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Chen J, Ye W. Molecular mechanisms underlying Tao-Hong-Si-Wu decoction treating hyperpigmentation based on network pharmacology, Mendelian randomization analysis, and experimental verification. PHARMACEUTICAL BIOLOGY 2024; 62:296-313. [PMID: 38555860 DOI: 10.1080/13880209.2024.2330609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/02/2024] [Indexed: 04/02/2024]
Abstract
CONTEXT Hyperpigmentation, a common skin condition marked by excessive melanin production, currently has limited effective treatment options. OBJECTIVE This study explores the effects of Tao-Hong-Si-Wu decoction (THSWD) on hyperpigmentation and to elucidate the underlying mechanisms. MATERIALS AND METHODS We employed network pharmacology, Mendelian randomization, and molecular docking to identify THSWD's hub targets and mechanisms against hyperpigmentation. The Cell Counting Kit-8 (CCK-8) assay determined suitable THSWD treatment concentrations for PIG1 cells. These cells were exposed to graded concentrations of THSWD-containing serum (2.5%, 5%, 10%, 15%, 20%, 30%, 40%, and 50%) and treated with α-MSH (100 nM) to induce an in vitro hyperpigmentation model. Assessments included melanin content, tyrosinase activity, and Western blotting. RESULTS ALB, IL6, and MAPK3 emerged as primary targets, while quercetin, apigenin, and luteolin were the core active ingredients. The CCK-8 assay indicated that concentrations between 2.5% and 20% were suitable for PIG1 cells, with a 50% cytotoxicity concentration (CC50) of 32.14%. THSWD treatment significantly reduced melanin content and tyrosinase activity in α-MSH-induced PIG1 cells, along with downregulating MC1R and MITF expression. THSWD increased ALB and p-MAPK3/MAPK3 levels and decreased IL6 expression in the model cells. DISCUSSION AND CONCLUSION THSWD mitigates hyperpigmentation by targeting ALB, IL6, and MAPK3. This study paves the way for clinical applications of THSWD as a novel treatment for hyperpigmentation and offers new targeted therapeutic strategies.
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Affiliation(s)
- Jun Chen
- Department of Geriatrics, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Wenyi Ye
- Department of Traditional Chinese Internal Medicine, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
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Huang L, Wang Y, He Y, Huang D, Wen T, Han Z. Association Between COVID-19 and Neurological Diseases: Evidence from Large-Scale Mendelian Randomization Analysis and Single-Cell RNA Sequencing Analysis. Mol Neurobiol 2024; 61:6354-6365. [PMID: 38300446 DOI: 10.1007/s12035-024-03975-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
Observational studies have suggested that SARS-CoV-2 infection increases the risk of neurological diseases, but it remains unclear whether the association is causal. The present study aims to evaluate the causal relationships between SARS-CoV-2 infections and neurological diseases and analyzes the potential routes of SARS-CoV-2 entry at the cellular level. We performed Mendelian randomization (MR) analysis with CAUSE method to investigate causal relationship of SARS-CoV-2 infections with neurological diseases. Then, we conducted single-cell RNA sequencing (scRNA-seq) analysis to obtain evidence of potential neuroinvasion routes by measuring SARS-CoV-2 receptor expression in specific cell subtypes. Fast gene set enrichment analysis (fGSEA) was further performed to assess the pathogenesis of related diseases. The results showed that the COVID-19 is causally associated with manic (delta_elpd, - 0.1300, Z-score: - 2.4; P = 0.0082) and epilepsy (delta_elpd: - 2.20, Z-score: - 1.80; P = 0.038). However, no significant effects were observed for COVID-19 on other traits. Moreover, there are 23 cell subtypes identified through the scRNA-seq transcriptomics data of epilepsy, and SARS-CoV-2 receptor TTYH2 was found to be specifically expressed in oligodendrocyte and astrocyte cell subtypes. Furthermore, fGSEA analysis showed that the cell subtypes with receptor-specific expression was related to methylation of lysine 27 on histone H3 (H3K27ME3), neuronal system, aging brain, neurogenesis, and neuron projection. In summary, this study shows causal links between SARS-CoV-2 infections and neurological disorders such as epilepsy and manic, supported by MR and scRNA-seq analysis. These results should be considered in further studies and public health measures on COVID-19 and neurological diseases.
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Affiliation(s)
- Lin Huang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Yongheng Wang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
- International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing, China
| | - Yijie He
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Dongyu Huang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Tong Wen
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Zhijie Han
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China.
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Shen L, Li J, Zhang H, Zhao Y. Causal effects of endometriosis stages and locations on menstruation, ovulation, reproductive function, and delivery modes: a two-sample Mendelian randomization study. Front Endocrinol (Lausanne) 2024; 15:1328403. [PMID: 39157682 PMCID: PMC11327065 DOI: 10.3389/fendo.2024.1328403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 07/09/2024] [Indexed: 08/20/2024] Open
Abstract
Background Endometriosis is a chronic inflammatory disease of women during their reproductive years. The relationship between the severity and location of endometriosis and menstruation, ovulation, reproductive function, and mode of delivery remains unclear. Methods We explored the association between the various phenotypes of endometriosis and menstruation, ovulation, reproductive function, and mode of delivery, using two-sample Mendelian randomization (MR) and summary data on endometriosis stages and locations from the FinnGen consortium and women's menstruation, ovulation, reproductive function, and mode of delivery from OpenGWAS and ReproGen. Inverse-variance weighting was used for the primary MR analysis. In addition, a series of sensitivity analyses, confounding analyses, co-localization analyses, and multivariate MR analyses were performed. Results MR analysis showed a negative effect of moderate to severe endometriosis on age at last live birth (OR = 0.973, 95% CI: 0.960-0.986) and normal delivery (OR = 0.999, 95% CI: 0.998-1.000; values for endpoint were excluded), ovarian endometriosis on age at last live birth (OR = 0.976, 95% CI: 0.965-0.988) and normal delivery (OR = 0.999, 95% CI: 0.998-1.000; values for endpoint were excluded), and fallopian tubal endometriosis on excessive irregular menstruation (OR = 0.966, 95% CI: 0.942-0.990). Bidirectional MR analysis showed that age at menarche had a negative causal effect on intestinal endometriosis (OR = 0.417, 95% CI: 0.216-0.804). All MR analyses were confirmed by sensitivity analyses, and only the genetic effects of moderate to severe endometriosis on normal delivery and age at last live birth were supported by co-localization evidence. Conclusion Our findings deepen the understanding of the relationship between various types of endometriosis and menstruation, ovulation, reproductive function, and mode of delivery and clarify the important role of moderate to severe endometriosis.
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Affiliation(s)
- Lin Shen
- Department of Reproductive Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Research Institute for Family Planning, Beijing, China
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Li
- Department of Reproductive Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hanwang Zhang
- Department of Reproductive Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yiqing Zhao
- Department of Reproductive Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Wang Y, Tang Y, Liu TH, Shao L, Li C, Wang Y, Tan P. Integrative Multi-omics Analysis to Characterize Herpes Virus Infection Increases the Risk of Alzheimer's Disease. Mol Neurobiol 2024; 61:5337-5352. [PMID: 38191694 DOI: 10.1007/s12035-023-03903-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/22/2023] [Indexed: 01/10/2024]
Abstract
Evidence suggests that herpes virus infection is associated with an increased risk of Alzheimer's disease (AD), and innate and adaptive immunity plays an important role in the association. Although there have been many studies, the mechanism of the association is still unclear. This study aims to reveal the underlying molecular and immune regulatory network through multi-omics data and provide support for the study of the mechanism of infection and AD in the future. Here, we found that the herpes virus infection significantly increased the risk of AD. Genes associated with the occurrence and development of AD and genetically regulated by herpes virus infection are mainly enrichment in immune-related pathways. The 22 key regulatory genes identified by machine learning are mainly immune genes. They are also significantly related to the infiltration changes of 3 immune cell in AD. Furthermore, many of these genes have previously been reported to be linked, or potentially linked, to the pathological mechanisms of both herpes virus infection and AD. In conclusion, this study contributes to the study of the mechanisms related to herpes virus infection and AD, and indicates that the regulation of innate and adaptive immunity may be an effective strategy for preventing and treating herpes virus infection and AD. Additionally, the identified key regulatory genes, whether previously studied or newly discovered, may serve as valuable targets for prevention and treatment strategies.
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Affiliation(s)
- Yongheng Wang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Yaqin Tang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Tai-Hang Liu
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Lizhen Shao
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Chunying Li
- Chongqing Vocational College of Resources and Environmental Protection, Chongqing, China.
| | - Yingxiong Wang
- Joint International Research Laboratory of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China.
| | - Pengcheng Tan
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China.
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Luo J, Liu P, Luo Y. Genetic prediction of asthma increases multiple sepsis risks: A Mendelian randomization study. World Allergy Organ J 2024; 17:100937. [PMID: 39156599 PMCID: PMC11327466 DOI: 10.1016/j.waojou.2024.100937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/24/2024] [Accepted: 07/03/2024] [Indexed: 08/20/2024] Open
Abstract
Background Observational epidemiological studies have indicated a potential association between asthma and sepsis, although the causal relationship between these 2 conditions remains uncertain. To further investigate this relationship, the present study utilized Mendelian randomization (MR) analysis approach to explore the potential links between asthma and various types of sepsis. Methods In a large-scale genome-wide association study, single nucleotide polymorphisms (SNPs) associated with asthma were selected as instrumental variables. Three methods, including inverse-variance weighted (IVW), MR-Egger regression, and weighted median were used to assess the causal relationship between asthma and sepsis. The odds ratio (OR) and 95% confidence interval (CI) were used as the evaluation metrics for causal relationships, and sensitivity analysis was conducted to assess pleiotropy and instrument validity. Finally, a reverse MR analysis was conducted to investigate whether there is a causal relationship between sepsis and asthma. Results We found a positive association between asthma and an increased risk of sepsis (OR=1.18, P<0.05), streptococcal sepsis (OR=1.23, P=0.04), pneumonia-related sepsis (OR=1.57, P<0.05), pneumococcal sepsis (OR=1.58, P=0.01), other sepsis (OR=1.15, P<0.05), and sepsis in intensive care unit (ICU) settings (OR=1.23, P=0.02). Sensitivity analysis showed consistent results without heterogeneity or pleiotropy. The reverse MR analysis reveals no causal relationship between various types of sepsis and asthma. Conclusion Our study demonstrates a causal relationship between asthma and different types of sepsis. These findings suggest the importance of healthcare providers paying attention to the potential risk of sepsis in asthma patients and implementing appropriate preventive and intervention measures in a timely manner.
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Affiliation(s)
- Jihang Luo
- Department of Infectious Diseases, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Puyu Liu
- Department of Pathology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yawen Luo
- Department of Infectious Diseases, Affiliated Hospital of Zunyi Medical University, Zunyi, China
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Wang S, Dan W, Wang Z, Sun Y, Zhang G. Causal relationships between dietary antioxidant vitamin intake and atopic dermatitis: A two-sample Mendelian randomization study. Skin Res Technol 2024; 30:e13883. [PMID: 39120057 PMCID: PMC11311120 DOI: 10.1111/srt.13883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 06/24/2024] [Indexed: 08/10/2024]
Abstract
OBJECTIVE Oxidative stress is strongly associated with atopic dermatitis (AD), and increased antioxidant intake could potentially reduce the risk of or alleviate its symptoms. However, the argument is disputed. Therefore, we conducted a Mendelian randomization (MR) analysis to explore the causal relationship between dietary antioxidant vitamin intake and AD. METHODS We applied MR analysis to examine the causative association between dietary antioxidant vitamin intake (vitamin C, vitamin E, carotene, and retinol) and AD. The genome-wide association study (GWAS) summary data for antioxidant vitamins intake and AD were obtained from the IEU OpenGWAS database and the UK biobank. Our study consisted of two major parts, MR analysis to detect the causal relationship between exposure and outcome, and sensitivity analysis as supplemental evidence to verify the robustness of the results. RESULT The results revealed a suggestive causal relationship between vitamin E intake and AD (p = 0.038, OR 95% CI = 0.745-0.992). However, there was no causal relationship between the other three vitamins (vitamin C, carotene, and retinol) and AD (p = 0.507, OR 95% CI = 0.826-1.099) (p = 0.890, OR 95% CI = 0.864-1.184) (p = 0.492, OR 95% CI = 0.893-1.264). None of the single nucleotide polymorphisms (SNPs) were detected as heterogeneous and pleiotropy in the sensitivity analysis (p > 0.05). CONCLUSION The analysis suggested that dietary intake of vitamin E may potentially lower the risk of AD. Conversely, intake of vitamin C, retinol, and carotene is not causally related to AD. Although vitamin E intake could be protective against AD, intake of dietary antioxidant vitamins to prevent or treat AD is not necessary.
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Affiliation(s)
- Siqing Wang
- Graduate SchoolBeijing University of Chinese Medicine, 11 North Third Ring East Road, Beijing, 100029, China
- Dermatological DepartmentBeijing Hospital of Traditional Chinese MedicineCapital Medical University, 23 Behind the Art Museum, Beijing, 100010, China
- Inner Mongolia Hospital of Beijing Chinese Medicine Hospital, 5 Guangming West Street, Inner Mongolia, 014400, China
| | - Wenchao Dan
- Dermatological DepartmentBeijing Hospital of Traditional Chinese MedicineCapital Medical University, 23 Behind the Art Museum, Beijing, 100010, China
- Inner Mongolia Hospital of Beijing Chinese Medicine Hospital, 5 Guangming West Street, Inner Mongolia, 014400, China
| | - Zixuan Wang
- Dermatological DepartmentBeijing Hospital of Traditional Chinese MedicineCapital Medical University, 23 Behind the Art Museum, Beijing, 100010, China
| | - Yujie Sun
- Graduate SchoolBeijing University of Chinese Medicine, 11 North Third Ring East Road, Beijing, 100029, China
- Dermatological DepartmentBeijing Hospital of Traditional Chinese MedicineCapital Medical University, 23 Behind the Art Museum, Beijing, 100010, China
| | - Guangzhong Zhang
- Dermatological DepartmentBeijing Hospital of Traditional Chinese MedicineCapital Medical University, 23 Behind the Art Museum, Beijing, 100010, China
- Inner Mongolia Hospital of Beijing Chinese Medicine Hospital, 5 Guangming West Street, Inner Mongolia, 014400, China
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Wu G, Zhang Q, Zhang J, Zhu J, Zheng D, Wang Y, Wu L. Exploring the impact of electrocardiographic parameters on the risk of common arrhythmias: a two-sample Mendelian randomization study. J Thorac Dis 2024; 16:4553-4566. [PMID: 39144314 PMCID: PMC11320266 DOI: 10.21037/jtd-24-814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 07/12/2024] [Indexed: 08/16/2024]
Abstract
Background Observational studies have shown that heart rate (HR), heart rate variability (HRV), P-wave terminal force, P-wave duration, T-wave amplitude and PR interval are associated with risk factors for atrial fibrillation (AF) or bradycardia. Arrhythmias are associated with many causes of hospitalization. However, observational studies are susceptible to confounding factors that have not yet been identified. The objective of this study was to clarify the causal relationships by Mendelian randomization analysis. Methods We conducted a two-sample and multivariate Mendelian randomization (MVMR) analysis using genome-wide association study (GWAS) data from a European population to assess the total and direct causal effects of HR, three HRV traits, P-wave terminal force, P-wave duration, T-wave top amplitude in five-lead modes, and the PR interval on the risk of AF (N=191,205), bradycardia (N=463,010), and supraventricular tachycardia (SVT) (N=463,010). Results The results of the univariate MR analysis revealed the following significant causal effects: the higher the genetically predicted PR interval, the lower the risk of AF; the higher the HR and T-wave top amplitude (aVR leads and V3 + V4 + aVL leads), the lower the risk of bradycardia; and the higher HR and the lower PR interval, the higher the risk of SVT. The multivariate MR results indicated that the HRV_standard deviation of the normal-to-normal (SDNN) interval had an independent causal effect on the risk of AF [odds ratio (OR): 0.515; 95% confidence interval (CI): 0.278-0.954; P=0.03], and the T-wave top amplitude in the aVR leads (OR: 0.998; 95% CI: 0.996-0.999; P<0.001) and the HRV_SDNN (OR: 0.988; 95% CI: 0.976-1.000; P=0.045) had independent causal effects on the risk of bradycardia. Conclusions The HRV_SDNN had an independent causal effect on AF, while the HRV_SDNN and T-wave top amplitude in the aVR leads had independent causal effects on bradycardia, which suggests that some of the electrocardiographic parameters have preventive effects on the incidence of AF and bradycardia.
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Affiliation(s)
- Guangheng Wu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Qiaoyun Zhang
- Department of Anesthesiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Jie Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Jinqi Zhu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Deqiang Zheng
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Youxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
- School of Public Health, North China University of Science and Technology, Tangshan, China
- Centre for Precision Medicine, Edith Cowan University, Perth, Australia
| | - Lijuan Wu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
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Kang J, Wu X, Li Y, Zhao S, Wang S, Yu D. Association between inflammatory bowel disease and osteoporosis in European and East Asian populations: exploring causality, mediation by nutritional status, and shared genetic architecture. Front Immunol 2024; 15:1425610. [PMID: 39136019 PMCID: PMC11317921 DOI: 10.3389/fimmu.2024.1425610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/24/2024] [Indexed: 08/15/2024] Open
Abstract
Background While previous research has established an association between inflammatory bowel disease (IBD) and osteoporosis (OP), the nature of this association in different populations remains unclear. Objective Our study used linkage disequilibrium scores(LDSC) regression analysis and Mendelian randomization(MR) to assess the genetic correlation and causal relationship between IBD and OP in European and East Asian populations. Methods We performed separate genetic correlation and causal analyses for IBD and OP in European and East Asian populations, used the product of coefficients method to estimate the mediating effect of nutritional status on the causal relationship, and used multi-trait analysis to explore the biological mechanisms underlying the IBD-nutrition-OP causal pathway. Results Our analysis revealed a significant genetic correlation and causal relationship between IBD and OP in the European population. Conversely, no such correlation or causal relationship was observed in the East Asian population. Mediation analysis revealed a significant mediating effect of nutritional status on the causal pathway between IBD and OP in the European population. Multi-trait analysis of the IBD-nutrition-OP causal pathway identified MFAP2, ATP13A2, SERPINA1, FTO and VCAN as deleterious variants. Conclusion Our findings establish a genetic correlation and causal relationship between IBD and OP in the European population, with nutritional status playing a crucial mediating role.
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Affiliation(s)
- Jian Kang
- Graduate School, Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Xize Wu
- Graduate School, Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Yue Li
- Department of Cardiology, Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Shuangli Zhao
- Orthopedics and Traumatology, The Second Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Shixuan Wang
- Orthopedics and Traumatology, The Second Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Dongdong Yu
- Orthopedics and Traumatology, Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, China
- Key Laboratory of Ministry of Education for Traditional Chinese Medicine Viscera-State Theory and Applications, Liaoning University of Traditional Chinese Medicine, Shenyang, China
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Ruan LC, Zhang Y, Su L, Zhu LX, Wang SL, Guo Q, Wan BG, Qiu SY, Hu S, Wei YP, Zheng QL. Causal effects of genetic birth weight and gestational age on adult esophageal diseases: Mendelian randomization study. World J Gastrointest Oncol 2024; 16:3055-3068. [PMID: 39072185 PMCID: PMC11271773 DOI: 10.4251/wjgo.v16.i7.3055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/23/2024] [Accepted: 05/07/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Few studies have investigated the association between gestational age, birth weight, and esophageal cancer risk; however, causality remains debated. We aimed to establish causal links between genetic gestational age and birth weight traits and gastroesophageal reflux disease (GERD), Barrett's esophagus (BE), and esophageal adenocarcinoma (EA). Additionally, we explored if known risk factors mediate these links. AIM To analyze of the relationship between gestational age, birth weight and GERD, BE, and EA. METHODS Genetic data on gestational age and birth weight (n = 84689 and 143677) from the Early Growth Genetics Consortium and outcomes for GERD (n = 467253), BE (n = 56429), and EA (n = 21271) from genome-wide association study served as instrumental variables. Mendelian randomization (MR) and mediation analyses were conducted using MR-Egger, weighted median, and inverse variance weighted methods. Robustness was ensured through heterogeneity, pleiotropy tests, and sensitivity analyses. RESULTS Birth weight was negatively correlated with GERD and BE risk [odds ratio (OR) = 0.78; 95% confidence interval (CI): 0.69-0.8] and (OR = 0.75; 95%CI: 0.60-0.9), respectively, with no significant association with EA. No causal link was found between gestational age and outcomes. Birth weight was positively correlated with five risk factors: Educational attainment (OR = 1.15; 95%CI: 1.01-1.31), body mass index (OR = 1.06; 95%CI: 1.02-1.1), height (OR = 1.12; 95%CI: 1.06-1.19), weight (OR = 1.13; 95%CI: 1.10-1.1), and alcoholic drinks per week (OR = 1.03; 95%CI: 1.00-1.06). Mediation analysis showed educational attainment and height mediated the birth weight-BE link by 13.99% and 5.46%. CONCLUSION Our study supports the protective role of genetically predicted birth weight against GERD, BE, and EA, independent of gestational age and partially mediated by educational attainment and height.
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Affiliation(s)
- Lian-Cheng Ruan
- Department of Thoracic Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Yang Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Lang Su
- Department of Thoracic Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Ling-Xiao Zhu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Si-Lin Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Qiang Guo
- Department of Thoracic Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Bin-Gen Wan
- Department of Thoracic Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Sheng-Yu Qiu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Sheng Hu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Yi-Ping Wei
- Department of Thoracic Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Qiao-Ling Zheng
- Nanchang Medical College, Nanchang 330004, Jiangxi Province, China
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Yue Y, She X, Ding W, Chen S, Xiao Q, Pan B, Zhou L, Yin Y, Li Y, Wang S, Xu M. A novel Senescence-Based prognostic model unveils tumor interactions and drug resistance in colorectal cancer. Int Immunopharmacol 2024; 134:112197. [PMID: 38733826 DOI: 10.1016/j.intimp.2024.112197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/12/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND In China, CRC incidence is escalating. The main hurdles are heterogeneity and drug resistance. This research delves into cellular senescence in CRC, aiming to devise a prognostic model and pinpoint mechanisms impacting drug resistance. METHODS Mendelian randomization (MR) analysis confirmed the association between CRC and cellular aging. The Cancer Genome Atlas (TCGA)-CRC data served as the training set, with GSE38832 and GSE39582 as validation sets. Various bioinformatics methods were employed to construct and validate a risk model. CRC cells with NADPH Oxidase 4 (NOX4) knockout were generated using CRISPR-Cas9 technology. Protein blotting and colony formation assays elucidated the role of NOX4 in CRC cell aging and drug resistance. RESULTS A prognostic model, derived from dataset analysis, uncovered a link between high-risk groups and cancer progression. Notable differences in the tumor microenvironment were observed between risk groups. Finally, NOX4 was found to be linked with aging and drug resistance in CRC. CONCLUSION This research presents a novel senescence-based CRC prognosis model. It identifies NOX4's role in CRC drug resistance, suggesting it is a potential treatment target.
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Affiliation(s)
- Yanzhe Yue
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, 211166, Nanjing, Jiangsu, China; School of Basic-Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, 211198, Nanjing, Jiangsu, China
| | - Xiangjian She
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, 211166, Nanjing, Jiangsu, China; School of Basic-Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, 211198, Nanjing, Jiangsu, China
| | - Wenbo Ding
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, 211166, Nanjing, Jiangsu, China; School of Basic-Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, 211198, Nanjing, Jiangsu, China
| | - Shuyu Chen
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, 211166, Nanjing, Jiangsu, China; School of Basic-Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, 211198, Nanjing, Jiangsu, China
| | - Qianni Xiao
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, 211166, Nanjing, Jiangsu, China; School of Basic-Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, 211198, Nanjing, Jiangsu, China
| | - Bei Pan
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, 211166, Nanjing, Jiangsu, China
| | - Linpeng Zhou
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, 211166, Nanjing, Jiangsu, China; School of Basic-Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, 211198, Nanjing, Jiangsu, China
| | - Yujuan Yin
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, 211166, Nanjing, Jiangsu, China
| | - Youyue Li
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, 211166, Nanjing, Jiangsu, China
| | - Shukui Wang
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, 211166, Nanjing, Jiangsu, China; School of Basic-Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, 211198, Nanjing, Jiangsu, China; Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, 211166, Nanjing, Jiangsu, China.
| | - Mu Xu
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, 211166, Nanjing, China.
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Chi G, Pei J, Li X. Inflammatory bowel disease and risk of autoimmune hepatitis: A univariable and multivariable Mendelian randomization study. PLoS One 2024; 19:e0305220. [PMID: 38848323 PMCID: PMC11161122 DOI: 10.1371/journal.pone.0305220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 05/25/2024] [Indexed: 06/09/2024] Open
Abstract
OBJECTIVE This study aimed to use Mendelian randomization (MR) to investigate the potential causal association between inflammatory bowel disease (IBD) and autoimmune hepatitis (AIH). METHODS Two-sample MR was performed to estimate the causal effect of IBD on AIH. The primary analysis employed the inverse variance weighted (IVW) method in univariable MR analysis, supplemented by additional methods including MR-Egger, weighted median, simple mode, and weighted mode. The p values were adjusted by FDR p-value adjustment. In the replication analysis, the primary IVW analysis was repeated and then pooled by meta-analysis. Sensitivity analyses were performed using Cochran's Q test, MR-Egger intercept test, MR-PRESSO, leave-one-out, and funnel plot analysis to evaluate the robustness of the MR findings. Additionally, multivariable MR (MVMR) was employed to estimate the direct causal effect of IBD on the risk of AIH. RESULTS In univariable MR analysis, a significant positive causal association was observed between IBD (both Crohn's disease (CD) or ulcerative colitis (UC)) and the risk of AIH (for CD and AIH, the IVW odds ratio (OR) = 1.10, 95% confidence interval (CI) = 1.00-1.16, P = 0.045, FDR P = 0.045; for UC and AIH, the IVW OR = 1.07, 95% CI = 1.00-1.13, P = 0.038, FDR P = 0.076). Furthermore, no significant positive correlation between IBD and the risk of AIH (OR = 1.13, 95% CI = 0.94-1.35, P = 0.194). Sensitivity analysis revealed no pleiotropic bias. MVMR analysis further confirmed the direct causal effect of CD or UC on the risk of AIH after adjusting for the common risk factors (cigarettes per day and osteoporosis). In the replication analysis, the positive causal association between UC and the risk of AIH remain significant (the IVW odds ratio (OR) = 1.32, 95% CI = 1.18-1.48, P = 2.90E-06). While no significant positive association was observed between CD or IBD and the risk of AIH in the replication analysis, a suggestive positive association between the identified risk factors (UC, CD, and IBD) and the risk of AIH was detected in the meta-analysis (OR = 1.09, 95% CI = 1.05-1.13, P<0.0001). CONCLUSION This MR study revealed a positive impact of the identified risk factors (CD, UC and IBD) on the risk of AIH within the European population.
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Affiliation(s)
- Gang Chi
- Department of Biochemistry, Changzhi Medical College, Changazhi, Shanxi, China
| | - Jinhong Pei
- Department of Biochemistry, Changzhi Medical College, Changazhi, Shanxi, China
| | - Xueqing Li
- Department of Biochemistry, Changzhi Medical College, Changazhi, Shanxi, China
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Zhang T, Qiao J, Wang Y, Zhou Y, Jabbar Abdl Sattar Hamoudi H, Hendi MAA, Wang J. Causal link between hypothyroidism and gastric cancer risk: insights gained through multivariable Mendelian randomization and mediation analysis. Front Endocrinol (Lausanne) 2024; 15:1388608. [PMID: 38904039 PMCID: PMC11186985 DOI: 10.3389/fendo.2024.1388608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/20/2024] [Indexed: 06/22/2024] Open
Abstract
Background Gastric cancer (GC) is the third leading cause of cancer death worldwide, and hypothyroidism has been identified as a potential influencing factor. Despite known associations between hypothyroidism and various cancers, the causal link between hypothyroidism and GC and potential mediators of this relationship remains unclear. This study aimed to clarify these relationships using Mendelian randomization (MR). Methods Utilizing genetic variant information from the FinnGen and MRC Integrative Epidemiology Unit open genome-wide association studies (GWAS) databases, we conducted univariable and multivariable MR analyses to explore the causal relationship between hypothyroidism and GC risk. The analysis was adjusted for confounders such as BMI, smoking status, and alcohol intake, and included mediator MR analysis to examine the role of high cholesterol. Results We identified a significant inverse association between hypothyroidism and GC risk (OR = 0.93, 95% CI= 0.89-0.98, P = 0.003), with no evidence of reverse causation or pleiotropy. Adjustments for Helicobacter pylori infection weakened this association. Mediator analysis highlighted high cholesterol levels, chronic hepatitis B infection, and diabetes/endocrine disease status as significant mediators of the protective effect of hypothyroidism on GC risk. Conclusion Our findings suggest that hypothyroidism may confer a protective effect against GC, mediated in part by high cholesterol and other factors. These results underscore the importance of thyroid function and metabolic health in GC risk, offering new insights for preventive strategies and highlighting the need for further research into these complex associations.
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Affiliation(s)
- Tianyue Zhang
- Department of Endocrinology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jie Qiao
- Department of Endocrinology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yuanyou Wang
- Department of Endocrinology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yinying Zhou
- Department of Endocrinology, Qingtian People’s Hospital, Lishui, Zhejiang, China
| | | | - Mhd Alaa Al Hendi
- Department of Endocrinology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jun Wang
- Department of Gastroenterology Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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13
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Teng F, Sun J, Chen Z, Li H. Genetically determined dietary habits and risk of Alzheimer's disease: a Mendelian randomization study. Front Nutr 2024; 11:1415555. [PMID: 38887501 PMCID: PMC11180739 DOI: 10.3389/fnut.2024.1415555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024] Open
Abstract
Background Emerging evidence have suggested that dietary habits have potential implication on the development of Alzheimer's disease (AD). However, elucidating the causal relationship between specific dietary factors and AD risk remains a challenge. Therefore, our study endeavors to investigate the causal association between dietary habits and the risk of AD. Materials and methods We analyzed data on 231 dietary habits sourced from the UK Biobank and MRC-IEU, and AD data obtained from the FinnGen database. Employing a framework based on the classic two-sample Mendelian randomization (MR) study, we utilized the inverse-variance weighted (IVW) method as the primary analysis. Additionally, we conducted Steiger filtering and other methods to mitigate horizontal pleiotropy. The robustness of our overall findings was confirmed through multiple sensitivity analysis methods, and forward MR and reverse MR to address potential reverse causality bias. Results Our study evaluated the causal effect between 231 dietary habits involving over 500,000 participants of European ancestry, and 10,520 AD cases. Only oily fish intake demonstrated a significant protective causal relationship with AD following FDR correction (raw p-value = 1.28e-4, FDR p-value = 0.011, OR = 0.60, 95%CI: 0.47-0.78). Additionally, six dietary habits potentially influenced AD risk, with protective causal effects observed for average monthly intake of other alcoholic drinks (raw p-value = 0.024, FDR p-value = 0.574, OR = 0.57, 95%CI: 0.35-0.93) and tea intake (raw p-value = 0.047, FDR p-value = 0.581, OR = 0.78, 95%CI: 0.603-1.00). Conversely, detrimental causal effects were observed for the average weekly champagne plus white wine intake (raw p-value = 0.006, FDR p-value = 0.243, OR = 2.96, 95%CI: 1.37-6.38), Danish pastry intake (raw p-value = 0.036, FDR p-value = 0.574, OR = 13.33, 95%CI: 1.19-149.69), and doughnut intake (raw p-value = 0.039, FDR p-value = 0.574, OR = 7.41, 95%CI: 1.11-49.57). Moreover, the protective effect of goat's cheese intake phenotype exhibited statistical significance only in the IVW method (raw p-value<0.05). Conclusion Our results provide genetic support for a protective causal effect of oily fish intake on AD risk. Additionally, average monthly intake of other alcoholic drinks and tea consumption were also related with a lower risk of AD. Conversely, average weekly champagne plus white wine intake, Danish pastry intake, and doughnut intake were causally associated with increased risk of AD.
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Affiliation(s)
- Fei Teng
- Department of Liver Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Jiahui Sun
- Wangjing Hospital of China Academy of Chinese Medicine Sciences, Beijing, China
| | - Zheyu Chen
- Department of Liver Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Hao Li
- Wangjing Hospital of China Academy of Chinese Medicine Sciences, Beijing, China
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14
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Tang T, Yu H, Xu S, Zhong Y, Ma J, Zhao T. Causal effects of endometriosis on cancer risk: A Mendelian randomization study. Int J Cancer 2024; 154:1948-1954. [PMID: 38323658 DOI: 10.1002/ijc.34876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/14/2023] [Accepted: 01/19/2024] [Indexed: 02/08/2024]
Abstract
Endometriosis has been reported in epidemiological studies to be associated with certain types of cancer. However, the presence of reverse causality and residual confounding due to common risk factors introduces uncertainty regarding the extent to which endometriosis itself contributes to the development of cancer. We performed the Mendelian randomization (MR) to investigate the causal associations between endometriosis and 34 different types of cancers. The results of the inverse-variance-weighted (IVW) model suggested that genetic predisposition to endometriosis was causally associated with an increased risk for ovarian cancer (OR = 3.2913; p-value = .0320). The genetic liabilities to endometriosis had causal associations with the decreased risk for skin cancer (OR = 0.9973; p-value = .0219), hematological cancer (OR = 0.9953; p-value = .0175) and ER- breast cancer (OR = 0.6960; p-value = .0381). The causal association of the above combinations were robust by test of heterogeneity and pleiotropy. Together, our study suggests that endometriosis had causal effect on cancer risk.
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Affiliation(s)
- Tianyou Tang
- The College of Pediatrics, Chongqing Medical University, Chongqing, China
| | - Huilin Yu
- The Second Medicine College, Chongqing Medical University, Chongqing, China
| | - Sipei Xu
- The First Medicine College, Chongqing Medical University, Chongqing, China
| | - Yi Zhong
- The College of Pediatrics, Chongqing Medical University, Chongqing, China
| | - Jie Ma
- Department of Pharmacology, Pharmaceutical Engineering College, Chongqing Chemical Industry Vocational College, Chongqing, China
| | - Tingting Zhao
- Laboratory of Human Function Experimental Teaching and Management Center of Chongqing Medical University, Chongqing, China
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Martins YC, Bhawsar PMS, Balasubramanian JB, Russ D, Wong WSW, Maass W, Almeida JS. FAIR privacy-preserving operation of large genomic variant calling format (VCF) data without download or installation. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2024; 2024:65-74. [PMID: 38827109 PMCID: PMC11141832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Motivation: The proliferation of genetic testing and consumer genomics represents a logistic challenge to the personalized use of GWAS data in VCF format. Specifically, the challenge of retrieving target genetic variation from large compressed files filled with unrelated variation information. Compounding the data traversal challenge, privacy-sensitive VCF files are typically managed as large stand-alone single files (no companion index file) composed of variable-sized compressed chunks, hosted in consumer-facing environments with no native support for hosted execution. Results: A portable JavaScript module was developed to support in-browser fetching of partial content using byte-range requests. This includes on-the-fly decompressing irregularly positioned compressed chunks, coupled with a binary search algorithm iteratively identifying chromosome-position ranges. The in-browser zero-footprint solution (no downloads, no installations) enables the interoperability, reusability, and user-facing governance advanced by the FAIR principles for stewardship of scientific data. Availability - https://episphere.github.io/vcf, including supplementary material.
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Affiliation(s)
| | - Praphulla MS Bhawsar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
| | - Jeya B Balasubramanian
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
| | - Daniel Russ
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
| | - Wendy SW Wong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
| | | | - Jonas S Almeida
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
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Kui L, Dong C, Wu J, Zhuo F, Yan B, Wang Z, Yang M, Xiong C, Qiu P. Causal association between type 2 diabetes mellitus and acute suppurative otitis media: insights from a univariate and multivariate Mendelian randomization study. Front Endocrinol (Lausanne) 2024; 15:1407503. [PMID: 38836234 PMCID: PMC11148255 DOI: 10.3389/fendo.2024.1407503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024] Open
Abstract
Background Type 2 diabetes mellitus (T2DM) and hearing loss (HL) constitute significant public health challenges worldwide. Recently, the association between T2DM and HL has aroused attention. However, possible residual confounding factors and other biases inherent to observational study designs make this association undetermined. In this study, we performed univariate and multivariable Mendelian Randomization (MR) analysis to elucidate the causal association between T2DM and common hearing disorders that lead to HL. Methods Our study employed univariate and multivariable MR analyses, with the Inverse Variance Weighted method as the primary approach to assessing the potential causal association between T2DM and hearing disorders. We selected 164 and 9 genetic variants representing T2DM from the NHGRI-EBI and DIAGRAM consortium, respectively. Summary-level data for 10 hearing disorders were obtained from over 500,000 participants in the FinnGen consortium and MRC-IEU. Sensitivity analysis revealed no significant heterogeneity of instrumental variables or pleiotropy was detected. Results In univariate MR analysis, genetically predicted T2DM from both sources was associated with an increased risk of acute suppurative otitis media (ASOM) (In NHGRI-EBI: OR = 1.07, 95% CI: 1.02-1.13, P = 0.012; In DIAGRAM: OR = 1.14, 95% CI: 1.02-1.26, P = 0.016). Multivariable MR analysis, adjusting for genetically predicted sleep duration, alcohol consumption, body mass index, and smoking, either individually or collectively, maintained these associations. Sensitivity analyses confirmed the robustness of the results. Conclusion T2DM was associated with an increased risk of ASOM. Strict glycemic control is essential for the minimization of the effects of T2DM on ASOM.
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Affiliation(s)
- Lihong Kui
- Xiamen Rehabilitation Hospital, Xiamen, Fujian, China
| | - Cheng Dong
- Depart of Rehabilitation Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junyu Wu
- School of Physical Education, Shanghai University of Sport, Shanghai, China
| | - Feinan Zhuo
- Department of Rehabilitation, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Bin Yan
- School of Rehabilitation Medicine, Jiangsu Vocational College of Medicine, Jiangsu, China
| | - Zhewei Wang
- Department of Rehabilitation, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Meiling Yang
- Xiamen Rehabilitation Hospital, Xiamen, Fujian, China
| | - Canhai Xiong
- Xiamen Rehabilitation Hospital, Xiamen, Fujian, China
| | - Peng Qiu
- Department of Rehabilitation, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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17
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Wang Y, Hu X, Wang X, Li L, Lou P, Liu Z. Exploring the Two-Way Link between Migraines and Venous Thromboembolism: A Bidirectional Two-Sample Mendelian Randomization Study. Thromb Haemost 2024. [PMID: 38657649 DOI: 10.1055/a-2313-0311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
BACKGROUND The objective of this study is to utilize Mendelian randomization to scrutinize the mutual causality between migraine and venous thromboembolism (VTE) thereby addressing the heterogeneity and inconsistency that were observed in prior observational studies concerning the potential interrelation of the two conditions. METHODS Employing a bidirectional Mendelian randomization approach, the study explored the link between migraine and VTE, incorporating participants of European descent from a large-scale meta-analysis. An inverse-variance weighted (IVW) regression model, with random-effects, leveraging single nucleotide polymorphisms (SNPs) as instrumental variables was utilized to endorse the mutual causality between migraine and VTE. SNP heterogeneity was evaluated using Cochran's Q-test and to account for multiple testing, correction was implemented using the intercept of the MR-Egger method, and a leave-one-out analysis. RESULTS The IVW model unveiled a statistically considerable causal link between migraine and the development of VTE (odds ratio [OR] = 96.155, 95% confidence interval [CI]: 4.342-2129.458, p = 0.004), implying that migraine poses a strong risk factor for VTE development. Conversely, both IVW and simple model outcomes indicated that VTE poses as a weaker risk factor for migraine (IVW OR = 1.002, 95% CI: 1.000-1.004, p = 0.016). The MR-Egger regression analysis denoted absence of evidence for genetic pleiotropy among the SNPs while the durability of our Mendelian randomization results was vouched by the leave-one-out sensitivity analysis. CONCLUSION The findings of this Mendelian randomization assessment provide substantiation for a reciprocal causative association between migraine and VTE within the European population.
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Affiliation(s)
- Yang Wang
- Vascular Surgery, Shandong Public Health Clinical Center, Shandong University, Jinan, China
| | - Xiaofang Hu
- Department of Neurology, Shandong Public Health Clinical Center, Shandong University, Jinan, China
| | - Xiaoqing Wang
- Interventional Department, Shandong Public Health Clinical Center, Shandong University, Jinan, China
| | - Lili Li
- Interventional Department, Shandong Public Health Clinical Center, Shandong University, Jinan, China
| | - Peng Lou
- Vascular Surgery, Shandong Public Health Clinical Center, Shandong University, Jinan, China
| | - Zhaoxuan Liu
- Vascular Surgery, Shandong First Medical University affiliated Central Hospital, Jinan, China
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18
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Yu Z, Guo M, Yu B, Wang Y, Yan Z, Gao R. Anorexia nervosa and bulimia nervosa: a Mendelian randomization study of gut microbiota. Front Microbiol 2024; 15:1396932. [PMID: 38784806 PMCID: PMC11111991 DOI: 10.3389/fmicb.2024.1396932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
Background Anorexia nervosa (AN) and bulimia nervosa (BN) poses a significant challenge to global public health. Despite extensive research, conclusive evidence regarding the association between gut microbes and the risk of AN and BN remains elusive. Mendelian randomization (MR) methods offer a promising avenue for elucidating potential causal relationships. Materials and methods Genome-wide association studies (GWAS) datasets of AN and BN were retrieved from the OpenGWAS database for analysis. Independent single nucleotide polymorphisms closely associated with 196 gut bacterial taxa from the MiBioGen consortium were identified as instrumental variables. MR analysis was conducted utilizing R software, with outlier exclusion performed using the MR-PRESSO method. Causal effect estimation was undertaken employing four methods, including Inverse variance weighted. Sensitivity analysis, heterogeneity analysis, horizontal multivariate analysis, and assessment of causal directionality were carried out to assess the robustness of the findings. Results A total of 196 bacterial taxa spanning six taxonomic levels were subjected to analysis. Nine taxa demonstrating potential causal relationships with AN were identified. Among these, five taxa, including Peptostreptococcaceae, were implicated as exerting a causal effect on AN risk, while four taxa, including Gammaproteobacteria, were associated with a reduced risk of AN. Similarly, nine taxa exhibiting potential causal relationships with BN were identified. Of these, six taxa, including Clostridiales, were identified as risk factors for increased BN risk, while three taxa, including Oxalobacteraceae, were deemed protective factors. Lachnospiraceae emerged as a common influence on both AN and BN, albeit with opposing effects. No evidence of heterogeneity or horizontal pleiotropy was detected for significant estimates. Conclusion Through MR analysis, we revealed the potential causal role of 18 intestinal bacterial taxa in AN and BN, including Lachnospiraceae. It provides new insights into the mechanistic basis and intervention targets of gut microbiota-mediated AN and BN.
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Affiliation(s)
- Zongliang Yu
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Manping Guo
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Postdoctoral Research Station, China Academy of Chinese Medical Sciences, Beijing, China
- Postdoctoral Works Station, Yabao Pharmaceutical Group Co., Ltd., Yuncheng, China
| | - Binyang Yu
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yiming Wang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zian Yan
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Rui Gao
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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Purdue MP, Dutta D, Machiela MJ, Gorman BR, Winter T, Okuhara D, Cleland S, Ferreiro-Iglesias A, Scheet P, Liu A, Wu C, Antwi SO, Larkin J, Zequi SC, Sun M, Hikino K, Hajiran A, Lawson KA, Cárcano F, Blanchet O, Shuch B, Nepple KG, Margue G, Sundi D, Diver WR, Folgueira MAAK, van Bokhoven A, Neffa F, Brown KM, Hofmann JN, Rhee J, Yeager M, Cole NR, Hicks BD, Manning MR, Hutchinson AA, Rothman N, Huang WY, Linehan WM, Lori A, Ferragu M, Zidane-Marinnes M, Serrano SV, Magnabosco WJ, Vilas A, Decia R, Carusso F, Graham LS, Anderson K, Bilen MA, Arciero C, Pellegrin I, Ricard S, Scelo G, Banks RE, Vasudev NS, Soomro N, Stewart GD, Adeyoju A, Bromage S, Hrouda D, Gibbons N, Patel P, Sullivan M, Protheroe A, Nugent FI, Fournier MJ, Zhang X, Martin LJ, Komisarenko M, Eisen T, Cunningham SA, Connolly DC, Uzzo RG, Zaridze D, Mukeria A, Holcatova I, Hornakova A, Foretova L, Janout V, Mates D, Jinga V, Rascu S, Mijuskovic M, Savic S, Milosavljevic S, Gaborieau V, Abedi-Ardekani B, McKay J, Johansson M, Phouthavongsy L, Hayman L, Li J, Lungu I, Bezerra SM, Souza AG, Sares CTG, Reis RB, Gallucci FP, Cordeiro MD, Pomerantz M, Lee GSM, Freedman ML, Jeong A, Greenberg SE, Sanchez A, Thompson RH, Sharma V, Thiel DD, Ball CT, Abreu D, Lam ET, Nahas WC, Master VA, Patel AV, Bernhard JC, Freedman ND, Bigot P, Reis RM, Colli LM, Finelli A, Manley BJ, Terao C, Choueiri TK, Carraro DM, Houlston R, Eckel-Passow JE, Abbosh PH, Ganna A, Brennan P, Gu J, Chanock SJ. Multi-ancestry genome-wide association study of kidney cancer identifies 63 susceptibility regions. Nat Genet 2024; 56:809-818. [PMID: 38671320 DOI: 10.1038/s41588-024-01725-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/13/2024] [Indexed: 04/28/2024]
Abstract
Here, in a multi-ancestry genome-wide association study meta-analysis of kidney cancer (29,020 cases and 835,670 controls), we identified 63 susceptibility regions (50 novel) containing 108 independent risk loci. In analyses stratified by subtype, 52 regions (78 loci) were associated with clear cell renal cell carcinoma (RCC) and 6 regions (7 loci) with papillary RCC. Notably, we report a variant common in African ancestry individuals ( rs7629500 ) in the 3' untranslated region of VHL, nearly tripling clear cell RCC risk (odds ratio 2.72, 95% confidence interval 2.23-3.30). In cis-expression quantitative trait locus analyses, 48 variants from 34 regions point toward 83 candidate genes. Enrichment of hypoxia-inducible factor-binding sites underscores the importance of hypoxia-related mechanisms in kidney cancer. Our results advance understanding of the genetic architecture of kidney cancer, provide clues for functional investigation and enable generation of a validated polygenic risk score with an estimated area under the curve of 0.65 (0.74 including risk factors) among European ancestry individuals.
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Affiliation(s)
- Mark P Purdue
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
| | - Diptavo Dutta
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Mitchell J Machiela
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Timothy Winter
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | | | | | - Paul Scheet
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aoxing Liu
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chao Wu
- Biosample Repository, Fox Chase Cancer Center-Temple Health, Philadelphia, PA, USA
| | - Samuel O Antwi
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - James Larkin
- Department of Medical Oncology, Royal Marsden NHS Foundation Trust, London, UK
| | - Stênio C Zequi
- Department of Urology, A.C. Camargo Cancer Center, São Paulo, Brazil
- National Institute for Science and Technology in Oncogenomics and Therapeutic Innovation INCIT-INOTE, São Paulo, Brazil
- Latin American Renal Cancer Group, São Paulo, Brazil
- Department of Surgery, Division of Urology, São Paulo Federal University, São Paulo, Brazil
| | - Maxine Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keiko Hikino
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ali Hajiran
- Department of Urology, Division of Urologic Oncology, West Virginia University Cancer Institute, Morgantown, WV, USA
| | - Keith A Lawson
- Department of Surgical Oncology, Division of Urology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Flavio Cárcano
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Brian Shuch
- Department of Urology, UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Kenneth G Nepple
- Department of Urology, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Gaëlle Margue
- Department of Urology, CHU Bordeaux, Bordeaux, France
| | - Debasish Sundi
- Department of Urology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - W Ryan Diver
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Maria A A K Folgueira
- Departments of Radiology and Oncology, Comprehensive Center for Precision Oncology-C2PO, Centro de Investigação Translacional em Oncologia, Instituto do Cancer do Estado de São Paulo, Hospital das Clinicas, Faculdade de Medicina Universidade de São Paulo, São Paulo, Brazil
| | - Adrie van Bokhoven
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jonathan N Hofmann
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jongeun Rhee
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory, Rockville, MD, USA
| | - Nathan R Cole
- Cancer Genomics Research Laboratory, Frederick National Laboratory, Rockville, MD, USA
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Frederick National Laboratory, Rockville, MD, USA
| | - Michelle R Manning
- Cancer Genomics Research Laboratory, Frederick National Laboratory, Rockville, MD, USA
| | - Amy A Hutchinson
- Cancer Genomics Research Laboratory, Frederick National Laboratory, Rockville, MD, USA
| | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Wen-Yi Huang
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Adriana Lori
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | | | | | - Sérgio V Serrano
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Ana Vilas
- Department of Pathology, Hospital Pasteur, Montevideo, Uruguay
| | - Ricardo Decia
- Department of Urology, Hospital Pasteur, Montevideo, Uruguay
| | | | - Laura S Graham
- Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kyra Anderson
- Oncology Clinical Research Support Team, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Mehmet A Bilen
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | - Cletus Arciero
- Department of Surgery, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Solène Ricard
- Department of Urology, CHU Bordeaux, Bordeaux, France
| | - Ghislaine Scelo
- Observational and Pragmatic Research Institute Pte Ltd, Singapore, Singapore
| | - Rosamonde E Banks
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Naveen S Vasudev
- Department of Oncology, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Naeem Soomro
- Department of Urology, Newcastle Hospitals NHS Foundation Trust, Newcastle, UK
| | - Grant D Stewart
- Department of Urology, Western General Hospital, NHS Lothian, Edinburgh, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Adebanji Adeyoju
- Department of Urology, Stockport NHS Foundation Trust, Stockport, UK
| | - Stephen Bromage
- Department of Urology, Stockport NHS Foundation Trust, Stockport, UK
| | - David Hrouda
- Department of Urology, Imperial College Healthcare NHS Trust, London, UK
| | - Norma Gibbons
- Department of Urology, Imperial College Healthcare NHS Trust, London, UK
| | - Poulam Patel
- Division of Oncology, University of Nottingham, Nottingham, UK
| | - Mark Sullivan
- Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Andrew Protheroe
- Department of Oncology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Francesca I Nugent
- Department of Urology, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | | | - Xiaoyu Zhang
- Department of Surgical Oncology, Division of Urology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Lisa J Martin
- Department of Surgical Oncology, Division of Urology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Maria Komisarenko
- Department of Surgical Oncology, Division of Urology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Timothy Eisen
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sonia A Cunningham
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Denise C Connolly
- Cancer Signaling and Microenvironment, Biosample Repository Facility, Fox Chase Cancer Center-Temple Health, Philadelphia, PA, USA
| | - Robert G Uzzo
- Department of Urology, Fox Chase Cancer Center-Temple Health, Philadelphia, PA, USA
| | - David Zaridze
- Department of Clinical Epidemiology, N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Anush Mukeria
- Department of Clinical Epidemiology, N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, Second Faculty of Medicine, Charles University, Prague, Czech Republic
- Department of Oncology, Second Faculty of Medicine and University Hospital Motol, Charles University, Prague, Czech Republic
| | - Anna Hornakova
- Institute of Hygiene and Epidemiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Dana Mates
- Department of Occupational Health and Toxicology, National Center for Environmental Risk Monitoring, National Institute of Public Health, Bucharest, Romania
| | - Viorel Jinga
- Urology Department, Academy of Romanian Scientists, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Stefan Rascu
- Urology Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Mirjana Mijuskovic
- Clinic of Nephrology, Faculty of Medicine, Military Medical Academy, Belgrade, Serbia
| | - Slavisa Savic
- Department of Urology, Clinical Hospital Center Dr Dragisa Misovic Dedinje, Belgrade, Serbia
| | - Sasa Milosavljevic
- International Organisation for Cancer Prevention and Research, Belgrade, Serbia
| | - Valérie Gaborieau
- Genomic Epidemiology Branch, International Agency for Research on Cancer, Lyon, France
| | | | - James McKay
- Genomic Epidemiology Branch, International Agency for Research on Cancer, Lyon, France
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer, Lyon, France
| | - Larry Phouthavongsy
- Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Lindsay Hayman
- Diagnostic Development Program, Tissue Portal, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jason Li
- Diagnostic Development Program, Tissue Portal, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Ilinca Lungu
- Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Diagnostic Development Program, Tissue Portal, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Aline G Souza
- Departments of Medical Imaging, Hematology and Oncology, Division of Medical Oncology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | - Claudia T G Sares
- Departments of Surgery and Anatomy, Division of Urology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | - Rodolfo B Reis
- Departments of Surgery and Anatomy, Division of Urology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | - Fabio P Gallucci
- Surgery Department, Urology Division, Instituto do Cancer do Estado de São Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Mauricio D Cordeiro
- Surgery Department, Urology Division, Instituto do Cancer do Estado de São Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | - Gwo-Shu M Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Anhyo Jeong
- Department of Urology, UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Samantha E Greenberg
- Department of Population Sciences, Genetic Counseling Shared Resource, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Alejandro Sanchez
- Department of Surgery, Division of Urology, Huntsman Cancer Institute and University of Utah, Salt Lake City, UT, USA
| | | | - Vidit Sharma
- Department of Urology, Mayo Clinic, Rochester, MN, USA
| | - David D Thiel
- Department of Urology, Mayo Clinic, Jacksonville, FL, USA
| | - Colleen T Ball
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Diego Abreu
- Department of Urology, Hospital Pasteur, Montevideo, Uruguay
| | - Elaine T Lam
- Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - William C Nahas
- Surgery Department, Urology Division, Instituto do Cancer do Estado de São Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Viraj A Master
- Department of Urology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | - Alpa V Patel
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | | | - Neal D Freedman
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Pierre Bigot
- Department of Urology, CHU Angers, Angers, France
| | - Rui M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
| | - Leandro M Colli
- Departament of Medical Image, Hematology and Oncology, Division of Medical Oncology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | - Antonio Finelli
- Department of Surgical Oncology, Division of Urology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Brandon J Manley
- Genitourinary Oncology Program, Moffitt Cancer Center, Tampa, FL, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dirce M Carraro
- Clinical and Functional Genomics Group, CIPE (International Research Center), A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Richard Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | | | - Philip H Abbosh
- Department of Nuclear Dynamics and Cancer, Fox Chase Cancer Center-Temple Health, Philadelphia, PA, USA
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer, Lyon, France
| | - Jian Gu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephen J Chanock
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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Sun M, Zhang Z, Zhang J, Zhang J, Jia Z, Zhao L, Han X, Sun X, Zong J, Zhu Y, Wang S. Causal relationships of Helicobacter pylori and related gastrointestinal diseases on Type 2 diabetes: Univariable and Multivariable Mendelian randomization. PLoS One 2024; 19:e0300835. [PMID: 38652719 PMCID: PMC11037534 DOI: 10.1371/journal.pone.0300835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/05/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Previous observational studies have demonstrated a connection between the risk of Type 2 diabetes mellitus (T2DM) and gastrointestinal problems brought on by Helicobacter pylori (H. pylori) infection. However, little is understood about how these factors impact on T2DM. METHOD This study used data from the GWAS database on H. pylori antibodies, gastroduodenal ulcers, chronic gastritis, gastric cancer, T2DM and information on potential mediators: obesity, glycosylated hemoglobin (HbA1c) and blood glucose levels. Using univariate Mendelian randomization (MR) and multivariate MR (MVMR) analyses to evaluate the relationship between H. pylori and associated gastrointestinal diseases with the risk of developing of T2DM and explore the presence of mediators to ascertain the probable mechanisms. RESULTS Genetic evidence suggests that H. pylori IgG antibody (P = 0.006, b = 0.0945, OR = 1.0995, 95% CI = 1.023-1.176), H. pylori GroEL antibody (P = 0.028, OR = 1.033, 95% CI = 1.004-1.064), gastroduodenal ulcers (P = 0.019, OR = 1.036, 95% CI = 1.006-1.068) and chronic gastritis (P = 0.005, OR = 1.042, 95% CI = 1.012-1.074) are all linked to an increased risk of T2DM, additionally, H. pylori IgG antibody is associated with obesity (P = 0.034, OR = 1.03, 95% CI = 1.002-1.055). The results of MVMR showed that the pathogenic relationship between H. pylori GroEL antibody and gastroduodenal ulcer in T2DM is mediated by blood glucose level and obesity, respectively. CONCLUSION Our study found that H. pylori IgG antibody, H. pylori GroEL antibody, gastroduodenal ulcer and chronic gastritis are all related to t T2DM, and blood glucose level and obesity mediate the development of H. pylori GroEL antibody and gastroduodenal ulcer on T2DM, respectively. These findings may inform new prevention and intervention strategies for T2DM.
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Affiliation(s)
- Mei Sun
- Department of Infectious Diseases, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Department of gastroenterology, Dalian Municipal Central Hospital, Dalian, China
| | - Zhe Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- College of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Jingjing Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Juewei Zhang
- Health Inspection and Quarantine, College of Medical Laboratory, Dalian Medical University, Dalian, China
| | - Zhuqiang Jia
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Naqu People’s Hospital, Tibet, China
| | - Lin Zhao
- Department of Quality Management, Dalian Municipal Central Hospital, Dalian, China
| | - Xin Han
- Naqu People’s Hospital, Tibet, China
- Department of Orthopaedic Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xiaohong Sun
- Department of Nursing, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Junwei Zong
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Ying Zhu
- Department of Infectious Diseases, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Shouyu Wang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
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21
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Xie T, Mao Y. The causal impact of maternal smoking around birth on offspring ADHD: A two-sample Mendelian randomization study. J Affect Disord 2024; 351:24-30. [PMID: 38266926 DOI: 10.1016/j.jad.2024.01.196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 01/06/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND The previous literature highlights a relationship between maternal smoking around birth (MSAB) and offspring attention-deficit/hyperactivity disorder (ADHD). These studies have focused on the causal effects of MSAB on offspring ADHD. METHOD A Mendelian randomization analysis was conducted using summary statistics. Data on MSAB were obtained from a recent study including 391,992 participants. ADHD data were obtained from six sources for 246,888 participants. The present study used five methods to examine the causal impact from outcomes on exposures. The inverse variance weighted (IVW) was the main method of analysis, while the other four methods were supplementary methods. RESULT The IVW revealed that MSAB was a risk factor for offspring ADHD (OR: 2.54; 95 % confidence interval [CI]: 1.61-4.00, p = 6.04 × 10-5). Concerning ADHD in both sexes, MSAB was associated with females (OR = 3.96, 95 % CI: 1.99-7.90, p = 8.98 × 10-5) and males (OR = 3.74, 95 % CI: 1.74-5.72, p = 1.48 × 10-4). In different diagnosis periods for ADHD, MSAB increased the risk of childhood (OR = 3.63, 95 % CI: 2.25-5.87, p = 1.31 × 10-7), late-diagnosed (OR = 2.99, 95 % CI: 1.74-5.14, p = 7.33 × 10-5), and persistent (OR = 4.77, 95 % CI: 1.88-12.14, p = 1.03 × 10-3) ADHD. The final analysis did not reveal heterogeneity. CONCLUSIONS A causal impact of MSAB on offspring ADHD was observed. These findings highlight the need for careful consideration of prenatal exposure (MSAB) during the assessment of offspring ADHD. Additionally, it can provide targeted guidance for prenatal interventions. Future studies should analyze the effects of different doses of maternal smoking on ADHD.
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Affiliation(s)
- Tao Xie
- School of Public Policy and Administration, Xi'an Jiaotong University, Xi'an 710049, China
| | - Ying Mao
- School of Public Policy and Administration, Xi'an Jiaotong University, Xi'an 710049, China.
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22
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Jeong R, Bulyk ML. Chromatin accessibility variation provides insights into missing regulation underlying immune-mediated diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589213. [PMID: 38659802 PMCID: PMC11042205 DOI: 10.1101/2024.04.12.589213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Most genetic loci associated with complex traits and diseases through genome-wide association studies (GWAS) are noncoding, suggesting that the causal variants likely have gene regulatory effects. However, only a small number of loci have been linked to expression quantitative trait loci (eQTLs) detected currently. To better understand the potential reasons for many trait-associated loci lacking eQTL colocalization, we investigated whether chromatin accessibility QTLs (caQTLs) in lymphoblastoid cell lines (LCLs) explain immune-mediated disease associations that eQTLs in LCLs did not. The power to detect caQTLs was greater than that of eQTLs and was less affected by the distance from the transcription start site of the associated gene. Meta-analyzing LCL eQTL data to increase the sample size to over a thousand led to additional loci with eQTL colocalization, demonstrating that insufficient statistical power is still likely to be a factor. Moreover, further eQTL colocalization loci were uncovered by surveying eQTLs of other immune cell types. Altogether, insufficient power and context-specificity of eQTLs both contribute to the 'missing regulation.'
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Affiliation(s)
- Raehoon Jeong
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Bioinformatics and Integrative Genomics Graduate Program, Harvard University, Cambridge, MA 02138, USA
| | - Martha L. Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Bioinformatics and Integrative Genomics Graduate Program, Harvard University, Cambridge, MA 02138, USA
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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23
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Li X, Huang L, Yan Y, Rong Y, Chen X, Gao M, Huang J. Deciphering the causal association and co-disease mechanisms between psoriasis and breast cancer. Front Immunol 2024; 15:1304888. [PMID: 38605947 PMCID: PMC11007022 DOI: 10.3389/fimmu.2024.1304888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
Background Prior research has indicated a link between psoriasis and the susceptibility to breast cancer (BC); however, a definitive causal relationship remains elusive. This study sought to elucidate the causal connection and shared underlying mechanisms between psoriasis and BC through bidirectional Mendelian randomization (MR) and bioinformatic approaches. Methods We employed a bidirectional MR approach to examine the potential causal connection between psoriasis and BC. Genetic data pertaining to psoriasis and BC were sourced from extensive published genome-wide association studies. The inverse -variance weighted or wald ratio served as the primary method for estimating causal effects. Sensitivity analysis of the MR results was applied with multiple methods. Leveraged datasets from the Gene Expression Omnibus and the Cancer Genome Atlas repositories to identify common differentially expressed genes, shedding light on the shared mechanisms underlying these two conditions. Results The MR analysis revealed that when considering psoriasis as an exposure factor, the incidences of BC (OR=1.027) and estrogen receptor negative (ER-) BC (OR=1.054) were higher than in the general population. When using Her2+ BC as an exposure factor, the risk of psoriasis was 0.822 times higher (OR=0.822) than in the general population. Sensitivity analysis indicated that the results were robust. Transcriptome analysis showed that CXCL13 and CCL20 were activated in both BC and psoriasis. Both diseases were also linked to neutrophil chemotaxis, the IL-17 pathway, and the chemokine pathway. Conclusion The results suggest that psoriasis may increase the risk of BC, especially ER- BC, while reverse MR suggests a decreased risk of psoriasis in Her2+ BC. Transcriptome analysis revealed a shared mechanism between psoriasis and BC.
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Affiliation(s)
- Xujia Li
- VIP Department, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, China
| | - Lingli Huang
- VIP Department, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, China
| | - Yue Yan
- VIP Department, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, China
| | - Yuming Rong
- VIP Department, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, China
| | - Xuxian Chen
- VIP Department, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, China
| | - Mengge Gao
- Department of Clinical Nutrition, Huadu District People’s Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jinsheng Huang
- VIP Department, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, China
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24
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Xie T, Zhu B, Li HR, Xu JF, Mao Y. Educational attainment, income, and attention deficit hyperactivity disorder: A mediation analysis based on two-step Mendelian randomization. Soc Sci Med 2024; 345:116680. [PMID: 38394947 DOI: 10.1016/j.socscimed.2024.116680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/17/2023] [Accepted: 02/08/2024] [Indexed: 02/25/2024]
Abstract
Previous studies have reported the relationship between educational attainment and attention deficit hyperactivity disorder (ADHD). However, the mechanism of this relationship remains unknown. It is well known that educational attainment correlates with income. Therefore, based on summary data from a genome-wide association study we used two-step Mendelian randomization (MR) to explore the role of income between education and ADHD. The inverse variance weighted (IVW) method was used in our analysis. The IVW results suggested that educational attainment and income were protective factors against ADHD. Educational attainment affects ADHD through income [ADHD: Beta = -0.68, 95% confidence interval (CI) = -0.87, -0.49; female: Beta = -0.87, 95% CI = -1.28, -0.47; male: Beta = -1.01, 95% CI = -1.34, -0.68; childhood: Beta = -0.52, 95% CI = -0.74, -0.30; late-diagnosed: Beta = -0.78, 95% CI = -1.11, -0.47; persistent: Beta = -0.82, 95% CI = -1.33, -0.31]. Income also affected ADHD through educational attainment [female: Beta = -1.08, 95% CI = -1.35, -0.83; male: Beta = -1.16, 95% CI = -1.57, -0.77; persistent: Beta = -1.48, 95% CI = -2.09, -0.94]. In the final analysis, data with heterogeneity were analyzed using IVW random effects results. The mechanism is that income will mediate the relationship between educational attainment and ADHD.
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Affiliation(s)
- Tao Xie
- School of Public Policy and Administration, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Bin Zhu
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China.
| | - Hao-Ran Li
- School of Public Policy and Administration, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Jin-Feng Xu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China; West China School of Medicine, Sichuan University, Chengdu, 610041, China.
| | - Ying Mao
- School of Public Policy and Administration, Xi'an Jiaotong University, Xi'an, 710049, China.
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Qiu Z, Jia X, Fu Y, Yang Y. Screen time in the development of cardiovascular diseases: A two-sample Mendelian randomization study. Nutr Metab Cardiovasc Dis 2024; 34:706-717. [PMID: 37996370 DOI: 10.1016/j.numecd.2023.09.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/27/2023] [Accepted: 09/29/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND AND AIMS Coronary artery disease (CAD), heart failure (HF), and ischemic heart disease (IHD) are three common cardiovascular diseases that are closely associated with metabolic activity. The global incidence and prevalence of these conditions are on the rise, primarily due to unhealthy lifestyles, aging populations, and the increasing prevalence of obesity and diabetes. Excessive screen time has emerged as a potential risk factor for various adverse health outcomes, although limited research has explored its relationship with cardiovascular disease outcomes. METHODS AND RESULTS A Mendelian randomization (MR) study was conducted, employing exposure-associated genetic variants as instrumental variables to explore the causal relationship between screen time use and cardiovascular disease outcomes. Single nucleotide polymorphisms (SNPs) were utilized as pooled data for the genetic variable instrument, investigating the association between screen use duration and three types of cardiovascular diseases: coronary artery disease (CAD), heart failure (HF), and ischemic heart disease (IHD). Through the MR analysis, it was revealed that the use of mobile phones and TV screens exhibited a significant causal association with the occurrence of CAD, heart failure, and IHD. However, no significant association was observed between the use of computers and these three types of cardiovascular diseases. CONCLUSION Our study suggests that excessive screen time use is associated with the development of cardiovascular disease. However, it should be noted that the consequences of screen time can vary depending on the reasons and purposes for its use. Implementing reasonable control over screen time, particularly for entertainment purposes, holds promise as a potential approach to mitigating cardiovascular disease.
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Affiliation(s)
- Zhengqi Qiu
- Faculty of Medicine, Macau University of Science and Technology, Room PP-R203, Est. Seak Pai Van Praia Park, Rés-Do-Chão R, Coloane, Macau 999078, China.
| | - Xueyuan Jia
- Faculty of Medicine, Macau University of Science and Technology, Room PP-R203, Est. Seak Pai Van Praia Park, Rés-Do-Chão R, Coloane, Macau 999078, China
| | - Yancheng Fu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Yanru Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
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Puvogel S, Alsema A, North HF, Webster MJ, Weickert CS, Eggen BJL. Single-Nucleus RNA-Seq Characterizes the Cell Types Along the Neuronal Lineage in the Adult Human Subependymal Zone and Reveals Reduced Oligodendrocyte Progenitor Abundance with Age. eNeuro 2024; 11:ENEURO.0246-23.2024. [PMID: 38351133 PMCID: PMC10913050 DOI: 10.1523/eneuro.0246-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 03/06/2024] Open
Abstract
The subependymal zone (SEZ), also known as the subventricular zone (SVZ), constitutes a neurogenic niche that persists during postnatal life. In humans, the neurogenic potential of the SEZ declines after the first year of life. However, studies discovering markers of stem and progenitor cells highlight the neurogenic capacity of progenitors in the adult human SEZ, with increased neurogenic activity occurring under pathological conditions. In the present study, the complete cellular niche of the adult human SEZ was characterized by single-nucleus RNA sequencing, and compared between four youth (age 16-22) and four middle-aged adults (age 44-53). We identified 11 cellular clusters including clusters expressing marker genes for neural stem cells (NSCs), neuroblasts, immature neurons, and oligodendrocyte progenitor cells. The relative abundance of NSC and neuroblast clusters did not differ between the two age groups, indicating that the pool of SEZ NSCs does not decline in this age range. The relative abundance of oligodendrocyte progenitors and microglia decreased in middle-age, indicating that the cellular composition of human SEZ is remodeled between youth and adulthood. The expression of genes related to nervous system development was higher across different cell types, including NSCs, in youth as compared with middle-age. These transcriptional changes suggest ongoing central nervous system plasticity in the SEZ in youth, which declined in middle-age.
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Affiliation(s)
- Sofía Puvogel
- Section Molecular Neurobiology, Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen 9700 AD, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen 6500 HB, The Netherlands
| | - Astrid Alsema
- Section Molecular Neurobiology, Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen 9700 AD, The Netherlands
| | - Hayley F North
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Sydney, New South Wales 2031, Australia
- School of Psychiatry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Maree J Webster
- Laboratory of Brain Research, Stanley Medical Research Institute, Rockville 20850, Maryland
| | - Cynthia Shannon Weickert
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Sydney, New South Wales 2031, Australia
- School of Psychiatry, University of New South Wales, Sydney, New South Wales 2052, Australia
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, New York 13201
| | - Bart J L Eggen
- Section Molecular Neurobiology, Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen 9700 AD, The Netherlands
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Ren Y, Jiang Y, Peng H, Jiang H. Causal association between several gender-driven factors and gout: A bidirectional Mendelian randomization study. Int J Rheum Dis 2024; 27:e15111. [PMID: 38519439 DOI: 10.1111/1756-185x.15111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/09/2024] [Accepted: 02/22/2024] [Indexed: 03/24/2024]
Affiliation(s)
- Yanshuang Ren
- Henan Key Laboratory of Rare Diseases, Endocrinology and Metabolism Center, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Yuqing Jiang
- Henan Key Laboratory of Rare Diseases, Endocrinology and Metabolism Center, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Huifang Peng
- Henan Key Laboratory of Rare Diseases, Endocrinology and Metabolism Center, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Hongwei Jiang
- Henan Key Laboratory of Rare Diseases, Endocrinology and Metabolism Center, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
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Wang X, Chen Q, Liu Y, Sun J, Li J, Zhao P, Cai L, Liu W, Yang Z, Wang Z, Lv H. Causal relationship between multiparameter brain MRI phenotypes and age: evidence from Mendelian randomization. Brain Commun 2024; 6:fcae077. [PMID: 38529357 PMCID: PMC10963122 DOI: 10.1093/braincomms/fcae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/05/2024] [Accepted: 02/29/2024] [Indexed: 03/27/2024] Open
Abstract
To explore the causal relationship between age and brain health (cortical atrophy, white matter integrity, white matter hyperintensities and cerebral microbleeds in various brain regions) related multiparameter imaging features using two-sample Mendelian randomization. Age was determined as chronological age of the subject. Cortical volume, white matter micro-integrity, white matter hyperintensity volume and cerebral microbleeds of each brain region were included as phenotypes for brain health. Age and imaging of brain health related genetic data were analysed to determine the causal relationship using inverse-variance weighted model, validated by heterogeneity and horizontal pleiotropy variables. Age is causally related to increased volumes of white matter hyperintensities (β = 0.151). For white matter micro-integrity, fibres of the inferior cerebellar peduncle (axial diffusivity β = -0.128, orientation dispersion index β = 0.173), cerebral peduncle (axial diffusivity β = -0.136), superior fronto-occipital fasciculus (isotropic volume fraction β = 0.163) and fibres within the limbic system were causally deteriorated. We also detected decreased cortical thickness of multiple frontal and temporal regions (P < 0.05). Microbleeds were not related with aging (P > 0.05). Aging is a threat of brain health, leading to cortical atrophy mainly in the frontal lobes, as well as the white matter degeneration especially abnormal hyperintensity and deteriorated white matter integrity around the hippocampus.
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Affiliation(s)
- Xinghao Wang
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Qian Chen
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Yawen Liu
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Jing Sun
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Jia Li
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Pengfei Zhao
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Linkun Cai
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Wenjuan Liu
- Department of Radiology, Aerospace Center Hospital, Beijing 100089, China
- Peking University Aerospace School of Clinical Medicine, Beijing 100089, China
| | - Zhenghan Yang
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Zhenchang Wang
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Han Lv
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
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Yao X, Zhang R, Wang X. The gut-joint axis: Genetic evidence for a causal association between gut microbiota and seropositive rheumatoid arthritis and seronegative rheumatoid arthritis. Medicine (Baltimore) 2024; 103:e37049. [PMID: 38394529 PMCID: PMC11309692 DOI: 10.1097/md.0000000000037049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/03/2024] [Indexed: 02/25/2024] Open
Abstract
This study aimed to assess the causal relationship between GM and RA (seropositive RA and seronegative RA). A two-sample Mendelian randomization (MR) analysis was performed to assess the causality of GM on seropositive RA and seronegative RA. GM's genome-wide association study (GWAS) was used as the exposure, whereas the GWAS datasets of seropositive RA and seronegative RA were the outcomes. The primary analysis approach was used as inverse-variance weighted (IVW), followed by 3 additional MR methods (MR-Egger, weighted median, and weighted mode). Cochran's Q test was used to identify heterogeneity. The MR-Egger intercept test and leave-one-out analyses were used to assess horizontal pleiotropy. All statistical analyses were performed in R software. We discovered that Alloprevotella (IVW OR 0.84, 95% CI 0.71-0.99, P = .04) and Christensenellaceae R 7 group (IVW OR 0.71, 95% CI 0.52-0.99, P = .04) were negatively correlated with seropositive RA, Ruminococcaceae UCG002 (IVW OR 1.30, 95% CI 1.10-1.54, P = .002) was positively associated with seropositive RA. Actinomyces (IVW OR 0.73, 95% CI 0.54-0.99, P = .04), Christensenellaceae R 7 group (IVW OR 0.62, 95% CI 0.39-0.97, P = .04), Terrisporobacter (IVW OR 0.64, 95% CI 0.44-0.93, P = .02), Lactobacillales (IVW OR 0.65, 95% CI 0.47-0.90, P = .01) were negatively correlated with seronegative RA. The present MR analysis showed a protective effect of Alloprevotella and Christensenellaceae R 7 group and a potentially anti-protective effect of Ruminococcaceae UCG002 on seropositive RA; and a protective effect of Actinomyces, Christensenellaceae R 7 group, Terrisporobacter, and Lactobacillales on seronegative RA. Further experimental studies and randomized controlled trials are needed to validate these findings.
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Affiliation(s)
- Xinyi Yao
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Runrun Zhang
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Xinchang Wang
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
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Huang A, Wu X, Lin J, Wei C, Xu W. Genetic insights into repurposing statins for hyperthyroidism prevention: a drug-target Mendelian randomization study. Front Endocrinol (Lausanne) 2024; 15:1331031. [PMID: 38425755 PMCID: PMC10902122 DOI: 10.3389/fendo.2024.1331031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Background Current therapeutic measures for thyroid dysfunction are limited and often accompanied by adverse effects. The use of lipid-lowering drugs like statins has recently been associated with lower thyroid eye diseases risk. Objective To investigate the implications of genetically proxied lipid-lowering drugs on thyroid dysfunction. Methods In this drug-target Mendelian randomization (MR) study, we utilized genetic variants within drug target genes associated with low-density lipoprotein (LDL) or triglyceride (TG), derived from a genome-wide association study (GWAS) meta-analysis (N ≤ 188,577), to simulate lifelong drug interventions. Genetic summary statistics for thyroid dysfunction outcomes were retrieved from GWAS datasets of Thyroid Omics Consortium (N ≤ 54,288) and UK Biobank (N = 484,598). Inverse-variance-weighted MR (IVW-MR) method was performed as primary analysis, followed by validation in colocalization analysis. A subsequent two-step MR analysis was conducted to identify biomarkers mediating the identified drug-outcome association. Results In IVW-MR analysis, genetic mimicry of 3-hydroxy-3-methylglutarylcoenzyme reductase (HMGCR) inhibitors (e.g. statins) was significantly associated with lower risk of hyperthyroidism in two independent datasets (OR1, 0.417 per 1-mmol/L lower in LDL-C; 95% CI 0.262 to 0.664; P1 = 2.262 × 10-4; OR2 0.996; 95% CI 0.993-0.998; P2 = 0.002). Two-step MR analysis revealed eighteen biomarkers linked to genetic mimicry of HMGCR inhibition, and identified insulin-like growth factor 1 (IGF-1) levels mediating 2.108% of the negative causal relationship between HMGCR inhibition and hyperthyroidism. Conclusion This study supports HMGCR inhibition as a promising therapeutic strategy for hyperthyroidism and suggests its underlying mechanisms may extend beyond lipid metabolism. Further investigations through laboratory studies and clinical trials are necessary to confirm and elucidate these findings.
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Affiliation(s)
- Anqi Huang
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Shantou University Medical College, Shantou, China
| | - Xinyi Wu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Shantou University Medical College, Shantou, China
| | - Jiaqi Lin
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Shantou University Medical College, Shantou, China
| | - Chiju Wei
- Multidisciplinary Research Center, Shantou University, Shantou, China
| | - Wencan Xu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
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Wu Y, Shi R, Chen H, Zhang Z, Bao S, Qu J, Zhou M. Effect of the gut microbiome in glaucoma risk from the causal perspective. BMJ Open Ophthalmol 2024; 9:e001547. [PMID: 38286567 PMCID: PMC10826588 DOI: 10.1136/bmjophth-2023-001547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/12/2024] [Indexed: 01/31/2024] Open
Abstract
OBJECTIVE Evidence from observational studies has reported possible associations between the gut microbiome (GM) and glaucoma. However, the causal effect of GM on glaucoma risk remains to be determined. METHODS AND ANALYSIS We conducted two-sample bidirectional Mendelian randomisation (MR) analyses to explore the causal association between GM and glaucoma. Genome-wide association study summary statistics of 196 GM taxa (n=18 340) and glaucoma (18 902 cases and 358 375 controls) were obtained from MiBioGen and FinnGen Consortium. Inverse variance weighted, MR-Egger, weighted median, weighted mode, Mendelian Randomisation Pleiotropy Residual Sum and Outlier, MR-Egger intercept and Cochran's Q statistical analyses were used to supplement MR results and sensitivity analysis. An independent cohort from the Medical Research Council (MRC) Integrative Epidemiology Unit at the University of Bristol (MRC-IEU) Consortium (1715 cases and 359 479 controls) was used to validate causal effects. RESULTS Results of the MR analysis suggested that the family Oxalobacteraceae (OR 0.900, 95% CI 0.843 to 0.961, p=0.002) and the genus Eggerthella (OR 0.881, 95% CI 0.811 to 0.957, p=0.003) had a negative effect on glaucoma, whereas the genus Bilophila (OR 1.202, 95% CI 1.074 to 1.346, p=0.001), LachnospiraceaeUCG010 (OR 1.256, 95% CI 1.109 to 1.423, p=0.0003) and Ruminiclostridium 9 (OR 1.258, 95% CI 1.083 to 1.461, p=0.003) had a positive effect on glaucoma. Among these, the positive causal effect of LachnospiraceaeUCG010 (OR 1.002, 95% CI 1.000 to 1.004, p=0.033) on glaucoma was replicated in an independent cohort. CONCLUSION This MR analysis from large population studies demonstrated the causal effect of GM on glaucoma risk and supported the role of GM in influencing glaucoma susceptibility.
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Affiliation(s)
- Yaxuan Wu
- School of Biomedical Engineering, School of Information and Communication Engineering, Hainan University, Haikou, People's Republic of China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, People's Republic of China
- Hainan Institute of Real World Data, Qionghai, People's Republic of China
| | - Ronghua Shi
- School of Biomedical Engineering, School of Information and Communication Engineering, Hainan University, Haikou, People's Republic of China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, People's Republic of China
- Hainan Institute of Real World Data, Qionghai, People's Republic of China
| | - He Chen
- School of Biomedical Engineering, School of Information and Communication Engineering, Hainan University, Haikou, People's Republic of China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, People's Republic of China
- Hainan Institute of Real World Data, Qionghai, People's Republic of China
| | - Zicheng Zhang
- School of Biomedical Engineering, School of Information and Communication Engineering, Hainan University, Haikou, People's Republic of China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, People's Republic of China
- Hainan Institute of Real World Data, Qionghai, People's Republic of China
| | - Siqi Bao
- School of Biomedical Engineering, School of Information and Communication Engineering, Hainan University, Haikou, People's Republic of China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, People's Republic of China
- Hainan Institute of Real World Data, Qionghai, People's Republic of China
| | - Jia Qu
- School of Biomedical Engineering, School of Information and Communication Engineering, Hainan University, Haikou, People's Republic of China
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, People's Republic of China
- Hainan Institute of Real World Data, Qionghai, People's Republic of China
| | - Meng Zhou
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, People's Republic of China
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Bhattacharyya U, John J, Lam M, Fisher J, Sun B, Baird D, Chen CY, Lencz T. Large-Scale Mendelian Randomization Study Reveals Circulating Blood-based Proteomic Biomarkers for Psychopathology and Cognitive Task Performance. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.18.24301455. [PMID: 38293198 PMCID: PMC10827252 DOI: 10.1101/2024.01.18.24301455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background Research on peripheral (e.g., blood-based) biomarkers for psychiatric illness has typically been low-throughput in terms of both the number of subjects and the range of assays performed. Moreover, traditional case-control studies examining blood-based biomarkers are subject to potential confounds of treatment and other exposures common to patients with psychiatric illnesses. Our research addresses these challenges by leveraging large-scale, high-throughput proteomics data and Mendelian Randomization (MR) to examine the causal impact of circulating proteins on psychiatric phenotypes and cognitive task performance. Methods We utilized plasma proteomics data from the UK Biobank (3,072 proteins assayed in 34,557 European-ancestry individuals) and deCODE Genetics (4,719 proteins measured across 35,559 Icelandic individuals). Significant proteomic quantitative trait loci (both cis-pQTLs and trans-pQTLs) served as MR instruments, with the most recent GWAS for schizophrenia, bipolar disorder, major depressive disorder, and cognitive task performance (all excluding overlapping UK Biobank participants) as phenotypic outcomes. Results MR revealed 109 Bonferroni-corrected causal associations (44 novel) involving 88 proteins across the four phenotypes. Several immune-related proteins, including interleukins and complement factors, stood out as pleiotropic across multiple outcome phenotypes. Drug target enrichment analysis identified several novel potential pharmacologic repurposing opportunities, including anti-inflammatory agents for schizophrenia and bipolar disorder and duloxetine for cognitive performance. Conclusions Identification of causal effects for these circulating proteins suggests potential biomarkers for these conditions and offers insights for developing innovative therapeutic strategies. The findings also indicate substantial evidence for the pleiotropic effects of many proteins across different phenotypes, shedding light on the shared etiology among psychiatric conditions and cognitive ability.
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Affiliation(s)
- Upasana Bhattacharyya
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY
| | - Jibin John
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY
| | - Max Lam
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY
| | - Jonah Fisher
- Biogen Inc., Cambridge, MA
- Harvard T.H. Chan School of Public Health, Cambridge, MA
| | | | | | | | - Todd Lencz
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY
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Cao C, Zhang S, Wang J, Tian M, Ji X, Huang D, Yang S, Gu N. PGS-Depot: a comprehensive resource for polygenic scores constructed by summary statistics based methods. Nucleic Acids Res 2024; 52:D963-D971. [PMID: 37953384 PMCID: PMC10767792 DOI: 10.1093/nar/gkad1029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/04/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
Polygenic score (PGS) is an important tool for the genetic prediction of complex traits. However, there are currently no resources providing comprehensive PGSs computed from published summary statistics, and it is difficult to implement and run different PGS methods due to the complexity of their pipelines and parameter settings. To address these issues, we introduce a new resource called PGS-Depot containing the most comprehensive set of publicly available disease-related GWAS summary statistics. PGS-Depot includes 5585 high quality summary statistics (1933 quantitative and 3652 binary trait statistics) curated from 1564 traits in European and East Asian populations. A standardized best-practice pipeline is used to implement 11 summary statistics-based PGS methods, each with different model assumptions and estimation procedures. The prediction performance of each method can be compared for both in- and cross-ancestry populations, and users can also submit their own summary statistics to obtain custom PGS with the available methods. Other features include searching for PGSs by trait name, publication, cohort information, population, or the MeSH ontology tree and searching for trait descriptions with the experimental factor ontology (EFO). All scores, SNP effect sizes and summary statistics can be downloaded via FTP. PGS-Depot is freely available at http://www.pgsdepot.net.
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Affiliation(s)
- Chen Cao
- Key Laboratory for Bio-Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Shuting Zhang
- Key Laboratory for Bio-Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jianhua Wang
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300203, China
| | - Min Tian
- Key Laboratory for Bio-Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xiaolong Ji
- Department of Biostatistics, Centre for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Dandan Huang
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300203, China
| | - Sheng Yang
- Department of Biostatistics, Centre for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Ning Gu
- Key Laboratory for Bio-Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Medical School, Nanjing University, Nanjing, Jiangsu 210093, China
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Richard-St-Hilaire A, Gamache I, Pelletier J, Grenier JC, Poujol R, Hussin JG. Signatures of Co-evolution and Co-regulation in the CYP3A and CYP4F Genes in Humans. Genome Biol Evol 2024; 16:evad236. [PMID: 38207129 PMCID: PMC10805436 DOI: 10.1093/gbe/evad236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024] Open
Abstract
Cytochromes P450 (CYP450) are hemoproteins generally involved in the detoxification of the body of xenobiotic molecules. They participate in the metabolism of many drugs and genetic polymorphisms in humans have been found to impact drug responses and metabolic functions. In this study, we investigate the genetic diversity of CYP450 genes. We found that two clusters, CYP3A and CYP4F, are notably differentiated across human populations with evidence for selective pressures acting on both clusters: we found signals of recent positive selection in CYP3A and CYP4F genes and signals of balancing selection in CYP4F genes. Furthermore, an extensive amount of unusual linkage disequilibrium is detected in this latter cluster, indicating co-evolution signatures among CYP4F genes. Several of the selective signals uncovered co-localize with expression quantitative trait loci (eQTL), which could suggest epistasis acting on co-regulation in these gene families. In particular, we detected a potential co-regulation event between CYP3A5 and CYP3A43, a gene whose function remains poorly characterized. We further identified a causal relationship between CYP3A5 expression and reticulocyte count through Mendelian randomization analyses, potentially involving a regulatory region displaying a selective signal specific to African populations. Our findings linking natural selection and gene expression in CYP3A and CYP4F subfamilies are of importance in understanding population differences in metabolism of nutrients and drugs.
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Affiliation(s)
- Alex Richard-St-Hilaire
- Département de biochimie et médecine moléculaire, Université de Montréal, Montreal, QC, Canada
- Sainte-Justine Hospital, Research Center, Montreal, QC, Canada
| | - Isabel Gamache
- Département de biochimie et médecine moléculaire, Université de Montréal, Montreal, QC, Canada
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
| | - Justin Pelletier
- Département de biochimie et médecine moléculaire, Université de Montréal, Montreal, QC, Canada
- McGill CERC in Genomic Medicine, McGill University, Montreal, Canada
| | | | - Raphaël Poujol
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
| | - Julie G Hussin
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
- Département de médecine, Université de Montréal, Montreal, QC, Canada
- Mila-Quebec AI institute, Montreal, QC, Canada
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Pan S, Kang H, Liu X, Li S, Yang P, Wu M, Yuan N, Lin S, Zheng Q, Jia P. COLOCdb: a comprehensive resource for multi-model colocalization of complex traits. Nucleic Acids Res 2024; 52:D871-D881. [PMID: 37941154 PMCID: PMC10767919 DOI: 10.1093/nar/gkad939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/01/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
Large-scale genome-wide association studies (GWAS) have provided profound insights into complex traits and diseases. Yet, deciphering the fine-scale molecular mechanisms of how genetic variants manifest to cause the phenotypes remains a daunting task. Here, we present COLOCdb (https://ngdc.cncb.ac.cn/colocdb), a comprehensive genetic colocalization database by integrating more than 3000 GWAS summary statistics and 13 types of xQTL to date. By employing two representative approaches for the colocalization analysis, COLOCdb deposits results from three key components: (i) GWAS-xQTL, pair-wise colocalization between GWAS loci and different types of xQTL, (ii) GWAS-GWAS, pair-wise colocalization between the trait-associated genetic loci from GWASs and (iii) xQTL-xQTL, pair-wise colocalization between the genetic loci associated with molecular phenotypes in xQTLs. These results together represent the most comprehensive colocalization analysis, which also greatly expands the list of shared variants with genetic pleiotropy. We expect that COLOCdb can serve as a unique and useful resource in advancing the discovery of new biological mechanisms and benefit future functional studies.
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Affiliation(s)
- Siyu Pan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Hongen Kang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xinxuan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Shuhua Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Peng Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Mingqiu Wu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Na Yuan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Shiqi Lin
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Qiwen Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
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Genovese G, Rockweiler NB, Gorman BR, Bigdeli TB, Pato MT, Pato CN, Ichihara K, McCarroll SA. BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies. Bioinformatics 2024; 40:btae038. [PMID: 38261650 PMCID: PMC10832354 DOI: 10.1093/bioinformatics/btae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/07/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024] Open
Abstract
MOTIVATION Many genetics studies report results tied to genomic coordinates of a legacy genome assembly. However, as assemblies are updated and improved, researchers are faced with either realigning raw sequence data using the updated coordinate system or converting legacy datasets to the updated coordinate system to be able to combine results with newer datasets. Currently available tools to perform the conversion of genetic variants have numerous shortcomings, including poor support for indels and multi-allelic variants, that lead to a higher rate of variants being dropped or incorrectly converted. As a result, many researchers continue to work with and publish using legacy genomic coordinates. RESULTS Here we present BCFtools/liftover, a tool to convert genomic coordinates across genome assemblies for variants encoded in the variant call format with improved support for indels represented by different reference alleles across genome assemblies and full support for multi-allelic variants. It further supports variant annotation fields updates whenever the reference allele changes across genome assemblies. The tool has the lowest rate of variants being dropped with an order of magnitude less indels dropped or incorrectly converted and is an order of magnitude faster than other tools typically used for the same task. It is particularly suited for converting variant callsets from large cohorts to novel telomere-to-telomere assemblies as well as summary statistics from genome-wide association studies tied to legacy genome assemblies. AVAILABILITY AND IMPLEMENTATION The tool is written in C and freely available under the MIT open source license as a BCFtools plugin available at http://github.com/freeseek/score.
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Affiliation(s)
- Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - Nicole B Rockweiler
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - Bryan R Gorman
- Center for Data and Computational Sciences, VA Boston HealthCare System, Boston, MA 02130, United States
- Booz Allen Hamilton Inc, McLean, VA 22102, United States
| | - Tim B Bigdeli
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, United States
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, United States
- Cooperative Studies Program, VA New York Harbor Healthcare System, Brooklyn, NY 11209, United States
| | - Michelle T Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, New Brunswick, NJ 08901, United States
| | - Carlos N Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, New Brunswick, NJ 08901, United States
| | - Kiku Ichihara
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
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Zuo M, Wang Z, Li W, Chen S, Yuan Y, Yang Y, Mao Q, Liu Y. Causal effects of potential risk factors on postpartum depression: a Mendelian randomization study. Front Psychiatry 2023; 14:1275834. [PMID: 38173707 PMCID: PMC10761415 DOI: 10.3389/fpsyt.2023.1275834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/09/2023] [Indexed: 01/05/2024] Open
Abstract
Background Postpartum depression (PPD) is a type of depressive episode related to parents after childbirth, which causes a variety of symptoms not only for parents but also affects the development of children. The causal relationship between potential risk factors and PPD remains comprehensively elucidated. Methods Linkage disequilibrium score regression (LDSC) analysis was conducted to screen the heritability of each instrumental variant (IV) and to calculate the genetic correlations between effective causal factors and PPD. To search for the causal effect of multiple potential risk factors on the incidence of PPD, random effects of the inverse variance weighted (IVW) method were applied. Sensitivity analyses, including weighted median, MR-Egger regression, Cochrane's Q test, and MR Pleiotropy Residual Sum and Outlier (MR-PRESSO), were performed to detect potential Mendelian randomization (MR) assumption violations. Multivariable MR (MVMR) was conducted to control potential multicollinearity. Results A total of 40 potential risk factors were investigated in this study. LDSC regression analysis reported a significant genetic correlation of potential traits with PPD. MR analysis showed that higher body mass index (BMI) (Benjamini and Hochberg (BH) corrected p = 0.05), major depression (MD) (BH corrected p = 5.04E-19), and schizophrenia (SCZ) (BH corrected p = 1.64E-05) were associated with the increased risk of PPD, whereas increased age at first birth (BH corrected p = 2.11E-04), older age at first sexual intercourse (BH corrected p = 3.02E-15), increased average total household income before tax (BH corrected p = 4.57E-02), and increased years of schooling (BH corrected p = 1.47E-11) led to a decreased probability of PPD. MVMR analysis suggested that MD (p = 3.25E-08) and older age at first birth (p = 8.18E-04) were still associated with an increased risk of PPD. Conclusion In our MR study, we found multiple risk factors, including MD and younger age at first birth, to be deleterious causal risk factors for PPD.
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Affiliation(s)
| | | | | | | | | | | | | | - Yanhui Liu
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, China
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38
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Qiu S, Hu Y, Liu G. Mendelian randomization study supports the causal effects of air pollution on longevity via multiple age-related diseases. NPJ AGING 2023; 9:29. [PMID: 38114504 PMCID: PMC10730819 DOI: 10.1038/s41514-023-00126-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 10/09/2023] [Indexed: 12/21/2023]
Abstract
Growing evidence suggests that exposure to fine particulate matter (PM2.5) may reduce life expectancy; however, the causal pathways of PM2.5 exposure affecting life expectancy remain unknown. Here, we assess the causal effects of genetically predicted PM2.5 concentration on common chronic diseases and longevity using a Mendelian randomization (MR) statistical framework based on large-scale genome-wide association studies (GWAS) (>400,000 participants). After adjusting for other types of air pollution and smoking, we find significant causal relationships between PM2.5 concentration and angina pectoris, hypercholesterolaemia and hypothyroidism, but no causal relationship with longevity. Mediation analysis shows that although the association between PM2.5 concentration and longevity is not significant, PM2.5 exposure indirectly affects longevity via diastolic blood pressure (DBP), hypertension, angina pectoris, hypercholesterolaemia and Alzheimer's disease, with a mediated proportion of 31.5, 70.9, 2.5, 100, and 24.7%, respectively. Our findings indicate that public health policies to control air pollution may help improve life expectancy.
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Affiliation(s)
- Shizheng Qiu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Yang Hu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, 150001, China.
| | - Guiyou Liu
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, 100069, China.
- Chinese Institute for Brain Research, Beijing, China.
- Key Laboratory of Cerebral Microcirculation in Universities of Shandong; Department of Neurology, Second Affiliated Hospital; Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China.
- Beijing Key Laboratory of Hypoxia Translational Medicine, National Engineering Laboratory of Internet Medical Diagnosis and Treatment Technology, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
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Deng CH, Naithani S, Kumari S, Cobo-Simón I, Quezada-Rodríguez EH, Skrabisova M, Gladman N, Correll MJ, Sikiru AB, Afuwape OO, Marrano A, Rebollo I, Zhang W, Jung S. Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences. Database (Oxford) 2023; 2023:baad088. [PMID: 38079567 PMCID: PMC10712715 DOI: 10.1093/database/baad088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/17/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023]
Abstract
Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.
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Affiliation(s)
- Cecilia H Deng
- Molecular and Digital Breeding, New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Auckland 1025, New Zealand
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York, NY 11724, USA
| | - Irene Cobo-Simón
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Institute of Forest Science (ICIFOR-INIA, CSIC), Madrid, Spain
| | - Elsa H Quezada-Rodríguez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Maria Skrabisova
- Department of Biochemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Nick Gladman
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York, NY 11724, USA
- U.S. Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853, USA
| | - Melanie J Correll
- Agricultural and Biological Engineering Department, University of Florida, 1741 Museum Rd, Gainesville, FL 32611, USA
| | | | | | - Annarita Marrano
- Phoenix Bioinformatics, 39899 Balentine Drive, Suite 200, Newark, CA 94560, USA
| | | | - Wentao Zhang
- National Research Council Canada, 110 Gymnasium Pl, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Sook Jung
- Department of Horticulture, Washington State University, 303c Plant Sciences Building, Pullman, WA 99164-6414, USA
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40
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Zhao X, Xu W, Gu Y, Li Z, Sun G. Causal associations between hand grip strength and pulmonary function: a two-sample Mendelian randomization study. BMC Pulm Med 2023; 23:459. [PMID: 37990169 PMCID: PMC10664596 DOI: 10.1186/s12890-023-02720-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/19/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Several observational studies have reported an association between hand grip strength (HGS) and pulmonary function (PF). However, causality is unclear. To investigate whether HGS and PF are causally associated, we performed Mendelian randomization (MR) analyses. METHODS We identified 110 independent single nucleotide polymorphisms (SNPs) for right-hand grip strength (RHGS) and 103 independent SNPs for left-hand grip strength (LHGS) at the genome-wide significant threshold (P < 5 × 10-8) from MRC-IEU Consortium and evaluated these related to PF. MR estimates were calculated using the inverse-variance weighted (IVW) method and multiple sensitivity analyses were further performed. RESULTS Genetical liability to HGS was positively causally associated with forced vital capacity (FVC) and forced expiratory volume in one second (FEV1), but not with FEV1/FVC. In addition, there was positive causal association between RHGS and FVC (OR=1.519; 95% CI, 1.418-1.627; P=8.96E-33), and FEV1 (OR=1.486; 95% CI, 1.390-1.589; P=3.19E-31); and positive causal association between LHGS and FVC (OR=1.464; 95% CI, 1.385-1.548; P=2.83E-41) and FEV1 (OR=1.419; 95% CI, 1.340-1.502; P=3.19E-33). Nevertheless, no associations were observed between RHGS and FEV1/FVC (OR=0.998; 95% CI, 0.902-1.103; P=9.62E-01) and between LHGS and FEV1/FVC (OR=0.966; 95% CI, 0.861-1.083; P=5.52E-01). Similar results were shown in several sensitivity analyses. CONCLUSION Our study provides support at the genetic level that HGS is positively causally associated with FVC and FEV1, but not with FEV1/FVC. Interventions for HGS in PF impairment deserve further exploration as potential indicators of PF assessment.
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Affiliation(s)
- Xianghu Zhao
- College of Sports Medicine, Wuhan Sports University, Wuhan, 430079, Hubei Province, China
- Department of Rehabilitation, Zhongda Hospital, Southeast University, Nanjing, 210009, Jiangsu Province, China
| | - Wenyuan Xu
- Graduate School, Anhui University of Chinese Medicine, Hefei, 230012, Anhui Province, China
| | - Yanchao Gu
- College of Sports Medicine, Wuhan Sports University, Wuhan, 430079, Hubei Province, China
| | - Zhanghua Li
- Department of Orthopedics, Wuhan Third Hospital, Tongren Hospital of Wuhan University, Wuhan, 430074, Hubei Province, China.
| | - Guiju Sun
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, and Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu Province, China.
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41
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Constantinescu AE, Bull CJ, Goudswaard LJ, Zheng J, Elsworth B, Timpson NJ, Moore SF, Hers I, Vincent EE. A phenome-wide approach to identify causal risk factors for deep vein thrombosis. BMC Med Genomics 2023; 16:284. [PMID: 37951941 PMCID: PMC10640748 DOI: 10.1186/s12920-023-01710-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
Deep vein thrombosis (DVT) is the formation of a blood clot in a deep vein. DVT can lead to a venous thromboembolism (VTE), the combined term for DVT and pulmonary embolism, a leading cause of death and disability worldwide. Despite the prevalence and associated morbidity of DVT, the underlying causes are not well understood. Our aim was to leverage publicly available genetic summary association statistics to identify causal risk factors for DVT. We conducted a Mendelian randomization phenome-wide association study (MR-PheWAS) using genetic summary association statistics for 973 exposures and DVT (6,767 cases and 330,392 controls in UK Biobank). There was evidence for a causal effect of 57 exposures on DVT risk, including previously reported risk factors (e.g. body mass index-BMI and height) and novel risk factors (e.g. hyperthyroidism and varicose veins). As the majority of identified risk factors were adiposity-related, we explored the molecular link with DVT by undertaking a two-sample MR mediation analysis of BMI-associated circulating proteins on DVT risk. Our results indicate that circulating neurogenic locus notch homolog protein 1 (NOTCH1), inhibin beta C chain (INHBC) and plasminogen activator inhibitor 1 (PAI-1) influence DVT risk, with PAI-1 mediating the BMI-DVT relationship. Using a phenome-wide approach, we provide putative causal evidence that hyperthyroidism, varicose veins and BMI enhance the risk of DVT. Furthermore, the circulating protein PAI-1 has a causal role in DVT aetiology and is involved in mediating the BMI-DVT relationship.
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Affiliation(s)
- Andrei-Emil Constantinescu
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK.
- Bristol Medical School, Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK.
- School of Translational Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK.
| | - Caroline J Bull
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- School of Translational Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- Health Data Research UK. Registered Office, 215 Euston Road, London, NW1 2BE, UK
| | - Lucy J Goudswaard
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Jie Zheng
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Benjamin Elsworth
- Our Future Health Ltd. Registered office: 2 New Bailey, 6 Stanley Street, Manchester, M3 5GS, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - Samantha F Moore
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
- UKRI Medical Research Council, Swindon, UK
| | - Ingeborg Hers
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Emma E Vincent
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- Bristol Medical School, Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- School of Translational Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
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42
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Cifello J, Kuksa PP, Saravanan N, Valladares O, Wang LS, Leung YY. hipFG: high-throughput harmonization and integration pipeline for functional genomics data. Bioinformatics 2023; 39:btad673. [PMID: 37947320 PMCID: PMC10660288 DOI: 10.1093/bioinformatics/btad673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/20/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023] Open
Abstract
SUMMARY Preparing functional genomic (FG) data with diverse assay types and file formats for integration into analysis workflows that interpret genome-wide association and other studies is a significant and time-consuming challenge. Here we introduce hipFG (Harmonization and Integration Pipeline for Functional Genomics), an automatically customized pipeline for efficient and scalable normalization of heterogenous FG data collections into standardized, indexed, rapidly searchable analysis-ready datasets while accounting for FG datatypes (e.g. chromatin interactions, genomic intervals, quantitative trait loci). AVAILABILITY AND IMPLEMENTATION hipFG is freely available at https://bitbucket.org/wanglab-upenn/hipFG. A Docker container is available at https://hub.docker.com/r/wanglab/hipfg.
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Affiliation(s)
- Jeffrey Cifello
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Pavel P Kuksa
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Naveensri Saravanan
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Otto Valladares
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Yuk Yee Leung
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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Zhang R, Wu M, Ma M, Liu B, Zhang X, Wei N, Wang T, Lv Y, Xu C, Wang J, Zhang Y, Liu F. Genetic evidence for the causal linkage between telomere length and aortic aneurysm risk: A Mendelian randomisation study. Eur J Clin Invest 2023; 53:e14056. [PMID: 37392033 DOI: 10.1111/eci.14056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/02/2023] [Accepted: 06/25/2023] [Indexed: 07/02/2023]
Abstract
BACKGROUND Evidence of a clear causal relationship between telomere length and aortic aneurysms is limited by the potential for confounding or reverse causation effects. In this study, we used a Mendelian randomisation (MR) approach to investigate this putative causal association. METHODS In total, 118 telomere length-associated single-nucleotide polymorphisms, identified in 472,174 individuals of European ancestry, were used as the instrumental variables. Summary statistics for genome-wide association studies of aortic aneurysms were obtained from the FinnGen consortium. For the primary MR analyses, the inverse-variance weighted random-effects method was used and was supplemented with multivariable MR, weighted median and MR-Egger approaches. The MR-Egger intercept test, Cochran's Q test and 'leave-one-out' sensitivity analysis were performed to evaluate the horizontal pleiotropy, heterogeneity and stability of the genetic variants. Forward and reverse MR analyses were performed. RESULTS All forward univariable MR analyses showed that longer telomere lengths decreased aortic aneurysm risks (total aortic aneurysms: OR = 0.80, 95% CI 0.67-0.96, p = .015; thoracic aortic aneurysms: OR = 0.82, 95% CI 0.68-0.98, p = .026; abdominal aortic aneurysms: OR = 0.525, 95% CI 0.398-0.69, p < .001), whereas all reverse MR analyses suggested the absence of aortic aneurysm liability on telomere length. The sensitivity analysis results were robust, and no evidence of horizontal pleiotropy was observed. CONCLUSIONS Our results support a possible causal association between telomere length and aortic aneurysms, providing new insights into the involvement of telomere biology in this condition and offering a potential avenue for targeted therapeutic interventions.
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Affiliation(s)
- Ronghuai Zhang
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, P. R. China
| | - Min Wu
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, P. R. China
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Shaanxi Provincial People's Hospital, Xi'an, P. R. China
| | - Meijuan Ma
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, P. R. China
| | - Bo Liu
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, P. R. China
| | - Xuejun Zhang
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, P. R. China
| | - Na Wei
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, P. R. China
| | - Ting Wang
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, P. R. China
| | - Ying Lv
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, P. R. China
| | - Cuixiang Xu
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Shaanxi Provincial People's Hospital, Xi'an, P. R. China
| | - Junkui Wang
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, P. R. China
| | - Yulian Zhang
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Shaanxi Provincial People's Hospital, Xi'an, P. R. China
- Department of Nursing, Shaanxi Provincial People's Hospital, Xi'an, P. R. China
| | - Fuqiang Liu
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, P. R. China
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Shaanxi Provincial People's Hospital, Xi'an, P. R. China
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Luo F, Zhou P, Ran X, Gu M, Zhou S. No evident causal association between Helicobacter pylori infection and colorectal cancer: a bidirectional mendelian randomization study. Sci Rep 2023; 13:18544. [PMID: 37899462 PMCID: PMC10613620 DOI: 10.1038/s41598-023-45545-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 10/20/2023] [Indexed: 10/31/2023] Open
Abstract
Observational studies have reported a correlation between Helicobacter pylori infection and colorectal cancer (CRC); however, the underlying cause has remained unclear. This research was aimed at determining whether there is a correlation between H. pylori infection and CRC by measuring the prevalence of H. pylori CagA antibodies and VacA antibodies. Using data from many genome-wide association studies (GWAS), we conducted a Mendelian randomization (MR) study with two sample GWAS. Then, we used bidirectional MR to evaluate the association between H. pylori infection and CRC for identifying causation. The most common method of analysis was the inverse variance-weighted technique. In addition, we performed supplementary analyses using the weighted median technique and MR-Egger regression. Horizontal pleiotropic outliers were identified and corrected using the MR Pleiotropy RESidual Sum and Outlier (MR-PRESSO) method. Genetically predicted anti-H. pylori IgG seropositivity was not causally associated with CRC [odds ratio (OR): 1.12; 95% confidence interval (CI): 0.98-1.27, P = 0.08] and neither were H. pylori VacA antibody levels (OR = 0.96, 95% CI: 0.90-1.02, P = 0.25) or H. pylori CagA antibody levels (OR = 1.00, 95% CI: 0.93-1.07, P = 0.92). Furthermore, reverse MR analysis did not reveal evidence for a causal effect of CRC on H. pylori infection. The weighted median, the MR-Egger method, and MR-PRESSO yielded identical results. Using genetic data, MR analysis showed there was no evidence for a causal association between seroprevalence of H. pylori infection and CRC. The relationship between H. pylori infection and CRC requires further research.
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Affiliation(s)
- Fang Luo
- Department of Gastroenterology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, 400021, China
| | - Peipei Zhou
- Department of Gastroenterology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, 400021, China
| | - Xiong Ran
- Department of Radiology, Chongqing General Hospital, No.118, Xingguang Avenue, Liangjiang New District, Chongqing, 400014, China
| | - Ming Gu
- Department of Radiology, Chongqing General Hospital, No.118, Xingguang Avenue, Liangjiang New District, Chongqing, 400014, China.
| | - Shaoquan Zhou
- Department of Radiology, Chongqing General Hospital, No.118, Xingguang Avenue, Liangjiang New District, Chongqing, 400014, China.
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Zhou X, Lian P, Liu H, Wang Y, Zhou M, Feng Z. Causal Associations between Gut Microbiota and Different Types of Dyslipidemia: A Two-Sample Mendelian Randomization Study. Nutrients 2023; 15:4445. [PMID: 37892520 PMCID: PMC10609956 DOI: 10.3390/nu15204445] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
The determination of a causal association between gut microbiota and a range of dyslipidemia remains uncertain. To clarify these associations, we employed a two-sample Mendelian randomization (MR) analysis utilizing the inverse-variance weighted (IVW) method. This comprehensive analysis investigated the genetic variants that exhibited a significant association (p < 5 × 10-8) with 129 distinct gut microbiota genera and their potential link to different types of dyslipidemia. The results indicated a potential causal association between 22 gut microbiota genera and dyslipidemia in humans. Furthermore, these findings suggested that the impact of gut microbiota on dyslipidemia regulation is dependent on the specific phylum, family, and genus. Bacillota phylum demonstrated the greatest diversity, with 15 distinct genera distributed among eight families. Notably, gut microbiota-derived from the Lachnospiraceae and Lactobacillaceae families exhibit statistically significant associations with lipid levels that contribute to overall health (p < 0.05). The sensitivity analysis indicated that our findings possess robustness (p > 0.05). The findings of our investigation provide compelling evidence that substantiates a causal association between the gut microbiota and dyslipidemia in the human body. It is noteworthy to highlight the significant influence of the Bacillota phylum as a crucial regulator of lipid levels, and the families Lachnospiraceae and Lactobacillaceae should be recognized as probiotics that significantly contribute to this metabolic process.
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Affiliation(s)
| | | | | | | | - Meijuan Zhou
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, NMPA Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou 510515, China; (X.Z.); (P.L.); (H.L.); (Y.W.)
| | - Zhijun Feng
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, NMPA Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou 510515, China; (X.Z.); (P.L.); (H.L.); (Y.W.)
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Qi B, Yang ZJ, Huang N, Zheng WB, Gui C. Searching for Intrinsic Causality between Colonic Dysbiosis and Non-Ischemic Cardiomyopathy: A Mendelian Randomization-Based Analysis. J Cardiovasc Dev Dis 2023; 10:420. [PMID: 37887867 PMCID: PMC10607801 DOI: 10.3390/jcdd10100420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/09/2023] [Accepted: 08/17/2023] [Indexed: 10/28/2023] Open
Abstract
Objective: Little is known about gut microbiota (GM) and cardiomyopathy. Their causal relationship was explored using two-sample Mendelian randomization (TSMR) performed by R software. Methods: The single nucleotide polymorphisms (SNPs) were further screened based on the genome-wide association studies (GWAS) of gut microbiota and cardiomyopathy obtained from an open database. TSMR was performed using an MR-Egger regression, simple estimator based on mode, weighted median method, inverse variance weighted (IVW), weighted estimator and CML-MA-BIC to explore the causal association. And the sensitivity analysis was carried out using an MR-Egger regression and the leave-one-out sensitivity test. Results: As for 211 GM taxa, IVW results confirmed that the class Actinobacteria (OR = 0.81, p = 0.021) and genus Coprobacter (OR = 0.85, p = 0.033) were protective factors for cardiomyopathy. The phylum Firmicutes (OR = 0.87, p < 0.01), family Acidaminococcaceae (OR = 0.89, p < 0.01), genus Desulfovibrio (OR = 0.92, p = 0.030) and genus Prevotella9 (OR = 0.93, p = 0.029) were protective factors for ischemic cardiomyopathy. The family Rhodospirillaceae (OR = 1.06, p = 0.036) and genus Turicibacter (OR = 1.09, p = 0.019) were risk factors for ischemic cardiomyopathy. The genus Olsenella (OR = 0.91, p = 0.032) was a protective factor for non-ischemic cardiomyopathy. The order Rhodospirillales (OR = 1.14, p = 0.024), family Rikenellaceae (OR = 1.21, p = 0.012) and genus Gordonibacter (OR = 1.12, p = 0.019) were risk factors for non-ischemic cardiomyopathy. The robustness of MR results was reflected in the heterogeneity (p > 0.05) and pleiotropy (p > 0.05) analyses. Conclusions: A potential causal relationship of cardiomyopathy with some GM taxa has been confirmed in the current study.
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Affiliation(s)
- Bin Qi
- Department of Cardiology, The First Affliated Hospital of Guangxi Medical University, Nanning 530021, China; (B.Q.); (Z.-J.Y.); (N.H.); (W.-B.Z.)
- Guangxi Key Laboratory Base of Precision Medicine in Cardiocerebrovascular Diseases Control and Prevention, Nanning 530021, China
- Guangxi Clinical Research Center for Cardiocerebrovascular Diseases, Nanning 530021, China
| | - Zhi-Jie Yang
- Department of Cardiology, The First Affliated Hospital of Guangxi Medical University, Nanning 530021, China; (B.Q.); (Z.-J.Y.); (N.H.); (W.-B.Z.)
- Guangxi Key Laboratory Base of Precision Medicine in Cardiocerebrovascular Diseases Control and Prevention, Nanning 530021, China
- Guangxi Clinical Research Center for Cardiocerebrovascular Diseases, Nanning 530021, China
| | - Nan Huang
- Department of Cardiology, The First Affliated Hospital of Guangxi Medical University, Nanning 530021, China; (B.Q.); (Z.-J.Y.); (N.H.); (W.-B.Z.)
- Guangxi Key Laboratory Base of Precision Medicine in Cardiocerebrovascular Diseases Control and Prevention, Nanning 530021, China
- Guangxi Clinical Research Center for Cardiocerebrovascular Diseases, Nanning 530021, China
| | - Wen-Bo Zheng
- Department of Cardiology, The First Affliated Hospital of Guangxi Medical University, Nanning 530021, China; (B.Q.); (Z.-J.Y.); (N.H.); (W.-B.Z.)
- Guangxi Key Laboratory Base of Precision Medicine in Cardiocerebrovascular Diseases Control and Prevention, Nanning 530021, China
- Guangxi Clinical Research Center for Cardiocerebrovascular Diseases, Nanning 530021, China
| | - Chun Gui
- Department of Cardiology, The First Affliated Hospital of Guangxi Medical University, Nanning 530021, China; (B.Q.); (Z.-J.Y.); (N.H.); (W.-B.Z.)
- Guangxi Key Laboratory Base of Precision Medicine in Cardiocerebrovascular Diseases Control and Prevention, Nanning 530021, China
- Guangxi Clinical Research Center for Cardiocerebrovascular Diseases, Nanning 530021, China
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Xu H, Sun Y, Francis M, Cheng CF, Modulla NT, Brenna JT, Chiang CWK, Ye K. Shared genetic basis informs the roles of polyunsaturated fatty acids in brain disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.03.23296500. [PMID: 37873425 PMCID: PMC10593041 DOI: 10.1101/2023.10.03.23296500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The neural tissue is rich in polyunsaturated fatty acids (PUFAs), components that are indispensable for the proper functioning of neurons, such as neurotransmission. PUFA nutritional deficiency and imbalance have been linked to a variety of chronic brain disorders, including major depressive disorder (MDD), anxiety, and anorexia. However, the effects of PUFAs on brain disorders remain inconclusive, and the extent of their shared genetic determinants is largely unknown. Here, we used genome-wide association summary statistics to systematically examine the shared genetic basis between six phenotypes of circulating PUFAs (N = 114,999) and 20 brain disorders (N = 9,725-762,917), infer their potential causal relationships, identify colocalized regions, and pinpoint shared genetic variants. Genetic correlation and polygenic overlap analyses revealed a widespread shared genetic basis for 77 trait pairs between six PUFA phenotypes and 16 brain disorders. Two-sample Mendelian randomization analysis indicated potential causal relationships for 16 pairs of PUFAs and brain disorders, including alcohol consumption, bipolar disorder (BIP), and MDD. Colocalization analysis identified 40 shared loci (13 unique) among six PUFAs and ten brain disorders. Twenty-two unique variants were statistically inferred as candidate shared causal variants, including rs1260326 (GCKR), rs174564 (FADS2) and rs4818766 (ADARB1). These findings reveal a widespread shared genetic basis between PUFAs and brain disorders, pinpoint specific shared variants, and provide support for the potential effects of PUFAs on certain brain disorders, especially MDD, BIP, and alcohol consumption.
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Affiliation(s)
- Huifang Xu
- Department of Genetics, University of Georgia, Athens, Georgia
| | - Yitang Sun
- Department of Genetics, University of Georgia, Athens, Georgia
| | - Michael Francis
- Institute of Bioinformatics, University of Georgia, Athens, Georgia
| | - Claire F. Cheng
- Department of Genetics, University of Georgia, Athens, Georgia
| | | | - J. Thomas Brenna
- Dell Pediatric Research Institute and Department of Pediatrics, The University of Texas at Austin, Texas
- Dell Pediatric Research Institute and Department of Chemistry, The University of Texas at Austin, Texas
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Texas
| | - Charleston W. K. Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Kaixiong Ye
- Department of Genetics, University of Georgia, Athens, Georgia
- Institute of Bioinformatics, University of Georgia, Athens, Georgia
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48
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Haycock PC, Borges MC, Burrows K, Lemaitre RN, Harrison S, Burgess S, Chang X, Westra J, Khankari NK, Tsilidis KK, Gaunt T, Hemani G, Zheng J, Truong T, O’Mara TA, Spurdle AB, Law MH, Slager SL, Birmann BM, Saberi Hosnijeh F, Mariosa D, Amos CI, Hung RJ, Zheng W, Gunter MJ, Davey Smith G, Relton C, Martin RM. Design and quality control of large-scale two-sample Mendelian randomization studies. Int J Epidemiol 2023; 52:1498-1521. [PMID: 38587501 PMCID: PMC10555669 DOI: 10.1093/ije/dyad018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 02/10/2023] [Indexed: 03/27/2024] Open
Abstract
Background Mendelian randomization (MR) studies are susceptible to metadata errors (e.g. incorrect specification of the effect allele column) and other analytical issues that can introduce substantial bias into analyses. We developed a quality control (QC) pipeline for the Fatty Acids in Cancer Mendelian Randomization Collaboration (FAMRC) that can be used to identify and correct for such errors. Methods We collated summary association statistics from fatty acid and cancer genome-wide association studies (GWAS) and subjected the collated data to a comprehensive QC pipeline. We identified metadata errors through comparison of study-specific statistics to external reference data sets (the National Human Genome Research Institute-European Bioinformatics Institute GWAS catalogue and 1000 genome super populations) and other analytical issues through comparison of reported to expected genetic effect sizes. Comparisons were based on three sets of genetic variants: (i) GWAS hits for fatty acids, (ii) GWAS hits for cancer and (iii) a 1000 genomes reference set. Results We collated summary data from 6 fatty acid and 54 cancer GWAS. Metadata errors and analytical issues with the potential to introduce substantial bias were identified in seven studies (11.6%). After resolving metadata errors and analytical issues, we created a data set of 219 842 genetic associations with 90 cancer types, generated in analyses of 566 665 cancer cases and 1 622 374 controls. Conclusions In this large MR collaboration, 11.6% of included studies were affected by a substantial metadata error or analytical issue. By increasing the integrity of collated summary data prior to their analysis, our protocol can be used to increase the reliability of downstream MR analyses. Our pipeline is available to other researchers via the CheckSumStats package (https://github.com/MRCIEU/CheckSumStats).
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Affiliation(s)
- Philip C Haycock
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Maria Carolina Borges
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | | | - Sean Harrison
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Xuling Chang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat—National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Jason Westra
- Department of Mathematics, Statistics, and Computer Science, Dordt College, Sioux Center, IA, USA
| | - Nikhil K Khankari
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kostas K Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Tom Gaunt
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jie Zheng
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Therese Truong
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, Team “Exposome, Heredity, Cancer and Health”, CESP, Villejuif, France
| | - Tracy A O’Mara
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Medicine, Faculty of Health Sciences, University of Queensland, Brisbane, Australia
| | - Amanda B Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Medicine, Faculty of Health Sciences, University of Queensland, Brisbane, Australia
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Daniela Mariosa
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Christopher I Amos
- Dan L Duncan Comprehensive Cancer Center Baylor College of Medicine, Houston, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health and University of Toronto, Toronto, Canada
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Marc J Gunter
- Section of Nutrition and Metabolism, International Agency for Research on Cancer (IARC), Lyon, France
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Richard M Martin
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Biomedical Research Centre at University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
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Liu M, Feng J. Association between adiposity and facial aging: results from a Mendelian randomization study. Eur J Med Res 2023; 28:350. [PMID: 37715292 PMCID: PMC10503104 DOI: 10.1186/s40001-023-01236-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/16/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Skin, as a sociologically meaningful interface, has psychological implications different from other organs, particularly in the context of the global population aging. Growing evidence suggests that facial aging is associated with an increased risk of adiposity. Existing research, however, were observational, and while they may find some correlations, it is difficult to simply disentangle non-causal or reverse-causal links because these associations may be confounded or fail to accurately reflect true causative linkages. OBJECTIVES We conducted a 2-sample Mendelian randomization (MR) study to examine the potential effect of facial aging on the risk of broad obesity and its three major adiposity indicators, including body mass index (BMI), body fat percentage (BF%) and waist circumference (WC). METHODS Genetic instruments from IEU OpenGWAS project, one of the largest available genome-wide association studies (GWAS) for facial aging (423,999 samples) were used to investigate the relation to broad obesity (32,858 cases, 65,839 controls). Using the inverse-variance weighted (IVW) technique, single nucleotide polymorphisms (SNPs) associated with adiposity indicators (BMI (461,460 samples), BF% (454,633 samples), and WC (462,166 samples)) were investigated in relationship to facial aging. Further sensitivity analyses were performed, including Mendelian randomization-Egger (MR-Egger), weighted median estimates, and leave-one-out analysis, to evaluate the consistency of the results and related potential issues in MR studies. RESULTS We identified strong and significant correlations between adiposity and facial aging in the 17 broad obesity-associated SNPs (IVW estimate of odds ratio OR = 1.020, 95% CI 1.010-1.029, P = 7.303e - 05), 458 BMI-associated SNPs (IVW estimate of odds ratio OR = 1.047, 95% CI 1.0357-1.058, P = 1.154e - 16),for the 395 BF%-associated SNPs (OR = 1.056, 95%CI 1.040-1.072,P = 7.617e - 12), or for the 374 WC-associated SNPs (OR = 1.072, 95% CI 1057-1.087,P = 1.229e - 23). A range of complementary methodologies have been employed to evaluate horizontal pleiotropy and related potential caveats occurring in MR research. CONCLUSIONS Using Mendelian randomization as an alternative approach to investigate causality, we found a causal relationship between adiposity and facial aging, which was statistically strong and significant.
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Affiliation(s)
- Meiqi Liu
- Department of Plastic and Cosmetic Surgery, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Jingwei Feng
- Department of Plastic and Cosmetic Surgery, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, 510515, Guangdong, People's Republic of China.
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Faber BG, Frysz M, Boer CG, Evans DS, Ebsim R, Flynn KA, Lundberg M, Southam L, Hartley A, Saunders FR, Lindner C, Gregory JS, Aspden RM, Lane NE, Harvey NC, Evans DM, Zeggini E, Davey Smith G, Cootes T, Van Meurs J, Kemp JP, Tobias JH. The identification of distinct protective and susceptibility mechanisms for hip osteoarthritis: findings from a genome-wide association study meta-analysis of minimum joint space width and Mendelian randomisation cluster analyses. EBioMedicine 2023; 95:104759. [PMID: 37619450 PMCID: PMC10470292 DOI: 10.1016/j.ebiom.2023.104759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Hip minimum joint space width (mJSW) provides a proxy for cartilage thickness. This study aimed to conduct a genome-wide association study (GWAS) of mJSW to (i) identify new genetic determinants of mJSW and (ii) identify which mJSW loci convey hip osteoarthritis (HOA) risk and would therefore be of therapeutic interest. METHODS GWAS meta-analysis of hip mJSW derived from plain X-rays and DXA was performed, stratified by sex and adjusted for age and ancestry principal components. Mendelian randomisation (MR) and cluster analyses were used to examine causal effect of mJSW on HOA. FINDINGS 50,745 individuals were included in the meta-analysis. 42 SNPs, which mapped to 39 loci, were identified. Mendelian randomisation (MR) revealed little evidence of a causal effect of mJSW on HOA (ORIVW 0.98 [95% CI 0.82-1.18]). However, MR-Clust analysis suggested the null MR estimates reflected the net effect of two distinct causal mechanisms cancelling each other out, one of which was protective, whereas the other increased HOA susceptibility. For the latter mechanism, all loci were positively associated with height, suggesting mechanisms leading to greater height and mJSW increase the risk of HOA in later life. INTERPRETATIONS One group of mJSW loci reduce HOA risk via increased mJSW, suggesting possible utility as targets for chondroprotective therapies. The second group of mJSW loci increased HOA risk, despite increasing mJSW, but were also positively related to height, suggesting they contribute to HOA risk via a growth-related mechanism. FUNDING Primarily funded by the Medical Research Council and Wellcome Trust.
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Affiliation(s)
- Benjamin G Faber
- Musculoskeletal Research Unit, University of Bristol, UK; Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK.
| | - Monika Frysz
- Musculoskeletal Research Unit, University of Bristol, UK; Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK
| | - Cindy G Boer
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, San Francisco, USA
| | - Raja Ebsim
- Division of Informatics, Imaging and Data Sciences, The University of Manchester, UK
| | - Kaitlyn A Flynn
- Mater Research Institute, The University of Queensland, Woolloongabba, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Mischa Lundberg
- UQ Frazer Institute, The University of Queensland, Woolloongabba, Australia
| | - Lorraine Southam
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
| | - April Hartley
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK
| | - Fiona R Saunders
- Centre for Arthritis and Musculoskeletal Health, University of Aberdeen, UK
| | - Claudia Lindner
- Division of Informatics, Imaging and Data Sciences, The University of Manchester, UK
| | - Jennifer S Gregory
- Centre for Arthritis and Musculoskeletal Health, University of Aberdeen, UK
| | - Richard M Aspden
- Centre for Arthritis and Musculoskeletal Health, University of Aberdeen, UK
| | - Nancy E Lane
- Center for Musculoskeletal Health, University of California Davis, Sacramento, USA
| | - Nicholas C Harvey
- Medical Research Council Lifecourse Epidemiology Centre, University of Southampton, UK; NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, UK
| | - David M Evans
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia; UQ Frazer Institute, The University of Queensland, Woolloongabba, Australia
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany; Technical University of Munich and Klinikum Rechts der Isar, TUM School of Medicine, Germany
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK
| | - Timothy Cootes
- Division of Informatics, Imaging and Data Sciences, The University of Manchester, UK
| | - Joyce Van Meurs
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - John P Kemp
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK; Mater Research Institute, The University of Queensland, Woolloongabba, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Jonathan H Tobias
- Musculoskeletal Research Unit, University of Bristol, UK; Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK
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