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Summary: Microbiome influences multiple human systems, but its effects on gene methylation is unknown. We investigated the relations between gene methylation in blood and the abundance of common gut bacteria profiled by 16s rRNA gene sequencing in two population-based Dutch cohorts: LifeLines-Deep (LLD, n = 616, discovery) and the Netherlands Twin Register (NTR, n = 296, replication). In LLD, we also explored microbial pathways using data generated by shotgun metagenomic sequencing (n = 683). Methylation in both cohorts was profiled in blood samples using the Illumina 450K array. Discovery and replication analysis identified two independent CpGs associated with the genus Eggerthella: cg16586104 (Pmeta−analysis = 3.21 × 10−11) and cg12234533 (Pmeta−analysis = 4.29 × 10−10). We also show that microbiome can mediate the effect of environmental factors on host gene methylation. In this first association study linking epigenome to microbiome, we found and replicated the associations of two CpGs to the abundance of genus Eggerthella and identified microbiome as a mediator of the exposome. These associations are observational and suggest further investigation in larger and longitudinal set-ups. [ABSTRACT FROM AUTHOR]

This study evaluates to what extent symptoms are present before, during, and after a positive SARS-CoV-2 polymerase chain reaction (PCR) test, and to evaluate how the symptom burden and quality of Life (QoL) compares to those with a negative PCR test. Participants from the Dutch Lifelines COVID-19 Cohort Study filled-out as of March 2020 weekly, later bi-weekly and monthly, questions about demographics, COVID-19 diagnosis and severity, QoL, and symptoms. The study population included those with one positive or negative PCR test who filled out two questionnaires before and after the test, resulting in 996 SARS-CoV-2 PCR positive and 3978 negative participants. Nearly all symptoms were more often reported after a positive test versus the period before the test (p < 0.05), except fever. A higher symptom prevalence after versus before a test was also found for nearly all symptoms in negatives (p < 0.05). Before the test, symptoms were already partly present and reporting of nearly all symptoms before did not differ between positives and negatives (p > 0.05). QoL decreased around the test for positives and negatives, with a larger deterioration for positives. Not all symptoms after a positive SARS-CoV-2 PCR test might be attributable to the infection and symptoms were also common in negatives. [ABSTRACT FROM AUTHOR]

Background: We examined whether the effect of maternal smoking during pregnancy on birthweight of the offspring was mediated by smoking-induced changes to DNA methylation in cord blood.Methods: First, we used cord blood of 129 Dutch children exposed to maternal smoking vs 126 unexposed to maternal and paternal smoking (53% male) participating in the GECKO Drenthe birth cohort. DNA methylation was measured using the Illumina HumanMethylation450 Beadchip. We performed an epigenome-wide association study for the association between maternal smoking and methylation followed by a mediation analysis of the top signals [false-discovery rate (FDR) < 0.05]. We adjusted both analyses for maternal age, education, pre-pregnancy BMI, offspring's sex, gestational age and white blood cell composition. Secondly, in 175 exposed and 1248 unexposed newborns from two independent birth cohorts, we replicated and meta-analysed results of eight cytosine-phosphate-guanine (CpG) sites in the GFI1 gene, which showed the most robust mediation. Finally, we performed functional network and enrichment analysis.Results: We found 35 differentially methylated CpGs (FDR < 0.05) in newborns exposed vs unexposed to smoking, of which 23 survived Bonferroni correction (P < 1 × 10(-7)). These 23 CpGs mapped to eight genes: AHRR, GFI1, MYO1G, CYP1A1, NEUROG1, CNTNAP2, FRMD4A and LRP5. We observed partial confirmation as three of the eight CpGs in GFI1 replicated. These CpGs partly mediated the effect of maternal smoking on birthweight (Sobel P < 0.05) in meta-analysis of GECKO and the two replication cohorts. Differential methylation of these three GFI1 CpGs explained 12-19% of the 202 g lower birthweight in smoking mothers. Functional enrichment analysis pointed towards activation of cell-mediated immunity.Conclusions: Maternal smoking during pregnancy was associated with cord blood methylation differences. We observed a potentially mediating role of methylation in the association between maternal smoking during pregnancy and birthweight of the offspring. Functional network analysis suggested a role in activating the immune system. [ABSTRACT FROM AUTHOR]

Background: Although sex differences are described in Coronavirus Disease 2019 (COVID-19) diagnoses and testing, many studies neglect possible gender-related influences. Additionally, research is often performed in clinical populations, while most COVID-19 patients are not hospitalized. Therefore, we investigated associations between sex and gender-related variables, and COVID-19 diagnoses and testing practices in a large general population cohort during the first wave of the pandemic when testing capacity was limited. Methods: We used data from the Lifelines COVID-19 Cohort (N = 74,722; 60.8% female). We applied bivariate and multiple logistic regression analyses. The outcomes were a COVID-19 diagnosis (confirmed by SARS-CoV-2 PCR testing or physician's clinical diagnosis) and PCR testing. Independent variables included among others participants' sex, age, somatic comorbidities, occupation, and smoking status. Sex-by-comorbidity and sex-by-occupation interaction terms were included to investigate sex differences in associations between the presence of comorbidities or an occupation with COVID-19 diagnoses or testing practices. Results: In bivariate analyses female sex was significantly associated with COVID-19 diagnoses and testing, but significance did not persist in multiple logistic regression analyses. However, a gender-related variable, being a health care worker, was significantly associated with COVID-19 diagnoses (OR = 1.68; 95%CI = 1.30–2.17) and testing (OR = 12.5; 95%CI = 8.55–18.3). Female health care workers were less often diagnosed and tested than male health care workers (ORinteraction = 0.54; 95%CI = 0.32–0.92, ORinteraction = 0.53; 95%CI = 0.29–0.97, respectively). Conclusions: We found no sex differences in COVID-19 diagnoses and testing in the general population. Among health care workers, a male preponderance in COVID-19 diagnoses and testing was observed. This could be explained by more pronounced COVID-19 symptoms in males or by gender inequities. [ABSTRACT FROM AUTHOR]

This document is a correction notice for an article titled "Symptoms and quality of life before, during, and after a SARS-CoV-2 PCR positive or negative test: data from Lifelines" published in Scientific Reports. The correction states that H. Marike Boezen, one of the authors, is deceased. Additionally, there was an error in the Consortium list, where Judith G. M. Rosmalen was incorrectly listed as an author. The correction has been made to the original article. The authors of the article are Yvonne M. J. Goërtz, Martijn A. Spruit, Maarten Van Herck, Nicole Dukers-Muijrers, H. Marike Boezen, Jochen O. Mierau, H. Lude Franke, Jackie Dekens, Patrick Deelen, Pauline Lanting, Judith M. Vonk, Ilja Nolte, Anil P. S. Ori, Annique Claringbould, Floranne Boulogne, Marjolein X. L. Dijkema, Henry H. Wiersma, Robert Warmerdam, Soesma A. Jankipersadsing, Irene van Blokland, Geertruida H. de Bock, Cisca Wijmenga, Carla J. H. van der Kallen, Chris Burtin, and Daisy J. A. Janssen. [Extracted from the article]

Background: DNA methylation has been found to associate with disease, aging and environmental exposure, but it is unknown how genome, environment and disease influence DNA methylation dynamics in childhood. Results: By analysing 538 paired DNA blood samples from children at birth and at 4-5 years old and 726 paired samples from children at 4 and 8 years old from four European birth cohorts using the Illumina Infinium Human Methylation 450 k chip, we have identified 14,150 consistent age-differential methylation sites (a-DMSs) at epigenomewide significance of p <1.14 x 10-7. Genes with an increase in age-differential methylation were enriched in pathways related to 'development', and were more often located in bivalent transcription start site (TSS) regions, which can silence or activate expression of developmental genes. Genes with a decrease in age-differential methylation were involved in cell signalling, and enriched on H3K27ac, which can predict developmental state. Maternal smoking tended to decrease methylation levels at the identified da-DMSs. We also found 101 a-DMSs (0.71%) that were regulated by genetic variants using cis-differential Methylation Quantitative Trait Locus (cis-dMeQTL) mapping. Moreover, a-DMS-associated genes during early development were significantly more likely to be linked with disease. Conclusion: Our study provides new insights into the dynamic epigenetic landscape of the first 8 years of life. [ABSTRACT FROM AUTHOR]

BACKGROUND: Prenatal exposure to air pollution is considered to be associated with adverse effects on child health. This may partly be mediated by mechanisms related to DNA methylation. OBJECTIVES: We investigated associations between exposure to air pollution, using nitrogen dioxide (NO2) as marker, and epigenome-wide cord blood DNA methylation. METHODS: We meta-analyzed the associations between NO2 exposure at residential addresses during pregnancy and cord blood DNA methylation (Illumina 450K) in four European and North American studies (n = 1,508) with subsequent look-up analyses in children ages 4 (n = 733) and 8 (n = 786) years. Additionally, we applied a literature-based candidate approach for antioxidant and anti-inflammatory genes. To assess influence of exposure at the transcriptornics level, we related mRNA expression in blood cells to NO2 exposure in 4- (n = 111) and 16-year-olds (n = 239). RESULTS: We found epigenome-wide significant associations [false discovery rate (FDR) p < 0.05] between maternal NO2 exposure during pregnancy and DNA methylation in newborns for 3 CpG sites in mitochondria-related genes: cgl2283362 (LONP1), cg24l72570 (3.8 kbp upstream of HIBADH), and cg08973675 (SLC25A28). The associations with cg08973675 methylation were also significant in the older children. Further analysis of antioxidant and anti-inflammatory genes revealed differentially methylated CpGs in CAT and TPO in newborns (FDR p < 0.05). NO2 exposure at the time of biosampling in childhood had a significant impact on CAT and TPO expression. CONCLUSIONS: NO2 exposure during pregnancy was associated with differential offspring DNA methylation in mitochondria-related genes. Exposure to NO2 was also linked to differential methylation as well as expression of genes involved in antioxidant defense pathways. CITATION: Gruzieva O, Xu CJ, Breton CV, Annesi-Maesano I, Antó JM, Auffray C, Ballereau S, Bellander T, Bousquet J, Bustamante M, Charles MA, de Kluizenaar Y, den Dekker HT, Duijts L, Felix JF, Gehring U, Guxens M, Jaddoe VV, Jankipersadsing SA, Merid SK, Kere J, Kumar A, Lemonnier N, Lepeule J, Nystad W, Page CM, Panasevich S, Postma D, Slama R, Sunyer J, Söderhäll C, Yao J, London SJ, Pershagen G, Koppelman GH, Melen E. 2017. Epigenome-wide meta-analysis of methylation in children related to prenatal NO2 air pollution exposure. Environ Health Perspect 125:104-110; http://dx.doi.org/10.1289/EHP36 [ABSTRACT FROM AUTHOR]

Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors. These factors collectively explain 18.7% of the variation seen in the interindividual distance of microbial composition. We could associate 110 factors to 125 species and observed that fecal chromogranin A (CgA), a protein secreted by enteroendocrine cells, was exclusively associated with 61 microbial species whose abundance collectively accounted for 53% of microbial composition. Low CgA concentrations were seen in individuals with a more diverse microbiome. These results are an important step toward a better understanding of environment-diet-microbe-host interactions. [ABSTRACT FROM AUTHOR]

Background The majority of coeliac disease (CD) patients are not being properly diagnosed and therefore remain untreated, leading to a greater risk of developing CD-associated complications. The major genetic risk heterodimer, HLA-DQ2 and DQ8, is already used clinically to help exclude disease. However, approximately 40% of the population carry these alleles and the majority never develop CD. Objective We explored whether CD risk prediction can be improved by adding non-HLA-susceptible variants to common HLA testing. Design We developed an average weighted genetic risk score with 10, 26 and 57 single nucleotide polymorphisms (SNP) in 2675 cases and 2815 controls and assessed the improvement in risk prediction provided by the non-HLA SNP. Moreover, we assessed the transferability of the genetic risk model with 26 non-HLA variants to a nested case-control population (n=1709) and a prospective cohort (n=1245) and then tested how well this model predicted CD outcome for 985 independent individuals. Results Adding 57 non-HLA variants to HLA testing showed a statistically significant improvement compared to scores from models based on HLA only, HLA plus 10 SNP and HLA plus 26 SNP. With 57 non-HLA variants, the area under the receiver operator characteristic curve reached 0.854 compared to 0.823 for HLA only, and 11.1% of individuals were reclassified to a more accurate risk group. We show that the risk model with HLA plus 26 SNP is useful in independent populations. Conclusions Predicting risk with 57 additional non-HLA variants improved the identification of potential CD patients. This demonstrates a possible role for combined HLA and non-HLA genetic testing in diagnostic work for CD. [ABSTRACT FROM AUTHOR]