Use of novel DNA methylation signatures to distinguish between human airway structural cell types

INTRODUCTION: Chronic inflammatory and fibrotic lung diseases like asthma, COPD and pulmonary fibrosis are characterised by modified phenotype of the airway structural cells. Airway walls are comprised of a robust epithelial layer that lines the lumen followed by the basement membrane, submucosa predominantly composed of fibroblasts and finally enveloped by a bulk of smooth muscle cells that determine the relaxation and constriction of the airways. The phenotype of airway structural cells is determined by epigenetic alterations such as DNA methylation, which alters the activation status of a range of important inflammatory and remodelling genes. Here we determined if airway structural cells (Epithelial cells, fibroblasts and smooth muscle cells) have different DNA methylome signatures that can be used to distinguish between them. This will offer a reference standard for identifying cell type specific DNA methylation changes induced by various inflammatory stimuli. EXPERIMENTAL METHODS: Illumina Human Methylation 450K Beadchip (HM450K) was used to perform genome-wide methylome screening on 17 bronchial fibroblast (BrF), 23 lung parenchymal fibroblast (LgF), 17 airway epithelial cell (Ep) and 6 airway smooth muscle cell (ASM) samples isolated from healthy individuals. The data was normalised using funtoonorm, a specialised algorithm in R developed for multiple tissue types. R packages minfi, limma and DMRcate was used for CpG site exclusion and identification of significant differentially methylated regions (DMR) specific to each of the four cell types. RESULTS AND DISCUSSION: Epithelial cells distinctly separated from other lung cells (791 DMR). LgF, BrF and ASM had 13, 10 and 1 signature DMR respectively. Despite close anatomical proximity, ASM and BrF displayed 2 DMR when compared to each other. Interestingly, fibroblasts obtained from airway showed 6 DMR in comparison to those obtained from lung parenchyma, suggesting that the same cell type obtained from different parts of the lung can have significantly different methylation patterns that might lead to phenotypic differences. CONCLUSION: We have identified cell and tissue specific methylation signatures which can be used to differentiate between different types of airway structural cells. The airway epithelial cells showed the greatest separation from other airway structural cells. The Bronchial fibroblasts varied minimally from airway smooth muscle cells despite its significant separation from airway epithelial cells and parenchymal fibroblasts

Investigating genome wide DNA methylation in bronchial and lung fibroblasts from healthy individuals and individuals with COPD

Rationale: Lung fibroblasts are implicated in respiratory disease pathology including chronic obstructive pulmonary disease (COPD). Phenotypic differences between fibroblasts isolated from the bronchi versus the lung parenchyma have been described but no studies have compared the cell types on a genome wide scale. DNA methylation is a reversible modification of the DNA structure with the ability to affect cell function via the alteration of gene expression. Here we compared genome wide DNA methylation profiles from bronchial and lung fibroblasts and assessed modification to these profiles in cells isolated from individuals with COPD. Methods: DNA was isolated from lung (LgF) and bronchial fibroblasts (BrF) at passage 4 and bisulphite treated. Site specific, quantitative genome wide methylation was determined using the Illumina 450K Infinium Methylation BeadChip array. Linear modelling and DMRcate functions identified differentially methylated sites and regions respectively between BrF and LgF and from cells isolated from healthy individuals versus those with COPD. Results: 3980 CpG (methylation) sites significantly differed, following Bonferroni correction, between BrF and LgF isolated from healthy individuals. These sites had a broad distribution of effect size, with 240 CpG sites displaying a difference in methylation of >50%. 78 of these sites were validated in a second cohort of matched BrF and LgF isolated from the same individuals. There was genomic proximity to these sites and DMRcate was used to refine the individual CpG sites to 5 regions of interest associated with 5 genes; HLX, TWIST1, CREB5, SKAP2 and PRDM16. Differences in methylation were less pronounced when comparing cells isolated from healthy individuals to those with COPD. In BrF 47 DMRcate regions were identified with a maximum difference in methylation of at least 20%. In LgF 3 DMRcate regions were identified with a maximum difference in methylation of at least 20%. Conclusions: DNA methylation profiles are significantly different between BrF and LgF but only small modifications are associated with COPD. Future work will focus on validating a methylation based marker of lung versus bronchial fibroblasts to differentiate cell types by validating our differential DNA methylation observations with gene/protein expression

Maternal antenatal depression and child mental health: moderation by genomic risk for attention-deficit/hyperactivity disorder

Maternal antenatal depression strongly influences child mental health but with considerable inter-individual variation that is, in part, linked to genotype. The challenge is to effectively capture the genotypic influence. We outline a novel approach to describe genomic susceptibility to maternal antenatal depression focusing on child emotional/behavioral difficulties. Two cohorts provided measures of maternal depression, child genetic variation, and child mental health symptoms. We constructed a conventional polygenic risk score (PRS) for attention-deficit/hyperactivity disorder (ADHD) (PRSADHD) that significantly moderated the association between maternal antenatal depression and internalizing problems at 60 months (p = 2.94 x 10(-4), R-2 = .18). We then constructed an interaction PRS (xPRS) based on a subset of those single nucleotide polymorphisms from the PRSADHD that most accounted for the moderation of the association between maternal antenatal depression and child outcome. The interaction between maternal antenatal depression and this xPRS accounted for a larger proportion of the variance in child emotional/behavioral problems than models based on any PRSADHD (p = 5.50 x 10(-9), R-2 = .27), with similar findings in the replication cohort. The xPRS was significantly enriched for genes involved in neuronal development and synaptic function. Our study illustrates a novel approach to the study of genotypic moderation on the impact of maternal antenatal depression on child mental health and highlights the utility of the xPRS approach. These findings advance our understanding of individual differences in the developmental origins of mental health.Stress and Psychopatholog

Integrated analysis of environmental and genetic influences on cord blood DNA methylation in new-borns

Epigenetic processes, including DNA methylation (DNAm), are among the mechanisms allowing integration of genetic and environmental factors to shape cellular function. While many studies have investigated either environmental or genetic contributions to DNAm, few have assessed their integrated effects. Here we examine the relative contributions of prenatal environmental factors and genotype on DNA methylation in neonatal blood at variably methylated regions (VMRs) in 4 independent cohorts (overall n = 2365). We use Akaike’s information criterion to test which factors best explain variability of methylation in the cohort-specific VMRs: several prenatal environmental factors (E), genotypes in cis (G), or their additive (G + E) or interaction (GxE) effects. Genetic and environmental factors in combination best explain DNAm at the majority of VMRs. The CpGs best explained by either G, G + E or GxE are functionally distinct. The enrichment of genetic variants from GxE models in GWAS for complex disorders supports their importance for disease risk

The effect of lobster meal on the growth performance and pigmentation of the common goldfish (Carassius auratus)

This study evaluated lobster meal (LM) as a source of carotenoids and protein in diets for the Common Goldfish (Carassius auratus). Fish were fed four experimental diets which included up to 15% LM. After 8 weeks, there were no significant differences among treatments in terms of weight gain, condition factor, specific growth rate (SGR), feed intake, and feed conversion ratio (FCR). Lobster meal inclusion had no significant effect on whole body composition. Although, there were no significant differences in growth across all treatments, fish gained >350% with an SGR between 2.5–3.7 and an average FCR of 1.8. There were no treatment differences in pigmentation of the fish, but the lightness, redness and yellowness scores did increase after the duration of the trial. LM could be used as a source of pigment and protein, and could reduce the need for synthetic carotenoids in commercial fish feeds. Keywords: Carotenoids, Common goldfish, Fish meal, Lobster meal, Pigmentatio

Use of novel DNA methylation signatures to distinguish between human airway structural cell types

INTRODUCTION: Chronic inflammatory and fibrotic lung diseases like asthma, COPD and pulmonary fibrosis are characterised by modified phenotype of the airway structural cells. Airway walls are comprised of a robust epithelial layer that lines the lumen followed by the basement membrane, submucosa predominantly composed of fibroblasts and finally enveloped by a bulk of smooth muscle cells that determine the relaxation and constriction of the airways. The phenotype of airway structural cells is determined by epigenetic alterations such as DNA methylation, which alters the activation status of a range of important inflammatory and remodelling genes. Here we determined if airway structural cells (Epithelial cells, fibroblasts and smooth muscle cells) have different DNA methylome signatures that can be used to distinguish between them. This will offer a reference standard for identifying cell type specific DNA methylation changes induced by various inflammatory stimuli. EXPERIMENTAL METHODS: Illumina Human Methylation 450K Beadchip (HM450K) was used to perform genome-wide methylome screening on 17 bronchial fibroblast (BrF), 23 lung parenchymal fibroblast (LgF), 17 airway epithelial cell (Ep) and 6 airway smooth muscle cell (ASM) samples isolated from healthy individuals. The data was normalised using funtoonorm, a specialised algorithm in R developed for multiple tissue types. R packages minfi, limma and DMRcate was used for CpG site exclusion and identification of significant differentially methylated regions (DMR) specific to each of the four cell types. RESULTS AND DISCUSSION: Epithelial cells distinctly separated from other lung cells (791 DMR). LgF, BrF and ASM had 13, 10 and 1 signature DMR respectively. Despite close anatomical proximity, ASM and BrF displayed 2 DMR when compared to each other. Interestingly, fibroblasts obtained from airway showed 6 DMR in comparison to those obtained from lung parenchyma, suggesting that the same cell type obtained from different parts of the lung can have significantly different methylation patterns that might lead to phenotypic differences. CONCLUSION: We have identified cell and tissue specific methylation signatures which can be used to differentiate between different types of airway structural cells. The airway epithelial cells showed the greatest separation from other airway structural cells. The Bronchial fibroblasts varied minimally from airway smooth muscle cells despite its significant separation from airway epithelial cells and parenchymal fibroblasts

Effect of angiotensin II receptor blocker and salt supplementation on short-term blood pressure variability in type 2 diabetes

High blood pressure variability (BPV) has been associated with increased cardiovascular (CV) risk. The effect of dietary salt and renin-angiotensin-aldosterone system (RAAS) activity on short-term BPV in type 2 diabetes mellitus (T2DM) is not well characterised. We aimed to determine the effect of dietary salt (sodium chloride, NaCl) supplementation on 24-h mean arterial BPV (24hBPV) during angiotensin II receptor blocker (telmisartan) use and to evaluate the effects of age, sex, plasma renin activity (PRA) and serum aldosterone on 24hBPV. In a randomised, double-blind, crossover study, patients with T2DM (n = 28), treated with telmisartan received NaCl (100 mmol/24 h) or placebo capsules during 2 weeks of telmisartan. Following a 6-week washout, the protocol was repeated in reverse. 24hBPV was evaluated as a co-efficient of variation [CV (%) = mean/standard deviation] × 100). Twenty-four hour urinary sodium excretion, ambulatory BP and biochemical tests were performed at each phase. Results were analysed using a linear mixed model to generate predicted values for 24hBPV. Predicted 24hBPV was higher with telmisartan vs baseline (p = 0.01), with a trend towards reduced 24hBPV with salt (p = 0.052). Predicted 24hBPV was lower in females (p = 0.017), increasing age (p = 0.001) and increasing PRA (p = 0.011). In patients with T2DM, predicted 24hBPV increased from baseline with telmisartan, but there was no additional increase in predicted 24hBPV with salt supplementation. This suggests that in the short-term, salt supplementation has no apparent deleterious effects on 24hBPV. Long-term studies are required to evaluate the effect of 24hBPV on CV outcomes in patients with T2DM.Angela X. Chen, John L. Moran, Renata Libianto, Sara Baqar, Christopher O'Callaghan, Richard J. MacIsaac, George Jerums, Elif I. Ekinc

The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells

Contains fulltext : 219496.pdf (Publisher’s version ) (Closed access)DNA methylation is the most studied modification in human population epigenetics. Its information content can be explored in 2 principal ways - epigenome-wide association studies and epigenetic age. The latter likely reflects cellular/biological age and works with impressive accuracy across most tissues. In adults, it associates with various environments and health. However, current epigenetic clocks are not very accurate in the pediatric age range perhaps because DNA methylation changes much faster in children. Addressing this crucial gap, we created a precise tool to estimate DNA methylation age specific to pediatric buccal epithelial cells. This tool has the potential to become the standard reference for epigenetic studies broadly relevant to child development across the spectrum from health to disease.The development of biological markers of aging has primarily focused on adult samples. Epigenetic clocks are a promising tool for measuring biological age that show impressive accuracy across most tissues and age ranges. In adults, deviations from the DNA methylation (DNAm) age prediction are correlated with several age-related phenotypes, such as mortality and frailty. In children, however, fewer such associations have been made, possibly because DNAm changes are more dynamic in pediatric populations as compared to adults. To address this gap, we aimed to develop a highly accurate, noninvasive, biological measure of age specific to pediatric samples using buccal epithelial cell DNAm. We gathered 1,721 genome-wide DNAm profiles from 11 different cohorts of typically developing individuals aged 0 to 20 y old. Elastic net penalized regression was used to select 94 CpG sites from a training dataset (n = 1,032), with performance assessed in a separate test dataset (n = 689). DNAm at these 94 CpG sites was highly predictive of age in the test cohort (median absolute error = 0.35 y). The Pediatric-Buccal-Epigenetic (PedBE) clock was characterized in additional cohorts, showcasing the accuracy in longitudinal data, the performance in nonbuccal tissues and adult age ranges, and the association with obstetric outcomes. The PedBE tool for measuring biological age in children might help in understanding the environmental and contextual factors that shape the DNA methylome during child development, and how it, in turn, might relate to child health and disease.7 p

Four priority areas to advance invasion science in the face of rapid environmental change

Unprecedented rates of introduction and spread of non-native species pose burgeoning challenges to biodiversity, natural resource management, regional economies, and human health. Current biosecurity efforts are failing to keep pace with globalization, revealing critical gaps in our understanding and response to invasions. Here, we identify four priority areas to advance invasion science in the face of rapid global environmental change. First, invasion science should strive to develop a more comprehensive framework for predicting how the behavior, abundance, and interspecific interactions of non-native species vary in relation to conditions in receiving environments and how these factors govern the ecological impacts of invasion. A second priority is to understand the potential synergistic effects of multiple co-occurring stressors— particularly involving climate change—on the establishment and impact of non-native species. Climate adaptation and mitigation strategies will need to consider the possible consequences of promoting non-native species, and appropriate management responses to non-native species will need to be developed. The third priority is to address the taxonomic impediment. The ability to detect and evaluate invasion risks is compromised by a growing deficit in taxonomic expertise, which cannot be adequately compensated by new molecular technologies alone. Management of biosecurity risks will become increasingly challenging unless academia, industry, and governments train and employ new personnel in taxonomy and systematics. Fourth, we recommend that internationally cooperative biosecurity strategies consider the bridgehead effects of global dispersal networks, in which organisms tend to invade new regions from locations where they have already established. Cooperation among countries to eradicate or control species established in bridgehead regions should yield greater benefit than independent attempts by individual countries to exclude these species from arriving and establishing