Impact of infection on proteome-wide glycosylation revealed by distinct signatures for bacterial and viral pathogens

Mechanisms of infection and pathogenesis have predominantly been studied based on differential gene or protein expression. Less is known about posttranslational modifications, which are essential for protein functional diversity. We applied an innovative glycoproteomics method to study the systemic proteome-wide glycosylation in response to infection. The protein site-specific glycosylation was characterized in plasma derived from well-defined controls and patients. We found 3862 unique features, of which we identified 463 distinct intact glycopeptides, that could be mapped to more than 30 different proteins. Statistical analyses were used to derive a glycopeptide signature that enabled significant differentiation between patients with a bacterial or viral infection. Furthermore, supported by a machine learning algorithm, we demonstrated the ability to identify the causative pathogens based on the distinctive host blood plasma glycopeptide signatures. These results illustrate that glycoproteomics holds enormous potential as an innovative approach to improve the interpretation of relevant biological changes in response to infection

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

Serum 25-Hydroxyvitamin D Concentrations ≥40 ng/ml Are Associated with >65% Lower Cancer Risk: Pooled Analysis of Randomized Trial and Prospective Cohort Study

<div><p>Background</p><p>Higher serum 25-hydroxyvitamin D [25(OH)D] concentrations have been associated with a lower risk of multiple cancer types across a range of 25(OH)D concentrations.</p><p>Objectives</p><p>To investigate whether the previously reported inverse association between 25(OH)D and cancer risk could be replicated, and if a 25(OH)D response region could be identified among women aged 55 years and older across a broad range of 25(OH)D concentrations.</p><p>Methods</p><p>Data from two cohorts representing different median 25(OH)D concentrations were pooled to afford a broader range of 25(OH)D concentrations than either cohort alone: the Lappe cohort (N = 1,169), a randomized clinical trial cohort (median 25(OH)D = 30 ng/ml) and the GrassrootsHealth cohort (N = 1,135), a prospective cohort (median 25(OH)D = 48 ng/ml). Cancer incidence over a multi-year period (median: 3.9 years) was compared according to 25(OH)D concentration. Kaplan-Meier plots were developed and the association between 25(OH)D and cancer risk was examined with multivariate Cox regression using multiple 25(OH)D measurements and spline functions. The study included all invasive cancers excluding skin cancer.</p><p>Results</p><p>Age-adjusted cancer incidence across the combined cohort (N = 2,304) was 840 cases per 100,000 person-years (1,020 per 100,000 person-years in the Lappe cohort and 722 per 100,000 person-years in the GrassrootsHealth cohort). Incidence was lower at higher concentrations of 25(OH)D. Women with 25(OH)D concentrations ≥40 ng/ml had a 67% lower risk of cancer than women with concentrations <20 ng/ml (HR = 0.33, 95% CI = 0.12–0.90).</p><p>Conclusions</p><p>25(OH)D concentrations ≥40 ng/ml were associated with substantial reduction in risk of all invasive cancers combined.</p></div

Association between serum 25(OH)D and risk of cancer, pooled cohort (N = 2304).

<p>Association between serum 25(OH)D and risk of cancer, pooled cohort (N = 2304).</p

Frequency distribution and cancer incidence rates by 25(OH)D concentration, pooled cohort (N = 2304).

<p>The bars represent the number of non-cases by groupings of 10 ng/ml, white dots represent the 25(OH)D concentration for each cancer case, black dots represent cancer incidence rates per 100,000 person-years for indicated 25(OH)D groupings (plotted at the median 25(OH)D value for each grouping: baseline 25(OH)D groups at 17, 25, 30, 37, 46, and 63 ng/ml; mean 25(OH)D groups at 17, 25, 31, 38, 47, 58, and 69 ng/ml). Vertical error bars indicate the 95% confidence intervals.</p

Association between serum 25(OH)D and risk of cancer adjusted for age, BMI, smoking status, and calcium supplement intake in the range of ≤100 ng/ml, pooled cohort (N = 2304).

<p>Solid black line represents the estimated hazard ratio for the Cox regression model with restricted cubic splines with 3 knots and dashed lines represent the 95% confidence interval of the estimate. The reduction in risk from 20 ng/ml to 40 ng/ml was approximately 70%.</p

Kaplan-Meier plot comparing the proportion of cancer-free participants by 25(OH)D concentration (allowing for participants switching groups), pooled cohort (N = 2304).

<p>Four-year cumulative cancer-free proportion was 98% among participants with 25(OH)D concentrations ≥40 ng/ml compared to 93% for those with 25(OH)D concentrations <20 ng/ml (proportion with cancer was 71% lower for ≥40 ng/ml vs. <20 ng/ml, <i>P</i> = 0.02).</p

Cancer incidence rates by 25(OH)D concentration with fitted curves, pooled cohort (N = 2304).

<p>Black dots represent cancer incidence rates per 100,000 person-years for indicated 25(OH)D groupings (rates are displayed at the median value for each grouping: baseline 25(OH)D groups at 17, 25, 30, 37, 46, and 63 ng/ml; mean 25(OH)D groups at 17, 25, 31, 38, 47, 58, 69 ng/ml), as seen in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152441#pone.0152441.g001" target="_blank">Fig 1</a>. Solid black lines represent the best fit line to the exponential equation: Y = A + B(e^(-X/C)), where Y = cancer incidence rate, X = serum 25(OH)D (dashed lines represent the 95% confidence intervals).</p