Search

Background: Fibrinogen plays an essential role in blood coagulation and inflammation. Circulating fibrinogen levels may be determined by inter-individual differences in DNA methylation at CpG sites, and vice versa., Methods: We performed an epigenome-wide association study (EWAS) of circulating fibrinogen levels in 18,037 White, Black, American Indian, and Hispanic participants representing 14 studies from the CHARGE consortium. Circulating leukocyte DNA methylation was measured in 12,904 participants using the Illumina 450K array, and in 5,133 participants using the EPIC array. Each study performed an EWAS of fibrinogen using linear mixed models adjusted for potential confounders. Study-specific results were combined using array-specific meta-analysis, followed by cross-replication of epigenome-wide significant associations. We compared models with and without C-reactive protein (CRP) adjustment to examine the role of inflammation., Results: We identified 208 and 87 significant CpG sites associated with fibrinogen from the 450K (p-value<1.03×10 -7 ) and EPIC arrays (p-value<5.78×10 -8 ), respectively. There were 78 associations from the 450K array that replicated in the EPIC array and 26 vice versa. After accounting for the overlapping sites, there were 83 replicated CpG sites located in 61 loci, of which only 4 have been previously reported for fibrinogen. Examples of genes located near these CpG sites were SOCS3 and AIM2, which are involved in inflammatory pathways. The associations for all 83 replicated CpG sites were attenuated after CRP adjustment, although many remained significant., Conclusion: We identified 83 CpG sites associated with circulating fibrinogen levels. These associations are partially driven by inflammatory pathways shared by both fibrinogen and CRP., (Copyright © 2023 International Society on Thrombosis and Haemostasis. All rights reserved.)

Background: Folate and vitamin B-12 are essential micronutrients involved in the donation of methyl groups in cellular metabolism. However, associations between intake of these nutrients and genome-wide DNA methylation levels have not been studied comprehensively in humans., Objective: The aim of this study was to assess whether folate and/or vitamin B-12 intake are asssociated with genome-wide changes in DNA methylation in leukocytes., Methods: A large-scale epigenome-wide association study of folate and vitamin B-12 intake was performed on DNA from 5841 participants from 10 cohorts using Illumina 450k arrays. Folate and vitamin B-12 intakes were calculated from food-frequency questionnaires (FFQs). Continuous and categorical (low compared with high intake) linear regression mixed models were applied per cohort, controlling for confounders. A meta-analysis was performed to identify significant differentially methylated positions (DMPs) and regions (DMRs), and a pathway analysis was performed on the DMR annotated genes., Results: The categorical model resulted in 6 DMPs, which are all negatively associated with folate intake, annotated to FAM64A, WRAP73, FRMD8, CUX1, and LCN8 genes, which have a role in cellular processes including centrosome localization, cell proliferation, and tumorigenesis. Regional analysis showed 74 folate-associated DMRs, of which 73 were negatively associated with folate intake. The most significant folate-associated DMR was a 400-base pair (bp) spanning region annotated to the LGALS3BP gene. In the categorical model, vitamin B-12 intake was associated with 29 DMRs annotated to 48 genes, of which the most significant was a 1100-bp spanning region annotated to the calcium-binding tyrosine phosphorylation-regulated gene (CABYR). Vitamin B-12 intake was not associated with DMPs., Conclusions: We identified novel epigenetic loci that are associated with folate and vitamin B-12 intake. Interestingly, we found a negative association between folate and DNA methylation. Replication of these methylation loci is necessary in future studies., (Copyright © American Society for Nutrition 2019.)

The distribution of mercury and methylmercury (MeHg) in sediment, mudflats, and marsh soils of the Hg-contaminated tidal Penobscot River was investigated, along with biogeochemical controls on production. Average total Hg in surface samples (0-3 cm) ranged from 100 to 1200 ng/g; average MeHg ranged from 5 to 50 ng/g. MeHg was usually highest at or near the surface except in highly mobile mudflats. Although total Hg concentrations in the Penobscot are elevated, it is the accumulation of MeHg that stands out in comparison to other ecosystems. Surface soils in the large Mendall Marsh, about 17 km downstream from the contamination source, contained particularly high %MeHg (averaging 8%). In Mendall marsh soil porewaters, MeHg often accounted for more than half of total Hg. Salt marshes are areas of particular concern in the Penobscot River, for they are depositional environments for a Hg-contaminated mobile pool of river sediment, hot spots for net MeHg production, and sources of risk to marsh animals. We hypothesized that exceptionally low mercury partitioning between the solid and aqueous phases (with log K d averaging ~4.5) drives high MeHg in Penobscot marshes. The co-occurrence of iron and sulfide in filtered soil porewaters, sometimes both above 100 μM, suggests the presence of nanoparticulate and/or colloidal metal sulfides. These colloids may be stabilized by high concentrations of aromatic and potentially sulfurized dissolved organic matter (DOM) in marsh soils. Thus, Hg in Penobscot marsh soils appears to be in a highly available for microbial methylation through the formation of DOM-associated HgS complexes. Additionally, low partitioning of MeHg to marsh soils suggests high MeHg bioavailability to animals. Overall, drivers of high MeHg in Penobscot marshes include elevated Hg in soils, low partitioning of Hg to solids, high Hg bioavailability for methylation, rapidly shifting redox conditions in surface marsh soils, and high rates of microbial activity., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Background: Glycosylation is one of the most common post-translation modifications with large influences on protein structure and function. The effector function of immunoglobulin G (IgG) alters between pro- and anti-inflammatory, based on its glycosylation. IgG glycan synthesis is highly complex and dynamic., Methods: With the use of two different analytical methods for assessing IgG glycosylation, we aim to elucidate the link between DNA methylation and glycosylation of IgG by means of epigenome-wide association studies. In total, 3000 individuals from 4 cohorts were analyzed., Results: The overlap of the results from the two glycan measurement panels yielded DNA methylation of 7 CpG-sites on 5 genomic locations to be associated with IgG glycosylation: cg25189904 (chr.1, GNG12); cg05951221, cg21566642 and cg01940273 (chr.2, ALPPL2); cg05575921 (chr.5, AHRR); cg06126421 (6p21.33); and cg03636183 (chr.19, F2RL3). Mediation analyses with respect to smoking revealed that the effect of smoking on IgG glycosylation may be at least partially mediated via DNA methylation levels at these 7 CpG-sites., Conclusion: Our results suggest the presence of an indirect link between DNA methylation and IgG glycosylation that may in part capture environmental exposures., General Significance: An epigenome-wide analysis conducted in four population-based cohorts revealed an association between DNA methylation and IgG glycosylation patterns. Presumably, DNA methylation mediates the effect of smoking on IgG glycosylation., (Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.)

Monozygotic (MZ) twins share the same STR profile, demonstrating a practical problem in forensic casework. DNA methylation has provided a suitable resource for MZ twin differentiation; however, studies addressing the forensic feasibility are lacking. Here, we investigated epigenetic MZ twin differentiation from blood under the forensic scenario comprising i) the discovery of candidate markers in reference-type blood DNA via genome-wide analysis, ii) the technical validation of candidate markers in reference-type blood DNA using a suitable targeted method, and iii) the analysis of the validated markers in trace-type DNA. Genome-wide methylation analysis in blood DNA from 10 MZ twin pairs resulted in 19-111 twin-differentially methylated sites (tDMSs) per pair with >0.3 twin-to-twin differences. Considering all top three candidate tDMSs across all pairs in the technical validation based on methylation-specific qPCR, 67.85% generated >0.1 twin-to-twin differences. Of the validated tDMSs, 68.4% showed >0.1 twin-to-twin differences with qPCR in trace-type DNA across 8 pairs. Using an updated marker selection strategy, 8 additional candidate tDMSs were obtained for an example MZ pair, of which 7 showed >0.1 twin-to-twin differences in both reference- and trace-type DNA. Lastly, we introduce a high-resolution melting curve analysis of the entire fragment that can complement the proposed approach. Overall, our study demonstrates the general feasibility of epigenetic twin differentiation in the forensic context and highlights that the number of informative tDMSs in the final trace DNA analysis is crucial, as some candidate markers identified in reference DNA were shown not informative in the trace DNA due to various, including technical, reasons. Future studies will need to address the optimal number of epigenetic markers required for reliable identification of MZ twin individuals including statistical considerations., (Copyright © 2017 Elsevier B.V. All rights reserved.)

High nevus count is the strongest risk factor for melanoma, and although gene variants have been discovered for both traits, epigenetic variation is unexplored. We investigated 322 healthy human skin DNA methylomes associated with total body nevi count, incorporating genetic and transcriptomic variation. DNA methylation changes were identified at genes involved in melanocyte biology, such as RAF1 (P = 1.2 × 10 -6 ) and CTC1 (region: P = 6.3 × 10 -4 ), and other genes including ARRDC1 (P = 3.1 × 10 -7 ). A subset exhibited coordinated methylation and transcription changes within the same biopsy. The total analysis was also enriched for melanoma-associated DNA methylation variation (P = 6.33 × 10 -6 ). In addition, we show that skin DNA methylation is associated in cis with known genome-wide association study single nucleotide polymorphisms for nevus count, at PLA2G6 (P = 1.7 × 10 -49 ) and NID1 (P = 6.4 × 10 -14 ), as well as melanoma risk, including in or near MC1R, MX2, and TERT/CLPTM1L (P < 1 × 10 -10 ). Our analysis using a uniquely large dataset comprising healthy skin DNA methylomes identified known and additional regulatory loci and pathways in nevi and melanoma biology. This integrative study improves our understanding of predisposition to nevi and their potential contribution to melanoma pathogenesis., (Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.)

Dosimeter data taken on the APEX (1994-1996), CRRES (1990-1991) and DMSP (1984-1987) satellites have been used to study the low altitude (down to 350 km) radiation environment. Of special concern has been the inner edge of the inner radiation belt due to its steep gradient. We have constructed dose models of the inner edge of the belt from all three spacecraft and put them into a personal computer utility, called APEXRAD, that calculates dose for user-selected orbits. The variation of dose for low altitude, circular orbits is given as a function of altitude, inclination and particle type. Dose-depth curves show that shielding greater than approximately 1/4 in Al is largely ineffectual for low altitude orbits. The contribution of outer zone electrons to low altitude dose is shown to be important only for thin shields and to have significant variation with magnetic activity and solar cycle.