Comparison of Two Meta-Analysis Methods: Inverse-Variance-Weighted Average and Weighted Sum of Z-Scores

Sex hormones and neuromyelitis optica spectrum disorder: a bidirectional Mendelian randomization study

BACKGROUND

Females are considered to have an increased susceptibility to neuromyelitis optica spectrum disorder (NMOSD) than males, especially aquaporin-4 (AQP4) antibody positive NMOSD, indicating that sex hormones may be involved in the NMOSD pathogenesis. However, the causality between sex hormones and NMOSD still remains unclear.

METHODS

Based on the genome-wide association study (GWAS) data of three sex hormones (estradiol (E2), progesterone (PROG) and bioavailable testosterone (BAT)), sex hormone-binding globulin (SHBG), age of menarche, age of menopause, and NMOSD (total, AQP4 + and AQP4 -), we performed a two-sample bidirectional Mendelian randomization (MR) study. Sex-stratified GWAS data of E2, PROG, BAT, and SHBG was obtained for gender-specific MR analysis. Causal inferences were based on the inverse variance weighted method, MR-Egger regression, and weighted median method. The reverse MR analysis was also performed to assess the impact of NMOSD on hormone levels.

RESULTS

PROG in females had aggravative effects on NMOSD (P < 0.001), especially AQP4 - NMOSD (P < 0.001). In the reverse MR analysis, total NMOSD was found to decrease the level of BAT (P < 0.001) and increase the level of SHBG (P = 0.001) in females.

CONCLUSION

Findings of this MR analysis revealed mutual causal associations between sex hormones and NMOSD, which provided novel perspectives about the gender-related pathogenesis of NMOSD.

A comprehensive analysis of the health effects associated with smoking in the largest population using UK Biobank genotypic and phenotypic data

Background

Smoking is a widespread behavior, while the relationship between smoking and various diseases remains a topic of debate.

Objective

We conducted analysis to further examine the identified associations and assess potential causal relationships.

Methods

We utilized seven single nucleotide polymorphisms (SNPs) known to be linked to smoking extracting genotype data from the UK Biobank, a large-scale biomedical repository encompassing comprehensive health-related and genetic information of European descent. Phenome-wide association study (PheWAS) analysis was conducted to map the association of genetically predicted smoking status with 1,549 phenotypes. The associations identified in the PheWAS were then meticulously examined through two-sample Mendelian randomization (MR) analysis, utilizing data from the UK Biobank (n = 487,365) and the Sequencing Consortium of Alcohol and Nicotine Use (GSCAN) (n = 337,334). This approach allowed us to comprehensively characterize the links between smoking and disease patterns.

Results

The PheWAS analysis produced 34 phenotypes that demonstrated significant associations with smoking (P = 0.05/1460). Importantly, sickle cell anemia and type 2 diabetes exhibited the most significant SNPs (both 85.71% significant SNPs). Furthermore, the MR analyses provided compelling evidence supporting causal associations between smoking and the risk of following diseases: obstructive chronic bronchitis (IVW: Beta = 0.48, 95% confidence interval (CI) 0.36-0.61, P = 1.62×10-13), cancer of the bronchus (IVW: Beta = 0.92, 95% CI 0.68-1.17, P = 2.02×10-13), peripheral vascular disease (IVW: Beta = 1.09, 95% CI 0.71-1.46, P = 1.63×10-8), emphysema (IVW: Beta = 1.63, 95% CI 0.90-2.36, P = 1.29×10-5), pneumococcal pneumonia (IVW: Beta = 0.30, 95% CI 0.11-0.49, P = 1.60×10-3), chronic airway obstruction (IVW: Beta = 0.83, 95% CI 0.30-1.36, P = 2.00×10-3) and type 2 diabetes (IVW: Beta = 0.53, 95% CI 0.16-0.90, P = 5.08×10-3).

Conclusion

This study affirms causal relationships between smoking and obstructive chronic bronchitis, cancer of the bronchus, peripheral vascular disease, emphysema, pneumococcal pneumonia, chronic airway obstruction, type 2 diabetes, in the European population. These findings highlight the broad health impacts of smoking and support smoking cessation efforts.

Blood metabolites mediate effects of breakfast skipping on heart failure via Mendelian randomization analysis

Numerous observational studies have suggested a potential causal relationship between skipping breakfast and cardiovascular diseases, including heart failure (HF). However, these studies are susceptible to inherent confounders and the challenge of reverse causation, and the underlying metabolic factors are not yet clear. Therefore, our aim is to assess the causal impact of breakfast skipping on HF and the role of potential mediating metabolic products from a genetic perspective, by conducting Mendelian Randomization (MR) studies and mediation analysis. We leveraged summary data from the most extensive genome-wide association studies to date on breakfast skipping (with 193,860 participants), blood metabolites (with 118,461 participants), and HF (involving 47,309 cases and 930,014 controls). To explore the causal relationship between breakfast skipping and HF, as well as the role of 249 potential blood metabolite mediators, we conducted bidirectional MR and mediation MR analyses. We primarily employed the Inverse Variance Weighted (IVW) method, complemented by various other techniques to ensure the comprehensiveness and reliability of our analysis. Our research confirms a causal association between breakfast skipping and an increased risk of HF (odds ratio [OR]: 1.378, 95% confidence interval [CI]: 1.047-1.813; p = 0.022). Furthermore, our research findings demonstrate that breakfast skipping is positively correlated with 6 blood metabolites and negatively correlated with 2 others. Notably, our mediation MR analysis further reveals that three blood metabolites act as mediators in the relationship between breakfast skipping and the risk of HF. Specifically, the mediating effects are attributed to the ratio of docosahexaenoic acid (DHA) to total fatty acids (proportion mediated = 9.41%, 95% CI: 2.10-28.61%), glucose (proportion mediated = 6.17%, 95% CI: 0.97-28.53%), and glycoprotein acetyls (GlycA) (proportion mediated = 5.68%, 95% CI: 0.94-21.62%). The combined mediating effects of these three factors total 20.53% (95%CI: 8.59-91.06%). Our research confirms the causal relationship between genetically instrumented breakfast skipping and HF, underscoring the potential mediating roles played by three key blood metabolites: ratio of DHA to total fatty acids, glucose and GlycA. This discovery offers valuable perspectives for clinical strategies targeting HF.

Male infertility risk and plasma lipidome: a Mendelian randomization study

Background

In recent years, the decline in sperm quality in men has become a global trend. There is a close relationship between sperm quality and pregnancy outcome. There is a large body of literature supporting the role of plasma lipidome in male infertility, while the complex mechanisms between them and male infertility are still less clear. Systematic study of the causal relationship between plasma lipidome and MI can help to provide new therapeutic ideas and targets for male infertility.

Methods

In this study, we used a two-sample Mendelian randomization analysis based on Genome-wide association studies pooled data of 179 causal relationships between plasma lipidome and male infertility. We used employed the inverse variance weighted method as the main analysis to assess causality between exposure and outcome, in addition to MR-Egger, Weighted median as complementary methods, and tests for multiplicity and heterogeneity.

Results

We identified 13 plasma lipidome comprising 4 types of plasma lipidome that were associated with male infertility. Among these, 9 plasma lipidome were found to be protective factors, while 4 were risk factors. Notably, the largest proportion of these plasma lipidome were triglyceride types, with Sphingomyelin (d40:1) exhibiting the strongest association with male infertility.

Conclusion

These findings contribute to the current better understanding of male infertility and provide new perspectives on the underlying etiology of male infertility as well as prevention and treatment strategies. In addition, clinical trial validation is needed to assess the potential of these plasma lipidome as biomarkers.

Causal relationship between breakfast skipping and myocardial infarction: Two-sample Mendelian randomization

While observational studies suggest a connection between skipping breakfast and myocardial infarction (MI), the causal nature of this relationship is unclear. This study aims to investigate the genetic causal relationships between breakfast skipping and MI through Mendelian randomization (MR). Employing genetic data from a public genome-wide association study, this research focuses on genetic variations linked to breakfast skipping and MI. The primary analytical method was the inverse variance-weighted approach, complemented by additional methods like MR-Egger, weighted median, and mode analyses. It also includes heterogeneity and horizontal pleiotropy tests such as the Cochrane Q test, MR-Egger intercept, and MR-PRESSO tests, with a leave-one-out analysis for enhanced sensitivity assessment reliability. The study discovered a notable association between breakfast skipping and an increased risk of MI (odds ratios: 1.34, 95% confidence intervals: 1.03-1.76, P = .027). The test revealed no heterogeneity or multiplicity, and the sensitivity analysis confirmed the robustness of the results. Our MR analysis suggests that habitual breakfast skipping might elevate the likelihood of MI, underlining the importance of regular breakfast consumption in potentially mitigating heart attack risks.

Casual effects of telomere length on sarcoidosis: a bidirectional Mendelian randomization analysis

Background

Telomere length, crucial for genomic stability, have been implicated in various inflamm-aging diseases, but their role in sarcoidosis remains unexplored.

Objective

This study aims to explore the casual effects between TL and sarcoidosis via a bidirectional Mendelian Randomization (MR) study.

Methods

We examined single nucleotide polymorphisms (SNPs) associated with TL and sarcoidosis, utilizing available open-access genome-wide association study (GWAS) databases from the UK Biobank and FinnGen. We employed five MR techniques, including Inverse Variance Weighted (IVW), MR Egger, weighted median (WM), Robust adjusted profile score (RAPS), and Maximum likelihood, to assess causal relationships and explore pleiotropy.

Results

Summary data extracted from GWAS datasets of TL (n = 472,174) and (n = 217,758) of European ancestry. Employing 130 SNPs with genome-wide significance as instrumental factors for TL, we detect a significant negative correlation between TL and sarcoidosis (OR: 0.682, 95% confidence interval: 0.524-0.888, p : 0.0045). Similarly, utilizing 6 SNPs with genome-wide significance as instrumental factors for sarcoidosis, we fail to identify a noteworthy association between sarcoidosis and TL (OR: 0.992, 95% confidence interval: 0.979-1.005, p : 0.2424).

Conclusion

Our results suggest that longer telomeres may reduce the risk of sarcoidosis, highlighting TL as a potential biomarker for diagnosis and long-term monitoring. Understanding the critical role of telomere shortening enables more effective focus on diagnosing, treating, and curing sarcoidosis linked to telomeres. Clinical investigations into treatments that enhance TL are warranted.

Assessing causal relationships between gut microbiota and abortion: evidence from two sample Mendelian randomization analysis

Background

While some studies have suggested a link between gut microbiota (GM) and abortion, the causal relationship remains unclear.

Methods

To explore the causal relationship between GM and abortion, including spontaneous abortion (SA) and habitual abortion (HA), we performed a two-sample Mendelian randomization (MR) analysis. We used summary statistics data from MiBioGen and FinnGen for genome-wide association studies (GWAS), with GM data as the exposure variable and abortion data as the outcome variable.

Results

In the absence of heterogeneity and horizontal pleiotropy, the inverse-variance weighted (IVW) method identified five genetically predicted GM genera linked to the risk of abortions. Lactococcus was negatively correlated with the risk of SA, whereas the Eubacterium fissicatena group was positively correlated with the risk of SA. Genetic predictions of Coprococcus3 and Odoribacter were linked to a reduced risk of HA, while the Eubacterium ruminantium group was associated with an increased risk of HA.

Conclusion

Our study suggests a genetic causal relationship between specific GM and two types of abortions, improving our understanding of the pathological relationship between GM and abortion.

Saturation genome editing of BAP1 functionally classifies somatic and germline variants

Many variants that we inherit from our parents or acquire de novo or somatically are rare, limiting the precision with which we can associate them with disease. We performed exhaustive saturation genome editing (SGE) of BAP1, the disruption of which is linked to tumorigenesis and altered neurodevelopment. We experimentally characterized 18,108 unique variants, of which 6,196 were found to have abnormal functions, and then used these data to evaluate phenotypic associations in the UK Biobank. We also characterized variants in a large population-ascertained tumor collection, in cancer pedigrees and ClinVar, and explored the behavior of cancer-associated variants compared to that of variants linked to neurodevelopmental phenotypes. Our analyses demonstrated that disruptive germline BAP1 variants were significantly associated with higher circulating levels of the mitogen IGF-1, suggesting a possible pathological mechanism and therapeutic target. Furthermore, we built a variant classifier with >98% sensitivity and specificity and quantify evidence strengths to aid precision variant interpretation.

Malnutrition as a potential predictor of mortality in chronic kidney disease patients on dialysis: A systematic review and meta-analysis

BACKGROUND & AIMS

Malnutrition, a significant problem in patients with chronic kidney disease (CKD), is linked to lower health-related quality of life, longer and more frequent hospital admissions, worse functional capacity, and higher levels of morbidity. However, the extent of its impact on mortality is poorly elucidated. This systematic review and meta-analysis aimed to investigate the impact of malnutrition on mortality among CKD patients on dialysis.

METHODS

This meta-analysis was designed and performed in accordance with the PRISMA guidelines (CRD42023394584). A systematic electronic literature search was conducted in PubMed, ScienceDirect, and Embase to identify relevant cohort studies. The studies that reported nutritional status and its impact on mortality in patients were considered for analysis. The generic inverse variance method was used to pool the hazard ratio effect estimates by employing a random effects model. The Newcastle-Ottawa scale was used for the quality assessment. The statistical analysis was performed by utilizing RevMan and CMA 2.0.

RESULTS

A total of 29 studies that comprised 11,063 patients on dialysis whose nutritional status was evaluated were eligible for quantitative analysis. Based on a comparison between the "malnutrition" category and the reference "normal nutrition status" category, the results showed that the overall pooled hazard risk (HR) for mortality was (HR 1.49, 95% CI: 1.36-1.64, p < 0.0001). According to the subgroup analysis, the hemodialysis subgroup had greater mortality hazards (HR 1.53; 95% CI 1.38-1.70, p < 0.0001), compared to the peritoneal dialysis subgroup (HR 1.26; 95% CI 1.15-1.37, p < 0.00001). Additionally, the overall incidence of mortality was explored but the authors were unable to combine the results due to limitations with the data.

CONCLUSION

The findings conclude that malnutrition is a strong predictor of mortality among patients on dialysis, with the hemodialysis subgroup having a higher mortality hazard compared to the peritoneal dialysis subgroup. The results of this study will advocate for early nutritional evaluation and timely dietary interventions to halt the progression of CKD and death.

Decoding connections in the European population: serum uric acid, sex hormone-binding globulin, total testosterone, estradiol, and female infertility - advanced bidirectional and mediative Mendelian randomization

Background

Despite observational links between serum uric acid (SUA), sex hormone-related phenotypes, and female infertility, the causality behind these associations remains uncertain.

Objective

This study utilizes Bidirectional Two-Sample and Mediation Mendelian Randomization to explore the causal relationships and mediation effects of sex hormone-binding globulin (SHBG), total testosterone (TT), and estradiol on these associations.

Methods

We analyzed single-nucleotide polymorphisms (SNPs) associated with SUA and sex hormone levels using data from large-scale GWAS of European populations. Female infertility data were sourced from 6,481 cases and 75,450 controls in the FinnGen Consortium. We employed methods including Inverse Variance Weighted (IVW), Weighted Median, and MR-Egger regression to assess causality.

Results

We found that elevated SUA levels causally increase the risk of female infertility (IVW OR: 1.13, P=0.047). Elevated SUA levels significantly decrease SHBG levels (β=-0.261; P=2.177e-04), with SHBG mediating 27.93% of the effect of SUA on infertility (OR=0.854; 95%CI, 0.793-0.920; P=2.853e-05). Additionally, elevated TT levels, which were associated with decreased SUA levels (β=-0.127), showed an indirect effect on infertility mediated by SUA (β=-0.0187; 95% CI, -0.041 to -0.003; P=0.046).

Conclusion

Our findings demonstrate causal links between high SUA and increased risk of female infertility mediated by hormonal factors such as SHBG and TT. These insights suggest new avenues for infertility treatment and highlight the need for further research into these mechanisms.

Casual associations between brain structure and sarcopenia: A large-scale genetic correlation and mendelian randomization study

Sarcopenia presenting a critical challenge in population-aging healthcare. The elucidation of the interplay between brain structure and sarcopenia necessitates further research. The aim of this study is to explore the casual association between brain structure and sarcopenia. Linkage disequilibrium score regression (LDSC) was conducted to estimate the genetic correlations; MR was then performed to explore the causal relationship between Brain imaging-derived phenotypes (BIDPs) and three sarcopenia-related traits: handgrip strength, walking pace, and appendicular lean mass (ALM). The main analyses were conducted using the inverse-variance weighted method. Moreover, weighted median and MR-Egger were conducted as sensitivity analyses. Genetic association between 6.41% of BIDPs and ALM was observed, and 4.68% of BIDPs exhibited causal MR association with handgrip strength, 2.11% of BIDPs were causally associated with walking pace, and 2.04% of BIDPs showed causal association with ALM. Volume of ventromedial hypothalamus was associated with increased odds of handgrip strength (OR: 1.18, 95% CI: 1.02 to 1.37) and ALM (OR: 1.05, 95% CI: 1.01 to 1.09). Mean thickness of G-pariet-inf-Angular was associated with decreased odds of handgrip strength (OR: 0.83, 95% CI: 0.70 to 0.97) and walking pace (OR: 0.97, 95% CI: 0.93 to 0.99). As part of the brain structure forward causally influences sarcopenia, which may provide new perspectives for the prevention of sarcopenia and offer valuable insights for further research on the brain-muscle axis.

Automated rating of background parenchymal enhancement in MRI of extremely dense breasts without compromising the association with breast cancer in the DENSE trial

OBJECTIVES

Background parenchymal enhancement (BPE) on dynamic contrast-enhanced MRI (DCE-MRI) as rated by radiologists is subject to inter- and intrareader variability. We aim to automate BPE category from DCE-MRI.

METHODS

This study represents a secondary analysis of the Dense Tissue and Early Breast Neoplasm Screening trial. 4553 women with extremely dense breasts who received supplemental breast MRI screening in eight hospitals were included. Minimal, mild, moderate and marked BPE rated by radiologists were used as reference. Fifteen quantitative MRI features of the fibroglandular tissue were extracted to predict BPE using Random Forest, Naïve Bayes, and KNN classifiers. Majority voting was used to combine the predictions. Internal-external validation was used for training and validation. The inverse-variance weighted mean accuracy was used to express mean performance across the eight hospitals. Cox regression was used to verify non inferiority of the association between automated rating and breast cancer occurrence compared to the association for manual rating.

RESULTS

The accuracy of majority voting ranged between 0.56 and 0.84 across the eight hospitals. The weighted mean prediction accuracy for the four BPE categories was 0.76. The hazard ratio (HR) of BPE for breast cancer occurrence was comparable between automated rating and manual rating (HR = 2.12 versus HR = 1.97, P = 0.65 for mild/moderate/marked BPE relative to minimal BPE).

CONCLUSION

It is feasible to rate BPE automatically in DCE-MRI of women with extremely dense breasts without compromising the underlying association between BPE and breast cancer occurrence. The accuracy for minimal BPE is superior to that for other BPE categories.

Navigating Pubertal Goldilocks: The Optimal Pace for Hierarchical Brain Organization

Adolescence is a timed process with an onset, tempo, and duration. Nevertheless, the temporal dimension, especially the pace of maturation, remains an insufficiently studied aspect of developmental progression. The primary objective is to estimate the precise influence of pubertal maturational tempo on the configuration of associative brain regions. To this end, the connection between maturational stages and the level of hierarchical organization of large-scale brain networks in 12-13-year-old females is analyzed. Skeletal maturity is used as a proxy for pubertal progress. The degree of maturity is defined by the difference between bone age and chronological age. To assess the level of hierarchical organization in the brain, the temporal dynamic of closed eye resting state high-density electroencephalography (EEG) in the alpha frequency range is analyzed. Different levels of hierarchical order are captured by the measured asymmetry in the directionality of information flow between different regions. The calculated EEG-based entropy production of participant groups is then compared with accelerated, average, and decelerated maturity. Results indicate that an average maturational trajectory optimally aligns with cerebral hierarchical order, and both accelerated and decelerated timelines result in diminished cortical organization. This suggests that a "Goldilocks rule" of brain development is favoring a particular maturational tempo.

Clinicopathological Characteristics and Risk Factors of Young-Onset Gastric Carcinoma: A Systematic Review and Meta-analysis

INTRODUCTION

The characteristics of gastric carcinoma in young individuals differ from that in older individuals. We conducted a systematic review and meta-analysis to explore the clinicopathological features and risk factors associated with young-onset (younger than 50 years) gastric carcinoma.

METHODS

We searched for studies published between January 1, 1990, and September 1, 2023, on patients with young-onset gastric carcinoma in PubMed, EMBASE, Web of Science, and MEDLINE to explore clinicopathological characteristics among this specific patient group. Extracted information included the proportion of patients with symptoms or family history of gastric cancer, tumor location, and histological features such as Lauren or World Health Organization histological classification and degree of differentiation. Additional analyses were conducted on risk factors such as positive family history, Helicobacter pylori infection, or high-risk nutritional or behavioral factors. The estimates were derived using random or fixed-effect models and included subgroup analyses based on different sex and age groups. This study was registered in PROSPERO (CRD42023466131).

RESULTS

We identified 5,696 records, 1,292 were included in the quality assessment stage. Finally, 84 studies from 18 countries or regions including 89,447 patients with young-onset gastric carcinoma were included. Young-onset gastric carcinoma has slight female predominance (53.7%, 95% confidence interval [CI]: 51.6-55.7%), with most having symptoms (87.0%, 95% CI: 82.4%-91.7%). Family history was reported in 12.1% (95% CI: 9.5%-14.7%). H. pylori infection was detected in 60.0% of cases (95% CI: 47.1%-72.8%). Most of these carcinomas were in the non-cardia region (89.6%, 95% CI: 82.4%-96.8%), exhibiting Lauren diffuse-type histology (71.1%, 95% CI: 66.8%-75.3%) and poor/undifferentiated features (81.9%, 95% CI%: 79.7-84.2%). A positive family history of gastric cancer was the most important risk factor associated with the development of gastric carcinoma in young individuals (pooled odds ratios 4.0, 95% CI: 2.8-5.2), followed by H. pylori infection (odds ratio 2.3; 95% CI: 1.4-3.2) and dietary and other lifestyle risk factors.

DISCUSSION

Young-onset gastric carcinoma exhibits specific clinicopathological characteristics, with positive family history being the most important risk factor. Most of the patients were symptomatic at diagnosis. These findings could help to inform future strategies for the early detection of gastric carcinoma among young individuals.

Bleeding Risk in Patients Receiving Omega-3 Polyunsaturated Fatty Acids: A Systematic Review and Meta-Analysis of Randomized Clinical Trials

BACKGROUND

There is a potential concern about increased bleeding risk in patients receiving omega-3 polyunsaturated fatty acids (PUFAs). The aims of this study-level meta-analysis were to determine the risk of bleeding and to assess whether this relationship is linked to the received dose of omega-3 PUFAs or the background use of antiplatelet treatment.

METHODS AND RESULTS

Electronic databases were searched through May 2023 to identify randomized clinical trials of patients receiving omega-3 PUFAs. Overall bleeding events, including fatal and central nervous system events, were identified and compared with those of a control group. A total of 120 643 patients from 11 randomized clinical trials were included. There was no difference in the pooled meta-analytic events of bleeding among patients receiving omega-3 PUFAs and those in the control group (rate ratio [RR], 1.09 [95% CI, 0.91-1.31]; P=0.34). Likewise, the incidence of hemorrhagic stroke, intracranial bleeding, and gastrointestinal bleeding were similar. A prespecified analysis was performed in patients receiving high-dose purified eicosapentaenoic acid (EPA), which demonstrated a 50% increase in the relative risk of bleeding but only a modest increase in the absolute risk of bleeding (0.6%) when compared with placebo. Bleeding risk was associated with the dose of EPA (risk difference, 0.24 [95% CI, 0.05-0.43]; P=0.02) but not the background use of antiplatelet therapy (risk difference, -0.01 [95% CI, -0.02 to 0]; P=0.056).

CONCLUSIONS

Omega-3 PUFAs were not associated with increased bleeding risk. Patients receiving high-dose purified EPA may incur additional bleeding risk, although its clinical significance is very modest.

Causal relationship between primary biliary cholangitis and inflammatory bowel disease: a Mendelian randomization study

Background

Several studies indicated that inflammatory bowel disease (IBD) may contribute to increased susceptibility to primary biliary cholangitis (PBC). However, the causal relationship between IBD and PBC remains unclear.

Methods

The genetic variant data of patients with IBD and PBC were obtained from published genome-wide association studies (GWASs). The IBD data were further divided into a discovery dataset and a validation dataset depending on the data source. We conducted a two-sample Mendelian randomization (MR) analysis using the inverse variance weighting (IVW), MR-Egger, weighted median (WM), MR robust adjusted profile score (MR-RAPS), and maximum likelihood (ML) methods, with IVW being the main focus, to verify the causal relationship between IBD and PBC. Additionally, a series of sensitivity analyses were performed to ensure the reliability of the results.

Results

In the discovery cohort, the IVW analysis results (OR = 1.114, P = 0.011) indicated a significant association between IBD and PBC. The MR-RAPS (OR = 1.130, P = 0.007) and ML (OR = 1.115, P = 0.011) analyses yielded results consistent with those of IVW in confirming IBD as a risk factor for PBC. In the validation cohort, consistent findings were observed regarding the causal relationship between IBD and PBC using IVW, MR-RAPS, and ML analyses; all three methods identified IBD as a risk factor for developing PBC. By the IVW analysis, Crohn's disease (CD) emerged as the most prominent subtype of IBD associated with an increased risk of developing PBC in both the discovery cohort (OR = 1.068, P = 0.049) and the validation cohort (OR = 1.082, P = 0.019).

Conclusion

The results of the MR analysis suggest a causal relationship between IBD and PBC, highlighting the necessity for proactive PBC prevention in patients with IBD, particularly those with CD.

Causal relationship between immune cells and atrial fibrillation: A Mendelian randomization study

Atrial fibrillation (AF) is a prevalent cardiac arrhythmia, with recent research indicating a correlation between immune system characteristics and the development of AF. However, it remains uncertain whether the immunological response is the primary underlying component or a secondary consequence of AF. Initially, we investigated the effect of immune cells on AF by performing forward Mendelian randomization (MR) analyses with immune cells as the exposure variable and their associated genetic variants as instrumental variables. Subsequently, we performed reverse MR analyses with AF as the exposure variable and immune cells as the outcome variable to exclude the interference of reverse causality, to distinguish between primary and secondary effects, and to further elucidate the causal relationship between the immune system and AF. We discovered that membrane proteins on specific immune cells, such as CD25 on memory B cells-which functions as a part of the interleukin-2 receptor-may be risk factors for AF development, with odds ratios of 1.0233 (95% confidence interval: 1.0012-1.0458, P = .0383). In addition, certain immune cell counts, such as the CD4 regulatory T cell Absolute Count, play a protective factor in the development of AF (odds ratio: 0.9513, 95% confidence interval: 0.9165-0.9874; P = .0086). More detailed results are elaborated in the main text. Our MR study has yielded evidence that substantiates a genetically inferred causal association between the immune system and AF. Identifying the risk factors associated with AF is vital to facilitate the development of innovative pharmaceutical treatments.

The causal relationship between gut microbiota and lymphoma: a two-sample Mendelian randomization study

Background

Previous studies have indicated a potential link between the gut microbiota and lymphoma. However, the exact causal interplay between the two remains an area of ambiguity.

Methods

We performed a two-sample Mendelian randomization (MR) analysis to elucidate the causal relationship between gut microbiota and five types of lymphoma. The research drew upon microbiome data from a research project of 14,306 participants and lymphoma data encompassing 324,650 cases. Single-nucleotide polymorphisms were meticulously chosen as instrumental variables according to multiple stringent criteria. Five MR methodologies, including the inverse variance weighted approach, were utilized to assess the direct causal impact between the microbial exposures and lymphoma outcomes. Moreover, sensitivity analyses were carried out to robustly scrutinize and validate the potential presence of heterogeneity and pleiotropy, thereby ensuring the reliability and accuracy.

Results

We discerned 38 potential causal associations linking genetic predispositions within the gut microbiome to the development of lymphoma. A few of the more significant results are as follows: Genus Coprobacter (OR = 0.619, 95% CI 0.438-0.873, P = 0.006) demonstrated a potentially protective effect against Hodgkin's lymphoma (HL). Genus Alistipes (OR = 0.473, 95% CI 0.278-0.807, P = 0.006) was a protective factor for diffuse large B-cell lymphoma. Genus Ruminococcaceae (OR = 0.541, 95% CI 0.341-0.857, P = 0.009) exhibited suggestive protective effects against follicular lymphoma. Genus LachnospiraceaeUCG001 (OR = 0.354, 95% CI 0.198-0.631, P = 0.0004) showed protective properties against T/NK cell lymphoma. The Q test indicated an absence of heterogeneity, and the MR-Egger test did not show significant horizontal polytropy. Furthermore, the leave-one-out analysis failed to identify any SNP that exerted a substantial influence on the overall results.

Conclusion

Our study elucidates a definitive causal link between gut microbiota and lymphoma development, pinpointing specific microbial taxa with potential causative roles in lymphomagenesis, as well as identifying probiotic candidates that may impact disease progression, which provide new ideas for possible therapeutic approaches to lymphoma and clues to the pathogenesis of lymphoma.

The Impact of Non-alcohol Fatty Liver Disease on Bone Mineral Density is Mediated by Sclerostin by Mendelian Randomization Study

Non-alcoholic fatty liver disease (NAFLD) has been found to be associated with osteoporosis (OP) in observational studies. However, the precise causal relationship between NAFLD and OP remains unclear. Here, we used Mendelian randomization (MR) to explore the causal relationship. We selected NAFLD-related single-nucleotide polymorphisms from a genome-wide meta-analysis (8434 cases and 434,770 controls) as instrumental variants. We used inverse variance weighted analysis for the primary MR analysis. Furthermore, we used similar methodologies in parallel investigations of other chronic liver diseases (CLDs). We performed sensitivity analyses to ensure the reliability of the results. We observed a causality between NAFLD and forearm bone mineral density (FABMD) (beta-estimate [β]: - 0.212; p-value: 0.034). We also found that sclerostin can act as a mediator to influence the NAFLD and FABMD pathways to form a mediated MR network (mediated proportion = 8.8%). We also identified indications of causal relationships between other CLDs and OP. However, we were unable to establish any associated mediators. Notably, our analyses did not yield any evidence of pleiotropy. Our findings have implications in the development of preventive and interventional measures aimed at managing low bone mineral density in patients with NAFLD.

No causal association between serum vitamin D levels and diabetes retinopathy: A Mendelian randomization analysis

BACKGROUND AND AIM

Diabetes retinopathy (DR) is a common microvascular complication of diabetes, and it is the main cause of global vision loss. The current observational research results show that the causal relationship between Vitamin D and DR is still controversial. Therefore, we conducted a Mendelian randomization study to determine the potential causal relationship between serum 25-hydroxyvitamin D 25(OH)D and DR.

METHODS AND RESULTS

In this study, we selected aggregated data on serum 25(OH)D levels (GWAS ID: ebi-a-GCST90000615) and DR (GWAS ID: finn-b-DM_RETINOPATHY) from a large-scale GWAS database. Then use MR analysis to evaluate the possible causal relationship between them. We mainly use inverse variance weighted (IVW), supplemented by MR Egger and weighted median methods. Sensitivity analysis is also used to ensure the stability of the results, such as Cochran's Q-test, MR-PRESSO, MR-Egger interception test, and retention method. The MR analysis results showed that there was no significant causal relationship between 25(OH)D and DR (OR = 1.0128, 95%CI=(0.9593,1.0693), P = 0.6447); Similarly, there was no significant causal relationship between DR and serum 25 (OH) D levels (OR = 0.9900, 95% CI=(0.9758,1.0045), P = 0.1771).

CONCLUSION

Our study found no significant causal relationship between serum 25(OH)D levels and DR, and vice versa. A larger sample size randomized controlled trial is needed to further reveal its potential causal relationship.

No bidirectional relationship between sleep phenotypes and risk of proliferative diabetic retinopathy: a two-sample Mendelian randomization study

This study aimed to investigate the probable existence of a causal relationship between sleep phenotypes and proliferative diabetic retinopathy (PDR). Single nucleotide polymorphisms associated with sleep phenotypes were selected as instrumental variables at the genome-wide significance threshold (P < 5 × 10-8). Inverse-variance weighted was applied as the primary Mendelian randomization (MR) analysis method, and MR Egger regression, weighted median, simple mode, and weighted mode methods were used as complementary analysis methods to estimate the causal association between sleep phenotypes and PDR. Results indicated that genetically predicted sleep phenotypes had no causal effects on PDR risk after Bonferroni correction (P = 0.05/10) [Chronotype: P = 0.143; Daytime napping: P = 0.691; Daytime sleepiness: P = 0.473; Insomnia: P = 0.181; Long sleep duration: P = 0.671; Morning person:P = 0.113; Short sleep duration: P = 0.517; Obstructive sleep apnea: P = 0.091; Sleep duration: P = 0.216; and snoring: P = 0.014]. Meanwhile, there are no reverse causality for genetically predicted PDR on sleep phenotypes [Chronotype: P = 0.100; Daytime napping: P = 0.146; Daytime sleepiness: P = 0.469; Insomnia: P = 0.571; Long sleep duration: P = 0.779; Morning person: P = 0.040; Short sleep duration: P = 0.875; Obstructive sleep apnea: P = 0.628; Sleep duration: P = 0.896; and snoring: P = 0.047]. This study's findings did not support the causal effect of between sleep phenotypes and PDR. Whereas, longitudinal studies can further verify results validation.

Associations between sex hormones, receptors, binding proteins and inflammatory bowel disease: a Mendelian randomization study

Background

Gender differences existed in inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC). Observational studies have revealed associations between sex hormones and IBD, such as estrogen and testosterone. However, the exact relationship between these sex hormones and IBD is unclear.

Method

Based on the genome-wide association studies data of eight sex hormones, two sex hormone receptors, sex hormone-binding globulin (SHBG), total IBD and its two subtypes, we performed a two-sample Mendelian randomization (MR) study to analyze their mutual relationship. For estradiol (E2), progesterone (PROG), bioavailable testosterone (BAT), total testosterone (TT) and SHBG, sex-stratified MR analyses were also performed. Inverse variance weighted method, MR-Egger regression and Weighted median method were used for causal analyses. Sensitivity analyses were conducted to test the stability of causal relationships. Besides, a reverse MR analysis was performed to estimate the reverse causation.

Results

E2 (P=0.028) and TT (P=0.034) had protective effects on CD. Sex-stratified analyses revealed protective roles of E2 in males on total IBD (P=0.038) and CD (P=0.020). TT in females had protective effects on total IBD (P=0.025) and CD (P=0.029), and BAT in females decreased the risk of developing CD (P=0.047) and UC (P=0.036). Moreover, SHBG in males was also associated with a decreased risk of CD (P=0.021). The reversed MR analysis showed that CD was negatively correlated with estrogen receptor (P=0.046). UC was negatively correlated with PROG in females (P=0.015) and positively correlated with SHBG levels in males (P=0.046).

Conclusion

Findings of this study revealed the mutual causal associations between sex hormones and the risk of developing IBD.

Causal association between asthma and periodontitis: A two-sample Mendelian randomization analysis

BACKGROUND

A unified view of whether asthma and periodontitis interact and the direction of action is not found in previous studies. Therefore, in this article, we will elucidate bidirectional causality by two-sample Mendelian randomization (MR).

METHODS

We obtained summary-level data for asthma and periodontitis from the massive GWAS databases of several publicly available. Meanwhile, it will ensure no confounders like smoking using the Phenoscanner website to have a search over each SNP. The F statistic value of each SNP is calculated as more significant than 10. This MR analysis mainly used five MR methods: MR-Egger, weighted median, inverse variance weighted (IVW), simple mode, and weighted mode. As a result, we performed heterogeneity and horizontal pleiotropy tests.

RESULTS

We have found supporting evidence to verify the hypothesis that asthma may be a protective factor for periodontitis (IVW OR = 0.34; 95% CI = [0.132,0.87]; p = 0.025). The consistent impact direction is shown when additional asthma GWAS dataset are used (MR-Egger OR = 0.118; 95%CI = [0.016,0.883]; p = 0.04). There is no evidence of a causal effect of periodontitis at the risk of asthma in the reverse analysis (p > 0.05).

CONCLUSIONS

Our analysis found that people with asthma may have a lower risk of periodontitis than those without. This MR analysis could have significant implications for the clinical process and future research.

Exploring the causal associations of micronutrients on urate levels and the risk of gout: A Mendelian randomization study

BACKGROUND & AIMS

Growing evidence has indicated a potential association between micronutrient levels, urate levels, and the risk of gout. However, the causal association underlying these associations still remains uncertain. Previous observational studies and randomized controlled trials investigating the association between micronutrients, urate levels, and the risk of gout have been limited in their scope and depth. The aim of this study was to utilize Mendelian randomization (MR) to investigate the causal associations between genetically predicted micronutrient levels, urate levels, and the risk of gout.

METHODS

In this study, we conducted a comprehensive examination of 10 specific micronutrients (vitamin B6, vitamin B12, vitamin C, vitamin D, folate, calcium, iron, copper, zinc, and selenium) as potential exposures. Two-sample MR analyses were performed to explore their causal associations with urate levels and the risk of gout. In these analyses, gout data were collected from the Global Biobank Meta-Analysis Initiative (N = 1,069,839, N cases = 30,549) and urate levels data from CKDGen Consortium (N = 288,649) by utilizing publicly available summary statistics from independent cohorts of European ancestry. We performed inverse-variance weighted MR analyses as main analyses, along with a range of sensitivity analyses, such as MR-Egger, weighted median, simple mode, weighted mode, Steiger filtering, MR-PRESSO, and Radial MR analysis, to ensure the robustness of our findings.

RESULTS

The results of our study indicate that there were negative associations between serum vitamin B12 and urate levels, as well as serum folate and the risk of gout. Specifically, we found a negative association between vitamin B12 levels and urate levels, with a β coefficient of -0.324 (95% CI -0.0581 to -0.0066, P = 0.0137) per one standard deviation (SD) increase. Similarly, a negative association was observed between folate levels and gout risk, with an odds ratio of 0.8044 (95% CI 0.6637 to 0.9750, P = 0.0265) per one SD increase. On the other hand, we identified positive associations between serum calcium levels and both urate levels and the risk of gout. Specifically, there was a positive association between serum calcium levels and urate levels (β coefficient: 0.0994, 95% CI 0.0519 to 0.1468, P = 4.11E-05) per one SD increase. Furthermore, a positive association was found between serum calcium levels and the risk of gout, with an odds ratio of 1.1479 (95% CI 1.0460 to 1.2598, P = 0.0036) per one SD increase. These findings were robust in extensive sensitivity analyses. By employing MR-PRESSO and Radial MR to eliminate outliers, the observed associations have been reinforced. No clear associations were found between the other micronutrients and the urate levels, as well as the risk of gout.

CONCLUSION

Our findings provided evidence that there were negative associations between serum vitamin B12 and urate levels, as well as serum folate and the risk of gout, while positive associations existed between the serum calcium levels and urate levels, as well as the risk of gout.

Evidence for Genetic Causal Relationships Between Multiple Immune-Mediated Inflammatory Diseases and Age-Related Macular Degeneration: A Univariable and Multivariable Mendelian Randomization Study

INTRODUCTION

With the global aging population on the rise, age-related macular degeneration (AMD) poses a growing healthcare burden. Prior research hints at immune-mediated inflammatory diseases (IMIDs) potentially elevating AMD risk via diverse mechanisms. However, causality remains disputed as a result of confounding factors. Hence, our Mendelian randomization (MR) study aims to untangle this link, mitigating confounding effects to explore the IMID-AMD causal relationship. This study aims to investigate the causal relationship between IMIDs and AMD, providing new strategies for the prevention and treatment of AMD in clinical practice.

METHODS

This study was registered with PROSPERO, CRD42023469815. We obtained data on IMIDs and AMD from Genome-Wide Association Studies (GWAS) summary statistics and the FinnGen consortium. Rigorous selection steps were applied to screen for eligible instrumental single nucleotide polymorphisms (SNPs). We conducted univariate Mendelian randomization, inverse variance-weighted (IVW), weighted median, Mendelian randomization-Egger (MR-Egger), and multivariate Mendelian randomization (MVMR) analyses. Various sensitivity analysis methods were employed to assess pleiotropy and heterogeneity. The aim was to explore the causal relationships between IMIDs and AMD.

RESULTS

The MR analysis revealed that Crohn's disease (CD) (IVW: odd ratios (OR) 1.05, 95% CI (confidence interval) 1.01-1.10, p = 0.007), rheumatoid arthritis (RA) (IVW: OR 1.09, 95% CI 1.04-1.15, p = 0.0001), and type 1 diabetes (T1D) (IVW: OR 1.05, 95% CI 1.02-1.09, p = 0.001) were correlated with an elevated risk of AMD, while multiple sclerosis (MS) (IVW: OR 2.78E-18, 95% CI 2.23E-31 to 3.48E-05, p = 0.008) appeared to be protective against AMD. These findings were supported by an array of MR analysis methodologies and the MVMR approach.

CONCLUSION

Our study results, based on MR, provide genetic evidence indicating a causal relationship between specific IMIDs and AMD. CD, RA, and T1D are factors increasing the risk of AMD, while MS may have a protective effect.

Causal Associations Between Gut Microbiota and Cerebrovascular Diseases

BACKGROUND

Numerous studies suggest that the gut microbiota closely linked to cerebrovascular diseases, such as Intracranial aneurysm (IA) and aneurysmal subarachnoid hemorrhage (aSAH). Nevertheless, the confirmation of a definitive causal connection between gut microbiota, IA, and aSAH is still pending. The aim of our research is to explore the potential bidirectional causality among them.

METHODS

This bidirectional Mendelian Randomization (MR) study used single nucleotide polymorphisms linked to gut microbiota, IA, and aSAH from Genome-Wide Association Studies. The Inverse Variance Weighted (IVW) method was used to explore causality. To assess the robustness of the result, sensitivity analyses were further performed, including weighted-median method, MR-Egger regression, Maximum-likelihood method, MR pleiotropy residual sum and outlier test and leave-one-out analysis.

RESULTS

In the IVW method, the family Porphyromonadaceae (odds ratio [OR] 0.63; 95% CI 0.47-0.85; P: 0.002) and genus Bilophila (OR 0.66; 95% CI 0.50-0.86; P: 0.002) showed a significant negative association with the risk of IA. Similarly, the genus Bilophila (OR: 0.68; 95% CI: 0.50-0.93; P: 0.017) and genus Ruminococcus1 (OR: 0.48; 95% CI: 0.30-0.78; P: 0.003) were linked to reduced risk of aSAH. The sensitivity analysis yielded similar outcomes in the IVW approach. Through the adoption of reverse MR analysis, a potential correlation between IA and decreased abundance of genus Ruminococcus1 was identified (OR 0.94; 95% CI 0.90-0.99; P 0.024).

CONCLUSIONS

This MR analysis investigated the causal associations between gut microbiota, IA, and aSAH risks. The findings expanded current knowledge of the microbiota-gut-brain axis and offered novel perspectives on preventing and managing these conditions.

CODA: an open-source platform for federated analysis and machine learning on distributed healthcare data

OBJECTIVES

Distributed computations facilitate multi-institutional data analysis while avoiding the costs and complexity of data pooling. Existing approaches lack crucial features, such as built-in medical standards and terminologies, no-code data visualizations, explicit disclosure control mechanisms, and support for basic statistical computations, in addition to gradient-based optimization capabilities.

MATERIALS AND METHODS

We describe the development of the Collaborative Data Analysis (CODA) platform, and the design choices undertaken to address the key needs identified during our survey of stakeholders. We use a public dataset (MIMIC-IV) to demonstrate end-to-end multi-modal FL using CODA. We assessed the technical feasibility of deploying the CODA platform at 9 hospitals in Canada, describe implementation challenges, and evaluate its scalability on large patient populations.

RESULTS

The CODA platform was designed, developed, and deployed between January 2020 and January 2023. Software code, documentation, and technical documents were released under an open-source license. Multi-modal federated averaging is illustrated using the MIMIC-IV and MIMIC-CXR datasets. To date, 8 out of the 9 participating sites have successfully deployed the platform, with a total enrolment of >1M patients. Mapping data from legacy systems to FHIR was the biggest barrier to implementation.

DISCUSSION AND CONCLUSION

The CODA platform was developed and successfully deployed in a public healthcare setting in Canada, with heterogeneous information technology systems and capabilities. Ongoing efforts will use the platform to develop and prospectively validate models for risk assessment, proactive monitoring, and resource usage. Further work will also make tools available to facilitate migration from legacy formats to FHIR and DICOM.

Investigating the Causal Relationship Between Sleep Behaviors and Primary Open-Angle Glaucoma: A Bidirectional Two-Sample Mendelian Randomization Study

Background

Although previous studies of sleep-related behaviors in relation to primary open-angle glaucoma (POAG) have been noted, the causal relationship remains unclear. The purpose of our present study was to investigate the relationships of genetically predicted sleep traits with POAG using a two-sample bidirectional Mendelian randomization (MR) method.

Methods

Summary-level data collected from publicly available genome-wide association studies (GWAS) of European decent were applied for the bidirectional MR analysis. After quality control steps, independent single-nucleotide polymorphisms for eight sleep behaviors and POAG were selected as the genetic instruments. The inverse-variance weighted (IVW) approach was adopted as the primary method, which was complemented by a series of sensitivity analyses to assess the robustness of the results by estimating heterogeneity and pleiotropy. Multivariable MR (MVMR) was used to assess the direct effect of sleep traits on POAG, after adjusting for several confounding factors.

Results

Our investigation revealed a positive correlation between genetically predicted ease of getting up in the morning and sleep duration and POAG using the IVW method (odds ratio (OR)=1.78, 95% confidence interval (CI):1.29-2.46, P = 4.33× 10-4; OR = 1.66, 95% CI:1.18-2.34, P = 3.38×10-3, respectively). Other supplementary MR methods also confirmed similar results. Moreover, the MVMR results also revealed that the adverse effects of these two sleep traits on POAG persisted after adjusting for body mass index, smoking, drinking, and education (all P < 0.05). Conversely, the relationships between genetic liability of POAG and different sleep behaviors were not statistically significant in the reverse-direction MR estimate (all P > 0.05).

Conclusion

Our study demonstrated that genetic prediction of getting up easily in the morning or sleep duration were associated with a higher risk of POAG, but not vice versa, in a European population. Further validation and clinical interventions are required to offer potential strategies to prevent and manage POAG.

The role of thyroid function in borderline personality disorder and schizophrenia: a Mendelian Randomisation study

BACKGROUND

Genome-wide association studies have reported a genetic overlap between borderline personality disorder (BPD) and schizophrenia (SCZ). Epidemiologically, the direction and causality of the association between thyroid function and risk of BPD and SCZ are unclear. We aim to test whether genetically predicted variations in TSH and FT4 levels or hypothyroidism are associated with the risk of BPD and SCZ.

METHODS

We employed Mendelian Randomisation (MR) analyses using genetic instruments associated with TSH and FT4 levels as well as hypothyroidism to examine the effects of genetically predicted thyroid function on BPD and SCZ risk. Bidirectional MR analyses were employed to investigate a potential reverse causal association.

RESULTS

Genetically predicted higher FT4 was not associated with the risk of BPD (OR: 1.18; P = 0.60, IVW) or the risk of SCZ (OR: 0.93; P = 0.19, IVW). Genetically predicted higher TSH was not associated with the risk of BPD (OR: 1.11; P = 0.51, IVW) or SCZ (OR: 0.98, P = 0.55, IVW). Genetically predicted hypothyroidism was not associated with BPD or SCZ. We found no evidence for a reverse causal effect between BPD or SCZ on thyroid function.

CONCLUSIONS

We report evidence for a null association between genetically predicted FT4, TSH or hypothyroidism with BPD or SCZ risk. There was no evidence for reverse causality.

The Causality between Gut Microbiota and Hypertension and Hypertension-related Complications: A Bidirectional Two-Sample Mendelian Randomization Analysis

BACKGROUND

Recent studies have highlighted a connection between gut microbiota and hypertension, yet the precise nature of this relationship remains unclear.

OBJECTIVE

This research aims to analyze the causal link between gut microbiota and hypertension, along with associated complications, utilizing two-sample bidirectional Mendelian randomization (MR).

MATERIALS AND METHODS

Summary data from genome-wide association studies (GWAS) meta-analyses, including gut microbiota GWAS data from 24 cohorts, and the latest GWAS data for hypertension-related conditions were acquired. Employing various MR methods, including Inverse-variance weighted (IVW), MR-Egger, Weighted Median, Simple Mode, and Weighted Mode, we investigated the association between gut microbiota and hypertension-related conditions. Sensitivity analyses were conducted for result stability, and reverse MR analysis assessed the potential for reverse causality.

RESULTS

The Mendelian randomization analysis involving 199 microbial taxa and four phenotypes identified 46 microbial taxa with potential causal links to hypertension and its complications. Following Bonferroni correction, genus.Victivallis showed a robust causal relationship with hypertension (OR = 1.08, 95% CI = 1.04-1.12, P = 9.82e-5). This suggests an 8% increased risk of hypertension with each unit rise in genus.Victivallis abundance.

CONCLUSION

In conclusion, this study establishes a causal connection between gut microbiota and hypertension, along with common associated complications. The findings unveil potential targets and evidence for future hypertension and complication treatment through gut microbiota interventions, offering a novel avenue for therapeutic exploration.

Mendelian randomization analysis of atopic dermatitis and esophageal cancer in East Asian and European populations

Background

Emerging observational studies showed an association between atopic dermatitis (AD) and gastrointestinal cancers. However, it remains unclear whether this association is causal, particularly in the case of cancers like esophageal cancer, which exhibit ancestral genetic traits.

Methods

To assess the potential causal relationship between AD and esophageal cancer across diverse ancestral backgrounds, we conducted a 2-sample Mendelian randomization study. Independent genetic instruments for AD from the FinnGen consortium (N case = 7024 and N control = 198 740), BioBank Japan (N case = 2385 and N control = 209 651) and Early Genetics and Lifecourse Epidemiology (EAGLE) eczema consortium (N case = 18 900 and N control = 84 166, without the 23andMe study) were used to investigate the association with esophageal cancer in the UK Biobank study (N case = 740 and N control = 372 016) and BioBank Japan esophageal cancer sample (N case = 1300 and N control = 197 045).

Results

When esophageal cancer extracted from East Asian ancestry was used as a outcome factor, AD data extracted from BioBank Japan (OR = 0.90, 95% CI: 0.83-0.98), FinnGen consortium (OR = 0.86, 95% CI: 0.77-0.96), and EAGLE consortium (OR = 0.92, 95% CI: 0.81-1.06) were negatively associated with esophageal cancer susceptibility. However, AD as a whole did not show an association with esophageal cancer from European ancestry.

Conclusion

This study provides support for a causal relationship between AD and esophageal cancer in East Asian populations but not between AD and esophageal cancer from European ancestry. The specific associations between esophageal cancer and AD appear to exhibit significant disparities between the East Asian and European regions.

Mendelian randomization analysis identifies a genetic casual association between circulating C-reactive protein and intracerebral hemorrhage

BACKGROUND

The causal effect of C-reactive protein (CRP) on intracerebral hemorrhage (ICH) remains controversial. We discussed the causal association of CRP with ICH based on two-sample Mendelian randomization.

METHODS

The data from two genome-wide association studies (GWAS) of European ancestry was extracted, including circulating CRP levels (204,402 individuals) and ICH (1,687 cases and 201,146 controls). The inverse variance weighted (IVW) method was primary tool to evaluate the causal relationship of circulating CRP levels on ICH risk. MR-Egger regression and MR-PRESSO global test were utilized to identify pleiotropy. Heterogeneity was discussed with Cochran's Q test. The leave-one-out analysis explored the reliability of the results.

RESULTS

54 SNPs were identified as instrumental variables (IVs) for circulating CRP levels, and these IVs had no significant horizontal pleiotropy, heterogeneity, or bias. MR analysis demonstrated a causal relationship between elevated circulating CRP levels and decreased risk of ICH (ORIVW = 0.828, 95% CI 0.692-0.992, P = 0.040).

CONCLUSION

Elevated circulating CRP levels demonstrated a significant potentially protective causal relationship with risk of ICH.

Performance Benefits of Pre- and Per-cooling on Self-paced Versus Constant Workload Exercise: A Systematic Review and Meta-analysis

BACKGROUND AND OBJECTIVE

Exercise in hot environments impairs endurance performance. Cooling interventions can attenuate the impact of heat stress on performance, but the influence of an exercise protocol on the magnitude of performance benefit remains unknown. This meta-analytical review compared the effects of pre- and per-cooling interventions on performance during self-paced and constant workload exercise in the heat.

METHODS

The study protocol was preregistered at the Open Science Framework ( https://osf.io/wqjb3 ). A systematic literature search was performed in PubMed, Web of Science, and MEDLINE from inception to 9 June, 2023. We included studies that examined the effects of pre- or per-cooling on exercise performance in male individuals under heat stress (> 30 °C) during self-paced or constant workload exercise in cross-over design studies. Risk of bias was assessed using the Cochrane Risk of Bias Tool for randomized trials.

RESULTS

Fifty-nine studies (n = 563 athletes) were identified from 3300 records, of which 40 (n = 370 athletes) used a self-paced protocol and 19 (n = 193 athletes) used a constant workload protocol. Eighteen studies compared multiple cooling interventions and were included more than once (total n = 86 experiments and n = 832 paired measurements). Sixty-seven experiments used a pre-cooling intervention and 19 used a per-cooling intervention. Average ambient conditions were 34.0 °C [32.3-35.0 °C] and 50.0% [40.0-55.3%] relative humidity. Cooling interventions attenuated the performance decline in hot conditions and were more effective during a constant workload (effect size [ES] = 0.62, 95% confidence interval [CI] 0.44-0.81) compared with self-paced exercise (ES = 0.30, 95% CI 0.18-0.42, p = 0.004). A difference in performance outcomes between protocols was only observed with pre-cooling (ES = 0.74, 95% CI 0.50-0.98 vs ES = 0.29, 95% CI 0.17-0.42, p = 0.001), but not per-cooling (ES = 0.45, 95% CI 0.16-0.74 vs ES = 0.35, 95% CI 0.01-0.70, p = 0.68).

CONCLUSIONS

Cooling interventions attenuated the decline in performance during exercise in the heat, but the magnitude of the effect is dependent on exercise protocol (self-paced vs constant workload) and cooling type (pre- vs per-cooling). Pre-cooling appears to be more effective in attenuating the decline in exercise performance during a constant workload compared with self-paced exercise protocols, whereas no differences were found in the effectiveness of per-cooling.

Interaction between systemic iron parameters and left ventricular structure and function in the preserved ejection fraction population: a two-sample bidirectional Mendelian randomization study

BACKGROUND

Left ventricular (LV) remodeling and diastolic function in people with heart failure (HF) are correlated with iron status; however, the causality is uncertain. This Mendelian randomization (MR) study investigated the bidirectional causal relationship between systemic iron parameters and LV structure and function in a preserved ejection fraction population.

METHODS

Transferrin saturation (TSAT), total iron binding capacity (TIBC), and serum iron and ferritin levels were extracted as instrumental variables for iron parameters from meta-analyses of public genome-wide association studies. Individuals without myocardial infarction history, HF, or LV ejection fraction (LVEF) < 50% (n = 16,923) in the UK Biobank Cardiovascular Magnetic Resonance Imaging Study constituted the outcome dataset. The dataset included LV end-diastolic volume, LV end-systolic volume, LV mass (LVM), and LVM-to-end-diastolic volume ratio (LVMVR). We used a two-sample bidirectional MR study with inverse variance weighting (IVW) as the primary analysis method and estimation methods using different algorithms to improve the robustness of the results.

RESULTS

In the IVW analysis, one standard deviation (SD) increased in TSAT significantly correlated with decreased LVMVR (β = -0.1365; 95% confidence interval [CI]: -0.2092 to -0.0638; P = 0.0002) after Bonferroni adjustment. Conversely, no significant relationships were observed between other iron and LV parameters. After Bonferroni correction, reverse MR analysis showed that one SD increase in LVEF significantly correlated with decreased TSAT (β = -0.0699; 95% CI: -0.1087 to -0.0311; P = 0.0004). No heterogeneity or pleiotropic effects evidence was observed in the analysis.

CONCLUSIONS

We demonstrated a causal relationship between TSAT and LV remodeling and function in a preserved ejection fraction population.

PASTRY: achieving balanced power for detecting risk and protective minor alleles in meta-analysis of association studies with overlapping subjects

BACKGROUND

Meta-analysis is a statistical method that combines the results of multiple studies to increase statistical power. When multiple studies participating in a meta-analysis utilize the same public dataset as controls, the summary statistics from these studies become correlated. To solve this challenge, Lin and Sullivan proposed a method to provide an optimal test statistic adjusted for the correlation. This method quickly became the standard practice. However, we identified an unexpected power asymmetry phenomenon in this standard framework. This can lead to unbalanced power for detecting protective minor alleles and risk minor alleles.

RESULTS

We found that the power asymmetry of the current framework is mainly due to the errors in approximating the correlation term. We then developed a meta-analysis method based on an accurate correlation estimator, called PASTRY (A method to avoid Power ASymmeTRY). PASTRY outperformed the standard method on both simulated and real datasets in terms of the power symmetry.

CONCLUSIONS

Our findings suggest that PASTRY can help to alleviate the power asymmetry problem. PASTRY is available at https://github.com/hanlab-SNU/PASTRY .

Causal Association Between Allergic Diseases and Dementia: Evidence from Multivariate Mendelian Randomization Study

Background

The link between allergic diseases and dementia remains controversial, and the genetic causality of this link is unclear.

Objective

This study investigated the causal relationship between allergic diseases and dementia using univariate and multivariate Mendelian randomization (MR) methods.

Methods

We selected genome-wide association studies including 66,645 patients with allergic diseases and 12,281 patients with dementia, with statistical datasets derived from the FinnGen Consortium of European origin. After a rigorous screening process for single nucleotide polymorphisms to eliminate confounding effects, MR estimation was performed mainly using the inverse variance weighting method and the MR-Egger method. Sensitivity analyses were performed using Cochran's Q test, MR-PRESSO test, MR Pleiotropy residuals and leave-one-out analysis.

Results

Univariate and multivariate MR together demonstrated a causal relationship between atopic dermatitis and reduced vascular dementia (VaD) risk (OR = 0.89, 95% CI: 0.81-0.99, p = 0.031; OR = 0.85, 95% CI: 0.76-0.95, p = 0.003). MVMR confirmed asthma was associated with a reduction in the risk of Alzheimer's disease (AD) (OR = 0.82, 95% CI: 0.71-0.94, p = 0.005) and may be associated with a reduction in the risk of VaD (OR = 0.80, 95% CI: 0.65-0.99, p = 0.042); allergic rhinitis may be causally associated with an increased risk of AD (OR = 1.16, 95% CI: 1.00-1.35, p = 0.046) and VaD (OR = 1.29, 95% CI: 1.03-1.62, p = 0.027). In sensitivity analyses, these findings were reliable.

Conclusions

MR methods have only demonstrated that allergic rhinitis dementia is associated with an increased risk of developing dementia. Previously observed associations between other allergic diseases and dementia may be influenced by comorbidities and confounding factors rather than causality.

Genome-wide association and Mendelian randomization analysis provide insights into the shared genetic architecture between high-dimensional electrocardiographic features and ischemic heart disease

Observational studies have revealed that ischemic heart disease (IHD) has a unique manifestation on electrocardiographic (ECG). However, the genetic relationships between IHD and ECG remain unclear. We took 12-lead ECG as phenotypes to conduct genome-wide association studies (GWAS) for 41,960 samples from UK-Biobank (UKB). By leveraging large-scale GWAS summary of ECG and IHD (downloaded from FinnGen database), we performed LD score regression (LDSC), Mendelian randomization (MR), and polygenic risk score (PRS) regression to explore genetic relationships between IHD and ECG. Finally, we constructed an XGBoost model to predict IHD by integrating PRS and ECG. The GWAS identified 114 independent SNPs significantly (P value < 5 × 10-8/800, where 800 denotes the number of ECG features) associated with ECG. LDSC analysis indicated significant (P value < 0.05) genetic correlations between 39 ECG features and IHD. MR analysis performed by five approaches showed a putative causal effect of IHD on four S wave related ECG features at lead III. Integrating PRS for these ECG features with age and gender, the XGBoost model achieved Area Under Curve (AUC) 0.72 in predicting IHD. Here, we provide genetic evidence supporting S wave related ECG features at lead III to monitor the IHD risk, and open up a unique approach to integrate ECG with genetic factors for pre-warning IHD.

The causal relationship between osteoarthritis and bladder cancer: A Mendelian randomization study

OBJECTIVE

The causal association between osteoarthritis (OA) and bladder cancer remains unclear. This Mendelian randomization (MR) study was carried out to assess the potential causal effects of any OA, knee OA and hip OA, and bladder cancer.

METHOD

Genome-wide association study (GWAS) summary data for OA and bladder cancer were obtained in GWAS CATALOG, UK Biobank, and FinnGen Consortium. Inverse-variance weighted (IVW) approach was primarily conducted to evaluate the causal relationships between OA and bladder cancer, and MR-Egger intercept and Cochran's Q test were mainly used to estimate heterogeneity and pleiotropy. MR-PRESSO was used to test the presence of horizontal outliers. Leave-one-out analysis was utilized to ensure the reliability of the results.

RESULTS

A higher genetic predisposition to any OA has a causal association with bladder cancer risk, while neither knee OA nor hip OA is causally linked to bladder cancer. MR-Egger intercept analysis exhibited that any OA and knee OA had no pleiotropic effect on the risk of bladder cancer, and Cochran's Q test showed that any OA, knee OA and hip OA had no heterogeneity on bladder cancer risk. Neither MR PRESSO analysis nor leave-one-out analysis revealed any outlier SNPs.

CONCLUSIONS

This MR study exhibited a positive cause-and-effect relationship between any type of OA and bladder cancer risk, but not between site-specific OA, knee OA and hip OA, and bladder cancer. Attention should be paid to the screening and prevention of bladder cancer in OA patients at any site.

Error Rates of Data Processing Methods in Clinical Research: A Systematic Review and Meta-Analysis of Manuscripts Identified Through PubMed

Background

In clinical research, prevention of systematic and random errors of data collected is paramount to ensuring reproducibility of trial results and the safety and efficacy of the resulting interventions. Over the last 40 years, empirical assessments of data accuracy in clinical research have been reported in the literature. Although there have been reports of data error and discrepancy rates in clinical studies, there has been little systematic synthesis of these results. Further, although notable exceptions exist, little evidence exists regarding the relative accuracy of different data processing methods. We aim to address this gap by evaluating error rates for 4 data processing methods.

Methods

A systematic review of the literature identified through PubMed was performed to identify studies that evaluated the quality of data obtained through data processing methods typically used in clinical trials: medical record abstraction (MRA), optical scanning, single-data entry, and double-data entry. Quantitative information on data accuracy was abstracted from the manuscripts and pooled. Meta-analysis of single proportions based on the Freeman-Tukey transformation method and the generalized linear mixed model approach were used to derive an overall estimate of error rates across data processing methods used in each study for comparison.

Results

A total of 93 papers (published from 1978 to 2008) meeting our inclusion criteria were categorized according to their data processing methods. The accuracy associated with data processing methods varied widely, with error rates ranging from 2 errors per 10,000 fields to 2,784 errors per 10,000 fields. MRA was associated with both high and highly variable error rates, having a pooled error rate of 6.57% (95% CI: 5.51, 7.72). In comparison, the pooled error rates for optical scanning, single-data entry, and double-data entry methods were 0.74% (0.21, 1.60), 0.29% (0.24, 0.35) and 0.14% (0.08, 0.20), respectively.

Conclusions

Data processing and cleaning methods may explain a significant amount of the variability in data accuracy. MRA error rates, for example, were high enough to impact decisions made using the data and could necessitate increases in sample sizes to preserve statistical power. Thus, the choice of data processing methods can likely impact process capability and, ultimately, the validity of trial results.

Saturation genome editing of DDX3X clarifies pathogenicity of germline and somatic variation

Loss-of-function of DDX3X is a leading cause of neurodevelopmental disorders (NDD) in females. DDX3X is also a somatically mutated cancer driver gene proposed to have tumour promoting and suppressing effects. We perform saturation genome editing of DDX3X, testing in vitro the functional impact of 12,776 nucleotide variants. We identify 3432 functionally abnormal variants, in three distinct classes. We train a machine learning classifier to identify functionally abnormal variants of NDD-relevance. This classifier has at least 97% sensitivity and 99% specificity to detect variants pathogenic for NDD, substantially out-performing in silico predictors, and resolving up to 93% of variants of uncertain significance. Moreover, functionally-abnormal variants can account for almost all of the excess nonsynonymous DDX3X somatic mutations seen in DDX3X-driven cancers. Systematic maps of variant effects generated in experimentally tractable cell types have the potential to transform clinical interpretation of both germline and somatic disease-associated variation.

Modifiable risk factors for diphtheria: A systematic review and meta-analysis

Objective

To identify modifiable risk factors for diphtheria and assess their strengths of association with the disease.

Methods

This review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) statement. Electronic databases and grey literature were searched from inception until January 2023. Studies had to report on diphtheria cases and estimates of association for at least one potential risk factor or sufficient data to calculate these. The quality of non-ecological studies was assessed using the Newcastle-Ottawa Scale (NOS), while the quality of evidence was evaluated using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) criteria.

Results

The search yielded 37,705 papers, of which 29 were ultimately included. All the non-ecological studies were of moderate to high quality. Meta-analysis of 20 studies identified three factors increasing the risk of diphtheria: incomplete vaccination (<3 doses) (pooled odds ratio (POR) = 2.2, 95% confidence interval (CI) = 1.4-3.4); contact with a person with skin lesions (POR = 4.8, 95% CI = 2.1-10.9); and low knowledge of diphtheria (POR = 2.4, 95% CI = 1.2-4.7). Contact with a case of diphtheria; sharing a bed or bedroom; sharing utensils, cups, and glasses; infrequent bathing; and low parental education were associated with diphtheria in multiple studies. Evidence for other factors was inconclusive. The quality of evidence was low or very low for all the risk factors.

Conclusions

Findings from the review suggest that countries seeking to control diphtheria need to strengthen surveillance, improve vaccination coverage, and increase people's knowledge of the disease. Future research should focus on understudied or inconclusive risk factors.

Systematic review and meta-analysis of the methionine utilization efficiency in piglets receiving different methionine sources

Methionine (Met) is an essential amino acid that can be supplied in different chemical forms: DL-Met, L-Met, and OH-Met. This study aimed (i) to model and compare the utilization efficiency of Met for protein deposition (PD) from all sources and (ii) to determine the efficacy and efficiency of these three free Met sources in average daily gain (ADG) of post-weaning pigs fed at or below the Met requirement. A systematic review of the literature resulted in 1 898 papers being screened for title and abstract, with 24 papers meeting the inclusion criteria. The resulting database containing 208 treatment means was used. Prior to model development, the standardized ileal digestible (SID) Met requirements in percentage in the diet were determined using initial and final BW according to the NRC (2012). Data from piglets fed above the SID Met requirements were excluded from the database prior to statistical analysis. Linear mixed-effects regression models predicting ADG as a function of free Met source and SID methionine intake (Meti) or methionine + cysteine intake (Met + cysi) were used to evaluate the efficacy and efficiency of free Met source for weight gain. Moreover, Met retention was modeled assuming that 16% of ADG is deposited as PD, and that Met accounts for 2% of PD. Met utilization efficiency was calculated as Meti after maintenance divided by Met retained in PD. Met utilization efficiency was 77% for the basal diet, decreased (P < 0.01) as Meti increased, and was equal among the three free Met sources. The mixed-effects models showed no difference in ADG for three free Met sources evaluated (P > 0.05). However, the efficacy (ADG per unit of SID Meti) of free Met sources for weight gain differed between piglets fed L and DL-Met (P < 0.05), while there was no difference (P > 0.05) between piglets fed DL and OH-Met or OH and L-Met. On average, piglets fed L-Met gained 40.3 g/d more weight per unit of increase in SID Meti than those fed DL-Met (model 4; P = 0.05). The efficacy of free Met sources for ADG was also compared using SID Met + cysi as covariable. Piglets fed L- (+11.7 g/d; P = 0.02) or OH-Met (+11.5 g/d; P = 0.04) gained more weight per gram of SID Met + cysi compared to those fed DL-Met. In conclusion, although the efficacy of DL- and L-Met for ADG differed, the efficiency for PD of L-, DL-, and OH-Met were not different in piglets fed at or below Meti requirement.

Endoscopic Submucosal Dissection Versus Surgery or Endoscopic Mucosal Resection for Metachronous Early Gastric Cancer: a Meta-analysis

BACKGROUND

Resection options for early gastric cancer (EGC) include endoscopic submucosal dissection (ESD), endoscopic mucosal resection (EMR), and surgery. In patients with metachronous EGC following previous resection, the optimal resection technique is not well elucidated. We conducted a systematic review and meta-analysis of studies comparing ESD to EMR, or ESD to surgery, in patients with metachronous EGC.

METHODS

We conducted an electronic search of studies reporting on outcomes and AEs following ESD versus either EMR or surgery for patients with metachronous EGC. Pooled odds ratios (OR) of included studies were obtained using DerSimonian and Laird random effects models. Funnel plots were produced and visually inspected for evidence of publication bias. The quality of the evidence was assessed using GRADE.

RESULTS

A total of 9367 abstracts were screened and 10 observational studies were included. The odds of complete resection were higher amongst patients undergoing ESD compared to EMR (OR 5.88, 95% confidence intervals, CI, 1.79-19.35), whereas the odds of complete resection were no different between ESD and surgery (OR 0.57, 95% CI 0.04-8.24). There were no differences in the odds of local recurrence with ESD versus surgery (OR 5.01, 95% CI 0.86-29.13). Post-procedural bleeding did not differ significantly between ESD and EMR (OR 0.70, 95% CI 0.16-3.00). There was no evidence of publication bias.

DISCUSSION

For metachronous EGC, ESD or surgery is preferred over EMR depending on local expertise and patient preferences, largely due to a higher risk of incomplete resection with EMR.

REVIEW REGISTRATION

PROSPERO CRD42021270445.

Bidirectional relationship between 56 peripheral inflammatory regulators and sleep apnea syndrome: A Mendelian randomization study

BACKGROUND

Peripheral inflammation plays an potential role in both pathogenesis and outcomes of sleep apnea syndrome (SAS). However, this topic has not been explored at the genetic level.

OBJECTIVES

The aim of the study was to investigate the genetic interaction between a total of 56 peripheral inflammatory regulators and SAS, and to further reveal the genetic association of SAS-related inflammatory regulators with several neurological disorders.

METHODS

Summary data for SAS, cerebral atherosclerosis, vascular dementia and peripheral concentrations of these inflammatory regulators were collected from genome-wide association studies. Instrumental variables were extracted from these data for causal inference of exposure and outcome using Two-sample Mendelian randomization methods. All analyses were performed using R (version 3.5.2).

RESULTS

First, of the included 56 inflammatory regulators, higher IL-25 level and lower IL-23, IL-24, IL-36γ and MIP-1a levels in peripheral circulation significantly increased the risk of SAS (P<0.05). Second, SAS significantly decreased the peripheral levels of IL-17A, IL-23, IL-27, IL-36α and TRAIL (P<0.05). Third, there was no genetic relationship between SAS and other inflammatory regulators (P>0.05). Fourth, in the SAS-related inflammatory regulators mentioned above, decreased levels of IL-17A and IL-27 in peripheral circulation were significantly associated with the increased risk of cerebral atherosclerosis, and decreased level of TRAIL promoted the elevation of vascular dementia risk (P<0.05).

CONCLUSION

There was a interaction between peripheral inflammation and SAS at the genetic level. Furthermore, peripheral inflammation might involved in the mechanism for SAS causing some neurological diseases mentioned above.

Correlation between diabetic retinopathy and diabetic nephropathy: a two-sample Mendelian randomization study

Rationale & objective

A causal relationship concerning diabetic retinopathy (DR) and diabetic nephropathy (DN) has been studied in many epidemiological observational studies. We conducted a two-sample mendelian randomization study from the perspective of genetics to assess these associations.

Methods

20 independent single nucleotide polymorphisms (SNPs) associated with diabetic retinopathy were selected from the FinnGen consortium. Summary-level data for diabetic nephropathy were obtained from the publicly available genome-wide association studies (GWAS) database, FinnGen and CKDGen consortium. Inverse variance weighted (IVW) was selected as the primary analysis. MR-Egger, weighted median (WM), simple mode and weighted mode were used as complementary methods to examine causality. Additionally, sensitivity analyses including Cochran's Q test, MR-Egger, MR-Pleiotropy Residual Sum and Outlier (MR-PRESSO), and leave-one-out analyses were conducted to guarantee the accuracy and robustness of our MR analysis.

Results

Our current study demonstrated positive associations of genetically predicted diabetic retinopathy with diabetic nephropathy (OR=1.32; P=3.72E-11), type 1 diabetes with renal complications (OR=1.96; P= 7.11E-11), and type 2 diabetes with renal complications (OR=1.26, P=3.58E-04). Further subtype analysis and multivariate mendelian randomization (MVMR) also reached the same conclusion. A significant casualty with DN was demonstrated both in non-proliferative DR (OR=1.07, P=0.000396) and proliferative DR (OR=1.67, P=3.699068E-14). All the findings were robust across several sensitivity analyses.

Conclusion

Consistent with previous clinical studies, our findings revealed a positive correlation between DR and DN, providing genetic evidence for the non-invasive nature of DR in predicting DN.

Building an optimal predictive model for imputing tissue-specific gene expression by combining genotype and whole-blood transcriptome data

Accurate imputation of tissue-specific gene expression can be a powerful tool for understanding the biological mechanisms underlying human complex traits. Existing imputation methods can be grouped into two categories according to the types of predictors used. The first category uses genotype data, while the second category uses whole-blood expression data. Both data types can be easily collected from blood, avoiding invasive tissue biopsies. In this study, we attempted to build an optimal predictive model for imputing tissue-specific gene expression by combining the genotype and whole-blood expression data. We first evaluated the imputation performance of each standalone model (using genotype data [GEN model] and using whole-blood expression data [WBE model]) using their respective data types across 47 human tissues. The WBE model outperformed the GEN model in most tissues by a large gain. Then, we developed several combined models that leverage both types of predictors to further improve imputation performance. We tried various strategies, including utilizing a merged dataset of the two data types (MERGED models) and integrating the imputation outcomes of the two standalone models (inverse variance-weighted [IVW] models). We found that one of the MERGED models noticeably outperformed the standalone models. This model involved a fixed ratio between the two regularization penalty factors for the two predictor types so that the contribution of the whole-blood transcriptome is upweighted compared with the genotype. Our study suggests that one can improve the imputation of tissue-specific gene expression by combining the genotype and whole-blood expression, but the improvement can be largely dependent on the combination strategy chosen.

Prevalence of tick-borne pathogens in Rhipicephalus species infesting domestic animals in Africa: A systematic review and meta-analysis

Rhipicephalus ticks transmit important tick-borne pathogens (TBPs) such as Anaplasma, Babesia, and Theileria spp. which cause major economic losses in livestock production and contribute to emerging zoonotic diseases. A vast amount of data is available based on the demonstration of these pathogens in various host tissues, with limited information on the prevalence of these TBPs and their vectors. Quantifying TBPs infection rates among Rhipicephalus spp. is essential for the effective control and management of TBDs in domestic animals and surveillance of emerging diseases in humans, as they have close social associations. This review summarizes the prevalence of TBPs in Rhipicephalus spp. from domestic animals of Africa. A thorough search was done in SCOPUS, Web of Knowledge, PubMed, Google Scholar, and library sources from 2000 to 2022. All research in Africa reporting TBPs infection rates in Rhipicephalus spp. were included in the selection criteria. The meta-analysis evaluated publication bias using funnel plots to analyze the observed heterogeneity and applied a quality effects model. Prevalence estimates were based on data from 46 studies reporting TBPs infection rates in Rhipicephalus spp. from northern and sub-Saharan Africa. Sub-group analysis was done by geographic region and tick genus. A total of 12,368 Rhipicephalus spp. collected from domestic animals in Africa were used in the meta-analysis. The quality effects model revealed a high degree of heterogeneity among studies on the various TBPs. The overall prevalence of detected TBPs such as Theileria spp. was 8% (95% CI: 3-15%), Rickettsia spp. 3% (95% CI: 0-9%), Ehrlichia spp. 7% (95% CI: 2-14%), Anaplasma spp. 8% (95% CI: 2-16%), Coxiella spp. 10% (95% CI: 1-26%) and Babesia spp. 6% (95% CI: 2-12%). Northern Africa had the highest prevalence of Anaplasma spp. 12% (95% CI: 3-25%) and Theileria spp. 16% (95% CI: 0-42%). Whilst West Africa had the highest prevalence for Ehrlichia spp. 12% (95% CI: 3-24%) and eastern Africa for Rickettsia spp. 8% (95% CI: 4-12%). This is a systematic and quantitative investigation of the various TBPs detected in Rhipicephalus tick vectors from domestic animal hosts in Africa. The findings demonstrate considerable species variation across the African continent and offer preliminary estimates of infection rates for the continent.

The causal effect of schizophrenia on fractures and bone mineral density: a comprehensive two-sample Mendelian randomization study of European ancestry

BACKGROUND

Schizophrenia was clinically documented to co-occur with fractures and aberrant bone mineral density (BMD), but the potential causal relationship remained unclear. This study aimed to test the causal effects between schizophrenia and fractures as well as aberrant BMD by conducting Mendelian randomization (MR) analyses.

METHODS

Two-sample MR was utilized, based on instrumental variables from large genome-wide association studies (GWAS) of schizophrenia as exposure, to identify the causal association of schizophrenia with mixed fractures, fractures at different body sites (including skull and facial bones, shoulder and upper arm, wrist and hand, and femur) and BMDs of forearm (FA), femoral neck (FN), lumbar spine (LS) and estimated BMD (eBMD). Multivariable Mendelian randomization (MVMR) analysis was performed to minimize the confounding effect of body mass index (BMI).

RESULTS

Result from inverse variance weighting (IVW) method provided evidence schizophrenia increased the risk of fractures of skull and facial bones [odds ratio (OR) = 1.0006, 95% confidence interval (CI): 1.0003 to 1.0010] and femur [OR =1.0007, 95% CI: 1.0003 to 1.0011], whereas, decreased the level of eBMD [β (95%CI): -0.013 (-0.021, -0.004)]. These causal effects still existed after adjusting for BMI. Sensitivity analyses showed similar results. However, no causal effect of schizophrenia on fracture or BMD in other parts was detected.

CONCLUSION

The current finding confirmed that schizophrenia was causally associated with the fractures of skull, face and femur as well as eBMD, which might remind psychiatrists to pay close attention to the fracture risk in schizophrenic patients when formulating their treatment strategies.

Causal association between common rheumatic diseases and glaucoma: a Mendelian randomization study

Background

Autoimmunity and inflammation are the main characteristics of rheumatic diseases and have both been found to be related to glaucoma. However, it remains unclear whether rheumatic diseases increase the risk of glaucoma. Here, we performed a Mendelian randomization (MR) analysis to investigate the causal effects of six common rheumatic diseases on glaucoma.

Methods

Six rheumatic diseases were included: ankylosing spondylitis (AS), rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), Sicca syndrome/Sjögren's sydrome (SS), dermatomyositis (DM), and gout. Glaucoma included primary open-angle glaucoma (POAG) and primary angle-closure glaucoma (PACG). Genetic variants associated with these rheumatic diseases and glaucoma were extracted from the genome-wide association studies and FinnGen8 database, respectively. First, a two-sample MR was used to investigate the potential causal association. Then, a multivariable MR was conducted to further verify the results. Inverse-variance weighted MR analysis was used as the main method, together with several sensitivity analyses.

Results

Two-sample MR suggests that AS is related to a higher risk of both POAG [odds ratio (OR): 1.28, 95% confidence interval (CI) 1.13-1.44; p = 1.1 × 10-4] and PACG (OR: 1.55, 95% CI: 1.09-2.09, p = 1.4 × 10-2). Multivariable MR shows a similar trend of the effect of AS on POAG (OR: 1.52, 95% CI: 1.22-1.90, p = 1.9 × 10-4) and PACG (OR: 2.05, 95% CI: 1.06-3.95, p = 3.2 × 10-2). No significant association was observed between the other five rheumatic diseases and glaucoma.

Conclusions

AS is related to an increased risk of POAG and PACG. We stress the importance of glaucoma screening for AS patients.

Differences in Dental Implant Survival between Immediate vs. Delayed Placement: A Systematic Review and Meta-Analysis

OBJECTIVES

To compare the impact of immediate and delayed implant placement upon the survival of implants and to investigate the differences in implant survival between immediate and delayed placement in adults.

METHODS

A search for the relevant literature was performed using the databases of CENTRAL, MEDLINE and Scopus. The studies found were limited to publications between 2014 and 2022, written in the English language, peer-reviewed, and were randomised trials or comparative studies. The quality of the evidence was assessed using the Cochrane Risk of Bias 2.0 and Risk of Bias in Non-randomised Studies-of Interventions appraisal tools and implant survival, and the primary outcome was meta-analysed using RevMan v.5.3.

RESULTS

A total of 10 studies were eligible for inclusion, including six randomised controlled trials and four non-randomised comparative studies. Five of the six randomised trials observed a low risk of bias, while the comparative studies had a moderate-to-serious risk of bias. The search strategy resulted in 341 implants placed immediately into fresh extraction sites (332 survived, 97.4%) and 359 implants inserted into delayed sites (350 survived, 97.5%).

CONCLUSION

The meta-analysis demonstrated that there was no significant difference in the implant survival rates between immediately placed implants and implants placed using a delayed timing protocol (risk ratio 0.99; 95% CI 0.96, 1.02, Z = 0.75, p = 0.45). However, the detailed analysis showed that slightly more implant failures happened in the immediate dental implant placement group, with survival rates in some studies ranging between 90 and 95%, while the delayed placement group had survival rates of more than 95%.