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Zhang Y, Bharadhwaj VS, Kodamullil AT, Herrmann C. A network of transcriptomic signatures identifies novel comorbidity mechanisms between schizophrenia and somatic disorders. DISCOVER MENTAL HEALTH 2024; 4:11. [PMID: 38573526 PMCID: PMC10994898 DOI: 10.1007/s44192-024-00063-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/28/2024] [Indexed: 04/05/2024]
Abstract
The clinical burden of mental illness, in particular schizophrenia and bipolar disorder, are driven by frequent chronic courses and increased mortality, as well as the risk for comorbid conditions such as cardiovascular disease and type 2 diabetes. Evidence suggests an overlap of molecular pathways between psychotic disorders and somatic comorbidities. In this study, we developed a computational framework to perform comorbidity modeling via an improved integrative unsupervised machine learning approach based on multi-rank non-negative matrix factorization (mrNMF). Using this procedure, we extracted molecular signatures potentially explaining shared comorbidity mechanisms. For this, 27 case-control microarray transcriptomic datasets across multiple tissues were collected, covering three main categories of conditions including psychotic disorders, cardiovascular diseases and type II diabetes. We addressed the limitation of normal NMF for parameter selection by introducing multi-rank ensembled NMF to identify signatures under various hierarchical levels simultaneously. Analysis of comorbidity signature pairs was performed to identify several potential mechanisms involving activation of inflammatory response auxiliarily interconnecting angiogenesis, oxidative response and GABAergic neuro-action. Overall, we proposed a general cross-cohorts computing workflow for investigating the comorbid pattern across multiple symptoms, applied it to the real-data comorbidity study on schizophrenia, and further discussed the potential for future application of the approach.
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Affiliation(s)
- Youcheng Zhang
- Institute of Pharmacy and Molecular Biotechnology (IPMB) & BioQuant, Universität Heidelberg, 69120, Heidelberg, Germany
| | - Vinay S Bharadhwaj
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53757, Sankt Augustin, Germany
| | - Alpha T Kodamullil
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53757, Sankt Augustin, Germany
| | - Carl Herrmann
- Institute of Pharmacy and Molecular Biotechnology (IPMB) & BioQuant, Universität Heidelberg, 69120, Heidelberg, Germany.
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Lee J, Xue X, Au E, McIntyre WB, Asgariroozbehani R, Panganiban K, Tseng GC, Papoulias M, Smith E, Monteiro J, Shah D, Maksyutynska K, Cavalier S, Radoncic E, Prasad F, Agarwal SM, Mccullumsmith R, Freyberg Z, Logan RW, Hahn MK. Glucose dysregulation in antipsychotic-naive first-episode psychosis: in silico exploration of gene expression signatures. Transl Psychiatry 2024; 14:19. [PMID: 38199991 PMCID: PMC10781725 DOI: 10.1038/s41398-023-02716-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/10/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
Antipsychotic (AP)-naive first-episode psychosis (FEP) patients display early dysglycemia, including insulin resistance and prediabetes. Metabolic dysregulation may therefore be intrinsic to psychosis spectrum disorders (PSDs), independent of the metabolic effects of APs. However, the potential biological pathways that overlap between PSDs and dysglycemic states remain to be identified. Using meta-analytic approaches of transcriptomic datasets, we investigated whether AP-naive FEP patients share overlapping gene expression signatures with non-psychiatrically ill early dysglycemia individuals. We meta-analyzed peripheral transcriptomic datasets of AP-naive FEP patients and non-psychiatrically ill early dysglycemia subjects to identify common gene expression signatures. Common signatures underwent pathway enrichment analysis and were then used to identify potential new pharmacological compounds via Integrative Library of Integrated Network-Based Cellular Signatures (iLINCS). Our search results yielded 5 AP-naive FEP studies and 4 early dysglycemia studies which met inclusion criteria. We discovered that AP-naive FEP and non-psychiatrically ill subjects exhibiting early dysglycemia shared 221 common signatures, which were enriched for pathways related to endoplasmic reticulum stress and abnormal brain energetics. Nine FDA-approved drugs were identified as potential drug treatments, of which the antidiabetic metformin, the first-line treatment for type 2 diabetes, has evidence to attenuate metabolic dysfunction in PSDs. Taken together, our findings support shared gene expression changes and biological pathways associating PSDs with dysglycemic disorders. These data suggest that the pathobiology of PSDs overlaps and potentially contributes to dysglycemia. Finally, we find that metformin may be a potential treatment for early metabolic dysfunction intrinsic to PSDs.
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Grants
- R01 DK124219 NIDDK NIH HHS
- R01 HL150432 NHLBI NIH HHS
- R01 MH107487 NIMH NIH HHS
- R01 MH121102 NIMH NIH HHS
- Holds the Meighen Family Chair in Psychosis Prevention, the Cardy Schizophrenia Research Chair, a Danish Diabetes Academy Professorship, a Steno Diabetes Center Fellowship, and a U of T Academic Scholar Award, and is funded by operating grants from the Canadian Institutes of Health Research (CIHR), the Banting and Best Diabetes Center, the Miners Lamp U of T award, CIHR and Canadian Psychiatric Association Glenda MacQueen Memorial Award, and the PSI Foundation.
- Hilda and William Courtney Clayton Paediatric Research Fund and Dr. LG Rao/Industrial Partners Graduate Student Award from the University of Toronto, and Meighen Family Chair in Psychosis Prevention
- U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- UofT | Banting and Best Diabetes Centre, University of Toronto (BBDC)
- Canadian Institutes of Health Research (CIHR) Canada Graduate Scholarship-Master’s program
- Cleghorn Award
- University of Toronto (UofT)
- Centre for Addiction and Mental Health (Centre de Toxicomanie et de Santé Mentale)
- U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)
- U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- U.S. Department of Defense (United States Department of Defense)
- Commonwealth of Pennsylvania Formula Fund, The Pittsburgh Foundation
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Affiliation(s)
- Jiwon Lee
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Xiangning Xue
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Emily Au
- Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - William B McIntyre
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Roshanak Asgariroozbehani
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Kristoffer Panganiban
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - George C Tseng
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Emily Smith
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
| | | | - Divia Shah
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kateryna Maksyutynska
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Samantha Cavalier
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Emril Radoncic
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Femin Prasad
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Sri Mahavir Agarwal
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Robert Mccullumsmith
- Department of Neurosciences, University of Toledo, Toledo, OH, USA
- ProMedica, Toledo, OH, USA
| | - Zachary Freyberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ryan W Logan
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Psychiatry, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Pharmacology, Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Margaret K Hahn
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Centre for Addiction and Mental Health, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
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Wu Y, Xing YH, Tao S, Jiao M, Zhu M, Han YT, Guo W, Tao XB. Integrated analysis of potential biomarkers associated with diabetic periodontitis development based on bioinformatics: An observational study. Medicine (Baltimore) 2023; 102:e36019. [PMID: 37986309 PMCID: PMC10659692 DOI: 10.1097/md.0000000000036019] [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: 08/24/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/22/2023] Open
Abstract
Based on the importance of chronic inflammation in the pathogenesis of periodontitis and diabetes, the bidirectional relationship between these 2 diseases has been widely confirmed. However, the molecular mechanisms of bidirectional relationship still need to be studied further. In this study, gene expression profile data for diabetes and periodontitis were obtained from Gene Expression Omnibus (GEO) database. Integrative analytical platform were constructed, including common differentially expressed genes (cDEGs), Gene Ontology-Kyoto Encyclopedia of Genes and Genomes (GO-KEGG), and protein-protein interaction. Hub genes and essential modules were detected via Cytoscape. Key hub genes and signaling pathway that mediate chronic inflammation were validated by qPCR and Western blot. Eleven cDEGs were identified. Function analysis showed that cDEGs plays an important role in inflammatory response, cytokine receptor binding, TNF signaling pathway. As hub genes, CXCR4, IL1B, IL6, CXCL2, and MMP9 were detected based on the protein-protein interactions network. IL1B, CXCR4 mRNA were up-regulated in gingivitis samples compared with normal tissues (P < .05). Western blot indicated that the levels of TNF were enhanced in gingivitis of type 2 diabetes compared with normal tissues (P < .01). Hub gene and TNF signaling pathway are helpful to elucidate the molecular mechanism of the bidirectional relationship between periodontitis and diabetes.
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Affiliation(s)
- Yiran Wu
- Department of Nursing, The First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Yong-Hu Xing
- Oral Medical Center, The First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Shuai Tao
- Department of Nursing, The First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Min Jiao
- Department of Nursing, The First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Min Zhu
- Department of Nursing, The First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Ya-Ting Han
- Department of Nursing, The First Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Wei Guo
- School of Basic Medicine, Wannan Medical College, Wuhu, China
| | - Xiu-Bin Tao
- Department of Nursing, The First Affiliated Hospital of Wannan Medical College, Wuhu, China
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Borovcanin MM, Vesic K, Petrovic I, Jovanovic IP, Mijailović NR. Diabetes mellitus type 2 as an underlying, comorbid or consequent state of mental disorders. World J Diabetes 2023; 14:481-493. [PMID: 37273248 PMCID: PMC10236997 DOI: 10.4239/wjd.v14.i5.481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/21/2023] [Accepted: 04/12/2023] [Indexed: 05/15/2023] Open
Abstract
Somatic disturbances that occur in parallel with psychiatric diseases are a major challenge in clinical practice. Various factors contribute to the development of mental and somatic disorders. Type 2 diabetes mellitus (T2DM) is a significant health burden worldwide, and the prevalence of diabetes in adults is increasing. The comorbidity of diabetes and mental disorders is very common. By sharing a bidirectional link, both T2DM and mental disorders influence each other in various manners, but the exact mechanisms underlying this link are not yet elucidated. The potential mechanisms of both mental disorders and T2DM are related to immune and inflammatory system dysfunction, oxidative stress, endothelial dysfunction, and metabolic disturbances. Moreover, diabetes is also a risk factor for cognitive dysfunction that can range from subtle diabetes-associated cognitive decline to pre-dementia and dementia. A complex re-lationship between the gut and the brain also represents a new therapeutic approach since gut-brain signalling pathways regulate food intake and hepatic glucose production. The aim of this minireview is to summarize and present the latest data on mutual pathogenic pathways in these disorders, emphasizing their complexity and interweaving. We also focused on the cognitive performances and changes in neurodegenerative disorders. The importance of implementing integrated approaches in treating both of these states is highlighted, along with the need for individual therapeutic strategies.
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Affiliation(s)
- Milica M Borovcanin
- Department of Psychiatry, Faculty of Medical Sciences, University of Kragujevac, Kragujevac 34 000, Serbia
| | - Katarina Vesic
- Department of Neurology, Faculty of Medical Sciences, University of Kragujevac, Kragujevac 34 000, Serbia
| | - Ivica Petrovic
- Department of Pathophysiology, Faculty of Medical Sciences, University of Kragujevac, Kragujevac 34 000, Serbia
| | - Ivan P Jovanovic
- Center for Molecular Medicine and Stem Cell Research, Faculty of Medical Sciences, University of Kragujevac, Kragujevac 34 000, Serbia
| | - Nataša R Mijailović
- Department of Pharmacy, Faculty of Medical Sciences, University of Kragujevac, Kragujevac 34 000, Serbia
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Shared Genes of PPARG and NOS2 in Alzheimer’s Disease and Ulcerative Colitis Drive Macrophages and Microglia Polarization: Evidence from Bioinformatics Analysis and Following Validation. Int J Mol Sci 2023; 24:ijms24065651. [PMID: 36982725 PMCID: PMC10058634 DOI: 10.3390/ijms24065651] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Emerging evidence shows that peripheral systemic inflammation, such as inflammatory bowel disease (IBD), has a close even interaction with central nervous disorders such as Alzheimer’s disease (AD). This study is designed to further clarify the relationship between AD and ulcerative colitis (UC, a subclass of IBD). The GEO database was used to download gene expression profiles for AD (GSE5281) and UC (GSE47908). Bioinformatics analysis included GSEA, KEGG pathway, Gene Ontology (GO), WikiPathways, PPI network, and hub gene identification. After screening the shared genes, qRT-PCR, Western blot, and immunofluorescence were used to verify the reliability of the dataset and further confirm the shared genes. GSEA, KEGG, GO, and WikiPathways suggested that PPARG and NOS2 were identified as shared genes and hub genes by cytoHubba in AD and UC and further validated via qRT-PCR and Western blot. Our work identified PPARG and NOS2 are shared genes of AD and UC. They drive macrophages and microglia heterogeneous polarization, which may be potential targets for treating neural dysfunction induced by systemic inflammation and vice versa.
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Special Issue: Genetics of Psychiatric Disease and the Basics of Neurobiology. Genes (Basel) 2022; 13:genes13112008. [DOI: 10.3390/genes13112008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
A psychiatric disorder is a mental illness involving significant disturbances in thinking, emotional regulation or behavior [...]
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Meta-Analysis of Long-Term Efficacy of Proliferative Diabetic Retinopathy Based on Intelligent Medical Treatment. CONTRAST MEDIA & MOLECULAR IMAGING 2022; 2022:6545553. [PMID: 36226268 PMCID: PMC9525783 DOI: 10.1155/2022/6545553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/26/2022] [Accepted: 09/08/2022] [Indexed: 01/26/2023]
Abstract
In order to solve some problems of subhealth and high chronic diseases, the diagnosis and treatment of value-added diabetic retinopathy are studied. In particular, diabetes, a high chronic disease, poses a great threat to people's health. With the continuous improvement of national health awareness, the medical field also begins to pay more attention to the diagnosis and treatment of value-added diabetic retinopathy. In order to improve the long-term treatment of value-added diabetic retinopathy through intelligent medical monitoring and systematic scientific efficacy analysis and evaluation, the purpose of this study is to explore how to effectively achieve the meta-analysis of long-term efficacy of proliferative diabetic retinopathy through intelligent medical treatment. Through the study of diabetic retinopathy, the system can help doctors to achieve unlimited further signs of parameter acquisition and transmission and build more mature after treatment of the results of the monitoring platform. At the same time, a conclusion based on vitrectomy was proposed to effectively improve the surgical efficacy of patients with proliferative diabetic retinopathy.
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Goh KK, Chen CYA, Wu TH, Chen CH, Lu ML. Crosstalk between Schizophrenia and Metabolic Syndrome: The Role of Oxytocinergic Dysfunction. Int J Mol Sci 2022; 23:ijms23137092. [PMID: 35806096 PMCID: PMC9266532 DOI: 10.3390/ijms23137092] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/23/2022] [Accepted: 06/23/2022] [Indexed: 02/01/2023] Open
Abstract
The high prevalence of metabolic syndrome in persons with schizophrenia has spurred investigational efforts to study the mechanism beneath its pathophysiology. Early psychosis dysfunction is present across multiple organ systems. On this account, schizophrenia may be a multisystem disorder in which one organ system is predominantly affected and where other organ systems are also concurrently involved. Growing evidence of the overlapping neurobiological profiles of metabolic risk factors and psychiatric symptoms, such as an association with cognitive dysfunction, altered autonomic nervous system regulation, desynchrony in the resting-state default mode network, and shared genetic liability, suggest that metabolic syndrome and schizophrenia are connected via common pathways that are central to schizophrenia pathogenesis, which may be underpinned by oxytocin system dysfunction. Oxytocin, a hormone that involves in the mechanisms of food intake and metabolic homeostasis, may partly explain this piece of the puzzle in the mechanism underlying this association. Given its prosocial and anorexigenic properties, oxytocin has been administered intranasally to investigate its therapeutic potential in schizophrenia and obesity. Although the pathophysiology and mechanisms of oxytocinergic dysfunction in metabolic syndrome and schizophrenia are both complex and it is still too early to draw a conclusion upon, oxytocinergic dysfunction may yield a new mechanistic insight into schizophrenia pathogenesis and treatment.
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Affiliation(s)
- Kah Kheng Goh
- Department of Psychiatry, Wan-Fang Hospital, Taipei Medical University, Taipei 116, Taiwan; (K.K.G.); (C.Y.-A.C.); (C.-H.C.)
- Psychiatric Research Center, Wan-Fang Hospital, Taipei Medical University, Taipei 116, Taiwan;
- Department of Psychiatry, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Cynthia Yi-An Chen
- Department of Psychiatry, Wan-Fang Hospital, Taipei Medical University, Taipei 116, Taiwan; (K.K.G.); (C.Y.-A.C.); (C.-H.C.)
- Psychiatric Research Center, Wan-Fang Hospital, Taipei Medical University, Taipei 116, Taiwan;
| | - Tzu-Hua Wu
- Psychiatric Research Center, Wan-Fang Hospital, Taipei Medical University, Taipei 116, Taiwan;
- Department of Clinical Pharmacy, School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan
| | - Chun-Hsin Chen
- Department of Psychiatry, Wan-Fang Hospital, Taipei Medical University, Taipei 116, Taiwan; (K.K.G.); (C.Y.-A.C.); (C.-H.C.)
- Psychiatric Research Center, Wan-Fang Hospital, Taipei Medical University, Taipei 116, Taiwan;
- Department of Psychiatry, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Mong-Liang Lu
- Department of Psychiatry, Wan-Fang Hospital, Taipei Medical University, Taipei 116, Taiwan; (K.K.G.); (C.Y.-A.C.); (C.-H.C.)
- Psychiatric Research Center, Wan-Fang Hospital, Taipei Medical University, Taipei 116, Taiwan;
- Department of Psychiatry, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Correspondence:
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Bioinformatics and Network-based Approaches for Determining Pathways, Signature Molecules, and Drug Substances connected to Genetic Basis of Schizophrenia etiology. Brain Res 2022; 1785:147889. [PMID: 35339428 DOI: 10.1016/j.brainres.2022.147889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/28/2022] [Accepted: 03/21/2022] [Indexed: 12/12/2022]
Abstract
Knowledge of heterogeneous etiology and pathophysiology of schizophrenia (SZP) is reasonably inadequate and non-deterministic due to its inherent complexity and underlying vast dynamics related to genetic mechanisms. The evolution of large-scale transcriptome-wide datasets and subsequent development of relevant, robust technologies for their analyses show promises toward elucidating the genetic basis of disease pathogenesis, its early risk prediction, and predicting drug molecule targets for therapeutic intervention. In this research, we have scrutinized the genetic basis of SZP through functional annotation and network-based system biology approaches. We have determined 96 overlapping differentially expressed genes (DEGs) from 2 microarray datasets and subsequently identified their interconnecting networks to reveal transcriptome signatures like hub proteins (FYN, RAD51, SOCS3, XIAP, AKAP13, PIK3C2A, CBX5, GATA3, EIF3K, and CDKN2B), transcription factors and miRNAs. In addition, we have employed gene set enrichment to highlight significant gene ontology (e.g., positive regulation of microglial cell activation) and relevant pathways (such as axon guidance and focal adhesion) interconnected to the genes associated with SZP. Finally, we have suggested candidate drug substances like Luteolin HL60 UP as a possible therapeutic target based on these key molecular signatures.
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Perry BI, Bowker N, Burgess S, Wareham NJ, Upthegrove R, Jones PB, Langenberg C, Khandaker GM. Evidence for Shared Genetic Aetiology Between Schizophrenia, Cardiometabolic, and Inflammation-Related Traits: Genetic Correlation and Colocalization Analyses. SCHIZOPHRENIA BULLETIN OPEN 2022; 3:sgac001. [PMID: 35156041 PMCID: PMC8827407 DOI: 10.1093/schizbullopen/sgac001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Schizophrenia commonly co-occurs with cardiometabolic and inflammation-related traits. It is unclear to what extent the comorbidity could be explained by shared genetic aetiology. METHODS We used GWAS data to estimate shared genetic aetiology between schizophrenia, cardiometabolic, and inflammation-related traits: fasting insulin (FI), fasting glucose, glycated haemoglobin, glucose tolerance, type 2 diabetes (T2D), lipids, body mass index (BMI), coronary artery disease (CAD), and C-reactive protein (CRP). We examined genome-wide correlation using linkage disequilibrium score regression (LDSC); stratified by minor-allele frequency using genetic covariance analyzer (GNOVA); then refined to locus-level using heritability estimation from summary statistics (ρ-HESS). Regions with local correlation were used in hypothesis prioritization multi-trait colocalization to examine for colocalisation, implying common genetic aetiology. RESULTS We found evidence for weak genome-wide negative correlation of schizophrenia with T2D (rg = -0.07; 95% C.I., -0.03,0.12; P = .002) and BMI (rg = -0.09; 95% C.I., -0.06, -0.12; P = 1.83 × 10-5). We found a trend of evidence for positive genetic correlation between schizophrenia and cardiometabolic traits confined to lower-frequency variants. This was underpinned by 85 regions of locus-level correlation with evidence of opposing mechanisms. Ten loci showed strong evidence of colocalization. Four of those (rs6265 (BDNF); rs8192675 (SLC2A2); rs3800229 (FOXO3); rs17514846 (FURIN)) are implicated in brain-derived neurotrophic factor (BDNF)-related pathways. CONCLUSIONS LDSC may lead to downwardly-biased genetic correlation estimates between schizophrenia, cardiometabolic, and inflammation-related traits. Common genetic aetiology for these traits could be confined to lower-frequency common variants and involve opposing mechanisms. Genes related to BDNF and glucose transport amongst others may partly explain the comorbidity between schizophrenia and cardiometabolic disorders.
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Affiliation(s)
- Benjamin I Perry
- Department of Psychiatry, University of Cambridge School of Clinical Medicine, Cambridge, UK,Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK,To whom correspondence should be addressed; Department of Psychiatry, University of Cambridge, Herchel Smith Building, Robinson Way, Cambridge, CB2 0SZ, UK; tel: +441223 336963, e-mail:
| | - Nicholas Bowker
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Rachel Upthegrove
- Institute for Mental Health, University of Birmingham, Birmingham, UK
| | - Peter B Jones
- Department of Psychiatry, University of Cambridge School of Clinical Medicine, Cambridge, UK,Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Golam M Khandaker
- Department of Psychiatry, University of Cambridge School of Clinical Medicine, Cambridge, UK,Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
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Auwul MR, Rahman MR, Gov E, Shahjaman M, Moni MA. Bioinformatics and machine learning approach identifies potential drug targets and pathways in COVID-19. Brief Bioinform 2021; 22:6220170. [PMID: 33839760 PMCID: PMC8083354 DOI: 10.1093/bib/bbab120] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/15/2021] [Accepted: 03/13/2021] [Indexed: 12/12/2022] Open
Abstract
Current coronavirus disease-2019 (COVID-19) pandemic has caused massive loss of lives. Clinical trials of vaccines and drugs are currently being conducted around the world; however, till now no effective drug is available for COVID-19. Identification of key genes and perturbed pathways in COVID-19 may uncover potential drug targets and biomarkers. We aimed to identify key gene modules and hub targets involved in COVID-19. We have analyzed SARS-CoV-2 infected peripheral blood mononuclear cell (PBMC) transcriptomic data through gene coexpression analysis. We identified 1520 and 1733 differentially expressed genes (DEGs) from the GSE152418 and CRA002390 PBMC datasets, respectively (FDR < 0.05). We found four key gene modules and hub gene signature based on module membership (MMhub) statistics and protein-protein interaction (PPI) networks (PPIhub). Functional annotation by enrichment analysis of the genes of these modules demonstrated immune and inflammatory response biological processes enriched by the DEGs. The pathway analysis revealed the hub genes were enriched with the IL-17 signaling pathway, cytokine-cytokine receptor interaction pathways. Then, we demonstrated the classification performance of hub genes (PLK1, AURKB, AURKA, CDK1, CDC20, KIF11, CCNB1, KIF2C, DTL and CDC6) with accuracy >0.90 suggesting the biomarker potential of the hub genes. The regulatory network analysis showed transcription factors and microRNAs that target these hub genes. Finally, drug-gene interactions analysis suggests amsacrine, BRD-K68548958, naproxol, palbociclib and teniposide as the top-scored repurposed drugs. The identified biomarkers and pathways might be therapeutic targets to the COVID-19.
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Affiliation(s)
- Md Rabiul Auwul
- School of Economics and Statistics, Guangzhou University, Guangzhou 510006, China
| | - Md Rezanur Rahman
- Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Sirajgonj-6751, Bangladesh
| | - Esra Gov
- Department of Bioengineering, Adana Alparslan Turkes Science and Technology University, Adana-01250, Turkey
| | - Md Shahjaman
- Department of Statistics, Begum Rokeya University, Rangpur-5400, Bangladesh
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Australia
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