MesaEpiGenomics

Methylomics of Gene Expression in Human Monocytes

Liu Y, Ding J, Reynolds LM, Lohman K, Register TC, De La Fuente A, Howard TD, Hawkins GA, Cui W, Morris J, Smith SG, Barr RG, Kaufman JD, Burke GL, Post W, Shea S, McCall CE, Siscovick D, Jacobs DR Jr, Tracy RP, Herrington DM, Hoeschele I.

Hum Mol Genet. 2013 Dec 15;22(24):5065-74. doi: 10.1093/hmg/ddt356. Epub 2013 Jul 29.

ABSTRACT:

DNA methylation is one of several epigenetic mechanisms that contribute to the regulation of gene expression; however, the extent to which methylation of CpG dinucleotides correlates with gene expression at the genome-wide level is still largely unknown. Using purified primary monocytes from subjects in a large community-based cohort (N=1,264), we characterized methylation (>485,000 CpG sites) and mRNA expression (>48K transcripts) and carried out genome-wide association analyses of 8,370 expression phenotypes. We identified 11,203 potential cis-acting CpG loci whose degree of methylation was associated with gene expression (eMS) at a False Discovery Rate (FDR) threshold of 0.001. Most of the associations were consistent in effect size and direction of effect across sex and three ethnicities. Contrary to expectation, these eMS were not predominately enriched in promoter regions, or CpG islands, but rather in the 3'UTR, gene bodies, CpG shores or "offshore" sites, and both positive and negative correlations between methylation and expression were observed across all locations. eMS were enriched for regions predicted to be regulatory by ENCODE data in multiple cell types, particularly enhancers. One of the strongest association signals detected (p<2.2x10^-308) was a methylation probe (cg17005068) in the promoter/enhancer region of the Glutathione S-transferase theta 1 gene (GSTT1, encoding the detoxification enzyme) with GSTT1 mRNA expression. Our study provides a detailed description of the epigenetic architecture in human monocytes and its relationship to gene expression. These data may help prioritize interrogation of biologically relevant methylation loci and provide new insights into the epigenetic basis of human health and diseases.

Reynolds LM¹, Taylor JR², Ding J³, Lohman K⁴, Johnson C⁵, Siscovick D⁶, Burke G⁷, Post W⁸, Shea S⁹, Jacobs DR Jr¹⁰, Stunnenberg H¹¹, Kritchevsky SB³, Hoeschele I¹², McCall CE¹³, Herrington DM¹⁴, Tracy RP¹⁵, Liu Y¹⁶.

Nat Commun. 2014 Nov 18;5:5366. doi: 10.1038/ncomms6366.

ABSTRACT:

Age-related variations in DNA methylation have been reported; however, the functional relevance of these differentially methylated sites (age-dMS) are unclear. Here we report potentially functional age-dMS, defined as age- and cis-gene expression-associated methylation sites (age-eMS), identified by integrating genome-wide CpG methylation and gene expression profiles collected ex vivo from circulating T cells (227 CD4+ samples) and monocytes (1,264 CD14+ samples, age range: 55-94 years). None of the age-eMS detected in 227 T-cell samples are detectable in 1,264 monocyte samples, in contrast to the majority of age-dMS detected in T cells that replicated in monocytes. Age-eMS tend to be hypomethylated with older age, located in predicted enhancers and preferentially linked to expression of antigen processing and presentation genes. These results identify and characterize potentially functional age-related methylation in human T cells and monocytes, and provide novel insights into the role age-dMS may have in the aging process.

Reynolds LM¹, Ding J², Taylor JR³, Lohman K⁴, Soranzo N⁵, de la Fuente A⁶, Liu TF⁷, Johnson C⁸, Barr RG⁹, Register TC¹⁰, Donohue KM¹¹, Talor MV¹², Cihakova D¹³, Gu C¹⁴, Divers J¹⁵, Siscovick D¹⁶, Burke G¹⁷, Post W¹⁸, Shea S¹⁹, Jacobs DR Jr²⁰, Hoeschele I²¹, McCall CE^22,23, Kritchevsky SB^24,25, Herrington D²⁶, Tracy RP²⁷, Liu Y²⁸.

BMC Genomics. 2015 Apr 22;16:333. doi: 10.1186/s12864-015-1522-4.

ABSTRACT:

BACKGROUND: Transcriptomic studies hold great potential towards understanding the human aging process. Previous transcriptomic studies have identified many genes with age-associated expression levels; however, small samples sizes and mixed cell types often make these results difficult to interpret.RESULTS: Using transcriptomic profiles in CD14+ monocytes from 1,264 participants of the Multi-Ethnic Study of Atherosclerosis (aged 55-94 years), we identified 2,704 genes differentially expressed with chronological age (false discovery rate, FDR ≤ 0.001). We further identified six networks of co-expressed genes that included prominent genes from three pathways: protein synthesis (particularly mitochondrial ribosomal genes), oxidative phosphorylation, and autophagy, with expression patterns suggesting these pathways decline with age. Expression of several chromatin remodeler and transcriptional modifier genes strongly correlated with expression of oxidative phosphorylation and ribosomal protein synthesis genes. 17% of genes with age-associated expression harbored CpG sites whose degree of methylation significantly mediated the relationship between age and gene expression (p < 0.05). Lastly, 15 genes with age-associated expression were also associated (FDR ≤ 0.01) with pulse pressure independent of chronological age. Comparing transcriptomic profiles of CD14+ monocytes to CD4+ T cells from a subset (n = 423) of the population, we identified 30 age-associated (FDR < 0.01) genes in common, while larger sets of differentially expressed genes were unique to either T cells (188 genes) or monocytes (383 genes). At the pathway level, a decline in ribosomal protein synthesis machinery gene expression with age was detectable in both cell types.CONCLUSIONS: An overall decline in expression of ribosomal protein synthesis genes with age was detected in CD14+ monocytes and CD4+ T cells, demonstrating that some patterns of aging are likely shared between different cell types. Our findings also support cell-specific effects of age on gene expression, illustrating the importance of using purified cell samples for future transcriptomic studies. Longitudinal work is required to establish the relationship between identified age-associated genes/pathways and aging-related diseases.

Ding J¹, Reynolds LM², Zeller T³, Müller C³, Lohman K², Nicklas BJ¹, Kritchevsky SB¹, Huang Z⁴, de la Fuente A⁵, Soranzo N⁶, Settlage RE⁷, Chuang CC⁸, Howard T¹, Xu N⁹, Goodarzi MO⁹, Chen YD¹⁰, Rotter JI¹⁰, Siscovick DS¹¹, Parks JS⁸, Murphy S⁴, Jacobs DR Jr¹², Post W¹³, Tracy RP¹⁴, Wild PS¹⁵, Blankenberg S³, Hoeschele I⁷, Herrington D¹, McCall CE¹, Liu Y¹⁶.

Diabetes. 2015 Oct;64(10):3464-74. doi: 10.2337/db14-1314. Epub 2015 Jul 7.

ABSTRACT:

Obesity is linked to type 2 diabetes (T2D) and cardiovascular diseases; however, the underlying molecular mechanisms remain unclear. We aimed to identify obesity-associated molecular features that may contribute to obesity-related diseases. Using circulating monocytes from 1,264 Multi-Ethnic Study of Atherosclerosis (MESA) participants, we quantified the transcriptome and epigenome. We discovered that alterations in a network of coexpressed cholesterol metabolism genes are a signature feature of obesity and inflammatory stress. This network included 11 BMI-associated genes related to sterol uptake (↑LDLR, ↓MYLIP), synthesis (↑SCD, FADS1, HMGCS1, FDFT1, SQLE, CYP51A1, SC4MOL), and efflux (↓ABCA1, ABCG1), producing a molecular profile expected to increase intracellular cholesterol. Importantly, these alterations were associated with T2D and coronary artery calcium (CAC), independent from cardiometabolic factors, including serum lipid profiles. This network mediated the associations between obesity and T2D/CAC. Several genes in the network harbored C-phosphorus-G dinucleotides (e.g., ABCG1/cg06500161), which overlapped Encyclopedia of DNA Elements (ENCODE)-annotated regulatory regions and had methylation profiles that mediated the associations between BMI/inflammation and expression of their cognate genes. Taken together with several lines of previous experimental evidence, these data suggest that alterations of the cholesterol metabolism gene network represent a molecular link between obesity/inflammation and T2D/CAC.

Reynolds LM, Wan M, Ding J, Taylor JR, Lohman K, Su D, Bennett BD, Porter DK, Gimple R, Pittman GS, Wang X, Howard TD, Siscovick D, Psaty BM, Shea S, Burke GL, Jacobs DR Jr, Rich SS, Hixson JE, Stein JH, Stunnenberg H, Barr RG, Kaufman JD, Post WS, Hoeschele I, Herrington DM, Bell DA, Liu Y.

Circ Cardiovasc Genet. 2015 Oct;8(5):707-16. doi: 10.1161/CIRCGENETICS.115.001097. Epub 2015 Aug 25.

ABSTRACT:

BACKGROUND: Tobacco smoke contains numerous agonists of the aryl hydrocarbon receptor (AhR) pathway, and activation of the AhR pathway was shown to promote atherosclerosis in mice. Intriguingly, cigarette smoking is most strongly and robustly associated with DNA modifications to an AhR pathway gene, the AhR repressor (AHRR). We hypothesized that altered AHRR methylation in monocytes, a cell type sensitive to cigarette smoking and involved in atherogenesis, may be a part of the biological link between cigarette smoking and atherosclerosis.METHODS AND RESULTS: DNA methylation profiles of AHRR in monocytes (542 CpG sites±150 kb of AHRR, using Illumina 450K array) were integrated with smoking habits and ultrasound-measured carotid plaque scores from 1256 participants of the Multi-Ethnic Study of Atherosclerosis (MESA). Methylation of cg05575921 significantly associated (P=6.1×10(-134)) with smoking status (current versus never). Novel associations between cg05575921 methylation and carotid plaque scores (P=3.1×10(-10)) were identified, which remained significant in current and former smokers even after adjusting for self-reported smoking habits, urinary cotinine, and well-known cardiovascular disease risk factors. This association replicated in an independent cohort using hepatic DNA (n=141). Functionally, cg05575921 was located in a predicted gene expression regulatory element (enhancer) and had methylation correlated with AHRR mRNA profiles (P=1.4×10(-17)) obtained from RNA sequencing conducted on a subset (n=373) of the samples.CONCLUSIONS: These findings suggest that AHRR methylation may be functionally related to AHRR expression in monocytes and represents a potential biomark