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Non-additive genome-wide association scan reveals a new gene associated with habitual coffee consumption.

ABSTRACT: Coffee is one of the most consumed beverages world-wide and one of the primary sources of caffeine intake. Given its important health and economic impact, the underlying genetics of its consumption has been widely studied. Despite these efforts, much has still to be uncovered. In particular, the use of non-additive genetic models may uncover new information about the genetic variants driving coffee consumption. We have conducted a genome-wide association study in two Italian populations using additive, recessive and dominant models for analysis. This has uncovered a significant association in the PDSS2 gene under the recessive model that has been replicated in an independent cohort from the Netherlands (ERF). The identified gene has been shown to negatively regulate the expression of the caffeine metabolism genes and can thus be linked to coffee consumption. Further bioinformatics analysis of eQTL and histone marks from Roadmap data has evidenced a possible role of the identified SNPs in regulating PDSS2 gene expression through enhancers present in its intron. Our results highlight a novel gene which regulates coffee consumption by regulating the expression of the genes linked to caffeine metabolism. Further studies will be needed to clarify the biological mechanism which links PDSS2 and coffee consumption.

SUBMITTER: Pirastu N

PROVIDER: S-EPMC4997959 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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Non-additive genome-wide association scan reveals a new gene associated with habitual coffee consumption.

Pirastu Nicola N Kooyman Maarten M Robino Antonietta A van der Spek Ashley A Navarini Luciano L Amin Najaf N Karssen Lennart C LC Van Duijn Cornelia M CM Gasparini Paolo P

Scientific reports 20160825

Coffee is one of the most consumed beverages world-wide and one of the primary sources of caffeine intake. Given its important health and economic impact, the underlying genetics of its consumption has been widely studied. Despite these efforts, much has still to be uncovered. In particular, the use of non-additive genetic models may uncover new information about the genetic variants driving coffee consumption. We have conducted a genome-wide association study in two Italian populations using ad ...[more]

PMID: 27561104

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Project description:BACKGROUND:Coffee intake may be inversely associated with colorectal cancer; however, previous studies have been inconsistent. Serum coffee metabolites are integrated exposure measures that may clarify associations with cancer and elucidate underlying mechanisms. OBJECTIVES:Our aims were 2-fold as follows: 1) to identify serum metabolites associated with coffee intake and 2) to examine these metabolites in relation to colorectal cancer. DESIGN:In a nested case-control study of 251 colorectal cancer cases and 247 matched control subjects from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial, we conducted untargeted metabolomics analyses of baseline serum by using ultrahigh-performance liquid-phase chromatography-tandem mass spectrometry and gas chromatography-mass spectrometry. Usual coffee intake was self-reported in a food-frequency questionnaire. We used partial Pearson correlations and linear regression to identify serum metabolites associated with coffee intake and conditional logistic regression to evaluate associations between coffee metabolites and colorectal cancer. RESULTS:After Bonferroni correction for multiple comparisons (P = 0.05 ÷ 657 metabolites), 29 serum metabolites were positively correlated with coffee intake (partial correlation coefficients: 0.18-0.61; P < 7.61 × 10(-5)); serum metabolites most highly correlated with coffee intake (partial correlation coefficients >0.40) included trigonelline (N'-methylnicotinate), quinate, and 7 unknown metabolites. Of 29 serum metabolites, 8 metabolites were directly related to caffeine metabolism, and 3 of these metabolites, theophylline (OR for 90th compared with 10th percentiles: 0.44; 95% CI: 0.25, 0.79; P-linear trend = 0.006), caffeine (OR for 90th compared with 10th percentiles: 0.56; 95% CI: 0.35, 0.89; P-linear trend = 0.015), and paraxanthine (OR for 90th compared with 10th percentiles: 0.58; 95% CI: 0.36, 0.94; P-linear trend = 0.027), were inversely associated with colorectal cancer. CONCLUSIONS:Serum metabolites can distinguish coffee drinkers from nondrinkers; some caffeine-related metabolites were inversely associated with colorectal cancer and should be studied further to clarify the role of coffee in the cause of colorectal cancer. The Prostate, Lung, Colorectal, and Ovarian trial was registered at clinicaltrials.gov as NCT00002540.

Project description:Abstract Objectives Epidemiological studies suggested the evidence that coffee consumption decreased risk of type 2 diabetes. Recently, Japanese genome-wide association studies (GWAS) of coffee consumption has identified rs2074356 (G > A) at 12q24.12–13 in HECTD4. This study aims to examine the associations of habitual coffee consumption with prediabetes and type 2 diabetes, and whether this association is modified by rs2074356 variant in Korean adults. Methods A total of 4010 participants (1890 men and 2120 women) who had genetic information from Korea Association REsource (KARE) study were included. Habitual coffee consumption was assessed through a food frequency questionnaire and categorized into five categories (non-consumers, <1 cup/day and ≥1 cups/day of black coffee, and <1 cup/day and ≥1 cups/day of sugared coffee). Incident prediabetes or type 2 diabetes were defined according to the self-report of physician-diagnosis, oral glucose tolerance test (OGTT) or hemoglobin A1c (HbA1c) test. Multivariable logistic regression models were used to calculate odds ratio (OR)s and 95% confidence interval (CI)s. Results A total of 2916 participants (72.7%) have developed prediabetes during a follow-up of 15 years. We found that black coffee consumption lowered risk of prediabetes and type 2 diabetes combined among men and women combined (OR = 0.63; 95% CI = 0.44–0.91 for ≥1 cups/day black coffee vs. non-consumers). When we separated men and women, compared with non-consumers, ORs (95% CIs) for ≥1 cups/day of black coffee were 0.50 (0.27–0.93) among men and 0.72 (0.45–1.14) among women and ORs (95% CIs) for ≥1 cups/day of sugared coffee were 1.41 (0.91–2.18) among men and 1.12 (0.80–1.58) among women. We observed a suggestive difference by rs2074356 (GG vs. AG + AA). Compared with non-consumers, participants with AG + AA genotypes consumed ≥ 1 cups/day of black coffee had a 60% lower risk of prediabetes and type 2 diabetes combined (95% CI 0.20–0.78), but we found a weaker association among those with GG genotype (OR = 0.81; 95% CI = 0.51–1.28). Conclusions We observed an inverse association between black coffee consumption and prediabetes and type 2 diabetes combined in Korean population. This association was more pronounced among carriers of minor allele of HECTD4 rs2074356 (AG/AA). Funding Sources None.

Project description:Background Globally, coffee is one of the most consumed beverages and recently, it has been a target of researchers to understand its effect on human health whether good or bad. Even though there is controversy on coffee consumption effect in cardiovascular diseases, several reports pointed out that coffee has a positive effect on the occurrence and progression of chronic non-communicable diseases including cardiovascular diseases. However, the impact of Ethiopian coffee Arabica consumption on cardiovascular diseases has not been well investigated thoroughly. Objective The aim of the present study was to investigate the effect of habitual consumption of Ethiopian Arabica coffee on the risk of cardiovascular diseases among non-diabetic individuals in Addis Ababa. Materials and methods A cross-sectional study was conducted in 70 healthy individuals in Addis Ababa. The participants were 35 coffee drinkers (16 males; 19 females) and 35 non-drinkers (15 males; 20 females). Coffee consumption and demographic data were obtained by using questionnaires. Anthropometric measurements were measured according to World Health Organization standards. Blood samples were collected by trained laboratory technicians through aseptic and sterile techniques for the analysis of biochemical parameters. Serum was separated via centrifugation and transported to Addis Ababa University, College of Health Sciences, Biochemistry laboratory with an ice pack for analysis or stored at -80 °C. Results were compared between coffee consumers and non -consumers using appropriate statistical parameter. Result The main finding of this study was that consumption of Ethiopian origin Arabica coffee leads to a significant increase in serum free fatty acids (FFAs) and high density lipoprotein (HDL) as well as a significant decrease in triacylglycerides (TAGs) but has no significant effect in both total cholesterol (TC) and low density lipoprotein (LDL). The magnitude of the effect is similar in both sexes. Conclusion The present study demonstrated that Ethiopian coffee Arabica consumption significantly affected most serum lipid levels and so it may be possible to say it has a protective effect against risks of cardiovascular diseases (CVDs). However, the correlations between coffee consumption habits and serum lipid levels require further investigation through experimental and epidemiological studies with larger sample size, including different age groups and nutritional habits. Food Science; Food Analysis; Cardiology; Coffee; Lipid; Cardiovascular diseases; Fatty acids; Lipoprotein

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Non-additive genome-wide association scan reveals a new gene associated with habitual coffee consumption.

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Non-additive genome-wide association scan reveals a new gene associated with habitual coffee consumption.

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