Educational attainment, health outcomes and mortality: a within-sibship Mendelian randomization study

Previous Mendelian randomization (MR) studies using population samples (population-MR) have provided evidence for beneficial effects of educational attainment on health outcomes in adulthood. However, estimates from these studies may have been susceptible to bias from population stratification, assortative mating and indirect genetic effects due to unadjusted parental genotypes. Mendelian randomization using genetic association estimates derived from within-sibship models (within-sibship MR) can avoid these potential biases because genetic differences between siblings are due to random segregation at meiosis. Applying both population and within-sibship MR, we estimated the effects of genetic liability to educational attainment on body mass index (BMI), cigarette smoking, systolic blood pressure (SBP) and all-cause mortality. MR analyses used individual-level data on 72,932 siblings from UK Biobank and the Norwegian HUNT study and summary-level data from a within-sibship Genome-wide Association Study including over 140,000 individuals. Both population and within-sibship MR estimates provided evidence that educational attainment influences BMI, cigarette smoking and SBP. Genetic variant-outcome associations attenuated in the within-sibship model, but genetic variant-educational attainment associations also attenuated to a similar extent. Thus, within-sibship and population MR estimates were largely consistent. The within-sibship MR estimate of education on mortality was imprecise but consistent with a putative effect. These results provide evidence of beneficial individual-level effects of education (or liability to education) on adulthood health, independent of potential demographic and family-level confounders.

SNP-level FST outperforms window statistics for detecting soft sweeps in local adaptation

Local adaptation can lead to elevated genetic differentiation at the targeted genetic variant and nearby sites. Selective sweeps come in different forms, and depending on the initial and final frequencies of a favored variant, very different patterns of genetic variation may be produced. If local selection favors an existing variant that had already recombined onto multiple genetic backgrounds, then the width of elevated genetic differentiation (high FST) may be too narrow to detect using a typical windowed genome scan, even if the targeted variant becomes highly differentiated. We therefore used a simulation approach to investigate the power of SNP-level FST (specifically, the maximum SNP FST value within a window) to detect diverse scenarios of local adaptation, and compared it against whole-window FST and the Comparative Haplotype Identity statistic. We found that SNP FST had superior power to detect complete or mostly complete soft sweeps, but lesser power than window-wide statistics to detect partial hard sweeps. To investigate the relative enrichment and nature of SNP FST outliers from real data, we applied the two FST statistics to a panel of Drosophila melanogaster populations. We found that SNP FST had a genome-wide enrichment of outliers compared to demographic expectations, and though it yielded a lesser enrichment than window FST, it detected mostly unique outlier genes and functional categories. Our results suggest that SNP FST is highly complementary to typical window-based approaches for detecting local adaptation, and merits inclusion in future genome scans and methodologies.

The Interaction Between Genetic Variant ZNF804A rs1344706 and Alcohol Withdrawal on Impulsivity: Evidence for the Diathesis-Stress Model

Objective: Alcohol use disorder (AUD) is the most common substance use disorder, which may relate to increased impulsivity. A more detailed understanding of the potential moderating factor on association between AUD and impulsivity is likely to have far-reaching effects. This study aims to examine whether the interaction between a genetic variant ZNF804A rs1344706 and alcohol use is related to impulsivity in Chinese Han adult males diagnosed with AUD.Methods: A total of 455 Chinese Han adult males diagnosed with AUD were included in this study. Impulsivity was assessed using Barratt Impulsiveness Scale. Alcohol dependence was measured by Michigan Alcoholism Screening Test. Genomic DNA was extracted from peripheral blood of participants and genotyped.Results: Hierarchical multiple regression yielded a significant interaction between ZNF804A rs1344706 and alcohol use (β = 0.20, p = 0.0237). Then, A region of significance (RoS) test was performed to interpret the interaction effect. Re-parameterized regression models revealed that the interaction between ZNF804A rs1344706 and alcohol problem severity fit to the weak diathesis-stress model (R2 = 0.15, p < 0.0010), indicating that the T allele carriers are more susceptible to alcohol problem severity, jointly contributing to impulsivity.Conclusions: This study, which analyzed a specific gene-environment interaction, demonstrated that carriers of the T allele of ZNF804A rs1344706 may be more susceptible to alcohol problem severity, correlated with higher levels of impulsivity during withdrawal.

Mendelian Randomization Integrating GWAS, eQTL, and mQTL Data Identified Genes Pleiotropically Associated With Atrial Fibrillation

Background: Atrial fibrillation (AF) is the most common arrhythmia. Genome-wide association studies (GWAS) have identified more than 100 loci associated with AF, but the underlying biological interpretation remains largely unknown. The goal of this study is to identify gene expression and DNA methylation (DNAm) that are pleiotropically or potentially causally associated with AF, and to integrate results from transcriptome and methylome.Methods: We used the summary data-based Mendelian randomization (SMR) to integrate GWAS with expression quantitative trait loci (eQTL) studies and methylation quantitative trait loci (mQTL) studies. The HEIDI (heterogeneity in dependent instruments) test was introduced to test against the null hypothesis that there is a single causal variant underlying the association.Results: We prioritized 22 genes by eQTL analysis and 50 genes by mQTL analysis that passed the SMR & HEIDI test. Among them, 6 genes were overlapped. By incorporating consistent SMR associations between DNAm and AF, between gene expression and AF, and between DNAm and gene expression, we identified several mediation models at which a genetic variant exerted an effect on AF by altering the DNAm level, which regulated the expression level of a functional gene. One example was the genetic variant-cg18693985-CPEB4-AF axis.Conclusion: In conclusion, our integrative analysis identified multiple genes and DNAm sites that had potentially causal effects on AF. We also pinpointed plausible mechanisms in which the effect of a genetic variant on AF was mediated by genetic regulation of transcription through DNAm. Further experimental validation is necessary to translate the identified genes and possible mechanisms into clinical practice.

Substance Use-Related Cognitive Decline in Families with Autosomal Dominant Alzheimer’s Disease: A Cohort Study

Background: Cigarette smoking is a known risk factor for Alzheimer’s disease (AD). However, the association between neurodegeneration and other substances has not been fully determined. It is of vital importance to evaluate this relationship in populations at high risk of dementia. Since substance use possibly modifies the progression rate of cognitive decline, we studied this association in a unique and well-phenotyped cohort from the University of Antioquia: carriers of the PSEN1-E280A genetic variant. Objective: To determine the association between substance use and cognitive decline in carriers of the PSEN1-E280A genetic variant. Methods: A retrospective cohort study was conducted with 94 carriers and 69 noncarriers recruited between January 2019 and April 2020. A psychiatrist interviewed the participants using the Consumption of Alcohol, Cigarettes and other Substances questionnaire. The participants were also submitted to cognitive evaluation. The relationship between cognitive decline and substance use was explored through a mixed effects regression model. Results: There was an association between cigarettes and better performance on tasks related to perceptual organization, verbal fluency, and memory in carriers. Alcohol had a positive or negative effect on memory according to the type of alcoholic beverage. Results on marijuana use were no conclusive. Coffee was associated with progressive improvements in executive function and verbal fluency. Conclusion: Cigarette and alcohol were associated with an improvement of some cognitive assessments, possibly by a survival bias. In addition, coffee was related to improvements in executive function and language; therefore, its short-term neuroprotective potential should be studied.

CCR5Δ32 in Brazil: Impacts of a European Genetic Variant on a Highly Admixed Population

The genetic background of Brazilians encompasses Amerindian, African, and European components as a result of the colonization of an already Amerindian inhabited region by Europeans, associated to a massive influx of Africans. Other migratory flows introduced into the Brazilian population genetic components from Asia and the Middle East. Currently, Brazil has a highly admixed population and, therefore, the study of genetic factors in the context of health or disease in Brazil is a challenging and remarkably interesting subject. This phenomenon is exemplified by the genetic variant CCR5Δ32, a 32 base-pair deletion in the CCR5 gene. CCR5Δ32 originated in Europe, but the time of origin as well as the selective pressures that allowed the maintenance of this variant and the establishment of its current frequencies in the different human populations is still a field of debates. Due to its origin, the CCR5Δ32 allele frequency is high in European-derived populations (~10%) and low in Asian and African native human populations. In Brazil, the CCR5Δ32 allele frequency is intermediate (4-6%) and varies on the Brazilian States, depending on the migratory history of each region. CCR5 is a protein that regulates the activity of several immune cells, also acting as the main HIV-1 co-receptor. The CCR5 expression is influenced by CCR5Δ32 genotypes. No CCR5 expression is observed in CCR5Δ32 homozygous individuals. Thus, the CCR5Δ32 has particular effects on different diseases. At the population level, the effect that CCR5Δ32 has on European populations may be different than that observed in highly admixed populations. Besides less evident due to its low frequency in admixed groups, the effect of the CCR5Δ32 variant may be affected by other genetic traits. Understanding the effects of CCR5Δ32 on Brazilians is essential to predict the potential use of pharmacological CCR5 modulators in Brazil. Therefore, this study reviews the impacts of the CCR5Δ32 on the Brazilian population, considering infectious diseases, inflammatory conditions, and cancer. Finally, this article provides a general discussion concerning the impacts of a European-derived variant, the CCR5Δ32, on a highly admixed population.