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Li X, Long H, Wen D, Chen B, Chen L, Li B. Genetic insights into the association between serum cytokines and frozen shoulder risk: A bidirectional mendelian randomization study. Cytokine 2024; 183:156736. [PMID: 39173280 DOI: 10.1016/j.cyto.2024.156736] [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: 06/03/2024] [Revised: 07/25/2024] [Accepted: 08/13/2024] [Indexed: 08/24/2024]
Abstract
BACKGROUND Although existing studies have indicated a connection between chronic low-grade inflammation and the onset of frozen shoulder (FS), the precise causal relationship between distinct circulating inflammatory factors and FS has yet to be thoroughly evaluated. In this study, we employed a bidirectional two-sample Mendelian randomization (MR) analysis to investigate the potential causal relationship between systemic cytokines and FS. METHODS A genome-wide association dataset comprising 41 serum cytokines from 8,293 individuals of Finnish descent was utilized, along with FS data from the UK Biobank included 10,104 FS cases and 451,099 controls. The primary MR method was the inverse variance weighted approach, and four additional MR techniques (MR-Egger, weighted median, simple mode, and weighted mode) were also employed to support and validate the findings. Heterogeneity and horizontal pleiotropy assessments were assessed using Cochrane's Q and MR-Egger intercept tests. Moreover, a series of sensitivity analyses were conducted to strengthen the accuracy and credibility of these findings. RESULTS Based on the IVW method, genetically predicted increasing levels of growth regulated oncogene alpha (GROa) (OR=1.08, 95 % CI 1.02-1.13, P=0.005), interferon gamma-induced protein 10 (IP-10) (OR=1.09, 95 % CI 1.02-1.17, P=0.010), regulated on activation, C-C Motif Chemokine Ligand 5 (CCL5) (OR=1.11, 95 % CI 1.03-1.20, P=0.007) were suggestively associated with an increased risk of FS. Reverse MR analysis revealed no significant causal effect of FS on the 41 systemic inflammatory factors. No heterogeneity or horizontal pleiotropy was observed in our analysis. CONCLUSION This study established a causal association between 41 systemic inflammatory factors and FS, indicating that elevated levels of GROa, IP-10 and CCL5 were associated with a higher risk of FS. Further research is warranted to explore the potential of these biomarkers as early predictors and therapeutic targets for FS.
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Affiliation(s)
- Xuefei Li
- Division of Joint Surgery and Sports Medicine, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China; Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Han Long
- Huazhong University of Science and Technology, Tongji Medical College, School of Medicine and Health Management, Wuhan 430022, China
| | - Dusu Wen
- Division of Joint Surgery and Sports Medicine, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Biao Chen
- Division of Joint Surgery and Sports Medicine, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.
| | - Liaobin Chen
- Division of Joint Surgery and Sports Medicine, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.
| | - Bin Li
- Division of Joint Surgery and Sports Medicine, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.
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Wang Y, Xie K, Wang J, Chen F, Li X, Zhang L. Mendelian randomization demonstrates a causal link between peripheral circulating acylcarnitines and intracranial aneurysms. Neurotherapeutics 2024:e00428. [PMID: 39098392 DOI: 10.1016/j.neurot.2024.e00428] [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: 03/03/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/06/2024] Open
Abstract
Intracranial aneurysm (IA) is the most prevalent type of cerebral vascular disease causing life-threatening subarachnoid hemorrhages (SAH). A long-term vascular structure remodeling is considered as the main pathophysiological feature of IAs. However, the causal factors triggering the pathophysiological process are not clear. Recently, the abnormalities of peripheral circulating proteins and metabolites have been found in IAs patients and associated with the ruptures. We comprehensively investigated the potential causal relationship between blood metabolites and proteins and IAs using the mendelian randomization (MR) analysis. We applied two-sample MR to explore the potential causal association between peripheral circulating metabolites (191 blood metabolites) and proteins (1398 proteins) and IAs using data from the FinnGen study and the GWAS datasets published by Bakker et al. We identified palmitoylcarnitine, stearoylcarnitine and 2-tetradecenoylcarnitine as causal contributors of IAs and ruptures. Further two-step mediation MR analysis suggested that hypertension as one of the contributors of IAs and ruptures mediated the causal relationship between palmitoylcarnitine, stearoylcarnitine and 2-tetradecenoylcarnitine and IAs. Together, our study demonstrates that blood metabolic palmitoylcarnitine, stearoylcarnitine and 2-tetradecenoylcarnitine are causally linked to the formation and rupture of IAs. Hypertension partially mediates the causal effects.
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Affiliation(s)
- Ying Wang
- Department of Neurosurgery, National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Kang Xie
- Department of Neurosurgery, National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Junyu Wang
- Department of Neurosurgery, National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Fenghua Chen
- Department of Neurosurgery, National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China; Research Center for Cerebrovascular Disease, Central South University, Changsha, 410008, China.
| | - Xi Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan, 410008, China.
| | - Longbo Zhang
- Departments of Neurosurgery, Changde Hospital, Xiangya School of Medicine, Central South University, 818 Renmin Street, Wuling District, Changde, Hunan 415003, China; Department of Neurosurgery, National Clinical Research Center of Geriatric Disorders, Research Center for Cerebrovascular Disease, Xiangya Hospital, Central South University, Changsha, 410008, China.
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Sayers I, John C, Chen J, Hall IP. Genetics of chronic respiratory disease. Nat Rev Genet 2024; 25:534-547. [PMID: 38448562 DOI: 10.1038/s41576-024-00695-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/08/2024]
Abstract
Chronic respiratory diseases, such as chronic obstructive pulmonary disease (COPD), asthma and interstitial lung diseases are frequently occurring disorders with a polygenic basis that account for a large global burden of morbidity and mortality. Recent large-scale genetic epidemiology studies have identified associations between genetic variation and individual respiratory diseases and linked specific genetic variants to quantitative traits related to lung function. These associations have improved our understanding of the genetic basis and mechanisms underlying common lung diseases. Moreover, examining the overlap between genetic associations of different respiratory conditions, along with evidence for gene-environment interactions, has yielded additional biological insights into affected molecular pathways. This genetic information could inform the assessment of respiratory disease risk and contribute to stratified treatment approaches.
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Affiliation(s)
- Ian Sayers
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, University Park, Nottingham, UK
- Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, UK
| | - Catherine John
- University of Leicester, Leicester, UK
- University Hospitals of Leicester, Leicester, UK
| | - Jing Chen
- University of Leicester, Leicester, UK
| | - Ian P Hall
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, University Park, Nottingham, UK.
- Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, UK.
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Pu KL, Kang H, Li L. Therapeutic targets for age-related macular degeneration: proteome-wide Mendelian randomization and colocalization analyses. Front Neurol 2024; 15:1400557. [PMID: 38903171 PMCID: PMC11187347 DOI: 10.3389/fneur.2024.1400557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/24/2024] [Indexed: 06/22/2024] Open
Abstract
Background Currently, effective therapeutic drugs for age-related macular degeneration (AMD) are urgently needed, and it is crucial to explore new treatment targets. The proteome is indispensable for exploring disease targets, so we conducted a Mendelian randomization (MR) of the proteome to identify new targets for AMD and its related subtypes. Methods The plasma protein level data used in this study were obtained from two large-scale studies of protein quantitative trait loci (pQTL), comprising 35,559 and 54,219 samples, respectively. The expression quantitative trait loci (eQTL) data were sourced from eQTLGen and GTEx Version 8. The discovery set for AMD data and subtypes was derived from the FinnGen study, consisting of 9,721 AMD cases and 381,339 controls, 5,239 wet AMD cases and 273,920 controls, and 6,651 dry AMD cases and 272,504 controls. The replication set for AMD data was obtained from the study by Winkler TW et al., comprising 14,034 cases and 91,234 controls. Summary Mendelian randomization (SMR) analysis was employed to assess the association between QTL data and AMD and its subtypes, while colocalization analysis was performed to determine whether they share causal variants. Additionally, chemical exploration and molecular docking were utilized to validate potential drugs targeting the identified proteins. Results SMR and colocalization analysis jointly identified risk-associated proteins for AMD and its subtypes, including 5 proteins (WARS1, BRD2, IL20RB, TGFB1, TNFRSF10A) associated with AMD, 2 proteins (WARS1, IL20RB) associated with Dry-AMD, and 9 proteins (COL10A1, WARS1, VTN, SDF2, LBP, CD226, TGFB1, TNFRSF10A, CSF2) associated with Wet-AMD. The results revealed potential therapeutic chemicals, and molecular docking indicated a good binding between the chemicals and protein structures. Conclusion Proteome-wide MR have identified risk-associated proteins for AMD and its subtypes, suggesting that these proteins may serve as potential therapeutic targets worthy of further clinical investigation.
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Affiliation(s)
- Kun-Lin Pu
- Pengzhou Hospital of Traditional Chinese Medicine, Chengdu, China
| | - Hong Kang
- Department of Thoracic Surgery, Sichuan Cancer Hospital, Chengdu, China
| | - Li Li
- Pengzhou Hospital of Traditional Chinese Medicine, Chengdu, China
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Chen Z, Gao N, Wang X, Chen X, Zeng Y, Li C, Yang X, Cai Q, Wang X. Shared genetic aetiology of respiratory diseases: a genome-wide multitraits association analysis. BMJ Open Respir Res 2024; 11:e002148. [PMID: 38834332 PMCID: PMC11163672 DOI: 10.1136/bmjresp-2023-002148] [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: 10/22/2023] [Accepted: 05/10/2024] [Indexed: 06/06/2024] Open
Abstract
OBJECTIVE This study aims to explore the common genetic basis between respiratory diseases and to identify shared molecular and biological mechanisms. METHODS This genome-wide pleiotropic association study uses multiple statistical methods to systematically analyse the shared genetic basis between five respiratory diseases (asthma, chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, lung cancer and snoring) using the largest publicly available genome wide association studies summary statistics. The missions of this study are to evaluate global and local genetic correlations, to identify pleiotropic loci, to elucidate biological pathways at the multiomics level and to explore causal relationships between respiratory diseases. Data were collected from 27 November 2022 to 30 March 2023 and analysed from 14 April 2023 to 13 July 2023. MAIN OUTCOMES AND MEASURES The primary outcomes are shared genetic loci, pleiotropic genes, biological pathways and estimates of genetic correlations and causal effects. RESULTS Significant genetic correlations were found for 10 paired traits in 5 respiratory diseases. Cross-Phenotype Association identified 12 400 significant potential pleiotropic single-nucleotide polymorphism at 156 independent pleiotropic loci. In addition, multitrait colocalisation analysis identified 15 colocalised loci and a subset of colocalised traits. Gene-based analyses identified 432 potential pleiotropic genes and were further validated at the transcriptome and protein levels. Both pathway enrichment and single-cell enrichment analyses supported the role of the immune system in respiratory diseases. Additionally, five pairs of respiratory diseases have a causal relationship. CONCLUSIONS AND RELEVANCE This study reveals the common genetic basis and pleiotropic genes among respiratory diseases. It provides strong evidence for further therapeutic strategies and risk prediction for the phenomenon of respiratory disease comorbidity.
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Affiliation(s)
- Zhe Chen
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University Department of Thoracic Surgery, Changsha, Hunan, China
| | - Ning Gao
- Department of Cardiovascular Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xuanye Wang
- Department of Oncology, Xi'an Jiaotong University Second Affiliated Hospital Department of Oncology, Xi'an, Shaanxi, China
| | - Xiangming Chen
- Department of Orthopaedics, Xiangya Hospital Central South University, Changsha, Hunan, China
| | - YaQi Zeng
- Department of Psychiatry, Brain Hospital of Hunan Province, Changsha, Hunan, China
| | - Cong Li
- Department of Radiology, The Second Xiangya Hospital of Central South University Department of Radiology, Changsha, Hunan, China
| | - Xiahong Yang
- Department of Anesthesiology, The Second Xiangya Hospital of Central South University Department of Anesthesiology, Changsha, Hunan, China
| | - Qidong Cai
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University Department of Thoracic Surgery, Changsha, Hunan, China
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University Department of Thoracic Surgery, Changsha, Hunan, China
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Wang Q, Song YX, Wu XD, Luo YG, Miao R, Yu XM, Guo X, Wu DZ, Bao R, Mi WD, Cao JB. Gut microbiota and cognitive performance: A bidirectional two-sample Mendelian randomization. J Affect Disord 2024; 353:38-47. [PMID: 38417715 DOI: 10.1016/j.jad.2024.02.083] [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: 08/21/2023] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 03/01/2024]
Abstract
PURPOSE Previous studies have suggested a potential association between gut microbiota and neurological and psychiatric disorders. However, the causal relationship between gut microbiota and cognitive performance remains uncertain. METHODS A two-sample Mendelian randomization (MR) study used SNPs linked to gut microbiota (n = 18,340) and cognitive performance (n = 257,841) from recent GWAS data. Inverse-variance weighted (IVW), MR Egger, weighted median, simple mode, and weighted mode were employed. Heterogeneity was assessed via Cochran's Q test for IVW. Results were shown with funnel plots. Outliers were detected through leave-one-out method. MR-PRESSO and MR-Egger intercept tests were conducted to address horizontal pleiotropy influence. LIMITATIONS Limited to European populations, generic level, and potential confounding factors. RESULTS IVW analysis revealed detrimental effects on cognitive perfmance associated with the presence of genus Blautia (P = 0.013, 0.966[0.940-0.993]), Catenibacterium (P = 0.035, 0.977[0.956-0.998]), Oxalobacter (P = 0.043, 0.979[0.960-0.999]). Roseburia (P < 0.001, 0.935[0.906-0.965]), in particular, remained strongly negatively associated with cognitive performance after Bonferroni correction. Conversely, families including Bacteroidaceae (P = 0.043, 1.040[1.001-1.081]), Rikenellaceae (P = 0.047, 1.026[1.000-1.053]), along with genera including Paraprevotella (P = 0.044, 1.020[1.001-1.039]), Ruminococcus torques group (P = 0.016, 1.062[1.011-1.115]), Bacteroides (P = 0.043, 1.040[1.001-1.081]), Dialister (P = 0.027, 1.039[1.004-1.074]), Paraprevotella (P = 0.044, 1.020[1.001-1.039]) and Ruminococcaceae UCG003 (P = 0.007, 1.040[1.011-1.070]) had a protective effect on cognitive performance. CONCLUSIONS Our results suggest that interventions targeting specific gut microbiota may offer a promising avenue for improving cognitive function in diseased populations. The practical application of these findings has the potential to enhance cognitive performance, thereby improving overall quality of life.
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Affiliation(s)
- Qian Wang
- Department of Anesthesiology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China; Medical School of Chinese People's Liberation Army, Beijing 100853, China
| | - Yu-Xiang Song
- Department of Anesthesiology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Xiao-Dong Wu
- Department of Anesthesiology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Yun-Gen Luo
- Department of Anesthesiology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China; Medical School of Chinese People's Liberation Army, Beijing 100853, China
| | - Ran Miao
- Department of Anesthesiology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Xiao-Meng Yu
- Department of Anesthesiology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Xu Guo
- Department of Anesthesiology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - De-Zhen Wu
- Department of Anesthesiology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Rui Bao
- Department of Anesthesiology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Wei-Dong Mi
- Department of Anesthesiology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Jiang-Bei Cao
- Department of Anesthesiology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China.
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Lu T, Chen Y, Yoshiji S, Ilboudo Y, Forgetta V, Zhou S, Greenwood CMT. Circulating Metabolite Abundances Associated With Risks of Bipolar Disorder, Schizophrenia, and Depression: A Mendelian Randomization Study. Biol Psychiatry 2024:S0006-3223(24)01285-X. [PMID: 38705554 DOI: 10.1016/j.biopsych.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND Preventive measures and treatments for psychiatric disorders are limited. Circulating metabolites are potential candidates for biomarker and therapeutic target identification, given their measurability and essential roles in biological processes. METHODS Leveraging large-scale genome-wide association studies, we conducted Mendelian randomization analyses to assess the associations between circulating metabolite abundances and the risks of bipolar disorder, schizophrenia, and depression. Genetic instruments were selected for 94 metabolites measured in the Canadian Longitudinal Study on Aging cohort (N = 8299). We repeated Mendelian randomization analyses based on the UK Biobank, INTERVAL, and EPIC (European Prospective Investigation into Cancer)-Norfolk studies. RESULTS After validating Mendelian randomization assumptions and colocalization evidence, we found that a 1 SD increase in genetically predicted circulating abundances of eicosapentaenoate and docosapentaenoate was associated with odds ratios of 0.72 (95% CI, 0.65-0.79) and 0.63 (95% CI, 0.55-0.72), respectively, for bipolar disorder. Genetically increased Ω-3 unsaturated fatty acids abundance and Ω-3-to-total fatty acids ratio, as well as genetically decreased Ω-6-to-Ω-3 ratio, were negatively associated with the risk of bipolar disorder in the UK Biobank. Genetically increased circulating abundances of 3 N-acetyl-amino acids were associated with an increased risk of schizophrenia with a maximum odds ratio of 1.31 (95% CI, 1.18-1.44) per 1 SD increase. Furthermore, a 1 SD increase in genetically predicted circulating abundance of hypotaurine was associated with an odds ratio of 0.85 (95% CI, 0.78-0.93) for depression. CONCLUSIONS The biological mechanisms that underlie Ω-3 unsaturated fatty acids, NAT8-catalyzed N-acetyl-amino acids, and hypotaurine warrant exploration to identify new biomarkers and potential therapeutic targets.
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Affiliation(s)
- Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada; Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada.
| | - Yiheng Chen
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada; Five Prime Sciences Inc., Montréal, Québec, Canada; Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Satoshi Yoshiji
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada; Department of Human Genetics, McGill University, Montréal, Québec, Canada; Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Japan Society for the Promotion of Science, Tokyo, Japan
| | - Yann Ilboudo
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | | | - Sirui Zhou
- Department of Human Genetics, McGill University, Montréal, Québec, Canada; McGill Genome Centre, McGill University, Montréal, Québec, Canada
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada; Department of Human Genetics, McGill University, Montréal, Québec, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada; Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada.
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Zhang W, Lu T, Sladek R, Li Y, Najafabadi H, Dupuis J. SharePro: an accurate and efficient genetic colocalization method accounting for multiple causal signals. Bioinformatics 2024; 40:btae295. [PMID: 38688586 PMCID: PMC11105950 DOI: 10.1093/bioinformatics/btae295] [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: 07/24/2023] [Revised: 04/11/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024] Open
Abstract
MOTIVATION Colocalization analysis is commonly used to assess whether two or more traits share the same genetic signals identified in genome-wide association studies (GWAS), and is important for prioritizing targets for functional follow-up of GWAS results. Existing colocalization methods can have suboptimal performance when there are multiple causal variants in one genomic locus. RESULTS We propose SharePro to extend the COLOC framework for colocalization analysis. SharePro integrates linkage disequilibrium (LD) modeling and colocalization assessment by grouping correlated variants into effect groups. With an efficient variational inference algorithm, posterior colocalization probabilities can be accurately estimated. In simulation studies, SharePro demonstrated increased power with a well-controlled false positive rate at a low computational cost. Compared to existing methods, SharePro provided stronger and more consistent colocalization evidence for known lipid-lowering drug target proteins and their corresponding lipid traits. Through an additional challenging case of the colocalization analysis of the circulating abundance of R-spondin 3 GWAS and estimated bone mineral density GWAS, we demonstrated the utility of SharePro in identifying biologically plausible colocalized signals. AVAILABILITY AND IMPLEMENTATION SharePro for colocalization analysis is written in Python and openly available at https://github.com/zhwm/SharePro_coloc.
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Affiliation(s)
- Wenmin Zhang
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec H3A 1E3, Canada
- Montreal Heart Institute, Université de Montréal, Montreal, Quebec H1T 1C8, Canada
| | - Tianyuan Lu
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Robert Sladek
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec H3A 1E3, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada
- Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Yue Li
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec H3A 1E3, Canada
- School of Computer Science, McGill University, Montreal, Quebec H3A 2A7, Canada
| | - Hamed Najafabadi
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec H3A 1E3, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada
- Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Josée Dupuis
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec H3A 1E3, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, McGill College, QC H3A 1Y7, Canada
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Sharma P, Klarin D, Voight BF, Tsao PS, Levin MG, Damrauer SM. Evaluation of Plasma Biomarkers for Causal Association With Peripheral Artery Disease. Arterioscler Thromb Vasc Biol 2024; 44:1114-1123. [PMID: 38545784 PMCID: PMC11043009 DOI: 10.1161/atvbaha.124.320674] [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: 01/04/2024] [Accepted: 03/14/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Hundreds of biomarkers for peripheral artery disease (PAD) have been reported in the literature; however, the observational nature of these studies limits causal inference due to the potential of reverse causality and residual confounding. We sought to evaluate the potential causal impact of putative PAD biomarkers identified in human observational studies through genetic causal inference methods. METHODS Putative circulating PAD biomarkers were identified from human observational studies through a comprehensive literature search based on terms related to PAD using PubMed, Cochrane, and Embase. Genetic instruments were generated from publicly available genome-wide association studies of circulating biomarkers. Two-sample Mendelian randomization was used to test the association of genetically determined biomarker levels with PAD using summary statistics from a genome-wide association study of 31 307 individuals with and 211 753 individuals without PAD in the Veterans Affairs Million Veteran Program and replicated in data from FinnGen comprised of 11 924 individuals with and 288 638 individuals without PAD. RESULTS We identified 204 unique circulating biomarkers for PAD from the observational literature, of which 173 were genetically instrumented using genome-wide association study results. After accounting for multiple testing (false discovery rate, <0.05), 10 of 173 (5.8%) biomarkers had significant associations with PAD. These 10 biomarkers represented categories including plasma lipoprotein regulation, lipid homeostasis, and protein-lipid complex remodeling. Observational literature highlighted different pathways including inflammatory response, negative regulation of multicellular organismal processes, and regulation of response to external stimuli. CONCLUSIONS Integrating human observational studies and genetic causal inference highlights several key pathways in PAD pathophysiology. This work demonstrates that a substantial portion of biomarkers identified in observational studies are not well supported by human genetic evidence and emphasizes the importance of triangulating evidence to understand PAD pathophysiology. Although the identified biomarkers offer insights into atherosclerotic development in the lower limb, their specificity to PAD compared with more widespread atherosclerosis requires further study.
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Affiliation(s)
- Pranav Sharma
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Derek Klarin
- Veterans Affairs Palo Alto Healthcare System, CA
- Division of Vascular Surgery, Stanford University School of Medicine, CA
| | - Benjamin F. Voight
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, United States
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, United States
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, United State
| | - Philip S. Tsao
- Veterans Affairs Palo Alto Healthcare System, CA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, CA
| | - Michael G. Levin
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, United States
- Division of Cardiovascular Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Scott M. Damrauer
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, United States
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, United States
- Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, United States
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10
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Luo J, Shi L, Liu J, Li G, Tu L, Hu S. SGLT2 inhibition, plasma proteins, and heart failure: a proteome-wide Mendelian Randomization and colocalization study. Front Cardiovasc Med 2024; 11:1371513. [PMID: 38725835 PMCID: PMC11079590 DOI: 10.3389/fcvm.2024.1371513] [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: 01/16/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Objective To investigate the causal contributions of Sodium-glucose cotransporter 2 (SGLT2) inhibition on Heart Failure (HF) and identify the circulating proteins that mediate SGLT2 inhibition's effects on HF. Methods Applying a two-sample, two-step Mendelian Randomization (MR) analysis, we aimed to estimate: (1) the causal impact of SGLT2 inhibition on HF; (2) the causal correlation of SGLT2 inhibition on 4,907 circulating proteins; (3) the causal association of SGLT2 inhibition-driven plasma proteins on HF. Genetic variants linked to SGLT2 inhibition derived from the previous studies. The 4,907 circulating proteins were derived from the deCODE study. Genetic links to HF were obtained through the Heart Failure Molecular Epidemiology for Therapeutic Targets (HERMES) consortium. Results SGLT2 inhibition demonstrated a lower risk of HF (odds ratio [OR] = 0.44, 95% CI [0.26, 0.76], P = 0.003). Among 4,907 circulating proteins, we identified leucine rich repeat transmembrane protein 2 (LRRTM2), which was related to both SGLT2 inhibition and HF. Mediation analysis revealed that the impact of SGLT2 inhibition on HF operates indirectly through LRRTM2 [β = -0.20, 95% CI (-0.39, -0.06), P = 0.02] with a mediation proportion of 24.6%. Colocalization analysis provided support for the connections between LRRTM2 and HF. Conclusion The study indicated a causative link between SGLT2 inhibition and HF, with plasma LRRTM2 potentially serving as a mediator.
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Affiliation(s)
- Jinlan Luo
- Department of Geriatric Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
| | - Lili Shi
- Department of Geriatric Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
| | - Jingrui Liu
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
- Division of Cardiology and Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gen Li
- Department of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ling Tu
- Department of Geriatric Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
| | - Shuiqing Hu
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
- Division of Cardiology and Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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11
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Wang J, Wang Y, Ou Q, Yang S, Jing J, Fang J. Computer gaming alters resting-state brain networks, enhancing cognitive and fluid intelligence in players: evidence from brain imaging-derived phenotypes-wide Mendelian randomization. Cereb Cortex 2024; 34:bhae061. [PMID: 38436466 DOI: 10.1093/cercor/bhae061] [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: 01/19/2024] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 03/05/2024] Open
Abstract
The debate on whether computer gaming enhances players' cognitive function is an ongoing and contentious issue. Aiming to delve into the potential impacts of computer gaming on the players' cognitive function, we embarked on a brain imaging-derived phenotypes (IDPs)-wide Mendelian randomization (MR) study, utilizing publicly available data from a European population. Our findings indicate that computer gaming has a positive impact on fluid intelligence (odds ratio [OR] = 6.264, P = 4.361 × 10-10, 95% confidence interval [CI] 3.520-11.147) and cognitive function (OR = 3.322, P = 0.002, 95% CI 1.563-7.062). Out of the 3062 brain IDPs analyzed, only one phenotype, IDP NET100 0378, was significantly influenced by computer gaming (OR = 4.697, P = 1.10 × 10-5, 95% CI 2.357-9.361). Further MR analysis suggested that alterations in the IDP NET100 0378 caused by computer gaming may be a potential factor affecting fluid intelligence (OR = 1.076, P = 0.041, 95% CI 1.003-1.153). Our MR study lends support to the notion that computer gaming can facilitate the development of players' fluid intelligence by enhancing the connectivity between the motor cortex in the resting-state brain and key regions such as the left dorsolateral prefrontal cortex and the language center.
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Affiliation(s)
- Jiadong Wang
- Department of Clinical Medicine, Hangzhou City University School of Medicine, 50 Huzhou Street, Hangzhou 310015, China
| | - Yu Wang
- Department of Clinical Medicine, The Second Clinical Medical College, Zhejiang Chinese Medical University, 548 Binwen Street, Hangzhou 310053, China
| | - Qian Ou
- Department of Basic Medical Sciences, Zhejiang University School of Medicine, 866 Yvhangtang Street, Hangzhou 310018, China
| | - Sengze Yang
- School of Economics and Management, Harbin University of Science and Technology, 4 Linyuan Street, Harbin 150080, China
| | - Jiajie Jing
- Department of Clinical Medicine, Hangzhou City University School of Medicine, 50 Huzhou Street, Hangzhou 310015, China
| | - Jiaqi Fang
- Department of Clinical Medicine, Hangzhou City University School of Medicine, 50 Huzhou Street, Hangzhou 310015, China
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12
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Li M, Zhao R, Dang X, Xu X, Chen R, Chen Y, Zhang Y, Zhao Z, Wu D. Causal Relationships Between Screen Use, Reading, and Brain Development in Early Adolescents. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307540. [PMID: 38165022 PMCID: PMC10953555 DOI: 10.1002/advs.202307540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/11/2023] [Indexed: 01/03/2024]
Abstract
The rise of new media has greatly changed the lifestyles, leading to increased time on these platforms and less time spent reading. This shift has particularly profound impacts on early adolescents, who are in a critical stage of brain development. Previous studies have found associations between screen use and mental health, but it remains unclear whether screen use is the direct cause of the outcomes. Here, the Adolescent Brain Cognitive Development (ABCD) dataset is utlized to examine the causal relationships between screen use and brain development. The results revealed adverse causal effects of screen use on language ability and specific behaviors in early adolescents, while reading has positive causal effects on their language ability and brain volume in the frontal and temporal regions. Interestingly, increased screen use is identified as a result, rather than a cause, of certain behaviors such as rule-breaking and aggressive behaviors. Furthermore, the analysis uncovered an indirect influence of screen use, mediated by changes in reading habits, on brain development. These findings provide new evidence for the causal influences of screen use on brain development and highlight the importance of monitoring media use and related habit change in children.
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Affiliation(s)
- Mingyang Li
- Key Laboratory for Biomedical Engineering of Ministry of EducationDepartment of Biomedical EngineeringCollege of Biomedical Engineering & Instrument ScienceZhejiang UniversityYuquan CampusHangzhou310027China
| | - Ruoke Zhao
- Key Laboratory for Biomedical Engineering of Ministry of EducationDepartment of Biomedical EngineeringCollege of Biomedical Engineering & Instrument ScienceZhejiang UniversityYuquan CampusHangzhou310027China
| | - Xixi Dang
- Department of PsychologyHangzhou Normal UniversityHangzhouChina
| | - Xinyi Xu
- Key Laboratory for Biomedical Engineering of Ministry of EducationDepartment of Biomedical EngineeringCollege of Biomedical Engineering & Instrument ScienceZhejiang UniversityYuquan CampusHangzhou310027China
| | - Ruike Chen
- Key Laboratory for Biomedical Engineering of Ministry of EducationDepartment of Biomedical EngineeringCollege of Biomedical Engineering & Instrument ScienceZhejiang UniversityYuquan CampusHangzhou310027China
| | - Yiwei Chen
- Key Laboratory for Biomedical Engineering of Ministry of EducationDepartment of Biomedical EngineeringCollege of Biomedical Engineering & Instrument ScienceZhejiang UniversityYuquan CampusHangzhou310027China
| | - Yuqi Zhang
- Key Laboratory for Biomedical Engineering of Ministry of EducationDepartment of Biomedical EngineeringCollege of Biomedical Engineering & Instrument ScienceZhejiang UniversityYuquan CampusHangzhou310027China
| | - Zhiyong Zhao
- Key Laboratory for Biomedical Engineering of Ministry of EducationDepartment of Biomedical EngineeringCollege of Biomedical Engineering & Instrument ScienceZhejiang UniversityYuquan CampusHangzhou310027China
| | - Dan Wu
- Key Laboratory for Biomedical Engineering of Ministry of EducationDepartment of Biomedical EngineeringCollege of Biomedical Engineering & Instrument ScienceZhejiang UniversityYuquan CampusHangzhou310027China
- Children's HospitalZhejiang University School of MedicineNational Clinical Research Center for Child HealthHangzhouChina
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13
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Li S, Gong M. Drug targets for haemorrhoidal disease: proteome-wide Mendelian randomisation and colocalisation analyses. Gut 2024:gutjnl-2023-330967. [PMID: 38316540 DOI: 10.1136/gutjnl-2023-330967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/25/2024] [Indexed: 02/07/2024]
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14
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Chen J, Ruan X, Sun Y, Lu S, Hu S, Yuan S, Li X. Multi-omic insight into the molecular networks of mitochondrial dysfunction in the pathogenesis of inflammatory bowel disease. EBioMedicine 2024; 99:104934. [PMID: 38103512 PMCID: PMC10765009 DOI: 10.1016/j.ebiom.2023.104934] [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: 09/17/2023] [Revised: 11/15/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Mitochondrial dysfunction has been linked to the development of inflammatory bowel disease (IBD), but the genetic pathophysiology was not fully elucidated. We employed Mendelian randomization and colocalization analyses to investigate the associations between mitochondrial-related genes and IBD via integrating multi-omics. METHODS Summary-level data of mitochondrial gene methylation, expression and protein abundance levels were obtained from corresponding methylation, expression and protein quantitative trait loci studies, respectively. We obtained genetic associations with IBD and its two subtypes from the Inflammatory Bowel Disease Genetics Consortium (discovery), the UK Biobank (replication), and the FinnGen study (replication). We performed summary-data-based Mendelian randomization analysis to assess the associations of mitochondrial gene-related molecular features with IBD. Colocalization analysis was further conducted to assess whether the identified signal pairs shared a causal genetic variant. FINDINGS After integrating the multi-omics data between mQTL-eQTL and eQTL-pQTL, we identified two mitochondrial genes, i.e., PARK7 and ACADM, with tier 1 evidence for their associations with IBD and ulcerative colitis (UC). PDK1 and FISI genes were associated with UC risk with tier 2 and tier 3 evidence, respectively. The methylation of cg05467918 in ACADM was associated with lower expression of ACADM, which fits with the positive effect of cg05467918 methylation on UC risk. Consistently, the inverse associations between gene methylation and gene expression were also observed in PARK7 (cg10385390) and PDK1 (cg17679246), which were corroborated with the protective role in UC. At circulating protein level, genetically predicted higher levels of PARK7 (OR 0.36, 95% CI 0.25-0.52) and HINT1 (OR 0.47, 95% CI 0.30-0.74) were inversely associated with IBD risk; genetically predicted higher level of HINT1 was associated with a decreased risk of Crohn's disease (CD) (OR 0.26, 95% CI 0.14-0.49) and a higher level of ACADM (OR 0.67, 95% CI 0.55-0.83), PDK1 (OR 0.63, 95% CI 0.49-0.81), FIS1 (OR 0.63, 95% CI 0.47-0.83) was associated with a decreased risk of UC. INTERPRETATION We found that the mitochondrial PARK7 gene was putatively associated with IBD risk, and mitochondrial FIS1, PDK1, and ACADM genes were associated with UC risk with evidence from multi-omics levels. This study identified mitochondrial genes in relation to IBD, which may enhance the understanding of the pathogenic mechanisms of IBD development. FUNDING XL is supported by the Natural Science Fund for Distinguished Young Scholars of Zhejiang Province (LR22H260001) and Healthy Zhejiang One Million People Cohort (K-20230085).
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Affiliation(s)
- Jie Chen
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xixian Ruan
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yuhao Sun
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Shiyuan Lu
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Shixian Hu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China; Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China.
| | - Shuai Yuan
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Xue Li
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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Yang F, Xu F, Zhang H, Gill D, Larsson SC, Li X, Cui H, Yuan S. Proteomic insights into the associations between obesity, lifestyle factors, and coronary artery disease. BMC Med 2023; 21:485. [PMID: 38049831 PMCID: PMC10696760 DOI: 10.1186/s12916-023-03197-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/27/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND We aimed to investigate the protein pathways linking obesity and lifestyle factors to coronary artery disease (CAD). METHODS Summary-level genome-wide association statistics of CAD were obtained from the CARDIoGRAMplusC4D consortium (60,801 cases and 123,504 controls) and the FinnGen study (R8, 39,036 cases and 303,463 controls). Proteome-wide Mendelian randomization (MR) analysis was conducted to identify CAD-associated blood proteins, supplemented by colocalization analysis to minimize potential bias caused by linkage disequilibrium. Two-sample MR analyses were performed to assess the associations of genetically predicted four obesity measures and 13 lifestyle factors with CAD risk and CAD-associated proteins' levels. A two-step network MR analysis was conducted to explore the mediating effects of proteins in the associations between these modifiable factors and CAD. RESULTS Genetically predicted levels of 41 circulating proteins were associated with CAD, and 17 of them were supported by medium to high colocalization evidence. PTK7 (protein tyrosine kinase-7), RGMB (repulsive guidance molecule BMP co-receptor B), TAGLN2 (transgelin-2), TIMP3 (tissue inhibitor of metalloproteinases 3), and VIM (vimentin) were identified as promising therapeutic targets. Several proteins were found to mediate the associations between some modifiable factors and CAD, with PCSK9, C1S, AGER (advanced glycosylation end product-specific receptor), and MST1 (mammalian Ste20-like kinase 1) exhibiting highest frequency among the mediating networks. CONCLUSIONS This study suggests pathways explaining the associations of obesity and lifestyle factors with CAD from alterations in blood protein levels. These insights may be used to prioritize therapeutic intervention for further study.
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Affiliation(s)
- Fangkun Yang
- Department of Cardiology, First Affiliated Hospital of Ningbo University (Ningbo First Hospital), School of Medicine, Ningbo University, 59 Liuting Road, Ningbo, 315010, China
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, China
- Cardiovascular Disease Clinical Medical Research Center of Ningbo, Ningbo, Zhejiang, China
| | - Fengzhe Xu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Han Zhang
- Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Susanna C Larsson
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Unit of Medical Epidemiology, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Xue Li
- Department of Big Data in Health Science School of Public Health, Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Hanbin Cui
- Department of Cardiology, First Affiliated Hospital of Ningbo University (Ningbo First Hospital), School of Medicine, Ningbo University, 59 Liuting Road, Ningbo, 315010, China.
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, China.
- Cardiovascular Disease Clinical Medical Research Center of Ningbo, Ningbo, Zhejiang, China.
| | - Shuai Yuan
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
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16
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Li X, Lu Z, Qi Y, Chen B, Li B. The Role of Polyunsaturated Fatty Acids in Osteoarthritis: Insights from a Mendelian Randomization Study. Nutrients 2023; 15:4787. [PMID: 38004181 PMCID: PMC10674676 DOI: 10.3390/nu15224787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/04/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
The prior observational research on the impact of polyunsaturated fatty acid (PUFA) supplementation on osteoarthritis (OA) patients had yielded inclusive outcomes. This study utilized the Mendelian randomization (MR) approach to explore potential causal relationships between PUFAs and OA. The MR study was performed using GWAS summary statistics for PUFAs, encompassing omega-3 and omega-6 fatty acids, and for knee OA (KOA) and hip OA (HOA). The primary inverse-variance-weighted (IVW) method and two supplementary MR approaches were used to establish robust causality. Heterogeneity and horizontal pleiotropy were assessed using Cochrane's Q and MR-Egger intercept tests. Additionally, a range of sensitivity analyses were conducted to strengthen the precision and reliability of the results. The IVW method indicated a potential genetic association between omega-3 fatty acids and KOA risk (odd ratio (OR) = 0.94, 95% confidence interval (CI): 0.89-1.00, p = 0.048). No significant correlation was found between omega-3 levels and HOA. Moreover, genetically predicted higher levels of omega-6 fatty acids were associated with a decreased risk of KOA (OR = 0. 93, 95% CI: 0.86-1.00, p = 0.041) and HOA (OR = 0.89, 95% CI: 0.82-0.96; p = 0.003). The MR-Egger intercept evaluation showed no horizontal pleiotropy affecting the MR analysis (all p > 0.05). Our findings supported the causal relationship between PUFAs and OA susceptibility and offered a novel insight that high omega-6 fatty acids may reduce the risk of KOA and HOA. These results underscore the importance of maintaining optimal levels of PUFAs, particularly omega-6 fatty acids, in individuals with a genetic predisposition to OA. Future research is necessary to validate these findings and elucidate the underlying mechanisms involved.
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Affiliation(s)
- Xuefei Li
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China;
| | - Zhengjie Lu
- Division of Joint Surgery and Sports Medicine, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China (B.C.)
| | - Yongjian Qi
- Department of Spine Surgery and Musculoskeletal Tumor, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Biao Chen
- Division of Joint Surgery and Sports Medicine, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China (B.C.)
| | - Bin Li
- Division of Joint Surgery and Sports Medicine, Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China (B.C.)
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Nakanishi T, Willett J, Farjoun Y, Allen RJ, Guillen-Guio B, Adra D, Zhou S, Richards JB. Alternative splicing in lung influences COVID-19 severity and respiratory diseases. Nat Commun 2023; 14:6198. [PMID: 37794074 PMCID: PMC10550956 DOI: 10.1038/s41467-023-41912-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
Alternative splicing generates functional diversity in isoforms, impacting immune response to infection. Here, we evaluate the causal role of alternative splicing in COVID-19 severity and susceptibility by applying two-sample Mendelian randomization to cis-splicing quantitative trait loci and the results from COVID-19 Host Genetics Initiative. We identify that alternative splicing in lung, rather than total expression of OAS1, ATP11A, DPP9 and NPNT, is associated with COVID-19 severity. MUC1 and PMF1 splicing is associated with COVID-19 susceptibility. Colocalization analyses support a shared genetic mechanism between COVID-19 severity with idiopathic pulmonary fibrosis at the ATP11A and DPP9 loci, and with chronic obstructive lung diseases at the NPNT locus. Last, we show that ATP11A, DPP9, NPNT, and MUC1 are highly expressed in lung alveolar epithelial cells, both in COVID-19 uninfected and infected samples. These findings clarify the importance of alternative splicing in lung for COVID-19 and respiratory diseases, providing isoform-based targets for drug discovery.
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Affiliation(s)
- Tomoko Nakanishi
- Department of Human Genetics, McGill University, Montréal, QC, Canada.
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada.
- Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
- Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.
- Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan.
| | - Julian Willett
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Yossi Farjoun
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Five Prime Sciences Inc, Montréal, QC, Canada
| | - Richard J Allen
- Department of Population Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Darin Adra
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Sirui Zhou
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada.
- Five Prime Sciences Inc, Montréal, QC, Canada.
- Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montréal, QC, Canada.
- Department of Twin Research, King's College London, London, UK.
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Willett JDS, Lu T, Nakanishi T, Yoshiji S, Butler-Laporte G, Zhou S, Farjoun Y, Richards JB. Colocalization of expression transcripts with COVID-19 outcomes is rare across cell states, cell types and organs. Hum Genet 2023; 142:1461-1476. [PMID: 37640912 PMCID: PMC10511363 DOI: 10.1007/s00439-023-02590-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 06/30/2023] [Indexed: 08/31/2023]
Abstract
Identifying causal genes at GWAS loci can help pinpoint targets for therapeutic interventions. Expression studies can disentangle such loci but signals from expression quantitative trait loci (eQTLs) often fail to colocalize-which means that the genetic control of measured expression is not shared with the genetic control of disease risk. This may be because gene expression is measured in the wrong cell type, physiological state, or organ. We tested whether Mendelian randomization (MR) could identify genes at loci influencing COVID-19 outcomes and whether the colocalization of genetic control of expression and COVID-19 outcomes was influenced by cell type, cell stimulation, and organ. We conducted MR of cis-eQTLs from single cell (scRNA-seq) and bulk RNA sequencing. We then tested variables that could influence colocalization, including cell type, cell stimulation, RNA sequencing modality, organ, symptoms of COVID-19, and SARS-CoV-2 status among individuals with symptoms of COVID-19. The outcomes used to test colocalization were COVID-19 severity and susceptibility as assessed in the Host Genetics Initiative release 7. Most transcripts identified using MR did not colocalize when tested across cell types, cell state and in different organs. Most that did colocalize likely represented false positives due to linkage disequilibrium. In general, colocalization was highly variable and at times inconsistent for the same transcript across cell type, cell stimulation and organ. While we identified factors that influenced colocalization for select transcripts, identifying 33 that mediate COVID-19 outcomes, our study suggests that colocalization of expression with COVID-19 outcomes is partially due to noisy signals even after following quality control and sensitivity testing. These findings illustrate the present difficulty of linking expression transcripts to disease outcomes and the need for skepticism when observing eQTL MR results, even accounting for cell types, stimulation state and different organs.
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Affiliation(s)
- Julian Daniel Sunday Willett
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- McGill University, Montreal, QC, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, QC, Canada
- Genome Centre, McGill University, Montreal, QC, Canada
| | - Tianyuan Lu
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- McGill University, Montreal, QC, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, QC, Canada
- Genome Centre, McGill University, Montreal, QC, Canada
| | - Tomoko Nakanishi
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Graduate School of Medicine, Kyoto-McGill International Collaborative Program in Genomic Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
- Genome Centre, McGill University, Montreal, QC, Canada
| | - Satoshi Yoshiji
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Graduate School of Medicine, Kyoto-McGill International Collaborative Program in Genomic Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
- Genome Centre, McGill University, Montreal, QC, Canada
| | - Guillaume Butler-Laporte
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
| | - Sirui Zhou
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- McGill University, Montreal, QC, Canada
- Genome Centre, McGill University, Montreal, QC, Canada
| | - Yossi Farjoun
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- Genome Centre, McGill University, Montreal, QC, Canada
| | - J Brent Richards
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada.
- McGill University, Montreal, QC, Canada.
- Genome Centre, McGill University, Montreal, QC, Canada.
- Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montréal, QC, Canada.
- Department of Twin Research, King's College London, London, UK.
- Five Prime Sciences Inc, Montréal, Québec, Canada.
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19
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Trajanoska K, Bhérer C, Taliun D, Zhou S, Richards JB, Mooser V. From target discovery to clinical drug development with human genetics. Nature 2023; 620:737-745. [PMID: 37612393 DOI: 10.1038/s41586-023-06388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/29/2023] [Indexed: 08/25/2023]
Abstract
The substantial investments in human genetics and genomics made over the past three decades were anticipated to result in many innovative therapies. Here we investigate the extent to which these expectations have been met, excluding cancer treatments. In our search, we identified 40 germline genetic observations that led directly to new targets and subsequently to novel approved therapies for 36 rare and 4 common conditions. The median time between genetic target discovery and drug approval was 25 years. Most of the genetically driven therapies for rare diseases compensate for disease-causing loss-of-function mutations. The therapies approved for common conditions are all inhibitors designed to pharmacologically mimic the natural, disease-protective effects of rare loss-of-function variants. Large biobank-based genetic studies have the power to identify and validate a large number of new drug targets. Genetics can also assist in the clinical development phase of drugs-for example, by selecting individuals who are most likely to respond to investigational therapies. This approach to drug development requires investments into large, diverse cohorts of deeply phenotyped individuals with appropriate consent for genetically assisted trials. A robust framework that facilitates responsible, sustainable benefit sharing will be required to capture the full potential of human genetics and genomics and bring effective and safe innovative therapies to patients quickly.
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Affiliation(s)
- Katerina Trajanoska
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Claude Bhérer
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Daniel Taliun
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Sirui Zhou
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
- Department of Epidemiology and Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Vincent Mooser
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada.
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Song H, Lei N, Zeng L, Li X, Li X, Liu Y, Liu J, Wu W, Mu J, Feng Q. Genetic predisposition to subjective well-being, depression, and suicide in relation to COVID-19 susceptibility and severity. J Affect Disord 2023; 335:233-238. [PMID: 37178830 PMCID: PMC10174343 DOI: 10.1016/j.jad.2023.05.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/27/2023] [Accepted: 05/06/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Epidemiological studies have reported associations between subjective well-being (SWB), depression, and suicide with COVID-19 illness, but the causality has not been established. We performed a two-sample Mendelian randomization (MR) analysis to investigate the causal link between SWB, depression, suicide and COVID-19 susceptibility and severity. METHODS Summary statistics for SWB (298,420 cases), depression (113,769 cases) and suicide (52,208 cases) were obtained from three large-scale GWAS. Data on the associations between the Single Nucleotide Polymorphisms (SNPs) and COVID-19 (159,840 cases), hospitalized COVID-19 (44,986 cases), and severe COVID-19 (18,152 cases) were collected from the COVID-19 host genetics initiative. The causal estimate was calculated by the Inverse Variance Weighted, MR Egger and Weighted Median methods. Sensitivity tests were used to evaluate the validity of the causal relationship. RESULTS Our results showed that genetically predicted SWB (OR = 0.98, 95 % CI: 0.86-1.10, P = 0.69), depression (OR = 0.76, 95 % CI: 0.54-1.06, P = 0.11), and suicide (OR = 0.99, 95 % CI: 0.96-1.02, P = 0.56) were not causally related to COVID-19 susceptibility. Similarly, we did not find a potential causal relationship between SWB, depression, suicide and COVID-19 severity. CONCLUSIONS This indicated that positive or negative emotions would not make COVID-19 better or worse, and strategies that attempted to use positive emotions to improve COVID-19 symptoms may be useless. Improving knowledge about the SARS-CoV-2 and timely medical intervention to reduce panic during a pandemic is one of the effective measures to deal with the current decrease in well-being and increase in depression and suicide rates.
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Affiliation(s)
- Hongfei Song
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, PR China
| | - Na Lei
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, PR China
| | - Ling Zeng
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, PR China
| | - Xue Li
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, PR China
| | - Xiuyan Li
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, PR China
| | - Yuqiao Liu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, PR China
| | - Jibin Liu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, PR China
| | - Wenjun Wu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, PR China.
| | - Jie Mu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, PR China.
| | - Quansheng Feng
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, PR China.
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21
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Au Yeung SL, Luo S, Kwok KO. Actionable targets to reduce COVID-19 severity. Nat Metab 2023; 5:195-196. [PMID: 36805565 DOI: 10.1038/s42255-023-00743-9] [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] [Indexed: 02/22/2023]
Affiliation(s)
- Shiu Lun Au Yeung
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
| | - Shan Luo
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kin On Kwok
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong SAR, China
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong SAR, China
- Hong Kong Institute of Asia-Pacific Studies, The Chinese University of Hong Kong, Hong Kong SAR, China
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