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Cao Z, Huang J, Long X. Associations between immune cell traits and autoimmune thyroid diseases: a bidirectional two-sample mendelian randomization study. Immunogenetics 2024; 76:219-231. [PMID: 38940861 DOI: 10.1007/s00251-024-01345-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024]
Abstract
Autoimmune thyroid diseases (AITDs), mainly including Graves' disease (GD) and Hashimoto's thyroiditis (HT), are common autoimmune disorders characterized by abnormal immune responses targeting the thyroid gland. We conducted a bidirectional two-sample MR analysis using the largest dataset of peripheral immune cell phenotypes from Sardinia, and the AITD dataset from the 10th round of the FinnGen and the UK Biobank project. Instrumental variables (IVs) were rigorously selected based on the three assumptions of MR and analyzed using the Wald ratio, inverse-variance weighted (IVW), MR-Egger, and weighted median methods. Additionally, sensitivity analyses were performed using Cochrane's Q, the Egger intercept, the MR-PRESSO, and the leave-one-out (LOO) method to ensure the robustness of the results. The Steiger test was utilized to identify and exclude potential reverse causation. The results showed that 3, 3, and 11 immune cell phenotypes were significantly associated with the risk of AITD. In GD, the proportion of naive CD4-CD8- (DN) T cells in T cells and the proportion of terminally differentiated CD4+T cells in T cells showed the strongest inducing and protective effects, respectively. In HT, lymphocyte count and CD45 on CD4+T cells showed the strongest inducing and protective effects, respectively. In autoimmune hypothyroidism, CD127 CD8+T cell count and terminally differentiated DN T cell count exhibited the strongest inducing and protective effects, respectively. Through MR analysis, our study provides direct genetic evidence of the impact of immune cell traits on AITD risk and lays the groundwork for potential therapeutic and diagnostic target discovery.
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Affiliation(s)
- ZheXu Cao
- Department of Thyroid Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - JiangSheng Huang
- Department of Thyroid Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xia Long
- Hospital Office, The Second Xiangya Hospital, Central South University, 139 Renmin Middle Road, Changsha City, Hunan Province, China.
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Tan Y, Yan Z, Yin J, Cao J, Xie B, Zhang F, Zhang W, Xiong W. Elucidating the role of genetically determined metabolites in Diabetic Retinopathy: insights from a mendelian randomization analysis. Acta Diabetol 2024:10.1007/s00592-024-02345-7. [PMID: 39090426 DOI: 10.1007/s00592-024-02345-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 07/06/2024] [Indexed: 08/04/2024]
Abstract
AIMS Diabetic retinopathy (DR) results from complex genetic and metabolic interactions. Unraveling the links between blood metabolites and DR can advance risk prediction and therapy. METHODS Leveraging Mendelian Randomization (MR) and Linkage Disequilibrium Score Regression (LDSC), we analyzed 10,413 DR cases and 308,633 controls. Data was sourced from the Metabolomics GWAS server and the FinnGen project. RESULTS Our research conducted a comprehensive MR analysis across 486 serum metabolites to investigate their causal role in DR. After stringent selection and validation of instrumental variables, we focused on 480 metabolites for analysis. Our findings revealed 38 metabolites potentially causally associated with DR. Specifically, 4-androsten-3beta,17beta-diol disulfate 2 was identified as significantly associated with a reduced risk of DR (OR = 0.471, 95% CI = 0.324-0.684, p = 7.87 × 10- 5), even after rigorous adjustments for multiple testing. Sensitivity analyses further validated the robustness of this association, and linkage disequilibrium score regression analyses showed no significant genetic correlation between this metabolite and DR, suggesting a specific protective effect against DR. CONCLUSIONS Our study identifies 4-androsten-3beta,17beta-diol disulfate 2, a metabolite of androgens, as a significant protective factor against diabetic retinopathy, suggesting androgens as potential therapeutic targets.
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Affiliation(s)
- Yao Tan
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, No. 138 Tongzipo Road, Yuelu District, Changsha City, 410013, Hunan Province, China
- Postdoctoral Station of Clinical Medicine, The Third Xiangya Hospital, Central South University, Changsha City, 410013, Hunan Province, China
| | - Zuyun Yan
- The Third Xiangya Hospital, Central South University, Changsha City, 410013, Hunan Province, China
| | - Jiayang Yin
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, No. 138 Tongzipo Road, Yuelu District, Changsha City, 410013, Hunan Province, China
| | - Jiamin Cao
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, No. 138 Tongzipo Road, Yuelu District, Changsha City, 410013, Hunan Province, China
| | - Bingyu Xie
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, No. 138 Tongzipo Road, Yuelu District, Changsha City, 410013, Hunan Province, China
| | - Feng Zhang
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, No. 138 Tongzipo Road, Yuelu District, Changsha City, 410013, Hunan Province, China
| | - Wenhua Zhang
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, No. 138 Tongzipo Road, Yuelu District, Changsha City, 410013, Hunan Province, China.
| | - Wei Xiong
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, No. 138 Tongzipo Road, Yuelu District, Changsha City, 410013, Hunan Province, China.
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Qian Q, Wu Y, Cui N, Li Y, Zhou Y, Li Y, Lian M, Xiao X, Miao Q, You Z, Wang Q, Shi Y, Cordell HJ, Timilsina S, Gershwin ME, Li Z, Ma X, Ruqi Tang. Epidemiologic and genetic associations between primary biliary cholangitis and extrahepatic rheumatic diseases. J Autoimmun 2024; 148:103289. [PMID: 39059058 DOI: 10.1016/j.jaut.2024.103289] [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: 05/03/2024] [Revised: 07/14/2024] [Accepted: 07/14/2024] [Indexed: 07/28/2024]
Abstract
Patients with primary biliary cholangitis (PBC) commonly experience extrahepatic rheumatic diseases. However, the epidemiologic and genetic associations as well as causal relationship between PBC and these extrahepatic conditions remain undetermined. In this study, we first conducted systematic review and meta-analyses by analyzing 73 studies comprising 334,963 participants across 17 countries and found strong phenotypic associations between PBC and rheumatic diseases. Next, we utilized large-scale genome-wide association study summary data to define the shared genetic architecture between PBC and rheumatic diseases, including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), systemic sclerosis (SSc) and Sjögren's syndrome (SS). We observed significant genetic correlations between PBC and each of the four rheumatic diseases. Pleiotropy and heritability enrichment analysis suggested the involvement of humoral immunity and interferon-associated processes for the comorbidity. Of note, we identified four variants shared between PBC and RA (rs80200208), SLE (rs9843053), and SSc (rs27524, rs3873182) using cross-trait meta-analysis. Additionally, several pleotropic loci for PBC and rheumatic diseases were found to share causal variants with gut microbes possessing immunoregulatory functions. Finally, Mendelian randomization revealed consistent evidence for a causal effect of PBC on RA, SLE, SSc, and SS, but no or inconsistent evidence for a causal effect of extrahepatic rheumatic diseases on PBC. Our study reveals a profound genetic overlap and causal relationships between PBC and extrahepatic rheumatic diseases, thus providing insights into shared biological mechanisms and novel therapeutic interventions.
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Affiliation(s)
- Qiwei Qian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yi Wu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Nana Cui
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yikang Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yujie Zhou
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - You Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Min Lian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Xiao Xiao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Qi Miao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Zhengrui You
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Qixia Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Suraj Timilsina
- Division of Rheumatology, Department of Medicine, Allergy and Clinical Immunology, University of California at Davis, Davis, CA, USA
| | - M Eric Gershwin
- Division of Rheumatology, Department of Medicine, Allergy and Clinical Immunology, University of California at Davis, Davis, CA, USA
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China.
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China; Institute of Aging & Tissue Regeneration, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China.
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Wu B, Pan F, Wang Q, Liang Q, Qiu H, Zhou S, Zhou X. Association between blood metabolites and basal cell carcinoma risk: a two-sample Mendelian randomization study. Front Endocrinol (Lausanne) 2024; 15:1413777. [PMID: 39045268 PMCID: PMC11263015 DOI: 10.3389/fendo.2024.1413777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 06/24/2024] [Indexed: 07/25/2024] Open
Abstract
Background Circulating metabolites, which play a crucial role in our health, have been reported to be disordered in basal cell carcinoma (BCC). Despite these findings, evidence is still lacking to determine whether these metabolites directly promote or prevent BCC's progression. Therefore, our study aims to examine the potential effects of circulating metabolites on BCC progression. Material and methods We conducted a two-sample Mendelian randomization (MR) analysis using data from two separate genome-wide association studies (GWAS). The primary study included data for 123 blood metabolites from a GWAS with 25,000 Finnish individuals, while the secondary study had data for 249 blood metabolites from a GWAS with 114,000 UK Biobank participants.GWAS data for BCC were obtained from the UK Biobank for the primary analysis and the FinnGen consortium for the secondary analysis. Sensitivity analyses were performed to assess heterogeneity and pleiotropy. Results In the primary analysis, significant causal relationships were found between six metabolic traits and BCC with the inverse variance weighted (IVW) method after multiple testing [P < 4 × 10-4 (0.05/123)]. Four metabolic traits were discovered to be significantly linked with BCC in the secondary analysis, with a significance level of P < 2 × 10-4 (0.05/249). We found that all the significant traits are linked to Polyunsaturated Fatty Acids (PUFAs) and their degree of unsaturation. Conclusion Our research has revealed a direct link between the susceptibility of BCC and Polyunsaturated Fatty Acids and their degree of unsaturation. This discovery implies screening and prevention of BCC.
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Affiliation(s)
- Bingliang Wu
- Department of Medical Cosmetology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - FuQiang Pan
- Department of Medical Cosmetology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - QiaoQi Wang
- Department of Health Examination Center, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Qian Liang
- Department of Medical Cosmetology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - HouHuang Qiu
- Department of Medical Cosmetology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - SiYuan Zhou
- Department of Medical Cosmetology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xiang Zhou
- Department of Medical Cosmetology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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Yu S, Lin Y, Yang Y, Jin X, Liao B, Lu D, Huang J. Shared genetic effect of kidney function on bipolar and major depressive disorders: a large-scale genome-wide cross-trait analysis. Hum Genomics 2024; 18:60. [PMID: 38858783 PMCID: PMC11165782 DOI: 10.1186/s40246-024-00627-3] [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] [Accepted: 05/27/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Epidemiological studies have revealed a significant association between impaired kidney function and certain mental disorders, particularly bipolar disorder (BIP) and major depressive disorder (MDD). However, the evidence regarding shared genetics and causality is limited due to residual confounding and reverse causation. METHODS In this study, we conducted a large-scale genome-wide cross-trait association study to investigate the genetic overlap between 5 kidney function biomarkers (eGFRcrea, eGFRcys, blood urea nitrogen (BUN), serum urate, and UACR) and 2 mental disorders (MDD, BIP). Summary-level data of European ancestry were extracted from UK Biobank, Chronic Kidney Disease Genetics Consortium, and Psychiatric Genomics Consortium. RESULTS Using LD score regression, we found moderate but significant genetic correlations between kidney function biomarker traits on BIP and MDD. Cross-trait meta-analysis identified 1 to 19 independent significant loci that were found shared among 10 pairs of 5 kidney function biomarkers traits and 2 mental disorders. Among them, 3 novel genes: SUFU, IBSP, and PTPRJ, were also identified in transcriptome-wide association study analysis (TWAS), most of which were observed in the nervous and digestive systems (FDR < 0.05). Pathway analysis showed the immune system could play a role between kidney function biomarkers and mental disorders. Bidirectional mendelian randomization analysis suggested a potential causal relationship of kidney function biomarkers on BIP and MDD. CONCLUSIONS In conclusion, the study demonstrated that both BIP and MDD shared genetic architecture with kidney function biomarkers, providing new insights into their genetic architectures and suggesting that larger GWASs are warranted.
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Affiliation(s)
- Simin Yu
- Department of Urology, Innovation Institute for Integration of Medicine and Engineering, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Yifei Lin
- Department of Urology, Innovation Institute for Integration of Medicine and Engineering, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Yong Yang
- Health Management Center, General Practice Medical Center, Innovation Institute for Integration of Medicine and Engineering, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Xi Jin
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Banghua Liao
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Donghao Lu
- Health Management Center, General Practice Medical Center, Innovation Institute for Integration of Medicine and Engineering, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.
- Institute of Environmental Medicine, Karolinska Institutet, Nobels Väg 13, 17177, Stockholm, Sweden.
| | - Jin Huang
- Department of Urology, Innovation Institute for Integration of Medicine and Engineering, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.
- Health Management Center, General Practice Medical Center, Innovation Institute for Integration of Medicine and Engineering, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.
- Health Management Center, General Practice Medical Center and Medical Device Regulatory Research and Evaluation Centre, West China Hospital, Sichuan University, Chengdu, People's Republic of China.
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Duan A, Qiu Y, Song B, Tao Y, Wang M, Yin Z, Xie M, Chen Z, Wang Z, Sun X. Metabolome-Wide Mendelian Randomization Assessing the Causal Role of Serum and Cerebrospinal Metabolites in Traumatic Brain Injury. Biomedicines 2024; 12:1178. [PMID: 38927385 PMCID: PMC11201266 DOI: 10.3390/biomedicines12061178] [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: 03/26/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 06/28/2024] Open
Abstract
Previous studies have identified metabolites as biomarkers or potential therapeutic targets for traumatic brain injury (TBI). However, the causal association between them remains unknown. Therefore, we investigated the causal effect of serum metabolites and cerebrospinal fluid (CSF) metabolites on TBI susceptibility through Mendelian randomization (MR). Genetic variants related to metabolites and TBI were extracted from a corresponding genome-wide association study (GWAS). Causal effects were estimated through the inverse variance weighted approach, supplemented by a weighted median, weight mode, and the MR-Egger test. In addition, sensitivity analyses were further performed to evaluate the stability of the MR results, including the MR-Egger intercept, leave-one-out analysis, Cochrane's Q-test, and the MR-PRESSO global test. Metabolic pathway analysis was applied to uncover the underlying pathways of the significant metabolites in TBI. In blood metabolites, substances such as 4-acetaminophen sulfate and kynurenine showed positive links, whereas beta-hydroxyisovalerate and creatinine exhibited negative correlations. CSF metabolites such as N-formylanthranilic acid were positively related, while kynurenate showed negative associations. The metabolic pathway analysis highlighted the potential biological pathways involved in TBI. Of these 16 serum metabolites, 11 CSF metabolites and metabolic pathways may serve as useful circulating biomarkers in clinical screening and prevention, and may be candidate molecules for the exploration of mechanisms and drug targets.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zhong Wang
- Department of Neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (A.D.); (Y.Q.)
| | - Xiaoou Sun
- Department of Neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (A.D.); (Y.Q.)
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Zhang Z, Cao B, Wu Q. Causality of Genetically Determined Metabolites on Chronic Kidney Disease: A Two-Sample Mendelian Randomization Study In Silico. Metab Syndr Relat Disord 2024. [PMID: 38742978 DOI: 10.1089/met.2024.0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Abstract
Introduction: Chronic kidney disease (CKD) is associated with metabolic disorders. However, the evidence for the causality of circulating metabolites to promote or prevent CKD is still lacking. Methods: The two-sample Mendelian randomization (MR) analysis was conducted to evaluate the latent causal relationship between the genetically proxied 486 blood metabolites and CKD. Genome-wide association study (GWAS) data for exposures were derived from 7824 European GWAS on metabolite levels, which have been extensively utilized in the medical field to elucidate the mechanisms underlying disease onset and progression. The random inverse variance weighted (IVW) is the primary analysis for causality analysis while MR-Egger and weighted median as complementary analyses. For the further identification of metabolites, reverse MR and linkage disequilibrium score regression were performed for further evaluation. The drug target for N-acetylornithine was subsequently supplemented into the analysis, with MR and colocalization analysis being utilized. Key metabolic pathways were identified via MetaboAnalyst 4.0 (https://www.metaboanalyst.ca/) online website. Results: N-acetylornithine was identified as a reliable metabolite that increases the susceptibility to estimated glomerular filtration rate (eGFR) decrease (β = 0.047; 95% confidence interval: -0.068 to -0.026; PIVW = 1.5E-5). The "glyoxylate and dicarboxylate metabolism" pathway showed significant relevance to CKD development (P = 6E-4), whereas the "glycine, serine, and threonine metabolism" pathway was also recognized as associated with CKD by general practitioners (P = 7E-4). Colocalization analysis revealed a robust genetic link between N-acetylornithine and both CKD and eGFR, with 85.1% and 99.4% colocalization rates, respectively. IVW-MR analysis substantiated these findings with a significant positive association for CKD (odds ratio = 1.43, P = 4.7E-5) and a negative correlation with eGFR (b = -0.04, P = 1.13E-31). Conclusions: MR was utilized to explore the potential causal links between 61 genetic serum metabolites and CKD. N-acetylornithine and NAT8 were further explored as a potential therapeutic target for CKD treatment.
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Affiliation(s)
- Zekai Zhang
- Second College of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Beibei Cao
- Academy of Paediatrics, Nanjing Medical University, Nanjing, China
| | - Qiutong Wu
- Second College of Clinical Medicine, Nanjing Medical University, Nanjing, China
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Zou X, Lu Y, Tan Y. Effect of serum metabolites on the risk of iridocyclitis: a bidirectional Mendelian randomization study. Sci Rep 2024; 14:10535. [PMID: 38719907 PMCID: PMC11078962 DOI: 10.1038/s41598-024-61441-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024] Open
Abstract
Previous research has linked serum metabolite levels to iridocyclitis, yet their causal relationship remains unexplored. This study investigated this potential causality by analyzing pooled data from 7824 iridocyclitis patients in a Genome-Wide Association Study (GWAS) using Mendelian randomization (MR) and linkage disequilibrium score regression (LDSC). Employing rigorous quality control and comprehensive statistical methods, including sensitivity analyses, we examined the influence of 486 serum metabolites on iridocyclitis. Our MR analysis identified 23 metabolites with significant causal effects on iridocyclitis, comprising 17 known and 6 unidentified metabolites. Further refinement using Cochran's Q test and MR-PRESSO indicated 16 metabolites significantly associated with iridocyclitis risk. LDSC highlighted the heritability of certain metabolites, underscoring genetic influences on their levels. Notably, tryptophan, proline, theobromine, and 7-methylxanthine emerged as risk factors, while 3,4-dihydroxybutyrate appeared protective. These findings enhance our understanding of the metabolic interactions in iridocyclitis, offering insights for diagnosis, unraveling pathophysiological mechanisms, and informing potential avenues for prevention and personalized treatment.
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Affiliation(s)
- Xuyan Zou
- Changsha Aier Eye Hospital, Changsha, Hunan Provine, 410015, China
| | - Yijie Lu
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, Guangdong Provine, 518000, China
| | - Yao Tan
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, No. 138 Tongzipo Road, Yuelu District, Changsha, Hunan Provine, 410013, China.
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Shi G, Wu T, Li X, Zhao D, Yin Q, Zhu L. Systematic genome-wide Mendelian randomization reveals the causal links between miRNAs and Parkinson's disease. Front Neurosci 2024; 18:1385675. [PMID: 38765669 PMCID: PMC11099245 DOI: 10.3389/fnins.2024.1385675] [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: 02/13/2024] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
Background MicroRNAs (miRNAs) have pivotal roles in gene regulation. Circulating miRNAs have been developed as novel candidate non-invasive biomarkers for diagnosis, prognosis, and treatment response for diseases. However, miRNAs that have causal effects on Parkinson's Disease (PD) remain largely unknown. To investigate the causal relationships between miRNAs and PD, here we conduct a Mendelian randomization (MR) study. Methods This study utilized the summary-level data of respective genome-wide association studies (GWAS) for 2083 miRNAs and seven PD-related outcomes to comprehensively reveal the causal associations between the circulating miRNAs and PD. Two-sample MR design was deployed and the causal effects were estimated with inverse variance weighted, MR-Egger, and weighted median. Comprehensively sensitive analyses were followed, including Cochran's Q test, MR-Egger intercept test, MR-PRESSO, and leave-one-out analysis, to validate the robustness of our results. Finally, we investigated the potential role of the MR significant miRNAs by predicting their target genes and functional enrichment analysis. Results Inverse variance weighted estimates suggested that two miRNAs, miR-205-5p (β = -0.46, 95%CI: -0.690 to -0.229, p = 9.3 × 10-5) and miR-6800-5p (β = -0.389, 95%CI: -0.575 to -0.202, p = 4.32 × 10-5), significantly decreased the rate of cognitive decline among PD patients. In addition, eight miRNAs were nominally associated with more than three PD-related outcomes each. No significant heterogeneity of instrumental variables or horizontal pleiotropy was found. Gene Ontology (GO) analysis showed that the targets of these causal miRNAs were significantly enriched in cell cycle, apoptotic, and aging pathways. Conclusion This MR study identified two miRNAs whose genetically regulated expression might have a causal role in the development of PD dementia. Our findings provided potential miRNA biomarkers to make better and early diagnoses and risk assessments of PD.
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Affiliation(s)
- Guolin Shi
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Tingting Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Xuetao Li
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Debin Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Qiuyuan Yin
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Lei Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
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10
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Iakunchykova O, Pan M, Amlien IK, Roe JM, Walhovd KB, Fjell AM, Chen CH, Benros ME, Wang Y. Genetic evidence for the causal effects of C-reactive protein on self-reported habitual sleep duration. Brain Behav Immun Health 2024; 37:100754. [PMID: 38511149 PMCID: PMC10950822 DOI: 10.1016/j.bbih.2024.100754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/13/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
Inflammatory responses to acute stimuli are proposed to regulate sleep, but the relationship between chronic inflammation and habitual sleep duration is elusive. Here, we study this relation using genetically predicted level of chronic inflammation, indexed by CRP and IL6 signaling, and self-reported sleep duration. By Mendelian randomization analysis, we show that elevated CRP level within <10 mg/L has a homeostatic effect that facilitates maintaining 7-8 h sleep duration per day - making short-sleepers sleep longer (p = 2.42 × 10-2) and long-sleepers sleep shorter (1.87 × 10-7); but it is not associated with the overall sleep duration (p = 0.17). This homeostatic effect replicated in an independent CRP dataset. We observed causal effects of the soluble interleukin 6 receptor and gp130 on overall sleep duration (p = 1.62 × 10-8, p = 2.61 × 10-58, respectively), but these effects disappeared when CRP effects were accounted for in the model. Using polygenic score analysis, we found that the homeostatic effect of CRP on sleep duration stems primarily from the genetic variants within the CRP gene region: when genetic variants outside of this region were used to predict CRP levels, the opposite direction of effect was observed. In conclusion, we show that elevated CRP level may causally facilitate maintaining an optimal sleep duration that is beneficial to health, thus updating our current knowledge of immune regulation on sleep.
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Affiliation(s)
- Olena Iakunchykova
- Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - Mengyu Pan
- Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - Inge K. Amlien
- Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - James M. Roe
- Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - Kristine B. Walhovd
- Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
- Division of Radiology and Nuclear Medicine, Oslo University Hospital, Rikshospitalet, POB 4950, Nydalen, 0424, Oslo, Norway
| | - Anders M. Fjell
- Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
- Division of Radiology and Nuclear Medicine, Oslo University Hospital, Rikshospitalet, POB 4950, Nydalen, 0424, Oslo, Norway
| | - Chi-Hua Chen
- Department of Radiology, University of California in San Diego, Gilman Drive 9500, 92093, La Jolla, CA, USA
| | - Michael E. Benros
- Copenhagen Research Centre for Mental Health, Mental Health Center Copenhagen, Copenhagen University Hospital, Gentofte Hospitalsvej 15, 2900, Hellerup, Denmark
| | - Yunpeng Wang
- Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
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11
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Yang W, Fan X, Li W, Chen Y. Causal influence of gut microbiota on small cell lung cancer: a Mendelian randomization study. THE CLINICAL RESPIRATORY JOURNAL 2024; 18:e13764. [PMID: 38685730 PMCID: PMC11058399 DOI: 10.1111/crj.13764] [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: 01/24/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Previous studies have hinted at a significant link between lung cancer and the gut microbiome, yet their causal relationship remains to be elucidated. METHODS GWAS data for small cell lung cancer (SCLC) was extracted from the FinnGen consortium, comprising 179 cases and 218 613 controls. Genetic variation data for 211 gut microbiota were obtained as instrumental variables from MiBioGen. Mendelian randomization (MR) was employed to determine the causal relationship between the two, with inverse variance weighting (IVW) being the primary method for causal analysis. The MR results were validated through several sensitivity analyses. RESULTS The study identified a protective effect against SCLC for the genus Eubacterium ruminantium group (OR = 0.413, 95% CI: 0.223-0.767, p = 0.00513), genus Barnesiella (OR = 0.208, 95% CI: 0.0640-0.678, p = 0.00919), family Lachnospiraceae (OR = 0.319, 95% CI: 0.107-0.948, p = 0.03979), and genus Butyricimonas (OR = 0.376, 95% CI: 0.144-0.984, p = 0.04634). Conversely, genus Intestinibacter (OR = 3.214, 95% CI: 1.303-7.926, p = 0.01125), genus Eubacterium oxidoreducens group (OR = 3.391, 95% CI: 1.215-9.467, p = 0.01973), genus Bilophila (OR = 3.547, 95% CI: 1.106-11.371, p = 0.03315), and order Bacillales (OR = 1.860, 95% CI: 1.034-3.347, p = 0.03842) were found to potentially promote the onset of SCLC. CONCLUSION We identified potential causal relationships between certain gut microbiota and SCLC, offering new insights into microbiome-mediated mechanisms of SCLC pathogenesis, resistance, mutations, and more.
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Affiliation(s)
- Wenjing Yang
- General Hospital of Ningxia Medical UniversityYinchuanNingxia Hui Autonomous RegionChina
| | - Xinxia Fan
- The Second Affiliated Hospital of Liaoning University of Traditional Chinese MedicineShenyangLiaoningChina
| | - Wangshu Li
- Dalian Women and Children's Medical Center (Group)DalianLiaoningChina
| | - Yan Chen
- Department of Respiratory and Critical Care MedicineGeneral Hospital of Northern Theater CommandShenyangLiaoningChina
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12
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Shang W, Qian H, Zhang S, Yuan M, Pan X, Huang S, Liu J, Chen D. Human blood metabolites and risk of sepsis: A Mendelian randomization investigation. Eur J Clin Invest 2024; 54:e14145. [PMID: 38041600 DOI: 10.1111/eci.14145] [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: 08/10/2023] [Revised: 11/14/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
BACKGROUND Evidence supports the observational correlations between human blood metabolites and sepsis. However, whether these associations represent a causal relationship is unknown. In this study, we applied two-sample Mendelian randomization (MR) analyses to examine causality between genetically proxied 486 blood metabolites and sepsis risk. METHODS We used summary data from genome-wide association studies (GWAS) on 486 metabolites involving 7824 individuals as exposure and a sepsis GWAS including 11,643 cases and 474,841 controls as the outcome. The inverse-variance weighted (IVW) was the primary method to estimate the causal relationship between exposure and outcome, with MR-Egger and weighted median serving as supplements. Sensitivity analyses were implemented with Cochrane's Q test, MR-Egger intercept, MR-PRESSO and leave-one-out analysis. In addition, we performed replication MR, meta-analysis, Steiger test, linkage disequilibrium score (LDSC) regression and multivariable MR (MVMR) to thoroughly verify the causation. RESULTS We identified that genetically determined high levels of 1-oleoylglycerophosphoethanolamine (odds ratio (OR) = .52, 95% confidence interval (CI): .31-.87, p = .0122), alpha-glutamyltyrosine (OR = .75, 95% CI: .60-.93, p = .0102), heptanoate (7:0) (OR = .51, 95% CI: .33-.81, p = .0041) and saccharin (OR = .84, 95% CI: .74-.94, p = .0036) were causally associated with a lower risk of sepsis. MVMR analysis demonstrated the independent causal effect of these metabolites on sepsis. CONCLUSIONS These findings indicated that four blood metabolites have a protective impact on sepsis, thus providing novel perspectives into the metabolite-mediated development mechanism of sepsis by combining genomics and metabolomics.
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Affiliation(s)
- Weifeng Shang
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hang Qian
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sheng Zhang
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingyang Yuan
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiaojun Pan
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sisi Huang
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiao Liu
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dechang Chen
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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13
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Kiltschewskij DJ, Reay WR, Geaghan MP, Atkins JR, Xavier A, Zhang X, Watkeys OJ, Carr VJ, Scott RJ, Green MJ, Cairns MJ. Alteration of DNA Methylation and Epigenetic Scores Associated With Features of Schizophrenia and Common Variant Genetic Risk. Biol Psychiatry 2024; 95:647-661. [PMID: 37480976 DOI: 10.1016/j.biopsych.2023.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/24/2023]
Abstract
BACKGROUND Unpacking molecular perturbations associated with features of schizophrenia is a critical step toward understanding phenotypic heterogeneity in this disorder. Recent epigenome-wide association studies have uncovered pervasive dysregulation of DNA methylation in schizophrenia; however, clinical features of the disorder that account for a large proportion of phenotypic variability are relatively underexplored. METHODS We comprehensively analyzed patterns of DNA methylation in a cohort of 381 individuals with schizophrenia from the deeply phenotyped Australian Schizophrenia Research Bank. Epigenetic changes were investigated in association with cognitive status, age of onset, treatment resistance, Global Assessment of Functioning scores, and common variant polygenic risk scores for schizophrenia. We subsequently explored alterations within genes previously associated with psychiatric illness, phenome-wide epigenetic covariance, and epigenetic scores. RESULTS Epigenome-wide association studies of the 5 primary traits identified 662 suggestively significant (p < 6.72 × 10-5) differentially methylated probes, with a further 432 revealed after controlling for schizophrenia polygenic risk on the remaining 4 traits. Interestingly, we uncovered many probes within genes associated with a variety of psychiatric conditions as well as significant epigenetic covariance with phenotypes and exposures including acute myocardial infarction, C-reactive protein, and lung cancer. Epigenetic scores for treatment-resistant schizophrenia strikingly exhibited association with clozapine administration, while epigenetic proxies of plasma protein expression, such as CCL17, MMP10, and PRG2, were associated with several features of schizophrenia. CONCLUSIONS Our findings collectively provide novel evidence suggesting that several features of schizophrenia are associated with alteration of DNA methylation, which may contribute to interindividual phenotypic variation in affected individuals.
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Affiliation(s)
- Dylan J Kiltschewskij
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Precision Medicine Program, Hunter Medical Research Institute, New Lambton, New South Wales, Australia
| | - William R Reay
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Precision Medicine Program, Hunter Medical Research Institute, New Lambton, New South Wales, Australia
| | - Michael P Geaghan
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Joshua R Atkins
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia
| | - Alexandre Xavier
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Centre for Information Based Medicine, Hunter Medical Research Institute, New Lambton, New South Wales, Australia
| | - Xiajie Zhang
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Centre for Information Based Medicine, Hunter Medical Research Institute, New Lambton, New South Wales, Australia
| | - Oliver J Watkeys
- School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
| | - Vaughan J Carr
- School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia; Department of Psychiatry, School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Centre for Information Based Medicine, Hunter Medical Research Institute, New Lambton, New South Wales, Australia
| | - Melissa J Green
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Precision Medicine Program, Hunter Medical Research Institute, New Lambton, New South Wales, Australia.
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14
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Sun J, Zhou J, Gong Y, Pang C, Ma Y, Zhao J, Yu Z, Zhang Y. Bayesian network-based Mendelian randomization for variant prioritization and phenotypic causal inference. Hum Genet 2024:10.1007/s00439-024-02640-x. [PMID: 38381161 DOI: 10.1007/s00439-024-02640-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/05/2024] [Indexed: 02/22/2024]
Abstract
Mendelian randomization is a powerful method for inferring causal relationships. However, obtaining suitable genetic instrumental variables is often challenging due to gene interaction, linkage, and pleiotropy. We propose Bayesian network-based Mendelian randomization (BNMR), a Bayesian causal learning and inference framework using individual-level data. BNMR employs the random graph forest, an ensemble Bayesian network structural learning process, to prioritize candidate genetic variants and select appropriate instrumental variables, and then obtains a pleiotropy-robust estimate by incorporating a shrinkage prior in the Bayesian framework. Simulations demonstrate BNMR can efficiently reduce the false-positive discoveries in variant selection, and outperforms existing MR methods in terms of accuracy and statistical power in effect estimation. With application to the UK Biobank, BNMR exhibits its capacity in handling modern genomic data, and reveals the causal relationships from hematological traits to blood pressures and psychiatric disorders. Its effectiveness in handling complex genetic structures and modern genomic data highlights the potential to facilitate real-world evidence studies, making it a promising tool for advancing our understanding of causal mechanisms.
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Affiliation(s)
- Jianle Sun
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Zhou
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Yuqiao Gong
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Chongchen Pang
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Yanran Ma
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Zhao
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, China
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Zhangsheng Yu
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China.
| | - Yue Zhang
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China.
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15
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Reay WR, Kiltschewskij DJ, Di Biase MA, Gerring ZF, Kundu K, Surendran P, Greco LA, Clarke ED, Collins CE, Mondul AM, Albanes D, Cairns MJ. Genetic influences on circulating retinol and its relationship to human health. Nat Commun 2024; 15:1490. [PMID: 38374065 PMCID: PMC10876955 DOI: 10.1038/s41467-024-45779-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/04/2024] [Indexed: 02/21/2024] Open
Abstract
Retinol is a fat-soluble vitamin that plays an essential role in many biological processes throughout the human lifespan. Here, we perform the largest genome-wide association study (GWAS) of retinol to date in up to 22,274 participants. We identify eight common variant loci associated with retinol, as well as a rare-variant signal. An integrative gene prioritisation pipeline supports novel retinol-associated genes outside of the main retinol transport complex (RBP4:TTR) related to lipid biology, energy homoeostasis, and endocrine signalling. Genetic proxies of circulating retinol were then used to estimate causal relationships with almost 20,000 clinical phenotypes via a phenome-wide Mendelian randomisation study (MR-pheWAS). The MR-pheWAS suggests that retinol may exert causal effects on inflammation, adiposity, ocular measures, the microbiome, and MRI-derived brain phenotypes, amongst several others. Conversely, circulating retinol may be causally influenced by factors including lipids and serum creatinine. Finally, we demonstrate how a retinol polygenic score could identify individuals more likely to fall outside of the normative range of circulating retinol for a given age. In summary, this study provides a comprehensive evaluation of the genetics of circulating retinol, as well as revealing traits which should be prioritised for further investigation with respect to retinol related therapies or nutritional intervention.
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Affiliation(s)
- William R Reay
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton, NSW, Australia.
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Melbourne, VIC, Australia.
| | - Dylan J Kiltschewskij
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - Maria A Di Biase
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Melbourne, VIC, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zachary F Gerring
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kousik Kundu
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
- Health Data Research UK, Wellcome Genome Campus and University of Cambridge, Hinxton, UK
| | - Laura A Greco
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - Erin D Clarke
- School of Health Sciences, The University of Newcastle, Callaghan, NSW, Australia
- Food and Nutrition Research Program, Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - Clare E Collins
- School of Health Sciences, The University of Newcastle, Callaghan, NSW, Australia
- Food and Nutrition Research Program, Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - Alison M Mondul
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda, MD, USA
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton, NSW, Australia.
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16
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Wang Z, Yang Q. The causal relationship between human blood metabolites and the risk of visceral obesity: a mendelian randomization analysis. Lipids Health Dis 2024; 23:39. [PMID: 38326855 PMCID: PMC10851536 DOI: 10.1186/s12944-024-02035-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/30/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND We aimed to explore the causal relationship between blood metabolites and the risk of visceral obesity, as measured by visceral adipose tissue (VAT). METHODS Summary statistics for 486 blood metabolites and total, as well as sex-stratified, MRI-derived VAT measurements, adjusted for body mass index (BMI) and height, were collected from previous genome-wide association studies (GWAS). A two-sample Mendelian Randomization (MR) design was used. Comprehensive evaluation was further conducted, including sensitivity analysis, linkage disequilibrium score (LDSC) regression, Steiger test, and metabolic pathway analysis. RESULTS After multiple testing correction, arachidonate (20:4n6) has been implicated in VAT accumulation (β = 0.35, 95%CI:0.18-0.52, P < 0.001; FDR = 0.025). Additionally, several blood metabolites were identified as potentially having causal relationship (FDR < 0.10). Among them, lysine (β = 0.67, 95%CI: 0.28-1.06, P < 0.001; FDR = 0.074), proline (β = 0.30, 95%CI:0.13-0.48, P < 0.001; FDR = 0.082), valerate (β = 0.50, 95%CI:0.23-0.78, P < 0.001, FDR = 0.091) are associated with an increased risk of VAT accumulation. On the other hand, glycine (β=-0.21, 95%CI: -0.33-0.09), P < 0.001, FDR = 0.076) have a protective effect against VAT accumulation. Most blood metabolites showed consistent trends between different sexes. Multivariable MR analysis demonstrated the effect of genetically predicted arachidonate (20:4n6) and proline on VAT remained after accounting for BMI and glycated hemoglobin (HbA1c). There is no evidence of heterogeneity, pleiotropy, and reverse causality. CONCLUSION Our MR findings suggest that these metabolites may serve as biomarkers, as well as for future mechanistic exploration and drug target selection of visceral obesity.
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Affiliation(s)
- Zhaoxiang Wang
- Department of Endocrinology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, Jiangsu, 215300, China
| | - Qichao Yang
- Department of Endocrinology, Affiliated Wujin Hospital of Jiangsu University, Changzhou, Jiangsu, 213017, China.
- Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, 213017, China.
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17
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MA XB, LIU YM, LV YL, QIAN L. Interaction between systemic iron parameters and left ventricular structure and function in the preserved ejection fraction population: a two-sample bidirectional Mendelian randomization study. J Geriatr Cardiol 2024; 21:64-80. [PMID: 38440342 PMCID: PMC10908583 DOI: 10.26599/1671-5411.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Left ventricular (LV) remodeling and diastolic function in people with heart failure (HF) are correlated with iron status; however, the causality is uncertain. This Mendelian randomization (MR) study investigated the bidirectional causal relationship between systemic iron parameters and LV structure and function in a preserved ejection fraction population. METHODS Transferrin saturation (TSAT), total iron binding capacity (TIBC), and serum iron and ferritin levels were extracted as instrumental variables for iron parameters from meta-analyses of public genome-wide association studies. Individuals without myocardial infarction history, HF, or LV ejection fraction (LVEF) < 50% (n = 16,923) in the UK Biobank Cardiovascular Magnetic Resonance Imaging Study constituted the outcome dataset. The dataset included LV end-diastolic volume, LV end-systolic volume, LV mass (LVM), and LVM-to-end-diastolic volume ratio (LVMVR). We used a two-sample bidirectional MR study with inverse variance weighting (IVW) as the primary analysis method and estimation methods using different algorithms to improve the robustness of the results. RESULTS In the IVW analysis, one standard deviation (SD) increased in TSAT significantly correlated with decreased LVMVR (β = -0.1365; 95% confidence interval [CI]: -0.2092 to -0.0638; P = 0.0002) after Bonferroni adjustment. Conversely, no significant relationships were observed between other iron and LV parameters. After Bonferroni correction, reverse MR analysis showed that one SD increase in LVEF significantly correlated with decreased TSAT (β = -0.0699; 95% CI: -0.1087 to -0.0311; P = 0.0004). No heterogeneity or pleiotropic effects evidence was observed in the analysis. CONCLUSIONS We demonstrated a causal relationship between TSAT and LV remodeling and function in a preserved ejection fraction population.
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Affiliation(s)
- Xiong-Bin MA
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Yong-Ming LIU
- Geriatric Cardiovascular Department and Gansu Clinical Research Center for Geriatric Diseases, First Hospital of Lanzhou University, Gansu, China
| | - Yan-Lin LV
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Lin QIAN
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
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18
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Iakunchykova O, Leonardsen EH, Wang Y. Genetic evidence for causal effects of immune dysfunction in psychiatric disorders: where are we? Transl Psychiatry 2024; 14:63. [PMID: 38272880 PMCID: PMC10810856 DOI: 10.1038/s41398-024-02778-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 01/06/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
The question of whether immune dysfunction contributes to risk of psychiatric disorders has long been a subject of interest. To assert this hypothesis a plethora of correlative evidence has been accumulated from the past decades; however, a variety of technical and practical obstacles impeded on a cause-effect interpretation of these data. With the advent of large-scale omics technology and advanced statistical models, particularly Mendelian randomization, new studies testing this old hypothesis are accruing. Here we synthesize these new findings from genomics and genetic causal inference studies on the role of immune dysfunction in major psychiatric disorders and reconcile these new data with pre-omics findings. By reconciling these evidences, we aim to identify key gaps and propose directions for future studies in the field.
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Affiliation(s)
- Olena Iakunchykova
- Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - Esten H Leonardsen
- Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway
| | - Yunpeng Wang
- Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, 0317, Oslo, Norway.
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19
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Bhattacharyya U, John J, Lam M, Fisher J, Sun B, Baird D, Chen CY, Lencz T. Large-Scale Mendelian Randomization Study Reveals Circulating Blood-based Proteomic Biomarkers for Psychopathology and Cognitive Task Performance. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.18.24301455. [PMID: 38293198 PMCID: PMC10827252 DOI: 10.1101/2024.01.18.24301455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background Research on peripheral (e.g., blood-based) biomarkers for psychiatric illness has typically been low-throughput in terms of both the number of subjects and the range of assays performed. Moreover, traditional case-control studies examining blood-based biomarkers are subject to potential confounds of treatment and other exposures common to patients with psychiatric illnesses. Our research addresses these challenges by leveraging large-scale, high-throughput proteomics data and Mendelian Randomization (MR) to examine the causal impact of circulating proteins on psychiatric phenotypes and cognitive task performance. Methods We utilized plasma proteomics data from the UK Biobank (3,072 proteins assayed in 34,557 European-ancestry individuals) and deCODE Genetics (4,719 proteins measured across 35,559 Icelandic individuals). Significant proteomic quantitative trait loci (both cis-pQTLs and trans-pQTLs) served as MR instruments, with the most recent GWAS for schizophrenia, bipolar disorder, major depressive disorder, and cognitive task performance (all excluding overlapping UK Biobank participants) as phenotypic outcomes. Results MR revealed 109 Bonferroni-corrected causal associations (44 novel) involving 88 proteins across the four phenotypes. Several immune-related proteins, including interleukins and complement factors, stood out as pleiotropic across multiple outcome phenotypes. Drug target enrichment analysis identified several novel potential pharmacologic repurposing opportunities, including anti-inflammatory agents for schizophrenia and bipolar disorder and duloxetine for cognitive performance. Conclusions Identification of causal effects for these circulating proteins suggests potential biomarkers for these conditions and offers insights for developing innovative therapeutic strategies. The findings also indicate substantial evidence for the pleiotropic effects of many proteins across different phenotypes, shedding light on the shared etiology among psychiatric conditions and cognitive ability.
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Affiliation(s)
- Upasana Bhattacharyya
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY
| | - Jibin John
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY
| | - Max Lam
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY
| | - Jonah Fisher
- Biogen Inc., Cambridge, MA
- Harvard T.H. Chan School of Public Health, Cambridge, MA
| | | | | | | | - Todd Lencz
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY
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Kiewa J, Meltzer-Brody S, Milgrom J, Guintivano J, Hickie IB, Whiteman DC, Olsen CM, Medland SE, Martin NG, Wray NR, Byrne EM. Comprehensive Sex-Stratified Genetic Analysis of 28 Blood Biomarkers and Depression Reveals a Significant Association between Depression and Low Levels of Total Protein in Females. Complex Psychiatry 2024; 10:19-34. [PMID: 38584764 PMCID: PMC10997320 DOI: 10.1159/000538058] [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: 09/13/2023] [Accepted: 02/14/2024] [Indexed: 04/09/2024] Open
Abstract
Introduction Major depression (MD) is more common amongst women than men, and MD episodes have been associated with fluctuations in reproductive hormones amongst women. To investigate biological underpinnings of heterogeneity in MD, the associations between depression, stratified by sex and including perinatal depression (PND), and blood biomarkers, using UK Biobank (UKB) data, were evaluated, and extended to include the association of depression with biomarker polygenic scores (PGS), generated as proxy for each biomarker. Method Using female (N = 39,761) and male (N = 38,821) UKB participants, lifetime MD and PND were tested for association with 28 blood biomarkers. A GWAS was conducted for each biomarker and genetic correlations with depression subgroups were estimated. Using independent data from the Australian Genetics of Depression Study, PGS were constructed for each biomarker, and tested for association with depression status (n [female cases/controls] = 9,006/6,442; n [male cases/controls] = 3,106/6,222). Regions of significant local genetic correlation between depression subgroups and biomarkers highlighted by the PGS analysis were identified. Results Depression in females was significantly associated with levels of twelve biomarkers, including total protein (OR = 0.90, CI = [0.86, 0.94], p = 3.9 × 10-6) and vitamin D (OR = 0.94, CI = [0.90, 0.97], p = 2.6 × 10-4), and PND with five biomarker levels, also including total protein (OR = 0.88, CI = [0.81, 0.96], p = 4.7 × 10-3). Depression in males was significantly associated with levels of eleven biomarkers. In the independent Australian Genetics of Depression Study, PGS analysis found significant associations for female depression and PND with total protein (female depression: OR = 0.93, CI = [0.88, 0.98], p = 3.6 × 10-3; PND: OR = 0.91, CI = [0.86, 0.96], p = 1.1 × 10-3), as well as with vitamin D (female depression: OR = 0.93, CI = [0.89, 0.97], p = 2.0 × 10-3; PND: OR = 0.92, CI = [0.87, 0.97], p = 1.4 × 10-3). The male depression sample did not report any significant results, and the point estimate of total protein (OR = 0.98, CI = [0.92-1.04], p = 4.7 × 10-1) did not indicate any association. Local genetic correlation analysis highlighted significant genetic correlation between PND and total protein, located in 5q13.3 (rG = 0.68, CI = [0.33, 1.0], p = 3.6 × 10-4). Discussion and Conclusion Multiple lines of evidence from genetic analysis highlight an association between total serum protein levels and depression in females. Further research involving prospective measurement of total protein and depressive symptoms is warranted.
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Affiliation(s)
- Jacqueline Kiewa
- Child Health Research Centre, University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | | | - Jeannette Milgrom
- Parent-Infant Research Institute, Austin Health, Melbourne, VIC, Australia
- Melbourne School of Psychological Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Jerry Guintivano
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Ian B. Hickie
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
| | | | | | - Sarah E. Medland
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Naomi R. Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Enda M. Byrne
- Child Health Research Centre, University of Queensland, Brisbane, QLD, Australia
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21
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Tan Y, Yin J, Cao J, Xie B, Zhang F, Xiong W. Genetically Determined Metabolites in Graves Disease: Insight From a Mendelian Randomization Study. J Endocr Soc 2023; 8:bvad149. [PMID: 38116129 PMCID: PMC10729855 DOI: 10.1210/jendso/bvad149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Indexed: 12/21/2023] Open
Abstract
Context Graves disease (GD) is a prevalent autoimmune disorder with a complex etiology. The association between serum metabolites and GD remains partially understood. Objective This study aimed to elucidate the causal connections between serum metabolites and predisposition to GD, examining potential genetic interplay. Methods A 1-sample Mendelian randomization (MR) study was conducted on the GD analysis that included 2836 cases and 374 441 controls. We utilized genome-wide association study summary data from the FinnGen project, analyzing the causal impact of 486 serum metabolites on GD. Approaches used were the inverse variance weighted methodology, Cochran's Q test, MR-Egger regression, MR-PRESSO, Steiger test, and linkage disequilibrium score regression analyses to assess genetic influence on metabolites and GD. Results 19 metabolites were identified as having a pronounced association with GD risk, of which 10 maintained noteworthy correlations after stringent sensitivity assessments. Three metabolites exhibited significant heritability: kynurenine (OR 3.851, P = 6.09 × 10-4), a risk factor; glycerol 2-phosphate (OR 0.549, P = 3.58 × 10-2) and 4-androsten-3beta,17beta-diol disulfate 2 (OR 0.461, P = 1.34 × 10-2) were recognized as protective factors against GD. Crucially, all 3 exhibited no shared genetic interrelation with GD, further substantiating their potential causal significance in the disease. Conclusion This study unveils pivotal insights into the intricate relationships between serum metabolites and GD risk. By identifying specific risk and protective factors, it opens avenues for more precise disease understanding and management. The findings underline the importance of integrating genomics with metabolomics to fathom the multifaceted nature of GD.
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Affiliation(s)
- Yao Tan
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, Changsha City 410013, China
- Postdoctoral Station of Clinical Medicine, The Third Xiangya Hospital, Central South University, Changsha City 410013, China
| | - Jiayang Yin
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, Changsha City 410013, China
| | - Jiamin Cao
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, Changsha City 410013, China
| | - Bingyu Xie
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, Changsha City 410013, China
| | - Feng Zhang
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, Changsha City 410013, China
| | - Wei Xiong
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, Changsha City 410013, China
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22
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Li L, Li W, Ma Q, Lin Y, Cui Z. Exploring the causal correlations between 486 serum metabolites and systemic lupus erythematosus: a bidirectional Mendelian randomization study. Front Mol Biosci 2023; 10:1281987. [PMID: 38028539 PMCID: PMC10672030 DOI: 10.3389/fmolb.2023.1281987] [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: 09/08/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
Objective: The observational association between circulating metabolites and systemic lupus erythematosus (SLE) has been well documented. However, whether the association is causal remains unclear. In this study, bidirectional Mendelian randomization (MR) was introduced to analyse the causal relationships and possible mechanisms. Methods: We conducted a two-sample bidirectional MR study. A genome-wide association study (GWAS) with 7,824 participants provided data on 486 human blood metabolites. Outcome information was obtained from a large-scale GWAS summary, which contained 5,201 single nucleotide polymorphisms (SNPs) cases and 9,066 control cases of Europeans and yielded a total of 7,071,163 SNPs. The inverse variance weighted (IVW) model was recruited as the primary two-sample MR analysis approach, followed by sensitivity analyses such as the heterogeneity test, horizontal pleiotropy test, leave-one-out analysis, and linkage disequilibrium score (LDSC) regression. Results: In this study, we discovered that 24 metabolites belonging to the lipid, carbohydrate, xenobiotic and amino acid superpathways may increase the risk of SLE occurrence (p < 0.05). In addition, the metabolic disorders of 51 metabolites belonging to the amino acid, energy, xenobiotics, peptide and lipid superpathways were affected by SLE (p < 0.05). Palmitoleate belonging to the lipid superpathway and isobutyrylcarnitine and phenol sulfate belonging to the amino acid superpathway were factors with two-way causation. The metabolic enrichment pathway of bile acid biosynthesis was significant in the forward MR analysis (p = 0.0435). Linolenic acid and linoleic acid metabolism (p = 0.0260), betaine metabolism (p = 0.0314), and glycerolipid metabolism (p = 0.0435) were the significant metabolically enriched pathways in the reverse MR analysis. Conclusion: The levels of some specific metabolites may either contribute to the immune response inducing SLE, or they may be intermediates in the development and progression of SLE. These metabolites can be used as auxiliary diagnostic tools for SLE and for the evaluation of disease progression and therapeutic effects.
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Affiliation(s)
- Li Li
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Wenyu Li
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qing Ma
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Youkun Lin
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhezhe Cui
- Guangxi Key Laboratory of Major Infectious Disease Prevention and Control and Biosafety Emergency Response, Guangxi Centre for Disease Control and Prevention, Nanning, China
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Hindley G, Drange OK, Lin A, Kutrolli G, Shadrin AA, Parker N, O'Connell KS, Rødevand L, Cheng W, Bahrami S, Karadag N, Holen B, Jaholkowski P, Woldeyohannes MT, Djurovic S, Dale AM, Frei O, Ueland T, Smeland OB, Andreassen OA. Cross-trait genome-wide association analysis of C-reactive protein level and psychiatric disorders. Psychoneuroendocrinology 2023; 157:106368. [PMID: 37659117 PMCID: PMC10802833 DOI: 10.1016/j.psyneuen.2023.106368] [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: 03/30/2023] [Revised: 07/10/2023] [Accepted: 08/13/2023] [Indexed: 09/04/2023]
Abstract
C-reactive protein (CRP) tends to be elevated in individuals with psychiatric disorders. Recent findings have suggested a protective effect of the genetic liability to elevated CRP on schizophrenia risk and a causative effect on depression despite weak genetic correlations, while causal relationships with bipolar disorder were inconclusive. We investigated the shared genetic underpinnings of psychiatric disorders and variation in CRP levels. Genome-wide association studies for CRP (n = 575,531), bipolar disorder (n = 413,466), depression (n = 480,359), and schizophrenia (n = 130,644) were used in causal mixture models to compare CRP with psychiatric disorders based on polygenicity, discoverability, and genome-wide genetic overlap. The conjunctional false discovery rate method was used to identify specific shared genetic loci. Shared variants were mapped to putative causal genes, which were tested for overrepresentation among gene ontology gene-sets. CRP was six to ten times less polygenic (n = 1400 vs 8600-14,500 variants) and had a discoverability one to two orders of magnitude higher than psychiatric disorders. Most CRP-associated variants were overlapping with psychiatric disorders. We identified 401 genetic loci jointly associated with CRP and psychiatric disorders with mixed effect directions. Gene-set enrichment analyses identified predominantly CNS-related gene sets for CRP and each of depression and schizophrenia, and basic cellular processes for CRP and bipolar disorder. In conclusion, CRP has a markedly different genetic architecture to psychiatric disorders, but the majority of CRP associated variants are also implicated in psychiatric disorders. Shared genetic loci implicated CNS-related processes to a greater extent than immune processes, which may have implications for how we conceptualise causal relationships between CRP and psychiatric disorders.
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Affiliation(s)
- Guy Hindley
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Akershus University Hospital, Division of Mental Health Services, Department for Special Psychiatry, Lorenskog, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway.
| | - Ole Kristian Drange
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Department of Psychiatry, Sørlandet Hospital, Kristiansand, Norway
| | - Aihua Lin
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Gleda Kutrolli
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Alexey A Shadrin
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway
| | - Nadine Parker
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Kevin S O'Connell
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Linn Rødevand
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Weiqiu Cheng
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Shahram Bahrami
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Naz Karadag
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Børge Holen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Piotr Jaholkowski
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Markos Tesfaye Woldeyohannes
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; NORMENT Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Anders M Dale
- Department of Radiology, University of California, San Diego, La Jolla, CA, United States; Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, CA, United States; Department of Cognitive Science, University of California, San Diego, La Jolla, CA, United States; Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States
| | - Oleksandr Frei
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Thor Ueland
- Research Institute of Internal Medicine, Oslo University Hospital and Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Olav B Smeland
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Department of Psychiatry, Sørlandet Hospital, Kristiansand, Norway
| | - Ole A Andreassen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; KG Jebsen Centre for Neurodevelopmental disorders, University of Oslo, Oslo, Norway.
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Yin Q, Shi G, Zhu L. Association between gut microbiota and sensorineural hearing loss: a Mendelian randomization study. Front Microbiol 2023; 14:1230125. [PMID: 37915857 PMCID: PMC10616596 DOI: 10.3389/fmicb.2023.1230125] [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: 05/31/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023] Open
Abstract
Background Several recent studies speculated that the gut microbiota is associated with sensorineural hearing loss (SNHL) and proposed the concept of the gut-inner ear axis. However, the causal effect of gut microbiota on SNHL is still unknown. In this study, we performed a two-sample Mendelian randomization (MR) analysis to estimate the causal effect of gut microbiota on SNHL. Methods Gut microbiota data were obtained from the largest available genome-wide association study (n = 18,340) conducted by the MiBioGen consortium. The summary statistics of SNHL were obtained from the FinnGen consortium R8 release data (28,310 cases and 302,750 controls). The causal effects were estimated with inverse-variance weighted, MR-Egger, and weighted median. Reverse Mendelian randomization analysis was performed on the bacteria that were found to be associated with SNHL in forward Mendelian randomization analysis. We then performed sensitivity analyses, including Cochran's Q-test, MR-Egger intercept test, MR-PRESSO, cML-MA-BIC, and leave-one-out analysis, to detect heterogeneity and pleiotropy. Results The inverse-variance weighted results suggested that Lachnospiraceae (UCG001) had a significant protective effect against SNHL (odds ratio = 0.85, 95% confidence interval: 0.78-0.93, P = 6.99 × 10-4). In addition, Intestinimonas (odds ratio = 0.89, 95% confidence interval: 0.82-0.97, P = 8.53 × 10-3) presented a suggestively protective effect on SNHL. Rikenellaceae (RC9gutgroup) (odds ratio = 1.08, 95% confidence interval: 1.02-1.15, P = 0.01) and Eubacterium (hallii group) (odds ratio = 1.12, 95% confidence interval: 1.00-1.24, P = 0.048) suggestively increase the risk of SNHL. The results of the reverse MR analysis showed that there is no significant causal effect of SNHL on the gut microbiota. No significant heterogeneity of instrumental variables or pleiotropy was detected. Conclusion The evidence that the four genera mentioned above are associated with SNHL supports the hypothesis of a gut-inner ear axis. Our study provides microbial markers for the prevention and treatment of SNHL, and further studies are needed to explore the mechanisms of the gut microbiome-inner ear axis in health and diseases.
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Affiliation(s)
- Qiuyuan Yin
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Guolin Shi
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Lei Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
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Greco LA, Reay WR, Dayas CV, Cairns MJ. Exploring opportunities for drug repurposing and precision medicine in cannabis use disorder using genetics. Addict Biol 2023; 28:e13313. [PMID: 37500481 PMCID: PMC10909568 DOI: 10.1111/adb.13313] [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: 01/21/2023] [Revised: 05/09/2023] [Accepted: 06/16/2023] [Indexed: 07/29/2023]
Abstract
Cannabis use disorder (CUD) remains a significant public health issue globally, affecting up to one in five adults who use cannabis. Despite extensive research into the molecular underpinnings of the condition, there are no effective pharmacological treatment options available. Therefore, we sought to further explore genetic analyses to prioritise opportunities to repurpose existing drugs for CUD. Specifically, we aimed to identify druggable genes associated with the disorder, integrate transcriptomic/proteomic data and estimate genetic relationships with clinically actionable biochemical traits. Aggregating variants to genes based on genomic position, prioritised the phosphodiesterase gene PDE4B as an interesting target for drug repurposing in CUD. Credible causal PDE4B variants revealed by probabilistic finemapping in and around this locus demonstrated an association with inflammatory and other substance use phenotypes. Gene and protein expression data integrated with the GWAS data revealed a novel CUD associated gene, NPTX1, in whole blood and supported a role for hyaluronidase, a key enzyme in the extracellular matrix in the brain and other tissues. Finally, genetic correlation with biochemical traits revealed a genetic overlap between CUD and immune-related markers such as lymphocyte count, as well as serum triglycerides.
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Affiliation(s)
- Laura A. Greco
- School of Biomedical Sciences and PharmacyThe University of NewcastleCallaghanNew South WalesAustralia
- Precision Medicine Research ProgramHunter Medical Research InstituteNew LambtonNew South WalesAustralia
| | - William R. Reay
- School of Biomedical Sciences and PharmacyThe University of NewcastleCallaghanNew South WalesAustralia
- Precision Medicine Research ProgramHunter Medical Research InstituteNew LambtonNew South WalesAustralia
| | - Christopher V. Dayas
- School of Biomedical Sciences and PharmacyThe University of NewcastleCallaghanNew South WalesAustralia
| | - Murray J. Cairns
- School of Biomedical Sciences and PharmacyThe University of NewcastleCallaghanNew South WalesAustralia
- Precision Medicine Research ProgramHunter Medical Research InstituteNew LambtonNew South WalesAustralia
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Ren F, Shang Q, Zhao S, Yang C, Feng K, Liu J, Kang X, Zhang R, Wang X, Wang X. An exploration of the correlations between seven psychiatric disorders and the risks of breast cancer, breast benign tumors and breast inflammatory diseases: Mendelian randomization analyses. Front Psychiatry 2023; 14:1179562. [PMID: 37448488 PMCID: PMC10338175 DOI: 10.3389/fpsyt.2023.1179562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/06/2023] [Indexed: 07/15/2023] Open
Abstract
Background Previous observational studies have showed that certain psychiatric disorders may be linked to breast cancer risk, there is, however, little understanding of relationships between mental disorders and a variety of breast diseases. This study aims to investigate if mental disorders influence the risks of overall breast cancer, the two subtypes of breast cancer (ER+ and ER-), breast benign tumors and breast inflammatory diseases. Methods During our research, genome-wide association study (GWAS) data for seven psychiatric disorders (schizophrenia, major depressive disorder, bipolar disorder, post-traumatic stress disorder, panic disorder, obsessive-compulsive disorder and anorexia nervosa) from the Psychiatric Genomics Consortium (PGC) and the UK Biobank were selected, and single-nucleotide polymorphisms (SNPs) significantly linked to these mental disorders were identified as instrumental variables. GWAS data for breast diseases came from the Breast Cancer Association Consortium (BCAC) as well as the FinnGen consortium. We performed two-sample Mendelian randomization (MR) analyses and multivariable MR analyses to assess these SNPs' effects on various breast diseases. Both heterogeneity and pleiotropy were evaluated by sensitivity analyses. Results When the GWAS data of psychiatric disorders were derived from the PGC, our research found that schizophrenia significantly increased the risks of overall breast cancer (two-sample MR: OR 1.05, 95%CI [1.03-1.07], p = 3.84 × 10-6; multivariable MR: OR 1.06, 95%CI [1.04-1.09], p = 2.34 × 10-6), ER+ (OR 1.05, 95%CI [1.02-1.07], p = 5.94 × 10-5) and ER- (two-sample MR: OR 1.04, 95%CI [1.01-1.07], p = 0.006; multivariable MR: OR 1.06, 95%CI [1.02-1.10], p = 0.001) breast cancer. Nevertheless, major depressive disorder only showed significant positive association with overall breast cancer (OR 1.12, 95%CI [1.04-1.20], p = 0.003) according to the two-sample MR analysis, but not in the multivariable MR analysis. In regards to the remainder of the mental illnesses and breast diseases, there were no significant correlations. While as for the data from the UK Biobank, schizophrenia did not significantly increase the risk of breast cancer. Conclusions The correlation between schizophrenia and breast cancer found in this study may be false positive results caused by underlying horizontal pleiotropy, rather than a true cause-and-effect relationship. More prospective studies are still needed to be carried out to determine the definitive links between mental illnesses and breast diseases.
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Affiliation(s)
- Fei Ren
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qingyao Shang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuangtao Zhao
- Department of Thoracic Surgery, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Chenxuan Yang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kexin Feng
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiaxiang Liu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiyu Kang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Xiang Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Chae WR, Baumert J, Nübel J, Brasanac J, Gold SM, Hapke U, Otte C. Associations between individual depressive symptoms and immunometabolic characteristics in major depression. Eur Neuropsychopharmacol 2023; 71:25-40. [PMID: 36966710 DOI: 10.1016/j.euroneuro.2023.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 05/29/2023]
Abstract
Inflammation and metabolic dysregulations are likely to underlie atypical, energy-related depressive symptoms such as appetite and sleep alterations. Indeed, increased appetite was previously identified as a core symptom of an immunometabolic subtype of depression. The aim of this study was 1) to replicate the associations between individual depressive symptoms and immunometabolic markers, 2) to extend previous findings with additional markers, and 3) to evaluate the relative contribution of these markers to depressive symptoms. We analyzed data from 266 persons with major depressive disorder (MDD) in the last 12 months from the German Health Interview and Examination Survey for Adults and its mental health module. Diagnosis of MDD and individual depressive symptoms were determined by the Composite International Diagnostic Interview. Associations were analyzed using multivariable regression models, adjusting for depression severity, sociodemographic/behavioral variables, and medication use. Increased appetite was associated with higher body mass index (BMI), waist circumference (WC), insulin, and lower high-density lipoprotein. In contrast, decreased appetite was associated with lower BMI, WC, and fewer metabolic syndrome (MetS) components. Insomnia was associated with higher BMI, WC, number of MetS components, triglycerides, insulin, and lower albumin, while hypersomnia was associated with higher insulin. Suicidal ideation was associated with higher number of MetS components, glucose, and insulin. None of the symptoms were associated with C-reactive protein after adjustment. Appetite alterations and insomnia were most important symptoms associated with metabolic markers. Longitudinal studies should investigate whether the candidate symptoms identified here are predicted by or predict the development of metabolic pathology in MDD.
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Affiliation(s)
- Woo Ri Chae
- Charité - Universitätsmedizin Berlin, Department of Psychiatry and Neurosciences, Campus Benjamin Franklin, Berlin, Germany.
| | - Jens Baumert
- Robert-Koch Institute, Department of Epidemiology and Health Monitoring, Berlin, Germany
| | - Julia Nübel
- Robert-Koch Institute, Department of Epidemiology and Health Monitoring, Berlin, Germany
| | - Jelena Brasanac
- Charité - Universitätsmedizin Berlin, Department of Psychiatry and Neurosciences, Campus Benjamin Franklin, Berlin, Germany
| | - Stefan M Gold
- Charité - Universitätsmedizin Berlin, Department of Psychiatry and Neurosciences, Campus Benjamin Franklin, Berlin, Germany; Charité - Universitätsmedizin Berlin, Medical Department, Section Psychosomatic Medicine, Hindenburgdamm 30, 12203 Berlin, Germany; Institute of Neuroimmunology and Multiple Sclerosis (INIMS), Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulfert Hapke
- Robert-Koch Institute, Department of Epidemiology and Health Monitoring, Berlin, Germany
| | - Christian Otte
- Charité - Universitätsmedizin Berlin, Department of Psychiatry and Neurosciences, Campus Benjamin Franklin, Berlin, Germany
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Yang Z, Li D, He Y, Chen X, Li Z. Unrevealing the shared genetic mechanisms underlying C-reactive protein and schizophrenia. Prog Neuropsychopharmacol Biol Psychiatry 2023; 126:110785. [PMID: 37150315 DOI: 10.1016/j.pnpbp.2023.110785] [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: 10/29/2022] [Revised: 04/18/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Longitudinal observational studies and Mendelian randomization research have obtained contradictory conclusions regarding the association between C-reactive protein (CRP) level and schizophrenia risk. However, the shared genetic mechanisms underlying CRP and schizophrenia remain poorly understood. Here, we examined the global and local genetic correlations using summary statistics from large-scale genome-wide association studies (GWAS) on CRP level and schizophrenia. Furthermore, we identified their shared genetic variants by applying the conditional false discovery rate approach and performed functional analyses of shared variants to explore the shared genetic mechanisms underlying CRP level and schizophrenia. We found a significant negative genetic correlation at the whole genome level and five significant local genetic correlations between CRP level and schizophrenia. Eight-three shared genetic loci were identified, from which single-nucleotide polymorphism (SNP) presents mixed effects on the increased CRP level and schizophrenia risk. Additionally, we identified 64 and 73 candidate genes that were mapped from SNPs with"concordant effect"(ceSNPs) and"discordant effect"(deSNPs) on the CRP level and schizophrenia risk respectively. Functional analyses revealed that genes mapped from ceSNPs and deSNPs exhibited similar patterns of human brain developmental expression trajectories and biological processes, but differed in expression levels and cell-type-specific enrichment in brain tissues. Our findings demonstrated mixed effects of shared genetic architecture between CRP level and schizophrenia, proving a deeper insight into the shared genetic aetiology underlying the CRP level and schizophrenia.
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Affiliation(s)
- Zihao Yang
- Department of Psychiatry, and National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, PR China
| | - David Li
- Department of Psychiatry, and National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, PR China
| | - Ying He
- Department of Psychiatry, and National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, PR China; China National Technology Institute on Mental Disorders & Hunan Key Laboratory of Psychiatry and Mental Health, Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, PR China
| | - Xiaogang Chen
- Department of Psychiatry, and National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, PR China; China National Technology Institute on Mental Disorders & Hunan Key Laboratory of Psychiatry and Mental Health, Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, PR China
| | - Zongchang Li
- Department of Psychiatry, and National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, PR China; China National Technology Institute on Mental Disorders & Hunan Key Laboratory of Psychiatry and Mental Health, Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, PR China.
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Zhao Q, Han B, Xu Q, Wang T, Fang C, Li R, Zhang L, Pei Y. Proteome and genome integration analysis of obesity. Chin Med J (Engl) 2023; 136:910-921. [PMID: 37000968 PMCID: PMC10278747 DOI: 10.1097/cm9.0000000000002644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Indexed: 04/03/2023] Open
Abstract
ABSTRACT The prevalence of obesity has increased worldwide in recent decades. Genetic factors are now known to play a substantial role in the predisposition to obesity and may contribute up to 70% of the risk for obesity. Technological advancements during the last decades have allowed the identification of many hundreds of genetic markers associated with obesity. However, the transformation of current genetic variant-obesity associations into biological knowledge has been proven challenging. Genomics and proteomics are complementary fields, as proteomics extends functional analyses. Integrating genomic and proteomic data can help to bridge a gap in knowledge regarding genetic variant-obesity associations and to identify new drug targets for the treatment of obesity. We provide an overview of the published papers on the integrated analysis of proteomic and genomic data in obesity and summarize four mainstream strategies: overlap, colocalization, Mendelian randomization, and proteome-wide association studies. The integrated analyses identified many obesity-associated proteins, such as leptin, follistatin, and adenylate cyclase 3. Despite great progress, integrative studies focusing on obesity are still limited. There is an increased demand for large prospective cohort studies to identify and validate findings, and further apply these findings to the prevention, intervention, and treatment of obesity. In addition, we also discuss several other potential integration methods.
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Affiliation(s)
- Qigang Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215123, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215213, China
| | - Baixue Han
- Department of Epidemiology and Biostatistics, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215123, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215213, China
| | - Qian Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215123, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215213, China
| | - Tao Wang
- Department of Endocrinology, The Second Affiliated Hospital, Soochow University, Suzhou, Jiangsu 215004, China
| | - Chen Fang
- Department of Endocrinology, The Second Affiliated Hospital, Soochow University, Suzhou, Jiangsu 215004, China
| | - Rui Li
- Department of Gastroenterology, The First Affiliated Hospital, Soochow University, Suzhou, Jiangsu 215006, China
| | - Lei Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215213, China
- Center for Genetic Epidemiology and Genomics, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215123, China
| | - Yufang Pei
- Department of Epidemiology and Biostatistics, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215123, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215213, China
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Househam AM. Effects of stress and mindfulness on epigenetics. VITAMINS AND HORMONES 2023; 122:283-306. [PMID: 36863798 DOI: 10.1016/bs.vh.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Epigenetics are heritable changes in the rate of gene expression without any modification of the DNA sequence and occur in response to environmental changes. Tangible changes to the external surroundings may be practical causes for epigenetic modifications, playing a potential evolutionary role. While fight, flight, or freeze responses once served a concrete role in survival, modern humans may not face similar existential threats that warrant psychological stress. Yet, chronic mental stress is predominant in modern life. This chapter elucidates the deleterious epigenetic changes that occur due to chronic stress. In an exploration of mindfulness-based interventions (MBIs) as a potential antidote to such stress-induced epigenetic modifications, several pathways of action are uncovered. The epigenetic changes that occur because of mindfulness practice are demonstrated across the hypothalamic-pituitary-adrenal axis, serotonergic transmission, genomic health and aging, and neurological biomarkers.
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Affiliation(s)
- Ayman Mukerji Househam
- Department of Social Work, New York University, New York, NY, United States; Department of Psychology, New York University, New York, NY, United States.
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Silveira PP, Meaney MJ. Examining the biological mechanisms of human mental disorders resulting from gene-environment interdependence using novel functional genomic approaches. Neurobiol Dis 2023; 178:106008. [PMID: 36690304 DOI: 10.1016/j.nbd.2023.106008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/30/2022] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
We explore how functional genomics approaches that integrate datasets from human and non-human model systems can improve our understanding of the effect of gene-environment interplay on the risk for mental disorders. We start by briefly defining the G-E paradigm and its challenges and then discuss the different levels of regulation of gene expression and the corresponding data existing in humans (genome wide genotyping, transcriptomics, DNA methylation, chromatin modifications, chromosome conformational changes, non-coding RNAs, proteomics and metabolomics), discussing novel approaches to the application of these data in the study of the origins of mental health. Finally, we discuss the multilevel integration of diverse types of data. Advance in the use of functional genomics in the context of a G-E perspective improves the detection of vulnerabilities, informing the development of preventive and therapeutic interventions.
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Affiliation(s)
- Patrícia Pelufo Silveira
- Department of Psychiatry, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada; Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada.
| | - Michael J Meaney
- Department of Psychiatry, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada; Translational Neuroscience Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (ASTAR), Singapore; Brain - Body Initiative, Agency for Science, Technology and Research (ASTAR), Singapore.
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Adams DM, Reay WR, Cairns MJ. Multiomic prioritisation of risk genes for anorexia nervosa. Psychol Med 2023; 53:1-9. [PMID: 36803885 PMCID: PMC10600818 DOI: 10.1017/s0033291723000235] [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: 08/14/2022] [Revised: 01/12/2023] [Accepted: 01/23/2023] [Indexed: 02/22/2023]
Abstract
BACKGROUND Anorexia nervosa (AN) is a psychiatric disorder associated with marked morbidity. Whilst AN genetic studies could identify novel treatment targets, integration of functional genomics data, including transcriptomics and proteomics, would assist to disentangle correlated signals and reveal causally associated genes. METHODS We used models of genetically imputed expression and splicing from 14 tissues, leveraging mRNA, protein, and mRNA alternative splicing weights to identify genes, proteins, and transcripts, respectively, associated with AN risk. This was accomplished through transcriptome, proteome, and spliceosome-wide association studies, followed by conditional analysis and finemapping to prioritise candidate causal genes. RESULTS We uncovered 134 genes for which genetically predicted mRNA expression was associated with AN after multiple-testing correction, as well as four proteins and 16 alternatively spliced transcripts. Conditional analysis of these significantly associated genes on other proximal association signals resulted in 97 genes independently associated with AN. Moreover, probabilistic finemapping further refined these associations and prioritised putative causal genes. The gene WDR6, for which increased genetically predicted mRNA expression was correlated with AN, was strongly supported by both conditional analyses and finemapping. Pathway analysis of genes revealed by finemapping identified the pathway regulation of immune system process (overlapping genes = MST1, TREX1, PRKAR2A, PROS1) as statistically overrepresented. CONCLUSIONS We leveraged multiomic datasets to genetically prioritise novel risk genes for AN. Multiple-lines of evidence support that WDR6 is associated with AN, whilst other prioritised genes were enriched within immune related pathways, further supporting the role of the immune system in AN.
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Affiliation(s)
- Danielle M. Adams
- School of Biomedical Sciences and Pharmacy, Centre for Complex Disease Neurobiology and Precision Medicine, The University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - William R. Reay
- School of Biomedical Sciences and Pharmacy, Centre for Complex Disease Neurobiology and Precision Medicine, The University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Murray J. Cairns
- School of Biomedical Sciences and Pharmacy, Centre for Complex Disease Neurobiology and Precision Medicine, The University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, Newcastle, NSW, Australia
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Yang Y, Zhou Y, Nyholt DR, Yap CX, Tannenberg RK, Wang Y, Wu Y, Zhu Z, Taylor BV, Gratten J. The shared genetic landscape of blood cell traits and risk of neurological and psychiatric disorders. CELL GENOMICS 2023; 3:100249. [PMID: 36819664 PMCID: PMC9932996 DOI: 10.1016/j.xgen.2022.100249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/03/2022] [Accepted: 12/20/2022] [Indexed: 01/27/2023]
Abstract
Phenotypic associations have been reported between blood cell traits (BCTs) and a range of neurological and psychiatric disorders (NPDs), but in most cases, it remains unclear whether these associations have a genetic basis and, if so, to what extent genetic correlations reflect causality. Here, we report genetic correlations and Mendelian randomization analyses between 11 NPDs and 29 BCTs, using genome-wide association study summary statistics. We found significant genetic correlations for four BCT-NPD pairs, all of which have prior evidence for a phenotypic correlation. We identified a previously unreported causal effect of increased platelet distribution width on susceptibility to Parkinson's disease. We identified multiple functional genes and regulatory elements for specific BCT-NPD pairs, some of which are targets of known drugs. These results enrich our understanding of the shared genetic landscape underlying BCTs and NPDs and provide a robust foundation for future work to improve prognosis and treatment of common NPDs.
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Affiliation(s)
- Yuanhao Yang
- Mater Research Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
- Corresponding author
| | - Yuan Zhou
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Dale R. Nyholt
- School of Biomedical Sciences, Faculty of Health, and Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia
| | - Chloe X. Yap
- Mater Research Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Rudolph K. Tannenberg
- Mater Research Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Ying Wang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Zhihong Zhu
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
- National Centre for Register-based Research, Aarhus University, Aarhus 8210, Denmark
| | - Bruce V. Taylor
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Jacob Gratten
- Mater Research Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
- Corresponding author
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Lin Y, Yang Y, Fu T, Lin L, Zhang X, Guo Q, Chen Z, Liao B, Huang J. Impairment of kidney function and kidney cancer: A bidirectional Mendelian randomization study. Cancer Med 2023; 12:3610-3622. [PMID: 36069056 PMCID: PMC9939186 DOI: 10.1002/cam4.5204] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 07/21/2022] [Accepted: 08/23/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Many observational epidemiology studies discovered that kidney cancer and impaired kidney function have a bidirectional relationship. However, it remains unclear whether these two kinds of traits are causally linked. In this study, we aimed to investigate the bidirectional causal relation between kidney cancer and kidney function biomarkers (creatinine-based estimated glomerular filtration rate (eGFRcrea), cystatin C-based estimated glomerular filtration rate (eGFRcys), blood urea nitrogen (BUN), serum urate, and urinary albumin-to-creatinine ratio (UACR)). METHODS For both directions, single-nucleotide polymorphisms (SNPs), as genetic instruments, for the five kidney function traits were selected from up to 1,004,040 individuals, and SNPs for kidney cancer were from 408,786 participants(1338 cases). In the main analysis, we applied two state-of-the-art MR methods, namely, contamination mixture and Robust Adjusted Profile Score to downweight the effect of weak instrument bias, pleiotropy, and extreme outliers. We additionally conducted traditional MR analyses as sensitivity analyses. Summary-level data of European ancestry were extracted from UK Biobank, Chronic Kidney Disease Genetics Consortium, and Kaiser Permanente. RESULTS Based on 99 SNPs, we found that the eGFRcrea had a significant negative causal effect on the risk of kidney cancer (OR = 0.007, 95% CI:2.6 × 10-4 -0.569, p = 0.041). After adjusting for body composition or diabetes, urate had a significant negative causal effect on kidney cancer (OR <1, p < 0.05). For UACR, it showed a strong causal effect on kidney cancer, after adjusting for body composition (OR = 14.503, 95% CI: 2.546-96.001, p = 0.032). Due to lacking significant signals and effect power for the reverse MR, further investigations are warranted. CONCLUSIONS Our study suggested a potential causal effect of damaged kidney function on kidney cancer. EGFRcrea and UACR might be causally associated with kidney cancer, especially when patients were comorbid with obesity or diabetes. We called for larger sample-size studies to further unravel the underlying causal relationship and the exact mechanism.
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Affiliation(s)
- Yifei Lin
- West China Hospital, Sichuan UniversityChengduPeople's Republic of China
- Program in Genetic Epidemiology and Statistical Genetics, Department of EpidemiologyHarvard T.H. Chan School of Public HealthBostonMassachusettsUSA
| | - Yong Yang
- Medical Device Regulatory Research and Evaluation Centre, West China HospitalSichuan UniversityChengduPeople's Republic of China
| | - Tingting Fu
- Medical Device Regulatory Research and Evaluation Centre, West China HospitalSichuan UniversityChengduPeople's Republic of China
| | - Ling Lin
- Medical Device Regulatory Research and Evaluation Centre, West China HospitalSichuan UniversityChengduPeople's Republic of China
| | - Xingming Zhang
- Department of UrologyInstitute of Urology, West China Hospital, Sichuan UniversityChengduPeople's Republic of China
| | - Qiong Guo
- Medical Device Regulatory Research and Evaluation Centre, West China HospitalSichuan UniversityChengduPeople's Republic of China
| | - Zhenglong Chen
- Medical Device Regulatory Research and Evaluation Centre, West China HospitalSichuan UniversityChengduPeople's Republic of China
| | - Banghua Liao
- Department of UrologyInstitute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan UniversityChengduPeople's Republic of China
| | - Jin Huang
- Medical Device Regulatory Research and Evaluation Centre, West China HospitalSichuan UniversityChengduPeople's Republic of China
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Andreassen OA, Hindley GFL, Frei O, Smeland OB. New insights from the last decade of research in psychiatric genetics: discoveries, challenges and clinical implications. World Psychiatry 2023; 22:4-24. [PMID: 36640404 PMCID: PMC9840515 DOI: 10.1002/wps.21034] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 01/15/2023] Open
Abstract
Psychiatric genetics has made substantial progress in the last decade, providing new insights into the genetic etiology of psychiatric disorders, and paving the way for precision psychiatry, in which individual genetic profiles may be used to personalize risk assessment and inform clinical decision-making. Long recognized to be heritable, recent evidence shows that psychiatric disorders are influenced by thousands of genetic variants acting together. Most of these variants are commonly occurring, meaning that every individual has a genetic risk to each psychiatric disorder, from low to high. A series of large-scale genetic studies have discovered an increasing number of common and rare genetic variants robustly associated with major psychiatric disorders. The most convincing biological interpretation of the genetic findings implicates altered synaptic function in autism spectrum disorder and schizophrenia. However, the mechanistic understanding is still incomplete. In line with their extensive clinical and epidemiological overlap, psychiatric disorders appear to exist on genetic continua and share a large degree of genetic risk with one another. This provides further support to the notion that current psychiatric diagnoses do not represent distinct pathogenic entities, which may inform ongoing attempts to reconceptualize psychiatric nosology. Psychiatric disorders also share genetic influences with a range of behavioral and somatic traits and diseases, including brain structures, cognitive function, immunological phenotypes and cardiovascular disease, suggesting shared genetic etiology of potential clinical importance. Current polygenic risk score tools, which predict individual genetic susceptibility to illness, do not yet provide clinically actionable information. However, their precision is likely to improve in the coming years, and they may eventually become part of clinical practice, stressing the need to educate clinicians and patients about their potential use and misuse. This review discusses key recent insights from psychiatric genetics and their possible clinical applications, and suggests future directions.
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Affiliation(s)
- Ole A Andreassen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Guy F L Hindley
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Oleksandr Frei
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Olav B Smeland
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
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Cai J, Li X, Wu S, Tian Y, Zhang Y, Wei Z, Jin Z, Li X, Chen X, Chen WX. Assessing the causal association between human blood metabolites and the risk of epilepsy. Lab Invest 2022; 20:437. [PMID: 36180952 PMCID: PMC9524049 DOI: 10.1186/s12967-022-03648-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/18/2022] [Indexed: 11/18/2022]
Abstract
Background Metabolic disturbance has been reported in patients with epilepsy. Still, the evidence about the causal role of metabolites in facilitating or preventing epilepsy is lacking. Systematically investigating the causality between blood metabolites and epilepsy would help provide novel targets for epilepsy screening and prevention. Methods We conducted two-sample Mendelian randomization (MR) analysis. Data for 486 human blood metabolites came from a genome-wide association study (GWAS) comprising 7824 participants. GWAS data for epilepsy were obtained from the International League Against Epilepsy (ILAE) consortium for primary analysis and the FinnGen consortium for replication and meta-analysis. Sensitivity analyses were conducted to evaluate heterogeneity and pleiotropy. Results 482 out of 486 metabolites were included for MR analysis following rigorous genetic variants selection. After IVW and sensitivity analysis filtration, six metabolites with causal effects on epilepsy were identified from the ILAE consortium. Only four metabolites remained significant associations with epilepsy when combined with the FinnGen consortium [uridine: odds ratio (OR) = 2.34, 95% confidence interval (CI) = 1.48–3.71, P = 0.0003; 2-hydroxystearate: OR = 1.61, 95% CI = 1.19–2.18, P = 0.002; decanoylcarnitine: OR = 0.82, 95% CI = 0.72–0.94, P = 0.004; myo-inositol: OR = 0.77, 95% CI = 0.62–0.96, P = 0.02]. Conclusion The evidence that the four metabolites mentioned above are associated with epilepsy in a causal way provides a novel insight into the underlying mechanisms of epilepsy by integrating genomics with metabolism, and has an implication for epilepsy screening and prevention. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03648-5.
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Affiliation(s)
- Jiahao Cai
- Department of Neurology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaoyu Li
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Shangbin Wu
- Department of Pediatrics, Guangdong Provincial Hospital of Traditional Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Yang Tian
- Department of Neurology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yani Zhang
- Department of Neurology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zixin Wei
- Department of Pulmonary and Critical Care Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zixiang Jin
- First School of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xiaojing Li
- Department of Neurology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiong Chen
- Department of Pediatric Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Wen-Xiong Chen
- Department of Neurology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China.
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Greco LA, Reay WR, Dayas CV, Cairns MJ. Pairwise genetic meta-analyses between schizophrenia and substance dependence phenotypes reveals novel association signals with pharmacological significance. Transl Psychiatry 2022; 12:403. [PMID: 36151087 PMCID: PMC9508072 DOI: 10.1038/s41398-022-02186-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/25/2022] [Accepted: 09/13/2022] [Indexed: 12/04/2022] Open
Abstract
Almost half of individuals diagnosed with schizophrenia also present with a substance use disorder, however, little is known about potential molecular mechanisms underlying this comorbidity. We used genetic analyses to enhance our understanding of the molecular overlap between these conditions. Our analyses revealed a positive genetic correlation between schizophrenia and the following dependence phenotypes: alcohol (rg = 0.368, SE = 0.076, P = 1.61 × 10-6), cannabis use disorder (rg = 0.309, SE = 0.033, P = 1.97 × 10-20) and nicotine (rg = 0.117, SE = 0.043, P = 7.0 × 10-3), as well as drinks per week (rg = 0.087, SE = 0.021, P = 6.36 × 10-5), cigarettes per day (rg = 0.11, SE = 0.024, P = 4.93 × 10-6) and life-time cannabis use (rg = 0.234, SE = 0.029, P = 3.74 × 10-15). We further constructed latent causal variable (LCV) models to test for partial genetic causality and found evidence for a potential causal relationship between alcohol dependence and schizophrenia (GCP = 0.6, SE = 0.22, P = 1.6 × 10-3). This putative causal effect with schizophrenia was not seen using a continuous phenotype of drinks consumed per week, suggesting that distinct molecular mechanisms underlying dependence are involved in the relationship between alcohol and schizophrenia. To localise the specific genetic overlap between schizophrenia and substance use disorders (SUDs), we conducted a gene-based and gene-set pairwise meta-analysis between schizophrenia and each of the four individual substance dependence phenotypes in up to 790,806 individuals. These bivariate meta-analyses identified 44 associations not observed in the individual GWAS, including five shared genes that play a key role in early central nervous system development. The results from this study further supports the existence of underlying shared biology that drives the overlap in substance dependence in schizophrenia, including specific biological systems related to metabolism and neuronal function.
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Affiliation(s)
- Laura A Greco
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - William R Reay
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - Christopher V Dayas
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton, NSW, Australia.
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Kiltschewskij DJ, Reay WR, Cairns MJ. Evidence of genetic overlap and causal relationships between blood-based biochemical traits and human cortical anatomy. Transl Psychiatry 2022; 12:373. [PMID: 36075890 PMCID: PMC9458732 DOI: 10.1038/s41398-022-02141-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 01/08/2023] Open
Abstract
Psychiatric disorders such as schizophrenia are commonly associated with structural brain alterations affecting the cortex. Recent genetic evidence suggests circulating metabolites and other biochemical traits play a causal role in many psychiatric disorders which could be mediated by changes in the cerebral cortex. Here, we leveraged publicly available genome-wide association study data to explore shared genetic architecture and evidence for causal relationships between a panel of 50 biochemical traits and measures of cortical thickness and surface area. Linkage disequilibrium score regression identified 191 genetically correlated biochemical-cortical trait pairings, with consistent representation of blood cell counts and other biomarkers such as C-reactive protein (CRP), haemoglobin and calcium. Spatially organised patterns of genetic correlation were additionally uncovered upon clustering of region-specific correlation profiles. Interestingly, by employing latent causal variable models, we found strong evidence suggesting CRP and vitamin D exert causal effects on region-specific cortical thickness, with univariable and multivariable Mendelian randomization further supporting a negative causal relationship between serum CRP levels and thickness of the lingual region. Our findings suggest a subset of biochemical traits exhibit shared genetic architecture and potentially causal relationships with cortical structure in functionally distinct regions, which may contribute to alteration of cortical structure in psychiatric disorders.
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Affiliation(s)
- Dylan J Kiltschewskij
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - William R Reay
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton, NSW, Australia.
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Reay WR, Geaghan MP, Atkins JR, Carr VJ, Green MJ, Cairns MJ. Genetics-informed precision treatment formulation in schizophrenia and bipolar disorder. Am J Hum Genet 2022; 109:1620-1637. [PMID: 36055211 PMCID: PMC9502060 DOI: 10.1016/j.ajhg.2022.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/13/2022] [Indexed: 12/02/2022] Open
Abstract
Genetically informed drug development and repurposing is an attractive prospect for improving patient outcomes in psychiatry; however, the effectiveness of these endeavors is confounded by heterogeneity. We propose an approach that links interventions implicated by disorder-associated genetic risk, at the population level, to a framework that can target these compounds to individuals. Specifically, results from genome-wide association studies are integrated with expression data to prioritize individual "directional anchor" genes for which the predicted risk-increasing direction of expression could be counteracted by an existing drug. While these compounds represent plausible therapeutic candidates, they are not likely to be equally efficacious for all individuals. To account for this heterogeneity, we constructed polygenic scores restricted to variants annotated to the network of genes that interact with each directional anchor gene. These metrics, which we call a pharmagenic enrichment score (PES), identify individuals with a higher burden of genetic risk, localized in biological processes related to the candidate drug target, to inform precision drug repurposing. We used this approach to investigate schizophrenia and bipolar disorder and reveal several compounds targeting specific directional anchor genes that could be plausibly repurposed. These genetic risk scores, mapped to the networks associated with target genes, revealed biological insights that cannot be observed in undifferentiated genome-wide polygenic risk score (PRS). For example, an enrichment of these partitioned scores in schizophrenia cases with otherwise low PRS. In summary, genetic risk could be used more specifically to direct drug repurposing candidates that target particular genes implicated in psychiatric and other complex disorders.
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Affiliation(s)
- William R Reay
- Centre for Complex Disease and Precision Medicine, School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia; Precision Medicine Research Program, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Michael P Geaghan
- Kinghorn Centre for Clinical Genomics, Garvan Medical Research Institute, Darlinghurst, NSW, Australia
| | - Joshua R Atkins
- Centre for Complex Disease and Precision Medicine, School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
| | - Vaughan J Carr
- Discipline of Psychiatry and Mental Health, School of Clinical Medicine, University of New South Wales, Randwick, NSW, Australia; Neuroscience Research Australia, Sydney, NSW, Australia; Department of Psychiatry, Monash University, Melbourne, VIC, Australia
| | - Melissa J Green
- Discipline of Psychiatry and Mental Health, School of Clinical Medicine, University of New South Wales, Randwick, NSW, Australia; Neuroscience Research Australia, Sydney, NSW, Australia
| | - Murray J Cairns
- Centre for Complex Disease and Precision Medicine, School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia; Precision Medicine Research Program, Hunter Medical Research Institute, Newcastle, NSW, Australia.
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Reay WR, Geaghan MP, Cairns MJ. The genetic architecture of pneumonia susceptibility implicates mucin biology and a relationship with psychiatric illness. Nat Commun 2022; 13:3756. [PMID: 35768473 PMCID: PMC9243103 DOI: 10.1038/s41467-022-31473-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/17/2022] [Indexed: 01/25/2023] Open
Abstract
Pneumonia remains one of the leading causes of death worldwide. In this study, we use genome-wide meta-analysis of lifetime pneumonia diagnosis (N = 391,044) to identify four association signals outside of the previously implicated major histocompatibility complex region. Integrative analyses and finemapping of these signals support clinically tractable targets, including the mucin MUC5AC and tumour necrosis factor receptor superfamily member TNFRSF1A. Moreover, we demonstrate widespread evidence of genetic overlap with pneumonia susceptibility across the human phenome, including particularly significant correlations with psychiatric phenotypes that remain significant after testing differing phenotype definitions for pneumonia or genetically conditioning on smoking behaviour. Finally, we show how polygenic risk could be utilised for precision treatment formulation or drug repurposing through pneumonia risk scores constructed using variants mapped to pathways with known drug targets. In summary, we provide insights into the genetic architecture of pneumonia susceptibility and genetics informed targets for drug development or repositioning.
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Affiliation(s)
- William R Reay
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Program, Hunter Medical Research Institute, Newcastle, NSW, 2305, Australia
| | - Michael P Geaghan
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Program, Hunter Medical Research Institute, Newcastle, NSW, 2305, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, 2308, Australia.
- Precision Medicine Program, Hunter Medical Research Institute, Newcastle, NSW, 2305, Australia.
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Abstract
Schizophrenia is increasingly recognized as a systemic disease, characterized by dysregulation in multiple physiological systems (eg, neural, cardiovascular, endocrine). Many of these changes are observed as early as the first psychotic episode, and in people at high risk for the disorder. Expanding the search for biomarkers of schizophrenia beyond genes, blood, and brain may allow for inexpensive, noninvasive, and objective markers of diagnosis, phenotype, treatment response, and prognosis. Several anatomic and physiologic aspects of the eye have shown promise as biomarkers of brain health in a range of neurological disorders, and of heart, kidney, endocrine, and other impairments in other medical conditions. In schizophrenia, thinning and volume loss in retinal neural layers have been observed, and are associated with illness progression, brain volume loss, and cognitive impairment. Retinal microvascular changes have also been observed. Abnormal pupil responses and corneal nerve disintegration are related to aspects of brain function and structure in schizophrenia. In addition, studying the eye can inform about emerging cardiovascular, neuroinflammatory, and metabolic diseases in people with early psychosis, and about the causes of several of the visual changes observed in the disorder. Application of the methods of oculomics, or eye-based biomarkers of non-ophthalmological pathology, to the treatment and study of schizophrenia has the potential to provide tools for patient monitoring and data-driven prediction, as well as for clarifying pathophysiology and course of illness. Given their demonstrated utility in neuropsychiatry, we recommend greater adoption of these tools for schizophrenia research and patient care.
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Affiliation(s)
- Steven M Silverstein
- Department of Psychiatry, University of Rochester Medical Center, Rochester, NY, USA
- Department of Ophthalmology, University of Rochester Medical Center, Rochester, NY, USA
- Department of Neuroscience, University of Rochester Medical Center, Rochester, NY, USA
- Center for Visual Science, University of Rochester, Rochester, NY, USA
| | - Joy J Choi
- Department of Psychiatry, University of Rochester Medical Center, Rochester, NY, USA
| | - Kyle M Green
- Department of Ophthalmology, University of Rochester Medical Center, Rochester, NY, USA
| | | | - Rajeev S Ramchandran
- Department of Ophthalmology, University of Rochester Medical Center, Rochester, NY, USA
- Department of Public Health Sciences, University of Rochester Medical Center, Rochester, NY, USA
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