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Opsasnick LA, Zhao W, Schmitz LL, Ratliff SM, Faul JD, Zhou X, Needham BL, Smith JA. Epigenome-wide association study of long-term psychosocial stress in older adults. Epigenetics 2024; 19:2323907. [PMID: 38431869 PMCID: PMC10913704 DOI: 10.1080/15592294.2024.2323907] [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: 11/13/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
Long-term psychosocial stress is strongly associated with negative physical and mental health outcomes, as well as adverse health behaviours; however, little is known about the role that stress plays on the epigenome. One proposed mechanism by which stress affects DNA methylation is through health behaviours. We conducted an epigenome-wide association study (EWAS) of cumulative psychosocial stress (n = 2,689) from the Health and Retirement Study (mean age = 70.4 years), assessing DNA methylation (Illumina Infinium HumanMethylationEPIC Beadchip) at 789,656 CpG sites. For identified CpG sites, we conducted a formal mediation analysis to examine whether smoking, alcohol use, physical activity, and body mass index (BMI) mediate the relationship between stress and DNA methylation. Nine CpG sites were associated with psychosocial stress (all p < 9E-07; FDR q < 0.10). Additionally, health behaviours and/or BMI mediated 9.4% to 21.8% of the relationship between stress and methylation at eight of the nine CpGs. Several of the identified CpGs were in or near genes associated with cardiometabolic traits, psychosocial disorders, inflammation, and smoking. These findings support our hypothesis that psychosocial stress is associated with DNA methylation across the epigenome. Furthermore, specific health behaviours mediate only a modest percentage of this relationship, providing evidence that other mechanisms may link stress and DNA methylation.
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Affiliation(s)
- Lauren A. Opsasnick
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Lauren L. Schmitz
- Robert M. La Follette School of Public Affairs, University of Wisconsin-Madison, Madison, WI, USA
| | - Scott M. Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Xiang Zhou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Belinda L. Needham
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
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Ziemann M, Abeysooriya M, Bora A, Lamon S, Kasu MS, Norris MW, Wong YT, Craig JM. Direction-aware functional class scoring enrichment analysis of infinium DNA methylation data. Epigenetics 2024; 19:2375022. [PMID: 38967555 PMCID: PMC11229754 DOI: 10.1080/15592294.2024.2375022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024] Open
Abstract
Infinium Methylation BeadChip arrays remain one of the most popular platforms for epigenome-wide association studies, but tools for downstream pathway analysis have their limitations. Functional class scoring (FCS) is a group of pathway enrichment techniques that involve the ranking of genes and evaluation of their collective regulation in biological systems, but the implementations described for Infinium methylation array data do not retain direction information, which is important for mechanistic understanding of genomic regulation. Here, we evaluate several candidate FCS methods that retain directional information. According to simulation results, the best-performing method involves the mean aggregation of probe limma t-statistics by gene followed by a rank-ANOVA enrichment test using the mitch package. This method, which we call 'LAM,' outperformed an existing over-representation analysis method in simulations, and showed higher sensitivity and robustness in an analysis of real lung tumour-normal paired datasets. Using matched RNA-seq data, we examine the relationship of methylation differences at promoters and gene bodies with RNA expression at the level of pathways in lung cancer. To demonstrate the utility of our approach, we apply it to three other contexts where public data were available. First, we examine the differential pathway methylation associated with chronological age. Second, we investigate pathway methylation differences in infants conceived with in vitro fertilization. Lastly, we analyse differential pathway methylation in 19 disease states, identifying hundreds of novel associations. These results show LAM is a powerful method for the detection of differential pathway methylation complementing existing methods. A reproducible vignette is provided to illustrate how to implement this method.
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Affiliation(s)
- Mark Ziemann
- Bioinformatics Working Group, Burnet Institute, Melbourne, Australia
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Mandhri Abeysooriya
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
- School of Exercise and Nutrition Sciences, Institute for Physical Activity and Nutrition, Deakin University, Geelong, Australia
| | - Anusuiya Bora
- Bioinformatics Working Group, Burnet Institute, Melbourne, Australia
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Séverine Lamon
- School of Exercise and Nutrition Sciences, Institute for Physical Activity and Nutrition, Deakin University, Geelong, Australia
| | - Mary Sravya Kasu
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Mitchell W. Norris
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Yen Ting Wong
- School of Medicine, Deakin University, Geelong, Australia
- Murdoch Children’s Research Institute, Melbourne, Australia
| | - Jeffrey M. Craig
- School of Medicine, Deakin University, Geelong, Australia
- Murdoch Children’s Research Institute, Melbourne, Australia
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Li W, Ballard J, Zhao Y, Long Q. Knowledge-guided learning methods for integrative analysis of multi-omics data. Comput Struct Biotechnol J 2024; 23:1945-1950. [PMID: 38736693 PMCID: PMC11087912 DOI: 10.1016/j.csbj.2024.04.053] [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: 02/15/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/14/2024] Open
Abstract
Integrative analysis of multi-omics data has the potential to yield valuable and comprehensive insights into the molecular mechanisms underlying complex diseases such as cancer and Alzheimer's disease. However, a number of analytical challenges complicate multi-omics data integration. For instance, -omics data are usually high-dimensional, and sample sizes in multi-omics studies tend to be modest. Furthermore, when genes in an important pathway have relatively weak signal, it can be difficult to detect them individually. There is a growing body of literature on knowledge-guided learning methods that can address these challenges by incorporating biological knowledge such as functional genomics and functional proteomics into multi-omics data analysis. These methods have been shown to outperform their counterparts that do not utilize biological knowledge in tasks including prediction, feature selection, clustering, and dimension reduction. In this review, we survey recently developed methods and applications of knowledge-guided multi-omics data integration methods and discuss future research directions.
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Affiliation(s)
- Wenrui Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Drive, Philadelphia, 19104, PA, USA
| | - Jenna Ballard
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, 19104, PA, USA
| | - Yize Zhao
- Department of Biostatistics, School of Public Health, Yale University, 60 College Street, New Haven, 06510, CT, USA
| | - Qi Long
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Drive, Philadelphia, 19104, PA, USA
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4
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Wang G, Zhang H, Shao M, Tian M, Feng H, Li Q, Cao C. Optimal variable identification for accurate detection of causal expression Quantitative Trait Loci with applications in heart-related diseases. Comput Struct Biotechnol J 2024; 23:2478-2486. [PMID: 38952424 PMCID: PMC11215961 DOI: 10.1016/j.csbj.2024.05.050] [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: 02/01/2024] [Revised: 05/31/2024] [Accepted: 05/31/2024] [Indexed: 07/03/2024] Open
Abstract
Gene expression plays a pivotal role in various diseases, contributing significantly to their mechanisms. Most GWAS risk loci are in non-coding regions, potentially affecting disease risk by altering gene expression in specific tissues. This expression is notably tissue-specific, with genetic variants substantially influencing it. However, accurately detecting the expression Quantitative Trait Loci (eQTL) is challenging due to limited heritability in gene expression, extensive linkage disequilibrium (LD), and multiple causal variants. The single variant association approach in eQTL analysis is limited by its susceptibility to capture the combined effects of multiple variants, and a bias towards common variants, underscoring the need for a more robust method to accurately identify causal eQTL variants. To address this, we developed an algorithm, CausalEQTL, which integrates L 0 +L 1 penalized regression with an ensemble approach to localize eQTL, thereby enhancing prediction performance precisely. Our results demonstrate that CausalEQTL outperforms traditional models, including LASSO, Elastic Net, Ridge, in terms of power and overall performance. Furthermore, analysis of heart tissue data from the GTEx project revealed that eQTL sites identified by our algorithm provide deeper insights into heart-related tissue eQTL detection. This advancement in eQTL mapping promises to improve our understanding of the genetic basis of tissue-specific gene expression and its implications in disease. The source code and identified causal eQTLs for CausalEQTL are available on GitHub: https://github.com/zhc-moushang/CausalEQTL.
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Affiliation(s)
- Guishen Wang
- College of Computer Science and Engineering, Changchun University of Technology, Changchun 130012, China
| | - Hangchen Zhang
- College of Computer Science and Engineering, Changchun University of Technology, Changchun 130012, China
| | - Mengting Shao
- Key Laboratory for Bio-Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Min Tian
- Key Laboratory for Bio-Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Hui Feng
- College of Computer Science and Engineering, Changchun University of Technology, Changchun 130012, China
| | - Qiaoling Li
- Department of Cardiology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing 210008, China
| | - Chen Cao
- Key Laboratory for Bio-Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
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Melton HJ, Zhang Z, Deng HW, Wu L, Wu C. MIMOSA: a resource consisting of improved methylome prediction models increases power to identify DNA methylation-phenotype associations. Epigenetics 2024; 19:2370542. [PMID: 38963888 PMCID: PMC11225927 DOI: 10.1080/15592294.2024.2370542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 06/12/2024] [Indexed: 07/06/2024] Open
Abstract
Although DNA methylation (DNAm) has been implicated in the pathogenesis of numerous complex diseases, from cancer to cardiovascular disease to autoimmune disease, the exact methylation sites that play key roles in these processes remain elusive. One strategy to identify putative causal CpG sites and enhance disease etiology understanding is to conduct methylome-wide association studies (MWASs), in which predicted DNA methylation that is associated with complex diseases can be identified. However, current MWAS models are primarily trained using the data from single studies, thereby limiting the methylation prediction accuracy and the power of subsequent association studies. Here, we introduce a new resource, MWAS Imputing Methylome Obliging Summary-level mQTLs and Associated LD matrices (MIMOSA), a set of models that substantially improve the prediction accuracy of DNA methylation and subsequent MWAS power through the use of a large summary-level mQTL dataset provided by the Genetics of DNA Methylation Consortium (GoDMC). Through the analyses of GWAS (genome-wide association study) summary statistics for 28 complex traits and diseases, we demonstrate that MIMOSA considerably increases the accuracy of DNA methylation prediction in whole blood, crafts fruitful prediction models for low heritability CpG sites, and determines markedly more CpG site-phenotype associations than preceding methods. Finally, we use MIMOSA to conduct a case study on high cholesterol, pinpointing 146 putatively causal CpG sites.
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Affiliation(s)
- Hunter J. Melton
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Zichen Zhang
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hong-Wen Deng
- Center of Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
| | - Lang Wu
- Center of Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
| | - Chong Wu
- Cancer Epidemiology Division, University of Hawaii Cancer Center, Honolulu, HI, USA
- Institute for Data Science in Oncology, The UT MD Anderson Cancer Center
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Li M, Yuan Y, Hou Z, Hao S, Jin L, Wang B. Human brain organoid: trends, evolution, and remaining challenges. Neural Regen Res 2024; 19:2387-2399. [PMID: 38526275 PMCID: PMC11090441 DOI: 10.4103/1673-5374.390972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/26/2023] [Accepted: 10/28/2023] [Indexed: 03/26/2024] Open
Abstract
Advanced brain organoids provide promising platforms for deciphering the cellular and molecular processes of human neural development and diseases. Although various studies and reviews have described developments and advancements in brain organoids, few studies have comprehensively summarized and analyzed the global trends in this area of neuroscience. To identify and further facilitate the development of cerebral organoids, we utilized bibliometrics and visualization methods to analyze the global trends and evolution of brain organoids in the last 10 years. First, annual publications, countries/regions, organizations, journals, authors, co-citations, and keywords relating to brain organoids were identified. The hotspots in this field were also systematically identified. Subsequently, current applications for brain organoids in neuroscience, including human neural development, neural disorders, infectious diseases, regenerative medicine, drug discovery, and toxicity assessment studies, are comprehensively discussed. Towards that end, several considerations regarding the current challenges in brain organoid research and future strategies to advance neuroscience will be presented to further promote their application in neurological research.
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Affiliation(s)
- Minghui Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yuhan Yuan
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Zongkun Hou
- School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Shilei Hao
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Liang Jin
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Bochu Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
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Alves VC, Carro E, Figueiro-Silva J. Unveiling DNA methylation in Alzheimer's disease: a review of array-based human brain studies. Neural Regen Res 2024; 19:2365-2376. [PMID: 38526273 PMCID: PMC11090417 DOI: 10.4103/1673-5374.393106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 12/05/2023] [Indexed: 03/26/2024] Open
Abstract
The intricacies of Alzheimer's disease pathogenesis are being increasingly illuminated by the exploration of epigenetic mechanisms, particularly DNA methylation. This review comprehensively surveys recent human-centered studies that investigate whole genome DNA methylation in Alzheimer's disease neuropathology. The examination of various brain regions reveals distinctive DNA methylation patterns that associate with the Braak stage and Alzheimer's disease progression. The entorhinal cortex emerges as a focal point due to its early histological alterations and subsequent impact on downstream regions like the hippocampus. Notably, ANK1 hypermethylation, a protein implicated in neurofibrillary tangle formation, was recurrently identified in the entorhinal cortex. Further, the middle temporal gyrus and prefrontal cortex were shown to exhibit significant hypermethylation of genes like HOXA3, RHBDF2, and MCF2L, potentially influencing neuroinflammatory processes. The complex role of BIN1 in late-onset Alzheimer's disease is underscored by its association with altered methylation patterns. Despite the disparities across studies, these findings highlight the intricate interplay between epigenetic modifications and Alzheimer's disease pathology. Future research efforts should address methodological variations, incorporate diverse cohorts, and consider environmental factors to unravel the nuanced epigenetic landscape underlying Alzheimer's disease progression.
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Affiliation(s)
- Victoria Cunha Alves
- Neurodegenerative Diseases Group, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain
- Network Center for Biomedical Research, Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- PhD Program in Neuroscience, Autonoma de Madrid University, Madrid, Spain
- Neurotraumatology and Subarachnoid Hemorrhage Group, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain
| | - Eva Carro
- Network Center for Biomedical Research, Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- Neurobiology of Alzheimer's Disease Unit, Functional Unit for Research Into Chronic Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Joana Figueiro-Silva
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Science, University of Zurich, Zurich, Switzerland
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Guo X, Chen Y, Huang H, Liu Y, Kong L, Chen L, Lyu H, Gao T, Lai J, Zhang D, Hu S. Serum signature of antibodies to Toxoplasma gondii, rubella virus, and cytomegalovirus in females with bipolar disorder: A cross-sectional study. J Affect Disord 2024; 361:82-90. [PMID: 38844171 DOI: 10.1016/j.jad.2024.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/13/2024]
Abstract
BACKGROUND AND AIM Immunity alterations have been observed in bipolar disorder (BD). However, whether serum positivity of antibodies to Toxoplasma gondii (T gondii), rubella, and cytomegalovirus (CMV) shared clinical relevance with BD, remains controversial. This study aimed to investigate this association. METHODS Antibody seropositivity of IgM and IgG to T gondii, rubella virus, and CMV of females with BD and controls was extracted based on medical records from January 2018 to January 2023. Family history, type of BD, onset age, and psychotic symptom history were also collected. RESULTS 585 individuals with BD and 800 healthy controls were involved. Individuals with BD revealed a lower positive rate of T gondii IgG in the 10-20 aged group (OR = 0.10), and a higher positive rate of rubella IgG in the 10-20 (OR = 5.44) and 20-30 aged group (OR = 3.15). BD with family history preferred a higher positive rate of T gondii IgG (OR = 24.00). Type-I BD owned a decreased positive rate of rubella IgG (OR = 0.37) and an elevated positive rate of CMV IgG (OR = 2.12) compared to type-II BD, while BD with early onset showed contrast results compared to BD without early onset (Rubella IgG, OR = 2.54; CMV IgG, OR = 0.26). BD with psychotic symptom history displayed a lower positive rate of rubella IgG (OR = 0.50). LIMITATIONS Absence of male evidence and control of socioeconomic status and environmental exposure. CONCLUSIONS Differential antibody seropositive rates of T gondii, rubella, and cytomegalovirus in BD were observed.
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Affiliation(s)
- Xiaonan Guo
- Department of Psychiatry, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
| | - Yiqing Chen
- Department of Psychiatry, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
| | - Huimin Huang
- Department of Psychiatry, The Third Affiliated Hospital of Wenzhou Medical University, 325800, Wenzhou, Zhejiang, China.
| | - Yifeng Liu
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China.
| | - Lingzhuo Kong
- Department of Psychiatry, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
| | - Lizichen Chen
- Department of Psychiatry, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
| | - Hailong Lyu
- Department of Psychiatry, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
| | | | - Jianbo Lai
- Department of Psychiatry, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; Zhejiang Key Laboratory of Precision Psychiatry, Hangzhou 310003, China; Brain Research Institute of Zhejiang University, Hangzhou 310058, China; Zhejiang Engineering Center for Mathematical Mental Health, Hangzhou 310003, China; MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China.
| | - Shaohua Hu
- Department of Psychiatry, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; Zhejiang Key Laboratory of Precision Psychiatry, Hangzhou 310003, China; Brain Research Institute of Zhejiang University, Hangzhou 310058, China; Zhejiang Engineering Center for Mathematical Mental Health, Hangzhou 310003, China; MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University School of Medicine, Hangzhou 310058, China; Department of Psychology and Behavioral Sciences, Graduate School, Zhejiang University, Hangzhou 310058, China; Nanhu Brain-computer Interface Institute, Hangzhou 311100, China.
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Park M, Shin JE, Yee J, Ahn YM, Joo EJ. Gene-gene interaction analysis for age at onset of bipolar disorder in a Korean population. J Affect Disord 2024; 361:97-103. [PMID: 38834091 DOI: 10.1016/j.jad.2024.05.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Multiple genes might interact to determine the age at onset of bipolar disorder. We investigated gene-gene interactions related to age at onset of bipolar disorder in the Korean population, using genome-wide association study (GWAS) data. METHODS The study population consisted of 303 patients with bipolar disorder. First, the top 1000 significant single-nucleotide polymorphisms (SNPs) associated with age at onset of bipolar disorder were selected through single SNP analysis by simple linear regression. Subsequently, the QMDR method was used to find gene-gene interactions. RESULTS The best 10 SNPs from simple regression were located in chromosome 1, 2, 3, 10, 11, 14, 19, and 21. Only five SNPs were found in several genes, such as FOXN3, KIAA1217, OPCML, CAMSAP2, and PTPRS. On QMDR analyses, five pairs of SNPs showed significant interactions with a CVC exceeding 1/5 in a two-locus model. The best interaction was found for the pair of rs60830549 and rs12952733 (CVC = 1/5, P < 1E-07). In three-locus models, four combinations of SNPs showed significant associations with age at onset, with a CVC of >1/5. The best three-locus combination was rs60830549, rs12952733, and rs12952733 (CVC = 2/5, P < 1E-6). The SNPs showing significant interactions were located in the KIAA1217, RBFOX3, SDK2, CYP19A1, NTM, SMYD3, and RBFOX1 genes. CONCLUSIONS Our analysis confirmed genetic interactions influencing the age of onset for bipolar disorder and identified several potential candidate genes. Further exploration of the functions of these promising genes, which may have multiple roles within the neuronal network, is necessary.
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Affiliation(s)
- Mira Park
- Department of Preventive Medicine, School of Medicine, Eulji University, Daejeon, Republic of Korea
| | - Ji-Eun Shin
- Department of Biomedical Informatics, School of Medicine, Konyang University, Daejeon, Republic of Korea
| | - Jaeyong Yee
- Department of Physiology and Biophysics, School of Medicine, Eulji University, Daejeon, Republic of Korea
| | - Yong Min Ahn
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Neuropsychiatry, Seoul National University Hospital, Seoul, Republic of Korea
| | - Eun-Jeong Joo
- Department of Psychiatry, Uijeongbu Eulji Medical Center, Eulji University, Gyeonggi, Republic of Korea; Department of Neuropsychiatry, School of Medicine, Eulji University, Daejeon, Republic of Korea.
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10
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Noble PA, Pozhitkov A, Singh K, Woods E, Liu C, Levin M, Javan G, Wan J, Abouhashem AS, Mathew-Steiner SS, Sen CK. Unraveling the Enigma of Organismal Death: Insights, Implications, and Unexplored Frontiers. Physiology (Bethesda) 2024; 39:0. [PMID: 38624244 DOI: 10.1152/physiol.00004.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/21/2024] [Accepted: 04/11/2024] [Indexed: 04/17/2024] Open
Abstract
Significant knowledge gaps exist regarding the responses of cells, tissues, and organs to organismal death. Examining the survival mechanisms influenced by metabolism and environment, this research has the potential to transform regenerative medicine, redefine legal death, and provide insights into life's physiological limits, paralleling inquiries in embryogenesis.
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Affiliation(s)
- Peter A Noble
- Department of Microbiology, University of Alabama Birmingham, Birmingham, Alabama, United States
| | - Alexander Pozhitkov
- Division of Research Informatics, Beckman Research Institute, City of Hope, Duarte, California, United States
| | - Kanhaiya Singh
- Department of Surgery, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Erik Woods
- Ossium Health, Indianapolis, Indiana, United States
| | - Chunyu Liu
- Institute for Human Performance, Upstate Medical University, Syracuse, New York, United States
| | - Michael Levin
- Department of Biology, Tufts University, Medford, Massachusetts, United States
| | - Gulnaz Javan
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, Alabama, United States
| | - Jun Wan
- Department of Surgery, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Ahmed Safwat Abouhashem
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Shomita S Mathew-Steiner
- Department of Surgery, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Chandan K Sen
- Department of Surgery, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
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11
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Breithaupt L, Holsen LM, Ji C, Hu J, Petterway F, Rosa-Caldwell M, Nilsson IA, Thomas JJ, Williams KA, Boutin R, Slattery M, Bulik CM, Arnold SE, Lawson EA, Misra M, Eddy KT. Identification of State Markers in Anorexia Nervosa: Replication and Extension of Inflammation-Associated Biomarkers Using Multiplex Profiling. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2024; 4:100332. [PMID: 38989135 PMCID: PMC11233894 DOI: 10.1016/j.bpsgos.2024.100332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 03/12/2024] [Accepted: 04/01/2024] [Indexed: 07/12/2024] Open
Abstract
Background Proteomics offers potential for detecting and monitoring anorexia nervosa (AN) and its variant, atypical AN (atyp-AN). However, research has been limited by small protein panels, a focus on adult AN, and lack of replication. Methods In this study, we performed Olink multiplex profiling of 92 inflammation-related proteins in females with AN/atyp-AN (n = 64), all of whom were ≤90% of expected body weight, and age-matched healthy control individuals (n = 44). Results Five proteins differed significantly between the primary AN/atyp-AN group and the healthy control group (lower levels: HGF, IL-18R1, TRANCE; higher levels: CCL23, LIF-R). The expression levels of 3 proteins (lower IL-18R1, TRANCE; higher LIF-R) were uniquely disrupted in participants with AN in our primary model. No unique expression levels emerged for atyp-AN. In the total sample, 12 proteins (ADA, CD5, CD6, CXCL1, FGF-21, HGF, IL-12B, IL18, IL-18R1, SIRT2, TNFSF14, TRANCE) were positively correlated with body mass index and 5 proteins (CCL11, FGF-19, IL8, LIF-R, OPG) were negatively correlated with body mass index in our primary models. Conclusions Our results replicate the results of a previous study that demonstrated a dysregulated inflammatory status in AN and extend those results to atyp-AN. Of the 17 proteins correlated with body mass index, 11 were replicated from a previous study that used similar methods, highlighting the promise of inflammatory protein expression levels as biomarkers of AN disease monitoring. Our findings underscore the complexity of AN and atyp-AN by highlighting the inability of the identified proteins to differentiate between these 2 subtypes, thereby emphasizing the heterogeneous nature of these disorders.
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Affiliation(s)
- Lauren Breithaupt
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
- Eating Disorders Clinical and Research Program, Massachusetts General Hospital, Boston, Massachusetts
- Mass General Brigham Multidisciplinary Eating Disorders Research Collaborative, Mass General Brigham, Boston, Massachusetts
| | - Laura M. Holsen
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
- Mass General Brigham Multidisciplinary Eating Disorders Research Collaborative, Mass General Brigham, Boston, Massachusetts
- Division of Women’s Health, Departments of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Chunni Ji
- Mass General Brigham Multidisciplinary Eating Disorders Research Collaborative, Mass General Brigham, Boston, Massachusetts
- Division of Women’s Health, Departments of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Jie Hu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Department of Anesthesia, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Felicia Petterway
- Mass General Brigham Multidisciplinary Eating Disorders Research Collaborative, Mass General Brigham, Boston, Massachusetts
- Neuroendocrine Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Megan Rosa-Caldwell
- Department of Neurology, Beth Israel Deaconess Hospital, Boston, Massachusetts
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | - Ida A.K. Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
- Centre for Eating Disorders Innovation, Karolinska Institutet, Stockholm, Sweden
| | - Jennifer J. Thomas
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
- Eating Disorders Clinical and Research Program, Massachusetts General Hospital, Boston, Massachusetts
- Mass General Brigham Multidisciplinary Eating Disorders Research Collaborative, Mass General Brigham, Boston, Massachusetts
| | - Kyle A. Williams
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
- Pediatric Neuropsychiatry and Immunology Program, Massachusetts General Hospital, Boston, Massachusetts
| | - Regine Boutin
- Neuroendocrine Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Meghan Slattery
- Mass General Brigham Multidisciplinary Eating Disorders Research Collaborative, Mass General Brigham, Boston, Massachusetts
- Neuroendocrine Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Cynthia M. Bulik
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Steven E. Arnold
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts
| | - Elizabeth A. Lawson
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
- Mass General Brigham Multidisciplinary Eating Disorders Research Collaborative, Mass General Brigham, Boston, Massachusetts
- Neuroendocrine Unit, Massachusetts General Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Madhusmita Misra
- Mass General Brigham Multidisciplinary Eating Disorders Research Collaborative, Mass General Brigham, Boston, Massachusetts
- Neuroendocrine Unit, Massachusetts General Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Neuroendocrine Unit, Massachusetts General Children’s Hospital, Boston, Massachusetts
| | - Kamryn T. Eddy
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
- Eating Disorders Clinical and Research Program, Massachusetts General Hospital, Boston, Massachusetts
- Mass General Brigham Multidisciplinary Eating Disorders Research Collaborative, Mass General Brigham, Boston, Massachusetts
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12
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Fu Y, Xie GM, Liu RQ, Xie JL, Zhang J, Zhang J. From aberrant neurodevelopment to neurodegeneration: Insights into the hub gene associated with autism and alzheimer's disease. Brain Res 2024; 1838:148992. [PMID: 38729333 DOI: 10.1016/j.brainres.2024.148992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/31/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Affiliation(s)
- Yu Fu
- Research Center for Translational Medicine at East Hospital, School of Medicine, Tongji University, Shanghai 200010, China
| | - Guang-Ming Xie
- Research Center for Translational Medicine at East Hospital, School of Medicine, Tongji University, Shanghai 200010, China
| | - Rong-Qi Liu
- Research Center for Translational Medicine at East Hospital, School of Life Science and Technology, Tongji University, Shanghai 200010, China
| | - Jun-Ling Xie
- Research Center for Translational Medicine at East Hospital, School of Medicine, Tongji University, Shanghai 200010, China
| | - Jing Zhang
- Research Center for Translational Medicine at East Hospital, School of Life Science and Technology, Tongji University, Shanghai 200010, China.
| | - Jun Zhang
- Research Center for Translational Medicine at East Hospital, School of Medicine, Tongji University, Shanghai 200010, China; Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200092, China.
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13
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Zhu S, He J, Yin L, Zhou J, Lian J, Ren Y, Zhang X, Yuan J, Wang G, Li X. Matrix metalloproteinases targeting in prostate cancer. Urol Oncol 2024; 42:275-287. [PMID: 38806387 DOI: 10.1016/j.urolonc.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/07/2024] [Accepted: 05/06/2024] [Indexed: 05/30/2024]
Abstract
Prostate cancer (PCa) is one of the most common tumors affecting men all over the world. PCa has brought a huge health burden to men around the world, especially for elderly men, but its pathogenesis is unclear. In prostate cancer, epigenetic inheritance plays an important role in the development, progression, and metastasis of the disease. An important role in cancer invasion and metastasis is played by matrix metalloproteinases (MMPs), zinc-dependent proteases that break down extracellular matrix. We review two important forms of epigenetic modification and the role of matrix metalloproteinases in tumor regulation, both of which may be of significant value as novel biomarkers for early diagnosis and prognosis monitoring. The author considers that both mechanisms have promising therapeutic applications for therapeutic agent research in prostate cancer, but that efforts should be made to mitigate or eliminate the side effects of drug therapy in order to maximize quality of life of patients. The understanding of epigenetic modification, MMPs, and their inhibitors in the functional regulation of prostate cancer is gradually advancing, it will provide a new technical means for the prevention of prostate cancer, early diagnosis, androgen-independent prostate cancer treatment, and drug research.
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Affiliation(s)
- Shuying Zhu
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, PR China
| | - Jing He
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, PR China
| | - Liliang Yin
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, PR China
| | - Jiawei Zhou
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, PR China
| | - Jiayi Lian
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, PR China
| | - Yanli Ren
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, PR China
| | - Xinling Zhang
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, PR China
| | - Jinghua Yuan
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, PR China
| | - Gang Wang
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, PR China
| | - Xiaoping Li
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, PR China.
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14
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Liu H, Ma L, Cao Z. DNA methylation and its potential roles in common oral diseases. Life Sci 2024; 351:122795. [PMID: 38852793 DOI: 10.1016/j.lfs.2024.122795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/26/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Oral diseases are among the most common diseases worldwide and are associated with systemic illnesses, and the rising occurrence of oral diseases significantly impacts the quality of life for many individuals. It is crucial to detect and treat these conditions early to prevent them from advancing. DNA methylation is a fundamental epigenetic process that contributes to a variety of diseases including various oral diseases. Taking advantage of its reversibility, DNA methylation becomes a viable therapeutic target by regulating various cellular processes. Understanding the potential role of this DNA alteration in oral diseases can provide significant advances and more opportunities for diagnosis and therapy. This article will review the biology of DNA methylation, and then mainly discuss the key findings on DNA methylation in oral cancer, periodontitis, endodontic disease, oral mucosal disease, and clefts of the lip and/or palate in the background of studies on global DNA methylation and gene-specific DNA methylation.
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Affiliation(s)
- Heyu Liu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, China
| | - Li Ma
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, China; Department of Periodontology, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
| | - Zhengguo Cao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, China; Department of Periodontology, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
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15
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Paljärvi T, Herttua K, Taipale H, Lähteenvuo M, Tanskanen A, Tiihonen J. Cardiovascular mortality in bipolar disorder: Population-based cohort study. Acta Psychiatr Scand 2024; 150:56-64. [PMID: 38826056 DOI: 10.1111/acps.13715] [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: 02/20/2024] [Revised: 04/26/2024] [Accepted: 05/20/2024] [Indexed: 06/04/2024]
Abstract
BACKGROUND Limited evidence base on cause-specific excess cardiovascular disease (CVD) mortality in bipolar disorder (BD) is a barrier to developing preventive interventions aimed at reducing the persistent mortality gap in BD. OBJECTIVE To investigate cause-specific CVD mortality in BD. METHODS We identified all individuals aged 15+ years during 2004-2018 with a diagnosis of BD using Finnish nationwide routine data. Standardised mortality ratios (SMR) with 95% confidence intervals (CI) were calculated using the mortality rates in the general population as weights. RESULTS 53,273 individuals with BD (57% women; median age at BD diagnosis, 40 years), were followed up for 428,426 person-years (median, 8.2 years). There were 5988 deaths due to any cause, of which 26% were due to CVD. The leading cause of absolute excess CVD mortality was coronary artery disease (CAD). The leading causes of relative excess mortality were cardiomegaly (SMR, 4.51; 95% CI, 3.58-5.43), venous thromboembolism (3.03; 2.26-3.81), cardiomyopathy (2.46; 1.95-2.97), and hypertensive heart disease (2.12; 1.71-2.54). The leading causes of absolute CVD mortality showed markedly lower relative excess, including CAD (1.47; 1.34-1.61), ischaemic stroke (1.31; 1.06-1.54), and acute myocardial infarction (1.12; 0.98-1.25). Due to the higher relative excess mortality, structural and functional heart disorders contributed as much as atherosclerotic and ischaemic disorders to the absolute excess mortality. CONCLUSIONS Cardiomyopathy and hypertensive heart disease as the leading causes of relative excess mortality emphasise the contribution of structural and functional heart disorders to the overall excess mortality alongside coronary artery disease. Interventions targeted at these modifiable causes of death should be priorities in the prevention of premature excess CVD mortality in BD.
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Affiliation(s)
- Tapio Paljärvi
- Department of Forensic Psychiatry, University of Eastern Finland, Niuvanniemi Hospital, Kuopio, Finland
| | - Kimmo Herttua
- Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Heidi Taipale
- Department of Forensic Psychiatry, University of Eastern Finland, Niuvanniemi Hospital, Kuopio, Finland
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Markku Lähteenvuo
- Department of Forensic Psychiatry, University of Eastern Finland, Niuvanniemi Hospital, Kuopio, Finland
| | - Antti Tanskanen
- Department of Forensic Psychiatry, University of Eastern Finland, Niuvanniemi Hospital, Kuopio, Finland
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Jari Tiihonen
- Department of Forensic Psychiatry, University of Eastern Finland, Niuvanniemi Hospital, Kuopio, Finland
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
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16
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Cabrera-Mendoza B, Aydin N, Fries GR, Docherty AR, Walss-Bass C, Polimanti R. Estimating the direct effects of the genetic liabilities to bipolar disorder, schizophrenia, and behavioral traits on suicide attempt using a multivariable Mendelian randomization approach. Neuropsychopharmacology 2024; 49:1383-1391. [PMID: 38396255 PMCID: PMC11250798 DOI: 10.1038/s41386-024-01833-2] [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: 08/15/2023] [Revised: 01/25/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024]
Abstract
Bipolar disorder (BD) and schizophrenia (SZ) are associated with higher odds of suicide attempt (SA). In this study, we aimed to explore the effect of BD and SZ genetic liabilities on SA, also considering the contribution of behavioral traits, socioeconomic factors, and substance use disorders. Leveraging large-scale genome-wide association data from the Psychiatric Genomics Consortium (PGC) and the UK Biobank (UKB), we conducted a two-sample Mendelian randomization (MR) analysis to evaluate the putative causal effect of BD (41,917 cases, 371,549 controls) and SZ (53,386 cases, 77,258 controls) on SA (26,590 cases, 492,022 controls). Then, we assessed the putative causal effect of BD and SZ on behavioral traits, socioeconomic factors, and substance use disorders. Considering the associations identified, we evaluated the direct causal effect of behavioral traits, socioeconomic factors, and substance use disorders on SA using a multivariable MR approach. The genetic liabilities to BD and SZ were associated with higher odds of SA (BD odds ratio (OR) = 1.24, p = 3.88 × 10-12; SZ OR = 1.09, p = 2.44 × 10-20). However, while the effect of mental distress (OR = 1.17, p = 1.02 × 10-4) and risk-taking (OR = 1.52, p = 0.028) on SA was independent of SZ genetic liability, the BD-SA relationship appeared to account for the effect of these risk factors. Similarly, the association with loneliness on SA was null after accounting for the effect of SZ genetic liability. These findings highlight the complex interplay between genetic risk of psychiatric disorders and behavioral traits in the context of SA, suggesting the need for a comprehensive mental health assessment for high-risk individuals.
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Affiliation(s)
- Brenda Cabrera-Mendoza
- Department of Psychiatry, Yale School of Medicine, West Haven, CT, 06516, USA.
- VA CT Healthcare System, West Haven, CT, 06516, USA.
| | - Necla Aydin
- Department of Psychiatry, Yale School of Medicine, West Haven, CT, 06516, USA
- Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Gabriel R Fries
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054, Houston, TX, USA
| | - Anna R Docherty
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Huntsman Mental Health Institute, Salt Lake City, UT, USA
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Consuelo Walss-Bass
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054, Houston, TX, USA
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine, West Haven, CT, 06516, USA
- VA CT Healthcare System, West Haven, CT, 06516, USA
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17
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Ding H, Zhang Y, Xie Y, Du X, Ji Y, Lin L, Chang Z, Zhang B, Liang M, Yu C, Qin W. Individualized Texture Similarity Network in Schizophrenia. Biol Psychiatry 2024; 96:176-187. [PMID: 38218309 DOI: 10.1016/j.biopsych.2023.12.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/14/2023] [Accepted: 12/23/2023] [Indexed: 01/15/2024]
Abstract
BACKGROUND Structural covariance network disruption has been considered an important pathophysiological indicator for schizophrenia. Here, we introduced a novel individualized structural covariance network measure, referred to as a texture similarity network (TSN), and hypothesized that the TSN could reliably reveal unique intersubject heterogeneity and complex dysconnectivity patterns in schizophrenia. METHODS The TSN was constructed by measuring the covariance of 180 three-dimensional voxelwise gray-level co-occurrence matrix feature maps between brain areas in each participant. We first tested the validity and reproducibility of the TSN in characterizing the intersubject variability in 2 longitudinal test-retest healthy cohorts. The TSN was further applied to elucidate intersubject variability and dysconnectivity patterns in 10 schizophrenia case-control datasets (609 schizophrenia cases vs. 579 controls) as well as in a first-episode depression dataset (69 patients with depression vs. 69 control participants). RESULTS The test-retest analysis demonstrated higher TSN intersubject than intrasubject variability. Moreover, the TSN reliably revealed higher intersubject variability in both chronic and first-episode schizophrenia, but not in depression. The TSN also reproducibly detected coexistent increased and decreased TSN strength in widespread brain areas, increased global small-worldness, and the coexistence of both structural hyposynchronization in the central networks and hypersynchronization in peripheral networks in patients with schizophrenia but not in patients with depression. Finally, aberrant intersubject variability and covariance strength patterns revealed by the TSN showed a missing or weak correlation with other individualized structural covariance network measures, functional connectivity, and regional volume changes. CONCLUSIONS These findings support the reliability of a TSN in revealing unique structural heterogeneity and complex dysconnectivity in patients with schizophrenia.
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Affiliation(s)
- Hao Ding
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China; School of Medical Imaging, Tianjin Medical University, Tianjin, China
| | - Yu Zhang
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China
| | - Yingying Xie
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaotong Du
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China
| | - Yi Ji
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China
| | - Liyuan Lin
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhongyu Chang
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China
| | - Bin Zhang
- Tianjin Anding Hospital, Tianjin Medical University, Tianjin, China; Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Meng Liang
- School of Medical Imaging, Tianjin Medical University, Tianjin, China
| | - Chunshui Yu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China; School of Medical Imaging, Tianjin Medical University, Tianjin, China.
| | - Wen Qin
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China.
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18
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Kalinowski A, Urban AE. Synaptic pruning in schizophrenia is not classical. Brain Behav Immun 2024; 120:117-118. [PMID: 38788966 DOI: 10.1016/j.bbi.2024.05.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024] Open
Affiliation(s)
- Agnieszka Kalinowski
- Stanford University School of Medicine, Department of Psychiatry and Behavioral Sciences, 401 Quarry Road, Palo Alto, CA, 94304, USA.
| | - Alexander E Urban
- Stanford University School of Medicine, Department of Psychiatry and Behavioral Sciences, 401 Quarry Road, Palo Alto, CA, 94304, USA
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19
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Stevenson A, Misra S, Girma E, Isvoranu AM, Akena D, Alemayehu M, Atwoli L, Gelaye B, Gichuru S, Kariuki SM, Kwobah EK, Kyebuzibwa J, Mwema RM, Newman CP, Newton CRJC, Ongeri L, Stroud RE, Teferra S, Koenen KC, Seedat S. Relationships between trauma types and psychotic symptoms: A network analysis of patients with psychotic disorders in a large, multi-country study in East Africa. Compr Psychiatry 2024; 133:152504. [PMID: 38876004 PMCID: PMC11253580 DOI: 10.1016/j.comppsych.2024.152504] [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: 12/11/2023] [Revised: 04/30/2024] [Accepted: 05/30/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND The link between trauma exposure and psychotic disorders is well-established. Further, specific types of trauma may be associated with specific psychotic symptoms. Network analysis is an approach that can advance our understanding of the associations across trauma types and psychotic symptoms. METHODS We conducted a network analysis with data from 16,628 adult participants (mean age [standard deviation] = 36.3 years [11.5]; 55.8% males) with psychotic disorders in East Africa recruited between 2018 and 2023. We used the Life Events Checklist and the Mini International Neuropsychiatric Interview to determine whether specific trauma types experienced over the life course and specific psychotic symptoms were connected. We used an Ising model to estimate the network connections and bridge centrality statistics to identify nodes that may influence trauma types and psychotic symptoms. RESULTS The trauma type "exposure to a war zone" had the highest bridge strength, betweenness, and closeness. The psychotic symptom "odd or unusual beliefs" had the second highest bridge strength. Exposure to a war zone was directly connected to visual hallucinations, odd or unusual beliefs, passivity phenomena, and disorganized speech. Odd or unusual beliefs were directly connected to transportation accidents, physical assault, war, and witnessing sudden accidental death. CONCLUSION Specific trauma types and psychotic symptoms may interact bidirectionally. Screening for psychotic symptoms in patients with war-related trauma and evaluating lifetime trauma in patients with odd or unusual beliefs in clinical care may be considered points of intervention to limit stimulating additional psychotic symptoms and trauma exposure. This work reaffirms the importance of trauma-informed care for patients with psychotic disorders.
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Affiliation(s)
- Anne Stevenson
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
| | - Supriya Misra
- Department of Public Health, San Francisco State University, San Francisco, CA, USA
| | - Engida Girma
- Department of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Dickens Akena
- Department of Psychiatry, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Melkam Alemayehu
- Department of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Lukoye Atwoli
- Department of Mental Health and Behavioural Sciences, School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya; Brain and Mind Institute, The Aga Khan University, Nairobi, Kenya; Department of Medicine, Medical College East Africa, The Aga Khan University, Nairobi, Kenya
| | - Bizu Gelaye
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Psychiatry, Harvard Medical School and the Chester M. Pierce MD, Division of Global Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Stella Gichuru
- Department of Mental Health, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Symon M Kariuki
- Neurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast, Kilifi, Kenya; Department of Psychiatry, University of Oxford, Oxford, UK
| | - Edith Kamaru Kwobah
- Department of Mental Health, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Joseph Kyebuzibwa
- Department of Psychiatry, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Rehema M Mwema
- Neurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast, Kilifi, Kenya
| | - Carter P Newman
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Charles R J C Newton
- Neurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast, Kilifi, Kenya; Department of Psychiatry, University of Oxford, Oxford, UK
| | - Linnet Ongeri
- Centre for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Rocky E Stroud
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Solomon Teferra
- Department of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Karestan C Koenen
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA; Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Soraya Seedat
- South African Medical Research Council Unit on the Genomics of Brain Disorders, Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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20
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Papageorgakopoulou MA, Bania A, Lagogianni IA, Birmpas K, Assimakopoulou M. The Role of Glia Telomere Dysfunction in the Pathogenesis of Central Nervous System Diseases. Mol Neurobiol 2024; 61:5868-5881. [PMID: 38240992 PMCID: PMC11249767 DOI: 10.1007/s12035-024-03947-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/09/2024] [Indexed: 07/16/2024]
Abstract
Maintaining the telomere length is decisive for the viability and homeostasis process of all the cells of an organism, including human glial cells. Telomere shortening of microglial cells has been widely associated with the onset and progression of neurodegenerative diseases such as Parkinson's and Alzheimer's disease. Additionally, traumatic brain injury appears to have a positive correlation with the telomere-shortening process of microglia, and telomere length can be used as a non-invasive biomarker for the clinical management of these patients. Moreover, telomere involvement through telomerase reactivation and homologous recombination also known as the alternative lengthening of telomeres (ALT) has been described in gliomagenesis pathways, and particular focus has been given in the translational significance of these mechanisms in gliomas diagnosis and prognostic classification. Finally, glia telomere shortening is implicated in some psychiatric diseases. Given that telomere dysfunction of glial cells is involved in the central nervous system (CNS) disease pathogenesis, it represents a promising drug target that could lead to the incorporation of new tools in the medicinal arsenal for the management of so far incurable conditions.
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Affiliation(s)
| | - Angelina Bania
- School of Medicine, University of Patras, 26504, Patras, Greece
| | | | | | - Martha Assimakopoulou
- Department of Anatomy, Histology and Embryology, School of Medicine, University of Patras, Preclinical Medicine Department Building, 1 Asklipiou, 26504, Patras, Greece.
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21
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Livingston NR, Kiemes A, Devenyi GA, Knight S, Lukow PB, Jelen LA, Reilly T, Dima A, Nettis MA, Casetta C, Agyekum T, Zelaya F, Spencer T, De Micheli A, Fusar-Poli P, Grace AA, Williams SCR, McGuire P, Egerton A, Chakravarty MM, Modinos G. Effects of diazepam on hippocampal blood flow in people at clinical high risk for psychosis. Neuropsychopharmacology 2024; 49:1448-1458. [PMID: 38658738 PMCID: PMC11250854 DOI: 10.1038/s41386-024-01864-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/11/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
Elevated hippocampal perfusion has been observed in people at clinical high risk for psychosis (CHR-P). Preclinical evidence suggests that hippocampal hyperactivity is central to the pathophysiology of psychosis, and that peripubertal treatment with diazepam can prevent the development of psychosis-relevant phenotypes. The present experimental medicine study examined whether diazepam can normalize hippocampal perfusion in CHR-P individuals. Using a randomized, double-blind, placebo-controlled, crossover design, 24 CHR-P individuals were assessed with magnetic resonance imaging (MRI) on two occasions, once following a single oral dose of diazepam (5 mg) and once following placebo. Regional cerebral blood flow (rCBF) was measured using 3D pseudo-continuous arterial spin labeling and sampled in native space using participant-specific hippocampus and subfield masks (CA1, subiculum, CA4/dentate gyrus). Twenty-two healthy controls (HC) were scanned using the same MRI acquisition sequence, but without administration of diazepam or placebo. Mixed-design ANCOVAs and linear mixed-effects models were used to examine the effects of group (CHR-P placebo/diazepam vs. HC) and condition (CHR-P diazepam vs. placebo) on rCBF in the hippocampus as a whole and by subfield. Under the placebo condition, CHR-P individuals (mean [±SD] age: 24.1 [±4.8] years, 15 F) showed significantly elevated rCBF compared to HC (mean [±SD] age: 26.5 [±5.1] years, 11 F) in the hippocampus (F(1,41) = 24.7, pFDR < 0.001) and across its subfields (all pFDR < 0.001). Following diazepam, rCBF in the hippocampus (and subfields, all pFDR < 0.001) was significantly reduced (t(69) = -5.1, pFDR < 0.001) and normalized to HC levels (F(1,41) = 0.4, pFDR = 0.204). In conclusion, diazepam normalized hippocampal hyperperfusion in CHR-P individuals, consistent with evidence implicating medial temporal GABAergic dysfunction in increased vulnerability for psychosis.
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Affiliation(s)
- Nicholas R Livingston
- Department of Psychological Medicine, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK.
| | - Amanda Kiemes
- Department of Psychological Medicine, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Gabriel A Devenyi
- Department of Psychiatry, McGill University, Montreal, QC, Canada
- Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal, QC, Canada
| | - Samuel Knight
- Department of Psychological Medicine, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Paulina B Lukow
- Institute of Cognitive Neuroscience, University College London, London, UK
- Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Luke A Jelen
- Department of Psychological Medicine, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Thomas Reilly
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Aikaterini Dima
- Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Maria Antonietta Nettis
- Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Cecilia Casetta
- Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Tyler Agyekum
- Department of Psychiatry, McGill University, Montreal, QC, Canada
- Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal, QC, Canada
| | - Fernando Zelaya
- Department of Neuroimaging, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Thomas Spencer
- Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
- Outreach and Support in South-London (OASIS) service, South London and Maudsley (SLaM) NHS Foundation Trust, London, UK
| | - Andrea De Micheli
- Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
- Outreach and Support in South-London (OASIS) service, South London and Maudsley (SLaM) NHS Foundation Trust, London, UK
| | - Paolo Fusar-Poli
- Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
- Outreach and Support in South-London (OASIS) service, South London and Maudsley (SLaM) NHS Foundation Trust, London, UK
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Anthony A Grace
- Departments of Neuroscience, Psychiatry and Psychology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Steve C R Williams
- Department of Neuroimaging, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Philip McGuire
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Alice Egerton
- Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - M Mallar Chakravarty
- Department of Psychiatry, McGill University, Montreal, QC, Canada
- Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal, QC, Canada
| | - Gemma Modinos
- Department of Psychological Medicine, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
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22
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Reid M, Lin A, Farhat LC, Fernandez TV, Olfson E. The genetics of trichotillomania and excoriation disorder: A systematic review. Compr Psychiatry 2024; 133:152506. [PMID: 38833896 DOI: 10.1016/j.comppsych.2024.152506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 05/09/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Trichotillomania (TTM) and excoriation disorder (ED) are impairing obsessive-compulsive related disorders that are common in the general population and for which there are no clear first-line medications, highlighting the need to better understand the underlying biology of these disorders to inform treatments. Given the importance of genetics in obsessive-compulsive disorder (OCD), evaluating genetic factors underlying TTM and ED may advance knowledge about the pathophysiology of these body-focused repetitive behaviors. AIM In this systematic review, we summarize the available evidence on the genetics of TTM and ED and highlight gaps in the field warranting further research. METHOD We systematically searched Embase, PsycInfo, PubMed, Medline, Scopus, and Web of Science for original studies in genetic epidemiology (family or twin studies) and molecular genetics (candidate gene and genome-wide) published up to June 2023. RESULTS Of the 3536 records identified, 109 studies were included in this review. These studies indicated that genetic factors play an important role in the development of TTM and ED, some of which may be shared across the OCD spectrum, but there are no known high-confidence specific genetic risk factors for either TTM or ED. CONCLUSIONS Our review underscores the need for additional genome-wide research conducted on the genetics of TTM and ED, for instance, genome-wide association and whole-genome/whole-exome DNA sequencing studies. Recent advances in genomics have led to the discovery of risk genes in several psychiatric disorders, including related conditions such as OCD, but to date, TTM and ED have remained understudied.
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Affiliation(s)
- Madison Reid
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA; The University of the South, USA
| | - Ashley Lin
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA
| | - Luis C Farhat
- Department of Psychiatry, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Thomas V Fernandez
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA; Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Emily Olfson
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA; Wu Tsai Institute, Yale University, New Haven, CT, USA.
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23
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Jefsen OH, Holde K, McGrath JJ, Rajagopal VM, Albiñana C, Vilhjálmsson BJ, Grove J, Agerbo E, Yilmaz Z, Plana-Ripoll O, Munk-Olsen T, Demontis D, Børglum A, Mors O, Bulik CM, Mortensen PB, Petersen LV. Polygenic Risk of Mental Disorders and Subject-Specific School Grades. Biol Psychiatry 2024; 96:222-229. [PMID: 38061465 DOI: 10.1016/j.biopsych.2023.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/04/2023] [Accepted: 11/18/2023] [Indexed: 01/21/2024]
Abstract
BACKGROUND Education is essential for socioeconomic security and long-term mental health; however, mental disorders are often detrimental to the educational trajectory. Genetic correlations between mental disorders and educational attainment do not always align with corresponding phenotypic associations, implying heterogeneity in the genetic overlap. METHODS We unraveled this heterogeneity by investigating associations between polygenic risk scores for 6 mental disorders and fine-grained school outcomes: school grades in language and mathematics in ninth grade and high school, as well as educational attainment by age 25, using nationwide-representative data from established cohorts (N = 79,489). RESULTS High polygenic liability of attention-deficit/hyperactivity disorder was associated with lower grades in language and mathematics, whereas high polygenic risk of anorexia nervosa or bipolar disorder was associated with higher grades in language and mathematics. Associations between polygenic risk and school grades were mixed for schizophrenia and major depressive disorder and neutral for autism spectrum disorder. CONCLUSIONS Polygenic risk scores for mental disorders are differentially associated with language and mathematics school grades.
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Affiliation(s)
- Oskar Hougaard Jefsen
- Psychosis Research Unit, Aarhus University Hospital, Psychiatry, Aarhus, Denmark; Center of Functionally Integrative Neuroscience, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
| | - Katrine Holde
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
| | - John J McGrath
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; Queensland Centre for Mental Health Research, Wacol, Queensland, Australia; Queensland Brain Institute, University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Veera Manikandan Rajagopal
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark; Department of Biomedicine, Aarhus University, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark; Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Clara Albiñana
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Bjarni Jóhann Vilhjálmsson
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Jakob Grove
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark; Department of Biomedicine, Aarhus University, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark; Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark; Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Esben Agerbo
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark; Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark; Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Zeynep Yilmaz
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Oleguer Plana-Ripoll
- Department of Clinical Epidemiology, Aarhus University and Aarhus University Hospital, Aarhus, Denmark
| | - Trine Munk-Olsen
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark; Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Ditte Demontis
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark; Department of Biomedicine, Aarhus University, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Anders Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark; Department of Biomedicine, Aarhus University, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark; Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Ole Mors
- Psychosis Research Unit, Aarhus University Hospital, Psychiatry, Aarhus, Denmark
| | - Cynthia M Bulik
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Preben Bo Mortensen
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Liselotte Vogdrup Petersen
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
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24
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Murphy J, Zierotin A, Mongan D, Healy C, Susai SR, O'Donoghue B, Clarke M, O'Connor K, Cannon M, Cotter DR. Associations between soluble urokinase plasminogen activator receptor (suPAR) concentration and psychiatric disorders - A systematic review and meta-analysis. Brain Behav Immun 2024; 120:327-338. [PMID: 38857636 DOI: 10.1016/j.bbi.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/29/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND There is some evidence of an association between inflammation in the pathogenesis of mental disorders. Soluble urokinase plasminogen activator receptor (suPAR) is a biomarker of chronic inflammation, which provides a more stable index of systemic inflammation than more widely used biomarkers. This review aims to synthesise studies that measured suPAR concentrations in individuals with a psychiatric disorder, to determine if these concentrations are altered in comparison to healthy participants. METHOD Comprehensive literature searches from inception to October 2023 were conducted of five relevant databases (PubMed, Web of Science, Embase, Scopus, APA PsychInfo). Random-effects meta-analyses were performed to compare the standardised mean difference of blood suPAR levels (i.e. plasma or serum) for individuals with any psychiatric disorder relative to controls. Separate meta-analyses of suPAR levels were conducted for individuals with schizophrenia or other psychotic disorder and depressive disorder. Risk of bias was assessed using the Newcastle Ottawa Scale. Post-hoc sensitivity analyses included excluding studies at high risk of bias, and analyses of studies that measured suPAR concentrations either in serum or in plasma separately. RESULTS The literature search identified 149 records. Ten full-text studies were screened for eligibility and 9 studies were included for review. Primary analyses revealed no significant difference in suPAR levels between individuals with any psychiatric disorder compared to controls (k = 7, SMD = 0.42, 95 % CI [-0.20, 1.04]). However, those with depressive disorder had elevated suPAR levels relative to controls (k = 3, SMD = 0.61, 95 % CI [0.34, 0.87]). Similarly, secondary analyses showed no evidence of a significant difference in suPAR levels in individuals with any psychiatric disorder when studies at high risk of bias were excluded (k = 6, SMD = 0.54, 95 % CI [-0.14, 1.22]), but elevated suPAR concentrations for those with schizophrenia or other psychotic disorder were found (k = 3, SMD = 0.98, 95 % CI [0.39, 1.58]). Furthermore, studies that analysed plasma suPAR concentrations found elevated plasma suPAR levels in individuals with any psychiatric disorder relative to controls (k = 5, SMD = 0.84, 95 % CI [0.38, 1.29]), while studies measuring serum suPAR levels in any psychiatric disorder did not find a difference (k = 2, SMD = -0.61, 95 % CI [-1.27, 0.04]). For plasma, elevated suPAR concentrations were also identified for those with schizophrenia or other psychotic disorder (k = 3, SMD = 0.98, 95 % CI [0.39, 1.58]). DISCUSSION When studies measuring either only serum or only plasma suPAR were considered, no significant difference in suPAR levels were observed between psychiatric disorder groups, although significantly elevated suPAR levels were detected in those with moderate to severe depressive disorder. However, plasma suPAR levels were significantly elevated in those with any psychiatric disorder relative to controls, while no difference in serum samples was found. A similar finding was reported for schizophrenia or other psychotic disorder. The plasma findings suggest that chronic inflammatory dysregulation may contribute to the pathology of schizophrenia and depressive disorder. Future longitudinal studies are required to fully elucidate the role of this marker in the psychopathology of these disorders.
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Affiliation(s)
- Jennifer Murphy
- Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin, Ireland.
| | - Anna Zierotin
- Department of Psychiatry, University College Dublin, Ireland
| | - David Mongan
- Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin, Ireland; Centre for Public Health, Queen's University Belfast, United Kingdom
| | - Colm Healy
- Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin, Ireland; School of Medicine, University College Dublin, Dublin, Ireland
| | - Subash R Susai
- Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin, Ireland; SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Brian O'Donoghue
- Department of Psychiatry, University College Dublin, Ireland; Department of Psychiatry, St Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - Mary Clarke
- Department of Psychiatry, University College Dublin, Ireland; DETECT Early Intervention for Psychosis Service, Blackrock, Co. Dublin, Ireland
| | - Karen O'Connor
- RISE, Early Intervention in Psychosis Team, South Lee Mental Health Services, Cork, Ireland; Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
| | - Mary Cannon
- Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin, Ireland; SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - David R Cotter
- Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin, Ireland; SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
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25
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Iraji A, Chen J, Lewis N, Faghiri A, Fu Z, Agcaoglu O, Kochunov P, Adhikari BM, Mathalon DH, Pearlson GD, Macciardi F, Preda A, van Erp TGM, Bustillo JR, Díaz-Caneja CM, Andrés-Camazón P, Dhamala M, Adali T, Calhoun VD. Spatial Dynamic Subspaces Encode Sex-Specific Schizophrenia Disruptions in Transient Network Overlap and Their Links to Genetic Risk. Biol Psychiatry 2024; 96:188-197. [PMID: 38070846 PMCID: PMC11156799 DOI: 10.1016/j.biopsych.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/15/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Schizophrenia research reveals sex differences in incidence, symptoms, genetic risk factors, and brain function. However, a knowledge gap remains regarding sex-specific schizophrenia alterations in brain function. Schizophrenia is considered a dysconnectivity syndrome, but the dynamic integration and segregation of brain networks are poorly understood. Recent advances in resting-state functional magnetic resonance imaging allow us to study spatial dynamics, the phenomenon of brain networks spatially evolving over time. Nevertheless, estimating time-resolved networks remains challenging due to low signal-to-noise ratio, limited short-time information, and uncertain network identification. METHODS We adapted a reference-informed network estimation technique to capture time-resolved networks and their dynamic spatial integration and segregation for 193 individuals with schizophrenia and 315 control participants. We focused on time-resolved spatial functional network connectivity, an estimate of network spatial coupling, to study sex-specific alterations in schizophrenia and their links to genomic data. RESULTS Our findings are consistent with the dysconnectivity and neurodevelopment hypotheses and with the cerebello-thalamo-cortical, triple-network, and frontoparietal dysconnectivity models, helping to unify them. The potential unification offers a new understanding of the underlying mechanisms. Notably, the posterior default mode/salience spatial functional network connectivity exhibits sex-specific schizophrenia alteration during the state with the highest global network integration and is correlated with genetic risk for schizophrenia. This dysfunction is reflected in regions with weak functional connectivity to corresponding networks. CONCLUSIONS Our method can effectively capture spatially dynamic networks, detect nuanced schizophrenia effects including sex-specific ones, and reveal the intricate relationship of dynamic information to genomic data. The results also underscore the clinical potential of dynamic spatial dependence and weak connectivity.
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Affiliation(s)
- Armin Iraji
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science, Atlanta, Georgia; Department of Computer Science, Georgia State University, Atlanta, Georgia.
| | - Jiayu Chen
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science, Atlanta, Georgia
| | - Noah Lewis
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science, Atlanta, Georgia; Department of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Ashkan Faghiri
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science, Atlanta, Georgia
| | - Zening Fu
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science, Atlanta, Georgia
| | - Oktay Agcaoglu
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science, Atlanta, Georgia
| | - Peter Kochunov
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Maryland
| | - Bhim M Adhikari
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Maryland
| | - Daniel H Mathalon
- Department of Psychiatry, University of California San Francisco, San Francisco, California; San Francisco Veteran Affairs Medical Center, San Francisco, California
| | - Godfrey D Pearlson
- Departments of Psychiatry and Neuroscience, Yale University School of Medicine, New Haven, Connecticut
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, California
| | - Adrian Preda
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, California
| | - Theo G M van Erp
- Clinical Translational Neuroscience Laboratory, Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, California
| | - Juan R Bustillo
- Department of Psychiatry and Behavioral Sciences, University of New Mexico, Albuquerque, New Mexico
| | - Covadonga M Díaz-Caneja
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Pablo Andrés-Camazón
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Mukesh Dhamala
- Department of Physics and Astronomy, Georgia State University, Atlanta, Georgia
| | - Tulay Adali
- Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, Baltimore, Maryland
| | - Vince D Calhoun
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science, Atlanta, Georgia; Department of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia.
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26
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Chen HW, Huang RD, Li LH, Zhou R, Cao BF, Liu K, Wang SA, Zhong Q, Wei YF, Wu XB. Impact of healthy lifestyle on the incidence and progression trajectory of mental disorders: A prospective study in the UK Biobank. J Affect Disord 2024; 358:383-390. [PMID: 38735583 DOI: 10.1016/j.jad.2024.05.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
BACKGROUND Healthier lifestyle decreased the risk of mental disorders (MDs) such as depression and anxiety. However, research on the effects of a comprehensive healthy lifestyle on their progression is lacking. METHODS 385,704 individuals without baseline MDs from the UK Biobank cohort were included. A composite healthy lifestyle score was computed by assessing alcohol intake, smoking status, television viewing time, physical activity, sleep duration, fruit and vegetable intake, oily fish intake, red meat intake, and processed meat intake. Follow-up utilized hospital and death register records. Multistate model was used to examine the role of healthy lifestyle on the progression of specific MDs, while a piecewise Cox regression model was utilized to assess the influence of healthy lifestyle across various phases of disease progression. RESULTS Higher lifestyle score reduced risks of transitions from baseline to anxiety and depression, as well as from anxiety and depression to comorbidity, with corresponding hazard ratios (HR) and 95 % confidence intervals (CI) of 0.94 (0.93, 0.95), 0.90 (0.89, 0.91), 0.94 (0.91, 0.98), and 0.95 (0.92, 0.98), respectively. Healthier lifestyle decreased the risk of transitioning from anxiety to comorbidity within 2 years post-diagnosis, with HR 0.93 (0.88, 0.98). Higher lifestyle scores at 2-4 years and 4-6 years post-depression onset were associated with reduced risk of comorbidity, with HR 0.93 (0.87, 0.99) and 0.92 (0.86, 0.99), respectively. LIMITATION The generalizability to other ethnic groups is limited. CONCLUSION This study observed a protective role of holistic healthy lifestyle in the trajectory of MDs and contributed to identifying critical progression windows.
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Affiliation(s)
- Hao-Wen Chen
- Department of Epidemiology, School of Public Health, Southern Medical University (Guangdong Provincial Key Laboratory of Tropical Disease Research), Guangzhou 510515, China
| | - Rui-Dian Huang
- Public Health Division, Hospital of Zhongluotan Town, Baiyun District, Guangzhou 510515, China
| | - Liang-Hua Li
- Public Health Division, Hospital of Zhongluotan Town, Baiyun District, Guangzhou 510515, China
| | - Rui Zhou
- Department of Epidemiology, School of Public Health, Southern Medical University (Guangdong Provincial Key Laboratory of Tropical Disease Research), Guangzhou 510515, China
| | - Bi-Fei Cao
- Department of Epidemiology, School of Public Health, Southern Medical University (Guangdong Provincial Key Laboratory of Tropical Disease Research), Guangzhou 510515, China
| | - Kuan Liu
- Department of Epidemiology, School of Public Health, Southern Medical University (Guangdong Provincial Key Laboratory of Tropical Disease Research), Guangzhou 510515, China
| | - Shi-Ao Wang
- Department of Epidemiology, School of Public Health, Southern Medical University (Guangdong Provincial Key Laboratory of Tropical Disease Research), Guangzhou 510515, China
| | - Qi Zhong
- Department of Epidemiology, School of Public Health, Southern Medical University (Guangdong Provincial Key Laboratory of Tropical Disease Research), Guangzhou 510515, China
| | - Yan-Fei Wei
- Department of Epidemiology, School of Public Health, Southern Medical University (Guangdong Provincial Key Laboratory of Tropical Disease Research), Guangzhou 510515, China
| | - Xian-Bo Wu
- Department of Epidemiology, School of Public Health, Southern Medical University (Guangdong Provincial Key Laboratory of Tropical Disease Research), Guangzhou 510515, China.
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Demircan K, Chillon TS, Jensen RC, Jensen TK, Sun Q, Bonnema SJ, Glintborg D, Bilenberg N, Andersen MS, Schomburg L. Maternal selenium deficiency during pregnancy in association with autism and ADHD traits in children: The Odense Child Cohort. Free Radic Biol Med 2024; 220:324-332. [PMID: 38704054 DOI: 10.1016/j.freeradbiomed.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND Selenoproteins regulate pathways controlling neurodevelopment, e.g., redox signaling and thyroid hormone metabolism. However, studies investigating maternal selenium in relation to child neurodevelopmental disorders are scarce. METHODS 719 mother-child pairs from the prospective population-based Odense Child Cohort study in Denmark were included. Three selenium biomarkers, i.e. concentrations of serum selenium, selenoprotein P (SELENOP), and activity of glutathione peroxidase 3 (GPX3), along with serum copper, zinc and iron were measured in early third trimester (at 28.9+/-0.8 weeks of pregnancy). ADHD and ASD traits in children were assessed systematically using the established Child Behaviour Checklist at 5 years of age, based on a Danish reference cohort with cut-off at 90th percentile. Multivariable regression models adjusted for biologically relevant confounders were applied. RESULTS 155 of 719 (21.6 %) children had ASD traits and 59 of 719 (8.2 %) children had traits of ADHD at 5 years of age. In crude and adjusted models, all three selenium biomarkers associated inversely with ADHD traits. For ADHD, fully adjusted OR for 10 μg/L increment in selenium was 0.76 (95 % CI 0.60, 0.94), for one mg/L increment in SELENOP was 0.73 (0.56, 0.95), and for 10 U/L increment in GPx3 was 0.93 (0.87,1.00). Maternal total selenium was inversely associated with child ASD traits, OR per 10 μg/L increment was 0.85 (0.74, 0,98). SELENOP and GPx3 were not associated with ASD traits. The associations were specific to selenium, as other trace elements such as copper, zinc, or iron were not associated with the outcomes. CONCLUSIONS The results provide coherent evidence for selenium deficiency as a risk factor for ADHD and ASD traits in an environment with borderline supply, the causality of which should be elucidated in a randomized controlled trial.
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Affiliation(s)
- Kamil Demircan
- Institute for Experimental Endocrinology, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Thilo Samson Chillon
- Institute for Experimental Endocrinology, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Richard Christian Jensen
- Department of Endocrinology, Odense University Hospital, Kløvervænget 6, 5000, Odense C, Denmark; University of Southern Denmark, Odense, Denmark; Department of Clinical Pharmacology, Pharmacy and Environmental Medicine, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Tina Kold Jensen
- Department of Clinical Pharmacology, Pharmacy and Environmental Medicine, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark; Odense Child Cohort, Hans Christian Andersen Children's Hospital, Odense University Hospital, Kløvervænget 23C, 5000, Odense C, Denmark; OPEN Patient Data Explorative Network (OPEN), SDU, Denmark
| | - Qian Sun
- Institute for Experimental Endocrinology, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Steen Joop Bonnema
- Department of Endocrinology, Odense University Hospital, Kløvervænget 6, 5000, Odense C, Denmark; University of Southern Denmark, Odense, Denmark
| | - Dorte Glintborg
- Department of Endocrinology, Odense University Hospital, Kløvervænget 6, 5000, Odense C, Denmark; University of Southern Denmark, Odense, Denmark
| | - Niels Bilenberg
- Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark; Department of Child and Adolescent Mental Health, Mental Health Services in the Region of Southern Denmark, Odense, Denmark
| | - Marianne Skovsager Andersen
- Department of Endocrinology, Odense University Hospital, Kløvervænget 6, 5000, Odense C, Denmark; University of Southern Denmark, Odense, Denmark.
| | - Lutz Schomburg
- Institute for Experimental Endocrinology, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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Reponen EJ, Ueland T, Rokicki J, Bettella F, Aas M, Werner MCF, Dieset I, Steen NE, Andreassen OA, Tesli M. Polygenic risk for schizophrenia and bipolar disorder in relation to cardiovascular biomarkers. Eur Arch Psychiatry Clin Neurosci 2024; 274:1223-1230. [PMID: 37145175 PMCID: PMC11226473 DOI: 10.1007/s00406-023-01591-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 02/20/2023] [Indexed: 05/06/2023]
Abstract
Individuals with schizophrenia and bipolar disorder are at an increased risk of cardiovascular disease (CVD), and a range of biomarkers related to CVD risk have been found to be abnormal in these patients. Common genetic factors are a putative underlying mechanism, alongside lifestyle factors and antipsychotic medication. However, the extent to which the altered CVD biomarkers are related to genetic factors involved in schizophrenia and bipolar disorder is unknown. In a sample including 699 patients with schizophrenia, 391 with bipolar disorder, and 822 healthy controls, we evaluated 8 CVD risk biomarkers, including BMI, and fasting plasma levels of CVD biomarkers from a subsample. Polygenic risk scores (PGRS) were obtained from genome-wide associations studies (GWAS) of schizophrenia and bipolar disorder from the Psychiatric Genomics Consortium. The CVD biomarkers were used as outcome variables in linear regression models including schizophrenia and bipolar disorder PGRS as predictors, age, sex, diagnostic category, batch and 10 principal components as covariates, controlling for multiple testing by Bonferroni correction for the number of independent tests. Bipolar disorder PGRS was significantly (p = 0.03) negatively associated with BMI after multiple testing correction, and schizophrenia PGRS was nominally negatively associated with BMI. There were no other significant associations between bipolar or schizophrenia PGRS, and other investigated CVD biomarkers. Despite a range of abnormal CVD risk biomarkers in psychotic disorders, we only found a significant negative association between bipolar disorder PGRS and BMI. This has previously been shown for schizophrenia PGRS and BMI, and warrants further exploration.
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Affiliation(s)
- Elina J Reponen
- NORMENT, Norwegian Centre for Mental Disorders Research, Oslo University Hospital and University of Oslo, Nydalen, P.O. Box 4956, N- 0424, Oslo, Norway.
| | - Thor Ueland
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
- K.G. Jebsen Thrombosis Research and Expertise Center, University of Tromsø, Tromsø, Norway
| | - Jaroslav Rokicki
- NORMENT, Norwegian Centre for Mental Disorders Research, Oslo University Hospital and University of Oslo, Nydalen, P.O. Box 4956, N- 0424, Oslo, Norway
- Centre for Research and Education in Forensic Psychiatry, Department of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Francesco Bettella
- NORMENT, Norwegian Centre for Mental Disorders Research, Oslo University Hospital and University of Oslo, Nydalen, P.O. Box 4956, N- 0424, Oslo, Norway
| | - Monica Aas
- NORMENT, Norwegian Centre for Mental Disorders Research, Oslo University Hospital and University of Oslo, Nydalen, P.O. Box 4956, N- 0424, Oslo, Norway
- Department of Mental Health Research and Development, Division of Mental Health and Addiction, Vestre Viken Hospital Trust, Drammen, Norway
| | - Maren C F Werner
- NORMENT, Norwegian Centre for Mental Disorders Research, Oslo University Hospital and University of Oslo, Nydalen, P.O. Box 4956, N- 0424, Oslo, Norway
| | - Ingrid Dieset
- NORMENT, Norwegian Centre for Mental Disorders Research, Oslo University Hospital and University of Oslo, Nydalen, P.O. Box 4956, N- 0424, Oslo, Norway
- Division of Mental Health and Addiction, Acute Psychiatric Department, Oslo University Hospital, Oslo, Norway
| | - Nils E Steen
- NORMENT, Norwegian Centre for Mental Disorders Research, Oslo University Hospital and University of Oslo, Nydalen, P.O. Box 4956, N- 0424, Oslo, Norway
| | - Ole A Andreassen
- NORMENT, Norwegian Centre for Mental Disorders Research, Oslo University Hospital and University of Oslo, Nydalen, P.O. Box 4956, N- 0424, Oslo, Norway
| | - Martin Tesli
- NORMENT, Norwegian Centre for Mental Disorders Research, Oslo University Hospital and University of Oslo, Nydalen, P.O. Box 4956, N- 0424, Oslo, Norway
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
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29
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Rana AK, Bhatt B, Kumar M. β-Hydroxybutyrate Improves the Redox Status, Cytokine Production and Phagocytic Potency of Glucose-Deprived HMC3 Human Microglia-like Cells. J Neuroimmune Pharmacol 2024; 19:35. [PMID: 39042253 DOI: 10.1007/s11481-024-10139-5] [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: 02/10/2024] [Accepted: 07/06/2024] [Indexed: 07/24/2024]
Abstract
Brain glucose deprivation is a component of the pathophysiology of ischemia, glucose transporter1 (GLUT1) deficiency, neurological disorders and occurs transiently in diabetes. Microglia, the neuroimmune cells must function effectively to offer immune defence and debris removal in low-energy settings. Brain glucose deprivation may compromise microglial functions further escalating the disease pathology and deteriorating the overall mental health. In the current study, HMC3 human microglia-like cells were cultured in vitro and exposed to glucose deprivation to investigate the effects of glucose deprivation on phenotypic state, redox status, secretion of cytokines and phagocytic capabilities of HMC3 cells. However, HMC3 cells were able to proliferate in the absence of glucose but showed signs of redox imbalance and mitochondrial dysfunction, as demonstrated by decreased MTT reduction and Mito Tracker™ staining of cells, along with a concomitant reduction in NOX2 protein, superoxide, and nitrite levels. Reduced levels of secreted TNF and IL-1β were the signs of compromised cytokine secretion by glucose-deprived HMC3 microglia-like cells. Moreover, glucose-deprived HMC3 cells also showed reduced phagocytic activity as assessed by fluorescently labelled latex beads-based functional phagocytosis assay. β-hydroxybutyrate (BHB) supplementation restored the redox status, mitochondrial health, cytokine secretion, and phagocytic activity of glucose-deprived HMC3 microglia-like cells. Overall, impaired brain glucose metabolism may hinder microglia's capacity to release diffusible immune factors and perform phagocytosis. This could escalate the mental health issues in neurological diseases where brain glucose metabolism is compromised. Moreover, nutritional ketosis or exogenous ketone supplementation such as BHB may be utilized as a potential metabolic therapies for these conditions.
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Affiliation(s)
- Anil Kumar Rana
- Centre for Excellence in Functional Foods, Food & Nutrition Biotechnology Division, National Agri-Food Biotechnology Institute, S.A.S Nagar, Sector 81 (Knowledge City), Punjab, 140306, India
| | - Babita Bhatt
- Centre for Excellence in Functional Foods, Food & Nutrition Biotechnology Division, National Agri-Food Biotechnology Institute, S.A.S Nagar, Sector 81 (Knowledge City), Punjab, 140306, India
| | - Mohit Kumar
- Centre for Excellence in Functional Foods, Food & Nutrition Biotechnology Division, National Agri-Food Biotechnology Institute, S.A.S Nagar, Sector 81 (Knowledge City), Punjab, 140306, India.
- Adjunct faculty, Regional Centre for Biotechnology, Faridabad, 121001, India.
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30
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Arraes GC, Barreto FS, Vasconcelos GS, Lima CNDC, da Silva FER, Ribeiro WLC, de Sousa FCF, Furtado CLM, Macêdo DS. Long-term Environmental Enrichment Normalizes Schizophrenia-like Abnormalities and Promotes Hippocampal Slc6a4 Promoter Demethylation in Mice Submitted to a Two-hit Model. Neuroscience 2024; 551:205-216. [PMID: 38843988 DOI: 10.1016/j.neuroscience.2024.05.023] [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: 01/02/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024]
Abstract
Here, we explored the impact of prolonged environmental enrichment (EE) on behavioral, neurochemical, and epigenetic changes in the serotonin transporter gene in mice subjected to a two-hit schizophrenia model. The methodology involved administering the viral mimetic PolyI:C to neonatal Swiss mice as a first hit during postnatal days (PND) 5-7, or a sterile saline solution as a control. At PND21, mice were randomly assigned either to standard environment (SE) or EE housing conditions. Between PND35-44, the PolyI:C-treated group was submitted to various unpredictable stressors, constituting the second hit. Behavioral assessments were conducted on PND70, immediately after the final EE exposure. Following the completion of behavioral assessments, we evaluated the expression of proteins in the hippocampus that are indicative of microglial activation, such as Iba-1, as well as related to neurogenesis, including doublecortin (Dcx). We also performed methylation analysis on the serotonin transporter gene (Slc6a4) to investigate alterations in serotonin signaling. The findings revealed that EE for 50 days mitigated sensorimotor gating deficits and working memory impairments in two-hit mice and enhanced their locomotor and exploratory behaviors. EE also normalized the overexpression of hippocampal Iba-1 and increased the expression of hippocampal Dcx. Additionally, we observed hippocampal demethylation of the Slc6a4 gene in the EE-exposed two-hit group, indicating epigenetic reprogramming. These results contribute to the growing body of evidence supporting the protective effects of long-term EE in counteracting behavioral disruptions caused by the two-hit schizophrenia model, pointing to enhanced neurogenesis, diminished microglial activation, and epigenetic modifications of serotonergic pathways as underlying mechanisms.
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Affiliation(s)
- Greicy Coelho Arraes
- Neuropsychopharmacology and Translational Psychiatry Laboratory, Drug Research and Development Center, Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil; Christus University Center (Unichristus-CE), Fortaleza, CE, Brazil
| | - Francisco Stefânio Barreto
- Neuropsychopharmacology and Translational Psychiatry Laboratory, Drug Research and Development Center, Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil; Laboratory of Experimental Oncology, Postgraduate Program in Translational Medicine, Drug Research and Development Center, Federal University of Ceara, Fortaleza, Ceará, Brazil
| | - Germana Silva Vasconcelos
- Neuropsychopharmacology and Translational Psychiatry Laboratory, Drug Research and Development Center, Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Camila Nayane de Carvalho Lima
- Neuropsychopharmacology and Translational Psychiatry Laboratory, Drug Research and Development Center, Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil; Translational Psychiatry Program, Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences at McGovern Medical School, The University of Texas Health Science Center at Houston (UT Health), Houston, TX, USA.
| | - Francisco Eliclécio Rodrigues da Silva
- Neuropsychopharmacology and Translational Psychiatry Laboratory, Drug Research and Development Center, Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | - Francisca Cléa Florenço de Sousa
- Neuropsychopharmacology and Translational Psychiatry Laboratory, Drug Research and Development Center, Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil.
| | - Cristiana Libardi Miranda Furtado
- Laboratory of Experimental Oncology, Postgraduate Program in Translational Medicine, Drug Research and Development Center, Federal University of Ceara, Fortaleza, Ceará, Brazil; Graduate Program in Medical Sciences, Experimental Biology Center - NUBEX, University of Fortaleza, UNIFOR, Fortaleza, Ceará, Brazil
| | - Danielle S Macêdo
- Neuropsychopharmacology and Translational Psychiatry Laboratory, Drug Research and Development Center, Department of Physiology and Pharmacology, Faculty of Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil; National Institute for Translational Medicine (INCT-TM. CNPq), Brazil.
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31
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Hartwell EE, Jinwala Z, Milone J, Ramirez S, Gelernter J, Kranzler HR, Kember RL. Application of polygenic scores to a deeply phenotyped sample enriched for substance use disorders reveals extensive pleiotropy with psychiatric and somatic traits. Neuropsychopharmacology 2024:10.1038/s41386-024-01922-2. [PMID: 39043921 DOI: 10.1038/s41386-024-01922-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/07/2024] [Accepted: 06/28/2024] [Indexed: 07/25/2024]
Abstract
Co-occurring psychiatric, medical, and substance use disorders (SUDs) are common, but the complex pathways leading to such comorbidities are poorly understood. A greater understanding of genetic influences on this phenomenon could inform precision medicine efforts. We used the Yale-Penn dataset, a cross-sectional sample enriched for individuals with SUDs, to examine pleiotropic effects of genetic liability for psychiatric and somatic traits. Participants completed an in-depth interview that provides information on demographics, environment, medical illnesses, and psychiatric and SUDs. Polygenic scores (PGS) for psychiatric disorders and somatic traits were calculated in European-ancestry (EUR; n = 5691) participants and, when discovery datasets were available, for African-ancestry (AFR; n = 4918) participants. Phenome-wide association studies (PheWAS) were then conducted. In AFR participants, the only PGS with significant associations was bipolar disorder (BD), all of which were with substance use phenotypes. In EUR participants, PGS for major depressive disorder (MDD), generalized anxiety disorder (GAD), post-traumatic stress disorder (PTSD), schizophrenia (SCZ), body mass index (BMI), coronary artery disease (CAD), and type 2 diabetes (T2D) all showed significant associations, the majority of which were with phenotypes in the substance use categories. For instance, PGSMDD was associated with over 200 phenotypes, 15 of which were depression-related (e.g., depression criterion count), 55 of which were other psychiatric phenotypes, and 126 of which were substance use phenotypes; and PGSBMI was associated with 138 phenotypes, 105 of which were substance related. Genetic liability for psychiatric and somatic traits is associated with numerous phenotypes across multiple categories, indicative of the broad genetic liability of these traits.
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Affiliation(s)
- Emily E Hartwell
- Crescenz VA Medical Center, Philadelphia, PA, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | - Zeal Jinwala
- Crescenz VA Medical Center, Philadelphia, PA, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Joel Gelernter
- West Haven VA Medical Center, West Haven, CT, USA
- Yale University, New Haven, CT, USA
| | - Henry R Kranzler
- Crescenz VA Medical Center, Philadelphia, PA, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | - Rachel L Kember
- Crescenz VA Medical Center, Philadelphia, PA, USA.
- University of Pennsylvania, Philadelphia, PA, USA.
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Lee PC, Jung IH, Thussu S, Patel V, Wagoner R, Burks KH, Amrute J, Elenbaas JS, Kang CJ, Young EP, Scherer PE, Stitziel NO. Instrumental variable and colocalization analyses identify endotrophin and HTRA1 as potential therapeutic targets for coronary artery disease. iScience 2024; 27:110104. [PMID: 38989470 PMCID: PMC11233907 DOI: 10.1016/j.isci.2024.110104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/26/2024] [Accepted: 05/22/2024] [Indexed: 07/12/2024] Open
Abstract
Coronary artery disease (CAD) remains a leading cause of disease burden globally, and there is a persistent need for new therapeutic targets. Instrumental variable (IV) and genetic colocalization analyses can help identify novel therapeutic targets for human disease by nominating causal genes in genome-wide association study (GWAS) loci. We conducted cis-IV analyses for 20,125 genes and 1,746 plasma proteins with CAD using molecular trait quantitative trait loci variant (QTLs) data from three different studies. 19 proteins and 119 genes were significantly associated with CAD risk by IV analyses and demonstrated evidence of genetic colocalization. Notably, our analyses validated well-established targets such as PCSK9 and ANGPTL4 while also identifying HTRA1 and endotrophin (a cleavage product of COL6A3) as proteins whose levels are causally associated with CAD risk. Further experimental studies are needed to confirm the causal role of the genes and proteins identified through our multiomic cis-IV analyses on human disease.
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Affiliation(s)
- Paul C. Lee
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - In-Hyuk Jung
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shreeya Thussu
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Ved Patel
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Ryan Wagoner
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Kendall H. Burks
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Junedh Amrute
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jared S. Elenbaas
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Chul Joo Kang
- McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - Erica P. Young
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - Philipp E. Scherer
- Touchstone Diabetes Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nathan O. Stitziel
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO 63108, USA
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
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Sullivan PF, Yao S, Hjerling-Leffler J. Schizophrenia genomics: genetic complexity and functional insights. Nat Rev Neurosci 2024:10.1038/s41583-024-00837-7. [PMID: 39030273 DOI: 10.1038/s41583-024-00837-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2024] [Indexed: 07/21/2024]
Abstract
Determining the causes of schizophrenia has been a notoriously intractable problem, resistant to a multitude of investigative approaches over centuries. In recent decades, genomic studies have delivered hundreds of robust findings that implicate nearly 300 common genetic variants (via genome-wide association studies) and more than 20 rare variants (via whole-exome sequencing and copy number variant studies) as risk factors for schizophrenia. In parallel, functional genomic and neurobiological studies have provided exceptionally detailed information about the cellular composition of the brain and its interconnections in neurotypical individuals and, increasingly, in those with schizophrenia. Taken together, these results suggest unexpected complexity in the mechanisms that drive schizophrenia, pointing to the involvement of ensembles of genes (polygenicity) rather than single-gene causation. In this Review, we describe what we now know about the genetics of schizophrenia and consider the neurobiological implications of this information.
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Affiliation(s)
- Patrick F Sullivan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA.
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
| | - Shuyang Yao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jens Hjerling-Leffler
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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34
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Fu Q, Li L, Zhuoma N, Ma R, Zhao Z, Quzuo Z, Wang Z, Yangzong D, Di J. Causality between six psychiatric disorders and digestive tract cancers risk: a two-sample Mendelian randomization study. Sci Rep 2024; 14:16689. [PMID: 39030227 DOI: 10.1038/s41598-024-66535-7] [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: 02/18/2024] [Accepted: 07/02/2024] [Indexed: 07/21/2024] Open
Abstract
Associations between psychiatric disorders and digestive tract cancers have been proposed. However, the causal link between these factors remains unclear. This study pioneers Mendelian randomization (MR) analysis to explore the genetic link between psychiatric disorders and digestive tract cancers risk. We analysed data on six psychiatric disorders [schizophrenia, bipolar disorder, major depressive disorder (MDD), attention deficit hyperactivity disorder, autism spectrum disorder, and panic disorder (PD)] and digestive tract cancers [esophagus cancer (EC), gastric cancer (GC), and colorectal cancer (CRC)] from genome-wide association studies databases. Using instrumental variables identified from significant single nucleotide polymorphism associations, we employed the inverse variance weighted (IVW) method alongside the weighted median (WM) method and MR-Egger regression. The results revealed no causal link between psychiatric disorders and the risk of EC or GC. Psychiatric disorders were not identified as risk factors for CRC. Notably, PD demonstrated a lower CRC risk (OR = 0.79, 95% CI 0.66-0.93, P = 0.01). This MR analysis underscores the lack of a causal association between psychiatric disorders and digestive tract cancers risk while suggesting a potential protective effect of PD against CRC.
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Affiliation(s)
- Qi Fu
- Qinghai University Affiliated Hospital (The Clinical Medical School), Qinghai University, Xining, 810000, Qinghai, China
| | - Linghui Li
- The Fifth People's Hospital of Qinghai Province, Xining, 810000, Qinghai, China
| | - Niyang Zhuoma
- Yushu City People's Hospital, Yushu, 815099, Qinghai, China
| | - Rui Ma
- Qinghai University Affiliated Hospital (The Clinical Medical School), Qinghai University, Xining, 810000, Qinghai, China
| | - Zhixi Zhao
- Yushu City People's Hospital, Yushu, 815099, Qinghai, China
| | - Zhaxi Quzuo
- Yushu City People's Hospital, Yushu, 815099, Qinghai, China
| | - Zhen Wang
- Yushu City People's Hospital, Yushu, 815099, Qinghai, China
| | - Deji Yangzong
- Yushu City People's Hospital, Yushu, 815099, Qinghai, China
| | - Ji Di
- Qinghai University Affiliated Hospital (The Clinical Medical School), Qinghai University, Xining, 810000, Qinghai, China.
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35
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Zhao B, Li Y, Fan Z, Wu Z, Shu J, Yang X, Yang Y, Wang X, Li B, Wang X, Copana C, Yang Y, Lin J, Li Y, Stein JL, O'Brien JM, Li T, Zhu H. Eye-brain connections revealed by multimodal retinal and brain imaging genetics. Nat Commun 2024; 15:6064. [PMID: 39025851 PMCID: PMC11258354 DOI: 10.1038/s41467-024-50309-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/02/2024] [Indexed: 07/20/2024] Open
Abstract
The retina, an anatomical extension of the brain, forms physiological connections with the visual cortex of the brain. Although retinal structures offer a unique opportunity to assess brain disorders, their relationship to brain structure and function is not well understood. In this study, we conducted a systematic cross-organ genetic architecture analysis of eye-brain connections using retinal and brain imaging endophenotypes. We identified novel phenotypic and genetic links between retinal imaging biomarkers and brain structure and function measures from multimodal magnetic resonance imaging (MRI), with many associations involving the primary visual cortex and visual pathways. Retinal imaging biomarkers shared genetic influences with brain diseases and complex traits in 65 genomic regions, with 18 showing genetic overlap with brain MRI traits. Mendelian randomization suggests bidirectional genetic causal links between retinal structures and neurological and neuropsychiatric disorders, such as Alzheimer's disease. Overall, our findings reveal the genetic basis for eye-brain connections, suggesting that retinal images can help uncover genetic risk factors for brain disorders and disease-related changes in intracranial structure and function.
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Affiliation(s)
- Bingxin Zhao
- Department of Statistics and Data Science, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA.
- Applied Mathematics and Computational Science Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Center for AI and Data Science for Integrated Diagnostics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Penn Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Population Aging Research Center, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Yujue Li
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Zirui Fan
- Department of Statistics and Data Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zhenyi Wu
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Juan Shu
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Xiaochen Yang
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Yilin Yang
- Department of Statistics and Data Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xifeng Wang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Bingxuan Li
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Xiyao Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Carlos Copana
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Yue Yang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jinjie Lin
- Yale School of Management, Yale University, New Haven, CT, 06511, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joan M O'Brien
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn Medicine Center for Ophthalmic Genetics in Complex Diseases, Philadelphia, PA, 19104, USA
| | - Tengfei Li
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Biomedical Research Imaging Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Hongtu Zhu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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36
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Wahbeh MH, Boyd RJ, Yovo C, Rike B, McCallion AS, Avramopoulos D. A functional schizophrenia-associated genetic variant near the TSNARE1 and ADGRB1 genes. HGG ADVANCES 2024; 5:100303. [PMID: 38702885 PMCID: PMC11130735 DOI: 10.1016/j.xhgg.2024.100303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/01/2024] [Accepted: 04/23/2024] [Indexed: 05/06/2024] Open
Abstract
Recent collaborative genome-wide association studies (GWAS) have identified >200 independent loci contributing to risk for schizophrenia (SCZ). The genes closest to these loci have diverse functions, supporting the potential involvement of multiple relevant biological processes, yet there is no direct evidence that individual variants are functional or directly linked to specific genes. Nevertheless, overlap with certain epigenetic marks suggest that most GWAS-implicated variants are regulatory. Based on the strength of association with SCZ and the presence of regulatory epigenetic marks, we chose one such variant near TSNARE1 and ADGRB1, rs4129585, to test for functional potential and assay differences that may drive the pathogenicity of the risk allele. We observed that the variant-containing sequence drives reporter expression in relevant neuronal populations in zebrafish. Next, we introduced each allele into human induced pluripotent cells and differentiated four isogenic clones homozygous for the risk allele and five clones homozygous for the non-risk allele into neural progenitor cells. Employing RNA sequencing, we found that the two alleles yield significant transcriptional differences in the expression of 109 genes at a false discovery rate (FDR) of <0.05 and 259 genes at a FDR of <0.1. We demonstrate that these genes are highly interconnected in pathways enriched for synaptic proteins, axon guidance, and regulation of synapse assembly. Exploration of genes near rs4129585 suggests that this variant does not regulate TSNARE1 transcripts, as previously thought, but may regulate the neighboring ADGRB1, a regulator of synaptogenesis. Our results suggest that rs4129585 is a functional common variant that functions in specific pathways likely involved in SCZ risk.
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Affiliation(s)
- Marah H Wahbeh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rachel J Boyd
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christian Yovo
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bailey Rike
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrew S McCallion
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dimitrios Avramopoulos
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Ratsika A, Codagnone MG, Bastiaanssen TFS, Hoffmann Sarda FA, Lynch CMK, Ventura-Silva AP, Rosell-Cardona C, Caputi V, Stanton C, Fülling C, Cryan JF. Maternal high-fat diet-induced microbiota changes are associated with alterations in embryonic brain metabolites and adolescent behaviour. Brain Behav Immun 2024:S0889-1591(24)00489-6. [PMID: 39032541 DOI: 10.1016/j.bbi.2024.07.020] [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: 02/23/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024] Open
Abstract
The developing central nervous system is highly sensitive to nutrient changes during the perinatal period, emphasising the potential impact of alterations of maternal diet on offspring brain development and behaviour. A growing body of research implicates the gut microbiota in neurodevelopment and behaviour. Maternal overweight and obesity during the perinatal period has been linked to changes in neurodevelopment, plasticity and affective disorders in the offspring, with implications for microbial signals from the maternal gut. Here we investigate the impact of maternal high-fat diet (mHFD)-induced changes in microbial signals on offspring brain development, and neuroimmune signals, and the enduring effects on behaviour into adolescence. We first demonstrate that maternal caecal microbiota composition at term pregnancy (embryonic day 18: E18) differs significantly in response to maternal diet. Moreover, mHFD resulted in the upregulation of microbial genes in the maternal intestinal tissue linked to alterations in quinolinic acid synthesis and elevated kynurenine levels in the maternal plasma, both neuronal plasticity mediators related to glutamate metabolism. Metabolomics of mHFD embryonic brains at E18 also detected molecules linked to glutamate-glutamine cycle, including glutamic acid, glutathione disulphide and kynurenine. During adolescence, the mHFD offspring exhibited increased locomotor activity and anxiety-like behaviour in a sex-dependent manner, along with upregulation of glutamate-related genes compared to controls. Overall, our results demonstrate that maternal exposure to high-fat diet results in microbiota changes, behavioural imprinting, altered brain metabolism and glutamate signalling during critical developmental windows during the perinatal period.
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Affiliation(s)
- Anna Ratsika
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland
| | - Martin G Codagnone
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland
| | - Thomaz F S Bastiaanssen
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland
| | - Fabiana A Hoffmann Sarda
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Caoimhe M K Lynch
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland
| | - Ana Paula Ventura-Silva
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland
| | - Cristina Rosell-Cardona
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland
| | - Valentina Caputi
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland
| | | | - Christine Fülling
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland
| | - John F Cryan
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland.
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38
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Lorincz-Comi N, Yang Y, Li G, Zhu X. MRBEE: A bias-corrected multivariable Mendelian randomization method. HGG ADVANCES 2024; 5:100290. [PMID: 38582968 PMCID: PMC11053334 DOI: 10.1016/j.xhgg.2024.100290] [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: 11/17/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024] Open
Abstract
Mendelian randomization (MR) is an instrumental variable approach used to infer causal relationships between exposures and outcomes, which is becoming increasingly popular because of its ability to handle summary statistics from genome-wide association studies. However, existing MR approaches often suffer the bias from weak instrumental variables, horizontal pleiotropy and sample overlap. We introduce MRBEE (MR using bias-corrected estimating equation), a multivariable MR method capable of simultaneously removing weak instrument and sample overlap bias and identifying horizontal pleiotropy. Our extensive simulations and real data analyses reveal that MRBEE provides nearly unbiased estimates of causal effects, well-controlled type I error rates and higher power than comparably robust methods and is computationally efficient. Our real data analyses result in consistent causal effect estimates and offer valuable guidance for conducting multivariable MR studies, elucidating the roles of pleiotropy, and identifying total 42 horizontal pleiotropic loci missed previously that are associated with myopia, schizophrenia, and coronary artery disease.
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Affiliation(s)
- Noah Lorincz-Comi
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Yihe Yang
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Gen Li
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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39
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Cote AC, Young HE, Huckins LM. Critical reasoning on the co-expression module QTL in the dorsolateral prefrontal cortex. HGG ADVANCES 2024; 5:100311. [PMID: 38773772 PMCID: PMC11214266 DOI: 10.1016/j.xhgg.2024.100311] [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: 10/23/2023] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 05/24/2024] Open
Abstract
Expression quantitative trait locus (eQTL) analysis is a popular method of gaining insight into the function of regulatory variation. While cis-eQTL resources have been instrumental in linking genome-wide association study variants to gene function, complex trait heritability may be additionally mediated by other forms of gene regulation. Toward this end, novel eQTL methods leverage gene co-expression (module-QTL) to investigate joint regulation of gene modules by single genetic variants. Here we broadly define a "module-QTL" as the association of a genetic variant with a summary measure of gene co-expression. This approach aims to reduce the multiple testing burden of a trans-eQTL search through the consolidation of gene-based testing and provide biological context to eQTLs shared between genes. In this article we provide an in-depth examination of the co-expression module eQTL (module-QTL) through literature review, theoretical investigation, and real-data application of the module-QTL to three large prefrontal cortex genotype-RNA sequencing datasets. We find module-QTLs in our study that are disease associated and reproducible are not additionally informative beyond cis- or trans-eQTLs for module genes. Through comparison to prior studies, we highlight promises and limitations of the module-QTL across study designs and provide recommendations for further investigation of the module-QTL framework.
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Affiliation(s)
- Alanna C Cote
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Hannah E Young
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura M Huckins
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06511, USA.
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40
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Zhao QG, Song ZT, Ma XL, Xu Q, Bu F, Li K, Zhang L, Pei YF. Human brain proteome-wide association study provides insights into the genetic components of protein abundance in obesity. Int J Obes (Lond) 2024:10.1038/s41366-024-01592-6. [PMID: 39025989 DOI: 10.1038/s41366-024-01592-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUNDS Genome-wide association studies have identified multiple genetic variants associated with obesity. However, most obesity-associated loci were waiting to be translated into new biological insights. Given the critical role of brain in obesity development, we sought to explore whether obesity-associated genetic variants could be mapped to brain protein abundances. METHODS We performed proteome-wide association studies (PWAS) and colocalization analyses to identify genes whose cis-regulated brain protein abundances were associated with obesity-related traits, including body fat percentage, trunk fat percentage, body mass index, visceral adipose tissue, waist circumference, and waist-to-hip ratio. We then assessed the druggability of the identified genes and conducted pathway enrichment analysis to explore their functional relevance. Finally, we evaluated the effects of the significant PWAS genes at the brain transcriptional level. RESULTS By integrating human brain proteomes from discovery (ROSMAP, N = 376) and validation datasets (BANNER, N = 198) with genome-wide summary statistics of obesity-related phenotypes (N ranged from 325,153 to 806,834), we identified 51 genes whose cis-regulated brain protein abundance was associated with obesity. These 51 genes were enriched in 11 metabolic processes, e.g., small molecule metabolic process and metabolic pathways. Fourteen of the 51 genes had high drug repurposing value. Ten of the 51 genes were also associated with obesity at the transcriptome level, suggesting that genetic variants likely confer risk of obesity by regulating mRNA expression and protein abundance of these genes. CONCLUSIONS Our study provides new insights into the genetic component of human brain protein abundance in obesity. The identified proteins represent promising therapeutic targets for future drug development.
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Affiliation(s)
- Qi-Gang Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, PR China
| | - Zi-Tong Song
- Department of Epidemiology and Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, PR China
| | - Xin-Ling Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, PR China
| | - Qian Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, PR China
| | - Fan Bu
- Department of Epidemiology and Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, PR China
| | - Kuan Li
- Department of Epidemiology and Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, PR China
| | - Lei Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, PR China.
| | - Yu-Fang Pei
- Department of Epidemiology and Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, PR China.
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41
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Dai Y, Itai T, Pei G, Yan F, Chu Y, Jiang X, Weinberg SM, Mukhopadhyay N, Marazita ML, Simon LM, Jia P, Zhao Z. DeepFace: Deep-learning-based framework to contextualize orofacial-cleft-related variants during human embryonic craniofacial development. HGG ADVANCES 2024; 5:100312. [PMID: 38796699 PMCID: PMC11193024 DOI: 10.1016/j.xhgg.2024.100312] [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: 02/08/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 05/28/2024] Open
Abstract
Orofacial clefts (OFCs) are among the most common human congenital birth defects. Previous multiethnic studies have identified dozens of associated loci for both cleft lip with or without cleft palate (CL/P) and cleft palate alone (CP). Although several nearby genes have been highlighted, the "casual" variants are largely unknown. Here, we developed DeepFace, a convolutional neural network model, to assess the functional impact of variants by SNP activity difference (SAD) scores. The DeepFace model is trained with 204 epigenomic assays from crucial human embryonic craniofacial developmental stages of post-conception week (pcw) 4 to pcw 10. The Pearson correlation coefficient between the predicted and actual values for 12 epigenetic features achieved a median range of 0.50-0.83. Specifically, our model revealed that SNPs significantly associated with OFCs tended to exhibit higher SAD scores across various variant categories compared to less related groups, indicating a context-specific impact of OFC-related SNPs. Notably, we identified six SNPs with a significant linear relationship to SAD scores throughout developmental progression, suggesting that these SNPs could play a temporal regulatory role. Furthermore, our cell-type specificity analysis pinpointed the trophoblast cell as having the highest enrichment of risk signals associated with OFCs. Overall, DeepFace can harness distal regulatory signals from extensive epigenomic assays, offering new perspectives for prioritizing OFC variants using contextualized functional genomic features. We expect DeepFace to be instrumental in accessing and predicting the regulatory roles of variants associated with OFCs, and the model can be extended to study other complex diseases or traits.
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Affiliation(s)
- Yulin Dai
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Toshiyuki Itai
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Guangsheng Pei
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Fangfang Yan
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yan Chu
- Center for Secure Artificial Intelligence for Healthcare, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaoqian Jiang
- Center for Secure Artificial Intelligence for Healthcare, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Seth M Weinberg
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Nandita Mukhopadhyay
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Mary L Marazita
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA; Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Lukas M Simon
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peilin Jia
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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42
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Yang Y, Chen Y, Xu S, Guo X, Jia G, Ping J, Shu X, Zhao T, Yuan F, Wang G, Xie Y, Ci H, Liu H, Qi Y, Liu Y, Liu D, Li W, Ye F, Shu XO, Zheng W, Li L, Cai Q, Long J. Integrating muti-omics data to identify tissue-specific DNA methylation biomarkers for cancer risk. Nat Commun 2024; 15:6071. [PMID: 39025880 PMCID: PMC11258330 DOI: 10.1038/s41467-024-50404-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
The relationship between tissue-specific DNA methylation and cancer risk remains inadequately elucidated. Leveraging resources from the Genotype-Tissue Expression consortium, here we develop genetic models to predict DNA methylation at CpG sites across the genome for seven tissues and apply these models to genome-wide association study data of corresponding cancers, namely breast, colorectal, renal cell, lung, ovarian, prostate, and testicular germ cell cancers. At Bonferroni-corrected P < 0.05, we identify 4248 CpGs that are significantly associated with cancer risk, of which 95.4% (4052) are specific to a particular cancer type. Notably, 92 CpGs within 55 putative novel loci retain significant associations with cancer risk after conditioning on proximal signals identified by genome-wide association studies. Integrative multi-omics analyses reveal 854 CpG-gene-cancer trios, suggesting that DNA methylation at 309 distinct CpGs might influence cancer risk through regulating the expression of 205 unique cis-genes. These findings substantially advance our understanding of the interplay between genetics, epigenetics, and gene expression in cancer etiology.
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Affiliation(s)
- Yaohua Yang
- Center for Public Health Genomics, Department of Public Health Sciences, UVA Comprehensive Cancer Center, School of Medicine, University of Virginia, Charlottesville, VA, USA.
| | - Yaxin Chen
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shuai Xu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Guochong Jia
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jie Ping
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiang Shu
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tianying Zhao
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Fangcheng Yuan
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gang Wang
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yufang Xie
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hang Ci
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hongmo Liu
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yawen Qi
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yongjun Liu
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Dan Liu
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Weimin Li
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fei Ye
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Li Li
- Department of Family Medicine, UVA Comprehensive Cancer Center, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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Wang X, Ma J, Dong Y, Ren X, Li R, Yang G, She G, Tan Y, Chen S. Exploration on the potential efficacy and mechanism of methyl salicylate glycosides in the treatment of schizophrenia based on bioinformatics, molecular docking and dynamics simulation. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2024; 10:64. [PMID: 39019913 PMCID: PMC11255270 DOI: 10.1038/s41537-024-00484-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 07/02/2024] [Indexed: 07/19/2024]
Abstract
The etiological and therapeutic complexities of schizophrenia (SCZ) persist, prompting exploration of anti-inflammatory therapy as a potential treatment approach. Methyl salicylate glycosides (MSGs), possessing a structural parent nucleus akin to aspirin, are being investigated for their therapeutic potential in schizophrenia. Utilizing bioinformation mining, network pharmacology, molecular docking and dynamics simulation, the potential value and mechanism of MSGs (including MSTG-A, MSTG-B, and Gaultherin) in the treatment of SCZ, as well as the underlying pathogenesis of the disorder, were examined. 581 differentially expressed genes related to SCZ were identified in patients and healthy individuals, with 349 up-regulated genes and 232 down-regulated genes. 29 core targets were characterized by protein-protein interaction (PPI) network, with the top 10 core targets being BDNF, VEGFA, PVALB, KCNA1, GRIN2A, ATP2B2, KCNA2, APOE, PPARGC1A and SCN1A. The pathogenesis of SCZ primarily involves cAMP signaling, neurodegenerative diseases and other pathways, as well as regulation of ion transmembrane transport. Molecular docking analysis revealed that the three candidates exhibited binding activity with certain targets with binding affinities ranging from -4.7 to -109.2 kcal/mol. MSTG-A, MSTG-B and Gaultherin show promise for use in the treatment of SCZ, potentially through their ability to modulate the expression of multiple genes involved in synaptic structure and function, ion transport, energy metabolism. Molecular dynamics simulation revealed good binding abilities between MSTG-A, MSTG-B, Gaultherin and ATP2B2. It suggests new avenues for further investigation in this area.
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Affiliation(s)
- Xiuhuan Wang
- Peking University HuiLongGuan Clinical Medical School, Beijing HuiLongGuan Hospital, Beijing, 100096, PR China
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, PR China
| | - Jiamu Ma
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, PR China
| | - Ying Dong
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, PR China
| | - Xueyang Ren
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, PR China
| | - Ruoming Li
- Peking University HuiLongGuan Clinical Medical School, Beijing HuiLongGuan Hospital, Beijing, 100096, PR China
| | - Guigang Yang
- Peking University HuiLongGuan Clinical Medical School, Beijing HuiLongGuan Hospital, Beijing, 100096, PR China
| | - Gaimei She
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, PR China.
| | - Yunlong Tan
- Peking University HuiLongGuan Clinical Medical School, Beijing HuiLongGuan Hospital, Beijing, 100096, PR China.
| | - Song Chen
- Peking University HuiLongGuan Clinical Medical School, Beijing HuiLongGuan Hospital, Beijing, 100096, PR China.
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Wang R, Su Y, O'Donnell K, Caron J, Meaney M, Meng X, Li Y. Differential interactions between gene expressions and stressors across the lifespan in major depressive disorder. J Affect Disord 2024; 362:688-697. [PMID: 39029669 DOI: 10.1016/j.jad.2024.07.069] [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: 01/24/2024] [Revised: 07/05/2024] [Accepted: 07/14/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND Both genetic predispositions and exposures to stressors have collectively contributed to the development of major depressive disorder (MDD). To deep dive into their roles in MDD, our study aimed to examine which susceptible gene expression interacts with various dimensions of stressors in the MDD risk among a large population cohort. METHODS Data analyzed were from a longitudinal community-based cohort from Southwest Montreal, Canada (N = 1083). Latent profile models were used to identify distinct patterns of stressors for the study cohort. A transcriptome-wide association study (TWAS) method was performed to examine the interactive effects of three dimensions of stressors (threat, deprivation, and cumulative lifetime stress) and gene expression on the MDD risk in a total of 48 tissues from GTEx. Additional analyses were also conducted to further explore and specify these associations including colocalization, and fine-mapping analyses, in addition to enrichment analysis investigations based on TWAS. RESULTS We identified 3321 genes linked to MDD at the nominal p-value <0.05 and found that different patterns of stressors can amplify the genetic susceptibility to MDD. We also observed specific genes and pathways that interacted with deprivation and cumulative lifetime stressors, particularly in specific brain tissues including basal ganglia, prefrontal cortex, brain amygdala, brain cerebellum, brain cortex, and the whole blood. Colocalization analysis also identified these genes as having a high probability of sharing MDD causal variants. LIMITATIONS The study cohort was composed exclusively of individuals of Caucasians, which restricts the generalizability of the findings to other ethnic population groups. CONCLUSIONS The findings of the study unveiled significant interactions between potential tissue-specific gene expression × stressors in the MDD risk and shed light on the intricate etiological attributes of gene expression and specific stressors across the lifespan in MDD. These genetic and environmental attributes in MDD corroborate the vulnerability-stress theory and direct future stress research to have a closer examination of genetic predisposition and potential involvements of omics studies to specify the intricate relationships between genes and stressful environments.
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Affiliation(s)
- Ruiyang Wang
- Department of Financial and Risk Engineering, New York University, NY, NYC, USA; Department of Psychiatry, McGill University, Montreal, QC, Canada; Douglas Research Centre, Montreal, QC, Canada
| | - Yingying Su
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Kieran O'Donnell
- Department of Psychiatry, McGill University, Montreal, QC, Canada; Douglas Research Centre, Montreal, QC, Canada; Yale Child Study Center, Department of Obstetrics Gynecology & Reproductive Sciences, Yale School of Medicine, Yale University, New Haven, CT, USA; Child & Brain Development Program, CIFAR, Toronto, ON, Canada
| | - Jean Caron
- Department of Psychiatry, McGill University, Montreal, QC, Canada; Douglas Research Centre, Montreal, QC, Canada
| | - Michael Meaney
- Department of Psychiatry, McGill University, Montreal, QC, Canada; Douglas Research Centre, Montreal, QC, Canada
| | - Xiangfei Meng
- Department of Psychiatry, McGill University, Montreal, QC, Canada; Douglas Research Centre, Montreal, QC, Canada.
| | - Yue Li
- School of Computer Science, McGill University, Montreal, QC, Canada.
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Kanjira SC, Adams MJ, Jiang Y, Tian C, Lewis CM, Kuchenbaecker K, McIntosh AM. Polygenic prediction of major depressive disorder and related traits in African ancestries UK Biobank participants. Mol Psychiatry 2024:10.1038/s41380-024-02662-x. [PMID: 39014000 DOI: 10.1038/s41380-024-02662-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 06/27/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
Genome-Wide Association Studies (GWAS) over-represent European ancestries, neglecting all other ancestry groups and low-income nations. Consequently, polygenic risk scores (PRS) more accurately predict complex traits in Europeans than African Ancestries groups. Very few studies have looked at the transferability of European-derived PRS for behavioural and mental health phenotypes to Africans. We assessed the comparative accuracy of depression PRS trained on European and African Ancestries GWAS studies to predict major depressive disorder (MDD) and related traits in African ancestry participants from the UK Biobank. UK Biobank participants were selected based on Principal component analysis clustering with an African genetic similarity reference population, MDD was assessed with the Composite International Diagnostic Interview (CIDI). PRS were computed using PRSice2 software using either European or African Ancestries GWAS summary statistics. PRS trained on European ancestry samples (246,363 cases) predicted case control status in Africans of the UK Biobank with similar accuracies (R2 = 2%, β = 0.32, empirical p-value = 0.002) to PRS trained on far much smaller samples of African Ancestries participants from 23andMe, Inc. (5045 cases, R² = 1.8%, β = 0.28, empirical p-value = 0.008). This suggests that prediction of MDD status from Africans to Africans had greater efficiency relative to discovery sample size than prediction of MDD from Europeans to Africans. Prediction of MDD status in African UK Biobank participants using GWAS findings of likely causal risk factors from European ancestries was non-significant. GWAS of MDD in European ancestries are inefficient for improving polygenic prediction in African samples; urgent MDD studies in Africa are needed.
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Affiliation(s)
- S C Kanjira
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Malawi Epidemiology and Intervention Research Unit, Lilongwe, Malawi
| | - M J Adams
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Y Jiang
- 23andMe Inc, Sunnyvale, CA, USA
| | - C Tian
- 23andMe Inc, Sunnyvale, CA, USA
| | - C M Lewis
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - K Kuchenbaecker
- UCL Genetics Institute, University College London, London, UK
| | - A M McIntosh
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK.
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D'Amico A, Sung H, Arbona-Lampaya A, Freifeld A, Hosey K, Garcia J, Lacbawan L, Besançon E, Kassem L, Akula N, Knowles EEM, Dickinson D, McMahon FJ. Independent inheritance of cognition and bipolar disorder in a family sample. Am J Med Genet B Neuropsychiatr Genet 2024:e33001. [PMID: 39011872 DOI: 10.1002/ajmg.b.33001] [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: 12/05/2023] [Revised: 05/28/2024] [Accepted: 06/17/2024] [Indexed: 07/17/2024]
Abstract
Cognitive deficits in people with bipolar disorder (BD) may be the result of the illness or its treatment, but they could also reflect genetic risk factors shared between BD and cognition. We investigated this question using empirical genetic relationships within a sample of patients with BD and their unaffected relatives. Participants with bipolar I, II, or schizoaffective disorder ("narrow" BD, n = 69), related mood disorders ("broad" BD, n = 135), and their clinically unaffected relatives (n = 227) completed five cognitive tests. General cognitive function (g) was quantified via principal components analysis (PCA). Heritability and genetic correlations were estimated with SOLAR-Eclipse. Participants with "narrow" or "broad" diagnoses showed deficits in g, although affect recognition was unimpaired. Cognitive performance was significantly heritable (h2 = 0.322 for g, p < 0.005). Coheritability between psychopathology and g was small (0.0184 for narrow and 0.0327 for broad) and healthy relatives of those with BD were cognitively unimpaired. In this family sample, cognitive deficits were present in participants with BD but were not explained by substantial overlaps in genetic determinants of mood and cognition. These findings support the view that cognitive deficits in BD are largely the result of the illness or its treatment.
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Affiliation(s)
- Alexander D'Amico
- Intramural Research Program, National Institute of Mental Health, NIH, DHHS, Bethesda, Maryland, USA
| | - Heejong Sung
- Intramural Research Program, National Institute of Mental Health, NIH, DHHS, Bethesda, Maryland, USA
| | - Alejandro Arbona-Lampaya
- Intramural Research Program, National Institute of Mental Health, NIH, DHHS, Bethesda, Maryland, USA
| | - Ally Freifeld
- Intramural Research Program, National Institute of Mental Health, NIH, DHHS, Bethesda, Maryland, USA
| | - Katie Hosey
- Intramural Research Program, National Institute of Mental Health, NIH, DHHS, Bethesda, Maryland, USA
| | - Joshua Garcia
- Intramural Research Program, National Institute of Mental Health, NIH, DHHS, Bethesda, Maryland, USA
| | - Ley Lacbawan
- Intramural Research Program, National Institute of Mental Health, NIH, DHHS, Bethesda, Maryland, USA
| | - Emily Besançon
- Intramural Research Program, National Institute of Mental Health, NIH, DHHS, Bethesda, Maryland, USA
| | - Layla Kassem
- Intramural Research Program, National Institute of Mental Health, NIH, DHHS, Bethesda, Maryland, USA
| | - Nirmala Akula
- Intramural Research Program, National Institute of Mental Health, NIH, DHHS, Bethesda, Maryland, USA
| | | | - Dwight Dickinson
- Intramural Research Program, National Institute of Mental Health, NIH, DHHS, Bethesda, Maryland, USA
| | - Francis J McMahon
- Intramural Research Program, National Institute of Mental Health, NIH, DHHS, Bethesda, Maryland, USA
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Lu Q, Zhou Y, Qian Q, Chen Z, Tan Q, Chen H, Yin F, Wang Y, Liu Z, Tian P, Sun D. Whole-exome sequencing identifies high-confidence genes for tic disorders in a Chinese Han population. Clin Chim Acta 2024; 561:119759. [PMID: 38880274 DOI: 10.1016/j.cca.2024.119759] [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: 03/26/2024] [Revised: 05/23/2024] [Accepted: 06/02/2024] [Indexed: 06/18/2024]
Abstract
BACKGROUND Tic disorder (TD) is a polygenic neurodevelopmental disorder with high susceptibility. However, identifying high-confidence risk genes has been challenging due to poor replication across multiple studies. METHODS Whole-exome sequencing was performed on 390 TD patients and 372 unaffected individuals in a Chinese Han population. Analysis of variance, burden analysis and in silico prediction were used to identify candidate genes for TD. To facilitate data analysis and to focus on high-confidence genes, we defined a panel of 160 genes as known causal or candidate TD genes from previous studies. Gene enrichment and protein-protein interaction analysis were utilized to detect potential novel TD risk genes. RESULTS Totally, 14 variants across 12 known TD candidate genes were considered potential susceptibility variants. Ten variants across 10 known TD candidate genes were identified as potential disease-causing variants. Burden analysis identified variants of 28 known genes were significantly excess in TD patients. In addition, 354 previously unproven TD genes are over-represented in patients. Genes enriched in the PI3K-Akt signaling, sphingolipid metabolism and serotonergic synaptic pathways, as well as those interacting with FN1, were considered potential new candidate genes for TD. CONCLUSIONS This is the largest WES study focusing on TD patients in a Chinese Han population. Several variants recurring in our cohort were identified as high-confidence risk loci for TD. Moreover, we provided potential new risk genes that may be prioritized for further investigation.
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Affiliation(s)
- Qing Lu
- Department of Neurology, Wuhan Children's Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Yong Zhou
- Puluo (Wuhan) Medical Biotechnology Co., LTD, Wuhan 430070, China; Department of Marketing, Wuhan Kindstar Clinical Diagnostic Institute Co., Ltd., Wuhan 430000, China
| | - Qiaoqiao Qian
- Department of Neurology, Wuhan Children's Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Zhigang Chen
- Puluo (Wuhan) Medical Biotechnology Co., LTD, Wuhan 430070, China
| | - Qianqian Tan
- Puluo (Wuhan) Medical Biotechnology Co., LTD, Wuhan 430070, China; Department of Marketing, Wuhan Kindstar Clinical Diagnostic Institute Co., Ltd., Wuhan 430000, China
| | - Haiyun Chen
- Puluo (Wuhan) Medical Biotechnology Co., LTD, Wuhan 430070, China; Department of Marketing, Wuhan Kindstar Clinical Diagnostic Institute Co., Ltd., Wuhan 430000, China
| | - Fan Yin
- Puluo (Wuhan) Medical Biotechnology Co., LTD, Wuhan 430070, China; Department of Marketing, Wuhan Kindstar Clinical Diagnostic Institute Co., Ltd., Wuhan 430000, China
| | - Yue Wang
- Department of Pediatrics, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhisheng Liu
- Department of Neurology, Wuhan Children's Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Peichao Tian
- Department of Pediatrics, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Dan Sun
- Department of Neurology, Wuhan Children's Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China.
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Ciulkinyte A, Mountford HS, Fontanillas P, Bates TC, Martin NG, Fisher SE, Luciano M. Genetic neurodevelopmental clustering and dyslexia. Mol Psychiatry 2024:10.1038/s41380-024-02649-8. [PMID: 39009701 DOI: 10.1038/s41380-024-02649-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 06/18/2024] [Accepted: 06/26/2024] [Indexed: 07/17/2024]
Abstract
Dyslexia is a learning difficulty with neurodevelopmental origins, manifesting as reduced accuracy and speed in reading and spelling. It is substantially heritable and frequently co-occurs with other neurodevelopmental conditions, particularly attention deficit-hyperactivity disorder (ADHD). Here, we investigate the genetic structure underlying dyslexia and a range of psychiatric traits using results from genome-wide association studies of dyslexia, ADHD, autism, anorexia nervosa, anxiety, bipolar disorder, major depressive disorder, obsessive compulsive disorder, schizophrenia, and Tourette syndrome. Genomic Structural Equation Modelling (GenomicSEM) showed heightened support for a model consisting of five correlated latent genomic factors described as: F1) compulsive disorders (including obsessive-compulsive disorder, anorexia nervosa, Tourette syndrome), F2) psychotic disorders (including bipolar disorder, schizophrenia), F3) internalising disorders (including anxiety disorder, major depressive disorder), F4) neurodevelopmental traits (including autism, ADHD), and F5) attention and learning difficulties (including ADHD, dyslexia). ADHD loaded more strongly on the attention and learning difficulties latent factor (F5) than on the neurodevelopmental traits latent factor (F4). The attention and learning difficulties latent factor (F5) was positively correlated with internalising disorders (.40), neurodevelopmental traits (.25) and psychotic disorders (.17) latent factors, and negatively correlated with the compulsive disorders (-.16) latent factor. These factor correlations are mirrored in genetic correlations observed between the attention and learning difficulties latent factor and other cognitive, psychological and wellbeing traits. We further investigated genetic variants underlying both dyslexia and ADHD, which implicated 49 loci (40 not previously found in GWAS of the individual traits) mapping to 174 genes (121 not found in GWAS of individual traits) as potential pleiotropic variants. Our study confirms the increased genetic relation between dyslexia and ADHD versus other psychiatric traits and uncovers novel pleiotropic variants affecting both traits. In future, analyses including additional co-occurring traits such as dyscalculia and dyspraxia will allow a clearer definition of the attention and learning difficulties latent factor, yielding further insights into factor structure and pleiotropic effects.
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Affiliation(s)
- Austeja Ciulkinyte
- Translational Neuroscience PhD Programme, University of Edinburgh, Edinburgh, UK
| | - Hayley S Mountford
- School of Philosophy, Psychology and Language Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Timothy C Bates
- School of Philosophy, Psychology and Language Sciences, University of Edinburgh, Edinburgh, UK
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
| | - Michelle Luciano
- School of Philosophy, Psychology and Language Sciences, University of Edinburgh, Edinburgh, UK.
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Zhang Q, Meng X, Luo H, Yu K, Li A, Zhou L, Chen R, Kan H. Air pollutants, genetic susceptibility, and incident schizophrenia in later life: A prospective study in the UK Biobank. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:173009. [PMID: 38734111 DOI: 10.1016/j.scitotenv.2024.173009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/10/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024]
Abstract
OBJECTIVE Air pollution has been linked to multiple psychiatric disorders, but little is known on its long-term association with schizophrenia. The interaction between air pollution and genetic susceptibility on incident schizophrenia has never been reported. We aimed to explore the associations between long-term air pollution exposure and late-onset schizophrenia and evaluate whether genetic susceptibility could modify the association. METHODS This population-based prospective cohort study included 437,802 middle-aged and elderly individuals free of schizophrenia at baseline in the UK Biobank. Land use regression models were applied in the estimation of the annual average concentrations of nitrogen dioxide (NO2), nitrogen oxides (NOx), fine particulate matter (PM2.5), and inhalable particulate matter (PM10) at residence. The associations between air pollutants and schizophrenia were evaluated by using Cox proportional hazard models. A polygenic risk score of schizophrenia was constructed for exploring potential interaction of air pollutants with genetic susceptibility. RESULTS An interquartile range increase in PM2.5, PM10, NO2, and NOx was associated with the hazard ratios (HR) for incident schizophrenia at 1.19, 1.16, 1.22, and 1.09, respectively. The exposure-response curves for the association of air pollution with incident schizophrenia were approximately linear. There are additive interactions of air pollution score (APS), PM10, NO2, and NOx with genetic risk. Specifically, compared with participants with low genetic susceptibility and low APS, the HR was 3.23 for individuals with high genetic risk and high APS, among which 0.49 excess risk could be attributed to the additive interaction, accounting for 15 % of the schizophrenia risk. CONCLUSION This large-scale, prospective cohort study conveys the first-hand evidence that long-term air pollution exposure could elevate schizophrenia incidence in later life, especially for individuals with higher genetic risks. The findings highlight the importance of improving air quality for preventing the late-onset schizophrenia in an aging era, especially among those with high genetic risks.
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Affiliation(s)
- Qingli Zhang
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai, China; Ministry of Education - Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xia Meng
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai, China
| | - Huihuan Luo
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai, China
| | - Kexin Yu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai, China
| | - Anni Li
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai, China
| | - Lu Zhou
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai, China
| | - Renjie Chen
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai, China; School of Public Health, University of South China, Hengyang, Hunan, China; School of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan, China..
| | - Haidong Kan
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai, China; Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China.
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Segura-Ortiz A, García-Nieto J, Aldana-Montes JF, Navas-Delgado I. Multi-objective context-guided consensus of a massive array of techniques for the inference of Gene Regulatory Networks. Comput Biol Med 2024; 179:108850. [PMID: 39013340 DOI: 10.1016/j.compbiomed.2024.108850] [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: 02/08/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
BACKGROUND AND OBJECTIVE Gene Regulatory Network (GRN) inference is a fundamental task in biology and medicine, as it enables a deeper understanding of the intricate mechanisms of gene expression present in organisms. This bioinformatics problem has been addressed in the literature through multiple computational approaches. Techniques developed for inferring from expression data have employed Bayesian networks, ordinary differential equations (ODEs), machine learning, information theory measures and neural networks, among others. The diversity of implementations and their respective customization have led to the emergence of many tools and multiple specialized domains derived from them, understood as subsets of networks with specific characteristics that are challenging to detect a priori. This specialization has introduced significant uncertainty when choosing the most appropriate technique for a particular dataset. This proposal, named MO-GENECI, builds upon the basic idea of the previous proposal GENECI and optimizes consensus among different inference techniques, through a carefully refined multi-objective evolutionary algorithm guided by various objective functions, linked to the biological context at hand. METHODS MO-GENECI has been tested on an extensive and diverse academic benchmark of 106 gene regulatory networks from multiple sources and sizes. The evaluation of MO-GENECI compared its performance to individual techniques using key metrics (AUROC and AUPR) for gene regulatory network inference. Friedman's statistical ranking provided an ordered classification, followed by non-parametric Holm tests to determine statistical significance. RESULTS MO-GENECI's Pareto front approximation facilitates easy selection of an appropriate solution based on generic input data characteristics. The best solution consistently emerged as the winner in all statistical tests, and in many cases, the median precision solution showed no statistically significant difference compared to the winner. CONCLUSIONS MO-GENECI has not only demonstrated achieving more accurate results than individual techniques, but has also overcome the uncertainty associated with the initial choice due to its flexibility and adaptability. It is shown intelligently to select the most suitable techniques for each case. The source code is hosted in a public repository at GitHub under MIT license: https://github.com/AdrianSeguraOrtiz/MO-GENECI. Moreover, to facilitate its installation and use, the software associated with this implementation has been encapsulated in a Python package available at PyPI: https://pypi.org/project/geneci/.
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Affiliation(s)
- Adrián Segura-Ortiz
- Department de Lenguajes y Ciencias de la Computación, ITIS Software, Universidad de Málaga, Málaga, 29071, Spain.
| | - José García-Nieto
- Department de Lenguajes y Ciencias de la Computación, ITIS Software, Universidad de Málaga, Málaga, 29071, Spain; Biomedical Research Institute of Málaga (IBIMA), Universidad de Málaga, Málaga, Spain
| | - José F Aldana-Montes
- Department de Lenguajes y Ciencias de la Computación, ITIS Software, Universidad de Málaga, Málaga, 29071, Spain; Biomedical Research Institute of Málaga (IBIMA), Universidad de Málaga, Málaga, Spain
| | - Ismael Navas-Delgado
- Department de Lenguajes y Ciencias de la Computación, ITIS Software, Universidad de Málaga, Málaga, 29071, Spain; Biomedical Research Institute of Málaga (IBIMA), Universidad de Málaga, Málaga, Spain
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