Using Mendelian randomization as the cornerstone for causal inference in epidemiology

Causal association between smoke and the risk of chronic knee pain: A Mendelian randomization study

A plethora of research has identified a comorbid association between smoke and an elevated risk of knee pain. Despite these findings, the causal link between genetically influenced smoke and the risk of knee pain remains to be elucidated. Considering this knowledge gap, we undertook a Mendelian randomization (MR) study to delineate the potential causal relationship. The instrumental variables were derived from genome-wide association studies (GWAS). We procured summary statistics for ever smoked from a GWAS dataset (280,508 cases and 180,558 controls, dataset: ukb-b-20261) to represent the exposure. The outcome was determined by GWAS data for knee pain for 3+ months, encompassing 76,910 cases and 20,979 controls (dataset: ukb-b-8906). The primary MR method employed was the inverse-variance weighted approach. Assessments for pleiotropy and heterogeneity were conducted utilizing the MR pleiotropy residual sum and outlier test, the MR-Egger intercept test, the leave-one-out analysis, and the Cochran Q test. There was a statistically significant genetic causal effect of smoke on the increased risk of knee pain (odds ratio = 1.08, 95% confidence interval = 1.01-1.16, P = .014]. Cochran Q statistic showed no heterogeneity (Q P = .66). The leave-one-out analysis chart, the global test P value in MR-pleiotropy residual sum, and outlier revealed no significant pleiotropy (global test P = 0.53). The intercept P value in MR-Egger revealed no significant pleiotropy (intercept P = 0.66). Our MR study showed no pleiotropy or heterogeneity. The findings from our study point toward an association between genetic predisposition to smoke and the incidence of knee pain. This genetic association underscores the clinical relevance of our findings, indicating that interventions aimed at smoking cessation could be particularly beneficial for those individuals who are predisposed to smoking or are at risk of developing knee pain.

Integrating Mendelian randomization and literature-mined evidence for breast cancer risk factors

OBJECTIVE

An increasing challenge in population health research is efficiently utilising the wealth of data available from multiple sources to investigate disease mechanisms and identify potential intervention targets. The use of biomedical data integration platforms can facilitate evidence triangulation from these different sources, improving confidence in causal relationships of interest. In this work, we aimed to integrate Mendelian randomization (MR) and literature-mined evidence from the EpiGraphDB biomedical knowledge graph to build a comprehensive overview of risk factors for developing breast cancer.

METHODS

We utilised MR-EvE ("Everything-vs-Everything") data to identify candidate risk factors for breast cancer and generate hypotheses for potential mediators of their effect. We also integrated this data with literature-mined relationships, which were extracted by overlapping literature spaces of risk factors and breast cancer. The literature-based discovery (LBD) results were followed up by validation with two-step MR to triangulate the findings from two data sources.

RESULTS

We identified 129 novel and established lifestyle risk factors and molecular traits with evidence of an effect on breast cancer, and made the MR results available in an R/Shiny app (https://mvab.shinyapps.io/MR_heatmaps/). We developed an LBD approach for identifying potential mechanistic intermediates of identified risk factors. We present the results of MR and literature evidence integration for two case studies (childhood body size and HDL-cholesterol), demonstrating their complementary functionalities.

CONCLUSION

We demonstrate that MR-EvE data offers an efficient hypothesis-generating approach for identifying disease risk factors. Moreover, we show that integrating MR evidence with literature-mined data may be used to identify causal intermediates and uncover the mechanisms behind the disease.

Assessment of the causal association between obstructive sleep apnea and telomere length: a bidirectional mendelian randomization study

Background

A plethora of observational studies has established a significant correlation between Obstructive Sleep Apnea (OSA) and Telomere Length (TL). Nevertheless, a universal consensus on precise causal association and its directionality has not yet been achieved. To shed light on this, we employed Mendelian Randomization (MR) to investigate the bidirectional causal association between OSA and TL.

Method

Utilizing publicly accessible Genome-Wide Association Studies (GWAS) datasets, we procured genetic data pertinent to MR analysis. The study incorporated samples from both the OSA (n = 217,955) and TL (n = 472,174) cohorts. In the forward MR analysis, OSA served as the exposure variable and TL as the outcome. Conversely, the reverse MR analysis treated TL as the exposure and OSA as the outcome. We employed the Inverse variance weighted (IVW) as the primary methodology for MR analysis. To ensure the robustness of our MR findings, multiple sensitivity analyses were performed.

Results

In the forward MR analysis, a negative correlation was indicated between OSA and TL (IVW: odds ratio (OR) = 0.964, 95% confidence interval (CI): 0.939-0.980, P = 0.006 < 0.05). However, no significant association was identified between TL and the risk of OSA in the reverse MR analysis (IVW: OR = 0.965, 95% CI: 0.870-1.070, P = 0.499 > 0.05).

Conclusion

Our study indicated a potential association between OSA and the increased risk of shorter TL, offering vital academic support for future clinical studies on this association.

Causal Association Between Childhood Body Mass Index and Phlebitis and Thrombophlebitis: An Analysis Using Mendelian Randomization

Background: Research has indicated a link between obesity and a greater likelihood of venous disorders. However, the specific relationship between obesity in children and conditions such as phlebitis and thrombophlebitis remains undetermined. To explore this, we undertook a two-sample Mendelian randomization (MR) study to investigate the possible causal impact of childhood body mass index (BMI) on the development of phlebitis and thrombophlebitis. Methods: This study utilized genome-wide association studies data from European populations. Childhood BMI was assessed in a sample of 39,620 individuals, while data on phlebitis and thrombophlebitis were obtained from 1613 cases and 335,586 controls. We selected 16 single nucleotide polymorphisms significantly associated with childhood BMI as instrumental variables (IVs). The inverse variance weighting (IVW) method was applied as the primary approach, with weighted median, MR-Egger regression, and weighted mode methods used as complementary analyses. Results: The IVW analysis indicates a significant causal link between childhood BMI and the occurrence of phlebitis and thrombophlebitis (Beta = 0.002739, Standard error (SE) = 0.000740, p = 0.0002147). Results from the weighted median method (Beta = 0.002446, SE = 0.001046, p = 0.01933) aligned with the IVW findings. However, the MR-Egger and weighted mode analyses did not show a significant association (p = 0.1051 and p = 0.2525, respectively). Leave-one-out sensitivity tests and heterogeneity assessments were performed, revealing no evidence of horizontal pleiotropy. Conclusion: The findings from the MR analysis suggest a potential causal relationship between childhood BMI and an elevated risk of phlebitis and thrombophlebitis. This study provides new insights into the impact of childhood obesity on venous health, emphasizing the need for early intervention and prevention strategies.

Objective assessment of cognitive fatigue: a bibliometric analysis

Aim

The objective of this study was to gain insight into the nature of cognitive fatigue and to identify future trends of objective assessment techniques in this field.

Methods

One thousand and eighty-five articles were retrieved from the Web of Science Core Collection database. R version 4.3.1, VOSviewer 1.6.20, CiteSpace 6.2.R4, and Microsoft Excel 2019 were used to perform the analysis.

Results

A total of 704 institutes from 56 countries participated in the relevant research, while the People's Republic of China contributed 126 articles and was the leading country. The most productive institute was the University of Gothenburg. Johansson Birgitta from the University of Gothenburg has posted the most articles (n = 13). The PLOS ONE published most papers (n = 38). The Neurosciences covered the most citations (n = 1,094). A total of 3,116 keywords were extracted and those with high frequency were mental fatigue, performance, quality-of-life, etc. Keywords mapping analysis indicated that cognitive fatigue caused by continuous work and traumatic brain injury, as well as its rehabilitation, have become the current research trend. The most co-cited literature was published in Sports Medicine. The strongest citation burst was related to electroencephalogram (EEG) event-related potential and spectral power analysis.

Conclusion

Publication information of related literature on the objective assessment of cognitive fatigue from 2007 to 2024 was summarized, including country and institute of origin, authors, and published journal, offering the current hotspots and novel directions in this field.

Mapping the evolving trend of research on leukocyte telomere length: a text-mining study

BACKGROUND

Substantial evidence indicates that measuring leukocyte telomere length (LTL) is a useful tool that may be considered as a valuable biomarker of individual biological age, correlating with numerous chronic disorders. However, to date, there has been a lack of in-depth understanding regarding the current landscape and forthcoming developments in the LTL field. Therefore, this study aimed to utilize bibliometric methods to summarize the knowledge structure, current focus, and emerging directions in this field.

METHOD

Scientific publications on LTL spanning the period from 2000 to 2022 were acquired from the Web of Science Core Collection database. Several bibliometric tools including CiteSpace, VOSviewer, and an online website were utilized for bibliometric analysis. The primary evaluations encompassed investigating the major contributors and their collaborative relationships among countries/regions, institutions, and authors, conducting co-citation analyses of authors, journals, as well as reference, examining reference bursts, as well as performing co-occurrence analyses of keywords.

RESULTS

There are 1818 papers with 66,668 citations identified. Both the annual publication and citation counts on LTL exhibited significant upward trends. The United States emerged as the most prominent contributor, as evidenced by the greatest volume of papers and the highest H-index value. University of California San Francisco and Aviv A were identified as the most productive institution and author in this domain, respectively. Reference analysis revealed that longitudinal study and mendelian randomization study are the most concerned research method in this field recently. Keywords analysis showed that the most concerned diseases in LTL fields were aging, inflammation, cardiovascular diseases, endocrine diseases, neurological and psychiatric diseases, and cancers. In addition, the following research directions such as "COPD", "mendelian randomization", "adiposity", "colorectal cancer", "National Health and Nutrition Examination Survey (NHNES)", "telomerase reverse transcriptase", "pregnancy" have garnered increasing attention in recent times and hold the potential to evolve into research foci in the foreseeable future.

CONCLUSION

This is the first bibliometric study that provides comprehensive overview of LTL research. The findings of this study could become valuable references for investigators to explore and address the current and emerging challenges in LTL research.

Multi-scale transcriptomics reveals that specific tumor cells promote lung adenocarcinoma metastasis through crosstalk with the microenvironment

Most advanced lung adenocarcinoma (LUAD) patient deaths are attributed to metastasis. However, the complete understanding of the metastatic mechanism in LUAD remains elusive. Single-cell RNA-seq (scRNA-seq), spatial RNA-seq (stRNA-seq) and bulk RNA-seq of primary LUAD were integrated to investigate metastatic driver genes, cell-cell interactions, and spatial colocalization of cells and ligand-receptor pairs. A lung adenocarcinoma metastasis risk scoring model (LMRS) was established to estimate the risk of metastasis in LUAD. Forty-two metastasis driver genes were identified and tumor epithelial cells were classified into two subtypes. Epithelial cell subclass characterized by susceptibility to metastasis are referred to as Epithelial_LM, and the remaining as Epithelial_LL. Epithelial_LM subtype has intimate ligand-receptor interactions with inflammatory endothelial cells (iendo), inflammatory cancer-associated fibroblasts (iCAF), and NKT cells. Epithelial_LM cells have a spatial colocalization relationship with these three types of cells. The LMRS was established and its efficacy was verified in bulk RNA-seq. We identified a subclass of epithelial cells prone to metastasis and demonstrated the contribution of inflammatory stromal cells and NKT cells in facilitating tumor metastasis.

Causal association between circulating inflammatory markers and sciatica development: a Mendelian randomization study

Background

This research explores the causal association between circulating inflammatory markers and the development of sciatica, a common and debilitating condition. While previous studies have indicated that inflammation may be a factor in sciatica, but a thorough genetic investigation to determine a cause-and-effect relationship has not yet been carried out. Gaining insight into these interactions may uncover novel treatment targets.

Methods

We utilized data from the OpenGWAS database, incorporating a large European cohort of 484,598 individuals, including 4,549 sciatica patients. Our study focused on 91 distinct circulating inflammatory markers. Genetic variations were employed as instrumental variables (IVs) for these markers. The analysis was conducted using inverse variance weighting (IVW) as the primary method, supplemented by weighted median-based estimation. Validation of the findings was conducted by sensitivity studies, utilizing the R software for statistical computations.

Results

The analysis revealed that 52 out of the 91 inflammatory markers studied showed a significant causal association with the risk of developing sciatica. Key markers like CCL2, monocyte chemotactic protein-4, and protein S100-A12 demonstrated a positive correlation. In addition, there was no heterogeneity or horizontal pleiotropy in these results. Interestingly, a reverse Mendelian randomization analysis also indicated potential causative effects of sciatica on certain inflammatory markers, notably Fms-related tyrosine kinase 3 ligands.

Discussion

The study provides robust evidence linking specific circulating inflammatory markers with the risk of sciatica, highlighting the role of inflammation in its pathogenesis. These findings could inform future research into targeted treatments and enhance our understanding of the biological mechanisms underlying sciatica.

Identification of early coagulation changes associated with survival outcomes post severe burns from multiple perspectives

Coagulation alterations manifest early after severe burns and are closely linked to mortality outcomes. Nevertheless, the precise characterization of coagulation changes associated with early mortality remains elusive. We examined alterations in indicators linked to mortality outcomes at both the transcriptomic and clinical characteristic levels. At the transcriptomic level, we pinpointed 28 differentially expressed coagulation-related genes (DECRGs) following burn injuries and endeavored to validate their causal relationships through Mendelian randomization. DECRGs tied to survival exhibit a significant association with neutrophil function, wherein the expression of CYP4F2 and P2RX1 serves as robust predictors of fatal outcomes. In terms of clinical indicators, early levels of D-dimer and alterations in serum calcium show a strong correlation with mortality outcomes. Coagulation depletion and fibrinolytic activation, stemming from the hyperactivation of coagulation pathways post-severe burns, are strongly linked to patient mortality. Monitoring these early coagulation markers with predictive value can effectively identify individuals necessitating priority critical care.

Utilizing systematic Mendelian randomization to identify potential therapeutic targets for mania

Background

Mania has caused incalculable economic losses for patients, their families, and even society, but there is currently no effective treatment plan for this disease without side effects.

Methods

Using bioinformatics and Mendelian randomization methods, potential drug target genes and key substances associated with mania were explored at the mRNA level. We used the chip expression profile from the GEO database to screen differential genes and used the eQTL and mania GWAS data from the IEU database for two-sample Mendelian randomization (MR) to determine core genes by colocalization. Next, we utilized bioinformatics analysis to identify key substances involved in the mechanism of action and determined related gene targets as drug targets.

Results

After differential expression analysis and MR, a causal relationship between the expression of 46 genes and mania was found. Colocalization analysis yielded six core genes. Five key substances were identified via enrichment analysis, immune-related analysis, and single-gene GSVA analysis of the core genes. MR revealed phenylalanine to be the only key substance that has a unidirectional causal relationship with mania. In the end, SBNO2, PBX2, RAMP3, and QPCT, which are significantly associated with the phenylalanine metabolism pathway, were identified as drug target genes.

Conclusion

SBNO2, PBX2, RAMP3, and QPCT could serve as potential target genes for mania treatment and deserve further basic and clinical research. Medicinal target genes regulate the phenylalanine metabolism pathway to achieve the treatment of mania. Phenylalanine is an important intermediate substance in the treatment of mania that is regulated by drug target genes.

Application of three-dimensional printing in cardiovascular diseases: a bibliometric analysis

AIM

This paper aimed to explore the application of three-dimensional (3D) printing in cardiovascular diseases, to reach an insight in this field and prospect the future trend.

METHODS

The articles were selected from the Web of Science Core Collection database. Excel 2019, VOSviewer 1.6.16, and CiteSpace 6.1.R6 were used to analyze the information.

RESULTS

A total of 467 papers of 3D printing in cardiovascular diseases were identified, and the first included literature appeared in 2000. A total of 692 institutions from 52 countries participated in the relevant research, while the United States of America contributed to 160 articles and were in a leading position. The most productive institution was Curtin University , and Zhonghua Sun who has posted the most articles ( n =8) was also from there. The Frontiers in Cardiovascular Medicine published most papers ( n =25). The Journal of Thoracic and Cardiovascular Surgery coveted the most citations ( n =520). Related topics of frontiers will still focus on congenital heart disease, valvular heart disease, and left atrial appendage closure.

CONCLUSIONS

The authors summarized the publication information of the application of 3D printing in cardiovascular diseases related literature from 2000 to 2023, including country and institution of origin, authors, and publication journal. This study can reflect the current hotspots and novel directions for the application of 3D printing in cardiovascular diseases.

Causal relationship between gut microbiota and tuberculosis: a bidirectional two-sample Mendelian randomization analysis

BACKGROUND

Growing evidence from observational studies and clinical trials suggests that the gut microbiota is associated with tuberculosis (TB). However, it is unclear whether any causal relationship exists between them and whether causality is bidirectional.

METHODS

A bidirectional two-sample Mendelian randomization (MR) analysis was performed. The genome-wide association study (GWAS) summary statistics of gut microbiota were obtained from the MiBioGen consortium, while the GWAS summary statistics of TB and its specific phenotypes [respiratory tuberculosis (RTB) and extrapulmonary tuberculosis (EPTB)] were retrieved from the UK Biobank and the FinnGen consortium. And 195 bacterial taxa from phylum to genus were analyzed. Inverse variance weighted (IVW), MR-Egger regression, maximum likelihood (ML), weighted median, and weighted mode methods were applied to the MR analysis. The robustness of causal estimation was tested using the heterogeneity test, horizontal pleiotropy test, and leave-one-out method.

RESULTS

In the UK Biobank database, we found that 11 bacterial taxa had potential causal effects on TB. Three bacterial taxa genus.Akkermansia, family.Verrucomicrobiacea, order.Verrucomicrobiales were validated in the FinnGen database. Based on the results in the FinnGen database, the present study found significant differences in the characteristics of gut microbial distribution between RTB and EPTB. Four bacterial taxa genus.LachnospiraceaeUCG010, genus.Parabacteroides, genus.RuminococcaceaeUCG011, and order.Bacillales were common traits in relation to both RTB and TB, among which order.Bacillales showed a protective effect. Additionally, family.Bacteroidacea and genus.Bacteroides were identified as common traits in relation to both EPTB and TB, positively associating with a higher risk of EPTB. In reverse MR analysis, no causal association was identified. No significant heterogeneity of instrumental variables (IVs) or horizontal pleiotropy was found.

CONCLUSION

Our study supports a one-way causal relationship between gut microbiota and TB, with gut microbiota having a causal effect on TB. The identification of characteristic gut microbiota provides scientific insights for the potential application of the gut microbiota as a preventive, diagnostic, and therapeutic tool for TB.

Causal relationship between levels of myeloperoxidase and obstructive sleep apnea: a bidirectional two-sample Mendelian randomization study

Background

Several observational studies have investigated the association between myeloperoxidase (MPO) and obstructive sleep apnea (OSA). However, the nature of this relationship remains uncertain due to potential selection and confounding biases. To resolve this, we conducted a bidirectional two-sample Mendelian randomization (MR) study to scrutinize the causal relationship between MPO and OSA.

Methods

Instrumental variables (IVs) for OSA were sourced from the publicly available FinnGen dataset, encompassing 38,998 OSA cases and 336,659 controls. Data on MPO were sourced from a study of 21,758 individuals conducted by the European Bioinformatics Institute (EBI). The primary MR analysis utilized the inverse-variance weighted (IVW) method, with MR-Egger intercept and leave-one-out methods assessing pleiotropy and Cochran's Q test determining heterogeneity.

Results

The IVW analysis indicated a causal relationship between heightened MPO levels and an increased incidence of OSA. Individuals with elevated MPO levels manifested a higher propensity to develop OSA, exhibiting an odds ratio (OR) of 1.075 and a 95% confidence interval (CI) of 1.011-1.143 (p = 0.021). Conversely, the reciprocal analysis unveiled no significant association between OSA and heightened MPO levels (p = 0.643). No directional pleiotropy was identified through the MR-Egger intercept test (p > 0.05).

Conclusion

Our study provides evidence of an association between elevated MPO levels and an increased incidence of OSA. However, OSA does not necessarily lead to elevated MPO levels. When patients present with high MPO levels, screening for OSA may be advisable, considering their clinical characteristics.

Eliminating COVID-19 as the immediate culprit for igniting pancreatitis

The impact of severe acute respiratory syndrome coronavirus 2 infection on the potential development of pancreatitis is a subject of ongoing debate within academic discourse. Establishing a causal link between COVID-19 and pancreatitis may not be fully supported by relying only on retrospective studies or case reports. This study examined the relationship between COVID-19 phenotypes and pancreatitis by Mendelian randomization (MR) method. The identification of instrumental variables (single nucleotide polymorphisms) that exhibit a robust association with the COVID-19 phenotypes was accomplished through a meticulous process of rigorous screening procedures. We included acute pancreatitis and chronic pancreatitis (CP) as the outcomes in the MR analysis, even though no definitive studies exist between COVID-19 and CP. A direct causal relationship between genetically predicted COVID-19 phenotypes and pancreatitis risk cannot be established. There is an ongoing debate over the designation of COVID-19 as a definitive cause of pancreatitis.

Gut Microbiota and Respiratory Infections: Insights from Mendelian Randomization

The role of the gut microbiota in modulating the risk of respiratory infections has garnered increasing attention. However, conventional clinical trials have faced challenges in establishing the precise relationship between the two. In this study, we conducted a Mendelian randomization analysis with single nucleotide polymorphisms employed as instrumental variables to assess the causal links between the gut microbiota and respiratory infections. Two categories of bacteria, family Lactobacillaceae and genus Family XIII AD3011, were causally associated with the occurrence of upper respiratory tract infections (URTIs). Four categories of gut microbiota existed that were causally associated with lower respiratory tract infections (LRTIs), with order Bacillales and genus Paraprevotella showing a positive association and genus Alistipes and genus Ruminococcaceae UCG009 showing a negative association. The metabolites and metabolic pathways only played a role in the development of LRTIs, with the metabolite deoxycholine acting negatively and menaquinol 8 biosynthesis acting positively. The identification of specific bacterial populations, metabolites, and pathways may provide new clues for mechanism research concerning therapeutic interventions for respiratory infections. Future research should focus on elucidating the potential mechanisms regulating the gut microbiota and developing effective strategies to reduce the incidence of respiratory infections. These findings have the potential to significantly improve global respiratory health.

Causal association between obstructive sleep apnea and gastroesophageal reflux disease: A bidirectional two-sample Mendelian randomization study

Objectives: Correlations between obstructive sleep apnea (OSA) and gastroesophageal reflux disease (GERD) have been detected in previous observational studies. However, this association remains uncertain due to the potential presence of selection and confounding biases. Therefore, this bidirectional two-sample Mendelian randomization (MR) study was conducted to evaluate the causal relationship between OSA and GERD.

Methods: In this study, instrumental variables (IVs) for OSA were selected from publicly available genetic summary data (27,207 cases and 280,720 controls). Summary statistics for GERD were obtained from a genome-wide association study of 602,604 individuals. The inverse variance weighted (IVW) method was used as the main MR method. The MR-Egger intercept test, MR pleiotropy residual sum and outlier, and leave-one-out analysis were used to detect pleiotropy. Heterogeneity was detected by Cochran’s Q test.

Results: The IVW results revealed that OSA [odds ratio (OR): 1.19, 95% confidence interval (CI): 1.11–1.28, p = 8.88E-07] was causally associated with the incidence of GERD. Moreover, there was evidence of GERD leading to OSA in the IVW analysis (OR: 1.44, 95%CI: 1.33–1.57, p = 7.74E-19). No directional pleiotropy was detected by the MR-Egger intercept test (all p &gt; 0.05).

Conclusion: This study found that OSA is linked to a higher incidence of GERD, and vice versa. This finding might be helpful for the screening and prevention of these two diseases.

A visual knowledge map analysis of mine fire research based on CiteSpace

Mine fire has always been a serious disaster in coal industry; many academic achievements have poured out in the past two decades for solving this problem. In this study, visual analysis was conducted to grasp the hotspots and development trend of mine fire research. Papers that published in 1999-2020 were retrieved as the data basis from Web of Science, and CiteSpace was used to carry out knowledge map analysis. The results shown that number of papers has increased steadily since 2005 and achieved explosive growth since 2014. Deng J is the first published author among many scholars. China, the USA, and Australia are active areas in mine fire research and China University of Mining and Technology ranks first in this field. The highest co-occurrence frequency keyword is "spontaneous combustion." International Journal of Coal Geology and Fuel provide guidance for mine fire research. Fire prevention technology, low carbon, ecology, and sustainable development are the hot research in recent years. The prevention and control of mine fire from combustion mechanism should be further strengthened.