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Pathogen-associated molecular patterns (PAMPs) have the capacity to couple inflammatory gene expression to changes in macrophage metabolism, both of which influence subsequent inflammatory activities. Similar to their microbial counterparts, several self-encoded damage-associated molecular patterns (DAMPs) induce inflammatory gene expression. However, whether this symmetry in host responses between PAMPs and DAMPs extends to metabolic shifts is unclear. Here, we report that the self-encoded oxidized phospholipid oxPAPC alters the metabolism of macrophages exposed to lipopolysaccharide. While cells activated by lipopolysaccharide rely exclusively on glycolysis, macrophages exposed to oxPAPC also use mitochondrial respiration, feed the Krebs cycle with glutamine, and favor the accumulation of oxaloacetate in the cytoplasm. This metabolite potentiates interleukin-1β production, resulting in hyperinflammation. Similar metabolic adaptions occur in vivo in hypercholesterolemic mice and human subjects. Drugs that interfere with oxPAPC-driven metabolic changes reduce atherosclerotic plaque formation in mice, thereby underscoring the importance of DAMP-mediated activities in pathophysiological conditions. Oxidized host-derived phospholipids such as oxPAPC can play important roles in atherosclerosis. Zanoni and colleagues demonstrate that oxPAPC generates a distinctive metabolic and hyperinflammatory profile in macrophages that can drive atherosclerosis in mice.

Identifying genetic variants associated with circulating protein concentrations (protein quantitative trait loci; pQTLs) and integrating them with variants from genome-wide association studies (GWAS) may illuminate the proteome’s causal role in disease and bridge a knowledge gap regarding SNP-disease associations. We provide the results of GWAS of 71 high-value cardiovascular disease proteins in 6861 Framingham Heart Study participants and independent external replication. We report the mapping of over 16,000 pQTL variants and their functional relevance. We provide an integrated plasma protein-QTL database. Thirteen proteins harbor pQTL variants that match coronary disease-risk variants from GWAS or test causal for coronary disease by Mendelian randomization. Eight of these proteins predict new-onset cardiovascular disease events in Framingham participants. We demonstrate that identifying pQTLs, integrating them with GWAS results, employing Mendelian randomization, and prospectively testing protein-trait associations holds potential for elucidating causal genes, proteins, and pathways for cardiovascular disease and may identify targets for its prevention and treatment. Genetic variation can influence levels of disease-related plasma proteins and, thus, contribute to the pathogenesis of complex diseases. Here, the authors perform genome-wide QTL analysis for 71 plasma proteins to identify causal proteins for coronary heart disease and provide a molecular QTL browser.

Identifying methylation quantitative trait loci (meQTLs) and integrating them with disease-associated variants from genome-wide association studies (GWAS) may illuminate functional mechanisms underlying genetic variant-disease associations. Here, we perform GWAS of >415 thousand CpG methylation sites in whole blood from 4170 individuals and map 4.7 million cis- and 630 thousand trans- meQTL variants targeting >120 thousand CpGs. Independent replication is performed in 1347 participants from two studies. By linking cis- meQTL variants with GWAS results for cardiovascular disease (CVD) traits, we identify 92 putatively causal CpGs for CVD traits by Mendelian randomization analysis. Further integrating gene expression data reveals evidence of cis CpG-transcript pairs causally linked to CVD. In addition, we identify 22 trans- meQTL hotspots each targeting more than 30 CpGs and find that trans- meQTL hotspots appear to act in cis on expression of nearby transcriptional regulatory genes. Our findings provide a powerful meQTL resource and shed light on DNA methylation involvement in human diseases. Differentially methylated CpGs can inform on disease mechanisms and be useful as biomarkers. Here, the authors perform GWAS for DNA methylation in whole blood, cis - and trans -meQTL mapping, followed by Mendelian randomization analysis that links meQTLs with cardiovascular diseases.

Atrial fibrillation (AF) is the most common cardiac arrhythmia, but little is known about the molecular mechanisms associated with AF arrhythmogenesis. DNA methylation is an important epigenetic mechanism that regulates gene expression and downstream biological processes. We hypothesize that DNA methylation might play an important role in the susceptibility to develop AF. A total of 2,639 participants from the Offspring Cohort of Framingham Heart Study were enrolled in the current study. These participants included 183 participants with prevalent AF and 220 with incident AF during up to 9 years follow up. Genome-wide methylation was profiled using the Illumina Infinium HumanMethylation450 BeadChip on blood-derived DNA collected during the eighth examination cycle (2005–2008). Two CpG sites were significantly associated with prevalent AF, and five CpGs were associated with incident AF after correction for multiple testing (FDR < 0.05). Fourteen previously reported genome-wide significant AF-related SNP were each associated with at least one CpG site; the most significant association was rs6490029 at the CUX2 locus and cg10833066 ( P  = 9.5 × 10 −279 ). In summary, we performed genome-wide methylation profiling in a community-based cohort and identified seven methylation signatures associated with AF. Our study suggests that DNA methylation might play an important role in AF arrhythmogenesis.

Transmembrane tumor necrosis factor (TNF) receptors are involved in inflammatory, apoptotic, and proliferative processes. In the bloodstream, soluble TNF receptor II (sTNFR2) can modify the inflammatory response of immune cells and is predictive of cardiovascular disease risk. We hypothesize that sTNFR2 is associated with epigenetic modifications of circulating leukocytes, which may relate to the pathophysiology underlying atherogenic risk. We conducted an epigenome-wide association study of sTNFR2 levels in the Framingham Heart Study Offspring cohort (examination 8; 2005-2008). sTNFR2 was quantitated by enzyme immunoassay and DNA methylation by microarray. The concentration of sTNFR2 was log -transformed and outliers were excluded. We conducted linear mixed effects models to test the association between sTNFR2 level and methylation at over 400,000 CpGs, adjusting for age, sex, BMI, smoking, imputed cell count, technical covariates, and accounting for familial relatedness. The study sample included 2468 participants (mean age: 67 ± 9 years, 52% women, mean sTNFR2 level 2661 ± 1078 pg/ml). After accounting for multiple testing, we identified 168 CpGs ( < 1.2 × 10 ) that were differentially methylated in relation to sTNFR2. A substantial proportion (27 CpGs; 16%) are in the major histocompatibility complex region and in loci overrepresented for antigen binding molecular functions ( = 1.7 × 10 ) and antigen processing and presentation biological processes ( = 1.3 × 10 ). Identified CpGs are enriched in active regulatory regions and associated with expression of 48 -genes (±500 kb) in whole blood ( < 1.1 × 10 ) that coincide with genes identified in GWAS of diseases of immune dysregulation (inflammatory bowel disease, type 1 diabetes, IgA nephropathy). Differentially methylated loci in leukocytes associated with sTNF2 levels reside in active regulatory regions, are overrepresented in antigen processes, and are linked to inflammatory diseases.

Background Payer-type (government-sponsored health coverage versus private health insurance) has been shown to influence a variety of cardiovascular disease outcomes in adults. However, it is unclear if the payer-type impacts the response to a lifestyle intervention in children with dyslipidemia. Methods We analyzed data prospectively collected from patients under the age of 25 years who were referred to a large regional preventive cardiology clinic from 2010 to 2016 in Massachusetts. We compared baseline high density lipoprotein cholesterol (HDL-C), triglycerides (TG), non-HDL-C, and low density lipoprotein cholesterol (LDL-C) by payer-type. Further, we analyzed the change in lipid values in response to a clinic-based multidisciplinary intervention over a nearly six-year period by payer-type with multi-variable adjusted linear regression models. We also tested for effect modifications by age, sex, race, and body mass index (BMI) category. Results Of the 1739 eligible patients (mean age 13 years, 52% female, 60% overweight and obese, 59% White), we found that patients with government-sponsored coverage ( n  = 354, 20%) presented to referral lipid clinic with lower HDL-C (− 3.5 mg/dL [1.0], p  < 0.001) and higher natural log-transformed TG (+ 0.14 [0.04], p  < 0.001) as compared to those with private insurance; however, the association was attenuated to the null after additionally adjusting for BMI category (− 1.1 [0.9], p  = 0.13, and + 0.05 [0.04], p  = 0.2 for HDL-C and natural log-transformed TG, respectively). We found no difference in baseline LDL-C between payer-types (+ 3.4 mg/dL [3.0], p  = 0.3). However, longitudinally, we found patients with private insurance and a self-reported race of White to have a clinically meaningful additional improvement in LDL-C, decreasing 12.8 (5.5) mg/dL ( p  = 0.02) between baseline and first follow-up, as compared to White patients with government-sponsored health coverage, after adjusting for age, sex, time between visits, and baseline LDL-C. Conclusions Our results suggest that youth with government-sponsored coverage are referred with poorer lipid profiles than those with private insurance, although this is largely explained by higher rates of overweight and obesity in the government-sponsored health coverage group. White patients with private insurance had substantially better improvement in LDL-C longitudinally, suggesting that higher socioeconomic status facilitates improvement in LDL-C, but is less beneficial for HDL-C and triglyceride levels.

In the originally published version of this Article, financial support was not fully acknowledged. The sentence “KS was supported by the ‘Biomedical Research Program’ funds at Weill Cornell Medicine in Qatar, a program funded by the Qatar Foundation” has been added to the acknowledgement section in both the PDF and HTML versions of the Article.

Threats to imperiled freshwater fauna in the U.S. were assessed through an experts survey addressing anthropogenic stressors and their sources. Specifically, causes of historic declines and current limits to recovery were identified for 135 imperiled freshwater species of fishes, crayfishes, dragonflies and damselflies, mussels, and amphibians. The survey was designed to identify threats with sufficient specificity to inform resource managers and regulators faced with translating information about predominant biological threats into specific, responsive actions. The findings point to altered sediment loads and nutrient inputs from agricultural nonpoint pollution; interference from exotic species; and altered hydrologic regimes associated with impoundment operations as the three leading threats nationwide, accompanied by many lesser but still significant threats. Variations in threats among regions and among taxa were also evident. Eastern species are most commonly affected by altered sediment loads from agricultural activities, whereas exotic species, habitat removal/damage, and altered hydrologic regimes predominate in the West. Altered sediment loading from agricultural activities and exotic species are dominant problems for both eastern mussels and fishes. However, eastern fishes also appear to be suffering from municipal nonpoint pollution (nutrients and sediments), whereas eastern mussels appear to be more severely affected by altered nutrient impacts from hydroelectric impoundments and agricultural runoff. Our findings suggest that control of nonpoint source pollution associated with agriculture activities should be a very high priority for agricultural producers and governmental support programs. Additionally, the large number of hydropower dams in the U.S. subject to federal re-licensing in coming years suggests a significant opportunity to restore natural hydrologic regimes in the affected rivers.

The link between DNA methylation, obesity, and adiposity-related diseases in the general population remains uncertain. We conducted an association study of body mass index (BMI) and differential methylation for over 400,000 CpGs assayed by microarray in whole-blood-derived DNA from 3,743 participants in the Framingham Heart Study and the Lothian Birth Cohorts, with independent replication in three external cohorts of 4,055 participants. We examined variations in whole blood gene expression and conducted Mendelian randomization analyses to investigate the functional and clinical relevance of the findings. We identified novel and previously reported BMI-related differential methylation at 83 CpGs that replicated across cohorts; BMI-related differential methylation was associated with concurrent changes in the expression of genes in lipid metabolism pathways. Genetic instrumental variable analysis of alterations in methylation at one of the 83 replicated CpGs, cg11024682 (intronic to sterol regulatory element binding transcription factor 1 [SREBF1]), demonstrated links to BMI, adiposity-related traits, and coronary artery disease. Independent genetic instruments for expression of SREBF1 supported the findings linking methylation to adiposity and cardiometabolic disease. Methylation at a substantial proportion (16 of 83) of the identified loci was found to be secondary to differences in BMI. However, the cross-sectional nature of the data limits definitive causal determination. We present robust associations of BMI with differential DNA methylation at numerous loci in blood cells. BMI-related DNA methylation and gene expression provide mechanistic insights into the relationship between DNA methylation, obesity, and adiposity-related diseases.