A Novel Approach Integrating Hierarchical Clustering and Weighted Combination for Association Study of Multiple Phenotypes and a Genetic Variant

Insights Into Causal Effects of Genetically Proxied Lipids and Lipid-Modifying Drug Targets on Cardiometabolic Diseases

BACKGROUND

The differential impact of serum lipids and their targets for lipid modification on cardiometabolic disease risk is debated. This study used Mendelian randomization to investigate the causal relationships and underlying mechanisms.

METHODS

Genetic variants related to lipid profiles and targets for lipid modification were sourced from the Global Lipids Genetics Consortium. Summary data for 10 cardiometabolic diseases were compiled from both discovery and replication data sets. Expression quantitative trait loci data from relevant tissues were employed to evaluate significant lipid-modifying drug targets. Comprehensive analyses including colocalization, mediation, and bioinformatics were conducted to validate the results and investigate potential mediators and mechanisms.

RESULTS

Significant causal associations were identified between lipids, lipid-modifying drug targets, and various cardiometabolic diseases. Notably, genetic enhancement of LPL (lipoprotein lipase) was linked to reduced risks of myocardial infarction (odds ratio [OR]1, 0.65 [95% CI, 0.57-0.75], P1=2.60×10-9; OR2, 0.59 [95% CI, 0.49-0.72], P2=1.52×10-7), ischemic heart disease (OR1, 0.968 [95% CI, 0.962-0.975], P1=5.50×10-23; OR2, 0.64 [95% CI, 0.55-0.73], P2=1.72×10-10), and coronary heart disease (OR1, 0.980 [95% CI, 0.975-0.985], P1=3.63×10-14; OR2, 0.64 [95% CI, 0.54-0.75], P2=6.62×10-8) across 2 data sets. Moreover, significant Mendelian randomization and strong colocalization associations for the expression of LPL in blood and subcutaneous adipose tissue were linked with myocardial infarction (OR, 0.918 [95% CI, 0.872-0.967], P=1.24×10-3; PP.H4, 0.99) and coronary heart disease (OR, 0.991 [95% CI, 0.983-0.999], P=0.041; PP.H4=0.92). Glucose levels and blood pressure were identified as mediators in the total effect of LPL on cardiometabolic outcomes.

CONCLUSIONS

The study substantiates the causal role of lipids in specific cardiometabolic diseases, highlighting LPL as a potent drug target. The effects of LPL are suggested to be influenced by changes in glucose and blood pressure, providing insights into its mechanism of action.

Effect of life course body composition on lipids and coronary atherosclerosis mediated by inflammatory biomarkers

OBJECTIVE

To investigate the mediating role of inflammatory biomarkers in the causal effect of body composition on lipids and atherosclerosis.

METHODS

Retrospective observational study and Mendelian randomization (MR) study were used. Observational analyses were undertaken using data from 4717 children and adolescents aged 6-18 years from Chinese who underwent dual-energy x-ray absorptiometry for body composition. MR analyses were based on summary statistics from UK Biobank, deCODE2021, GLGC, FinnGen and other large consortiums. Inflammatory biomarkers included leptin, insulin, adiponectin, osteocalcin, fibroblast growth factor 23 (FGF23) and parathyroid hormone (PTH).

RESULTS

In retrospective observational study, through osteocalcin, body composition had effects on total cholesterol (TC), triglyceride and low-density lipoprotein cholesterol (LDL). Conversely, fat mass vs. fat-free mass demonstrated opposing effects. Insulin played a role in the association of fat mass with TC and LDL (all P < 0.05). Mediation MR results indicated the causal effect of fat-free mass on coronary atherosclerosis via insulin (indirect effect, OR (odds ratio): 0.95 [95%CI, 0.92-0.98]) and adiponectin (OR: 0.96 [95%CI, 0.93-0.99]). Adiponectin also mediated the causal association of fat mass with coronary heart disease (OR: 1.06 [95%CI, 1.02-1.10]) and coronary atherosclerosis (OR: 1.05 [95%CI, 1.01, 1.09]). Leptin, adiponectin and insulin played roles in mediating the casual effects of body composition on triglyceride and high-density lipoprotein cholesterol.

CONCLUSIONS

Our findings suggest different body composition exert varying influences on lipids and atherosclerosis through distinct inflammatory biomarkers. The findings may be helpful in tailoring management of body composition based on inflammatory biomarkers with different lipid profiles.

Pleiotropic genetic association analysis with multiple phenotypes using multivariate response best-subset selection

Genetic pleiotropy refers to the simultaneous association of a gene with multiple phenotypes. It is widely distributed in the whole genome and can help to understand the common genetic mechanism of diseases or traits. In this study, a multivariate response best-subset selection (MRBSS) model based pleiotropic association analysis method is proposed. Different from the traditional genetic association model, the high-dimensional genotypic data are viewed as response variables while the multiple phenotypic data as predictor variables. Moreover, the response best-subset selection procedure is converted into an 0-1 integer optimization problem by introducing a separation parameter and a tuning parameter. Furthermore, the model parameters are estimated by using the curve search under the modified Bayesian information criterion. Simulation experiments show that the proposed method MRBSS remarkably reduces the computational time, obtains higher statistical power under most of the considered scenarios, and controls the type I error rate at a low level. The application studies in the datasets of maize yield traits and pig lipid traits further verifies the effectiveness.

Genetically proxied vitamin B12 and homocysteine in relation to life course adiposity and body composition

OBJECTIVE

Observational studies explore the association between vitamin B12 and obesity. However, causality is not reflected by such observations. We performed a bi-directional Mendelian randomization (MR) study to elucidate the causal relationship of vitamin B12 and homocysteine (Hcy) with life course adiposity and body composition.

METHODS

Two-sample MR analysis was conducted. Independent genetic variants associated with vitamin B12 and Hcy from large-scale genome-wide association studies (GWASs) were utilized as genetic instruments, and their causal effects on five life course adiposity phenotypes (birth weight, body mass index (BMI), childhood BMI, waist circumference, waist-to-hip ratio) and three body compositions (body fat mass, body fat-free mass, body fat percentage) were estimated from UK Biobank, other consortia, and large-scale GWASs. The inverse variance weighting (IVW, main analysis), bi-directional MR, and other six sensitivity MR analyses were performed.

RESULTS

Genetically proxied higher vitamin B12 concentrations were robustly associated with reduced BMI (Beta = -0.01, 95% confidence interval (CI) -0.016 to -0.004, P = 7.60E-04), body fat mass (Beta = -0.012, 95%CI -0.018 to -0.007, P = 1.69E-05), and body fat percentage (Beta = -0.005, 95%CI -0.009 to -0.002, P = 4.12E-03) per SD unit by IVW and other sensitivity analyses. Stratification analysis showed that these results remained significant in females and at different body sites (all P < 0.05 after Bonferroni correction). Bi-directional analyses showed no reverse causation.

CONCLUSIONS

This study provides strong evidence for the causal effect of vitamin B12 on adiposity. This gives novel clues for intervening obesity in public health and nutrition.

Bi-directional causal effect between vitamin B12 and non-alcoholic fatty liver disease: Inferring from large population data

OBJECTIVES

Many observational studies evaluate the association between vitamin B12 and non-alcoholic fatty liver disease (NAFLD). However, the causality of this association remains uncertain, especially in European populations. We conducted a bidirectional Mendelian randomization study to explore the association between vitamin B12 and NAFLD.

METHODS

Two-sample Mendelian randomization study was conducted. Summary statistics for vitamin B12 were acquired from a genome-wide association studies (GWAS) meta-analysis including 45,576 subjects. Summary-level data for NAFLD was obtained from a GWAS meta-analysis of 8,434 cases and 770,180 non-cases and another GWAS meta-analysis of 1,483 cases and 17,781 non-cases. Summary-level data for 4 enzymes including alkaline phosphatase (ALP), alanine aminotransferase (ALT), aspartate aminotransferase (AST), and gamma glutamyltransferase (GGT), was available from the UK Biobank. Inverse variance weighting (as main analysis), weighted median estimate, robust adjusted profile score, MR-Egger, and MR-PRESSO (sensitivity analyses) were performed to calculate causal estimates.

RESULTS

Genetically predicted higher vitamin B12 concentrations were consistently associated with an increased NAFLD in two sources. The combined odds ratio (OR) of NAFLD was 1.30 (95% confidence interval (CI), 1.13 to 1.48; p < 0.001) per SD-increase in vitamin B12 concentrations. Genetic liability to NAFLD was also positively associated with vitamin B12 concentrations (Beta 0.08, 95%CI, 0.01 to 0.16; p = 0.034). Sensitivity analyses also revealed consistent results. Genetically predicted vitamin B12 concentrations showed no significant association with liver enzymes.

CONCLUSION

The present study indicates that increased serum vitamin B12 concentrations may play a role in NAFLD risk. NAFLD also has a causal impact on elevated vitamin B12 concentrations in the circulation. Notably, vitamin B12 concentrations imply the levels of vitamin B12 in the circulation, and higher intake of vitamin B12 may not directly lead to higher levels of serum vitamin B12, instead the higher levels of vitamin B12 in the circulation may be caused by the dysregulation of the metabolism of this vitamin in this study. There exist bidirectional causal effects between serum vitamin B12 concentrations and risk of NAFLD in European individuals.

Association between homocysteine and nonalcoholic fatty liver disease: Mendelian randomisation study

BACKGROUND

Many observational studies explore the relationship between homocysteine (Hcy) and nonalcoholic fatty liver disease (NAFLD), whereas the causality of this association remains uncertain, especially in European populations. We performed a bidirectional Mendelian randomisation study to elucidate the causal association between Hcy and NAFLD. Furthermore, we explored the relationship of Hcy with liver enzymes, including alkaline phosphatase (ALP), alanine aminotransferase (ALT) and aspartate aminotransferase (AST).

METHODS

Two-sample Mendelian randomisation study was conducted. Summary statistics for Hcy were obtained from a genome-wide association studies (GWAS) meta-analysis comprising 44,147 subjects. Summary-level data for NAFLD were acquired from a GWAS meta-analysis of 8434 cases and 770,180 noncases and another GWAS meta-analysis of 1483 cases and 17,781 noncases. Summary-level data for three liver enzymes were available from the UK Biobank.

RESULTS

Genetic associations of Hcy concentrations with NAFLD and liver enzymes were observed. Genetically predicted higher Hcy concentrations were consistently associated with an increased NAFLD risk in two data sources. The combined odds ratio of NAFLD was 1.25 (95% confidence interval [CI], 1.05-1.45) per SD increase in Hcy concentrations. Genetically predicted higher Hcy concentrations showed significant association with ALP (Beta .69; 95% CI, 0.04-1.34), ALT (Beta 0.56; 95% CI, 0.15-0.97) and AST levels (Beta .57; 95% CI, 0.10-1.04). Genetic liability to NAFLD was not associated with Hcy concentrations.

CONCLUSIONS

This study has clinical implications as it indicates that increased Hcy concentrations increase the relevant liver enzymes and may play a role in NAFLD risk in European populations.

Inferring causal effects of homocysteine and B-vitamin concentrations on bone mineral density and fractures: Mendelian randomization analyses

OBJECTIVES

In the progress of bone metabolism, homocysteine (Hcy) and B vitamins play substantial roles. However, the causal associations of homocysteine, B-vitamin concentrations with bone mineral density (BMD), and fractures remain unclear. Therefore, we employed a two-sample Mendelian randomization (MR) design to infer the causal effects of Hcy and B vitamins on BMD and fractures.

METHODS

We selected instrumental variables from large genome-wide association studies (GWASs). Specifically, the exposures mainly included Hcy (sample size: 44,147), vitamin B12 (sample size: 45,576), folate (sample size: 37,465), and vitamin B6 (sample size: 1,864). The outcome variables included total body BMD (sample size: 66,628), heel BMD (sample size: 142,487), femoral neck BMD (sample size: 32,735), lumbar spine BMD (sample size: 28,498), and forearm BMD (sample size: 8143). Additionally, the total body BMD in several age strata was also included. Furthermore, the fractures of the forearm, femoral neck, lumbar spine, heel corresponding with the BMD regions, and femoral neck and lumbar spine BMD in men and women, separately, were added as additional outcomes. Two-sample MR approaches were utilized in this study. Inverse variance weighting (IVW) was adopted as the main analysis. MR-PRESSO, MR-Egger, the weighted median estimate, and multivariable MR were performed as sensitivity methods.

RESULTS

In the main analysis, Hcy concentrations have an inverse association with heel BMD (Beta = 0.046, 95% confidence interval (CI) -0.073 to -0.019, P = 9.59E-04) per SD unit. In addition, for one SD increase of vitamin B12, the total body BMD decreased 0.083 unit (95%CI -0.126 to -0.040, P = 1.65E-04). The trend was more obvious in age over 45 years (Beta = -0.135, 95%CI -0.203-0.067, P = 9.86E-05 for age 45-60; Beta = -0.074, 95%CI -0.141 to -0.007, P = 0.031 for age over 60 years). No association of B vitamins and Hcy levels with the risk of fractures and femoral neck and lumbar spine BMD in men and women was found in this study. Other sensitivity MR methods elucidated consistent results.

CONCLUSIONS

Our findings indicated that there exist the inversely causal effects of Hcy and vitamin B12 on BMD in certain body sites and age strata. These give novel clues for intervening bone-related diseases in public health and nutrition.

Causal effects of B vitamins and homocysteine on obesity and musculoskeletal diseases: A Mendelian randomization study

OBJECTIVES

Although homocysteine (Hcy) increases the risk of cardiovascular diseases, its effects on obesity and musculoskeletal diseases remain unclear. We performed a Mendelian randomization study to estimate the associations between Hcy and B vitamin concentrations and their effects on obesity and musculoskeletal-relevant diseases in the general population.

METHODS

We selected independent single nucleotide polymorphisms of Hcy (n = 44,147), vitamin B12 (n = 45,576), vitamin B6 (n = 1864), and folate (n = 37,465) at the genome-wide significance level as instruments and applied them to the studies of summary-level data for fat and musculoskeletal phenotypes from the UK Biobank study (n = 331,117), the FinnGen consortium (n = 218,792), and other consortia. Two-sample Mendelian randomization (MR) approaches were utilized in this study. The inverse variance weighting (IVW) was adopted as the main analysis. MR-PRESSO, MR-Egger, the weighted median estimate, bidirectional MR, and multivariable MR were performed as sensitivity methods.

RESULTS

Higher Hcy concentrations were robustly associated with an increased risk of knee osteoarthritis [odds ratio (OR) 1.119; 95% confidence interval (CI) 1.032-1.214; P = 0.007], hospital-diagnosed osteoarthritis (OR 1.178; 95% CI 1.012-1.37; P = 0.034), osteoporosis with pathological fracture (OR 1.597; 95% CI 1.036-2.46; P = 0.034), and soft tissue disorder (OR 1.069; 95% CI 1.001-1.141; P = 0.045) via an inverse variance weighting method and other MR approaches. Higher vitamin B12 levels were robustly associated with decreased body fat percentage and its subtypes (all P < 0.05). Bidirectional analyses showed no reverse causation. Multivariable MR analyses and other sensitivity analyses showed directionally similar results.

CONCLUSIONS

There exist significant causal effects of vitamin B12 in the serum and Hcy in the blood on fat and musculoskeletal diseases, respectively. These findings may have an important insight into the pathogenesis of obesity and musculoskeletal diseases and other possible future therapies.

A Novel Hierarchical Clustering Approach for Joint Analysis of Multiple Phenotypes Uncovers Obesity Variants Based on ARIC

Genome-wide association studies (GWASs) have successfully discovered numerous variants underlying various diseases. Generally, one-phenotype one-variant association study in GWASs is not efficient in identifying variants with weak effects, indicating that more signals have not been identified yet. Nowadays, jointly analyzing multiple phenotypes has been recognized as an important approach to elevate the statistical power for identifying weak genetic variants on complex diseases, shedding new light on potential biological mechanisms. Therefore, hierarchical clustering based on different methods for calculating correlation coefficients (HCDC) is developed to synchronously analyze multiple phenotypes in association studies. There are two steps involved in HCDC. First, a clustering approach based on the similarity matrix between two groups of phenotypes is applied to choose a representative phenotype in each cluster. Then, we use existing methods to estimate the genetic associations with the representative phenotypes rather than the individual phenotypes in every cluster. A variety of simulations are conducted to demonstrate the capacity of HCDC for boosting power. As a consequence, existing methods embedding HCDC are either more powerful or comparable with those of without embedding HCDC in most scenarios. Additionally, the application of obesity-related phenotypes from Atherosclerosis Risk in Communities via existing methods with HCDC uncovered several associated variants. Among these, UQCC1-rs1570004 is reported as a significant obesity signal for the first time, whose differential expression in subcutaneous fat, visceral fat, and muscle tissue is worthy of further functional studies.