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Liu Y, Rao J, Hu W, Yu Y, Wang P, Chen X, Zhang Y, Wang Z. Genetic Causality between Type 1 Diabetes and Arrhythmia Identified by a Two-sample Mendelian Randomization Study. Diabetes Res Clin Pract 2024; 213:111725. [PMID: 38823455 DOI: 10.1016/j.diabres.2024.111725] [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: 03/04/2024] [Revised: 05/10/2024] [Accepted: 05/28/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Clinical studies have shown that cardiovascular diseases in patients with type 1 diabetes (T1D) are often atypical or asymptomatic. The link between T1D and arrhythmia remains unclear. To infer causality between T1D and arrhythmia at the genetic level, we conducted a Mendelian randomization study through the genetic tools of T1D. METHODS In this study, we used genetic variables and summary statistics from genome-wide association studies of T1D and arrhythmia. Single nucleotide polymorphisms were selected based on the assumptions of instrumental variables. The inverse variance-weighted method was used as the primary analysis to summarize the causal effects between exposure and outcome. The weighted median and weighted mode methods were used as secondary methods. We tested for horizontal pleiotropy using the MR-Egger method and detected heterogeneity using the Q-test. A leave-one-out sensitivity analysis was performed. Scatter plots, forest plots, and funnel plots were used to visualize the results of the MR analysis. RESULTS In this study, we selected 28 T1D-related SNPs as instrumental variables. The IVW [odds ratio (OR) = 0.98, 95 % confidence interval (CI) = 0.97-1.00, P = 0.008], weighted median (OR = 0.98, 95 % CI = 0.96 - 0.99, P = 0.009), and weighted mode (OR = 0.98, 95 % CI = 0.96-0.99, P = 0.018) analysis methods suggested a causal effect of T1D on arrhythmia. The MR-Egger method indicated no horizontal pleiotropy (P = 0.649), and the Q-test showed no heterogeneity (IVW, P = 0.653). CONCLUSIONS Our MR analysis revealed a causal association between T1D and the development of arrhythmia, indicating that patients with T1D had a higher risk of arrhythmia.
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Affiliation(s)
- Yudi Liu
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jin Rao
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Wei Hu
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yue Yu
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Pei Wang
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Xiangyu Chen
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yufeng Zhang
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China.
| | - Zhinong Wang
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China.
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Bagheri M, Bombin A, Shi M, Murthy VL, Shah R, Mosley JD, Ferguson JF. Genotype-based "virtual" metabolomics in a clinical biobank identifies novel metabolite-disease associations. Front Genet 2024; 15:1392622. [PMID: 38812968 PMCID: PMC11133605 DOI: 10.3389/fgene.2024.1392622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/03/2024] [Indexed: 05/31/2024] Open
Abstract
Introduction: Circulating metabolites act as biomarkers of dysregulated metabolism and may inform disease pathophysiology. A portion of the inter-individual variability in circulating metabolites is influenced by common genetic variation. We evaluated whether a genetics-based "virtual" metabolomics approach can identify novel metabolite-disease associations. Methods: We examined the association between polygenic scores for 724 metabolites with 1,247 clinical phenotypes in the BioVU DNA biobank, comprising 57,735 European ancestry and 15,754 African ancestry participants. We applied Mendelian randomization (MR) to probe significant relationships and validated significant MR associations using independent GWAS of candidate phenotypes. Results and Discussion: We found significant associations between 336 metabolites and 168 phenotypes in European ancestry and 107 metabolites and 56 phenotypes in African ancestry. Of these metabolite-disease pairs, MR analyses confirmed associations between 73 metabolites and 53 phenotypes in European ancestry. Of 22 metabolitephenotype pairs evaluated for replication in independent GWAS, 16 were significant (false discovery rate p < 0.05). These included associations between bilirubin and X-21796 with cholelithiasis, phosphatidylcholine (16:0/22:5n3,18:1/20:4) and arachidonate with inflammatory bowel disease and Crohn's disease, and campesterol with coronary artery disease and myocardial infarction. These associations may represent biomarkers or potentially targetable mediators of disease risk.
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Affiliation(s)
- Minoo Bagheri
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Andrei Bombin
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Mingjian Shi
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Venkatesh L Murthy
- Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Ravi Shah
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jonathan D Mosley
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jane F Ferguson
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
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Elhage KG, Kranyak A, Jin JQ, Haran K, Spencer RK, Smith PL, Davis MS, Hakimi M, Bhutani T, Liao W. Mendelian Randomization Studies in Atopic Dermatitis: A Systematic Review. J Invest Dermatol 2024; 144:1022-1037. [PMID: 37977498 DOI: 10.1016/j.jid.2023.10.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 10/17/2023] [Accepted: 10/22/2023] [Indexed: 11/19/2023]
Abstract
Prior studies have found associations between atopic dermatitis (AD) and comorbidities, including depression, obesity, asthma, and allergic rhinitis. Although observational studies often cannot establish robust causality between potential risk factors and AD, Mendelian randomization minimizes confounding when exploring causality by relying on random allelic assortment at birth. In this study, we systematically reviewed 30 Mendelian randomization studies in AD. Body mass index, gut microbial flora, the IL-18 signaling pathway, and gastroesophageal reflux disease were among the causal factors for AD, whereas AD was causal for several medical conditions, including heart failure, rheumatoid arthritis, and conjunctivitis. These insights may improve preventive counseling in AD.
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Affiliation(s)
- Kareem G Elhage
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA
| | - Allison Kranyak
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA
| | - Joy Q Jin
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA; School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Kathryn Haran
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA
| | - Riley K Spencer
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA
| | - Payton L Smith
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA
| | - Mitchell S Davis
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA
| | - Marwa Hakimi
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA
| | - Tina Bhutani
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA
| | - Wilson Liao
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA.
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Pang S, Han T, Huang X, Zhao Y, Qian J, Zhong J, Xie P, Liao L. Exploring the potential causal relationship between gut microbiota and heart failure: A two-sample mendelian randomization study combined with the geo database. Curr Probl Cardiol 2024; 49:102235. [PMID: 38040216 DOI: 10.1016/j.cpcardiol.2023.102235] [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: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023]
Abstract
OBJECTIVE In recent years, researchers have observed a potential association between alterations in gut microbiota and the onset and progression of heart failure. Nevertheless, the causal relationship between gut microbiota and heart failure remains a topic of controversy. This study employed a two-sample Mendelian randomization approach to investigate the causal link between gut microbiota and heart failure. METHOD We extracted single nucleotide polymorphism (SNPs) data for heart failure (ebi-a-gcst009541) and gut microbiota from the publicly available genome-wide association analysis (GWAS) summary database. The primary analytical method employed was inverse variance weighting (IVW), complemented by validation using MR-PRESSO, weighted median, and MR pleiotropic residual methods. Additionally, gene pleiotropy (MR-Egger), heterogeneity testing, and a "leave-one-out" analysis were conducted to assess the robustness of the findings. Utilizing the limma package, differentially expressed genes (DEGs) from the Gut Microbiota datasets (GSE3586, GSE5406) and Heart Failure datasets (GSE47908, GSE87466) sourced from the Gene Expression Omnibus (GEO) were curated. Subsequent enrichment analysis was conducted using the Cluster Profiler and GO plot packages to validate the MR analysis outcomes. RESULTS The results of our analysis revealed seven distinct bacterial groups in the intestines that exhibited associations.with.the.risk.of.heart.failure. These.included.class.negativicutes (P = 0.02,OR:1.11,95%CI:1.02,1.21), gene.eubacterium.eligensgroup (P = 0.02,OR:1.10,95%CI:1.01,1.20),gene.eubacteriummoxidoreducensgroup (P = 0.01,OR:1.10,95%CI:1.02,1.19),Order.selenium (P = 0.02,OR:1.11,95%CI:1.02,1.21), gene.familyxiiiucg001 (P = 0.03,OR=1.09.95%CI:1.01,1.19), gene.familyxiiiad3011group (P = 0.03,OR:0.92,95%CI:0.86,0.99), and.gene.anaerostipes (P = 0.00,OR:0.87,95%CI:0.80,0.94). Nevertheless, upon conducting reverse causal MR analysis, no evidence of a causal relationship between heart failure and the aforementioned seven gut microbiota groups was found.Bioinformatics analysis reveals shared DEGs between gut microbiota and heart failure. CONCLUSION This Mendelian randomization study represents the first endeavor to explore the causal relationship between specific gut microbiota and heart failure. The findings suggest a significant correlation between these seven specific gut microbiota groups and the risk of heart failure, potentially offering valuable insights for heart failure prevention and control efforts.
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Affiliation(s)
- Shuwen Pang
- Shenzhen Hospital of Shanghai University of Traditional Chinese Medicine, No. 16 Xiantong Road, Luohu District, Shenzhen, 518001,Guangdong , China; General Hospital of the Southern Theater Command of the People's Liberation Army of China, 111 Liuhua Road, Yuexiu District, Guangzhou, 5100102, Guangdong, China; Graduate School of Guangzhou University of Traditional Chinese Medicine, No.12 Airport Road, Baiyun District, Guangzhou, 510100, Guangdong, China.
| | - Tao Han
- Wangjing Hospital, China Academy of Chinese Medical Sciences, 6 Wangjing Zhonghuan South Road, Chaoyang District, 100102, Beijing, China.
| | - Xiwei Huang
- General Hospital of the Southern Theater Command of the People's Liberation Army of China, 111 Liuhua Road, Yuexiu District, Guangzhou, 5100102, Guangdong, China; Graduate School of Guangzhou University of Traditional Chinese Medicine, No.12 Airport Road, Baiyun District, Guangzhou, 510100, Guangdong, China.
| | - Yueli Zhao
- General Hospital of the Southern Theater Command of the People's Liberation Army of China, 111 Liuhua Road, Yuexiu District, Guangzhou, 5100102, Guangdong, China.
| | - Jing Qian
- The Second Affiliated Hospital of Naval Medical University (Shanghai Long March Hospital), 415 Fengyang Road, Huangpu District, 200003, Shanghai, China.
| | - Jiahui Zhong
- Guangdong Provincial People's Hospital, No. 106 Zhongshan Second Road, Yuexiu District, Guangzhou, 510080,Guangdong, China.
| | - Pingjin Xie
- Shenzhen Hospital of Shanghai University of Traditional Chinese Medicine, No. 16 Xiantong Road, Luohu District, Shenzhen, 518001,Guangdong , China.
| | - Lu Liao
- Shenzhen Hospital of Shanghai University of Traditional Chinese Medicine, No. 16 Xiantong Road, Luohu District, Shenzhen, 518001,Guangdong , China.
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Yang T, Bi S, Zhang X, Yin M, Feng S, Li H. The Impact of Different Intensities of Physical Activity on Serum Urate and Gout: A Mendelian Randomization Study. Metabolites 2024; 14:66. [PMID: 38276301 PMCID: PMC10819057 DOI: 10.3390/metabo14010066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/07/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Physical activity is a potential protective factor against gout, but the role of exercise intensity in this context remains unclear. To overcome the limitations of observational studies in causal inference, this study employed a two-sample Mendelian randomization approach to explore the impact of different genetically proxied/predicted intensities of physical activity on serum urate concentration and the incidence of gout. Our data related to physical activity, serum urate, and gout were obtained from the UK Biobank, the Global Urate Genetics Consortium (GUGC), and the FinnGen dataset, respectively. Walking was included as representative of typical low-intensity physical activity in the analysis, and the other two types were moderate and vigorous physical activities. The estimation methods we used included the inverse-variance-weighted (IVW) method, MR-Egger regression, weighted-median method, simple-mode method, and weighted-mode method. Sensitivity analyses involved Rucker's framework, Cochran's Q test, funnel plots, MR-PRESSO outlier correction, and leave-one-out analysis. We found suggestive evidence from the inverse-variance-weighted method that moderate physical activity was a potential factor in reducing the incidence of gout (OR = 0.628, p = 0.034), and this association became more substantial in our subsequent sensitivity analysis (OR = 0.555, p = 0.006). However, we observed no distinctive effects of physical activity on serum urate concentration. In conclusion, our study supports some findings from observational studies and emphasizes the preventive role of moderate physical activity against gout. Given the limitations of the existing datasets, we call for future reexamination and expansion of our findings using new GWAS data.
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Affiliation(s)
- Tangxun Yang
- School of Physical Education, Xihua University, Chengdu 610039, China
| | - Shilin Bi
- National Institute of Education, Nanyang Technological University, Singapore 637616, Singapore
| | - Xing Zhang
- Department of Physical Education and Sport, Faculty of Sport Sciences, University of Granada, 18071 Granada, Spain
| | - Mingyue Yin
- School of Athletic Performance, Shanghai University of Sport, Shanghai 200438, China
| | - Siyuan Feng
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hansen Li
- Institute of Sports Science, College of Physical Education, Southwest University, Chongqing 400715, China
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Zhang Y, Li X, Song Z, Yang Y. Association between allergic rhinitis and hypertension risk: A bidirectional 2-sample mendelian randomization study. Medicine (Baltimore) 2023; 102:e36700. [PMID: 38115257 PMCID: PMC10727617 DOI: 10.1097/md.0000000000036700] [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: 09/22/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023] Open
Abstract
Previous studies have suggested a potential association between allergic rhinitis (AR) and hypertension, but the genetic basis remains unclear. In this study, we aimed to explore the genetic correlation and potential causal association between AR and hypertension. Using a large-scale genome-wide association study (GWAS) public database, we conducted meticulous screening to acquire the most up-to-date GWAS data on single nucleotide polymorphisms (SNPs) relevant to AR and hypertension, with a significance threshold of P < 5 × 10-8. Then, we investigated the causal association between AR and hypertension through mendelian randomization (MR) analysis. We also performed reverse MR analysis to assess the possibility of reverse causality. Sensitivity analyses encompassed various factors, including horizontal pleiotropy, heterogeneity testing, and stepwise exclusion sensitivity checks. To investigate the causal relationship between AR and hypertension, we utilize the odds ratio (OR) and 95% confidence interval (CI) as our evaluative metric. This study leveraged a database comprising 112583 samples for AR and 461880 samples for hypertension. After meticulous screening, we identified 32 SNPs as instrumental variables. By employing the aforementioned 2-sample Mendelian randomization approaches, the estimated causal effects showed striking concordance. A discernible causal association between AR and hypertension was found using the IVW method (OR = 0.91, 95% CI: 0.86-0.98, P = .008), with horizontal pleiotropy and heterogeneity tests supporting the validity of our MR study. MR-Egger regression findings provided reassurance against bias stemming from genetic pleiotropy (intercept = -0.0006802, P = .6947). Interestingly, "leave-one-out" analysis yielded no evidence of nonspecific SNP influences, further consolidating our findings. Moreover, our reverse MR analysis yielded no indication of reverse causality from hypertension to AR, effectively discounting any influence from the latter on the former. Our study found evidence of a causal association between AR and hypertension in individuals of European ancestry. It demonstrated that AR reduced the risk of hypertension, suggesting a protective effect on hypertension due to the negative correlation with AR.
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Affiliation(s)
- Yanhua Zhang
- Department of Cardiology, The Third People’s Hospital of Datong, Datong, Shanxi, China
| | - Xia Li
- The Third Clinical College, Shanxi University of Chinese Medicine, Taiyuan, Shanxi, China
- Clinical Research Center, The Third People’s Hospital of Datong, Datong, Shanxi, China
| | - Zhizhou Song
- Department of Cardiology, The Third People’s Hospital of Datong, Datong, Shanxi, China
| | - Youdong Yang
- Department of Cardiology, The Third People’s Hospital of Datong, Datong, Shanxi, China
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Zou X, Lu RL, Liao B, Liu SJ, Dai SX. Causal relationship between asthma and ulcerative colitis and the mediating role of interleukin-18: a bidirectional Mendelian study and mediation analysis. Front Immunol 2023; 14:1293511. [PMID: 38162651 PMCID: PMC10757619 DOI: 10.3389/fimmu.2023.1293511] [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: 09/13/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024] Open
Abstract
Objective Numerous observational investigations have documented a correlation between asthma and ulcerative colitis(UC). In this Mendelian Randomization (MR) study, we utilized extensive summary data from Genome-Wide Association Studies (GWAS) to further estimate the association between adult-onset asthma and the risk of UC, and to investigate the role of Interleukin-18 (IL-18) as a potential mediator. Materials and methods A two-step, two-sample MR study was conducted through mediation analysis. For this study, we employed a two-sample MR analysis using the inverse variance-weighted (IVW), weighted median, weighted mode, and MR-Egger regression techniques. We utilized publicly accessible summary statistics from a GWAS meta-analysis of adult-onset asthma in the UK Biobank (n=327,253; cases=26,582; controls=300,671) as the exposure factor. The outcomes were derived from GWAS data of individuals with European ancestry (n=26,405; cases=6,687; controls=19,718). GWAS data for IL-18 were obtained from individuals of European ancestry (n=9,785,222; cases=3,636; controls=9,781,586). Results The MR analysis indicates that adult-onset asthma is associated with an increased risk of UC, with an odds ratio (OR) of 1.019 (95% CI 1.001-1.045, P=0.006). However, there is no strong evidence to suggest that UC significantly impacts the risk of adult-onset asthma. IL-18 may act as a potential mediator in the causal relationship between adult-onset asthma and UC, with a mediation proportion of 3.9% (95% CI, 0.6%-6.9%). Conclusion In summary, our study established a causal relationship between asthma and UC, in which IL-18 contributes to a small extent. However, the primary factors underlying the influence of asthma on UC remain unclear. Future research should focus on identifying other potential mediators. In clinical practice, it is important to pay greater attention to intestinal lesions in patients with asthma.
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Affiliation(s)
- Xin Zou
- Department of Gastroenterology, Ganzhou Municipal Hospital(Guangdong Provincial People’s Hospital Ganzhou Hospital), Ganzhou, Jiangxi, China
| | - Rui-Ling Lu
- Department of Gastroenterology, Ganzhou Municipal Hospital(Guangdong Provincial People’s Hospital Ganzhou Hospital), Ganzhou, Jiangxi, China
- Department of Rheumatology and Immunology, The Second Clinical Medical College, Jinan University (Shenzhen People’s Hospital), Shenzhen, Guangdong, China
| | - Bin Liao
- Department of Gastroenterology, Ganzhou Municipal Hospital(Guangdong Provincial People’s Hospital Ganzhou Hospital), Ganzhou, Jiangxi, China
| | - Shi-Jie Liu
- Department of Gastroenterology, Geriatric Center, National Regional Medical Center, Guangdong Provincial People’s Hospital Ganzhou Hospital, Ganzhou, Jiangxi, China
| | - Shi-Xue Dai
- Department of Gastroenterology, Geriatric Center, National Regional Medical Center, Guangdong Provincial People’s Hospital Ganzhou Hospital, Ganzhou, Jiangxi, China
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Wu D, Liu B, Xian W, Yang Y, Li J, Hong S, Li Y, Xiao H. New insight into the causal relationship between Graves' disease liability and drug eruption: a Mendelian randomization study. Front Immunol 2023; 14:1267814. [PMID: 38077385 PMCID: PMC10703291 DOI: 10.3389/fimmu.2023.1267814] [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: 07/29/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Background Graves' disease (GD) and drug eruption are closely associated and frequently observed in the clinical setting. However, it remains unclear whether a causal relationship exists between these two conditions. The aim of the study is to investigate whether GD is causal to drug eruptions using two-sample Mendelian randomization. Methods We launched a two-sample MR to investigate whether GD is causal to drug eruption using Genome-wide association study (GWAS) summary data from Biobank Japan and FinnGen. Genetic variants were used as instrumental variables to avoid confounding bias. Statistical methods including inverse variance weighted (IVW), weighted median, MR-Egger, and MR-PRESSO were conducted to identify the robustness of the causal effect. Results Genetically predicted GD may increase the risk of drug eruption by 30.3% (OR=1.303, 95% CI 1.119-1.516, p<0.001) in the Asian population. In European populations, GD may increase the generalized drug eruption by 15.9% (OR=1.159, 95%CI 0.982-1.367, p=0.080). Conclusions We found GD is potentially causal to drug eruption. This finding expanded the view of the frequently observed co-existence of GD and adverse drug reactions involving the skin. The mechanism remains for further investigation.
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Affiliation(s)
- Dide Wu
- Department of Endocrinology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Boyuan Liu
- Department of Endocrinology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wei Xian
- Department of Endocrinology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuxin Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jinjian Li
- Department of Endocrinology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shubin Hong
- Department of Endocrinology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yanbing Li
- Department of Endocrinology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Haipeng Xiao
- Department of Endocrinology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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Liao Q, Li SZ, Tian FF, Huang K, Bi FF. No genetic causal association between dental caries and Alzheimer's disease: a bidirectional two-sample Mendelian randomization analysis. PeerJ 2023; 11:e15936. [PMID: 37637178 PMCID: PMC10460150 DOI: 10.7717/peerj.15936] [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: 01/30/2023] [Accepted: 07/31/2023] [Indexed: 08/29/2023] Open
Abstract
Background An increasing number of observational studies have suggested an association between dental caries and Alzheimer's disease (AD). The association between dental caries and Alzheimer's disease may be mediated by confounders or reverse causality. In this study, we conducted bidirectional two-sample Mendelian randomization (MR) to estimate the bidirectional causality between dental caries and AD. Materials and Methods Genome-wide association study (GWAS) summary statistics of dental caries were extracted from a published meta-analysis which included a total of 487,823 participants. GWAS datasets of AD and AD onset age were obtained from the FinnGen bank. A bidirectional two-sample analysis was performed to explore the causality between dental caries and AD. Results For the dental caries-AD causality estimation, there was no significant association between dental caries and AD, neither with the AD GWASs from the FinnGen database (OR: 1.041, p = 0.874) nor with those from the International Genomics of Alzheimer's Project (OR: 1.162, p = 0.409). In addition, the genetic susceptibility to dental caries was not related to the onset age of AD. No causality existed between dental caries and early-onset AD (OR: 0.515, p = 0.302) or late-onset AD (OR: 1.329, p = 0.347). For the AD-dental caries relationship, no causality was detected by the IVW method (OR: 1.000, p = 0.717). Findings from other MR methods were consistent. The pleiotropy test and sensitivity analysis confirmed the validity of these MR results. Conclusions In this bidirectional MR study, robust evidence to support a bidirectional causal effect between dental caries and AD from the GWAS results within large-scale European-descent populations was absent. Having dental caries would not alter the onset age of AD.
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Affiliation(s)
- Qiao Liao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Si-Zhuo Li
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fa-Fa Tian
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Kun Huang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fang-Fang Bi
- Department of Neurology, Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, Guangdong, China
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Li H, Zhang X, Cao Y, Zhang G. Potential protection of computer gaming against mental health issues: Evidence from a Mendelian randomization study. COMPUTERS IN HUMAN BEHAVIOR 2023. [DOI: 10.1016/j.chb.2023.107722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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Lorincz-Comi N, Yang Y, Li G, Zhu X. MRBEE: A novel bias-corrected multivariable Mendelian Randomization method. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523480. [PMID: 37066391 PMCID: PMC10103949 DOI: 10.1101/2023.01.10.523480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Mendelian randomization (MR) is an instrumental variable approach used to infer causal relationships between exposures and outcomes and can apply to summary data from genome-wide association studies (GWAS). Since GWAS summary statistics are subject to estimation errors, most existing MR approaches suffer from measurement error bias, whose scale and direction are influenced by weak instrumental variables and GWAS sample overlap, respectively. We introduce MRBEE (MR using Bias-corrected Estimating Equation), a novel multivariable MR method capable of simultaneously removing measurement error bias and identifying horizontal pleiotropy. In simulations, we showed that MRBEE is capable of effectively removing measurement error bias in the presence of weak instrumental variables and sample overlap. In two independent real data analyses, we discovered that the causal effect of BMI on coronary artery disease risk is entirely mediated by blood pressure, and that existing MR methods may underestimate the causal effect of cannabis use disorder on schizophrenia risk compared to MRBEE. MRBEE possesses significant potential for advancing genetic research by providing a valuable tool to study causality between multiple risk factors and disease outcomes, particularly as a large number of GWAS summary statistics become publicly available.
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Affiliation(s)
- Noah Lorincz-Comi
- Department of Population and Quantitative Health Sciences, School of Medicine
- Case Western Reserve University, Cleveland, OH 44106, USA June 12, 2023
| | - Yihe Yang
- Department of Population and Quantitative Health Sciences, School of Medicine
- Case Western Reserve University, Cleveland, OH 44106, USA June 12, 2023
| | - Gen Li
- Department of Population and Quantitative Health Sciences, School of Medicine
- Case Western Reserve University, Cleveland, OH 44106, USA June 12, 2023
| | - Xiaofeng Zhu
- This work was supported by grant HG011052 (to X.Z.) from the National Human Genome Research Institute (NHGRI), USA.
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Ding P, Gurney M, Perry G, Xu R. Association of COVID-19 with Risk and Progression of Alzheimer's Disease: Non-Overlapping Two-Sample Mendelian Randomization Analysis of 2.6 Million Subjects. J Alzheimers Dis 2023; 96:1711-1720. [PMID: 38007657 PMCID: PMC11037518 DOI: 10.3233/jad-230632] [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] [Indexed: 11/27/2023]
Abstract
BACKGROUND Epidemiological studies showed that COVID-19 increases risk of Alzheimer's disease (AD). However, it remains unknown if there is a potential genetic predispositional effect. OBJECTIVE To examine potential effects of genetic susceptibility of COVID-19 on the risk and progression of AD, we performed a non-overlapping 2-sample Mendelian randomization (MR) study using summary statistics from genome-wide association studies (GWAS). METHODS Two-sample Mendelian randomization (MR) analysis of over 2.6 million subjects was used to examine whether genetic susceptibility of COVID-19 is not associated with the risk of AD, cortical amyloid burden, hippocampal volume, or AD progression score. Additionally, a validation analysis was performed on a combined sample size of 536,190 participants. RESULTS We show that the AD risk was not associated with genetic susceptibility of COVID-19 risk (OR = 0.98, 95% CI 0.81-1.19) and COVID-19 severity (COVID-19 hospitalization: OR = 0.98, 95% CI 0.9-1.07, and critical COVID-19: OR = 0.98, 95% CI 0.92-1.03). Genetic predisposition to COVID-19 is not associated with AD progression as measured by hippocampal volume, cortical amyloid beta load, and AD progression score. These findings were replicated in a set of 536,190 participants. Consistent results were obtained across models based on different GWAS summary statistics, MR estimators and COVID-19 definitions. CONCLUSIONS Our findings indicated that the genetic susceptibility of COVID-19 is not associated with the risk and progression of AD.
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Affiliation(s)
- Pingjian Ding
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Mark Gurney
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - George Perry
- Department of Neuroscience, Development and Regenerative Biology, College of Sciences, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Rong Xu
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
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Astore C, Nagpal S, Gibson G. Mendelian Randomization Indicates a Causal Role for Omega-3 Fatty Acids in Inflammatory Bowel Disease. Int J Mol Sci 2022; 23:ijms232214380. [PMID: 36430859 PMCID: PMC9698476 DOI: 10.3390/ijms232214380] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal system. Omega-3 (ω3) fatty acids are polyunsaturated fatty acids (PUFAs) that are largely obtained from diet and have been speculated to decrease the inflammatory response that is involved in IBD; however, the causality of this association has not been established. A two-sample Mendelian randomization (MR) was used to assess genetic associations between 249 circulating metabolites measured in the UK Biobank as exposures and IBD as the outcome. The genome-wide association study summary level data for metabolite measurements and IBD were derived from large European ancestry cohorts. We observed ω3 fatty acids as a significant protective association with IBD, with multiple modes of MR evidence replicated in three IBD summary genetic datasets. The instrumental variables that were involved in the causal association of ω3 fatty acids with IBD highlighted an intronic SNP, rs174564, in FADS2, a protein engaged in the first step of alpha-linolenic acid desaturation leading to anti-inflammatory EPA and thence DHA production. A low ratio of ω3 to ω6 fatty acids was observed to be a causal risk factor, particularly for Crohn's disease. ω3 fatty acid supplementation may provide anti-inflammatory responses that are required to attenuate inflammation that is involved in IBD.
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Liao Q, He J, Huang K. Physical activities and risk of neurodegenerative diseases: A two-sample Mendelian randomization study. Front Aging Neurosci 2022; 14:991140. [PMID: 36212040 PMCID: PMC9541335 DOI: 10.3389/fnagi.2022.991140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
Objectives Physical activity (PA) is considered beneficial in slowing the progression and improving the neurodegenerative disease prognosis. However, the association between PA and neurodegenerative diseases remains unknown. In this study, we conducted a two-sample Mendelian randomization (MR) analysis to estimate the causal association between PA phenotypes and neurodegenerative diseases. Materials and methods Genetic variants robustly associated with PA phenotypes, used as instrumental variables, were extracted from public genome-wide association study (GWAS) summary statistics. Neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), Parkinson’s disease (PD), and Alzheimer’s disease (AD), were considered outcomes. GWAS information was also obtained from the most recent large population study of individuals with European ancestry. Multiple MR methods, pleiotropy tests and sensitivity analyses were performed to obtain a robust and valid estimation. Results We found a positive association between moderate-to-vigorous physical activities and ALS based on the inverse variance weighted MR analysis method (OR: 2.507, 95% CI: 1.218–5.160, p = 0.013). The pleiotropy test and sensitivity analysis confirmed the robustness and validity of these MR results. No causal effects of PA phenotypes were found on PD and AD. Conclusion Our study indicates a causal effect of PA on the risk of neurodegenerative diseases. Genetically predicted increases in self-reported moderate-to-vigorous PA participation could increase the risk of ALS in individuals of European ancestry. Precise and individualized prescriptions of physical activity should be provided to the elderly population.
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Affiliation(s)
- Qiao Liao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jian He
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Kun Huang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Kun Huang,
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Balogh L, Pulay AJ, Réthelyi JM. Genetics in the ADHD Clinic: How Can Genetic Testing Support the Current Clinical Practice? Front Psychol 2022; 13:751041. [PMID: 35350735 PMCID: PMC8957927 DOI: 10.3389/fpsyg.2022.751041] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 01/03/2022] [Indexed: 12/12/2022] Open
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a neurodevelopmental disorder with a childhood prevalence of 5%. In about two-thirds of the cases, ADHD symptoms persist into adulthood and often cause significant functional impairment. Based on the results of family and twin studies, the estimated heritability of ADHD approximates 80%, suggests a significant genetic component in the etiological background of the disorder; however, the potential genetic effects on disease risk, symptom severity, and persistence are unclear. This article provides a brief review of the genome-wide and candidate gene association studies with a focus on the clinical aspects, summarizing findings of ADHD disease risk, ADHD core symptoms as dimensional traits, and other traits frequently associated with ADHD, which may contribute to the susceptibility to other comorbid psychiatric disorders. Furthermore, neuropsychological impairment and measures from neuroimaging and electrophysiological paradigms, emerging as potential biomarkers, also provide a prominent target for molecular genetic studies, since they lie in the pathway from genes to behavior; therefore, they can contribute to the understanding of the underlying neurobiological mechanisms and the interindividual heterogeneity of clinical symptoms. Beyond the aforementioned aspects, throughout the review, we also give a brief summary of the genetic results, including polygenic risk scores that can potentially predict individual response to different treatment options and may offer a possibility for personalized treatment for the therapy of ADHD in the future.
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Affiliation(s)
- Lívia Balogh
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Attila J Pulay
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - János M Réthelyi
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
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Lin Z, Deng Y, Pan W. Combining the strengths of inverse-variance weighting and Egger regression in Mendelian randomization using a mixture of regressions model. PLoS Genet 2021; 17:e1009922. [PMID: 34793444 PMCID: PMC8639093 DOI: 10.1371/journal.pgen.1009922] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 12/02/2021] [Accepted: 11/02/2021] [Indexed: 11/19/2022] Open
Abstract
With the increasing availability of large-scale GWAS summary data on various traits, Mendelian randomization (MR) has become commonly used to infer causality between a pair of traits, an exposure and an outcome. It depends on using genetic variants, typically SNPs, as instrumental variables (IVs). The inverse-variance weighted (IVW) method (with a fixed-effect meta-analysis model) is most powerful when all IVs are valid; however, when horizontal pleiotropy is present, it may lead to biased inference. On the other hand, Egger regression is one of the most widely used methods robust to (uncorrelated) pleiotropy, but it suffers from loss of power. We propose a two-component mixture of regressions to combine and thus take advantage of both IVW and Egger regression; it is often both more efficient (i.e. higher powered) and more robust to pleiotropy (i.e. controlling type I error) than either IVW or Egger regression alone by accounting for both valid and invalid IVs respectively. We propose a model averaging approach and a novel data perturbation scheme to account for uncertainties in model/IV selection, leading to more robust statistical inference for finite samples. Through extensive simulations and applications to the GWAS summary data of 48 risk factor-disease pairs and 63 genetically uncorrelated trait pairs, we showcase that our proposed methods could often control type I error better while achieving much higher power than IVW and Egger regression (and sometimes than several other new/popular MR methods). We expect that our proposed methods will be a useful addition to the toolbox of Mendelian randomization for causal inference.
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Affiliation(s)
- Zhaotong Lin
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Yangqing Deng
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Wei Pan
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota, United States of America
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Zhu X, Li X, Xu R, Wang T. An iterative approach to detect pleiotropy and perform Mendelian Randomization analysis using GWAS summary statistics. Bioinformatics 2021; 37:1390-1400. [PMID: 33226062 DOI: 10.1093/bioinformatics/btaa985] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 01/01/2023] Open
Abstract
MOTIVATION The overall association evidence of a genetic variant with multiple traits can be evaluated by cross-phenotype association analysis using summary statistics from genome-wide association studies. Further dissecting the association pathways from a variant to multiple traits is important to understand the biological causal relationships among complex traits. RESULTS Here, we introduce a flexible and computationally efficient Iterative Mendelian Randomization and Pleiotropy (IMRP) approach to simultaneously search for horizontal pleiotropic variants and estimate causal effect. Extensive simulations and real data applications suggest that IMRP has similar or better performance than existing Mendelian Randomization methods for both causal effect estimation and pleiotropic variant detection. The developed pleiotropy test is further extended to detect colocalization for multiple variants at a locus. IMRP will greatly facilitate our understanding of causal relationships underlying complex traits, in particular, when a large number of genetic instrumental variables are used for evaluating multiple traits. AVAILABILITY AND IMPLEMENTATION The software IMRP is available at https://github.com/XiaofengZhuCase/IMRP. The simulation codes can be downloaded at http://hal.case.edu/∼xxz10/zhu-web/ under the link: MR Simulations software. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Xiaoyin Li
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Rong Xu
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Tao Wang
- Division of Biostatistics, Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA.,Division of Epidemiology, Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
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Lorincz-Comi N, Zhu X. Cardiometabolic risks of SARS-CoV-2 hospitalization using Mendelian Randomization. Sci Rep 2021; 11:7848. [PMID: 33846372 PMCID: PMC8042041 DOI: 10.1038/s41598-021-86757-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/19/2021] [Indexed: 01/31/2023] Open
Abstract
Many cardiometabolic conditions have demonstrated associative evidence with COVID-19 hospitalization risk. However, the observational designs of the studies in which these associations are observed preclude causal inferences of hospitalization risk. Mendelian Randomization (MR) is an alternative risk estimation method more robust to these limitations that allows for causal inferences. We applied four MR methods (MRMix, IMRP, IVW, MREgger) to publicly available GWAS summary statistics from European (COVID-19 GWAS n = 2956) and multi-ethnic populations (COVID-19 GWAS n = 10,908) to better understand extant causal associations between Type II Diabetes (GWAS n = 659,316), BMI (n = 681,275), diastolic and systolic blood pressure, and pulse pressure (n = 757,601 for each) and COVID-19 hospitalization risk across populations. Although no significant causal effect evidence was observed, our data suggested a trend of increasing hospitalization risk for Type II diabetes (IMRP OR, 95% CI 1.67, 0.96-2.92) and pulse pressure (OR, 95% CI 1.27, 0.97-1.66) in the multi-ethnic sample. Type II diabetes and Pulse pressure demonstrates a potential causal association with COVID-19 hospitalization risk, the proper treatment of which may work to reduce the risk of a severe COVID-19 illness requiring hospitalization. However, GWAS of COVID-19 with large sample size is warranted to confirm the causality.
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Affiliation(s)
- Noah Lorincz-Comi
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Wolstein Research Building Room 1317, 2103 Cornell Rd, Cleveland, OH, 44106, USA.
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