Fernando Pires Hartwig

Robust inference in summary data Mendelian randomisation via the zero modal pleiotropy assumption

Abstract Background Mendelian randomization (MR) is being increasingly used to strengthen causal inference in observational studies. Availability of summary data of genetic associations for a variety of phenotypes from large genome-wide association studies (GWAS) allows straightforward application of MR using summary data methods, typically in a two-sample design. In addition to the conventional inverse variance weighting (IVW) method, recently developed summary data MR methods, such as the MR-Egger and weighted median approaches, allow a relaxation of the instrumental variable assumptions. Methods Here, a new method - the mode-based estimate (MBE) - is proposed to obtain a single causal effect estimate from multiple genetic instruments. The MBE is consistent when the largest number of similar (identical in infinite samples) individual-instrument causal effect estimates comes from valid instruments, even if the majority of instruments are invalid. We evaluate the performance of the method in simulations designed to mimic the two-sample summary data setting, and demonstrate its use by investigating the causal effect of plasma lipid fractions and urate levels on coronary heart disease risk. Results The MBE presented less bias and lower type-I error rates than other methods under the null in many situations. Its power to detect a causal effect was smaller compared with the IVW and weighted median methods, but was larger than that of MR-Egger regression, with sample size requirements typically smaller than those available from GWAS consortia. Conclusions The MBE relaxes the instrumental variable assumptions, and should be used in combination with other approaches in sensitivity analyses.

Two-sample Mendelian randomisation: avoiding the downsides of a powerful, widely applicable but potentially fallible technique

Two-sample Mendelian randomization: avoiding the downsides of a powerful, widely applicable but potentially fallible technique Fernando Pires Hartwig*, Neil Martin Davies, Gibran Hemani and George Davey Smith Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil, Medical Research Council Integrative Epidemiology Unit at the University of Bristol and School of Social and Community Medicine, University of Bristol, Bristol, UK

From stem cells to the law courts: DNA methylation, the forensic epigenome and the possibility of a biosocial archive

The growth in epigenetics continues to attract considerable cross-disciplinary interest, apparently representing an opportunity to move beyond genomics towards the goal of understanding phenotypic variability from molecular through organismal to the societal level. The epigenome may also harbour useful information about life-time exposures (measured or unmeasured) irrespective of their influence on health or disease, creating the potential for a person-specific biosocial archive. Furthermore, such data may prove of use in providing identifying information, providing the possibility of a future forensic epigenome. The mechanisms involved in ensuring that environmentally induced epigenetic changes perpetuate across the life course remain unclear. Here we propose that a potential role of adult stem cells in maintaining epigenetic states provides a useful basis for formulating such epidemiologically-relevant concepts. Epigenetics encompasses different mechanisms of gene expression regulation, the most commonly discussed ones being DNA methylation, histone modifications and noncoding RNAs. The epigenetic mechanism most studied to date is DNA methylation—addition of a methyl group (CH3) at the 5’ position of a cytosine base, typically at CpG dinucleotides which are often clustered in CpG-rich DNA segments called CpG islands. This chemical addition is made by a covalent bond and is stable over time. Since epigenetic processes are believed to be modifiable by environmental (i.e. non-genetic) factors, much of the current interest in epigenetics lies in understanding how the environment influences gene expression—even though, as currently analysable, epigenetics is unlikely to hold all of the answers for this broad and rather complex question. Technological advances now allow epigenome-wide investigations to be performed in large human populations at affordable costs—especially with respect to DNA methylation. Although other measures are technically possible, they remain prohibitively expensive on a population scale. Epidemiological studies involving DNA methylation pertain to one of the most recent branches of epidemiology—epigenetic epidemiology. Large-scale profiling of DNA methylation levels has been applied to case-control studies, densely-phenotyped cohorts and in some instances serial samples from the same longitudinal cohort. This allows investigation of the determinants of variation in DNA methylation and their importance in the context of different health outcomes and traits, as evidenced by the steady rise in epigenetic epidemiology publications (Figure 1) and the numerous studies reported in this issue of the IJE.

Education and coronary heart disease: mendelian randomisation study

Objective To determine whether educational attainment is a causal risk factor in the development of coronary heart disease. Design Mendelian randomisation study, using genetic data as proxies for education to minimise confounding. Setting The main analysis used genetic data from two large consortia (CARDIoGRAMplusC4D and SSGAC), comprising 112 studies from predominantly high income countries. Findings from mendelian randomisation analyses were then compared against results from traditional observational studies (164 170 participants). Finally, genetic data from six additional consortia were analysed to investigate whether longer education can causally alter the common cardiovascular risk factors. Participants The main analysis was of 543 733 men and women (from CARDIoGRAMplusC4D and SSGAC), predominantly of European origin. Exposure A one standard deviation increase in the genetic predisposition towards higher education (3.6 years of additional schooling), measured by 162 genetic variants that have been previously associated with education. Main outcome measure Combined fatal and non-fatal coronary heart disease (63 746 events in CARDIoGRAMplusC4D). Results Genetic predisposition towards 3.6 years of additional education was associated with a one third lower risk of coronary heart disease (odds ratio 0.67, 95% confidence interval 0.59 to 0.77; P=3×10−8). This was comparable to findings from traditional observational studies (prevalence odds ratio 0.73, 0.68 to 0.78; incidence odds ratio 0.80, 0.76 to 0.83). Sensitivity analyses were consistent with a causal interpretation in which major bias from genetic pleiotropy was unlikely, although this remains an untestable possibility. Genetic predisposition towards longer education was additionally associated with less smoking, lower body mass index, and a favourable blood lipid profile. Conclusions This mendelian randomisation study found support for the hypothesis that low education is a causal risk factor in the development of coronary heart disease. Potential mechanisms could include smoking, body mass index, and blood lipids. In conjunction with the results from studies with other designs, these findings suggest that increasing education may result in substantial health benefits.

African ancestry, lung function and the effect of genetics

African-Americans have smaller lung function compared with European-Americans. The aim of this study was to disentangle the contribution of genetics from other variables on lung function. A cohort was followed from birth to 30 years of age in Brazil. Several variables were collected: genomic analysis based on DNA; forced expiratory volume in 1 s (FEV1) and forced vital capacity (FVC) obtained by spirometry; height measured by anthropometrists; and thorax circumference evaluated by photonic scanner. Crude and adjusted linear regression models were calculated according to African ancestry. The sample comprised 2869 participants out of 3701 members of the cohort. Males with higher African ancestry by DNA analysis had a smaller FEV1 (−0.13 L, 95% CI −0.23– −0.03 L) and FVC (−0.21 L, 95% CI −0.32– −0.09 L) compared with those with less African ancestry, having accounted for height, sitting to standing height ratio and other confounders. Similar effects were seen in females. After adjustment, ancestry remained significantly associated with lung function, but the large effect of adjustment for confounding among males (but not females) does not allow us to exclude the possibility that residual confounding may still account for these findings. Smaller lung function is related to African ancestry but adjustments for confounders reduced the effect sizes http://ow.ly/Iq0Ve

Telomeres and Tissue Engineering: The Potential Roles of TERT in VEGF-mediated Angiogenesis

Telomeres are protective structures located at the end of eukaryotic chromosomes which are shortened after each cell division, leading to senescence. Telomerase activity prevents telomere shortening by reverse transcription catalyzed by the subunit called TERT (telomerase reverse transcriptase). TERT expression has shown interesting cellular properties, which may be appealing for tissue engineering, such as the enhancement of cell proliferation and differentiation abilities in vitro. Despite some evidence for playing these roles in VEGF (vascular endothelial growth factor)-mediated angiogenesis, it is still unclear whether TERT can contribute to this essential event to generate functional organs. This review suggests a hypothesis that TERT and VEGF potentially regulates the transcriptional expression of each other, which would give new perspectives in the roles of telomerase in regulating several cellular processes, and also contributing for a better comprehension of the molecular mechanisms underlying VEGF signaling (both paracrine and autocrine). In general, based on the literature revised, it is possible to conclude that TERT is a potential VEGF enhancer; however, it is necessary to elaborate methodological approaches to explore this potential and to assess the potential benefits on tissue engineering approaches.Telomeres are protective structures located at the end of eukaryotic chromosomes which are shortened after each cell division, leading to senescence. Telomerase activity prevents telomere shortening by reverse transcription catalyzed by the subunit called TERT (telomerase reverse transcriptase). TERT expression has shown interesting cellular properties, which may be appealing for tissue engineering, such as the enhancement of cell proliferation and differentiation abilities in vitro. Despite some evidence for playing these roles in VEGF (vascular endothelial growth factor)-mediated angiogenesis, it is still unclear whether TERT can contribute to this essential event to generate functional organs. This review suggests a hypothesis that TERT and VEGF potentially regulates the transcriptional expression of each other, which would give new perspectives in the roles of telomerase in regulating several cellular processes, and also contributing for a better comprehension of the molecular mechanisms underlying VEGF signaling (both paracrine and autocrine). In general, based on the literature revised, it is possible to conclude that TERT is a potential VEGF enhancer; however, it is necessary to elaborate methodological approaches to explore this potential and to assess the potential benefits on tissue engineering approaches.

Inflammatory Biomarkers and Risk of Schizophrenia: A 2-Sample Mendelian Randomization Study

Importance Positive associations between inflammatory biomarkers and risk of psychiatric disorders, including schizophrenia, have been reported in observational studies. However, conventional observational studies are prone to bias, such as reverse causation and residual confounding, thus limiting our understanding of the effect (if any) of inflammatory biomarkers on schizophrenia risk. Objective To evaluate whether inflammatory biomarkers have an effect on the risk of developing schizophrenia. Design, Setting, and Participants Two-sample mendelian randomization study using genetic variants associated with inflammatory biomarkers as instrumental variables to improve inference. Summary association results from large consortia of candidate gene or genome-wide association studies, including several epidemiologic studies with different designs, were used. Gene-inflammatory biomarker associations were estimated in pooled samples ranging from 1645 to more than 80 000 individuals, while gene-schizophrenia associations were estimated in more than 30 000 cases and more than 45 000 ancestry-matched controls. In most studies included in the consortia, participants were of European ancestry, and the prevalence of men was approximately 50%. All studies were conducted in adults, with a wide age range (18 to 80 years). Exposures Genetically elevated circulating levels of C-reactive protein (CRP), interleukin-1 receptor antagonist (IL-1Ra), and soluble interleukin-6 receptor (sIL-6R). Main Outcomes and Measures Risk of developing schizophrenia. Individuals with schizophrenia or schizoaffective disorders were included as cases. Given that many studies contributed to the analyses, different diagnostic procedures were used. Results The pooled odds ratio estimate using 18 CRP genetic instruments was 0.90 (random effects 95% CI, 0.84-0.97; P = .005) per 2-fold increment in CRP levels; consistent results were obtained using different mendelian randomization methods and a more conservative set of instruments. The odds ratio for sIL-6R was 1.06 (95% CI, 1.01-1.12; P = .02) per 2-fold increment. Estimates for IL-1Ra were inconsistent among instruments, and pooled estimates were imprecise and centered on the null. Conclusions and Relevance Under mendelian randomization assumptions, our findings suggest a protective effect of CRP and a risk-increasing effect of sIL-6R (potentially mediated at least in part by CRP) on schizophrenia risk. It is possible that such effects are a result of increased susceptibility to early life infection.

Is there a causal role for homocysteine concentration in blood pressure? A Mendelian randomization study

Background: An understanding of whether homocysteine is a cause or a marker of increased blood pressure is relevant because blood homocysteine can be effectively lowered by safe and inexpensive interventions (e.g., vitamin B-6, B-9, and B-12 supplementation). Objective: The aim was to assess the causal influence of homocysteine on systolic and diastolic blood pressure (SBP and DBP, respectively) in adults with the use of Mendelian randomization (MR). Design: Data from the 1982 Pelotas Birth Cohort (Brazil) were used. A total of 4297 subjects were evaluated in 2004–2005 (mean age: 22.8 y). The association of homocysteine concentration with SBP and DBP was assessed by conventional ordinary least-squares (OLS) linear regression and 2-stage least-squares (2SLS) regression (MR analysis). The single nucleotide polymorphism (SNP) methylenetetrahydrofolate reductase (MTHFR) C677T (rs1801133) was used as proxy for homocysteine concentration. We also applied MR to data from the International Consortium for Blood Pressure (ICBP) genomewide association studies (>69,000 participants) using rs1801133 and additional homocysteine-associated SNPs as instruments. Results: In OLS regression, a 1-SD unit increase in log homocysteine concentration was associated with an increase of 0.9 (95% CI: 0.4, 1.4) mm Hg in SBP and of 1.0 (95% CI: 0.6, 1.4) mm Hg in DBP. In 2SLS regression, for the same increase in homocysteine, the coefficients were −1.8 mm Hg for SBP (95% CI: −3.9, 0.4 mm Hg; P = 0.01) and 0.1 mm Hg for DBP (95% CI: −1.5, 1.7 mm Hg; P = 0.24). In the MR analysis of ICBP data, homocysteine concentration was not associated with SBP (β = 0.6 mm Hg for each 1-SD unit increase in log homocysteine; 95% CI: −0.8, 1.9 mm Hg) but was positively associated with DBP (β = 1.1 mm Hg; 95% CI: 0.2, 1.9 mm Hg). The association of genetically increased homocysteine with DBP was not consistent across different SNPs. Conclusion: Overall, the present findings do not corroborate the hypothesis that homocysteine has a causal role in blood pressure, especially in SBP.

Association of lactase persistence genotype with milk consumption, obesity and blood pressure: a Mendelian randomization study in the 1982 Pelotas (Brazil) Birth Cohort, with a systematic review and meta-analysis

Background: Milk intake has been associated with lower blood pressure (BP) in observational studies, and randomized controlled trials suggested that milk-derived tripeptides have BP-lowering effects. Milk intake has also been associated with body mass index (BMI). Nevertheless, it is unclear whether increasing milk consumption would reduce BP in the general population. Methods: We investigated the association of milk intake with obesity and BP using genetically-defined lactase persistence (LP) based on the rs4988235 polymorphism in a Mendelian randomization design in the 1982 Pelotas (Southern Brazil) Birth Cohort. These results were combined with published reports identified through a systematic review using meta-analysis. Results: In the 1982 Pelotas Birth Cohort, milk intake was 42 [95% confidence interval (CI): 18; 67) ml/day higher in LP individuals. In conventional observational analysis, each 1-dl/day increase in milk intake was associated with −0.26 (95% CI: −0.33; −0.19) kg/m2 in BMI and −0.31 (95% CI: −0.46; −0.16) and -0.35 (95% CI: −0.46; −0.23) mmHg in systolic and diastolic BP, respectively. These results were not corroborated when analysing LP status, but confidence intervals were large. In random effects meta-analysis, LP individuals presented higher BMI [0.17 (95% CI: 0.07; 0.27) kg/m2] and higher odds of overweight-obesity [1.09 (95% CI: 1.02; 1.17)]. There were no reliable associations for BP. Conclusions: Our study supports that LP is positively associated with obesity, suggesting that the negative association of milk intake with obesity is likely due to limitations of conventional observational studies. Our findings also do not support that increased milk intake leads to lower BP.

Telomere dysfunction and tumor suppression responses in dyskeratosis congenita: Balancing cancer and tissue renewal impairment

Dyskeratosis congenita (DC) encompasses a large spectrum of diseases and clinical manifestations generally related to premature aging, including bone marrow failure and cancer predisposition. The major risk factor for DC is to carry germline telomere-related mutations - in telomerase or telomere shelterin genes - which results in premature telomere dysfunction, thus increasing the risk of premature aging impairments. Despite the advances that have been accomplished in DC research, the molecular aspects underlying the phenotypic variability of the disease remain poorly understood. Here different aspects of telomere biology, concerning adult stem cells senescence, tumor suppression and cancer are considered in the context of DC, resulting in two translational models: late onset of DC symptoms in telomere-related mutations carriers is a potential indicator of increased cancer risk and differences in tumor suppression capacities among the genetic subgroups are (at least partial) causes of different clinical manifestations of the disease. The limitations of both models are presented, and further experiments for their validation, as well as clinical implications, are discussed.