scholarly journals Integration of whole blood genome-wide DNA methylation and gene expression identifies epigenetically controlled modules in relation to NO2 air pollution exposure

2019 ◽  
Vol 3 ◽  
pp. 269
Author(s):  
Merid S ◽  
Bustamante M ◽  
Standl M ◽  
Sunyer J ◽  
Heinrich J ◽  
...  
2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Mi Kyeong Lee ◽  
◽  
Cheng-Jian Xu ◽  
Megan U. Carnes ◽  
Cody E. Nichols ◽  
...  

2018 ◽  
Vol 126 (2) ◽  
pp. 027004 ◽  
Author(s):  
Ana Julia de F.C. Lichtenfels ◽  
Diana A. van der Plaat ◽  
Kim de Jong ◽  
Cleo C. van Diemen ◽  
Dirkje S. Postma ◽  
...  

Epigenetics ◽  
2021 ◽  
pp. 1-17
Author(s):  
Gloria C. Chi ◽  
Yongmei Liu ◽  
James W. MacDonald ◽  
Lindsay M. Reynolds ◽  
Daniel A. Enquobahrie ◽  
...  

2018 ◽  
Vol 2017 (1) ◽  
pp. 172
Author(s):  
Olena Gruzieva ◽  
Carrie V. Breton ◽  
Herman T. den Dekker ◽  
Akram Ghantous ◽  
Allan C. Just ◽  
...  

2017 ◽  
Vol 195 (10) ◽  
pp. 1373-1383 ◽  
Author(s):  
Anna Gref ◽  
Simon K. Merid ◽  
Olena Gruzieva ◽  
Stéphane Ballereau ◽  
Allan Becker ◽  
...  

2016 ◽  
Vol 75 (11) ◽  
pp. 2029-2036 ◽  
Author(s):  
Juliana Imgenberg-Kreuz ◽  
Johanna K Sandling ◽  
Jonas Carlsson Almlöf ◽  
Jessica Nordlund ◽  
Linnea Signér ◽  
...  

ObjectivesIncreasing evidence suggests an epigenetic contribution to the pathogenesis of autoimmune diseases, including primary Sjögren's Syndrome (pSS). The aim of this study was to investigate the role of DNA methylation in pSS by analysing multiple tissues from patients and controls.MethodsGenome-wide DNA methylation profiles were generated using HumanMethylation450K BeadChips for whole blood, CD19+ B cells and minor salivary gland biopsies. Gene expression was analysed in CD19+ B cells by RNA-sequencing. Analysis of genetic regulatory effects on DNA methylation at known pSS risk loci was performed.ResultsWe identified prominent hypomethylation of interferon (IFN)-regulated genes in whole blood and CD19+ B cells, including at the genes MX1, IFI44L and PARP9, replicating previous reports in pSS, as well as identifying a large number of novel associations. Enrichment for genomic overlap with histone marks for enhancer and promoter regions was observed. We showed for the first time that hypomethylation of IFN-regulated genes in pSS B cells was associated with their increased expression. In minor salivary gland biopsies we observed hypomethylation of the IFN-induced gene OAS2. Pathway and disease analysis resulted in enrichment of antigen presentation, IFN signalling and lymphoproliferative disorders. Evidence for genetic control of methylation levels at known pSS risk loci was observed.ConclusionsOur study highlights the role of epigenetic regulation of IFN-induced genes in pSS where replication is needed for novel findings. The association with altered gene expression suggests a functional mechanism for differentially methylated CpG sites in pSS aetiology.


Circulation ◽  
2014 ◽  
Vol 129 (suppl_1) ◽  
Author(s):  
Sharine Wittkopp ◽  
Norbert Staimer ◽  
Thomas Tjoa ◽  
Daniel L Gillen ◽  
Nancy Daher ◽  
...  

Background: Epidemiological and toxicological studies support an adverse effect of air pollution exposure on cardiovascular outcomes, and proposed mechanisms include increased thrombosis and coagulation. Previously, we showed increased plasma levels of soluble platelet selectin (sP-selectin) and increased expression of the platelet selectin gene ( SELP ) in association with higher air pollution exposure; both indicating probable increased platelet activation. A functional polymorphism in SELP , Thr715Pro, decreases circulating levels of sP-selectin and is associated with decreased risk for venous thromboembolism and myocardial infarction. We hypothesized that carriers of the Pro allele would have weaker associations of gene expression and protein level with air pollution exposure versus non-carriers. Methods: We used a cohort-panel design, with repeated measures of exposures and outcomes among 60 elderly, non-smoking subjects with coronary artery disease, living in the Los Angeles air basin. This population is shown to have higher susceptibility to pollutant exposure. We measured plasma sP-selectin levels weekly for all 60 subjects using an ELISA assay. Genotypes were determined using restriction fragment length polymorphism analysis. Whole blood gene expression levels were measured using quantitative polymerase chain reactions, for a subset of 40 subjects. Pollutant exposures measured at subject residences included the following: NO 2 /NO x , O 3 , CO, PM 2.5 organic, elemental and black carbon; particulate matter size fractions (PM 0.25 , PM 0.25-2.5 , PM 2.5-10 ); and organic components and oxidative potential of PM. Primary and secondary organic carbon were estimated from total organic carbon. T-tests and linear mixed effects models were used to analyze the data. Results: We determined that the 12 subjects who were carriers of the protective, Pro715, allele had lower sP-selectin levels versus Thr715 homozygotes (34.78 ng/mL vs 42.03 ng/mL, p<0.001 by t-test). Pro715 allele carriers also had 0.396-fold lower SELP expression versus Thr715 homozygotes (p<0.005). However, in pollutant models, there was no significant interaction between carrier status and pollutant level (p-value= 0.1 or greater). Conclusions: While it appears that both SELP gene and protein expression increases in association with air pollution exposure and these levels are lower in Pro715 carriers, we found no effect modification of these relationships by genotype. Recent data suggests that lower plasma sP-selectin in 715Pro carriers results from decreased N-glycosylation and subsequent sequestration in the Golgi apparatus. To our knowledge, there is no data indicating that N-glycosylation changes as a result of air pollution exposure. We conclude that differences in the soluble protein levels due to the presence of this polymorphism are not altered as a result of changes in air pollution exposure.


2021 ◽  
Vol 2021 (1) ◽  
Author(s):  
Jiawen Liao ◽  
Duncan C. Thomas ◽  
Fred Lurmann ◽  
Roya Gheissari ◽  
Frank D. Gilliland ◽  
...  

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