Genetic and Epigenetic Variations in Asthma and Wheeze Illnesses

Asthma, a chronic respiratory condition, is common worldwide with no cure and limited effective prevention strategies. It is well recognized that asthma has a multifaceted etiology, though many of the underlying mechanisms involved in asthma development, persistence and remission are still convoluted. Epigenetic mechanisms, such as DNA methylation, regulate gene-expression but are not related to changes in the actual DNA sequence. Recently, differential patterns of DNA methylation within many genes have been associated with asthma, particularly within genes involved in the differentiation of pro-inflammatory T-helper 2 (Th2) cells. DNA methylation patterns within less known biologic pathways undoubtedly are involved in asthma pathogenesis as well. The purpose of this dissertation was three-fold. First, we explored whether genetic and epigenetic variations within Th2-genes differed among persons with different phenotypic presentations of wheeze illnesses. Second, we conducted an epigenome-wide association study (EWAS) to identify novel DNA methylation loci associated with asthma. Last, we conducted a follow-up study of our top EWAS findings, to investigate whether the expression of the associated genes were predictive of infant wheeze. We found that DNA-M within GATA3 and IL4 varied based on different wheeze-illness phenotypes, suggesting that Th2-genes are under differential epigenetic regulation for different presentations of asthma. We also identified nine novel DNA methylation loci (cg25578728 in CHD7, cg16658191 in HK1, cg00100703 in UNC45B, cg07948085 [intergenic], cg04359558 in LITAF, cg20417424 in ST6GALNAC5, cg19974715 [intergenic], cg01046943 in NUP210 and cg14727512 in DGCR14) associated with asthma at age 18. For two of those genes (HK1 and LITAF), expression levels in cord blood were predictive of infant wheeze. Interestingly, the observed methylation and expression patterns of HK1 and LITAF could be consistent with increased resistance to apoptotic signaling. Apoptotic-resistance among pro-inflammatory cells can increase the duration of an inflammatory response and is affiliated with asthmatic pathophysiology. Thus we may have identified under-studied genes and their epigenetic regulation, which could play important roles in asthma pathophysiology. These genes may offer new insights into the etiology of asthma, be investigated as potential targets for therapy, or be considered for inclusion in algorithms used to predict early-life wheeze and later-life asthma

The interplay of DNA methylation over time with Th2 pathway genetic variants on asthma risk and temporal asthma transition

BackgroundGenetic effects on asthma of genes in the T-helper 2 (Th2) pathway may interact with epigenetic factors including DNA methylation. We hypothesized that interactions between genetic variants and methylation in genes in this pathway (IL4, IL4R, IL13, GATA3, and STAT6) influence asthma risk, that such influences are age-dependent, and that methylation of some CpG sites changes over time in accordance with asthma transition. We tested these hypotheses in subsamples of girls from a population-based birth cohort established on the Isle of Wight, UK, in 1989.ResultsLogistic regression models were applied to test the interaction effect of DNA methylation and SNP on asthma within each of the five genes. Bootstrapping was used to assess the models identified. From 1,361 models fitted at each age of 10 and 18 years, 8 models, including 4 CpGs and 8 SNPs, showed potential associations with asthma risk. Of the 4 CpGs, methylation of cg26937798 (IL4R) and cg23943829 (IL4) changes between ages 10 and 18 (both higher at 10; P?=?9.14?×?10?6 and 1.07?×?10?5, respectively).At age 10, the odds of asthma tended to decrease as cg12405139 (GATA3) methylation increased (log-OR?=??12.15; P?=?0.049); this effect disappeared by age 18. At age 18, methylation of cg09791102 (IL4R) was associated with higher risk of asthma among subjects with genotype GG compared to AG (P?=?0.003), increased cg26937798 methylation among subjects with rs3024685 (IL4R) genotype AA (P?=?0.003) or rs8832 (IL4R) genotype GG (P?=?0.01) was associated with a lower asthma risk; these CpGs had no effect at age 10. Increasing cg26937798 methylation over time possibly reduced the risk of positive asthma transition (asthma-free at age 10???asthma at age 18; log-OR?=??3.11; P?=?0.069) and increased the likelihood of negative transition (asthma at age 10???asthma-free at age 18; log-OR?=?3.97; P?=?0.074).ConclusionsThe interaction of DNA methylation and SNPs in Th2 pathway genes is likely to contribute to asthma risk. This effect may vary with age. Methylation of some CpGs changed over time, which may influence asthma transition

Placental DNA methylation signatures of maternal smoking during pregnancy and potential impacts on fetal growth

Maternal smoking during pregnancy (MSDP) contributes to poor birth outcomes, in part through disrupted placental functions, which may be reflected in the placental epigenome. Here we present a meta-analysis of the associations between MSDP and placental DNA methylation (DNAm) and between DNAm and birth outcomes within the Pregnancy And Childhood Epigenetics (PACE) consortium (N = 1700, 344 with MSDP). We identify 443 CpGs that are associated with MSDP, of which 142 associated with birth outcomes, 40 associated with gene expression, and 13 CpGs are associated with all three. Only two CpGs have consistent associations from a prior meta-analysis of cord blood DNAm, demonstrating substantial tissue-specific responses to MSDP. The placental MSDP-associated CpGs are enriched for environmental response genes, growth-factor signaling, and inflammation, which play important roles in placental function. We demonstrate links between placental DNAm, MSDP and poor birth outcomes, which may better inform the mechanisms through which MSDP impacts placental function and fetal growth

Increased protein intake derived from leucine-enriched protein enhances the integrated myofibrillar protein synthetic response to short-term resistance training in untrained men and women: a 4-day randomized controlled trial

Leucine is a critical amino acid stimulating myofibrillar protein synthesis (MyoPS). The consumption of higher leucine-containing drinks stimulates MyoPS, but we know less about higher leucine solid foods. Here we examined the effect of short-term resistance exercise training (STRT) combined with supplementation of a protein and leucine-enriched bar, compared with STRT alone, on integrated (%/d) rates of MyoPS and anabolic protein signaling. In a non-blinded, randomized crossover trial, eight young adults performed four sessions of STRT without or while consuming the study bar (STRT+Leu, 16g of protein containing ∼3g of leucine) for two 4d phases, separated by 2d non-exercise (Rest) washout. In combination with serial muscle biopsies, deuterated water permitted the measurement of myofibrillar protein synthesis and protein signaling phosphorylation. MyoPS during STRT (1.43 ± 0.06 %/d) and STRT+Leu (1.53 ± 0.06 %/d) were greater than Rest (1.31 ± 0.05 %/d), and MyoPS during STRT+Leu (1.53 ± 0.06 %/d) was greater than STRT alone (1.43 ± 0.06 %/d). STRT+Leu increased the ratio of phosphorylated to total mTOR and 4EBP1 compared to Rest. Engaging in STRT increased integrated MyoPS and protein signaling in young adults and was enhanced with increased protein intake derived from a leucine-enriched protein bar. This study was registered at clinicaltrials.gov as NCT03796897

Epigenome-wide association study of asthma- and wheeze characterizes loci within HK1

Background:To identify novel epigenetic markers of adolescent asthma and replicate findings in an independent cohort, then explore whether such markers are detectable at birth, predictive of early-life wheeze, and associated with gene expression in cord blood.Methods:We performed epigenome-wide screening with recursive random forest feature selection and internal validation in the IOW birth cohort. We then tested whether we could replicate these findings in the independent cohort ALSPAC and followed-up our top finding with children of the IOW cohort.Results:We identified 10 CpG sites associated with adolescent asthma at a 5% false discovery rate (IOW, n = 370), five of which exhibited evidence of associations in the replication study (ALSPAC, n = 720). One site, cg16658191, within HK1 displayed particularly strong associations after cellular heterogeneity adjustments in both cohorts (ORIOW = 0.17, 95% CI 0.04–0.57) (ORALSPAC = 0.57, 95% CI 0.38–0.87). Additionally, higher expression of HK1 (OR = 3.81, 95% CI 1.41–11.77) in cord blood was predictive of wheezing in infancy (n = 82).Conclusion:We identified novel associations between asthma and wheeze with methylation at cg16658191 and the expression of HK1, which may serve as markers of, predictors of, and potentially etiologic factors involved in asthma and early life wheeze

Hepatitis C disease severity in living versus deceased donor liver transplant recipients: An extended observation study

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106731/1/hep26920.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/106731/2/hep26920-sup-0001-suppinfo.pd

A meta-analysis of pre-pregnancy maternal body mass index and placental DNA methylation identifies 27 CpG sites with implications for mother-child health

Higher maternal pre-pregnancy body mass index (ppBMI) is associated with increased neonatal morbidity, as well as with pregnancy complications and metabolic outcomes in offspring later in life. The placenta is a key organ in fetal development and has been proposed to act as a mediator between the mother and different health outcomes in children. The overall aim of the present work is to investigate the association of ppBMI with epigenome-wide placental DNA methylation (DNAm) in 10 studies from the PACE consortium, amounting to 2631 mother-child pairs. We identify 27 CpG sites at which we observe placental DNAm variations of up to 2.0% per 10 ppBMI-unit. The CpGs that are differentially methylated in placenta do not overlap with CpGs identified in previous studies in cord blood DNAm related to ppBMI. Many of the identified CpGs are located in open sea regions, are often close to obesity-related genes such as GPX1 and LGR4 and altogether, are enriched in cancer and oxidative stress pathways. Our findings suggest that placental DNAm could be one of the mechanisms by which maternal obesity is associated with metabolic health outcomes in newborns and children, although further studies will be needed in order to corroborate these findings.We would like to thank the Pregnancy and Childhood Epigenetics (PACE) consortium, as well as all the families that participated in these studies for their generous contribution. This work was partially funded by GVSAN2018111086 from the Basque Department of Health and PI18/01142 from ISCIII - Spanish Ministry of Science and Innovation - cofounded by the ERDF “A way to make Europe” to JRB and LSM, respectively; and by the Joint Programming Initiative – A Healthy Diet for a Healthy Life (JPI HDHL) (NutriPROGRAM). ACP was supported by grant GVSAN2019111085 from the Basque Department of Health to NFJ. Detailed acknowledgements and funding for each participating cohort are described in Supplementary Note 1

Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A

The major histocompatibility complex (MHC) on chromosome 6 is associated with susceptibility to more common diseases than any other region of the human genome, including almost all disorders classified as autoimmune. In type 1 diabetes the major genetic susceptibility determinants have been mapped to the MHC class II genes HLA-DQB1 and HLA-DRB1 (refs 1-3), but these genes cannot completely explain the association between type 1 diabetes and the MHC region. Owing to the region's extreme gene density, the multiplicity of disease-associated alleles, strong associations between alleles, limited genotyping capability, and inadequate statistical approaches and sample sizes, which, and how many, loci within the MHC determine susceptibility remains unclear. Here, in several large type 1 diabetes data sets, we analyse a combined total of 1,729 polymorphisms, and apply statistical methods - recursive partitioning and regression - to pinpoint disease susceptibility to the MHC class I genes HLA-B and HLA-A (risk ratios >1.5; Pcombined = 2.01 × 10-19 and 2.35 × 10-13, respectively) in addition to the established associations of the MHC class II genes. Other loci with smaller and/or rarer effects might also be involved, but to find these, future searches must take into account both the HLA class II and class I genes and use even larger samples. Taken together with previous studies, we conclude that MHC-class-I-mediated events, principally involving HLA-B*39, contribute to the aetiology of type 1 diabetes. ©2007 Nature Publishing Group

Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight

Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, we find that DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from -183 to 178 grams per 10% increase in methylation (P-Bonferroni <1.06 x 10(-7)). In additional analyses in 7,278 participants,Peer reviewe