct profiles of epitope dominance, which were correlated with the distribution of conformational flexibility, as measured by crystallographic B factors, solvent-accessible surface, COREX residue stability, and sequence entropy.</p> <p>Results</p> <p>Epitopes associated with allergy tended to be excluded from and lie adjacent to flexible segments of the allergen.</p> <p>Conclusion</p> <p>During the initiation of allergy, the N- and/or C-terminal ends of proteolytic processing intermediates were preferentially loaded into antigen presenting proteins for the priming of CD4+ T cells.</p

Serum 25-Hydroxyvitamin D and the Incidence of Acute Viral Respiratory Tract Infections in Healthy Adults

Declining serum concentrations of 25-hydroxyvitamin D seen in the fall and winter as distance increases from the equator may be a factor in the seasonal increased prevalence of influenza and other viral infections. This study was done to determine if serum 25-hydroxyvitamin D concentrations correlated with the incidence of acute viral respiratory tract infections.In this prospective cohort study serial monthly concentrations of 25-hydroxyvitamin D were measured over the fall and winter 2009-2010 in 198 healthy adults, blinded to the nature of the substance being measured. The participants were evaluated for the development of any acute respiratory tract infections by investigators blinded to the 25-hydroxyvitamin D concentrations. The incidence of infection in participants with different concentrations of vitamin D was determined. One hundred ninety-five (98.5%) of the enrolled participants completed the study. Light skin pigmentation, lean body mass, and supplementation with vitamin D were found to correlate with higher concentrations of 25-hydroxyvitamin D. Concentrations of 38 ng/ml or more were associated with a significant (p<0.0001) two-fold reduction in the risk of developing acute respiratory tract infections and with a marked reduction in the percentages of days ill.Maintenance of a 25-hydroxyvitamin D serum concentration of 38 ng/ml or higher should significantly reduce the incidence of acute viral respiratory tract infections and the burden of illness caused thereby, at least during the fall and winter in temperate zones. The findings of the present study provide direction for and call for future interventional studies examining the efficacy of vitamin D supplementation in reducing the incidence and severity of specific viral infections, including influenza, in the general population and in subpopulations with lower 25-hydroxyvitamin D concentrations, such as pregnant women, dark skinned individuals, and the obese

Teaching clinical informatics to third-year medical students: negative results from two controlled trials

BACKGROUND: Prior educational interventions to increase seeking evidence by medical students have been unsuccessful. METHODS: We report two quasirandomized controlled trials to increase seeking of medical evidence by third-year medical students. In the first trial (1997–1998), we placed computers in clinical locations and taught their use in a 6-hour course. Based on negative results, we created SUMSearch(TM), an Internet site that automates searching for medical evidence by simultaneous meta-searching of MEDLINE and other sites. In the second trial (1999–2000), we taught SUMSearch's use in a 5½-hour course. Both courses were taught during the medicine clerkship. For each trial, we surveyed the entire third-year class at 6 months, after half of the students had taken the course (intervention group). The students who had not received the intervention were the control group. We measured self-report of search frequency and satisfaction with search quality and speed. RESULTS: The proportion of all students who reported searching at least weekly for medical evidence significantly increased from 19% (1997–1998) to 42% (1999–2000). The proportion of all students who were satisfied with their search results increased significantly between study years. However, in neither study year did the interventions increase searching or satisfaction with results. Satisfaction with the speed of searching was 27% in 1999–2000. This did not increase between studies years and was not changed by the interventions. CONCLUSION: None of our interventions affected searching habits. Even with automated searching, students report low satisfaction with search speed. We are concerned that students using current strategies for seeking medical evidence will be less likely to seek and appraise original studies when they enter medical practice and have less time

Alternative Promoters Influence Alternative Splicing at the Genomic Level

Background: More and more experiments have shown that transcription and mRNA processing are not two independent events but are tightly coupled to each other. Both promoter and transcription rate were found to influence alternative splicing. More than half of human genes have alternative promoters, but it is still not clear why there are so many alternative promoters and what their biological roles are. Methodology/Principal Findings: In this study, we explored whether there is a functional correlation between alternative promoters and alternative splicing by a genome-wide analysis of human and mouse genes. We constructed a large data set of genes with alternative promoter and alternative splicing annotations. By analyzing these genes, we showed that genes with alternative promoters tended to demonstrate alternative splicing compare to genes with single promoter, and, genes with more alternative promoters tend to have more alternative splicing variants. Furthermore, transcripts from different alternative promoters tended to splice differently. Conclusions/Significance: Thus at the genomic level, alternative promoters are positively correlated with alternativ

Missing paternal demographics: A novel indicator for identifying high risk population of adverse pregnancy outcomes

BACKGROUND: One of every 6 United Status birth certificates contains no information on fathers. There might be important differences in the pregnancy outcomes between mothers with versus those without partner information. The object of this study was to assess whether and to what extent outcomes in pregnant women who did not have partner information differ from those who had. METHODS: We carried out a population-based retrospective cohort study based on the registry data in the United States for the period of 1995–1997, which was a matched multiple birth file (only twins were included in the current analysis). We divided the study subjects into three groups according to the availability of partner information: available, partly missing, and totally missing. We compared the distribution of maternal characteristics, maternal morbidity, labor and delivery complications, obstetric interventions, preterm birth, fetal growth restriction, low birth weight, congenital anomalies, fetal death, neonatal death, post-neonatal death, and neonatal morbidity among three study groups. RESULTS: There were 304466 twins included in our study. Mothers whose partner's information was partly missing and (especially) totally missing tended to be younger, of black race, unmarried, with less education, smoking cigarette during pregnancy, and with inadequate prenatal care. The rates of preterm birth, fetal growth restriction, low birth weight, Apgar score <7, fetal mortality, neonatal mortality, and post-neonatal mortality were significantly increased in mothers whose partner's information was partly or (especially) totally missing. CONCLUSIONS: Mothers whose partner's information was partly and (especially) totally missing are at higher risk of adverse pregnant outcomes, and clinicians and public health workers should be alerted to this important social factor

Bridging the gaps among research, policy and practice in ten low- and middle-income countries: Development and testing of a questionnaire for health-care providers

<p>Abstract</p> <p>Background</p> <p>The reliability and validity of instruments used to survey health-care providers' views about and experiences with research evidence have seldom been examined.</p> <p>Methods</p> <p>Country teams from ten low- and middle-income countries (China, Ghana, India, Iran, Kazakhstan, Laos, Mexico, Pakistan, Senegal and Tanzania) participated in the development, translation, pilot-testing and administration of a questionnaire designed to measure health-care providers' views and activities related to improving their clinical practice and their awareness of, access to and use of research evidence, as well as changes in their clinical practice that they attribute to particular sources of research evidence that they have used. We use internal consistency as a measure of the questionnaire's reliability and, whenever possible, we use explanatory factor analyses to assess the degree to which questions that pertain to a single domain actually address common themes. We assess the questionnaire's face validity and content validity and, to a lesser extent, we also explore its criterion validity.</p> <p>Results</p> <p>The questionnaire has high internal consistency, with Cronbach's alphas between 0.7 and 0.9 for 16 of 20 domains and sub-domains (identified by factor analyses). Cronbach's alphas are greater than 0.9 for two domains, suggesting some item redundancy. Pre- and post-field work assessments indicate the questionnaire has good face validity and content validity. Our limited assessment of criterion validity shows weak but statistically significant associations between the general influence of research evidence among providers and more specific measures of providers' change in approach to preventing or treating a clinical condition.</p> <p>Conclusion</p> <p>Our analysis points to a number of strengths of the questionnaire - high internal consistency (reliability) and good face and content validity - but also to areas where it can be shortened without losing important conceptual domains.</p

Temporal and spatial instability in neutral and adaptive (MHC) genetic variation in marginal salmon populations

The role of marginal populations for the long-term maintenance of species’ genetic diversity and evolutionary potential is particularly timely in view of the range shifts caused by climate change. The Centre-Periphery hypothesis predicts that marginal populations should bear reduced genetic diversity and have low evolutionary potential. We analysed temporal stability at neutral microsatellite and adaptive MHC genetic variation over five decades in four marginal Atlantic salmon populations located at the southern limit of the species’ distribution with a complicated demographic history, which includes stocking with foreign and native salmon for at least 2 decades. We found a temporal increase in neutral genetic variation, as well as temporal instability in population structuring, highlighting the importance of temporal analyses in studies that examine the genetic diversity of peripheral populations at the margins of the species’ range, particularly in face of climate change