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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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Zhu S, Ding Z. Acute pancreatitis and metabolic syndrome: genetic correlations and causal associations. Endocrine 2024; 84:380-387. [PMID: 37922090 DOI: 10.1007/s12020-023-03584-4] [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: 09/18/2023] [Accepted: 10/22/2023] [Indexed: 11/05/2023]
Abstract
BACKGROUND Although there is a definite correlation between the Metabolic Syndrome (MetS) and Acute Pancreatitis (AP), cause is yet unknown. The current work combined linkage disequilibrium score (LDSC) regression and Mendelian randomization (MR) approaches to fill this important information gap. METHODS In this study, we harnessed the power of publicly available gene-wide association databases (GWAS) to explore the intricate relationship between MetS and its components with AP. The cornerstone of our analysis was the Inverse-Variance Weighted (IVW) method, serving as our primary analytical tool. In addition to IVW, we complemented our investigation with several other robust MR methods, including MR-Egger, Weighted Median, Maximum Likelihood, and MR-PRESSO. By employing this diverse set of analytical approaches, we sought to ensure the comprehensiveness and robustness of our findings. RESULT LDSC regression indicated a genetic correlation between MetS and AP. Univariate MR results indicated a genetic association between MetS (OR = 1.084; 95% CI, 1.005-1.170; P = 0.037), BMI (OR = 1.459; 95% CI, 1.325-1.606; P = 1.46E-14), WHR (OR = 1.189; 95% CI, 1.068-1.323; P = 1.56 E-03), TG (OR = 1.110; 95% CI, 1.001-1.231; P = 0.047), and FI (OR = 1.798; 95% CI, 1.245-2.595; P = 1.74E-03) were able to significantly increase the risk of AP. The results of multivariate MR analysis revealed that these causality associations still existed. CONCLUSION Our investigation has yielded compelling evidence that substantiates the presence of both a genetic correlation and a causal relationship between MetS and AP.
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Affiliation(s)
- ShuangJing Zhu
- Department of Hepatobiliary Surgery, Chaohu Hospital of Anhui Medical University, Hefei, 238001, China
| | - Zhen Ding
- Department of Hepatobiliary Surgery, Chaohu Hospital of Anhui Medical University, Hefei, 238001, China.
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Zhang X, Cai Y, Jiang Y, Du W, An W, Fu Q, Chen Y. Genetic correlation between circulating metabolites and chalazion: a two-sample Mendelian randomization study. Front Mol Biosci 2024; 11:1368669. [PMID: 38577173 PMCID: PMC10991826 DOI: 10.3389/fmolb.2024.1368669] [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: 01/19/2024] [Accepted: 03/06/2024] [Indexed: 04/06/2024] Open
Abstract
Background: Lipid metabolism disorders were observationally associated with chalazion, but the causality of the related circulating metabolites on chalazion remained unknown. Here, we investigated the potential causal relationship between circulating metabolites and chalazion using two-sample Mendelian randomization (MR) analysis. Methods: For the primary analysis, 249 metabolic biomarkers were obtained from the UK Biobank, and 123 circulating metabolites were obtained from the publication by Kuttunen et al. for the secondary analysis. Chalazion summary data were obtained from the FinnGen database. Inverse variance weighted (IVW) is the main MR analysis method, and the MR assumptions were evaluated in sensitivity and colocalization analyses. Results: Two MR analyses results showed that the common metabolite, alanine, exhibited a genetic protective effect against chalazion (primary analysis: odds ratio [OR] = 0.680; 95% confidence interval [CI], 0.507-0.912; p = 0.010; secondary analysis: OR = 0.578; 95% CI, 0.439-0.759; p = 0.00008). The robustness of the findings was supported by heterogeneity and horizontal pleiotropy analysis. Two colocalization analyses showed that alanine did not share a region of genetic variation with chalazion (primary analysis: PPH4 = 1.95%; secondary analysis: PPH4 = 25.3%). Moreover, previous studies have suggested that an increase in the degree of unsaturation is associated with an elevated risk of chalazion (OR = 1.216; 95% CI, 1.055-1.401; p = 0.007), with omega-3 fatty acids (OR = 1.204; 95% CI, 1.054-1.377; p = 0.006) appearing to be the major contributing factor, as opposed to omega-6 fatty acids (OR = 0.850; 95% CI, 0.735-0.982; p = 0.027). Conclusion: This study suggests that alanine and several unsaturated fatty acids are candidate molecules for mechanistic exploration and drug target selection in chalazion.
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Affiliation(s)
- Xin Zhang
- Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yuying Cai
- Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yaping Jiang
- Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Wei Du
- Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Weishu An
- Department of Oncology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiangqiang Fu
- Department of General Practice, Clinical Research Center for General Practice, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yihui Chen
- Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
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Mi J, Jiang Q, Qi Z, Liu Z, Bai X, Zheng X, Wu J, Fang Y, Yang A, Chen H. Plasma campesterol and ABCG5/ABCG8 gene loci on the risk of cholelithiasis and cholecystitis: evidence from Mendelian randomization and colocalization analyses. Hum Genomics 2024; 18:19. [PMID: 38347599 PMCID: PMC10863091 DOI: 10.1186/s40246-024-00583-y] [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: 11/21/2023] [Accepted: 02/01/2024] [Indexed: 02/15/2024] Open
Abstract
The causal relationships between plasma metabolites and cholelithiasis/cholecystitis risks remain elusive. Using two-sample Mendelian randomization, we found that genetic proxied plasma campesterol level showed negative correlation with the risk of both cholelithiasis and cholecystitis. Furthermore, the increased risk of cholelithiasis is correlating with the increased level of plasma campesterol. Lastly, genetic colocalization study showed that the leading SNP, rs4299376, which residing at the ABCG5/ABCG8 gene loci, was shared by plasma campesterol level and cholelithiasis, indicating that the aberrant transportation of plant sterol/cholesterol from the blood stream to the bile duct/gut lumen might be the key in preventing cholesterol gallstone formation.
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Affiliation(s)
- Jiarui Mi
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Qingwei Jiang
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zhengwei Qi
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Zhengye Liu
- Department of Plastic and Aesthetic Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Xiaoyin Bai
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xia Zheng
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Jiaguo Wu
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Yanfei Fang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Aiming Yang
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Haotian Chen
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
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Mi J, Wang F, Liu Z, Bai X. Antioxidant, selenium and risk of nonalcoholic fatty liver disease, more than causality. Hepatol Int 2024; 18:289-291. [PMID: 36821046 DOI: 10.1007/s12072-023-10500-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 02/04/2023] [Indexed: 02/24/2023]
Affiliation(s)
- Jiarui Mi
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Fang Wang
- Department of Clinical Nutrition, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zhengye Liu
- Department of Plastic and Aesthetic Center, College of Medicine, the First Affiliated Hospital, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Xiaoyin Bai
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
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Louck LE, Cara KC, Klatt K, Wallace TC, Chung M. The Relationship of Circulating Choline and Choline-Related Metabolite Levels with Health Outcomes: A Scoping Review of Genome-Wide Association Studies and Mendelian Randomization Studies. Adv Nutr 2024; 15:100164. [PMID: 38128611 PMCID: PMC10819410 DOI: 10.1016/j.advnut.2023.100164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023] Open
Abstract
Choline is essential for proper liver, muscle, brain, lipid metabolism, cellular membrane composition, and repair. Understanding genetic determinants of circulating choline metabolites can help identify new determinants of choline metabolism, requirements, and their link to disease endpoints. We conducted a scoping review to identify studies assessing the association of genetic polymorphisms on circulating choline and choline-related metabolite concentrations and subsequent associations with health outcomes. This study follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement scoping review extension. Literature was searched to September 28, 2022, in 4 databases: Embase, MEDLINE, Web of Science, and the Biological Science Index. Studies of any duration in humans were considered. Any genome-wide association study (GWAS) investigating genetic variant associations with circulating choline and/or choline-related metabolites and any Mendelian randomization (MR) study investigating the association of genetically predicted circulating choline and/or choline-related metabolites with any health outcome were considered. Qualitative evidence is presented in summary tables. From 1248 total reviewed articles, 53 were included (GWAS = 27; MR = 26). Forty-two circulating choline-related metabolites were tested in association with genetic variants in GWAS studies, primarily trimethylamine N-oxide, betaine, sphingomyelins, lysophosphatidylcholines, and phosphatidylcholines. MR studies investigated associations between 52 total unique choline metabolites and 66 unique health outcomes. Of these, 47 significant associations were reported between 16 metabolites (primarily choline, lysophosphatidylcholines, phosphatidylcholines, betaine, and sphingomyelins) and 27 health outcomes including cancer, cardiovascular, metabolic, bone, and brain-related outcomes. Some articles reported significant associations between multiple choline types and the same health outcome. Genetically predicted circulating choline and choline-related metabolite concentrations are associated with a wide variety of health outcomes. Further research is needed to assess how genetic variability influences choline metabolism and whether individuals with lower genetically predicted circulating choline and choline-related metabolite concentrations would benefit from a dietary intervention or supplementation.
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Affiliation(s)
- Lauren E Louck
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, United States
| | - Kelly C Cara
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, United States
| | - Kevin Klatt
- Nutritional Sciences and Toxicology, University of California, Berkeley, CA, United States
| | - Taylor C Wallace
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, United States; Think Health Group, Inc, Washington, DC, United States
| | - Mei Chung
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, United States.
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Xie XM, Liu T, Wang GY. Associations of fatty acids with the risk of biliary tract calculus and inflammation: a Mendelian randomization study. Lipids Health Dis 2024; 23:8. [PMID: 38191483 PMCID: PMC10773125 DOI: 10.1186/s12944-023-01989-8] [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: 10/26/2023] [Accepted: 12/24/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND The presence of gallstones in both the gallbladder and bile ducts is referred to as cholelithiasis. The prevalence of cholecystolithiasis and bile duct stones differs. Observational and Mendelian randomization (MR) studies have elucidated the significant contributing role of numerous fatty acids (FAs) in the development of cholelithiasis. Despite numerous studies about cholelithiasis, evidence on the relationship between serum FA levels and cholecystolithiasis, as well as bile duct stones with or without inflammation, remains insufficient. METHODS A two-sample MR study was designed to clarify the impact of serum FA levels on various bile duct inflammatory diseases. The summary statistics of single nucleotide polymorphisms (SNPs) associated with fatty acids were obtained from the UK Biobank (UKB) and included data from 114,999 participants. The researchers obtained GWAS summary statistics for cholecystolithiasis and bile duct stones in 463,010 and 361,194 European participants, including cases with and without inflammation. No sample overlap between the exposure and outcome was verified through the "mr-lap" package. The SNPs were screened to identify instrumental variables (IVs). Cochran's Q test was applied for heterogeneity assessment. Inverse variance weighting (IVW) (fixed effects or random effects), MR-Egger regression and weighted median methods were used for MR. Multivariable MR was applied to determine the direct effect of each exposure on the outcome. A false discovery rate (FDR) was applied to adjust for multiple testing correction based on the Benjamini-Hochberg method. Finally, the FinnGen Consortium was used to validate some results. RESULTS The overall concentration of polyunsaturated fatty acids (PUFAs) in the serum was negatively associated with the risk of calculus of the gallbladder with acute cholecystitis (IVW, OR = 0.996, P = 0.038, CI 0.992-0.999; weighted median, OR = 0.995, P = 0.025, CI 0.991-0.999). The percentage of PUFAs to total monounsaturated fatty acids(MUFAs) (IVW, OR = 0.998, P = 0.045, CI 0.997-0.999) and the percentage of PUFAs to total FAs (IVW, OR = 0.997, P = 0.025, CI 0.995-0.999) had a protective role against cholecystitis. The percentage of PUFAs to total FAs had a protective role against calculus of the gallbladder without cholecystitis (IVW, OR = 0.995, P = 0.026, CI 0.990-0.999; MR Egger, OR = 0.99, P = 0.03, CI 0.982-0.998; weighted median, OR = 0.991, P = 5.41e-06, CI 0.988-0.995). Conversely, the percentage of MUFAs to total FAs increased the risk for cholecystitis (IVW, OR = 1.001, P = 0.034, CI 1.0001-1.002). However, there were no causal effects of the above exposures on the outcomes through multivariable MR and multiple testing correction. Finally, the causal effects of the above exposures on cholecystitis were validated in the FinnGen Consortium, which suggested that the percentage of PUFAs to total FAs (IVW, OR = 0.744, P = 0.021, CI 0.579-0.957) had a protective role against cholecystitis. CONCLUSION These Mendelian randomization findings suggested that more attention should be focused on people who have low serum PUFA levels, which may have a potential role in the occurrence of calculus of the gallbladder or cholecystitis rather than calculus of the bile duct without cholangitis or cholecystitis.
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Affiliation(s)
- Xing-Ming Xie
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, People's Republic of China
| | - Tao Liu
- Department of Hepatobiliary Surgery, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, 445000, People's Republic of China
| | - Guo-Ying Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, People's Republic of China.
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Ji L, Wang Y, Lu T, Yang J, Luo C, Qiu B. Identification of blood metabolites linked to the risk of intervertebral disc diseases: a comprehensive Mendelian randomization study. Postgrad Med J 2023; 99:1148-1153. [PMID: 37399049 DOI: 10.1093/postmj/qgad052] [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: 04/04/2023] [Revised: 05/08/2023] [Accepted: 05/23/2023] [Indexed: 07/04/2023]
Abstract
BACKGROUND Intervertebral disc degeneration (IVDD) has affected millions of people worldwide and dramatically affects human beings' quality of life. Observational studies hypothesize that metabolites play key roles as markers and effectors of IVDD, but their causality has not yet been illustrated. METHODS We conducted comprehensive Mendelian randomization (MR) to determine the causal relationship between 249 plasma metabolites and IVDD. Inverse-variance weighting was used as the primary estimate, whereas MR-Egger and weighed median were used to detect robustness. A series of sensitivity analyses including Cochran Q test, leave one out, and MR-Egger intercept analysis were also conducted. RESULTS In total, we found 13 blood metabolites significantly associated with IVDD, including phospholipids in very large high-density lipoprotein (HDL), free cholesterol to total lipids ratio in very large HDL, average diameter for HDL particles, cholesteryl esters to total lipids ratio in large HDL, free cholesterol to total lipids ratio in medium HDL, creatinine, free cholesterol to total lipids ratio in large HDL, phospholipids to total lipids ratio in very large HDL, cholesterol to total lipids ratio in very large HDL, cholesteryl esters to total lipids ratio in large HDL, phospholipids in large HDL, total lipids in very large HDL, and total lipids in large HDL. No pleiotropy was detected. Heterogeneity existed in several estimates and random-effect inverse-variance weighting was applied. CONCLUSIONS Our study highlighted the causal association of blood metabolites with the risk of IVDD. Our results provide new insights into possible treatment protocols controlling the concentration of specific blood metabolites in IVDD patients. Key messages What is already known on this topic Low back pain is the most common symptom for patients with intervertebral disc degeneration (IVDD) and influences the quality of life of large populations. Observational studies have indicated the association between metabolites and IVDD. However, causality has not been determined yet. What this study adds We conducted a comprehensive Mendelian randomization study to reveal the causal effect from 249 blood metabolites on low back pain. A total of 13 metabolites were found to causally affect the risk of IVDD, among which 11 were negatively associated and 2 were positively asscociated. How this study might affect research, practice, or policy These 13 significant metabolites could serve as biomarkers for IVDD and our results provide new insights into possible treatment protocols for IVDD patients.
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Affiliation(s)
- Linsong Ji
- Department of Spine Surgery, Beijing Jishuitan Hospital Guizhou Hospital, Guiyang 550014, China
| | - Yanping Wang
- Department of Gastroenterology, Beijing Jishuitan Hospital Guizhou Hospital, Guiyang 550014, China
| | - Tingsheng Lu
- Department of Spine Surgery, Beijing Jishuitan Hospital Guizhou Hospital, Guiyang 550014, China
| | - Jianwen Yang
- Department of Spine Surgery, Beijing Jishuitan Hospital Guizhou Hospital, Guiyang 550014, China
| | - Chunshan Luo
- Department of Spine Surgery, Beijing Jishuitan Hospital Guizhou Hospital, Guiyang 550014, China
| | - Bing Qiu
- Department of Spine Surgery, Beijing Jishuitan Hospital Guizhou Hospital, Guiyang 550014, 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. RESEARCH SQUARE 2023:rs.3.rs-3222588. [PMID: 37790512 PMCID: PMC10543429 DOI: 10.21203/rs.3.rs-3222588/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
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. We examined the association between polygenic scores for 726 metabolites (derived from OMICSPRED) with 1,247 clinical phenotypes in 57,735 European ancestry and 15,754 African ancestry participants from the BioVU DNA Biobank. We probed significant relationships through Mendelian randomization (MR) using genetic instruments constructed from the METSIM Study, and validated significant MR associations using independent GWAS of candidate phenotypes. We found significant associations between 336 metabolites and 168 phenotypes in European ancestry and 107 metabolites and 56 phenotypes among African ancestry. Of these metabolite-disease pairs, MR analyses confirmed associations between 73 metabolites and 53 phenotypes in European ancestry. Of 22 metabolite-phenotype pairs evaluated for replication in independent GWAS, 16 were significant (false discovery rate p<0.05). Validated findings included the metabolites bilirubin and X-21796 with cholelithiasis, phosphatidylcholine(16:0/22:5n3,18:1/20:4) and arachidonate(20:4n6) 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)
| | | | | | | | - Ravi Shah
- Vanderbilt University Medical Center
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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. RESEARCH SQUARE 2023:rs.3.rs-3222588. [PMID: 37790512 PMCID: PMC10543429 DOI: 10.21203/rs.3.rs-3222588/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
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. We examined the association between polygenic scores for 726 metabolites (derived from OMICSPRED) with 1,247 clinical phenotypes in 57,735 European ancestry and 15,754 African ancestry participants from the BioVU DNA Biobank. We probed significant relationships through Mendelian randomization (MR) using genetic instruments constructed from the METSIM Study, and validated significant MR associations using independent GWAS of candidate phenotypes. We found significant associations between 336 metabolites and 168 phenotypes in European ancestry and 107 metabolites and 56 phenotypes among African ancestry. Of these metabolite-disease pairs, MR analyses confirmed associations between 73 metabolites and 53 phenotypes in European ancestry. Of 22 metabolite-phenotype pairs evaluated for replication in independent GWAS, 16 were significant (false discovery rate p<0.05). Validated findings included the metabolites bilirubin and X-21796 with cholelithiasis, phosphatidylcholine(16:0/22:5n3,18:1/20:4) and arachidonate(20:4n6) 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)
| | | | | | | | - Ravi Shah
- Vanderbilt University Medical Center
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Joshi AD, McCormick N, Yokose C, Yu B, Tin A, Terkeltaub R, Merriman TR, Eliassen AH, Curhan GC, Raffield LM, Choi HK. Prediagnostic Glycoprotein Acetyl Levels and Incident and Recurrent Flare Risk Accounting for Serum Urate Levels: A Population-Based, Prospective Study and Mendelian Randomization Analysis. Arthritis Rheumatol 2023; 75:1648-1657. [PMID: 37043280 PMCID: PMC10524152 DOI: 10.1002/art.42523] [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: 02/06/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 04/13/2023]
Abstract
OBJECTIVE To prospectively investigate population-based metabolomics for incident gout and reproduce the findings for recurrent flares, accounting for serum urate. METHODS We conducted a prediagnostic metabolome-wide analysis among 105,615 UK Biobank participants with nuclear magnetic resonance metabolomic profiling data (168 total metabolites) from baseline blood samples collected 2006-2010 in those without history of gout. We calculated hazard ratios (HRs) for incident gout, adjusted for gout risk factors, excluding and including serum urate levels, overall and according to fasting duration before sample collection. Potential causal effects were tested with 2-sample Mendelian randomization. Poisson regression was used to calculate rate ratios (RRs) for the association with recurrent flares among incident gout cases. RESULTS Correcting for multiple testing, 88 metabolites were associated with risk of incident gout (N = 1,303 cases) before serum urate adjustment, including glutamine and glycine (inversely), and lipids, branched-chain amino acids, and most prominently, glycoprotein acetyls (GlycA; P = 9.17 × 10-32 ). Only GlycA remained associated with incident gout following urate adjustment (HR 1.52 [95% confidence interval (95% CI) 1.22-1.88] between extreme quintiles); the HR increased progressively with fasting duration before sample collection, reaching 4.01 (95% CI 1.36-11.82) for ≥8 hours of fasting. Corresponding HRs per SD change in GlycA levels were 1.10 (95% CI 1.04-1.17) overall and 1.54 (95% CI 1.21-1.96) for ≥8 hours of fasting. GlycA levels were also associated with recurrent gout flares among incident gout cases (RR 1.90 [95% CI 1.27-2.85] between extreme quintiles) with larger associations with fasting. Mendelian randomization corroborated a potential causal role for GlycA on gout risk. CONCLUSION This prospective, population-based study implicates GlycA, a stable long-term biomarker reflecting neutrophil overactivity, in incident and recurrent gout flares (central manifestation from neutrophilic synovitis) beyond serum urate.
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Affiliation(s)
- Amit D. Joshi
- Clinical and Translational Epidemiology Unit, Department of Medicine, Massachusetts General Hospital, Boston MA USA
| | - Natalie McCormick
- Clinical Epidemiology Program, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston MA USA
- The Mongan Institute, Department of Medicine, Massachusetts General Hospital, Boston MA USA
- Department of Medicine, Harvard Medical School, Boston MA USA
- Arthritis Research Canada, Vancouver BC Canada
| | - Chio Yokose
- Clinical Epidemiology Program, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston MA USA
- The Mongan Institute, Department of Medicine, Massachusetts General Hospital, Boston MA USA
- Department of Medicine, Harvard Medical School, Boston MA USA
| | - Bing Yu
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston TX USA
| | - Adrienne Tin
- Department of Medicine, University of Mississippi Medical Center, Jackson MS USA
| | - Robert Terkeltaub
- San Diego VA Healthcare Service and University of California San Diego, La Jolla, CA
| | - Tony R. Merriman
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham AL USA
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - A. Heather Eliassen
- Departments of Nutrition and Epidemiology, Harvard TH Chan School of Public Health, Boston MA USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston MA USA
| | - Gary C. Curhan
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston MA USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill NC USA
| | - Hyon K. Choi
- Clinical Epidemiology Program, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston MA USA
- The Mongan Institute, Department of Medicine, Massachusetts General Hospital, Boston MA USA
- Department of Medicine, Harvard Medical School, Boston MA USA
- Arthritis Research Canada, Vancouver BC Canada
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Huang T, Long Y, Ou Y, Li J, Huang Y, Gao J. Association between circulating fatty acid metabolites and asthma risk: a two-sample bidirectional Mendelian randomization study. BMC Med Genomics 2023; 16:112. [PMID: 37221513 DOI: 10.1186/s12920-023-01545-4] [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: 10/11/2022] [Accepted: 05/13/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND Fatty acids are involved in a wide range of immunological responses in humans. Supplementation of polyunsaturated fatty acids has been reported to help alleviate symptoms and airway inflammation in asthma patients, whereas the effects of fatty acids on the actual risk of asthma remain controversial. This study comprehensively investigated the causal effects of serum fatty acids on asthma risk using two-sample bidirectional Mendelian Randomization (MR) analysis. METHODS Genetic variants strongly associated with 123 circulating fatty acid metabolites were extracted as instrumental variables, and a large GWAS data of asthma was used to test effects of the metabolites on this outcome. The inverse-variance weighted method was used for primary MR analysis. The weighted median, MR-Egger regression, MR-PRESSO, and leave-one-out analyses were utilized to evaluate heterogeneity and pleiotropy. Potential confounders were adjusted by performing multivariable MR analyses. Reverse MR analysis was also conducted to estimate the causal effect of asthma on candidate fatty acid metabolites. Further, we performed colocalization analysis to examine the pleiotropy of variants within the fatty acid desaturase 1 (FADS1) locus between the significant metabolite traits and the risk of asthma. Cis-eQTL-MR and colocalization analysis were also performed to determine the association between RNA expression of FADS1 and asthma. RESULTS Genetically instrumented higher average number of methylene groups was causally associated with a lower risk of asthma in primary MR analysis, while inversely, the higher ratio of bis-allylic groups to double bonds and the higher ratio of bis-allylic groups to total fatty acids, were associated with higher probabilities of asthma. Consistent results were obtained in multivariable MR when adjusted for potential confounders. However, these effects were completely eliminated after SNPs correlated with the FADS1 gene were excluded. The reverse MR also found no causal association. The colocalization analysis suggested that the three candidate metabolite traits and asthma likely share causal variants within the FADS1 locus. In addition, the cis-eQTL-MR and colocalization analyses demonstrated a causal association and shared causal variants between FADS1 expression and asthma. CONCLUSIONS Our study supports a negative association between several PUFA traits and the risk of asthma. However, this association is largely attributed to the influence of FADS1 polymorphisms. The results of this MR study should be carefully interpreted given the pleiotropy of SNPs associated with FADS1.
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Affiliation(s)
- Tingting Huang
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yichen Long
- Department of Epidemiology, School of Public Health, Southeast University, Jiangsu, Nanjing, China
| | - Yang Ou
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai, China
| | - Jia Li
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yilin Huang
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinming Gao
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Beijing, China.
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Liu Z, Mi J, Wu H. Relationships between circulating metabolites and facial skin aging: a Mendelian randomization study. Hum Genomics 2023; 17:23. [PMID: 36927485 PMCID: PMC10022075 DOI: 10.1186/s40246-023-00470-y] [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: 11/07/2022] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Blood metabolites are important to various aspects of our health. However, currently, there is little evidence about the role of circulating metabolites in the process of skin aging. OBJECTIVES To examine the potential effects of circulating metabolites on the process of skin aging. METHOD In the primary analyses, we applied several MR methods to study the associations between 249 metabolites and facial skin aging risk. In the secondary analyses, we replicated the analyses with another array of datasets including 123 metabolites. MR Bayesian model averaging (MR-BMA) method was further used to prioritize the metabolites for the identification of predominant metabolites that are associated with skin aging. RESULTS In the primary analyses, only the unsaturation degree of fatty acids was found significantly associated with skin aging with the IVW method after multiple testing (odds ratio = 1.084, 95% confidence interval = 1.049-1.120, p = 1.737 × 10-06). Additionally, 11 out of 17 unsaturation-related biomarkers showed a significant or suggestively significant causal effect [p < 0.05 and > 2 × 10-4 (0.05/249 metabolites)]. In the secondary analyses, seven metabolic biomarkers were found significantly associated with skin aging [p < 4 × 10-4 (0.05/123)], while six of them were related to the unsaturation degree. MR-BMA method validated that the unsaturation degree of fatty acids plays a dominant role in facial skin aging. CONCLUSIONS Our study used systemic MR analyses and provided a comprehensive atlas for the associations between circulating metabolites and the risk of facial skin aging. Genetically proxied unsaturation degree of fatty acids was highlighted as a dominant factor correlated with the risk of facial skin aging.
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Affiliation(s)
- Zhengye Liu
- Department of Plastic and Aesthetic Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiarui Mi
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Huiling Wu
- Department of Plastic and Aesthetic Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
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