Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption

Habitual caffeine intake, genetics and cognitive performance

BACKGROUND

Research on caffeine and cognitive performance remains controversial. Variations in genes associated with caffeine metabolism and response such as CYP1A2, AHR and ADORA2A may account for variable findings.

AIM

To investigate caffeine × gene interactions on cognitive performance in all key domains of cognition in healthy individuals.

METHODS

Participants completed a lifestyle and food frequency questionnaire and a cognitive test battery including validated tasks to assess the domains of social cognition, memory, attention and executive function. Genotyping was performed for AHR rs6968554, CYP1A2 rs2472297, ADORA2A rs5751876, ADA rs73598374 and APOE rs429358 and rs7412.

RESULTS

Significant gene × caffeine interactions were observed for the domains of social cognition, (F2, 123 = 5.848, p = 0.004) and executive function (F2, 109 = 3.690, p = 0.028). 'Slow' metabolisers had a higher performance in social cognition compared with 'fast' metabolisers among high-caffeine consumers (p = 0.004), while 'fast' metabolisers had a higher performance in executive function compared with 'slow' metabolisers among moderate caffeine consumers (p = 0.002).

CONCLUSIONS

The present findings suggest an association between genetic caffeine metabolism, habitual caffeine intake and cognitive function in the domains of social cognition and executive function. More research in naturalistic environments using larger cohorts is needed to confirm these findings to add to our understanding of how habitual caffeine may influence cognitive function based on individual genotype.

Caffeine Consumption and Interaction with ADORA2A, CYP1A2 and NOS1 Variants Do Not Influence Age at Onset of Machado-Joseph Disease

BACKGROUND

The age at onset (AO) of Machado-Joseph disease (SCA3/MJD), a disorder due to an expanded CAG repeat (CAGexp) in ATXN3, is quite variable and the role of environmental factors is still unknown. Caffeine was associated with protective effects against other neurodegenerative diseases, and against SCA3/MJD in transgenic mouse models. We aimed to evaluate whether caffeine consumption and its interaction with variants of caffeine signaling/metabolization genes impact the AO of this disease.

METHODS

a questionnaire on caffeine consumption was applied to adult patients and unrelated controls living in Rio Grande do Sul, Brazil. AO and CAGexp were previously determined. SNPs rs5751876 (ADORA2A), rs2298383 (ADORA2A), rs762551 (CYP1A2) and rs478597 (NOS1) were genotyped. AO of subgroups were compared, adjusting the CAGexp to 75 repeats (p < 0.05).

RESULTS

171/179 cases and 98/100 controls consumed caffeine. Cases with high and low caffeine consumption (more or less than 314.5 mg of caffeine/day) had mean (SD) AO of 35.05 (11.44) and 35.43 (10.08) years (p = 0.40). The mean (SD) AO of the subgroups produced by the presence or absence of caffeine-enhancing alleles in ADORA2A (T allele at rs5751876 and rs2298383), CYP1A2 (C allele) and NOS1 (C allele) were all similar (p between 0.069 and 0.516).

DISCUSSION

Caffeine consumption was not related to changes in the AO of SCA3/MJD, either alone or in interaction with protective genotypes at ADORA2A, CYP1A2 and NOS1.

Impact of coffee intake on human aging: Epidemiology and cellular mechanisms

The conception of coffee consumption has undergone a profound modification, evolving from a noxious habit into a safe lifestyle actually preserving human health. The last 20 years also provided strikingly consistent epidemiological evidence showing that the regular consumption of moderate doses of coffee attenuates all-cause mortality, an effect observed in over 50 studies in different geographic regions and different ethnicities. Coffee intake attenuates the major causes of mortality, dampening cardiovascular-, cerebrovascular-, cancer- and respiratory diseases-associated mortality, as well as some of the major causes of functional deterioration in the elderly such as loss of memory, depression and frailty. The amplitude of the benefit seems discrete (17 % reduction) but nonetheless corresponds to an average increase in healthspan of 1.8 years of lifetime. This review explores evidence from studies in humans and human tissues supporting an ability of coffee and of its main components (caffeine and chlorogenic acids) to preserve the main biological mechanisms responsible for the aging process, namely genomic instability, macromolecular damage, metabolic and proteostatic impairments with particularly robust effects on the control of stress adaptation and inflammation and unclear effects on stem cells and regeneration. Further studies are required to detail these mechanistic benefits in aged individuals, which may offer new insights into understanding of the biology of aging and the development of new senostatic strategies. Additionally, the safety of this lifestyle factor in the elderly prompts a renewed attention to recommending the maintenance of coffee consumption throughout life as a healthy lifestyle and to further exploring who gets the greater benefit with what schedules of which particular types and doses of coffee.

Maternal coffee consumption and biomarkers of reproductive health in young, adult sons: a cohort study

It has been proposed that poor semen quality may have its origins from fetal programming due to environmental factors. We investigated whether maternal coffee consumption during early pregnancy was associated with biomarkers of reproductive health in adult sons in the Fetal Programming of Semen Quality (FEPOS) cohort. In 2017-2019, 1058 young men provided a semen and blood sample and self-measured their testis volume. Daily maternal coffee consumption was reported by the mothers around gestational week 17. We estimated relative percentage differences with 95 % confidence intervals (CI) for semen quality measures, testis volume, and reproductive hormone levels according to maternal coffee consumption during pregnancy. Maternal coffee consumption (yes/no (reference)) was associated with lower semen volume (-7.0 % (95 % CI:-12.9;-0.7)), lower proportion of morphologically normal spermatozoa (-8.3 % (95 % CI:-16.5;0.8)), higher proportion of non-progressive and immotile spermatozoa (4.3 % (95 % CI:-1.5;10.3)), and lower testis volume (-4.8 % (95 % CI:-9.0;-0.4)). No indication of a dose-response association or threshold effects was observed in the categorized and continuous analyses. No associations with reproductive hormone levels were observed in any of the analyses. Overall, the study does not provide obvious indications that maternal coffee consumption in early pregnancy deteriorates male offspring fecundity. While some minor changes were observed, most estimates were small with confidence intervals overlapping the null. Future studies, preferably with greater exposure contrast, are warranted before a conclusion can be drawn as to whether maternal coffee consumption during pregnancy constitutes a risk for reproductive health in adult sons.

Association of coffee consumption and caffeine metabolism with arrhythmias and cardiac morphology: An observational, genetic, and Mendelian randomization study

BACKGROUND

The association of coffee intake and caffeine metabolism with arrhythmias and cardiac structure is not fully understood.

OBJECTIVE

We aim to explore the associations of coffee intake and caffeine metabolism with the risk of certain types of arrhythmias, a broad range of cardiovascular imaging phenotypes, and a potential gene-coffee interaction.

METHODS

On the basis of the UK Biobank imaging study, heart metrics were extracted via cardiovascular magnetic resonance using machine learning. Caffeine metabolism was determined by cytochrome P4501A2 gene (CYP1A2) or a polygenetic score of different genetic variants influencing caffeine metabolism. Genome-wide association data for 2-sample Mendelian randomization originated predominantly from individuals of European descent.

RESULTS

A total of 34,992 individuals (mean age 63.5 ± 7.5 years; 52.9% female) were assessed in the principal imaging analysis. Higher daily consumption of coffee was independently associated with higher left ventricular mass, larger global ventricular volume, higher ventricular stroke volume, and larger atrial volume. The results were further supported by Mendelian randomization analysis. CYP1A2 and genetic score for caffeine metabolism were not associated with cardiovascular measurements (P>.053 for all tests). Coffee consumption was associated with a lower risk of sinus rhythm with short PR (per cup increase: odds ratio 0.90; 95% confidence interval 0.82-0.99) and atrial fibrillation (odds ratio 0.89; 95% confidence interval 0.84-0.93).

CONCLUSION

Coffee consumption was associated with a lower risk of atrial fibrillation, increased left ventricular mass, elevated ventricular volume, and larger atrial volume. Caffeine metabolism did not significantly alter the association. Our results suggest that customary caffeine consumption limitations aimed at arrhythmia risk reduction might be unnecessary.

Navigating Nutritional Inequality in Schizophrenia: A Comprehensive Exploration of Diet, Genetics, and Holistic Management Across the Life Cycle

This review explores the understudied topic of nutritional inequality among individuals with schizophrenia, highlighting the complex interplay between diet, genetics, and mental health. Unhealthy dietary patterns, socioeconomic factors, and disordered eating behaviors contribute to malnutrition, increasing the risk of physical health issues and premature mortality. Socioeconomic factors exacerbate nutritional disparities, necessitating targeted interventions. Genetic influences on nutrient metabolism remain under-researched, although nutritional genomics shows potential for personalized interventions. Current research reveals methodological gaps, urging larger sample sizes and standardized approaches. The integration of nutrigenomics, encompassing various omics disciplines, emerges as a transformative tool. The holistic life-cycle approach to schizophrenia management underscores the vital role of nutrition, calling for personalized interventions to enhance mental health outcomes.

Genetic susceptibility to caffeine intake and metabolism: a systematic review

BACKGROUND

Coffee and tea consumption account for most caffeine intake and 2-3 billion cups are taken daily around the world. Caffeine dependence is a widespread but under recognized problem.

OBJECTIVES

To conduct a systematic review on the genetic susceptibility factors affecting caffeine metabolism and caffeine reward and their association with caffeine intake.

METHODOLOGY

We conducted PubMed and Embase searches using the terms "caffeine", "reward", "gene", "polymorphism", "addiction", "dependence" and "habit" from inception till 2024. The demographics, genetic and clinical data from included studies were extracted and analyzed. Only case-control studies on habitual caffeine drinkers with at least 100 in each arm were included.

RESULTS

A total of 2552 studies were screened and 26 studies involving 1,851,428 individuals were included. Several genes that were involved with caffeine metabolism such as CYP1A2, ADORA2A, AHR, POR, ABCG2, CYP2A6, PDSS2 and HECTD4 rs2074356 (A allele specific to East Asians and monomorphic in Europeans, Africans and Americans) were associated with habitual caffeine consumption with effect size difference of 3% to 32% in number of cups of caffeinated drink per day per effect allele. In addition, ALDH2 was linked to the Japanese population. Genes associated with caffeine reward included BDNF, SLC6A4, GCKR, MLXIPL and dopaminergic genes such as DRD2 and DAT1 which had around 2-5% effect size difference in number of cups of caffeinated drink for each allele per day.

CONCLUSION

Several genes that were involved in caffeine metabolism and reward were associated with up to 30% effect size difference in number of cups of caffeinated drink per day, and some associations were specific to certain ethnicities. Identification of at-risk caffeine dependence individuals can lead to early diagnosis and stratification of at-risk vulnerable individuals such as pregnant women and children, and can potentially lead to development of drug targets for dependence to caffeine.

Phenome-Wide Analysis of Coffee Intake on Health over 20 Years of Follow-Up Among Adults in Hong Kong Osteoporosis Study

BACKGROUND/OBJECTIVES

There has been limited evidence on the long-term impacts of coffee intake on health. We aimed to investigate the association between coffee intake and the incidence of diseases and mortality risk over 20 years among community-dwelling Chinese adults.

METHODS

Participants were from the Hong Kong Osteoporosis Study who attended baseline assessments during 1995-2010. Coffee intake was self-reported through a food frequency questionnaire and was previously validated. Disease diagnoses, which were mapped into 1795 distinct phecodes, and mortality data were obtained from linkage with territory-wide electronic health records. Cox models were used to estimate the association between coffee intake and the incidence of each disease outcome and mortality among individuals without a history of the respective medical condition at baseline. All models were adjusted for age, sex, body mass index, smoking, alcohol drinking, and education.

RESULTS

Among the 7420 included participants (mean age 53.2 years, 72.2% women), 54.0% were non-coffee drinkers, and only 2.7% consumed more than one cup of coffee per day. Over a median follow-up of 20.0 years, any coffee intake was associated with a reduced risk of dementia, atrial fibrillation, painful respirations, infections, atopic dermatitis, and dizziness at a false discovery rate (FDR) of <0.05. Furthermore, any coffee intake was associated with an 18% reduced risk of all-cause mortality (95% confidence interval = 0.73-0.93).

CONCLUSION

In a population with relatively low coffee consumption, any coffee intake is linked to a lower risk of several neurological, circulatory, and respiratory diseases and symptoms, as well as mortality.

Mendelian randomization analysis of maternal coffee consumption during pregnancy on offspring neurodevelopmental difficulties in the Norwegian Mother, Father and Child Cohort Study (MoBa)

BACKGROUND

Previous observational epidemiological studies have suggested that coffee consumption during pregnancy may affect fetal neurodevelopment. However, results are inconsistent and may represent correlational rather than causal relationships. The present study investigated whether maternal coffee consumption was observationally associated and causally related to offspring childhood neurodevelopmental difficulties (NDs) in the Norwegian Mother, Father and Child Cohort Study.

METHODS

The observational relationships between maternal/paternal coffee consumption (before and during pregnancy) and offspring NDs were assessed using linear regression analyses (N = 58694 mother-child duos; N = 22 576 father-child duos). To investigate potential causal relationships, individual-level (N = 46 245 mother-child duos) and two-sample Mendelian randomization (MR) analyses were conducted using genetic variants previously associated with coffee consumption as instrumental variables.

RESULTS

We observed positive associations between maternal coffee consumption and offspring difficulties with social-communication/behavioral flexibility, and inattention/hyperactive-impulsive behavior (multiple testing corrected p < 0.005). Paternal coffee consumption (negative control) was not observationally associated with the outcomes. After adjusting for potential confounders (smoking, alcohol, education and income), the maternal associations attenuated to the null. MR analyses suggested that increased maternal coffee consumption was causally associated with social-communication difficulties (individual-level: beta = 0.128, se = 0.043, p = 0.003; two-sample: beta = 0.348, se = 0.141, p = 0.010). However, individual-level MR analyses that modelled potential pleiotropic pathways found the effect diminished (beta = 0.088, se = 0.049, p = 0.071). Individual-level MR analyses yielded similar estimates (heterogeneity p = 0.619) for the causal effect of coffee consumption on social communication difficulties in maternal coffee consumers (beta = 0.153, se = 0.071, p = 0.032) and non-consumers (beta = 0.107, se = 0.134, p = 0.424).

CONCLUSIONS

Together, our results provide little evidence for a causal effect of maternal coffee consumption on offspring NDs.

Potential genetic association between coffee/caffeine consumption and erectile dysfunction: a Mendelian randomization study and meta-analysis

Background

Coffee is a widely consumed beverage with potential benefits for various chronic diseases. Its effect on reducing erectile dysfunction (ED) risk is unclear. This Mendelian randomization (MR) study investigates the impact of coffee/caffeine consumption on ED.

Methods

Two sets of coffee consumption-associated genetic variants at the genome-wide significance level were obtained from recent studies of coffee consumption. Taking into account other sources of caffeine, genetic variants associated with caffeine consumption from tea were also obtained. The inverse variance weighted (IVW) method was utilized as the primary analysis. Sensitivity analysis methods and meta-analysis methods were performed to confirm the robustness of the results, while the genetic variants associated with confounders, e.g., diabetes and hypertension, were excluded.

Results

Genetically predicted coffee/caffeine consumption was unlikely to be associated with the risk of ED in the Bovijn datasets, with similar directional associations observed in the FinnGen datasets. The combined odds ratio for ED was 1.011 (95% CI 0.841-1.216, p=0.906) for coffee consumption from the genome-wide meta-analysis, 1.049 (95% CI 0.487-2.260, p=0.903) for coffee consumption from the genome-wide association study, and 1.061 (95% CI 0.682-1.651, p=0.793) for caffeine from tea.

Conclusion

Using genetic data, this study found no association between coffee/caffeine consumption and the risk of ED.

Association between coffee consumption and metabolic syndrome: A cross-sectional and Mendelian randomization study

BACKGROUND

This study investigates the associations between coffee consumption and metabolic syndrome and its components, as well as the effect of milk, sugar, and artificial sweeteners on these associations.

METHODS

A cross-sectional analysis was conducted with 351805 UK Biobank participants. Coffee consumption data were collected via food frequency questionnaires and 24-h recall. Metabolic syndrome was identified through blood biochemistry and self-reported medication use. Odds ratios were calculated using multivariable logistic regression, and results were verified with two-sample Mendelian randomization.

RESULTS

Consuming up to two cups of coffee per day was inversely associated with metabolic syndrome (1 cup/day: odds ratio [OR]: 0.88, 95% confidence interval [CI]: 0.85-0.92; 2 cups/day: OR: 0.90, 95% CI: 0.86-0.93). Higher intakes showed near-null associations. Mendelian randomization did not support a causal link between coffee intake and metabolic syndrome. Both self-reported and genetically predicted high coffee consumption (four cups per day or more) were associated with central obesity. The inverse association between coffee consumption and metabolic syndrome was more profound among drinkers of ground coffee than those of instant coffee. Results were similar when stratified by the use of milk and sugar, yet the use of artificial sweetener with coffee was positively associated with metabolic syndrome and all component conditions.

CONCLUSIONS

Coffee consumption may increase the risk of central obesity but is unlikely to impact the risk of metabolic syndrome. The potential health effects of artificial sweeteners in coffee need further investigation.

Identification of Sweetness Preference-Related Single-Nucleotide Polymorphisms for Polygenic Risk Scores Associated with Obesity

Our study aimed to identify sweetness preference-associated single-nucleotide polymorphisms (SNPs), characterize the related genetic loci, and develop SNP-based polygenic risk scores (PRS) to analyze their associations with obesity. For genotyping, we utilized a pooled genome-wide association study (GWAS) dataset of 18,499 females and 10,878 males. We conducted genome-wide association analyses, functional annotation, and employed the weighted method to calculate the levels of PRS from 677 sweetness preference-related SNPs. We used Cox proportional hazards modeling with time-varying covariates to estimate age-adjusted and multivariable hazard ratios (HRs) and 95% confidence intervals (CIs) for obesity incidence. We also tested the correlation between PRS and environmental factors, including smoking and dietary components, on obesity. Our results showed that in males, the TT genotype of rs4861982 significantly increased obesity risk compared to the GG genotype in the Health Professionals Follow-up Study (HPFS) cohort (HR = 1.565; 95% CI, 1.122-2.184; p = 0.008) and in the pooled analysis (HR = 1.259; 95% CI, 1.030-1.540; p = 0.025). Protein tyrosine phosphatase receptor type O (PTPRO) was identified as strongly associated with sweetness preference, indicating a positive correlation between sweetness preference and obesity risk. Moreover, each 10 pack-year increment in smoking was significantly associated with an increased risk of obesity in the HPFS cohort (HR = 1.024; 95% CI, 1.000-1.048) in males but not in females. In conclusion, significant associations between rs4861982, sweetness preference, and obesity were identified, particularly among males, where environmental factors like smoking are also correlated with obesity risk.

Genome-wide association studies of coffee intake in UK/US participants of European ancestry uncover cohort-specific genetic associations

Coffee is one of the most widely consumed beverages. We performed a genome-wide association study (GWAS) of coffee intake in US-based 23andMe participants (N = 130,153) and identified 7 significant loci, with many replicating in three multi-ancestral cohorts. We examined genetic correlations and performed a phenome-wide association study across hundreds of biomarkers, health, and lifestyle traits, then compared our results to the largest available GWAS of coffee intake from the UK Biobank (UKB; N = 334,659). We observed consistent positive genetic correlations with substance use and obesity in both cohorts. Other genetic correlations were discrepant, including positive genetic correlations between coffee intake and psychiatric illnesses, pain, and gastrointestinal traits in 23andMe that were absent or negative in the UKB, and genetic correlations with cognition that were negative in 23andMe but positive in the UKB. Phenome-wide association study using polygenic scores of coffee intake derived from 23andMe or UKB summary statistics also revealed consistent associations with increased odds of obesity- and red blood cell-related traits, but all other associations were cohort-specific. Our study shows that the genetics of coffee intake associate with substance use and obesity across cohorts, but also that GWAS performed in different populations could capture cultural differences in the relationship between behavior and genetics.

Caffeine consumption outcomes on amyotrophic lateral sclerosis disease progression and cognition

Caffeine consumption outcomes on Amyotrophic Lateral Sclerosis (ALS) including progression, survival and cognition remain poorly defined and may depend on its metabolization influenced by genetic variants. 378 ALS patients with a precise evaluation of their regular caffeine consumption were monitored as part of a prospective multicenter study. Demographic, clinical characteristics, functional disability as measured with revised ALS Functional Rating Scale (ALSFRS-R), cognitive deficits measured using Edinburgh Cognitive and Behavioural ALS Screen (ECAS), survival and riluzole treatment were recorded. 282 patients were genotyped for six single nucleotide polymorphisms tagging different genes involved in caffeine intake and/or metabolism: CYP1A1 (rs2472297), CYP1A2 (rs762551), AHR (rs4410790), POR (rs17685), XDH (rs206860) and ADORA2A (rs5751876) genes. Association between caffeine consumption and ALSFRS-R, ALSFRS-R rate, ECAS and survival were statistically analyzed to determine the outcome of regular caffeine consumption on ALS disease progression and cognition. No association was observed between caffeine consumption and survival (p = 0.25), functional disability (ALSFRS-R; p = 0.27) or progression of ALS (p = 0.076). However, a significant association was found with higher caffeine consumption and better cognitive performance on ECAS scores in patients carrying the C/T and T/T genotypes at rs2472297 (p-het = 0.004). Our results support the safety of regular caffeine consumption on ALS disease progression and survival and also show its beneficial impact on cognitive performance in patients carrying the minor allele T of rs2472297, considered as fast metabolizers, that would set the ground for a new pharmacogenetic therapeutic strategy.

Causal role of immune cells in uveitis: Mendelian randomization study

Background

Uveitis, characterized by inflammation of the iris, ciliary body, and choroid, presents a significant global clinical challenge, contributing substantially to visual impairment. Risk factors include autoimmune diseases and immune cell dysfunctions, yet many remain unidentified. Immune cells, notably T cells, B cells, and monocytes, play pivotal roles in uveitis pathogenesis. While biologic agents show promise, comprehensive studies on immune cell types in ocular diseases are lacking. Genome-wide association studies (GWAS) and Mendelian randomization (MR) present promising avenues to elucidate genetic susceptibilities and causal relationships between immune cell traits and uveitis risk.

Methods

Two-sample MR analysis was used to evaluate the causal relationship between 731 immune cells and uveitis, and genome-wide significance analysis was performed for genetic variation in 731 immune cells traits (P < 5 × 10-8). Immune characteristics include median fluorescence intensity (MFI), relative cell counts (RC), absolute cell counts (AC), and morphological parameters (MP), which were determined by published GWAS, and public data from the IEU Open GWAS database. The main analysis method of MR is inverse variance weighting (IVW). Heterogeneity and horizontal pleiotropy were also assessed.

Results

5 immunophenotypes, including CD62L-DC %DC, IgD+ CD38dim %B cell, CD3 on CM CD4+T cell, CD3 on CD45RA-CD4 +T cell, and CD3 on CD39+ CD4+ Treg may increase the risk of uveitis. 5 immunophenotypes, including CD11b on CD33dim HLA DR-Myeloid cell, HLA DR on CD33dim HLA DR+ CD11b-myeloid cell, CD14-CD16 + %monocyte, HLA DR on CD14-CD16 + monocyte and PDL-1 on CD14-CD16 + monocyte was negatively associated with the risk of uveitis. Among them, HLA DR on CD14-CD16 + monocyte (OR=0.921, 95%CI =0.875-0.970, P=0.001) and HLA DR on CD33dim HLA DR+ CD11b- (OR=0.879, 95%CI = 0.833-0.927, P=0.00) were negatively associated with the risk of uveitis in bi-direction.

Conclusion

These results indicate that 10 immune cells traits are significantly associated with the risk of developing uveitis and 2 of them were strongly associated with uveitis bi-directionally, after excluding the effects of confounding factors such as some immune diseases, which provided new ideas and therapeutic targets for the study of immune mechanism of uveitis.

The relationship between height and fruit/vegetable intakes in adults: A nationwide cross-sectional study

Background: Worldwide, fruit and vegetable intake is below recommendations. There is increasing evidence to suggest an association between height and diet. Aim: to analyse the associations of fruit and vegetable intake with attained height in Portuguese adults. Methods: A representative sample of 17 480 Portuguese adults (56.7% women) participated in this cross-sectional study. The survey comprised sociodemographic characteristics and self-reported height and weight. We performed regression models to assess the associations between height and fruit and vegetable consumption. Results: Compared with no intakes, those men with higher fruit and vegetables intake had 0.54 cm (95% CI 0.04; 1.04) greater height. Also, women with higher intakes of vegetables, fruit and vegetables combined were directly associated with a greater height of 0.29 cm (95% CI 0.03; 0.56 in vegetables) and 0.51 cm (95% CI 0.09; 0.93 in fruit and vegetables combined). Conclusion: Greater consumption of fruit and vegetables was directly associated with higher height in adults. From a health promotion perspective, intervention programmes aiming at improving fruit and vegetable intake should be highlighted so that full height potential is achieved.

Causal association of genetically determined caffeine intake from tea or coffee with bone health: a two-sample Mendelian randomization study

BACKGROUND

Relationship of caffeine intake and consumption of caffeinated beverages, such as tea and coffee, with bone health remains controversial. This study aimed to evaluate whether genetically determined caffeine intake from tea or coffee has causal effects on overall total body bone mineral density (TB-BMD) and fracture. We also assessed the association with TB-BMD in five age strata.

METHODS

Using two-sample Mendelian randomization approach, summary statistics were retrieved from genome-wide association studies (GWAS)/GWAS meta-analyses of caffeine intake from tea (n = 395 866)/coffee (n = 373 522), TB-BMD (n = 66 628), and fracture (n = 426 795). Inverse variance weighted method was adopted as the main univariable analysis. Multivariable analysis was conducted to evaluate whether the causal effect is independent.

RESULTS

In univariable analysis, genetically determined caffeine intake from tea had positive association with overall TB-BMD (per SD increase in genetically determined caffeine intake, beta of TB-BMD [in SD]: 0.166; 95% confidence interval (CI): 0.006-0.326) and inverse association with fracture (OR = 0.79; 95% CI: 0.654-0.954). Genetically determined caffeine intake from coffee was also positively associated with overall TB-BMD (beta = 0.231; 95% CI: 0.093-0.369). The association remained significant after adjustment for smoking in multivariable analysis. Genetically determined caffeine intake from tea or coffee was both positively associated with TB-BMD in the age strata of 45-60 years, but we lacked evidence of association in other strata.

CONCLUSIONS

Genetically, caffeine intake from tea or coffee may be beneficial to bone health. Due to the ascertainment method of caffeine intake from tea, our study also implied genetically higher tea consumption may improve TB-BMD and lower fracture risk.

Mendelian randomization analysis reveals causal relationship between obstetric-related diseases and COVID-19

BACKGROUND

Several observational studies demonstrated that pregnant individuals with COVID-19 had a higher risk of preeclampsia and preterm birth. We aimed to determine whether women with COVID-19 diagnosis had adverse pregnancy outcomes.

METHODS

A two-sample Mendelian randomization (MR) analysis in this study was used to evaluate the casual relationships between COVID-19 infection and obstetric-related diseases based on genome-wide association studies (GWAS) dataset. Inverse-variance weighted (IVW), MR-Egger and MR-PRESSO were used to infer the connection and estimate the pleiotropy respectively.

RESULTS

The significant connection was observed between COVID-19 and placental disorders with betaIVW of 1.57 and odds ratio (OR) of 4.81 (95% confidence interval [CI]: 1.05-22.05, p = 0.04). However, there were no associations between COVID-19 infection and gestational diabetes mellitus (GDM) (OR = 1.12; 95% CI: 0.85-1.45, p = 0.41), other disorders of amniotic fluid and membranes (OR = 0.90; 95% CI: 0.61-1.32, p = 0.59), Intrahepatic Cholestasis of Pregnancy (ICP) (OR = 1.42; 95% CI: 0.85-2.36, p = 0.18), birth weight (OR = 1.02; 95% CI: 0.99-1.05, p = 0.19), gestational hypertension (OR = 1.00; 95% CI: 1.00-1.00, p = 0.85), spontaneous miscarriages (OR = 1.00; 95% CI: 0.96-1.04, p = 0.90) and stillbirth (OR = 1.00; 95% CI: 0.98-1.01, p = 0.62).

CONCLUSION

There was no direct causal relationship between COVID-19 infection and maternal and neonatal poor outcomes. Our study could alleviate the anxiety of pregnant women under the COVID-19 pandemic conditions partly.

Coffee consumption affects kidney function based on GCKR polymorphism in a Korean population

Kidney function can be preserved through pharmacological interventions and nonpharmacological strategies, such as lifestyle and dietary adjustments. Among these, coffee has been linked to protective effects on kidney function. However, few studies have investigated the effect of coffee consumption on kidney function according to specific genes. We hypothesized that the impact of coffee consumption on kidney function might vary depending on GCKR polymorphism. GCKR rs1260326 polymorphism was examined using the Korean genome and epidemiology data from 656 chronic kidney disease (CKD) cases and 38,540 individuals without CKD (non-CKD). GCKR polymorphism has been previously associated with both coffee consumption and kidney function in Europeans. We replicated the associations between GCKR rs1260326 and coffee consumption and kidney function in Korean individuals. We also explored the effect of coffee consumption on kidney function by multivariate logistic regression analysis. Individuals with the rs1260326 (TC/CC) genotype did not experience significant changes in CKD risk based on their coffee consumption habits. In contrast, individuals with the TT genotype exhibited a significantly lower risk of CKD based on coffee consumption. Interestingly, in the non-CKD group, a beneficial effect on estimated glomerular filtration rate was observed in individuals with the T allele as coffee consumption increased. Our findings supported the hypothesis and revealed that the impact of coffee consumption habits on kidney function may vary based on the GCKR rs1260326 genotype of Korean individuals.

ChREBP is activated by reductive stress and mediates GCKR-associated metabolic traits

Common genetic variants in glucokinase regulator (GCKR), which encodes GKRP, a regulator of hepatic glucokinase (GCK), influence multiple metabolic traits in genome-wide association studies (GWASs), making GCKR one of the most pleiotropic GWAS loci in the genome. It is unclear why. Prior work has demonstrated that GCKR influences the hepatic cytosolic NADH/NAD+ ratio, also referred to as reductive stress. Here, we demonstrate that reductive stress is sufficient to activate the transcription factor ChREBP and necessary for its activation by the GKRP-GCK interaction, glucose, and ethanol. We show that hepatic reductive stress induces GCKR GWAS traits such as increased hepatic fat, circulating FGF21, and circulating acylglycerol species, which are also influenced by ChREBP. We define the transcriptional signature of hepatic reductive stress and show its upregulation in fatty liver disease and downregulation after bariatric surgery in humans. These findings highlight how a GCKR-reductive stress-ChREBP axis influences multiple human metabolic traits.

Mendelian randomization for cardiovascular diseases: principles and applications

Large-scale genome-wide association studies conducted over the last decade have uncovered numerous genetic variants associated with cardiometabolic traits and risk factors. These discoveries have enabled the Mendelian randomization (MR) design, which uses genetic variation as a natural experiment to improve causal inferences from observational data. By analogy with the random assignment of treatment in randomized controlled trials, the random segregation of genetic alleles when DNA is transmitted from parents to offspring at gamete formation is expected to reduce confounding in genetic associations. Mendelian randomization analyses make a set of assumptions that must hold for valid results. Provided that the assumptions are well justified for the genetic variants that are employed as instrumental variables, MR studies can inform on whether a putative risk factor likely has a causal effect on the disease or not. Mendelian randomization has been increasingly applied over recent years to predict the efficacy and safety of existing and novel drugs targeting cardiovascular risk factors and to explore the repurposing potential of available drugs. This review article describes the principles of the MR design and some applications in cardiovascular epidemiology.

Genetic association between coffee/caffeine consumption and the risk of obstructive sleep apnea in the European population: a two-sample Mendelian randomization study

BACKGROUND

The association between coffee/caffeine consumption and obstructive sleep apnea (OSA) risk remains unclear.

PURPOSE

To determine the relationship between coffee/caffeine consumption and the risk of OSA, using the Mendelian randomization (MR) method in the European population.

METHODS

Two sets of coffee consumption-associated genetic variants were, respectively, extracted from the recent genome-wide meta-analysis (GWMA) and genome-wide association study (GWAS) of coffee consumption. Taking other caffeine sources into account, genetic variants associated with caffeine consumption from tea and plasma caffeine (reflecting total caffeine intake) were also obtained. The inverse variance weighted (IVW) technique was utilized as the primary analysis, supplemented by the MR-Egger, weighted-median, and MR-Pleiotropy RESidual Sum and Outlier (PRESSO) techniques. Leave-one-out (LOO) analysis was performed to assess whether the overall casual estimates were driven by a single SNP. Additional sensitivity analyses were performed using similar methods, while the genetic variants associated with confounders, e.g., body mass index and hypertension, were excluded.

RESULTS

The IVW method demonstrated that coffee consumption GWMA (OR: 1.065, 95% CI 0.927-1.224, p = 0.376), coffee consumption GWAS (OR: 1.665, 95% CI 0.932-2.977, p = 0.086), caffeine from tea (OR: 1.198, 95% CI 0.936-1.534, p = 0.151), and blood caffeine levels (OR: 1.054, 95% CI 0.902-1.231, p = 0.508) were unlikely to be associated with the risk of OSA. The other three methods presented similar results, where no significant associations were found. No single genetic variant was driving the overall estimates by the LOO analysis. These findings were also supported by the sensitivity analyses with no confounding genetic variants.

CONCLUSION

Our study found no association between coffee/caffeine consumption and the risk of OSA.

Current therapeutic targets and multifaceted physiological impacts of caffeine

Caffeine, which shares consubstantial structural similarity with purine adenosine, has been demonstrated as a nonselective adenosine receptor antagonist for eliciting most of the biological functions at physiologically relevant dosages. Accumulating evidence supports caffeine's beneficial effects against different disorders, such as total cardiovascular diseases and type 2 diabetes. Conversely, paradoxical effects are also linked to caffeine ingestion in humans including hypertension-hypotension and tachycardia-bradycardia. These observations suggest the association of caffeine action with its ingested concentration and/or concurrent interaction with preferential molecular targets to direct explicit events in the human body. Thus, a coherent analysis of the functional targets of caffeine, relevant to normal physiology, and disease pathophysiology, is required to understand the pharmacology of caffeine. This review provides a broad overview of the experimentally validated targets of caffeine, particularly those of therapeutic interest, and the impacts of caffeine on organ-specific physiology and pathophysiology. Overall, the available empirical and epidemiological evidence supports the dose-dependent functional activities of caffeine and advocates for further studies to get insights into the caffeine-induced changes under specific conditions, such as asthma, DNA repair, and cancer, in view of its therapeutic applications.

Genetics of caffeine and brain-related outcomes - a systematic review of observational studies and randomized trials

CONTEXT

Although the stimulant and anxiogenic properties of caffeine are widely accepted, research on its specific effects on the brain remains controversial. Growing evidence shows that interindividual differences in caffeine response may be partly due to variations in genes such as CYP1A2 and ADORA2A, which have been used to identify individuals as "fast" or "slow" caffeine metabolizers and as having a "high" or "low" caffeine sensitivity, respectively.

OBJECTIVE

The objective of this review was to identify, evaluate, and discuss current evidence on the associations between common genetic variants, caffeine consumption, and brain-related outcomes in humans.

DATA SOURCES

PubMed and Embase databases were searched for relevant reports based on a predetermined search strategy.

DATA EXTRACTION

Reports of observational and experimental studies on healthy adults who underwent (a) genetic analysis for polymorphisms in genes associated with caffeine metabolism and effects and (b) measurements of brain-related effects such as anxiety, insomnia, and cognitive performance associated with the consumption of caffeine (habitual intake or supplementation) were included.

DATA ANALYSIS

Of the 22 records included, 15 were randomized controlled trials, 6 were cross-sectional studies, and 1 was a genome-wide association study. The main outcomes identified were cognitive performance (n = 9), anxiety (n = 7), and sleep disturbance/insomnia (n = 6). Polymorphisms in the CYP1A2 gene were associated with cognitive function, while variations in the ADORA2A gene were associated with anxiety and sleep disturbance.

CONCLUSION

The present review has provided evidence that variability in the CYP1A2 and the ADORA2A genes may modulate the association between caffeine and brain-related outcomes. Future studies are warranted to investigate the specific polymorphisms implicated in each brain outcome, which cognitive functions are particularly related to caffeine (simple vs complex), whether there are gender differences in anxiety effects, and how habitual caffeine intake may influence the acute effects of caffeine.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO registration no. CRD42021257556.

Maternal caffeine consumption during pregnancy and offspring cord blood DNA methylation: an epigenome-wide association study meta-analysis

Background: Prenatal caffeine exposure may influence offspring health via DNA methylation, but no large studies have tested this. Materials & methods: Epigenome-wide association studies and differentially methylated regions in cord blood (450k or EPIC Illumina arrays) were meta-analyzed across six European cohorts (n = 3725). Differential methylation related to self-reported caffeine intake (mg/day) from coffee, tea and cola was compared with assess whether caffeine is driving effects. Results: One CpG site (cg19370043, PRRX1) was associated with caffeine and another (cg14591243, STAG1) with cola intake. A total of 12-22 differentially methylated regions were detected with limited overlap across caffeinated beverages. Conclusion: We found little evidence to support an intrauterine effect of caffeine on offspring DNA methylation. Statistical power limitations may have impacted our findings.

Genetics of vegetarianism: A genome-wide association study

A substantial body of evidence points to the heritability of dietary preferences. While vegetarianism has been practiced for millennia in various societies, its practitioners remain a small minority of people worldwide, and the role of genetics in choosing a vegetarian diet is not well understood. Dietary choices involve an interplay between the physiologic effects of dietary items, their metabolism, and taste perception, all of which are strongly influenced by genetics. In this study, we used a genome-wide association study (GWAS) to identify loci associated with strict vegetarianism in UK Biobank participants. Comparing 5,324 strict vegetarians to 329,455 controls, we identified one SNP on chromosome 18 that is associated with vegetarianism at the genome-wide significant level (rs72884519, β = -0.11, P = 4.997 x 10-8), and an additional 201 suggestively significant variants. Four genes are associated with rs72884519: TMEM241, RIOK3, NPC1, and RMC1. Using the Functional Mapping and Annotation (FUMA) platform and the Multi-marker Analysis of GenoMic Annotation (MAGMA) tool, we identified 34 genes with a possible role in vegetarianism, 3 of which are GWAS-significant based on gene-level analysis: RIOK3, RMC1, and NPC1. Several of the genes associated with vegetarianism, including TMEM241, NPC1, and RMC1, have important functions in lipid metabolism and brain function, raising the possibility that differences in lipid metabolism and their effects on the brain may underlie the ability to subsist on a vegetarian diet. These results support a role for genetics in choosing a vegetarian diet and open the door to future studies aimed at further elucidating the physiologic pathways involved in vegetarianism.

AHR rs4410790 genotype and IgG levels: Effect modification by lifestyle factors

Inflammation is a multifaceted marker resulting from complex interactions between genetic and lifestyle factors. Emerging evidence suggests Aryl hydrocarbon receptor (AHR) protein may be implicated in the regulation of immune system and inflammatory responses. To investigate whether rs4410790 genotype (TT, TC, CC) near AHR gene is related to serum IgG levels, a marker of chronic inflammation, and whether lifestyle factors modifies the relationship, we conducted a cross-sectional study by recruiting 168 Korean adults. Participants responded to a lifestyle questionnaire and provided oral epithelial cells and blood samples for biomarker assessment. Among these participants, C allele was the minor allele, with the minor allele frequency of 40%. The rs4410790 TT genotype was significantly associated with elevated IgG levels compared with TC/CC genotypes, after adjusting for potential confounders (p = 0.04). The relationship varied significantly by levels of alcohol consumption (P interaction = 0.046) and overweight/obese status (P interaction = 0.02), but not by smoking status (P interaction = 0.64) and coffee consumption (P interaction = 0.55). Specifically, higher IgG levels associated with the TT genotype were evident in frequent drinkers and individuals with BMI≥23kg/m2, but not in their counterparts. Thus, rs4410790 genotype may be associated with IgG levels and the genetic predisposition to higher IgG levels may be mitigated by healthy lifestyle factors like infrequent drinking and healthy weight.

Genome-Wide Association Studies of Coffee Intake in UK/US Participants of European Ancestry Uncover Gene-Cohort Influences

Coffee is one of the most widely consumed beverages. We performed a genome-wide association study (GWAS) of coffee intake in US-based 23andMe participants (N=130,153) and identified 7 significant loci, with many replicating in three multi-ancestral cohorts. We examined genetic correlations and performed a phenome-wide association study across thousands of biomarkers and health and lifestyle traits, then compared our results to the largest available GWAS of coffee intake from UK Biobank (UKB; N=334,659). The results of these two GWAS were highly discrepant. We observed positive genetic correlations between coffee intake and psychiatric illnesses, pain, and gastrointestinal traits in 23andMe that were absent or negative in UKB. Genetic correlations with cognition were negative in 23andMe but positive in UKB. The only consistent observations were positive genetic correlations with substance use and obesity. Our study shows that GWAS in different cohorts could capture cultural differences in the relationship between behavior and genetics.

Potential role of plasma branched-chain amino acids in the differential diagnosis of acute cerebral venous thrombosis

Cerebral venous thrombosis (CVT) is a special and easily misdiagnosed or undiagnosed subtype of stroke. To identify specific biomarkers with a high predictive ability for the diagnosis of acute CVT, we performed metabolomic analysis in plasma samples from acute CVT patients and healthy controls and confirmed the results in validation cohorts. In the discovery stage, there were 343 differential metabolites, and the caffeine metabolism pathway and the biosynthesis pathway for the branched chain amino acids (BCAAs) valine, leucine, and isoleucine were two significant pathways between the CVT and healthy cohorts. The area under the curve (AUC) for metabolites associated with valine, leucine, and isoleucine biosynthesis was 0.934. In the validation stage, the BCAA concentrations demonstrated an AUC of 0.935 to differentiate patients with acute CVT from the control cohort. In addition, BCAAs combined with D-dimer levels were used to establish a diagnostic model for CVT, and the AUC was 0.951, showing good diagnostic efficacy of separating CVT patients from the control cohort. BCAAs as plasma biomarkers deserve to be further studied and even developed in clinical CVT management.

Association of coffee consumption with type 2 diabetes and glycemic traits: a Mendelian randomization study

BACKGROUND/OBJECTIVES

Habitual coffee consumption was inversely associated with type 2 diabetes (T2D) and hyperglycemia in observational studies, but the causality of the association remains uncertain. This study tested a causal association of genetically predicted coffee consumption with T2D using the Mendelian randomization (MR) method.

SUBJECTS/METHODS

We used five single-nucleotide polymorphisms (SNPs) as instrumental variables (IVs) associated with habitual coffee consumption in a previous genome-wide association study among Koreans. We analyzed the associations between IVs and T2D, fasting blood glucose (FBG), 2h-postprandial glucose (2h-PG), and glycated haemoglobin (HbA1C) levels. The MR results were further evaluated by standard sensitivity tests for possible pleiotropism.

RESULTS

MR analysis revealed that increased genetically predicted coffee consumption was associated with a reduced prevalence of T2D; ORs per one-unit increment of log-transformed cup per day of coffee consumption ranged from 0.75 (0.62-0.90) for the weighted mode-based method to 0.79 (0.62-0.99) for Wald ratio estimator. We also used the inverse-variance-weighted method, weighted median-based method, MR-Egger method, and MR-PRESSO method. Similarly, genetically predicted coffee consumption was inversely associated with FBG and 2h-PG levels but not with HbA1c. Sensitivity measures gave similar results without evidence of pleiotropy.

CONCLUSIONS

A genetic predisposition to habitual coffee consumption was inversely associated with T2D prevalence and lower levels of FBG and 2h-PG profiles. Our study warrants further exploration.

Caffeine for Headaches: Helpful or Harmful? A Brief Review of the Literature

Consumption of caffeine in the diet, both daily and occasional, has a significant biological effect on the nervous system. Caffeine, through various and not yet fully investigated mechanisms, affects headaches. This is especially noticeable in migraine. In other headaches such as hypnic headache, post-dural puncture headache and spontaneous intracranial hypotension, caffeine is an important therapeutic agent. In turn, abrupt discontinuation of chronically used caffeine can cause caffeine-withdrawal headache. Caffeine can both relieve and trigger headaches.

Genetically predicted coffee and tea consumption and risk of intracranial aneurysm

OBJECTIVES

Observational studies have shown associations between coffee and tea consumption and risk of intracranial aneurysm (IA). However, the results are not consistent. We conducted a Mendelian randomization study to clarify whether genetically predicted coffee and tea consumption has a causal effect on IA and its subtypes.

METHODS

Genetic variants associated with coffee and tea consumption (cups/day) were obtained from large genome-wide association studies (GWASs), up to 349,376 subjects. Summary-level data for IA were adopted from a GWAS in 79,429 subjects (23 cohorts, 7495 cases, and 71,934 controls).

RESULTS

Genetically predicted coffee consumption was associated with a higher risk of any IA and aneurysmal subarachnoid hemorrhage (SAH), but not with unruptured IA. The ORs per 1 cup/day increase in genetically predicted coffee consumption were 1.42 (95% CI: 1.09-1.86; P = 0.010) for IA, 1.51 (95% CI: 1.13-2.03; P = 0.005) for aneurysmal SAH, and 1.20 (95% CI: 0.74-1.96; P = 0.460) for unruptured IA. Genetically predicted tea consumption was not associated with risk of any IA and its subtypes (P > 0.05). The associations remained consistent in sensitivity analyses, and no evidence of pleiotropy was detected.

CONCLUSIONS

Our study provides evidence to support that coffee consumption may increase the risk of IA and associated hemorrhage. Coffee should be limited for those at high risk of IA and associated hemorrhage.

Effect of coffee consumption on thyroid function: NHANES 2007-2012 and Mendelian randomization

Background

Coffee is one of the most consumed beverages worldwide, but the effects on the thyroid are unknown. This study aims to examine the association between coffee and thyroid function.

Methods

Participant data (≥ 20 years, n = 6578) for the observational study were obtained from NHANES 2007-2012. Analysis was performed using weighted linear regression models and multiple logistic regression models. Genetic datasets for Hyperthyroidism and Hypothyroidism were obtained from the IEU database and contained 462,933 European samples. Mendelian randomization (MR) was used for the analysis, inverse variance weighting (IVW) was the main method of analysis.

Results

In the model adjusted for other covariates, participants who drank 2-4 cups of coffee per day had significantly lower TSH concentrations compared to non-coffee drinkers (b=-0.23, 95% CI: -0.30, -0.16), but no statistically significant changes in TT4, FT4, TT3 and FT3. In addition, participants who drank <2 cups of coffee per day showed a low risk of developing subclinical hypothyroidism. (OR=0.60, 95% CI: 0.41, 0.88) Observational studies and MR studies have demonstrated both that coffee consumption has no effect on the risk of hyperthyroidism and hypothyroidism.

Conclusions

Our study showed that drinking <2 cups of coffee per day reduced the risk of subclinical hypothyroidism and drinking 2-4 cups of coffee reduced serum TSH concentrations. In addition, coffee consumption was not associated with the risk of hyperthyroidism and hypothyroidism.

Decoding the genetic relationship between Alzheimer's disease and type 2 diabetes: potential risk variants and future direction for North Africa

Introduction

Alzheimer's disease (AD) and Type 2 diabetes (T2D) are both age-associated diseases. Identification of shared genes could help develop early diagnosis and preventive strategies. Although genetic background plays a crucial role in these diseases, we noticed an underrepresentation tendency of North African populations in omics studies.

Materials and methods

First, we conducted a comprehensive review of genes and pathways shared between T2D and AD through PubMed. Then, the function of the identified genes and variants was investigated using annotation tools including PolyPhen2, RegulomeDB, and miRdSNP. Pathways enrichment analyses were performed with g:Profiler and EnrichmentMap. Next, we analyzed variant distributions in 16 worldwide populations using PLINK2, R, and STRUCTURE software. Finally, we performed an inter-ethnic comparison based on the minor allele frequency of T2D-AD common variants.

Results

A total of 59 eligible papers were included in our study. We found 231 variants and 363 genes shared between T2D and AD. Variant annotation revealed six single nucleotide polymorphisms (SNP) with a high pathogenic score, three SNPs with regulatory effects on the brain, and six SNPs with potential effects on miRNA-binding sites. The miRNAs affected were implicated in T2D, insulin signaling pathways, and AD. Moreover, replicated genes were significantly enriched in pathways related to plasma protein binding, positive regulation of amyloid fibril deposition, microglia activation, and cholesterol metabolism. Multidimensional screening performed based on the 363 shared genes showed that main North African populations are clustered together and are divergent from other worldwide populations. Interestingly, our results showed that 49 SNP associated with T2D and AD were present in North African populations. Among them, 11 variants located in DNM3, CFH, PPARG, ROHA, AGER, CLU, BDNF1, CST9, and PLCG1 genes display significant differences in risk allele frequencies between North African and other populations.

Conclusion

Our study highlighted the complexity and the unique molecular architecture of North African populations regarding T2D-AD shared genes. In conclusion, we emphasize the importance of T2D-AD shared genes and ethnicity-specific investigation studies for a better understanding of the link behind these diseases and to develop accurate diagnoses using personalized genetic biomarkers.

Addressing the ethical and societal challenges posed by genome-wide association studies of behavioral and brain-related traits

Genome-wide association studies have led to the identification of robust statistical associations of genetic variants with numerous brain-related traits, including neurological and psychiatric conditions, and psychological and behavioral measures. These results may provide insight into the biology underlying these traits and may facilitate clinically useful predictions. However, these results also carry the risk of harm, including possible negative effects of inaccurate predictions, violations of privacy, stigma and genomic discrimination, raising serious ethical and legal implications. Here, we discuss ethical concerns surrounding the results of genome-wide association studies for individuals, society and researchers. Given the success of genome-wide association studies and the increasing availability of nonclinical genomic prediction technologies, better laws and guidelines are urgently needed to regulate the storage, processing and responsible use of genetic data. Also, researchers should be aware of possible misuse of their results, and we provide guidance to help avoid such negative impacts on individuals and society.

Multi-trait genome-wide association study identifies a novel endometrial cancer risk locus that associates with testosterone levels

To detect novel endometrial cancer risk variants, we leveraged information from endometrial cancer risk factors in a multi-trait GWAS analysis. We first assessed causal relationships between established and suspected endometrial cancer risk factors, and endometrial cancer using Mendelian randomization. Following multivariable analysis, five independent risk factors (waist circumference, testosterone levels, sex hormone binding globulin levels, age at menarche, and age at natural menopause) were included in a multi-trait Bayesian GWAS analysis. We identified three potentially novel loci that associate with endometrial cancer risk, one of which (7q22.1) replicated in an independent endometrial cancer GWAS dataset and was genome-wide significant in a meta-analysis. This locus may affect endometrial cancer risk through altered testosterone levels. Consistent with this, we observed colocalization between the signals for endometrial cancer risk and expression of CYP3A7, a gene involved in testosterone metabolism. Thus, our findings suggest opportunities for hormone therapy to prevent or treat endometrial cancer.

Associations between health behaviours, fertility and reproductive outcomes: triangulation of evidence in the Norwegian Mother, Father and Child Cohort Study (MoBa)

BACKGROUND

Guidance to improve fertility includes reducing alcohol and caffeine consumption, achieving healthy weight-range and stopping smoking. Advice is informed by observational evidence, which is often biased by confounding.

METHODS

This study primarily used data from a pregnancy cohort, the Norwegian Mother, Father and Child Cohort Study. First, we conducted multivariable regression of health behaviours (alcohol and caffeine consumption, body-mass index (BMI), and smoking) on fertility outcomes (e.g. time to conception) and reproductive outcomes (e.g. age at first birth) (n = 84,075 females, 68,002 males), adjusting for birth year, education and attention-deficit and hyperactive-impulsive (ADHD) traits. Second, we used individual-level Mendelian randomisation (MR) to explore possible causal effects of health behaviours on fertility/reproductive outcomes (n = 63,376 females, 45,460 males). Finally, we performed summary-level MR for available outcomes in UK Biobank (n = 91,462-1,232,091) and controlled for education and ADHD liability using multivariable MR.

RESULTS

In multivariable regression analyses, higher BMI associated with fertility (longer time to conception, increased odds of infertility treatment and miscarriage), and smoking was associated with longer time to conception. In individual-level MR analyses, there was strong evidence for effects of smoking initiation and higher BMI on younger age at first birth, of higher BMI on increased time to conception, and weak evidence for effects of smoking initiation on increased time to conception. Age at first birth associations were replicated in summary-level MR analysis; however, effects attenuated using multivariable MR.

CONCLUSIONS

Smoking behaviour and BMI showed the most consistent associations for increased time to conception and a younger age at first birth. Given that age at first birth and time to conception are positively correlated, this suggests that the mechanisms for reproductive outcomes are distinct to the mechanisms acting on fertility outcomes. Multivariable MR suggested that effects on age at first birth might be explained by underlying liability to ADHD and education.

Acute Effects of Coffee Consumption on Health among Ambulatory Adults

BACKGROUND

Coffee is one of the most commonly consumed beverages in the world, but the acute health effects of coffee consumption remain uncertain.

METHODS

We conducted a prospective, randomized, case-crossover trial to examine the effects of caffeinated coffee on cardiac ectopy and arrhythmias, daily step counts, sleep minutes, and serum glucose levels. A total of 100 adults were fitted with a continuously recording electrocardiogram device, a wrist-worn accelerometer, and a continuous glucose monitor. Participants downloaded a smartphone application to collect geolocation data. We used daily text messages, sent over a period of 14 days, to randomly instruct participants to consume caffeinated coffee or avoid caffeine. The primary outcome was the mean number of daily premature atrial contractions. Adherence to the randomization assignment was assessed with the use of real-time indicators recorded by the participants, daily surveys, reimbursements for date-stamped receipts for coffee purchases, and virtual monitoring (geofencing) of coffee-shop visits.

RESULTS

The mean (±SD) age of the participants was 39±13 years; 51% were women, and 51% were non-Hispanic White. Adherence to the random assignments was assessed to be high. The consumption of caffeinated coffee was associated with 58 daily premature atrial contractions as compared with 53 daily events on days when caffeine was avoided (rate ratio, 1.09; 95% confidence interval [CI], 0.98 to 1.20; P = 0.10). The consumption of caffeinated coffee as compared with no caffeine consumption was associated with 154 and 102 daily premature ventricular contractions, respectively (rate ratio, 1.51; 95% CI, 1.18 to 1.94); 10,646 and 9665 daily steps (mean difference, 1058; 95% CI, 441 to 1675); 397 and 432 minutes of nightly sleep (mean difference, 36; 95% CI, 25 to 47); and serum glucose levels of 95 mg per deciliter and 96 mg per deciliter (mean difference, -0.41; 95% CI, -5.42 to 4.60).

CONCLUSIONS

In this randomized trial, the consumption of caffeinated coffee did not result in significantly more daily premature atrial contractions than the avoidance of caffeine. (Funded by the University of California, San Francisco, and the National Institutes of Health; CRAVE ClinicalTrials.gov number, NCT03671759.).

Investigating modifiable pathways in psoriasis: A Mendelian randomization study

BACKGROUND

Potentially modifiable risk factors have previously been investigated only in conventional observational studies.

OBJECTIVE

To assess whether genetically predicted exposures to modifiable factors are associated with the risk of psoriasis.

METHODS

Two-sample Mendelian randomization (MR) analysis.

RESULTS

An increased risk of psoriasis was noted for genetically predicted lifetime smoking index (odds ratio [OR]_MR-IVW = 2.11; 95% confidence interval [CI], 1.28-3.51), childhood (OR _MR-IVW = 1.40; 95% CI, 1.14-1.71) and adult body mass index (OR _MR-IVW = 1.63; 95% CI, 1.32-2), waist (OR _IVW = 1.86; 95% CI, 1.31-2.64), and hip circumference (OR _MR-IVW = 1.55; 95% CI, 1.15-2.07). Protective association was also reported between genetically predicted longer sleep duration (OR _MR-IVW = 0.56; 95% CI 0.37-0.84) and increased years of education (OR _MR-IVW = 0.78; 95% CI, 0.62-0.98). This effect of education persisted in multivariable MR after adjusting for genetic predictors of smoking and adult body mass index (OR_MVMR-IVW = 0.72; 95% CI, 0.56-0.92).

LIMITATIONS

It was not possible to stratify for psoriasis severity.

CONCLUSION

Smoking cessation and prevention of obesity are important strategies for decreasing the incidence of psoriasis. Similarly, targeting education inequality is expected to lead further to reductions in cases of psoriasis.

Anti-Inflammatory Effect of Caffeine on Muscle under Lipopolysaccharide-Induced Inflammation

Evidence has shown that caffeine administration reduces pro-inflammatory biomarkers, delaying fatigue and improving endurance performance. This study examined the effects of caffeine administration on the expression of inflammatory-, adenosine receptor- (the targets of caffeine), epigenetic-, and oxidative metabolism-linked genes in the vastus lateralis muscle of mice submitted to lipopolysaccharide (LPS)-induced inflammation. We showed that caffeine pre-treatment before LPS administration reduced the expression of Il1b, Il6, and Tnfa, and increased Il10 and Il13. The negative modulation of the inflammatory response induced by caffeine involved the reduction of inflammasome components, Asc and Casp1, promoting an anti-inflammatory scenario. Caffeine treatment per se promoted the upregulation of adenosinergic receptors, Adora1 and Adora2A, an effect that was counterbalanced by LPS. Moreover, there was observed a marked Adora2A promoter hypermethylation, which could represent a compensatory response towards the increased Adora2A expression. Though caffeine administration did not alter DNA methylation patterns, the expression of DNA demethylating enzymes, Tet1 and Tet2, was increased in mice receiving Caffeine+LPS, when compared with the basal condition. Finally, caffeine administration attenuated the LPS-induced catabolic state, by rescuing basal levels of Ampk expression. Altogether, the anti-inflammatory effects of caffeine in the muscle can be mediated by modifications on the epigenetic landscape.

Analysis of genetically determined gene expression suggests role of inflammatory processes in exfoliation syndrome

BACKGROUND

Exfoliation syndrome (XFS) is an age-related systemic disorder characterized by excessive production and progressive accumulation of abnormal extracellular material, with pathognomonic ocular manifestations. It is the most common cause of secondary glaucoma, resulting in widespread global blindness. The largest global meta-analysis of XFS in 123,457 multi-ethnic individuals from 24 countries identified seven loci with the strongest association signal in chr15q22-25 region near LOXL1. Expression analysis have so far correlated coding and a few non-coding variants in the region with LOXL1 expression levels, but functional effects of these variants is unclear. We hypothesize that analysis of the contribution of the genetically determined component of gene expression to XFS risk can provide a powerful method to elucidate potential roles of additional genes and clarify biology that underlie XFS.

RESULTS

Transcriptomic Wide Association Studies (TWAS) using PrediXcan models trained in 48 GTEx tissues leveraging on results from the multi-ethnic and European ancestry GWAS were performed. To eliminate the possibility of false-positive results due to Linkage Disequilibrium (LD) contamination, we i) performed PrediXcan analysis in reduced models removing variants in LD with LOXL1 missense variants associated with XFS, and variants in LOXL1 models in both multiethnic and European ancestry individuals, ii) conducted conditional analysis of the significant signals in European ancestry individuals, and iii) filtered signals based on correlated gene expression, LD and shared eQTLs, iv) conducted expression validation analysis in human iris tissues. We observed twenty-eight genes in chr15q22-25 region that showed statistically significant associations, which were whittled down to ten genes after statistical validations. In experimental analysis, mRNA transcript levels for ARID3B, CD276, LOXL1, NEO1, SCAMP2, and UBL7 were significantly decreased in iris tissues from XFS patients compared to control samples. TWAS genes for XFS were significantly enriched for genes associated with inflammatory conditions. We also observed a higher incidence of XFS comorbidity with inflammatory and connective tissue diseases.

CONCLUSION

Our results implicate a role for connective tissues and inflammation pathways in the etiology of XFS. Targeting the inflammatory pathway may be a potential therapeutic option to reduce progression in XFS.

Mendelian randomization study of maternal coffee consumption and its influence on birthweight, stillbirth, miscarriage, gestational age and pre-term birth

BACKGROUND

Coffee consumption has been associated with several adverse pregnancy outcomes, although data from randomized-controlled trials are lacking. We investigate whether there is a causal relationship between coffee consumption and miscarriage, stillbirth, birthweight, gestational age and pre-term birth using Mendelian randomization (MR).

METHODS

A two-sample MR study was performed using summary results data from a genome-wide association meta-analysis of coffee consumption (N = 91 462) from the Coffee and Caffeine Genetics Consortium. Outcomes included self-reported miscarriage (N = 49 996 cases and 174 109 controls from a large meta-analysis); the number of stillbirths [N = 60 453 from UK Biobank (UKBB)]; gestational age and pre-term birth (N = 43 568 from the 23andMe, Inc cohort) and birthweight (N = 297 356 reporting own birthweight and N = 210 248 reporting offspring's birthweight from UKBB and the Early Growth Genetics Consortium). Additionally, a one-sample genetic risk score (GRS) analysis of coffee consumption in UKBB women (N up to 194 196) and the Avon Longitudinal Study of Parents and Children (N up to 6845 mothers and 4510 children) and its relationship with offspring outcomes was performed.

RESULTS

Both the two-sample MR and one-sample GRS analyses showed no change in risk of sporadic miscarriages, stillbirths, pre-term birth or effect on gestational age connected to coffee consumption. Although both analyses showed an association between increased coffee consumption and higher birthweight, the magnitude of the effect was inconsistent.

CONCLUSION

Our results suggest that coffee consumption during pregnancy might not itself contribute to adverse outcomes such as stillbirth, sporadic miscarriages and pre-term birth or lower gestational age or birthweight of the offspring.

Genetic Associations Between Smoking- and Glaucoma-Related Traits

Purpose

The purpose of this study was to describe the genetic relationship between smoking and glaucoma.

Methods

We used summary-level genetic data for smoking initiation, smoking intensity (cigarettes per day [CPD]), intraocular pressure (IOP), vertical cup-disc ratio, and open-angle glaucoma (OAG) to estimate global genetic correlations (rg) and perform two-sample Mendelian randomization (MR) experiments that explored relations between traits. Finally, we examined associations between smoking genetic risk scores (GRS) and smoking traits with measured IOP and OAG in Rotterdam Study participants.

Results

We identified weak inverse rg between smoking- and glaucoma-related traits that were insignificant after Bonferroni correction. However, MR analysis revealed that genetically predicted smoking initiation was associated with lower IOP (-0.18 mm Hg per SD, 95% confidence interval [CI] = -0.30 to -0.06, P = 0.003). Furthermore, genetically predicted smoking intensity was associated with decreased OAG risk (odds ratio [OR] = 0.74 per SD, 95% CI = 0.61 to 0.90, P = 0.002). In the Rotterdam Study, the smoking initiation GRS was associated with lower IOP (-0.09 mm Hg per SD, 95% CI = -0.17 to -0.01, P = 0.04) and lower odds of OAG (OR = 0.84 per SD, 95% CI = 0.73 to 0.98, P = 0.02) in multivariable-adjusted analyses. In contrast, neither smoking history nor CPD was associated with IOP (P ≥ 0.38) or OAG (P ≥ 0.54). Associations between the smoking intensity GRS and glaucoma traits were null (P ≥ 0.13).

Conclusions

MR experiments and GRS generated from Rotterdam Study participants support an inverse relationship between smoking and glaucoma.

Translational Relevance

Understanding the genetic drivers of the inverse relationship between smoking and glaucoma could yield new insights into glaucoma pathophysiology.

Relationship between genetic polymorphisms of cytokines and self-reported sleep complaints and habitual caffeine consumption

Pro-inflammatory cytokines are involved in sleep-wake regulation and are associated with caffeine consumption. This is a cross-sectional study in 1023 active French workers investigating associations between self-reported sleep complaints (>3months) and total sleep time (TST) with nine single-nucleotide-polymorphisms (SNPs) including pro-inflammatory cytokines, according to caffeine consumption. Participants were characterized as low, moderate and high (0-50, 51-300, and >300 mg/day) caffeine consumers. After adjusting the odd ratios (OR) for age, gender, and smoking, the risk of sleep complaints was higher in subjects with genetic mutations in tumor necrosis factor alpha (TNF-α, rs 1800629) (ORa [95%CI] = 1.43 [1.07-1.92] for both G/A and A/A aggregate genotypes) or interleukin-1 beta (IL-1β, rs1143627) (ORa = 1.61 [1.08-2.44] for homozygous A/A genotype), and the risk was higher when subjects carry the mutations in TNF-α plus IL-1β regardless of caffeine consumption. When stratified with caffeine consumption, the risk of sleep complaints was higher in TNF-α A allele carriers in high caffeine consumers, and in homozygous A/A genotype of IL-1β in moderate and high consumers. None of the nine SNPs influence TST, with the exception of the mutation on CYP1A2 and only when stratified with caffeine consumption. Our results also indicated more caffeine side-effects when carrying mutation on IL1β. This study showed that polymorphisms in TNF-α and/or IL-1β influenced sleep complaints but did not influence total sleep time. This suggests that management of sleep complaints, which can be addressed by clinical interventions, should consider the influence of the genetic profile of pro-inflammatory cytokines.

The causal association between smoking initiation, alcohol and coffee consumption, and women's reproductive health: A two-sample Mendelian randomization analysis

Objective: A number of epidemiological studies have demonstrated that smoking initiation and alcohol and coffee consumption were closely related to women's reproductive health. However, there was still insufficient evidence supporting their direct causality effect. Methods: We utilized two-sample Mendelian randomization (TSMR) analysis with summary datasets from genome-wide association study (GWAS) to investigate the causal relationship between smoking initiation, alcohol and coffee consumption, and women's reproductive health-related traits. Exposure genetic instruments were used as variants significantly related to traits. The inverse-variance weighted (IVW) method was used as the main analysis approach, and we also performed MR-PRESSO, MR-Egger, weighted median, and weighted mode to supplement the sensitivity test. Then, the horizontal pleiotropy was detected by using MRE intercept and MR-PRESSO methods, and the heterogeneity was assessed using Cochran's Q statistics. Results: We found evidence that smoking women showed a significant inverse causal association with the sex hormone-binding globulin (SHBG) levels (corrected β = -0.033, p = 9.05E-06) and age at menopause (corrected β = -0.477, p = 6.60E-09) and a potential positive correlation with the total testosterone (TT) levels (corrected β = 0.033, p = 1.01E-02). In addition, there was suggestive evidence for the alcohol drinking effect on the elevated TT levels (corrected β = 0.117, p = 5.93E-03) and earlier age at menopause (corrected β = -0.502, p = 4.14E-02) among women, while coffee consumption might decrease the female SHBG levels (corrected β = -0.034, p = 1.33E-03). Conclusion: Our findings suggested that smoking in women significantly decreased their SHBG concentration, promoted earlier menopause, and possibly reduced the TT levels. Alcohol drinking had a potential effect on female higher TT levels and earlier menopause, while coffee consumption might lead to lower female SHBG levels.

Variability of caffeine content in green and roasted Coffea arabica regarding the origin, post-harvest processing, and altitude, and overview of recommended daily allowance

Caffeine content is a crucial attribute of coffee. Its concentration and thus maximum cups of Coffea arabica from Africa, Asia, Central America, and South America from different altitudes of growing areas, altitude, and process using different post-harvest processing (dry, wet, and pulped natural). Our results suggest that geographical origin might affect the alkaloid concentration in C. arabica. The caffeine concentration pattern in green samples was as follows: Central America > South America > Asia > Africa. Altitude affected the concentrations, lowlands > midlands > highlands, however, not significantly. Given caffeine is thermostable, the medium roasting process did not affect the concentration of caffeine directly, but a small increase was observed. Scientific opinion on the safety of habitual caffeine consumption of up to 400 mg per day does not raise safety concerns for non-pregnant adults. A cup (7 g coffee in 120 mL of water) was used for recalculation. Results suggest that mostly highlands and midlands coffee from Africa reached levels of caffeine that might be consumed in more than 5.5 cups a day.

Genome-wide association study identifies novel loci associated with skin autofluorescence in individuals without diabetes

BACKGROUND

Skin autofluorescence (SAF) is a non-invasive measure reflecting accumulation of advanced glycation endproducts (AGEs) in the skin. Higher SAF levels are associated with an increased risk of developing type 2 diabetes and cardiovascular disease. An earlier genome-wide association study (GWAS) revealed a strong association between NAT2 variants and SAF. The aim of this study was to calculate SAF heritability and to identify additional genetic variants associated with SAF through genome-wide association studies (GWAS).

RESULTS

In 27,534 participants without diabetes the heritability estimate of lnSAF was 33% ± 2.0% (SE) in a model adjusted for covariates. In meta-GWAS for lnSAF five SNPs, on chromosomes 8, 11, 15 and 16 were associated with lnSAF (P < 5 × 10^-8): 1. rs2846707 (Chr11:102,576,358,C > T), which results in a Met30Val missense variant in MMP27 exon 1 (NM_022122.3); 2. rs2470893 (Chr15:75,019,449,C > T), in intergenic region between CYP1A1 and CYP1A2; with attenuation of the SNP-effect when coffee consumption was included as a covariate; 3. rs12931267 (Chr16:89,818,732,C > G) in intron 30 of FANCA and near MC1R; and following conditional analysis 4. rs3764257 (Chr16:89,800,887,C > G) an intronic variant in ZNF276, 17.8 kb upstream from rs12931267; finally, 30 kb downstream from NAT2 5. rs576201050 (Chr8:18,288,053,G > A).

CONCLUSIONS

This large meta-GWAS revealed five SNPs at four loci associated with SAF in the non-diabetes population. Further unravelling of the genetic architecture of SAF will help in improving its utility as a tool for screening and early detection of diseases and disease complications.

Whole Exome Sequencing Study Identifies Novel Rare Risk Variants for Habitual Coffee Consumption Involved in Olfactory Receptor and Hyperphagia

Habitual coffee consumption is an addictive behavior with unknown genetic variations and has raised public health issues about its potential health-related outcomes. We performed exome-wide association studies to identify rare risk variants contributing to habitual coffee consumption utilizing the newly released UK Biobank exome dataset (n = 200,643). A total of 34,761 qualifying variants were imported into SKAT to conduct gene-based burden and robust tests with minor allele frequency <0.01, adjusting the polygenic risk scores (PRS) of coffee intake to exclude the effect of common coffee-related polygenic risk. The gene-based burden and robust test of the exonic variants found seven exome-wide significant associations, such as OR2G2 (PSKAT = 1.88 × 10−9, PSKAT-Robust = 2.91 × 10−17), VEZT1 (PSKAT = 3.72 × 10−7, PSKAT-Robust = 1.41 × 10−7), and IRGC (PSKAT = 2.92 × 10−5, PSKAT-Robust = 1.07 × 10−7). These candidate genes were verified in the GWAS summary data of coffee intake, such as rs12737801 (p = 0.002) in OR2G2, and rs34439296 (p = 0.008) in IRGC. This study could help to extend genetic insights into the pathogenesis of coffee addiction, and may point to molecular mechanisms underlying health effects of habitual coffee consumption.

In silico analysis of a SLC6A4 G100V mutation in lung cancers

SLC6A4 is a serotonin re-uptake transporter which has been a target for anti-depressant therapies but recently some mutations have been described in cancer cells. Here, we characterize mutations in SLC6A4 that appear in cancer cells. We employed several validated computational and artificial intelligence algorithms to characterize the mutations. We identified a previously uncharacterized G100V mutation in lung cancers. In sillico structural analysis reveals that this mutation may affect SLC6A4 ligand binding and subsequently its function. We also identified several other mutations that may affect the structure of the protein. This preliminary analysis highlights the role of SLC6A4 in human cancers.

Tea Consumption and All-Cause and Cause-Specific Mortality in the UK Biobank : A Prospective Cohort Study

BACKGROUND

Tea is frequently consumed worldwide, but the association of tea drinking with mortality risk remains inconclusive in populations where black tea is the main type consumed.

OBJECTIVE

To evaluate the associations of tea consumption with all-cause and cause-specific mortality and potential effect modification by genetic variation in caffeine metabolism.

DESIGN

Prospective cohort study.

SETTING

The UK Biobank.

PARTICIPANTS

498 043 men and women aged 40 to 69 years who completed the baseline touchscreen questionnaire from 2006 to 2010.

MEASUREMENTS

Self-reported tea intake and mortality from all causes and leading causes of death, including cancer, all cardiovascular disease (CVD), ischemic heart disease, stroke, and respiratory disease.

RESULTS

During a median follow-up of 11.2 years, higher tea intake was modestly associated with lower all-cause mortality risk among those who drank 2 or more cups per day. Relative to no tea drinking, the hazard ratios (95% CIs) for participants drinking 1 or fewer, 2 to 3, 4 to 5, 6 to 7, 8 to 9, and 10 or more cups per day were 0.95 (95% CI, 0.91 to 1.00), 0.87 (CI, 0.84 to 0.91), 0.88 (CI, 0.84 to 0.91), 0.88 (CI, 0.84 to 0.92), 0.91 (CI, 0.86 to 0.97), and 0.89 (CI, 0.84 to 0.95), respectively. Inverse associations were seen for mortality from all CVD, ischemic heart disease, and stroke. Findings were similar regardless of whether participants also drank coffee or not or of genetic score for caffeine metabolism.

LIMITATION

Potentially important aspects of tea intake (for example, portion size and tea strength) were not assessed.

CONCLUSION

Higher tea intake was associated with lower mortality risk among those drinking 2 or more cups per day, regardless of genetic variation in caffeine metabolism. These findings suggest that tea, even at higher levels of intake, can be part of a healthy diet.

PRIMARY FUNDING SOURCE

National Cancer Institute Intramural Research Program.