Consistent Estimation in Mendelian Randomization with Some Invalid Instruments Using a Weighted Median Estimator

Association between depression and vascular aging: a comprehensive analysis of predictive value and mortality risks

BACKGROUND

Depression is a significant global health concern, projected to become the leading disease burden. Vascular burden has been implicated in the pathogenesis of depression. Conversely, whether depression independently influences the process of vascular aging is unknown. This study aims to investigate the mutual relationship between vascular age and depression.

METHODS

Utilizing data from the National Health and Nutrition Examination Survey (NHANES), the study included 27,764 participants after exclusions. Depression was assessed using the Patient Health Questionnaire (PHQ-9). Vascular aging was assessed by estimated pulse wave velocity (ePWV) and the heart age/vascular age (HVA) based on Framingham Risk Score (FRS). The study employed weighted logistic regression and Cox proportional hazards models to analyze the association between vascular age and depression as well as its mortality risk. Mendelian randomization was utilized to explore the causal associations.

RESULTS

Individuals with depression exhibited a higher risk of an advanced vascular age over their chronological age. Mendelian randomization analysis indicated a causal relationship between depression and arterial stiffness. A significant association was found between vascular age and depression incidence with odds ratios ranging from 1.10 to 1.38. As vascular age increased, the risk of mortality in individuals with depression increased by 22 % and 46 %, respectively.

LIMITATIONS

The study design limits the exploration of the dynamic relationship between changes in vascular age and depression due to the single timepoint measurement.

CONCLUSION

This study highlights the bidirectional relationship between depression and vascular age. Vascular age is a significant biomarker for the risk and prognosis of depression, while depression may contribute to vascular aging, which underscores the importance of integrated strategies for managing both vascular health and depression.

Causal associations between circulating immune cells and osteoarthritis: A bidirectional mendelian randomization study

PURPOSE

Osteoarthritis (OA) is a common degenerative joint disease, with its etiology remaining poorly understood. Our study aims to explore the causal associations between immune cells and OA, with the goal of generating a new perspective for targeted intervention strategies.

METHODS

A bidirectional two-sample Mendelian randomization (MR) analysis was performed to estimate the causality between multiple circulating immune cells and different sites of OA. The immune cell traits analyzed included the counts of circulating white blood cells (WBC), lymphocytes, monocytes, neutrophils, eosinophils, and basophils, as well as certain subsets of T and B lymphocytes. The OA types included were OA at any site, knee OA, hip OA, spine OA, thumb OA, and hand OA. Inverse-variance weighted (IVW), MR-Egger, weight median and weight mode were used to evaluate causal effects, with IVW being the main analysis method. Sensitivity analyses were conducted to assess heterogeneity and pleiotropy.

RESULTS

Our findings indicated that resting regulatory T cell (Treg) absolute counts (AC) were causally associated with an increased risk for spine OA [odds ratio (OR), 1.051; 95 % confidence interval (CI), 1.018-1.086; P=0.0005, PFDR=0.0350], and spine OA showed a positive causal relationship with the neutrophils count (OR, 1.104; 95 %CI, 1.032-1.181; P=0.0039, PFDR=0.0233). Besides, OA at any site was correlated with a rise in circulating eosinophils count (OR, 1.05; 95 %CI, 1.021-1.079; P=0.0007, PFDR=0.0041), while knee OA was associated with decreased total WBC (OR, 0.945; 95 %CI, 0.912-0.979; P=0.0016, PFDR=0.0048) and monocytes counts (OR, 0.958; 95 %CI, 0.934-0.982; P=0.0007, PFDR = 0.0041). No evidence of heterogeneity or horizontal pleiotropy was detected.

CONCLUSIONS

Our study has demonstrated the causal associations between multiple immune cells and diverse joint OA. These results highlight the intricate interplay between immune cells and OA, suggesting potential targets for therapeutic interventions to manage disease progression and alleviate symptoms.

Integrative analysis revealed novel putative therapeutic targets of ulcerative colitis: Role of creatine

BACKGROUND

Ulcerative colitis (UC) is becoming a global burden. Previous observational studies have unveiled associations between serum metabolites and UC, but their causal relationship remains unclear.

METHODS

Serum samples from patients and mice with UC were utilized for untargeted metabolomics to identify UC-associated metabolites. Then, a two-sample mendelian randomization (MR) analysis was employed to estimate their causal relationship. Finally, mice with chronic colitis induced by dextran sodium sulfate (DSS) and macrophages were used to evaluate the protective role of creatine and underlying mechanism.

RESULTS

16 serum metabolites showed associations with UC after adjusting for confounders and multiple testing. Among them, creatine exhibited a robust protective effect against UC (OR=0.39; 95 % CI=0.27-0.56). Significant reduction of creatine was also observed in mice with acute UC induced by DSS. The inverse variance weighted (IVW) MR analysis further confirmed a causal effect of creatine on UC risk (OR IVW=0.45; 95 % CI: 0.27-0.76). Furthermore, creatine supplementation could significantly suppress weight loss, disease activity index, mucosal damage and the infiltration of macrophages in mice with chronic colitis. Remarkably, creatine promoted the polarization of bone marrow-derived macrophage (BMDM) towards M2 phenotype and upregulated the expression of il-10, il-12 and arg-1.

CONCLUSIONS

This study revealed a causal relationship between creatine and UC. Creatine supplementation ameliorated chronic colitis by inhibiting the colonic infiltration of macrophages and promoting its polarization towards M2 phenotype. These results offer new insight into the pathogenesis of UC, emphasizing a potential protective role of creatine for UC.

Role of metabolites in mediating the effect of triacylglycerol on aplastic anemia

BACKGROUND

Observational studies have found a link between lipid metabolism disorders and aplastic anemia (AA). However, due to confounding variables and reverse causation, it is difficult to conclude such a causal link. The precise mechanism and potential implications of lipid metabolism disorder in AA remain unclear, necessitating further studies in this area.

METHOD

This study aimed to examine the causal relationship between 38 different subtypes of triacylglycerols and AA using two-sample Mendelian randomization (MR). Additionally, two-step MR analyses were conducted to investigate the mediating effects of vitamin A to oleoyl-linoleoyl-glycerol (18:1-18:2) ratio.

RESULTS

MR analysis showed that triacylglycerol (53:3) levels were positively associated with the risk of AA [inverse variance weighting (IVW): odds ratio (OR) = 1.131,95% confidence interval (CI):1.029-1.243, P = 0.011; Bayesian weighted MR (BWMR): OR = 1.137,95% CI:1.031-1.254, P = 0.010]. Triacylglycerol (53:3) level showed no inverse causality with AA (IVW:P = 0.834; BWMR:P = 0.349). Mediation analyses showed that increasing the vitamin A to oleoyl-linoleoyl-glycerol (18:1-18:2) ratio can decrease the risk of AA.

CONCLUSION

This study revealed the association between vitamin A to oleoyl-linoleoyl-glycerol (18:1-18:2) ratio, triacylglycerol (53:3) levels and AA, and indicated that lowering triacylglycerol (53:3) levels can reduce the risk of AA.

Absence of Causal Relationship Between Levels of Unsaturated Fatty Acids and ADHD: Evidence From Mendelian Randomization Study

OBJECTIVE

Previous research suggests a potential link between unsaturated fatty acids (UFAs) and ADHD, but the causal relationship remains uncertain. This study aims to investigate the causal association between ADHD and UFAs using Mendelian randomization (MR) analysis.

METHODS

Summary data from genome-wide association studies were used to estimate the concentration of circulating UFAs, including Monounsaturated Fatty Acids (MUFAs), Polyunsaturated Fatty Acids (PUFAs), Omega-3 PUFAs, Omega-6 PUFAs, Linoleic Acid (LA), and Docosahexaenoic Acid (DHA). Data from the Psychiatric Genomics Consortium, including both childhood and adult ADHD, were respectively used to examine the relationship between genetically predicted UFAs levels and ADHD. Various MR methods, including Inverse-variance weighted (IVW), MR Pleiotropy RESidual Sum and Outlier, MR-Egger, weighted median, and weighted mode, were employed to assess heterogeneity and pleiotropy.

RESULTS

The IVW revealed only nominal evidence suggesting a potential causal relationship between genetically predicted PUFAs (OR = 0.92, 95% CI [0.85, 0.99], p = .031), Omega-6 PUFAs (OR = 0.90, 95% CI [0.83, 0.98], p = .020), and LA levels (OR = 0.90, 95% CI [0.82, 0.98], p = .021) with childhood ADHD risk. However, after false discovery rate correction, the p-values for PUFAs, Omega-6 PUFAs, and LA levels all exceeded the threshold for significance. For adult ADHD, we did not find any significant associations between the six circulating UFA levels and adult ADHD.

CONCLUSION

Our findings do not support a causal relationship between UFAs levels and ADHD. This suggests that UFAs supplements may not be effective in improving ADHD symptoms and importantly, it appears that UFAs levels may not have a long-term effect on ADHD.

Role of blood lipids in mediating the effect of dietary factors on gastroesophageal reflux disease: a two-step mendelian randomization study

BACKGROUND

Growing studies have indicated an association between dietary factors and gastroesophageal reflux disease (GERD). However, whether these associations refer to a causal relationship and the potential mechanism by which dietary factors affect GERD is still unclear.

METHODS

A two-step mendelian randomization analysis was performed to obtain causal estimates of dietary factors, blood lipids on GERD. Independent genetic variants associated with 13 kinds of dietary factors and 5 kinds of blood lipids at the genome-wide significance level were selected as instrumental variables. The summary statistics for GERD were obtained from European Bioinformatics Institute, including 129,080 cases and 473,524 controls. Inverse variance weighted was utilized as the main statistical method. MR-Egger intercept test, Cochran's Q test, and leave-one-out analysis were performed to evaluate possible heterogeneity and pleiotropy. And the potential reverse causality was assessed using Steiger filtering.

RESULTS

The results of the inverse variance weighted method indicated that genetically predicted total pork intake (OR = 2.60, 95% CI: 1.21-5.58, p = 0.0143), total bread intake (OR = 0.68, 95% CI: 0.46-0.99, p = 0.0497), total cereal intake (OR = 0.42, 95% CI: 0.31-0.56, p = 2.98E-06), and total cheese intake (OR = 0.41, 95% CI: 0.27-0.61, p = 1.06E-05) were associated with the risk of GERD. Multivariable Mendelian randomization analysis also revealed a negative association between total cereal intake, total cheese intake and the risk of GERD, but the effect of total pork intake and total bread intake on GERD disappeared after adjustment of smoking, alcohol consumption, use of calcium channel blockers, BMI, physical activity levels, and biological sex (age adjusted). Furthermore, the concentration of low-density lipoprotein cholesterol (LDL-C) is negatively correlated with total cheese intake, which mediates the impact of total cheese intake on GERD. The proportion mediated by LDL-C is 2.27% (95%CI: 1.57%, 4.09%).

CONCLUSIONS

This study provides evidence that an increase in total cereal intake and total cheese intake will decrease the risk of GERD. Additionally, LDL-C mediates the causal effect of total cheese intake on GERD. These results provide new insights into the role of dietary factors and blood lipids in GERD, which is beneficial for disease prevention.

Insomnia and sleep duration for kidney function: Mendelian randomization study

OBJECTIVES

Extensive researches highlight the detrimental impact of sleep disorders such as insomnia and insufficient sleep duration on kidney function. However, establishing a clear causal relationship between insomnia, sleep duration, and kidney function remains challenging. This study aims to estimate this relationship using Mendelian randomization (MR).

METHODS

Independent genetic variants strongly associated with insomnia (N = 462,341) and sleep duration (N = 460,099) were selected as instrumental variables from corresponding genome-wide association studies (GWAS). Kidney function parameters, including serum creatinine, estimated glomerular filtration rate by cystatin C (eGFRcys), acute renal failure (ARF), chronic renal failure (CRF), kidney injury molecule-1, neutrophil gelatinase associated lipocalin, microalbuminuria, cystatin C, and β2 microglobulin, were derived from GWAS databases. A two-sample MR study was conducted to assess the causal relationship between sleep disorders and kidney function, and multivariable MR was used to identify potential mediators. The inverse-variance weighted was used as the primary estimate.

RESULTS

MR analysis found robust evidence indicating that insomnia and short sleep duration were associated with an increased risk of elevated serum creatinine, regardless of adjusting for obesity. Causal links between sleep duration and eGFRcys or cystatin C were also identified. While genetically predicted insomnia and sleep duration were found to potentially impact ARF, CRF, microalbuminuria, and β2 microglobulin, the p-values in multivariable MR analysis became nonsignificant. No pleiotropy was detected.

CONCLUSIONS

This study demonstrates a causal impact of insomnia on the risk of elevated serum creatinine and a positive effect of sleep duration on serum creatinine, eGFRcys, and cystatin C. Our findings also suggest their potential indirect effects on ARF, CRF, microalbuminuria, and β2 microglobulin mediated by obesity.

Exploring the relationship between creatine supplementation and renal function: insights from Mendelian randomization analysis

BACKGROUND

Creatine supplementation is ubiquitously consumed by fitness enthusiasts due to its perceived advantages in enhancing athletic performance. Although there is an increasing concern within this demographic regarding its possible impact on renal function, there is still a lack of rigorous scientific investigations into this alleged association.

METHODS

Data were collected through an online survey on the participants' demographics, creatine usage and concerns related to renal function. The reliability and validity of the survey were assessed using SPSS software. A total of 1129 participants responded to the survey, and chi-square tests were utilized for data analysis. To explore the potential association between creatine levels (as the exposure) and renal function (as the outcome), we utilized open-access genetic databases, and Mendelian randomization (MR) techniques were used to confirm this correlation.

RESULTS

Chi-square analysis revealed no significant association between creatine usage and renal function among the participants. Our MR analysis further supported this finding, demonstrating no significant association between creatine levels and six indicators assessing renal function (IVW, all with p values exceeding 0.05). Similar p values were consistently observed across other MR methods, confirming the absence of a statistical correlation.

CONCLUSIONS

This MR study offers compelling evidence indicating that creatine levels are not statistically associated with renal function, suggesting the potential to alleviate concerns within the fitness community and emphasizing the significance of evidence-based decision-making when considering nutritional supplementation.

Causal effects between gut microbiota and endometriosis: a two-sample Mendelian randomisation study

BACKGROUND

Previous observational evidence has indicated the potential involvement of the gut microbiota (GM) in the development of endometriosis. However, the causal relationship of the association remains to be investigated.

METHOD

Genome-wide association study (GWAS) data of GM was obtained from the MiBioGen consortium, and GWAS for endometriosis data was from the FinnGen consortium. Initially, a two-sample Mendelian randomisation (MR) analysis was performed to identify specific bacteria associated with endometriosis. Inverse variance-weighted (IVW) was used as the main MR analysis to infer causal relationships. The other four popular MR methods including MR-Egger regression, weighted mode, weighted median, and simple mode were used for secondary confirmation. Subsequently, these selected bacteria were employed as exposure to investigate their causal effects on six sub-types of endometriosis. Furthermore, reverse MR analysis was implemented to evaluate the reverse causal effects. Cochran's Q statistics was used to test the heterogeneity of instrumental variables (IVs); MR-Egger regression was used to test horizontal pleiotropy; MR-PRESSO and leave-one-out sensitivity analysis were applied to find significant outliers.

RESULT

A total of 1131 single nucleotide polymorphisms (SNPs) were collected as IVs for 196 GM taxa with endometriosis as the outcome. We identified 12 causal relationships between endometriosis and GM taxa including 1 phylum, 3 families, 2 orders, and 6 genera (Rikenellaceae RC9 gut group, Eubacterium ruminantium group, Faecalibacterium, Peptococcus, Clostridium sensu stricto 1, and Ruminococcaceae UCG005). Utilizing the Bonferroni method, we identified phylum Cyanobacteria as the strongest associated GM taxa. Subsequently, 6 significant causal effects were uncovered between the 12 selected specific GM and 6 sub-types of endometriosis. Meanwhile, no reverse causal relationship was found. Further, no horizontal pleiotropy and no significant outliers were detected in the sensitive analysis.

CONCLUSIONS

This MR analysis revealed significant causal effects between GM and endometriosis and phylum Cyanobacteria had the strongest association.

Mendelian randomization analysis of the association between childhood overweight or obesity and gestational diabetes mellitus

OBJECTIVE

To investigate the association between childhood overweight or obesity and gestational diabetes mellitus (GDM).

METHODS

Data were sourced from the Genome-Wide Association Studies database on childhood body mass index (BMI), with 39 620 samples and 8 173 382 single-nucleotide polymorphisms (SNPs), and GDM, with 143 441 samples, including 12 332 GDM cases and 20 149 608 SNPs. Mendelian randomization (MR) was conducted, including inverse variance weighting (IVW), MR-Egger regression, and the weighted median method. Statistical heterogeneity among SNPs was assessed using Cochran's Q test. MR-Egger's intercept, the MR-Pleiotropy RESidual Sum and Outlier (PRESSO) test, and funnel plots were used to evaluate pleiotropy. The leave-one-out method tested the robustness of the IVW results by excluding individual SNPs.

RESULTS

Fifteen SNPs highly related to childhood BMI were identified. IVW analysis indicated that higher childhood BMI is a significant risk factor for GDM (odds ratio 1.50 [95% confidence interval 1.20-1.87]; p < 0.001). The direction of the β value derived from the weighted median method analysis was consistent with that from the IVW analysis. Cochran's Q test showed statistical heterogeneity among SNPs highly related to childhood BMI (p = 0.001), thus prioritizing IVW analysis results. The MR-Egger regression intercept, MR-PRESSO test, and funnel plot analyses demonstrated no horizontal pleiotropy among SNPs highly related to childhood BMI. The leave-one-out analysis indicated that the MR analysis results were largely unchanged after the exclusion of individual SNPs.

CONCLUSION

Elevated childhood BMI is associated with an increased risk of developing GDM, underscoring the need to address childhood obesity as a preventive strategy. Effective interventions to reduce childhood obesity could be crucial in mitigating this risk.

Causal association and shared genetics between telomere length and COVID-19 outcomes: New evidence from the latest large-scale summary statistics

Background

Observational studies suggested that leukocyte telomere length (LTL) is shortened in COVID-19 patients. However, the genetic association and causality remained unknown.

Methods

Based on the genome-wide association of LTL (N = 472,174) and COVID-19 phenotypes (N = 1086,211-2597,856), LDSC and SUPERGNOVA were used to estimate the genetic correlation. Cross-trait GWAS meta-analysis, colocalization, fine-mapping analysis, and transcriptome-wide association study were conducted to explore the shared genetic etiology. Mendelian randomization (MR) was utilized to infer the causality. Upstream and downstream two-step MR was performed to investigate the potential mediating effects.

Results

LDSC identified a significant genetic association between LTL and all COVID-19 phenotypes (rG < 0, p < 0.05). Six significant regions were observed for LTL and COVID-19 susceptibility and hospitalization, respectively. Colocalization analysis found rs144204502, rs34517439, and rs56255908 were shared causal variants between LTL and COVID-19 phenotypes. Numerous biological pathways associated with LTL and COVID-19 outcomes were identified, mainly involved in -immune-related pathways. MR showed that longer LTL was significantly associated with a lower risk of COVID-19 severity (OR [95% CI] = 0.81 [0.71-0.92], p = 1.24 ×10-3) and suggestively associated with lower risks of COVID-19 susceptibility (OR [95% CI] = 0.96 [0.92-1.00], p = 3.44 ×10-2) and COVID-19 hospitalization (OR [95% CI] = 0.89 [0.80-0.98], p = 1.89 ×10-2). LTL partially mediated the effects of BMI, smoking, and education on COVID-19 outcomes. Furthermore, six proteins partially mediated the causality of LTL on COVID-19 outcomes, including BNDF, QPCT, FAS, MPO, SFTPB, and APOF.

Conclusions

Our findings suggested that shorter LTL was genetically associated with a higher risk of COVID-19 phenotypes, with shared genetic etiology and potential causality.

Genetic association between celiac disease and chronic kidney disease: a two-sample Mendelian randomization study

OBJECTIVE

A two-sample Mendelian randomization (MR) analysis was performed to elucidate the causal impact of celiac disease on the risk of chronic kidney disease (CKD).

METHODS

The study comprised data from three genome-wide association studies involving individuals of European ancestry. The study groups included participants with celiac disease (n = 24,269), CKD (n = 117,165), and estimated glomerular filtration rate levels based on serum creatinine (eGFRcrea, n = 133,413). We employed four widely recognized causal inference algorithms: MR-Egger, inverse variance weighted (IVW), weighted median, and weighted mode. To address potential issues related to pleiotropy and overall effects, MR-Egger regression and the MR-PRESSO global test were performed. Heterogeneity was assessed using Cochran's Q test.

RESULTS

We identified 14 genetic variants with genome-wide significance. The MR analysis provided consistent evidence across the various methodologies, supporting a causal relationship between celiac disease and an elevated risk of CKD (odds ratio (OR)IVW = 1.027, p = 0.025; ORweighted median = 1.028, P = 0.049; ORweighted mode = 1.030, p = 0.044). Furthermore, we observed a causal link between celiac disease and a decreased eGFRcrea (ORIVW = 0.997, P = 2.94E-06; ORweighted median = 0.996, P = 1.68E-05; ORweighted mode = 0.996, P = 3.11E-04; ORMR Egger = 0.996, P = 5.00E-03). We found no significant evidence of horizontal pleiotropy, heterogeneity, or bias based on MR-Egger regression, MR-PRESSO, and Cochran's Q test.

CONCLUSION

The results of this study indicate a causal relationship between celiac disease and an increased risk of CKD.

Association Between Periodontitis and Preeclampsia: A Bidirectional Mendelian Randomisation Analysis

OBJECTIVES

Studies have increasingly focussed on the relationship between periodontitis (PD) and preeclampsia (PE). However, conclusions have not been consistent, and it is unclear whether any causal relationship exists between them and whether causality is bidirectional. This study employed Mendelian randomisation (MR) analysis to investigate the potential bidirectional causal relationship between PD and PE.

METHODS

Genetic variants strongly linked to PD (17,353 cases and 28,210 controls), chronic periodontitis (CP; 1817 cases and 2215 controls), aggressive periodontitis (AgP; 851 cases and 6580 controls), and PE (7212 cases and 194,266 controls) in the genome-wide association study (GWAS) of European ancestry were used as instrumental variables (IVs). Inverse variance weighting (IVW) served as the primary method for causal inference. MR Pleiotropy RESidual Sum and Outlier (MR-PRESSO) was utilised to analyse horizontal pleiotropy. Cochrane Q tests and leave-one-out analyses were used to assess heterogeneity and stability amongst IVs.

RESULTS

The MR analysis revealed no causal impacts of PD or its 2 subtypes-CP and AgP-on PE. Similarly, no significant causal effect of PE on PD was found in the reverse-MR analysis (IVW odds ratio, 0.97; 95% confidence interval, 0.91-1.05; P = .58). The findings from MR-Egger, weighted median, weighted mode, and the simple modelling approaches, as well as the pleiotropy and sensitivity analyses, aligned with those of the IVW method.

CONCLUSIONS

The MR analysis suggests no bidirectional causal relationship between PD and PE; hence, PD and PE might not increase or prevent the risk of one other.

CLINICAL RELEVANCE

Genetically, periodontitis or its subtypes chronic periodontitis and aggressive periodontitis may not require specific clinical attention to prevent the development of preeclampsia.

Exploring the shared genetic basis of major depressive disorder and frailty

BACKGROUND

Major depressive disorder (MDD) and frailty impose substantial health and economic burdens. MDD is recognized as a significant risk factor for frailty, but the genetic associations between these conditions remain unclear. This study investigates the genetic correlation, shared pleiotropic loci, causal relationships, and comorbid genes between MDD and frailty.

METHODS

The genetic correlation between MDD and frailty was assessed using linkage disequilibrium score regression (LDSC) based on data from genome-wide association studies (GWAS). A detailed analysis was performed to identify shared pleiotropic loci and causal relationships through cross-phenotype association tests and Mendelian randomization. Additionally, tissue enrichment analysis was conducted using stratified LDSC, gene-based associations with both conditions were assessed using Multimarker Analysis of Genomic Annotation (MAGMA), and pathway analysis of comorbid genes was performed using the g: GOSt tool.

RESULTS

Our findings revealed a significant positive genetic correlation between MDD and frailty (rg = 0.65, P = 1.49E-219). We identified 57 shared risk SNPs between the two conditions, including 6 novel SNPs. Mendelian randomization analyses indicated robust causal effects of MDD on frailty and vice versa. Furthermore, we observed tissue-specific heritability enrichment in 9 brain tissues. By combining MAGMA and CPASSOC analyses, we identified 10 comorbid genes associated with both MDD and frailty, primarily involved in synapse formation, modulation, plasticity, and desaturase activity.

CONCLUSION

This study provides strong evidence for a shared genetic basis between MDD and frailty. The identification of comorbid genes offers new insights into the mechanisms underlying the relationship between these conditions.

Causal associations between kidney function and aortic valve stenosis: a bidirectional Mendelian randomization analysis

BACKGROUND

Aortic valve stenosis (AVS) is currently the most common heart valve disease. The results of observational studies on the incidence of AVS in the renal dysfunction population are contradictory due to the short follow-up period and different diagnostic criteria, etc. This study aimed to explore the causal relationship between kidney function and AVS using Mendelian randomization (MR) analysis.

METHODS

We acquired summary statistics of estimated glomerular filtration rate (eGFR) and chronic kidney disease (CKD) from the CKDGen Consortium and a study on AVS from the FinnGen biobank. Univariate and multivariable MR analyses were conducted to evaluate the causal associations. The MR-Egger intercept and MR-PRESSO Global test were applied to assess the pleiotropic effects. The heterogeneity of MR results was tested by Cochran's Q statistic. Moreover, the Bonferroni and FDR corrections were performed for multiple tests.

RESULTS

Genetically predicted decreased eGFR may be associated with a raised risk of AVS (OR = 0.045, p = 1.317e-04 by IVW; OR = 0.002, p = 0.004 by MR-Egger, OR = 0.091, p = 0.057 by WM). The causal association still established after multiple comparisons. Quality control analyses indicated the absence of heterogeneity and pleiotropy in our MR research. In addition, the causality of eGFR and AVS remained significant in multivariable MR analysis after adjusting BMI, hypertension, T2DM, LDL-C, and smoking.

CONCLUSION

Our MR study discovered that reduced eGFR may be a causative risk factor for AVS. In addition, the evidence did not support a significant causal association of AVS on kidney function.

Decoding the genetic landscape of juvenile dermatomyositis: insights from phosphorylation-associated single nucleotide polymorphisms

Genome-wide association studies (GWASs) have identified genetic susceptibility loci associated with juvenile dermatomyositis (JDM). Single nucleotide polymorphisms related to phosphorylation (phosSNPs) are critical nonsynonymous mutations exerting substantial influence on gene expression regulation. The aim of this study was to identify JDM susceptibility genes in the GWAS loci by the use of phosSNPs. We explored quantitative trait loci (QTLs) among the phosSNPs associated with JDM using data from eQTL (bulk tissues and single-cell) and pQTL studies. For gene expression and protein levels significantly influenced by JDM-associated phosSNPs, we assessed their associations with JDM through MR analyses. Additionally, we conducted differential expression gene analyses, incorporating single-cell transcriptomic profiling of 6 JDM cases and 11 juvenile controls (99,396 cells). We identified 31 phosSNPs situated in the 6p21 locus that were associated with JDM. Half of these phosSNPs showed effects on gene expression in various cells and circulating protein levels. In MR analyses, we established associations between the expression levels of pivotal JDM-associated genes, including MICB, C4A, HLA-DRB1, HLA-DRB5, and PSMB9, in skin, muscle, or blood cells and circulating levels of C4A, with JDM. Utilizing single-cell eQTL data, we identified a total of 276 association signals across 14 distinct immune cell types for 28 phosSNPs. Further insights were gained through single-cell differential expression analysis, revealing differential expression of PSMB9, HLA-A, HLA-B, HLA-C, HLA-DPB1, HLA-DQA1, HLA-DQB1, and HLA-DRB1 in immune cells. The present study pinpointed phosSNPs within susceptibility genes for JDM and unraveled the intricate relationships among these SNPs, gene expression levels, and JDM.

Recent advances in the application of Mendelian randomization to chronic kidney disease

OBJECTIVE

Chronic kidney disease (CKD) is a condition influenced by both genetic and environmental factors and has been a focus of extensive research. Utilizing Mendelian randomization, researchers have begun to untangle the complex causal relationships underlying CKD. This review delves into the advances and challenges in the application of MR in the field of nephrology, shifting from a mere summary of its principles and limitations to a more nuanced exploration of its contributions to our understanding of CKD.

METHODS

Key findings from recent studies have been pivotal in reshaping our comprehension of CKD. Notably, evidence indicates that elevated testosterone levels may impair renal function, while higher sex hormone-binding globulin (SHBG) levels appear to be protective, predominantly in men. Surprisingly, variations in plasma glucose and glycated hemoglobin levels seem unaffected by genetically induced changes in the estimated glomerular filtration rate (eGFR), suggesting an independent pathway for renal function impairment.

RESULTS

Furthermore, lifestyle factors such as physical activity and socioeconomic status emerge as significant influencers of CKD risk and kidney health. The relationship between sleep duration and CKD is nuanced; short sleep duration is linked to increased risk, while long sleep duration does not exhibit a clear causal effect. Additionally, lifestyle factors, including diet, exercise, and mental wellness activities, play a crucial role in kidney health. New insights also reveal a substantial causal connection between both central and general obesity and CKD onset, while no significant links were found between genetically modified LDL cholesterol or triglyceride levels and kidney function.

CONCLUSION

This review not only presents the recent achievements of MR in CKD research but also illuminates the path forwards, underscoring critical unanswered questions and proposing future research directions in this dynamic field.

Multi-omics combined to investigate potential druggable therapeutic targets for stroke: A systematic Mendelian randomization study and transcriptome verification

OBJECTIVE

Stroke is a highly prevalent and disabling disease whose disease mechanisms are not fully understood. The discovery of disease-associated proteins with genetic evidence of pathogenicity provides an opportunity to identify new therapeutic targets.

METHOD

We examined the observed and causal associations of thousands of plasma and inflammatory proteins that were measured using affinity-based proteomic assays. First, we pooled >3000 relevant proteins using a fixed-effects meta-analysis of 2 population-based studies involving 48,383 participants, then investigated the causal effects of stroke and its subtype-associated proteins by forward Mendelian randomization using cis-protein quantitative locus genetic tools identified from genome-wide association studies of these >48,000 individuals. To improve the accuracy of causal estimation, we implemented a systematic Mendelian randomization model that accounts for cascading imbalances between instruments and tested the robustness of causal estimation through multi-method analyses. To further validate the hypothesis that ginsenoside Rg1 monomer acts on the five protein targets screened for drug-targeted regulation, we conducted a comparative analysis of the mRNA (gene) expression levels of a limited number of genes in the brain tissues of different groups of SD rats. The druggability of the candidate proteins was investigated and the mechanism of action and potential targeting side effects were explored by Phenome-wide MR.

RESULTS

Six circulating proteins were identified to have a significant genetic association with stroke (PFDR < 0.05). For example, in patients with cardioembolic stroke, higher genetically predicted APRT was associated with a lower risk of cardioembolic stroke (ORivw [95 % CI] = 0.641 [0.517, 0.795]; P = 5.25 × 10-5, ORSMR [95 % CI] = 0.572, [0.397, 0.825], PSMR = 0.003). Mediation analyses suggested that atrial fibrillation, angina pectoris, and heart failure may mediate the association of CD40L, LIFR, and UPA with stroke. Molecular docking revealed promising interactions between the identified proteins and glycosides. Transcriptomic sequencing in animal models indicated that ginsenoside Rg1 may act through APRT, IL15RA, and VSIR pathways, with APRT showing significant variability in mRNA sequencing expression. Phenome-wide MR of the six target proteins showed an overwhelming predominance of PFDR > 0.05, indicating less toxicity.

CONCLUSIONS

The present study provides genetic evidence to support the potential efficacy of targeting the three druggable protein targets for the treatment of stroke. This is achieved by triangulating population genomic and proteomic data. Furthermore, the study validates the pathway mechanisms by which APRT, IL15RA, and VSIR dock ginsenoside Rg1 in animal models. This will help to prioritize stroke drug development.

Mitochondrial DNA copy number and the risk of autoimmune diseases: A Mendelian randomization study with meta-analysis

Background

Mitochondrial DNA plays a crucial role in the pathophysiology of autoimmune diseases (ADs). However, the association between mitochondrial DNA copy number (mtDNA-CN) and ADs risk is controversial. In this study, Mendelian randomization (MR) analysis and meta-analysis were performed using three sets of independent instrumental variables (IVs) to investigate the potential association between mtDNA-CN and 20 types of ADs.

Methods

The three sets of IVs were drawn primarily from participants in the UK Biobank and the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium using different methods. Outcome data for ADs were investigated using summary statistics from the FinnGen cohort. The potential causal associations were assessed using inverse-variance weighting (IVW), MR-Egger, and weighted median methods. Sensitivity analysis and the Steiger test were used to verify the robustness of the MR estimates. In addition, a meta-analysis was conducted to pool the results from three IV groups.

Results

Overall, genetically predicted mtDNA-CN was not associated with ADs risk (OR = 1.046, 95 % CI: 0.964-1.135, P = 0.283). However, subgroup analyses showed positive causal associations of mtDNA-CN with autoimmune hypothyroidism (OR = 1.133, 95 % CI: 1.016-1.262, P = 0.024) and rheumatoid arthritis (OR = 1.219, 95 % CI: 1.028-1.445, P = 0.023). In contrast, there was no causal association between mtDNA-CN and atopic dermatitis as well as psoriasis, ulcerative colitis, adult-onset Still disease, type1 diabetes, Crohn disease, sarcoidosis, ankylosing spondylitis, multiple sclerosis, autoimmune hyperthyroidism, primary sclerosing cholangitis, systemic lupus erythematosus, systemic sclerosis, alopecia areata, myasthenia gravis, Guillain-Barre syndrome, dermatopolymyositis, and vitiligo.

Conclusions

This MR analysis showed mtDNA-CN is causally associated with an increased risk of autoimmune hypothyroidism and rheumatoid arthritis at the genetic level. The findings have important implications for the use of mtDNA-CN as a biomarker for risk assessment of autoimmune hypothyroidism and rheumatoid arthritis in clinical practice.

Causal association between metabolites and upper gastrointestinal tumors: A Mendelian randomization study

Upper gastrointestinal (UGI) tumors, notably gastric cancer (GC) and esophageal cancer (EC), are significant global health concerns due to their high morbidity and mortality rates. However, only a limited number of metabolites have been identified as biomarkers for these cancers. To explore the association between metabolites and UGI tumors, the present study conducted a comprehensive two‑sample Mendelian randomization (MR) analysis using publicly available genetic data. In the present study, the causal relationships were examined between 1,400 metabolites and UGI cancer using methods such as inverse variance weighting and weighted medians, along with sensitivity analyses for heterogeneity and pleiotropy. Functional experiments were conducted to validate the MR results. The analysis identified 57 metabolites associated with EC and 58 with GC. Key metabolites included fructosyllysine [EC: Odds ratio (OR)=1.450, 95% confidence interval (CI)=1.087‑1.934, P=0.011; GC: OR=1.728, 95% CI=1.202‑2.483, P=0.003], 2'‑deoxyuridine to cytidine ratio (EC: OR=1.464, 95% CI=1.111‑1.929, P=0.007; GC: OR=1.464, 95% CI=1.094‑1.957, P=0.010) and carnitine to protonylcarnitine (C3) ratio (EC: OR=0.655, 95% CI=0.499‑0.861, P=0.002; GC: OR=0.664, 95% CI=0.486‑0.906, P=0.010). Notably, fructosyllysine levels and the 2'‑deoxyuridine to cytidine ratio were identified as risk factors for both EC and GC, while the C3 ratio served as a protective factor. Functional experiments demonstrated that fructosyllysine and the 2'‑deoxyuridine to cytidine ratio promoted the proliferation of EC and GC cells, whereas carnitine inhibited their proliferation. In conclusion, the present findings provide insights into the causal factors and biomarkers associated with UGI tumors, which may be instrumental in guiding targeted dietary and pharmacological interventions, thereby contributing to the prevention and treatment of UGI cancer.

The role of moderate to vigorous physical activity level and number of treatments/medications in mediating the effect of body mass index on diabetic nephropathy: a Mendelian randomization study

BACKGROUND

Body mass index (BMI) is associated with diabetic nephropathy (DN). However, the mediator factors in the BMI-DN effects remain unclear.

METHODS

Univariate and multivariate Mendelian randomization (MR) analysis were performed to estimate the association between six lifestyles (moderate to vigorous physical activity levels, years of schooling, BMI, nap during day, number of treatments/medications taken and coffee intake) and DN. MR Egger, Weighted median, Simple mode, and Weighted mode was supplemental methods to Inverse variance weighted. Sensitivity analysis included heterogeneity test, horizontal pleiotropy test, and Leave-One-Out. Additionally, mediation MR was conducted to evaluate the mediating role of lifestyles between BMI and DN. Finally, functional enrichment analysis based on the mediation MR results was performed.

RESULTS

univariate and multivariate Mendelian randomization (MR) analysis were performed to estimate the association between six lifestyles (moderate to vigorous physical activity levels, years of schooling, BMI, nap during day, number of treatments/medications taken and coffee intake) and DN. MR Egger, Weighted median, Simple mode, and Weighted mode was supplemental methods to Inverse variance weighted. Sensitivity analysis included heterogeneity test, horizontal pleiotropy test, and Leave-One-Out. Additionally, mediation MR was conducted to evaluate the mediating role of lifestyles between BMI and DN. Finally, functional enrichment analysis based on the mediation MR results was performed.

CONCLUSION

our results supported mediation role of vigorous physical activity level and number of treatments/medications in BMI-DN effects.

A Mendelian randomization study: physical activities and chronic kidney disease

Increasing evidence has shown that physical activity is related to a lower risk of chronic kidney disease (CKD), thus indicating a potential target for prevention. However, the causality is not clear; specifically, physical activity may protect against CKD, and CKD may lead to a reduction in physical activity. Our study examined the potential bidirectional relationship between physical activity and CKD by using a genetically informed method. Genome-wide association studies from the UK Biobank baseline data were used for physical activity phenotypes and included 460,376 participants. For kidney function (estimated Glomerular Filtration Rate (eGFR) and CKD, with eGFR < 60 mL/min/1.73 m2), CKDGen Consortium data were used, which included 480,698 CKD participants of European ancestry. Mendelian randomization (MR) analysis was used to determine the causal relationship between physical activities and kidney function. Two-sample MR genetically predicted that heavy DIY (do it yourself) (e.g., weeding, lawn mowing, carpentry, and digging) decreased the risk of CKD (odds ratio [OR] = 0.287, 95% CI = 0.117-0.705, p = 0.0065) and improved the level of eGFR (β = 0.036, 95% CI = 0.005-0.067, p = 0.021). The bidirectional MR showed no reverse causality. It is worth noting that other physical activities, such as walking for pleasure, strenuous sports, light DIY (e.g., pruning and watering the lawn), and other exercises (e.g., swimming, cycling, keeping fit, and bowling), were not significantly correlated with CKD and eGFR. This study used genetic data to provide reliable and robust causal evidence that heavy physical activity (e.g., weeding, lawn mowing, carpentry, and digging) can protect kidney function and further lower the risk of CKD.

Depression and the risk of non-alcohol fatty liver disease: Results from a cross-sectional study and a Mendelian randomization analysis

BACKGROUND

Previous studies have suggested that psychiatric factors may be pathogenic for NAFLD. However, the association between depression and NAFLD is not been consistent, and whether depression plays a causal role in the development of NAFLD remains unclear.

METHODS

We extracted data from the National Health and Nutrition Examination Survey (NHANES) 2017-2018 to assess the correlation between depression and NAFLD risk. Based on previous genome-wide association studies (GWAS) meta-analyses on NAFLD and depression, we performed a Mendelian randomization (MR) analysis to explore the causal effect of depression on NAFLD. The primary analysis method used in the MR analysis was inverse variance weighted.

RESULTS

We ultimately extracted the data from 3878 individuals in the NHANES database to perform the cross-sectional study. Multivariable-adjusted logistic regression showed that depressed individuals had a higher risk of NAFLD than controls (odds ratio [OR] 1.33, 95 % CI 1.03-1.72, p = 0.027) among women. Based on GWAS data, we included 36 genetic variants as instrumental variables to estimate the causal effect of depression on NAFLD risk. The MR analysis revealed a causal association between genetically predicted depression and an increased risk of NAFLD (OR = 1.504, 95 % CI 1.13-2.00, p = 0.005).

LIMITATIONS

The consistency of these findings in Eastern populations requires further longitudinal studies.

CONCLUSIONS

This cross-sectional study suggested that depression might increase the risk of NAFLD in women. The MR analysis demonstrated that there exists a causal association between genetically predicated depression and NAFLD risk.

Appraising non-linear association between pre-diagnostic platelet counts and cancer survival outcomes: observational and genetic analysis

Previous studies have reported inconsistent associations between platelet count (PLT) and cancer survival. However, whether there is linear causal effect merits in-depth investigations. We conducted a cohort study using the UK Biobank and a two-sample Mendelian randomization (MR) analysis. PLT levels were measured prior to cancer diagnosis. We adopted overall survival (OS) as the primary outcome. Cox models were utilized to estimate the effects of PLTs on survival outcomes at multiple lag times for cancer diagnosis. We employed 34 genetic variants as PLT proxies for MR analysis. Linear and non-linear effects were modeled. Prognostic effects of gene expression harboring the instrumental variants were also investigated. A total of 65 471 cancer patients were included. We identified a significant association between elevated PLTs (per 100 × 109/L) and inferior OS (HR: 1.07; 95% CI: 1.04-1.10; p < .001). Similar significant associations were observed for several cancer types. We further observed a U-shaped relationship between PLTs and cancer survival (p < .001). Our MR analysis found null evidence to support a causal association between PLTs and overall cancer survival (HR: 1.000; 95% CI: 0.998-1.001; p = .678), although non-linear MR analysis unveiled a potential greater detrimental effect at lower PLT range. Expression of eleven PLT-related genes were associated with cancer survival. Early detection of escalated PLTs indicated possible occult cancer development and inferior subsequent survival outcomes. The observed associations could potentially be non-linear. However, PLT is less likely to be a promising therapeutic target.

The causal impact of gut microbiota on circulating adipokine concentrations: a two-sample Mendelian randomization study

PURPOSE

Evidence from previous experimental and observational research demonstrates that the gut microbiota is related to circulating adipokine concentrations. Nevertheless, the debate as to whether gut microbiome composition causally influences circulating adipokine concentrations remains unresolved. This study aimed to take an essential step in elucidating this issue.

METHODS

We used two-sample Mendelian randomization (MR) to causally analyze genetic variation statistics for gut microbiota and four adipokines (including adiponectin, leptin, soluble leptin receptor [sOB-R], and plasminogen activator inhibitor-1 [PAI-1]) from large-scale genome-wide association studies (GWAS) datasets. A range of sensitivity analyses was also conducted to assess the stability and reliability of the results.

RESULTS

The composite results of the MR and sensitivity analyses revealed 22 significant causal associations. In particular, there is a suggestive causality between the family Clostridiaceae1 (IVW: β = 0.063, P = 0.034), the genus Butyrivibrio (IVW: β = 0.029, P = 0.031), and the family Alcaligenaceae (IVW: β=-0.070, P = 0.014) and adiponectin. Stronger causal effects with leptin were found for the genus Enterorhabdus (IVW: β=-0.073, P = 0.038) and the genus Lachnospiraceae (NK4A136 group) (IVW: β=-0.076, P = 0.01). Eight candidate bacterial groups were found to be associated with sOB-R, with the phylum Firmicutes (IVW: β = 0.235, P = 0.03) and the order Clostridiales (IVW: β = 0.267, P = 0.028) being of more interest. In addition, the genus Roseburia (IVW: β = 0.953, P = 0.022) and the order Lactobacillales (IVW: β=-0.806, P = 0.042) were suggestive of an association with PAI-1.

CONCLUSION

This study reveals a causal relationship between the gut microbiota and circulating adipokines and may help to offer novel insights into the prevention of abnormal concentrations of circulating adipokines and obesity-related diseases.

Circulating interleukin-27 is associated with the risk of chronic periodontitis and allergic rhinitis: A Mendelian randomization analysis

BACKGROUND

Chronic periodontitis (CP) and allergic rhinitis (AR) have attracted wide attention as global public health problems with high incidence. Recent studies have shown that circulating interleukin-27 (IL-27) is associated with the risk of CP and AR. The aim of this study is to analyze the causal effect between them using Mendelian randomization (MR).

METHODS

Bidirectional MR analyses were performed with the use of publicly available genome-wide association study (GWAS) data. Summary data on circulating IL-27, CP, and AR published in genome-wide association studies were collected. Instrumental variables (IV) were extracted using assumptions of correlation, independence and exclusivity as criteria. Inverse variance weighting (IVW) was used as the main method, combined with weighted median method (WM) and MR-Egger and other MR Analysis methods for causal inference of exposure and outcome. Cochran's Q and MR-Egger intercept were used for sensitivity analysis.

RESULTS

The IVW study showed a causal effect between increased circulating IL-27 levels and increased risk of CP (OR = 1.14, 95%CI = 1.02-1.26, p = .020). Similarly, the increase of circulating IL-27 level had a causal effect on the decreased risk of AR (OR = 0.88, 95%CI = 0.80-0.97, p = .012). In addition, IVW study found that there was a causal between the increased risk of CP and circulating IL-27 level (OR = 1.05, 95%CI = 1.01-1.10, p = .016). However, there was no significant causal relationship between the risk of AR and circulating IL-27 levels (OR = 0.97, 95%CI = 0.91-1.02, p = .209). no significant heterogeneity or horizontal pleiotropy was found in sensitivity analysis.

CONCLUSIONS

There is a causal effect between circulating IL-27 level and CP, AR, which will help to find new ideas and methods for the diagnosis and treatment of CP and AR.

The effect of histo-blood group ABO system transferase (BGAT) on pregnancy related outcomes：A Mendelian randomization study

Protein level of Histo-Blood Group ABO System Transferase (BGAT) has been reported to be associated with cardiometabolic diseases. But its effect on pregnancy related outcomes still remains unclear. Here we conducted a two-sample Mendelian randomization (MR) study to ascertain the putative causal roles of protein levels of BGAT in pregnancy related outcomes. Cis-acting protein quantitative trait loci (pQTLs) robustly associated with protein level of BGAT (P < 5 ×10-8) were used as instruments to proxy the BGAT protein level (N = 35,559, data from deCODE), with two additional pQTL datasets from Fenland (N = 10,708) and INTERVAL (N = 3301) used as validation exposures. Ten pregnancy related diseases and complications were selected as outcomes. We observed that a higher protein level of BGAT showed a putative causal effect on venous complications and haemorrhoids in pregnancy (VH) (odds ratio [OR]=1.19, 95% confidence interval [95% CI]=1.12-1.27, colocalization probability=91%), which was validated by using pQTLs from Fenland and INTERVAL. The Mendelian randomization results further showed effects of the BGAT protein on gestational hypertension (GH) (OR=0.97, 95% CI=0.96-0.99), despite little colocalization evidence to support it. Sensitivity analyses, including proteome-wide Mendelian randomization of the cis-acting BGAT pQTLs, showed little evidence of horizontal pleiotropy. Correctively, our study prioritised BGAT as a putative causal protein for venous complications and haemorrhoids in pregnancy. Future epidemiology and clinical studies are needed to investigate whether BGAT can be considered as a drug target to prevent adverse pregnancy outcomes.

Causal effect of lipoprotein(a) level on chronic kidney disease of European ancestry: a two-sample Mendelian randomization study

INTRODUCTION

Chronic kidney disease is a growing health issue, and the options of prevention and therapy remain limited. Although a number of observational studies have linked higher Lp(a) [lipoprotein(a)] levels to the kidney impairment, the causal relationship remains to be determined. The purpose of this study was to assess the causal association between Lp(a) levels and CKD.

METHODS

We selected eight single-nucleotide polymorphisms (SNPs) significantly associated with Lp(a) levels as instrumental variables. Genome-wide association study (GWAS) from CKDGen consortium yielded the summary data information for CKD. We designed the bidirectional two-sample Mendelian randomization (MR) analyses. The estimates were computed using inverse-variance weighted (IVW), simple median, weighted median, and maximum likelihood. MR-Egger regression was used to detect pleiotropy.

RESULTS

Fixed-effect IVW analysis indicated that genetically predicted Lp(a) levels were associated with CKD significantly (odds ratio, 1.039; 95% CI, 1.009-1.069; p = 0.010). The SNPs showed no pleiotropy according to result of MR-Egger test. Results from sensitivity analyses were consistent. In the inverse MR analysis, random-effect IVW method showed CKD had no causal effect on the elevated Lp(a) (odds ratio, 1.154; 95% CI, 0.845-1.576; p = 0.367).

CONCLUSION

In this bidirectional two-sample MR analysis, the causal deteriorating effects of genetically predicted plasma Lp(a) levels on the risk of CKD were identified. On the contrary, there is no evidence to support a causal effect of CKD on Lp(a) levels.

Methylation patterns associated with C-reactive protein in racially and ethnically diverse populations

Systemic low-grade inflammation is a feature of chronic disease. C-reactive protein (CRP) is a common biomarker of inflammation and used as an indicator of disease risk; however, the role of inflammation in disease is not completely understood. Methylation is an epigenetic modification in the DNA which plays a pivotal role in gene expression. In this study we evaluated differential DNA methylation patterns associated with blood CRP level to elucidate biological pathways and genetic regulatory mechanisms to improve the understanding of chronic inflammation. The racially and ethnically diverse participants in this study were included as 50% White, 41% Black or African American, 7% Hispanic or Latino/a, and 2% Native Hawaiian, Asian American, American Indian, or Alaska Native (total n = 13,433) individuals. We replicated 113 CpG sites from 87 unique loci, of which five were novel (CADM3, NALCN, NLRC5, ZNF792, and cg03282312), across a discovery set of 1,150 CpG sites associated with CRP level (p < 1.2E-7). The downstream pathways affected by DNA methylation included the identification of IFI16 and IRF7 CpG-gene transcript pairs which contributed to the innate immune response gene enrichment pathway along with NLRC5, NOD2, and AIM2. Gene enrichment analysis also identified the nuclear factor-kappaB transcription pathway. Using two-sample Mendelian randomization (MR) we inferred methylation at three CpG sites as causal for CRP levels using both White and Black or African American MR instrument variables. Overall, we identified novel CpG sites and gene transcripts that could be valuable in understanding the specific cellular processes and pathogenic mechanisms involved in inflammation.

A review on trends in development and translation of omics signatures in cancer

The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents. In this review, we summarized the current development of genomic, methylomic, transcriptomic, proteomic and metabolic signatures in the field of cancer research and highlighted their potentials in clinical applications to improve diagnosis, prognosis, and treatment decision in cancer patients.

Integrated approach of machine learning, Mendelian randomization and experimental validation for biomarker discovery in diabetic nephropathy

AIM

To identify potential biomarkers and explore the mechanisms underlying diabetic nephropathy (DN) by integrating machine learning, Mendelian randomization (MR) and experimental validation.

METHODS

Microarray and RNA-sequencing datasets (GSE47184, GSE96804, GSE104948, GSE104954, GSE142025 and GSE175759) were obtained from the Gene Expression Omnibus database. Differential expression analysis identified the differentially expressed genes (DEGs) between patients with DN and controls. Diverse machine learning algorithms, including least absolute shrinkage and selection operator, support vector machine-recursive feature elimination, and random forest, were used to enhance gene selection accuracy and predictive power. We integrated summary-level data from genome-wide association studies on DN with expression quantitative trait loci data to identify genes with potential causal relationships to DN. The predictive performance of the biomarker gene was validated using receiver operating characteristic (ROC) curves. Gene set enrichment and correlation analyses were conducted to investigate potential mechanisms. Finally, the biomarker gene was validated using quantitative real-time polymerase chain reaction in clinical samples from patients with DN and controls.

RESULTS

Based on identified 314 DEGs, seven characteristic genes with high predictive performance were identified using three integrated machine learning algorithms. MR analysis revealed 219 genes with significant causal effects on DN, ultimately identifying one co-expressed gene, carbonic anhydrase II (CA2), as a key biomarker for DN. The ROC curves demonstrated the excellent predictive performance of CA2, with area under the curve values consistently above 0.878 across all datasets. Additionally, our analysis indicated a significant association between CA2 and infiltrating immune cells in DN, providing potential mechanistic insights. This biomarker was validated using clinical samples, confirming the reliability of our findings in clinical practice.

CONCLUSION

By integrating machine learning, MR and experimental validation, we successfully identified and validated CA2 as a promising biomarker for DN with excellent predictive performance. The biomarker may play a role in the pathogenesis and progression of DN via immune-related pathways. These findings provide important insights into the molecular mechanisms underlying DN and may inform the development of personalized treatment strategies for this disease.

Association between the gut microbiota and diabetic nephropathy: a two-sample Mendelian randomization study

Numerous studies have revealed a correlation between the risk of developing diabetic nephropathy (DN) and the gut microbiota (GM) composition. However, it remains uncertain whether the GM composition causes DN. We aimed to explore any potential causal links between the GM composition and the risk of developing DN. A meta-analysis conducted by the MiBioGen consortium of the largest genome-wide association study (GWAS) provided aggregated data on the GM. DN data were obtained from the IEU database. The inverse-variance weighting (IVW) method was employed as the primary analytical approach. The IVW analysis indicated that genus Dialister (OR = 0.51, 95% CI: 0.34-0.77, p = 0.00118) was protective against DN. In addition, class Gammaproteobacteria (OR = 0.47, 95% CI: 0.27-0.83, p = 0.0096), class Lentisphaeria (OR =0.76, 95% CI: 0.68-0.99, p = 0.04), order Victivallales (OR = 0.76, 95% CI: 0.58-0.99, p = 0.04), and phylum Proteobacteria (OR = 0.53, 95% CI: 0.33-0.85, p = 0.00872) were negatively associated with the risk of developing DN. Genus LachnospiraceaeUCG008 (OR =1.45, 95% CI: 1.08-1.95, p = 0.01), order Bacteroidales (OR = 1.59, 95% CI: 1.02-2.49, p = 0.04), and genus Terrisporobacter (OR = 1.98, 95% CI: 1.14-3.45, p = 0.015) were positively associated with the risk of developing DN. In this study, we established a causal relationship between the genus Dialister and the risk of developing DN. Further trials are required to confirm the protective effects of probiotics on DN and to elucidate the precise protective mechanisms involving genus Dialister and DN.

Causal relationship between 731 immune cells and the risk of diabetic nephropathy: a two‑sample bidirectional Mendelian randomization study

OBJECTIVE

Previous observational studies have indicated associations between various immune cells and diabetic nephropathy (DN). However, the causality remains unclear. We aimed to further evaluate the causal association between immune cells and DN using bidirectional two-sample Mendelian randomization (MR) analysis.

METHOD

The DN data were retrieved from the IEU OpenGWAS Project database, while the data for 731 immune cells were sourced from GWAS summary statistics by Orru ̀ et al. The investigation into the causal relationship between immune cells and DN employed the inverse variance weighted (IVW), weighted median (WME), and MR-Egger methods. The stability and reliability of the findings underwent evaluation through Cochran's Q test, MR-Egger intercept's P-value, MR-PRESSO, and Leave-One-Out (LOO) method.

RESULT

The IVW estimates suggested a positive causal effect of CD25 on IgD-CD38dim B cell, CD25 on naive-mature B cell, CD127 on granulocyte, SSC-A on HLA DR + Natural Killer, HLA DR on plasmacytoid Dendritic Cell, and HLA DR on Dendritic Cell on DN. Conversely, the abundance of Myeloid Dendritic Cell, CD62L- Dendritic Cell %Dendritic Cell, CD86+ myeloid Dendritic Cell %Dendritic Cell, CD14- CD16-, CX3CR1 on CD14- CD16-, and SSC-A on CD4+ T cell had negative causal effects on DN. However, after correcting the P value for significant causality results using the FDR method, it was concluded that only Myeloid Dendritic Cells had a causal relationship with DN (FDR-p = 0.041), while the other immune cells showed no significant association with DN, so their relationship was suggestive. The results were stable with no observed horizontal pleiotropy and heterogeneity. Reverse MR analysis indicated no causal relationship between DN and the increased risk of positively identified immune cells.

CONCLUSION

This study provides an initial insight into the genetic perspective of the causal relationship between immune cells and DN. It establishes a crucial theoretical foundation for future endeavors in precision medicine and individualized treatment.

Association between hypothyroidism and nephrotic syndrome: a bidirectional two-sample Mendelian randomization analysis

BACKGROUND

There is a close clinical association between hypothyroidism and nephrotic syndrome (NS) was close, but whether there is genetic causality between the two is not known.

OBJECTIVE

Using pooled data from a genome-wide association study (GWAS), the association between hypothyroidism and NS was explored via Mendelian randomization (MR) analysis.

METHODS

Single-nucleotide polymorphisms (SNPs) associated with hypothyroidism (or NS) were screened as genetic instrumental variables (IVs) from pooled GWAS data, and inverse-variance weighting (IVW) was used for the main analysis to estimate causal effects, with MR-Egger, weighted median, and weighted mode used as complementary methods. Sensitivity analyses, including Cochran's Q test, MR-Egger intercept, MR-PRESSO and leave-one-out, were also conducted to assess the robustness of the results.

RESULTS

Genetically predicted hypothyroidism was positively associated with the risk of developing NS (IVW: OR = 1.18, 95% CI: 1.07-1.30, p = 0.00; MR-Egger: OR = 1.36, 95% CI: 1.10-1.68, p = 0.01), and the MR-Egger intercept (intercept = -0.02, p = 0.14), MR-PRESSO test (p = 0.14), Cochran's Q test (p = 0.15) and leave-one-out test results supported the robustness of the results. Genetically predicted NS status might not be associated with an increased risk of developing hypothyroidism (IVW: OR = 1.01, 95% CI: 1.00-1.03, p = 0.08; MR-Egger: OR = 1.01, 95% CI: 0.98-1.04, p = 0.43), and the MR-Egger intercept (intercept < 0.01, p = 0.69), MR-PRESSO test (p = 0.64), Cochran's Q test (p = 0.61) and leave-one-out test results supported the robustness of the results.

CONCLUSION

Hypothyroidism status could increase the risk of developing NS.

Elucidating the causal nexus and immune mediation between frailty and chronic kidney disease: integrative multi-omics analysis

BACKGROUND

Empirical research has consistently documented the concurrent manifestation of frailty and chronic kidney disease (CKD). However, the existence of a reverse causal association or the influence of confounding variables on these correlations remains ambiguous.

METHODS

Our analysis of 7,078 participants from National Health and Nutrition Examination Survey(NHANES) (1999-2018) applied weighted logistic regression and Mendelian Randomization (MR) to investigate the correlation between the frailty index (FI) and renal function. The multivariate MR analysis was specifically adjusted for type 2 diabetes and hypertension. Further analysis explored 3282 plasma proteins to link FI to CKD. A two-step network MR highlighted immune cells' mediating roles in the FI-CKD relationship.

RESULT

Genetically inferred FI and various renal function markers are significantly correlated, as supported by NHANES analyses. Multivariate MR analysis revealed a direct causal association between the FI and CKD. Additionally, our investigation into plasma proteins identified Tmprss11D and MICB correlated with FI and CKD, respectively. A two-step network MR to reveal 15 immune cell types, notably Central Memory CD4+ T cells and Lymphocytes, as crucial mediators between FI and CKD.

CONCLUSION

Our work establishes a causal connection between frailty and CKD, mediated by specific immune cell profiles. These findings highlight the importance of immune mechanisms in the frailty-CKD interplay and suggest that targeting shared risk factors and immune pathways could improve management strategies for these conditions. Our research contributes to a more nuanced understanding of frailty and CKD, offering new avenues for intervention and patient care in an aging population.

The shared genetic etiology of antisocial behavior and psychiatric disorders: Insights from pleiotropy and causality analysis

BACKGROUND

Antisocial behavior (ASB) infringes on the rights of others and significantly disrupts social order. Studies have shown that ASB is phenotypically associated with various psychiatric disorders. However, these studies often neglected the importance of genetic foundations.

METHODS

This study utilized genome-wide association studies and pleiotropy analysis to explore the genetic correlation between ASB and psychiatric disorders. Linkage disequilibrium score regression (LDSC) and high-definition likelihood (HDL) methods were employed to assess genetic correlations, and the PLACO method was used for pleiotropy analysis. Functional annotation and biological pathway analysis of identified pleiotropic genes were performed using enrichment analysis. Furthermore, Mendelian randomization (MR) analysis was conducted to validate these causal relationships.

RESULTS

LDSC and HDL analysis showed that significant positive genetic correlations were between ASB and attention deficit hyperactivity disorder (ADHD), schizophrenia (SCZ), major depressive disorder (MDD), and post-traumatic stress disorder (PTSD). Multiple potential pleiotropic genetic loci were identified, particularly the FOXP2 and MDFIC genes located at the 7q31.1 locus. Enrichment analysis showed that these pleiotropic genes are highly expressed in several brain regions (such as the hypothalamus, cerebellar hemisphere, cortex, and amygdala) and immune-related cells. MR analysis further confirmed the causal effects ADHD, SCZ, and MDD on ASB risk.

CONCLUSION

This study reveals significant genetic correlations and potential causal mechanisms between ASB and various psychiatric disorders. The MR analysis confirmed the causal effects of psychiatric disorders on ASB. These findings deepen our understanding of the genetic architecture of psychiatric disorders and ASB.

Association between human blood metabolome and risk of myocarditis: a mendelian randomization study

Myocarditis is a common disease of the cardiovascular and immune systems, but the relationship between relevant blood metabolites and the risk of myocarditis has not been well-established. To identify potential biometabolic markers associated with myocarditis, we conducted a two-sample Mendelian randomization (MR) study. We performed preliminary MR analysis using the inverse variance weighted (IVW) method, supplemented by MR-Egger, weighted median, and weighted mode methods to adjust for false discovery rate (FDR). Confounders were screened using the GWAS Catalog website. Sensitivity analyses included Cochrane Q-test, Egger regression, Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO), scatterplots, funnel plots, and forest plots. For genetic and directional analysis, we employed co-localization analysis and the Steiger test. MR analysis was performed using the FinnGen database and meta-analysis was performed using the IEU database. MR analysis identified significant correlations for five metabolic biomarkers after FDR correction. These included four known metabolites: kynurenine, 1-stearoyl-GPE (18:0), deoxycarnitine, and 5-acetylamino-6-formylamino-3-methyluracil, as well as one unknown metabolite, X-25,422. Among these, kynurenine (OR = 1.441, 95%CI = 1.089-1.906, p-value = 0.018) and 1-stearoyl-GPE (18:0) (OR = 1.263, 95%CI = 1.029-1.550, p-value = 0.029) were identified as risk factors for myocarditis, while deoxycarnitine (OR = 0.813, 95%CI = 0.676-0.979, p-value = 0.029), 5-acetylamino-6-formylamino-3-methyluracil (OR = 0.864, 95% CI = 0.775-0.962, p-value = 0.018), and X-25,422 (OR = 0.721, 95%CI = 0.587-0.886, p-value = 0.009) were found to be protective factors. No evidence of heterogeneity, horizontal pleiotropy, or sensitivity issues was observed, and no shared genetic factors between exposure and outcome were detected. The causality was in the correct direction. Meta-analysis further confirmed the causal relationship between the five metabolites and myocarditis. This study identifies a causal relationship between five circulating metabolites and myocarditis. Kynurenine, 1-stearoyl-GPE (18:0), deoxycarnitine, X-25,422, and 5-acetylamino-6-formylamino-3-methyluracil may serve as potential drug targets for myocarditis, providing a theoretical basis for the prevention, diagnosis, and treatment of the condition.

Causal Effects of Gastroesophageal Reflux on Chronic Rhinosinusitis: A Bidirectional Two-Sample Mendelian Randomization Study

INTRODUCTION

Observational studies have shown a bidirectional association between gastroesophageal reflux (GER) and chronic rhinosinusitis (CRS) or chronic rhinitis (CR), but it is not clear whether this association is causal.

OBJECTIVES

This study was to investigate the causality between GER and CRS or CR using bidirectional two-sample Mendelian randomization (MR) analysis.

METHODS

Using pooled data from large genome-wide association studies (GWAS), genetic loci independently associated with GER, CRS and CR in populations of European and American ancestry were selected as instrumental variables (IVs). The inverse variance weighted (IVW) method was used to analyse the random effects model of MR, and the odds ratio (OR) was used as the evaluation index to explore the bidirectional causality between GER and CRS or CR. Single nucleotide polymorphism (SNP) outliers were detected using MR-pleiotropy Residual Sum and Outliers (MR-PRESSO). The MR-Egger intercept test examined the horizontal pleiotropy of SNPs. The "leave-one-out" sensitivity analysis examined whether MR results were affected by a single SNP.

RESULTS

The main results of IVW showed that GER increased the risk of CRS (OR = 1.3795, 95% CI = 1.188-1.603, p < 0.0500) and CR (OR = 1.3941, 95% CI = 1.1671-1.6652, p < 0.0500). The obtained SNPs as IVs for GER, CRS and CR had no significant horizontal pleiotropy, heterogeneity or bias. Regarding the reverse directions, no notable associations could be found.

CONCLUSION

This MR analysis revealed that genetically predicted GER had a causal effect on an increased risk of CRS or CR, but not vice versa. These results have great implications for the management of CRS (especially for refractory CRS) or CR in clinical practice.

Skimmed milk intake reduces the risk of ER- breast cancer: a Mendelian randomization analysis

BACKGROUND

In prior observational investigations, it has been demonstrated that the consumption of milk is associated with the incidence of breast cancer (BC). Despite the existence of a two-sample Mendelian randomization (MR) that suggests a causal relationship between milk intake and breast cancer risk, the outcomes still lack a definitive conclusion. This ambiguity may be attributed to variables such as the variety of milk ingested, estrogen levels, the specific type of BC, and potential confounding factors. Therefore, our principal objective is to establish the causal association between the consumption of skimmed milk and full cream milk and the risk of different types of BC through the utilization of two-sample and two-step MR analyses.

METHODS

In this study, we analyzed single nucleotide polymorphisms associated with skimmed and full-cream milk consumption in a cohort of 360,806 individuals from European populations through genome-wide association studies. We conducted a two-sample MR analysis using three different methods: inverse variance weighting (IVW) was used as the main analysis, and MR-Egger and Weighted median were used as supplementary analyses to IVW. We also performed sensitivity analysis, which included leave-one-out analysis, Cochran's Q test to detect heterogeneity, and MR-Egger intercept analysis to detect potential biases caused by pleiotropy. We used two-step MR analysis to evaluate potential mediators of associations.

RESULTS

In the two-sample MR analysis, IVW analysis suggests a potential inverse causal relationship between skimmed milk and BC [OR 0.34, 95% CI (0.12-1.00), P = 0.05]. Subgroup analysis revealed that skimmed milk reduces the risk of estrogen receptor-negative (ER-) breast cancer [OR 0.18, 95% CI (0.04-0.90), P = 0.04], but not estrogen receptor-positive (ER+) breast cancer [OR 0.42, 95% CI (0.15-1.22), P = 0.11]. MR Egger reached similar results, that is, skimmed milk reduces the risk of ER- breast cancer [OR 0.006, 95% CI (0.00-0.70), P = 0.04], but not BC [OR 0.16, 95% CI (0.01-4.66), P = 0.30] and ER+ breast cancer [OR 0.50, 95% CI (0.02-12.61), P = 0.65]. Additionally, we found no causal relationship between full cream milk and BC (P > 0.05). In two-step MR analysis, we found evidence for a mediating role of BMI in the relationship between skimmed milk intake and ER-breast cancer risk.

CONCLUSION

Our findings strengthen the evidence for a protective effect of skimmed milk consumption on ER-breast cancer risk. Further two-step MR analyses suggest that this protective effect may partly result from body mass index (BMI). There is no evidence that full cream milk consumption affects the risk of BC.

Deciphering the genetic underpinnings of neuroticism: A Mendelian randomization study of druggable gene targets

BACKGROUND

Neuroticism, known for its association with a greater risk of psychiatric conditions such as depression and anxiety, is a critical focus of research.

METHODS

Cis-expression quantitative trait loci (eQTLs) from 31,684 whole blood samples provided by the eQTLGen Consortium, alongside data from a large neuroticism cohort, were analyzed to identify genes causally linked to neuroticism. To further explore the influence of gene expression changes on neuroticism, colocalization analysis was conducted. Identified drug targets were assessed for potential side effects using a phenome-wide association study (PheWAS). Additionally, we utilized multiple databases to explore the interactions between drugs and genes for drug prediction and assess the current medications for drug repurposing.

RESULTS

The analysis involved a total of 4473 druggable genes, with two-sample Mendelian randomization (MR) identifying 186 genes that are causally linked to neuroticism. Colocalization analysis highlighted 11 genes (TLR4, MMRN1, EP300, BRAF, ORM1, ACVR1B, LRRC17, NOS2, ADAMTS6, GPX1, and VCL) with a posterior probability of colocalization (PPH4) >0.8. PheWAS revealed that drugs targeting BRAF, LRRC17, ADAMTS6, and GPX1 were also associated with other traits. Notably, six of these genes (TLR4, MMRN1, BRAF, ACVR1B, NOS2, and GPX1) are already being explored for drug development in psychiatric and other diseases.

CONCLUSION

This study pinpointed six genes as promising therapeutic targets for neuroticism. The repurposing and development of drugs targeting these genes hold potential for managing neuroticism and associated psychiatric disorders.

Evaluating the relationship between standing height, body mass index, body fat percentage with risk of inguinal hernia: a Mendelian randomization study

Observational studies have suggested links between standing height, BMI, body fat percentage, and inguinal hernia risk, but with inconsistent results. We conducted Mendelian randomization (MR) method to investigate their causal relationships. Independent SNPs associated with standing height, BMI, and body fat percentage were extracted from GWAS data as instrumental variables (IVs). Two-sample MR initially explored causal relationships between these factors and inguinal hernia risk. Multivariable Mendelian randomization (MVMR) assessed the direct causal effects of exposures on inguinal hernia. Positive findings from the MVMR analysis were independently validated. The inverse-variance weighted Methods (IVW), weighted median(WM), and MR-Egger were used for the MR estimates. Sensitivity analyses were used to examine the stability and reliability of the results. Two-sample MR analysis revealed a suggestive causal association between height and inguinal hernia (OR = 1.091, 95% CI = 1.003-1.186, P = 0.042). BMI (OR = 0.846, 95% CI = 0.774-0.924, P < 0.001) and body fat percentage (OR = 0.793, 95% CI = 0.690-0.911, P = 0.001) were significantly protective factors. After MVMR adjustment, BMI (OR = 0.746,95%CI = 0.638-0.872, P < 0.001) remained protective. Independent validation yielded consistent result. Genetically predicted BMI is a significant protective factor for inguinal hernia, providing valuable guidance for individualized prevention strategies.

Genetic Evidence for GLP-1 and GIP Receptors as Targets for Treatment and Prevention of MASLD/MASH

BACKGROUND AND AIMS

Glucagon-like peptide-1 receptor (GLP1R) agonists and glucose-dependent insulinotropic polypeptide receptor (GIPR) agonists may help treat metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic dysfunction-associated steatohepatitis (MASH). However, their definitive effects are still unclear. Our study aims to clarify this uncertainty.

METHODS

We utilised conventional Mendelian randomisation (MR) analysis to explore potential causal links between plasma GLP-1/GIP concentrations and MASLD and its related traits. Next, we conducted drug-target MR analysis using highly expressed tissue data to assess the effects of corresponding drug perturbation on these traits. Finally, mediation analysis was performed to ascertain whether the potential causal effect is direct or mediated by other MASLD-related traits.

RESULTS

Circulating 2-h GLP-1 and GIP concentrations measured during an oral glucose tolerance test showed hepatoprotective effects on MASLD risk (ORGLP-1 = 0.168 [95% CI 0.033-0.839], p = 0.030; ORGIP = 0.331 [95% CI 0.222-0.494], p = 6.31 × 10-8). GLP1R expression in the blood had a minimal causal effect on MASLD risk, whereas GIPR expression significantly affected MASLD risk (OR = 0.671 [95% CI 0.531-0.849], p = 9.07 × 10-4). Expression levels of GLP1R or GIPR in the blood significantly influenced MASLD-related clinical traits. Mediation analysis revealed that GIPR expression protected against MASLD, even after adjusting for type 2 diabetes or body mass index.

CONCLUSIONS

GLP-1/GIP receptor agonists offer promise in lowering MASLD/MASH risk. GIP receptor agonists can exert direct and indirect effects on MASLD mediated by weight reduction or glycemic control improvement.

Causal effect of immune cells on idiopathic pulmonary fibrosis: A mendelian randomization study

BACKGROUND

A key component of idiopathic pulmonary fibrosis (IPF) is the involvement of immune cells. However, the causal interaction between different immune cell signatures and IPF remain inconclusive.

OBJECTIVES

Based on publicly accessible data, our study utilized the Mendelian randomization (MR) approach to determine the causative relevance of complex immune cell phenotypes in IPF.

METHODS

We deployed a two-sample Mendelian randomization approach to evaluate the causal interaction between immune cell markers and IPF. All data regarding 731 immune signatures and IPF were acquired from two genome-wide association studies (GWAS) that are accessible to the public. The original study adopted the inverse variance weighted (IVW) method, followed by sensitivity analyses aimed at eliminating heterogeneity and pleiotropy. Additionally, Multivariate Mendelian randomization (MVMR) was utilized to identify the independent risk factors in our study.

RESULTS

The summary dataset for IPF was accessed from the Finnish Genetic Consortium R9, comprising 2018 patients and 373,064 controls. And the dataset for immune signatures was conducted in 3,757 Sardinian individuals. By conducting IVW and extensive sensitivity analyses, univariate Mendelian randomization (UVMR) identified one immunophenotype that remained causally associated with IPF after false discovery rate (FDR) correction: CD39 on CD39+ CD8+T cells (odd ratio [OR] = 0.850, 95 % confidence interval [CI] = 0.787-0.918, P = 3.68 × 10-5). The causal association with IPF was further validated using MVMR.

CONCLUSIONS

Based on rigorous MR analysis methods and FDR correction, our study demonstrated that CD39 on CD39+ CD8+T cells showed a protective effect against IPF, providing effective insights for preventing and diagnosing pulmonary fibrosis.

Causal effect of cerebral small vessel disease on unexplained dizziness: A Mendelian randomization study

BACKGROUND

Previous cohort studies have suggested an association between cerebral small vessel disease (cSVD) and "unexplained dizziness". The causality of this link remains uncertain, but it would be of significant clinical importance, considering the substantial number of patients presenting with unexplained dizziness is large. We aimed to investigate the causal effect of cSVD-related phenotypes on unexplained dizziness using a Mendelian randomization approach.

METHODS

Genetic instruments for each cSVD-related phenotype - white matter hyperintensity (WMH) volume, lacunar stroke (LS), perivascular spaces (PVS), and cerebral microbleeds (CMBs) - as well as unexplained dizziness were identified through large-scale genome-wide association studies. We conducted 2-sample Mendelian randomization analyses. The random-effects inverse-variance weighted (IVW) method was chosen for the primary analysis. For sensitivity analyses, we employed the weighted-median, MR-Egger, MR pleiotropy residual sum and outlier (MR-PRESSO), and leave-one-out analysis methods were implemented for the sensitivity analyses.

RESULTS

We successfully identified a significant causal effect of WMH volume on unexplained dizziness (odds ratio [95% CI], 1.12 [1.01-1.23]). However, we were unable to detect any significant causal effects of the other cSVD-related phenotypes on unexplained dizziness, with odds ratios [95% CI] of 1.03 [0.98-1.09] for LS, 0.75 [0.55-1.02] for white matter PVS, 1.02 [0.68-1.52] for basal ganglia PVS, 0.80 [0.43-1.51] for hippocampal PVS, 0.95 [0.90-1.00] for lobar CMBs, and 0.97 [0.92-1.01] for mixed CMBs respectively. The results from the sensitivity analyses were generally consistent with those of the primary analyses.

CONCLUSIONS

This MR study supports a causal relationship between WMH, a phenotype associated with cSVD, and the risk of unexplained dizziness, but does not support such a relationship between other cSVD-related phenotypes and unexplained dizziness. These findings require further validation through randomized controlled trials, larger cohort studies, and MR studies based on more extensive GWASs.

Genetic relations between type 1 diabetes, coronary artery disease and leukocyte counts

AIMS/HYPOTHESIS

Type 1 diabetes is associated with excess coronary artery disease (CAD) risk even when known cardiovascular risk factors are accounted for. Genetic perturbation of haematopoiesis that alters leukocyte production is a novel independent modifier of CAD risk. We examined whether there are shared genetic determinants and causal relationships between type 1 diabetes, CAD and leukocyte counts.

METHODS

Genome-wide association study summary statistics were used to perform pairwise linkage disequilibrium score regression and heritability estimation from summary statistics (ρ-HESS) to respectively estimate the genome-wide and local genetic correlations, and two-sample Mendelian randomisation to estimate the causal relationships between leukocyte counts (335,855 healthy individuals), type 1 diabetes (18,942 cases, 501,638 control individuals) and CAD (122,733 cases, 424,528 control individuals). A latent causal variable (LCV) model was performed to estimate the genetic causality proportion of the genetic correlation between type 1 diabetes and CAD.

RESULTS

There was significant genome-wide genetic correlation (rg) between type 1 diabetes and CAD (rg=0.088, p=8.60 × 10-3) and both diseases shared significant genome-wide genetic determinants with eosinophil count (rg for type 1 diabetes [rg(T1D)]=0.093, p=7.20 × 10-3, rg for CAD [rg(CAD)]=0.092, p=3.68 × 10-6) and lymphocyte count (rg(T1D)=-0.052, p=2.76 × 10-2, rg(CAD)=0.176, p=1.82 × 10-15). Sixteen independent loci showed stringent Bonferroni significant local genetic correlations between leukocyte counts, type 1 diabetes and/or CAD. Cis-genetic regulation of the expression levels of genes within shared loci between type 1 diabetes and CAD was associated with both diseases as well as leukocyte counts, including SH2B3, CTSH, MORF4L1, CTRB1, CTRB2, CFDP1 and IFIH1. Genetically predicted lymphocyte, neutrophil and eosinophil counts were associated with type 1 diabetes and CAD (lymphocyte OR for type 1 diabetes [ORT1D]=0.67, p=2.02-19, ORCAD=1.09, p=2.67 × 10-6; neutrophil ORT1D=0.82, p=5.63 × 10-5, ORCAD=1.17, p=5.02 × 10-14; and eosinophil ORT1D=1.67, p=5.45 × 10-25, ORCAD=1.07, p=2.03 × 10-4. The genetic causality proportion between type 1 diabetes and CAD was 0.36 ± 0.16 (pLCV=1.30 × 10-2), suggesting a possible intermediary causal variable.

CONCLUSIONS/INTERPRETATION

This study sheds light on shared genetic mechanisms underlying type 1 diabetes and CAD, which may contribute to their co-occurrence through regulation of gene expression and leukocyte counts and identifies cellular and molecular targets for further investigation for disease prediction and potential drug discovery.

Exploring Causal Relationships between Circulating Inflammatory Proteins and Thromboangiitis Obliterans: A Mendelian Randomization Study

BACKGROUND

 Thromboangiitis obliterans (TAO) is a vascular condition characterized by poor prognosis and an unclear etiology. This study employs Mendelian randomization (MR) to investigate the causal impact of circulating inflammatory proteins on TAO.

METHODS

 In this MR analysis, summary statistics from a genome-wide association study meta-analysis of 91 inflammation-related proteins were integrated with independently sourced TAO data from the FinnGen consortium's R10 release. Methods such as inverse variance weighting, MR-Egger regression, weighted median approaches, MR-PRESSO, and multivariable MR (MVMR) analysis were utilized.

RESULTS

 The analysis indicated an association between higher levels of C-C motif chemokine 4 and a reduced risk of TAO, with an odds ratio (OR) of 0.44 (95% confidence interval [CI]: 0.29-0.67; p = 1.4 × 10-4; adjusted p = 0.013). Similarly, glial cell line-derived neurotrophic factor exhibited a suggestively protective effect against TAO (OR: 0.43, 95% CI: 0.22-0.81; p = 0.010; adjusted p = 0.218). Conversely, higher levels of C-C motif chemokine 23 were suggestively linked to an increased risk of TAO (OR: 1.88, 95% CI: 1.21-2.93; p = 0.005; adjusted p = 0.218). The sensitivity analysis and MVMR revealed no evidence of heterogeneity or pleiotropy.

CONCLUSION

 This study identifies C-C motif chemokine 4 and glial cell line-derived neurotrophic factor as potential protective biomarkers for TAO, whereas C-C motif chemokine 23 emerges as a suggestive risk marker. These findings elucidate potential causal relationships and highlight the significance of these proteins in the pathogenesis and prospective therapeutic strategies for TAO.

Gut microbiota and risk of ankylosing spondylitis

OBJECTIVE

Observational studies have established a connection between gut microbiota and ankylosing spondylitis (AS) risk; however, whether the observed associations are causal remains unclear. Therefore, we conducted a two-sample Mendelian randomization (MR) analysis to assess the potential causal associations of gut microbiota with AS risk.

METHODS

Instrumental variants of gut microbiota were obtained from the MiBioGen consortium (n = 18,340) and the Dutch Microbiome Project (n = 7738). The FinnGen consortium provided genetic association summary statistics for AS, encompassing 2860 cases and 270,964 controls. We used the inverse-variance weighted (IVW) method as the primary analysis, supplemented with the weighted median method, maximum likelihood-based method, MR pleiotropy residual sum and outlier test, and MR-Egger regression. In addition, we conducted a reverse MR analysis to assess the likelihood of reverse causality.

RESULTS

After the Bonferroni correction, species Bacteroides vulgatus remained statistically significantly associated with AS risk (odds ratio (OR) 1.55, 95% confidence interval (CI) 1.22-1.95, P = 2.55 × 10-4). Suggestive evidence of associations of eleven bacterial traits with AS risk was also observed (P < 0.05 by IVW). Among them, eight were associated with an elevated AS risk (OR 1.37, 95% CI 1.07-1.74, P = 0.011 for phylum Verrucomicrobia; OR 1.31, 95% CI 1.03-1.65, P = 0.026 for class Verrucomicrobiae; OR 1.17, 95% CI 1.01-1.36, P = 0.035 for order Bacillales; OR 1.31, 95% CI 1.03-1.65, P = 0.026 for order Verrucomicrobiales; OR 1.43, 95% CI 1.13-1.82, P = 0.003 for family Alcaligenaceae; OR 1.31, 95% CI 1.03-1.65, P = 0.026 for family Verrucomicrobiaceae; OR 1.31, 95% CI 1.03-1.65, P = 0.026 for genus Akkermansia; OR 1.55, 95% CI 1.19-2.02, P = 0.001 for species Sutterella wadsworthensis). Three traits exhibited a negative association with AS risk (OR 0.68, 95% CI 0.53-0.88, P = 0.003 for genus Dialister; OR 0.84, 95% CI 0.72-0.97, P = 0.020 for genus Howardella; OR 0.75, 95% CI 0.59-0.97, P = 0.026 for genus Oscillospira). Consistent associations were observed when employing alternate MR methods. In the reverse MR, no statistically significant correlations were detected between AS and these bacterial traits.

CONCLUSION

Our results revealed the associations of several gut bacterial traits with AS risk, suggesting a potential causal role of gut microbiota in AS development. Nevertheless, additional research is required to clarify the mechanisms by which these bacteria influence AS risk. Key Points • The association of gut microbiota with AS risk in observational studies is unclear. • This MR analysis revealed associations of 12 gut bacterial traits with AS risk.

Bidirectional association between abnormal cardiac conditions and epilepsy: A two-sample Mendelian randomization study

BACKGROUND

Observational studies have consistently indicated a significant correlation between abnormal cardiac conditions and epilepsy. However, the association and direction of this relationship remain a subject of debate. This study employs a two-sample bidirectional Mendelian randomization (MR) approach to investigate the association between abnormal cardiac conditions and epilepsy.

METHODS

Instrumental variables, represented by single nucleotide polymorphisms (SNPs) associated with epilepsy and various abnormal cardiac conditions, were derived from large-scale genome-wide association studies databases, including FinnGen and UK Biobank. Bidirectional MR analysis was conducted to estimate the association between epilepsy and abnormal cardiac conditions. Sensitivity analyses were performed using MR-Egger, weighted median, Inverse Variance Weighted, and MR pleiotropy residual sum and outlier methods.

RESULTS

The forward MR analysis suggested a potential positive effect of atrial fibrillation and flutter (AF) and valvular heart diseases (VHD) on the risk of epilepsy. Conversely, the reverse MR analysis indicated that epilepsy might increase the susceptibility to AF, VHD, and heart failure.

CONCLUSION

The findings support a bidirectional relationship between AF, VHD, and epilepsy, indicating that AF and VHD can elevate the risk of developing epilepsy, while epilepsy, in turn, can also increase the risk of developing AF and VHD. Furthermore, the study suggest that epilepsy may contribute to the development of heart failure. These results underscore the importance of screening for cardiac abnormalities in patients with epilepsy and vice versa, to better understand their clinical significance and potential as modifiable risk factors.

Relationship between myocardial infarction and atrial fibrillation: A bidirectional Mendelian randomization study

Many studies have shown that myocardial infarction (MI) is significantly associated with atrial fibrillation (AF), but the causal relationship between MI and AF has not been established. Therefore, we performed this Mendelian randomization (MR) study to investigate the relationship between MI and AF. We used a publicly available summary statistical dataset for MI based on genome-wide analysis studies (GWAS; ebi-a-GCST011364; 14,825 cases and 2680 controls) and a summary statistical dataset for AF based on an European GWAS (finn-b-I9_AF_REIMB; 10,516 cases and 116,926 controls). The 2-sample bidirectional MR analysis was performed using the inverse-variance weighted (IVW), MR-Egger, and weighted median methods. The causal effect of MI on AF was analyzed using 30 MI-specific single nucleotide polymorphisms (SNPs) that were characterized as instrumental variables (IVs) based on the GWAS data. The causal effect of MI on AF was confirmed by the IVW (odds ratio [OR] 1.42; 95% confidence interval [CI] 1.27-1.58; P < .001), MR-Egger (OR: 1.49; 95% CI: 1.15-1.93; P = .005), and weighted median (OR: 1.42; 95% CI: 1.24-1.63; P < .001) analyses. Furthermore, in the reverse MR analyses, the causal effect of AF on MI was analyzed using 20 AF-specific SNPs that were screened as IVs. The causal effect of AF on MI was significant based on the results from the IVW method (OR: 1.05; 95% CI: 1.00-1.09; P = .033). In conclusion, the bidirectional MR analyses demonstrated a clear bidirectional causal association between MI and AF.

Identifying genetic determinants of sarcopenia-related traits: a Mendelian randomization study of druggable genes

BACKGROUND

Sarcopenia, characterized by progressive muscle mass and function loss, particularly affects the elderly, and leads to severe consequences such as falls and mortality. Despite its prevalence, targeted pharmacotherapies for sarcopenia are lacking. Utilizing large-sample genome-wide association studies (GWAS) data is crucial for cost-effective drug discovery.

METHODS

Herein, we conducted four studies to understand the putative causal effects of genetic components on muscle mass and function. Study 1 employed a two-sample Mendelian randomization (MR) on 15,944 potential druggable genes, investigating their potential causality with muscle quantity and quality in a European population (N up to 461,089). Study 2 validated MR results through sensitivity analyses and colocalization analyses. Study 3 extended validation across other European cohorts, and study 4 conducted quantitative in vivo verification.

RESULTS

MR analysis revealed significant causality between four genes (BLOC-1 related complex subunit 7, BORCS7; peptidase m20 domain containing 1, PM20D1; nuclear casein kinase and cyclin dependent kinase substrate 1, NUCKS1 and ubiquinol-cytochrome c reductase complex assembly factor 1, UQCC1) and muscle mass and function (p-values range 5.98 × 10-6 to 9.26 × 10-55). To be specific, BORCS7 and UQCC1 negatively regulated muscle quantity and quality, whereas enhancing PM20D1 and NUCKS1 expression showed promise in promoting muscle mass and function. Causal relationships remained robust across sensitivity analyses, with UQCC1 exhibiting notable colocalization effects (PP·H4 93.4 % to 95.8 %). Further validation and in vivo replication verified the potential causality between these genes and muscle mass as well as function.

CONCLUSIONS

Our druggable genome-wide MR analysis identifies BORCS7, PM20D1, NUCKS1, and UQCC1 as causally associated with muscle mass and function. These findings offer insights into the genetic basis of sarcopenia, paving the way for these genes to become promising drug targets in mitigating this debilitating condition.