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Schröder S, Fuchs U, Gisa V, Pena T, Krüger DM, Hempel N, Burkhardt S, Salinas G, Schütz AL, Delalle I, Sananbenesi F, Fischer A. PRDM16-DT: A Brain and Astrocyte-Specific lncRNA Implicated in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.600964. [PMID: 39005272 PMCID: PMC11244882 DOI: 10.1101/2024.06.27.600964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Astrocytes provide crucial support for neurons, contributing to synaptogenesis, synaptic maintenance, and neurotransmitter recycling. Under pathological conditions, deregulation of astrocytes contributes to neurodegenerative diseases such as Alzheimer's disease (AD), highlighting the growing interest in targeting astrocyte function to address early phases of AD pathogenesis. While most research in this field has focused on protein-coding genes, non-coding RNAs, particularly long non-coding RNAs (lncRNAs), have emerged as significant regulatory molecules. In this study, we identified the lncRNA PRDM16-DT as highly enriched in the human brain, where it is almost exclusively expressed in astrocytes. PRDM16-DT and its murine homolog, Prdm16os, are downregulated in the brains of AD patients and in AD models. In line with this, knockdown of PRDM16-DT and Prdm16os revealed its critical role in maintaining astrocyte homeostasis and supporting neuronal function by regulating genes essential for glutamate uptake, lactate release, and neuronal spine density through interactions with the RE1-Silencing Transcription factor (Rest) and Polycomb Repressive Complex 2 (PRC2). Notably, CRISPR-mediated overexpression of Prdm16os mitigated functional deficits in astrocytes induced by stimuli linked to AD pathogenesis. These findings underscore the importance of PRDM16-DT in astrocyte function and its potential as a novel therapeutic target for neurodegenerative disorders characterized by astrocyte dysfunction.
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Affiliation(s)
- Sophie Schröder
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Ulrike Fuchs
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Verena Gisa
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Tonatiuh Pena
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
- Bioinformatics Unit, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Dennis M Krüger
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
- Bioinformatics Unit, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Nina Hempel
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Susanne Burkhardt
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Gabriela Salinas
- NGS- Integrative Genomics Core Unit, Institute of Pathology, University Medical Center Göttingen, Germany
| | - Anna-Lena Schütz
- Research Group for Genome Dynamics in Brain Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Ivana Delalle
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, 670 Albany Street, Boston, MA 02118, USA
| | - Farahnaz Sananbenesi
- Research Group for Genome Dynamics in Brain Diseases, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Andre Fischer
- Department for Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
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Cheng Y, Chen X, Zhang XQ, Ju PJ, Wang WD, Fang Y, Lin GN, Cui DH. Interaction between RNF4 and SART3 is associated with the risk of schizophrenia. Heliyon 2024; 10:e32743. [PMID: 38975171 PMCID: PMC11226853 DOI: 10.1016/j.heliyon.2024.e32743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 06/03/2024] [Accepted: 06/07/2024] [Indexed: 07/09/2024] Open
Abstract
The pathogenesis of schizophrenia (SCZ) is heavily influenced by genetic factors. Ring finger protein 4 (RNF4) and squamous cell carcinoma antigen recognized by T cells 3 (SART3) are thought to be involved in nervous system growth and development via oxidative stress pathways. Moreover, they have previously been linked to SCZ. Yet the role of RNF4 and SART3 in SCZ remains unclear. Here, we investigated how these two genes are involved in SCZ by studying their variants observed in patients. We first observed significantly elevated mRNA levels of RNF4 and SART3 in the peripheral blood in both first-episode (n = 30) and chronic (n = 30) SCZ patients compared to controls (n = 60). Next, we targeted-sequenced three single nucleotide polymorphisms (SNPs) in SART3 and six SNPs in RNF4 for association with SCZ using the genomic DNA extracted from peripheral blood leukocytes from SCZ participants (n = 392) and controls (n = 572). We observed a combination of SNPs that included rs1203860, rs2282765 (both in RNF4), and rs2287550 (in SART3) was associated with increased risk of SCZ, suggesting common pathogenic mechanisms between these two genes. We then conducted experiments in HEK293T cells to better understand the interaction between RNF4 and SART3. We observed that SART3 lowered the expression of RNF4 through ubiquitination and downregulated the expression of nuclear factor E2-related factor 2 (NRF2), a downstream factor of RNF4, implicating the existence of a possible shared regulatory mechanism for RNF4 and SART3. In conclusion, our study provides evidence that the interaction between RNF4 and SART3 contributes to the risk of SCZ. The findings shed light on the underlying molecular mechanisms of SCZ and may lead to the development of new therapies and interventions for this disorder.
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Affiliation(s)
- Ying Cheng
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Xi Chen
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Xiao Qing Zhang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Pei Jun Ju
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Di Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Division of Imaging, Computational and Systems Biomedicine, School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Fang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Guan Ning Lin
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Division of Imaging, Computational and Systems Biomedicine, School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Dong Hong Cui
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
- Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
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Xu S, Wang J, Mao K, Jiao D, Li Z, Zhao H, Sun Y, Feng J, Lai Y, Peng R, Fu Y, Gan R, Chen S, Zhao HY, Wei HJ, Cheng Y. Generation and transcriptomic characterization of MIR137 knockout miniature pig model for neurodevelopmental disorders. Cell Biosci 2024; 14:86. [PMID: 38937838 PMCID: PMC11212353 DOI: 10.1186/s13578-024-01268-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Neurodevelopmental disorders (NDD), such as autism spectrum disorders (ASD) and intellectual disorders (ID), are highly debilitating childhood psychiatric conditions. Genetic factors are recognized as playing a major role in NDD, with a multitude of genes and genomic regions implicated. While the functional validation of NDD-associated genes has predominantly been carried out using mouse models, the significant differences in brain structure and gene function between mice and humans have limited the effectiveness of mouse models in exploring the underlying mechanisms of NDD. Therefore, it is important to establish alternative animal models that are more evolutionarily aligned with humans. RESULTS In this study, we employed CRISPR/Cas9 and somatic cell nuclear transplantation technologies to successfully generate a knockout miniature pig model of the MIR137 gene, which encodes the neuropsychiatric disorder-associated microRNA miR-137. The homozygous knockout of MIR137 (MIR137-/-) effectively suppressed the expression of mature miR-137 and led to the birth of stillborn or short-lived piglets. Transcriptomic analysis revealed significant changes in genes associated with neurodevelopment and synaptic signaling in the brains of MIR137-/- miniature pig, mirroring findings from human ASD transcriptomic data. In comparison to miR-137-deficient mouse and human induced pluripotent stem cell (hiPSC)-derived neuron models, the miniature pig model exhibited more consistent changes in critical neuronal genes relevant to humans following the loss of miR-137. Furthermore, a comparative analysis identified differentially expressed genes associated with ASD and ID risk genes in both miniature pig and hiPSC-derived neurons. Notably, human-specific miR-137 targets, such as CAMK2A, known to be linked to cognitive impairments and NDD, exhibited dysregulation in MIR137-/- miniature pigs. These findings suggest that the loss of miR-137 in miniature pigs affects genes crucial for neurodevelopment, potentially contributing to the development of NDD. CONCLUSIONS Our study highlights the impact of miR-137 loss on critical genes involved in neurodevelopment and related disorders in MIR137-/- miniature pigs. It establishes the miniature pig model as a valuable tool for investigating neurodevelopmental disorders, providing valuable insights for potential applications in human research.
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Affiliation(s)
- Shengyun Xu
- Institute of Biomedical Research, Yunnan University, Kunming, 650500, China
| | - Jiaoxiang Wang
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
| | - Kexin Mao
- Institute of Biomedical Research, Yunnan University, Kunming, 650500, China
- Southwest United Graduate School, Kunming, 650092, China
| | - Deling Jiao
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
| | - Zhu Li
- Institute of Biomedical Research, Yunnan University, Kunming, 650500, China
| | - Heng Zhao
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
| | - Yifei Sun
- Institute of Biomedical Research, Yunnan University, Kunming, 650500, China
| | - Jin Feng
- Institute of Biomedical Research, Yunnan University, Kunming, 650500, China
- Southwest United Graduate School, Kunming, 650092, China
| | - Yuanhao Lai
- Institute of Biomedical Research, Yunnan University, Kunming, 650500, China
| | - Ruiqi Peng
- Institute of Biomedical Research, Yunnan University, Kunming, 650500, China
| | - Yu Fu
- Institute of Biomedical Research, Yunnan University, Kunming, 650500, China
| | - Ruoyi Gan
- Institute of Biomedical Research, Yunnan University, Kunming, 650500, China
- Southwest United Graduate School, Kunming, 650092, China
| | - Shuhan Chen
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
| | - Hong-Ye Zhao
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China.
| | - Hong-Jiang Wei
- Key Laboratory for Porcine Gene Editing and Xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China.
| | - Ying Cheng
- Institute of Biomedical Research, Yunnan University, Kunming, 650500, China.
- Southwest United Graduate School, Kunming, 650092, China.
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Ye J, Chen H, Wang Y, Chen H, Huang J, Yang Y, Feng Z, Li W. A preliminary metabolomics study of the database for biological samples of schizophrenia among Chinese ethnic minorities. BMC Psychiatry 2024; 24:262. [PMID: 38594695 PMCID: PMC11003042 DOI: 10.1186/s12888-024-05660-z] [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: 01/07/2024] [Accepted: 03/05/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Schizophrenia (SCZ) is a profound mental disorder with a multifactorial etiology, including genetics, environmental factors, and demographic influences such as ethnicity and geography. Among these, the studies of SCZ also shows racial and regional differences. METHODS We first established a database of biological samples for SCZ in China's ethnic minorities, followed by a serum metabolomic analysis of SCZ patients from various ethnic groups within the same region using the LC-HRMS platform. RESULTS Analysis identified 47 metabolites associated with SCZ, with 46 showing significant differences between Miao and Han SCZ patients. These metabolites, primarily fatty acids, amino acids, benzene, and derivatives, are involved in fatty acid metabolism pathways. Notably, L-Carnitine, L-Cystine, Aspartylphenylalanine, and Methionine sulfoxide demonstrated greater diagnostic efficacy in Miao SCZ patients compared to Han SCZ patients. CONCLUSION Preliminary findings suggest that there are differences in metabolic levels among SCZ patients of different ethnicities in the same region, offering insights for developing objective diagnostic or therapeutic monitoring strategies that incorporate ethnic considerations of SCZ.
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Affiliation(s)
- Jun Ye
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guizhou Medical University, 556000, Guizhou, China
| | - Haixia Chen
- Department of Clinical Biochemistry and Laboratory Medicine, Guizhou Medical University, 550001, Guizhou, China
| | - Yang Wang
- Shandong Yingsheng Biotechnology Co., Ltd., 250101, Jinan, Shandong, China
| | - Haini Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guizhou Medical University, 556000, Guizhou, China
| | - Jiang Huang
- Department of Psychiatry, The Second Affiliated Hospital of Guizhou Medical University, Kangfu Road, 556000, Guizhou, China
| | - Yixia Yang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guizhou Medical University, 556000, Guizhou, China
| | - Zhen Feng
- Shandong Yingsheng Biotechnology Co., Ltd., 250101, Jinan, Shandong, China.
| | - Wenfeng Li
- Department of Psychiatry, The Second Affiliated Hospital of Guizhou Medical University, Kangfu Road, 556000, Guizhou, China.
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5
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Egilmezer E, Hamilton ST, Foster CSP, Marschall M, Rawlinson WD. Human cytomegalovirus (CMV) dysregulates neurodevelopmental pathways in cerebral organoids. Commun Biol 2024; 7:340. [PMID: 38504123 PMCID: PMC10951402 DOI: 10.1038/s42003-024-05923-1] [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: 02/09/2023] [Accepted: 02/16/2024] [Indexed: 03/21/2024] Open
Abstract
Human cytomegalovirus (CMV) infection is the leading non-genetic aetiology of congenital malformation in developed countries, causing significant fetal neurological injury. This study investigated potential CMV pathogenetic mechanisms of fetal neural malformation using in vitro human cerebral organoids. Cerebral organoids were permissive to CMV replication, and infection dysregulated cellular pluripotency and differentiation pathways. Aberrant expression of dual-specificity tyrosine phosphorylation-regulated kinases (DYRK), sonic hedgehog (SHH), pluripotency, neurodegeneration, axon guidance, hippo signalling and dopaminergic synapse pathways were observed in CMV-infected organoids using immunofluorescence and RNA-sequencing. Infection with CMV resulted in dysregulation of 236 Autism Spectrum Disorder (ASD)-related genes (p = 1.57E-05) and pathways. This notable observation suggests potential links between congenital CMV infection and ASD. Using DisGeNET databases, 103 diseases related to neural malformation or mental disorders were enriched in CMV-infected organoids. Cytomegalovirus infection-related dysregulation of key cerebral cellular pathways potentially provides important, modifiable pathogenetic mechanisms for congenital CMV-induced neural malformation and ASD.
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Affiliation(s)
- Ece Egilmezer
- Serology and Virology Division, Microbiology, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, 2031, Australia
- School of Medical Science, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Stuart T Hamilton
- Serology and Virology Division, Microbiology, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, 2031, Australia
- School of Clinical Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Charles S P Foster
- Serology and Virology Division, Microbiology, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, 2031, Australia
- School of Medical Science, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - William D Rawlinson
- Serology and Virology Division, Microbiology, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, 2031, Australia.
- School of Medical Science, University of New South Wales, Sydney, NSW, 2052, Australia.
- School of Clinical Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
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6
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Zadok N, Ast G, Sharan R. A network-based method for associating genes with autism spectrum disorder. FRONTIERS IN BIOINFORMATICS 2024; 4:1295600. [PMID: 38525240 PMCID: PMC10960359 DOI: 10.3389/fbinf.2024.1295600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
Autism spectrum disorder (ASD) is a highly heritable complex disease that affects 1% of the population, yet its underlying molecular mechanisms are largely unknown. Here we study the problem of predicting causal genes for ASD by combining genome-scale data with a network propagation approach. We construct a predictor that integrates multiple omic data sets that assess genomic, transcriptomic, proteomic, and phosphoproteomic associations with ASD. In cross validation our predictor yields mean area under the ROC curve of 0.87 and area under the precision-recall curve of 0.89. We further show that it outperforms previous gene-level predictors of autism association. Finally, we show that we can use the model to predict genes associated with Schizophrenia which is known to share genetic components with ASD.
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Affiliation(s)
- Neta Zadok
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Roded Sharan
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
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Singh M, Pradhan D, Kkani P, Prasad Rao G, Dhagudu NK, Kumar L, Ramasubramanian C, Kumar SG, Sonttineni S, Mohan KN. Genome-scale copy number variant analysis in schizophrenia patients and controls from South India. Front Mol Neurosci 2023; 16:1268827. [PMID: 38178910 PMCID: PMC10764592 DOI: 10.3389/fnmol.2023.1268827] [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: 07/28/2023] [Accepted: 11/22/2023] [Indexed: 01/06/2024] Open
Abstract
Copy number variants (CNVs) are among the main genetic factors identified in schizophrenia (SZ) through genome-scale studies conducted mostly in Caucasian populations. However, to date, there have been no genome-scale CNV reports on patients from India. To address this shortcoming, we generated, for the first time, genome-scale CNV data for 168 SZ patients and 168 controls from South India. In total, 63 different CNVs were identified in 56 patients and 46 controls with a significantly higher proportion of medium-sized deletions (100 kb-1 Mb) after multiple testing (FDR = 2.7E-4) in patients. Of these, 13 CNVs were previously reported; however, when searched against GWAS, transcriptome, exome, and DNA methylation studies, another 17 CNVs with candidate genes were identified. Of the total 30 CNVs, 28 were present in 38 patients and 12 in 27 controls, indicating a significantly higher representation in the former (p = 1.87E-5). Only 4q35.1-q35.2 duplications were significant (p = 0.020) and observed in 11 controls and 2 patients. Among the others that are not significant, a few examples of patient-specific and previously reported CNVs include deletions of 11q14.1 (DLG2), 22q11.21, and 14q21.1 (LRFN5). 16p13.3 deletion (RBFOX1), 3p14.2 duplication (CADPS), and 7p11.2 duplication (CCT6A) were some of the novel CNVs containing candidate genes. However, these observations need to be replicated in a larger sample size. In conclusion, this report constitutes an important foundation for future CNV studies in a relatively unexplored population. In addition, the data indicate that there are advantages in using an integrated approach for better identification of candidate CNVs for SZ and other mental health disorders.
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Affiliation(s)
- Minali Singh
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani – Hyderabad Campus, Hyderabad, India
| | - Dibyabhabha Pradhan
- Centralized Core Research Facility, All India Institute of Medical Sciences, New Delhi, India
| | - Poornima Kkani
- Department of Zoology, Thiagarajar College, Madurai, India
| | | | | | - Lov Kumar
- Department of Computer Engineering, National Institute of Technology, Kurukshetra, India
| | | | | | | | - Kommu Naga Mohan
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani – Hyderabad Campus, Hyderabad, India
- Centre for Human Disease Research, Birla Institute of Technology and Science, Pilani – Hyderabad Campus, Hyderabad, India
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8
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Ye J, Huang Z, Li Q, Li Z, Lan Y, Wang Z, Ni C, Wu X, Jiang T, Li Y, Yang Q, Lim J, Ren CY, Jiang M, Li S, Jin P, Chen JH, Zhao C. Transition of allele-specific DNA hydroxymethylation at regulatory loci is associated with phenotypic variation in monozygotic twins discordant for psychiatric disorders. BMC Med 2023; 21:491. [PMID: 38082312 PMCID: PMC10714646 DOI: 10.1186/s12916-023-03177-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Major psychiatric disorders such as schizophrenia (SCZ) and bipolar disorder (BPD) are complex genetic mental illnesses. Their non-Mendelian features, such as those observed in monozygotic twins discordant for SCZ or BPD, are likely complicated by environmental modifiers of genetic effects. 5-Hydroxymethylcytosine (5hmC) is an important epigenetic mark in gene regulation, and whether it is linked to genetic variants that contribute to non-Mendelian features remains largely unexplored. METHODS We combined the 5hmC-selective chemical labeling method (5hmC-seq) and whole-genome sequencing (WGS) analysis of peripheral blood DNA obtained from monozygotic (MZ) twins discordant for SCZ or BPD to identify allelic imbalances in hydroxymethylome maps, and examined association of allele-specific hydroxymethylation (AShM) transition with disease susceptibility based on Bayes factors (BF) derived from the Bayesian generalized additive linear mixed model. We then performed multi-omics integrative analysis to determine the molecular pathogenic basis of those AShM sites. We finally employed luciferase reporter, CRISPR/Cas9 technology, electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation (ChIP), PCR, FM4-64 imaging analysis, and RNA sequencing to validate the function of interested AShM sites in the human neuroblastoma SK-N-SH cells and human embryonic kidney 293T (HEK293T) cells. RESULTS We identified thousands of genetic variants associated with AShM imbalances that exhibited phenotypic variation-associated AShM changes at regulatory loci. These AShM marks showed plausible associations with SCZ or BPD based on their effects on interactions among transcription factors (TFs), DNA methylation levels, or other epigenomic marks and thus contributed to dysregulated gene expression, which ultimately increased disease susceptibility. We then validated that competitive binding of POU3F2 on the alternative allele at the AShM site rs4558409 (G/T) in PLLP-enhanced PLLP expression, while the hydroxymethylated alternative allele, which alleviated the POU3F2 binding activity at the rs4558409 site, might be associated with the downregulated PLLP expression observed in BPD or SCZ. Moreover, disruption of rs4558409 promoted neural development and vesicle trafficking. CONCLUSION Our study provides a powerful strategy for prioritizing regulatory risk variants and contributes to our understanding of the interplay between genetic and epigenetic factors in mediating SCZ or BPD susceptibility.
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Affiliation(s)
- Junping Ye
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zhanwang Huang
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Qiyang Li
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Department of Rehabilitation, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Zhongwei Li
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yuting Lan
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Department of Psychiatry, the Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, Guangdong, China
| | - Zhongju Wang
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Chaoying Ni
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaohui Wu
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Tingyun Jiang
- The Third People's Hospital of Zhongshan, Zhongshan, Guangdong, China
| | - Yujing Li
- Departments of Human Genetics, Emory University, Atlanta, GA, USA
| | - Qiong Yang
- Department of Psychiatry, the Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, Guangdong, China
| | - Junghwa Lim
- Departments of Human Genetics, Emory University, Atlanta, GA, USA
| | - Cun-Yan Ren
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Meijun Jiang
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Science), Guangdong Mental Health Center, Southern Medical University, Guangzhou, China
| | - Shufen Li
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Peng Jin
- Departments of Human Genetics, Emory University, Atlanta, GA, USA
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China.
| | - Cunyou Zhao
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
- Department of Rehabilitation, Zhujiang Hospital of Southern Medical University, Guangzhou, China.
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Science), Guangdong Mental Health Center, Southern Medical University, Guangzhou, China.
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, China.
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Sun Y, Wen L, Luo YY, Hu WJ, Ren HW, Lv Y, Zhang C, Gao P, Xuan LN, Wang GY, Li CJ, Xiang ZX, Luan ZL. Positive Association of TEAD1 With Schizophrenia in a Northeast Chinese Han Population. Psychiatry Investig 2023; 20:1168-1176. [PMID: 38163656 PMCID: PMC10758319 DOI: 10.30773/pi.2023.0069] [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: 03/16/2023] [Revised: 08/02/2023] [Accepted: 09/04/2023] [Indexed: 01/03/2024] Open
Abstract
OBJECTIVE Schizophrenia is a complex and devastating psychiatric disorder with a strong genetic background. However, much uncertainty still exists about the role of genetic susceptibility in the pathophysiology of schizophrenia. TEA domain transcription factor 1 (TEAD1) is a transcription factor associated with neurodevelopment and has modulating effects on various nervous system diseases. In the current study, we performed a case-control association study in a Northeast Chinese Han population to explore the characteristics of pathogenic TEAD1 polymorphisms and potential association with schizophrenia. METHODS We recruited a total of 721 schizophrenia patients and 1,195 healthy controls in this study. The 9 single nucleotide polymorphisms (SNPs) in the gene region of TEAD1 were selected and genotyped. RESULTS The genetic association analyses showed that five SNPs (rs12289262, rs6485989, rs4415740, rs7113256, and rs1866709) were significantly different between schizophrenia patients and healthy controls in allele or/and genotype frequencies. After Bonferroni correction, the association of three SNPs (rs4415740, rs7113256, and rs1866709) with schizophrenia were still evident. Haplotype analysis revealed that two strong linkage disequilibrium blocks (rs6485989-rs4415740-rs7113256 and rs16911710-rs12364619-rs1866709) were globally associated with schizophrenia. Four haplotypes (C-C-C and T-T-T, rs6485989-rs4415740-rs7113256; G-T-A and G-T-G, rs16911710-rs12364619-rs1866709) were significantly different between schizophrenia patients and healthy controls. CONCLUSION The current findings indicated that the human TEAD1 gene has a genetic association with schizophrenia in the Chinese Han population and may act as a susceptibility gene for schizophrenia.
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Affiliation(s)
- Yang Sun
- Department of Psychiatry, Dalian Seventh People’s Hospital, Dalian, China
| | - Lin Wen
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Yi-Yang Luo
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Wen-Juan Hu
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Hui-Wen Ren
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Ye Lv
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Cong Zhang
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Ping Gao
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Li-Na Xuan
- Department of Neurosurgery, Epileptic Center of Liaoning, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Guan-Yu Wang
- Department of Neurosurgery, Epileptic Center of Liaoning, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Cheng-Jie Li
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Zhi-Xin Xiang
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Zhi-Lin Luan
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
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10
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Zhang W, Zhang M, Xu Z, Yan H, Wang H, Jiang J, Wan J, Tang B, Liu C, Chen C, Meng Q. Human forebrain organoid-based multi-omics analyses of PCCB as a schizophrenia associated gene linked to GABAergic pathways. Nat Commun 2023; 14:5176. [PMID: 37620341 PMCID: PMC10449845 DOI: 10.1038/s41467-023-40861-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
Identifying genes whose expression is associated with schizophrenia (SCZ) risk by transcriptome-wide association studies (TWAS) facilitates downstream experimental studies. Here, we integrated multiple published datasets of TWAS, gene coexpression, and differential gene expression analysis to prioritize SCZ candidate genes for functional study. Convergent evidence prioritized Propionyl-CoA Carboxylase Subunit Beta (PCCB), a nuclear-encoded mitochondrial gene, as an SCZ risk gene. However, the PCCB's contribution to SCZ risk has not been investigated before. Using dual luciferase reporter assay, we identified that SCZ-associated SNPs rs6791142 and rs35874192, two eQTL SNPs for PCCB, showed differential allelic effects on transcriptional activities. PCCB knockdown in human forebrain organoids (hFOs) followed by RNA sequencing analysis revealed dysregulation of genes enriched with multiple neuronal functions including gamma-aminobutyric acid (GABA)-ergic synapse. The metabolomic and mitochondrial function analyses confirmed the decreased GABA levels resulted from inhibited tricarboxylic acid cycle in PCCB knockdown hFOs. Multielectrode array recording analysis showed that PCCB knockdown in hFOs resulted into SCZ-related phenotypes including hyper-neuroactivities and decreased synchronization of neural network. In summary, this study utilized hFOs-based multi-omics analyses and revealed that PCCB downregulation may contribute to SCZ risk through regulating GABAergic pathways, highlighting the mitochondrial function in SCZ.
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Affiliation(s)
- Wendiao Zhang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
- The First Affiliated Hospital, Multi-Omics Research Center for Brain Disorders, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
- The First Affiliated Hospital, Clinical Research Center for Immune-Related Encephalopathy of Hunan Province, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
- The First Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
| | - Ming Zhang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Zhenhong Xu
- The First Affiliated Hospital, Multi-Omics Research Center for Brain Disorders, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
- The First Affiliated Hospital, Clinical Research Center for Immune-Related Encephalopathy of Hunan Province, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
- The First Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
| | - Hongye Yan
- The First Affiliated Hospital, Multi-Omics Research Center for Brain Disorders, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
- The First Affiliated Hospital, Clinical Research Center for Immune-Related Encephalopathy of Hunan Province, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
- The First Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
| | - Huimin Wang
- The First Affiliated Hospital, Multi-Omics Research Center for Brain Disorders, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
- The First Affiliated Hospital, Clinical Research Center for Immune-Related Encephalopathy of Hunan Province, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
- The First Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
| | - Jiamei Jiang
- The First Affiliated Hospital, Multi-Omics Research Center for Brain Disorders, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
- The First Affiliated Hospital, Clinical Research Center for Immune-Related Encephalopathy of Hunan Province, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
- The First Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
| | - Juan Wan
- The First Affiliated Hospital, Multi-Omics Research Center for Brain Disorders, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
- The First Affiliated Hospital, Clinical Research Center for Immune-Related Encephalopathy of Hunan Province, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
- The First Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
| | - Beisha Tang
- The First Affiliated Hospital, Multi-Omics Research Center for Brain Disorders, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
- The First Affiliated Hospital, Clinical Research Center for Immune-Related Encephalopathy of Hunan Province, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
- The First Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China
- Department of Neurology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Chunyu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China.
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China.
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan, 410008, China.
- Hunan Key Laboratory of Molecular Precision Medicine, Central South University, Changsha, Hunan, 410008, China.
| | - Qingtuan Meng
- The First Affiliated Hospital, Multi-Omics Research Center for Brain Disorders, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China.
- The First Affiliated Hospital, Clinical Research Center for Immune-Related Encephalopathy of Hunan Province, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China.
- The First Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, 421000, Hengyang, Hunan, China.
- MOE Key Lab of Rare Pediatric Diseases & School of Life Sciences, University of South China, 421001, Hengyang, Hunan, China.
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11
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Mısır E, Akay GG. Synaptic dysfunction in schizophrenia. Synapse 2023:e22276. [PMID: 37210696 DOI: 10.1002/syn.22276] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 04/25/2023] [Accepted: 05/07/2023] [Indexed: 05/22/2023]
Abstract
Schizophrenia is a chronic disease presented with psychotic symptoms, negative symptoms, impairment in the reward system, and widespread neurocognitive deterioration. Disruption of synaptic connections in neural circuits is responsible for the disease's development and progression. Because deterioration in synaptic connections results in the impaired effective processing of information. Although structural impairments of the synapse, such as a decrease in dendritic spine density, have been shown in previous studies, functional impairments have also been revealed with the development of genetic and molecular analysis methods. In addition to abnormalities in protein complexes regulating exocytosis in the presynaptic region and impaired vesicle release, especially, changes in proteins related to postsynaptic signaling have been reported. In particular, impairments in postsynaptic density elements, glutamate receptors, and ion channels have been shown. At the same time, effects on cellular adhesion molecular structures such as neurexin, neuroligin, and cadherin family proteins were detected. Of course, the confusing effect of antipsychotic use in schizophrenia research should also be considered. Although antipsychotics have positive and negative effects on synapses, studies indicate synaptic deterioration in schizophrenia independent of drug use. In this review, the deterioration in synapse structure and function and the effects of antipsychotics on the synapse in schizophrenia will be discussed.
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Affiliation(s)
- Emre Mısır
- Department of Psychiatry, Baskent University Faculty of Medicine, Ankara, Turkey
- Department of Interdisciplinary Neuroscience, Ankara University, Ankara, Turkey
| | - Güvem Gümüş Akay
- Department of Interdisciplinary Neuroscience, Ankara University, Ankara, Turkey
- Faculty of Medicine, Department of Physiology, Ankara University, Ankara, Turkey
- Brain Research Center (AÜBAUM), Ankara University, Ankara, Turkey
- Department of Cellular Neuroscience and Advanced Microscopic Neuroimaging, Neuroscience and Neurotechnology Center of Excellence (NÖROM), Ankara, Turkey
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12
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Medina AM, Hagenauer MH, Krolewski DM, Hughes E, Forrester LCT, Walsh DM, Waselus M, Richardson E, Turner CA, Sequeira PA, Cartagena PM, Thompson RC, Vawter MP, Bunney BG, Myers RM, Barchas JD, Lee FS, Schatzberg AF, Bunney WE, Akil H, Watson SJ. Neurotransmission-related gene expression in the frontal pole is altered in subjects with bipolar disorder and schizophrenia. Transl Psychiatry 2023; 13:118. [PMID: 37031222 PMCID: PMC10082811 DOI: 10.1038/s41398-023-02418-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/10/2023] Open
Abstract
The frontal pole (Brodmann area 10, BA10) is the largest cytoarchitectonic region of the human cortex, performing complex integrative functions. BA10 undergoes intensive adolescent grey matter pruning prior to the age of onset for bipolar disorder (BP) and schizophrenia (SCHIZ), and its dysfunction is likely to underly aspects of their shared symptomology. In this study, we investigated the role of BA10 neurotransmission-related gene expression in BP and SCHIZ. We performed qPCR to measure the expression of 115 neurotransmission-related targets in control, BP, and SCHIZ postmortem samples (n = 72). We chose this method for its high sensitivity to detect low-level expression. We then strengthened our findings by performing a meta-analysis of publicly released BA10 microarray data (n = 101) and identified sources of convergence with our qPCR results. To improve interpretation, we leveraged the unusually large database of clinical metadata accompanying our samples to explore the relationship between BA10 gene expression, therapeutics, substances of abuse, and symptom profiles, and validated these findings with publicly available datasets. Using these convergent sources of evidence, we identified 20 neurotransmission-related genes that were differentially expressed in BP and SCHIZ in BA10. These results included a large diagnosis-related decrease in two important therapeutic targets with low levels of expression, HTR2B and DRD4, as well as other findings related to dopaminergic, GABAergic and astrocytic function. We also observed that therapeutics may produce a differential expression that opposes diagnosis effects. In contrast, substances of abuse showed similar effects on BA10 gene expression as BP and SCHIZ, potentially amplifying diagnosis-related dysregulation.
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Affiliation(s)
- Adriana M Medina
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | | | - David M Krolewski
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Evan Hughes
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Maria Waselus
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Evelyn Richardson
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Cortney A Turner
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Robert C Thompson
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | | | | | - Huda Akil
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Stanley J Watson
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
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13
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Shriebman Y, Yitzhaky A, Kosloff M, Hertzberg L. Gene expression meta-analysis in patients with schizophrenia reveals up-regulation of RGS2 and RGS16 in Brodmann Area 10. Eur J Neurosci 2023; 57:360-372. [PMID: 36443250 DOI: 10.1111/ejn.15876] [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] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 09/10/2022] [Accepted: 11/17/2022] [Indexed: 11/30/2022]
Abstract
Regulator of G-protein signalling (RGS) proteins inhibit signalling by G-protein-coupled receptors (GPCRs). GPCRs mediate the functions of several important neurotransmitters and serve as targets of many anti-psychotics. RGS2, RGS4, RGS5 and RGS16 are located on chromosome 1q23.3-31, a locus found to be associated with schizophrenia. Although previous gene expression analysis detected down-regulation of RGS4 expression in brain samples of patients with schizophrenia, the results were not consistent. In the present study, we performed a systematic meta-analysis of differential RGS2, RGS4, RGS5 and RGS16 expression in Brodmann Area 10 (BA10) samples of patients with schizophrenia and from healthy controls. Two microarray datasets met the inclusion criteria (overall, 41 schizophrenia samples and 38 controls were analysed). RGS2 and RGS16 were found to be up-regulated in BA10 samples of individuals with schizophrenia, whereas no differential expression of RGS4 and RGS5 was detected. Analysis of dorso-lateral prefrontal cortex samples of the CommonMind Consortium (258 schizophrenia samples vs. 279 controls) further validated the results. Given their central role in inactivating G-protein-coupled signalling pathways, our results suggest that differential gene expression might lead to enhanced inactivation of G-protein signalling in schizophrenia. This, in turn, suggests that additional studies are needed to further explore the consequences of the differential expression we detected, this time at the protein and functional levels.
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Affiliation(s)
- Yaen Shriebman
- Shalvata Mental Health Center, affiliated with the Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Assif Yitzhaky
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Mickey Kosloff
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - Libi Hertzberg
- Shalvata Mental Health Center, affiliated with the Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
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14
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Chen J, Ding Q, An L, Wang H. Ca2+-stimulated adenylyl cyclases as therapeutic targets for psychiatric and neurodevelopmental disorders. Front Pharmacol 2022; 13:949384. [PMID: 36188604 PMCID: PMC9523369 DOI: 10.3389/fphar.2022.949384] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
As the main secondary messengers, cyclic AMP (cAMP) and Ca2+ trigger intracellular signal transduction cascade and, in turn, regulate many aspects of cellular function in developing and mature neurons. The group I adenylyl cyclase (ADCY, also known as AC) isoforms, including ADCY1, 3, and 8 (also known as AC1, AC3, and AC8), are stimulated by Ca2+ and thus functionally positioned to integrate cAMP and Ca2+ signaling. Emerging lines of evidence have suggested the association of the Ca2+-stimulated ADCYs with bipolar disorder, schizophrenia, major depressive disorder, post-traumatic stress disorder, and autism. In this review, we discuss the molecular and cellular features as well as the physiological functions of ADCY1, 3, and 8. We further discuss the recent therapeutic development to target the Ca2+-stimulated ADCYs for potential treatments of psychiatric and neurodevelopmental disorders.
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15
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Pan S, Zhou Y, Yan L, Xuan F, Tong J, Li Y, Huang J, Feng W, Chen S, Cui Y, Yang F, Tan S, Wang Z, Tian B, Hong LE, Tan YL, Tian L. TGF-β1 is associated with deficits in cognition and cerebral cortical thickness in first-episode schizophrenia. J Psychiatry Neurosci 2022; 47:E86-E98. [PMID: 35301253 PMCID: PMC9259382 DOI: 10.1503/jpn.210121] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/04/2021] [Accepted: 11/23/2021] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Evidence indicates that cytokines are associated with cognitive deficits in schizophrenia; however, the underlying brain-behaviour mechanisms remain unclear. We hypothesized that aberrations in brain structural connectivity mediate the cytokine effect in schizophrenia. METHODS In this study, we recruited patients with first-episode schizophrenia (n = 75, average illness duration 12.3 months, average medication period 0.6 days) and healthy controls (n = 44) of both sexes. We first conducted whole-blood RNA sequencing to detect differentially expressed genes. We also explored transcriptomic data on the dorsal lateral prefrontal cortices (dlPFC) retrieved from the CommonMind Consortium for gene functional clustering; we measured plasma transforming growth factor β1 (TGF-β1) levels by enzyme-linked immunosorbent assay; we acquired high-resolution T 1-weighted MRI data on cortical thickness MRI; and we assessed cognitive function using the validated Chinese version of the MATRICS Consensus Cognitive Battery. We compared these parameters in patients with schizophrenia and controls, and analyzed their associations. RESULTS Patients with schizophrenia had higher TGF-β1 at both the mRNA level (log2 fold change = 0.24; adjusted p = 0.026) and the protein level (12.85 ± 6.01 μg/mL v. 8.46 ± 5.15 μg/mL, adjusted p < 0.001) compared to controls. Genes coexpressed with TGFB1 in the dlPFC were less abundant in patients with schizophrenia compared to healthy controls. In patients with schizophrenia, TGF-β1 protein levels were inversely correlated with cortical thickness, especially of the lateral occipital cortex (r = -0.47, adjusted p = 0.001), and with the MATRICS Consensus Cognitive Battery visual learning and memory domain (r = -0.50, adjusted p < 0.001). We found a complete mediation effect of the thickness of the lateral occipital cortex on the negative relationship between TGF-β1 and visual cognition (p < 0.05). LIMITATIONS We did not explore the effect of other blood cytokines on neurocognitive performance and cortical thickness. Participants from the CommonMind Consortium did not all have first-episode schizophrenia and they were not all antipsychotic-naive, so we could not exclude an effect of antipsychotics on TGF-β1 signalling in the dlPFC. The sample size and cross-sectional design of our study were additional limitations. CONCLUSION These findings highlighted an association between upregulated blood levels of TGF-β1 and impairments in brain structure and function in schizophrenia.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yun-Long Tan
- From the Peking University Huilongguan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China (Pan, Zhou, Tong, Li, Huang, Feng, Chen, Yang, S. Tan, Wang, B. Tian, Y. Tan, L. Tian); the Institute of Biomedicine and Translational Medicine, Department of Physiology, Faculty of Medicine, University of Tartu, Tartu, Estonia (Yan, Xuan, L. Tian); the Department of Pharmacy, Peking University First Hospital, Beijing, China (Cui); and the Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, USA (Hong)
| | - Li Tian
- From the Peking University Huilongguan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China (Pan, Zhou, Tong, Li, Huang, Feng, Chen, Yang, S. Tan, Wang, B. Tian, Y. Tan, L. Tian); the Institute of Biomedicine and Translational Medicine, Department of Physiology, Faculty of Medicine, University of Tartu, Tartu, Estonia (Yan, Xuan, L. Tian); the Department of Pharmacy, Peking University First Hospital, Beijing, China (Cui); and the Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, USA (Hong)
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16
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Chen R, Liu J, Li S, Li X, Huo Y, Yao YG, Xiao X, Li M, Luo XJ. Functional genomics elucidates regulatory mechanisms of Parkinson's disease-associated variants. BMC Med 2022; 20:68. [PMID: 35168626 PMCID: PMC8848643 DOI: 10.1186/s12916-022-02264-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/18/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWASs) have identified multiple risk loci for Parkinson's disease (PD). However, identifying the functional (or potential causal) variants in the reported risk loci and elucidating their roles in PD pathogenesis remain major challenges. To identify the potential causal (or functional) variants in the reported PD risk loci and to elucidate their regulatory mechanisms, we report a functional genomics study of PD. METHODS We first integrated chromatin immunoprecipitation sequencing (ChIP-Seq) (from neuronal cells and human brain tissues) data and GWAS-identified single-nucleotide polymorphisms (SNPs) in PD risk loci. We then conducted a series of experiments and analyses to validate the regulatory effects of these (i.e., functional) SNPs, including reporter gene assays, allele-specific expression (ASE), transcription factor (TF) knockdown, CRISPR-Cas9-mediated genome editing, and expression quantitative trait loci (eQTL) analysis. RESULTS We identified 44 SNPs (from 11 risk loci) affecting the binding of 12 TFs and we validated the regulatory effects of 15 TF binding-disrupting SNPs. In addition, we also identified the potential target genes regulated by these TF binding-disrupting SNPs through eQTL analysis. Finally, we showed that 4 eQTL genes of these TF binding-disrupting SNPs were dysregulated in PD cases compared with controls. CONCLUSION Our study systematically reveals the gene regulatory mechanisms of PD risk variants (including widespread disruption of CTCF binding), generates the landscape of potential PD causal variants, and pinpoints promising candidate genes for further functional characterization and drug development.
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Affiliation(s)
- Rui Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, Yunnan, China
| | - Jiewei Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Shiwu Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Xiaoyan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Yongxia Huo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China. .,Zhongda Hospital, School of Life Sciences and Technology, Advanced Institute for Life and Health, Southeast University, Nanjing, 210096, Jiangsu, China. .,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
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17
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Liu R, Tang W, Wang W, Xu F, Fan W, Zhang Y, Zhang C. NLRP3 Influences Cognitive Function in Schizophrenia in Han Chinese. Front Genet 2021; 12:781625. [PMID: 34956329 PMCID: PMC8702823 DOI: 10.3389/fgene.2021.781625] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/19/2021] [Indexed: 12/14/2022] Open
Abstract
It has been proposed that immune abnormalities may be implicated with pathophysiology of schizophrenia. The nod-like receptor pyrin domain-contraining protein 3 (NLRP3) can trigger immune-inflammatory cascade reactions. In this study, we intended to identify the role of gene encoding NLRP3 (NLRP3) in susceptibility to schizophrenia and its clinical features. For the NLRP3 mRNA expression analysis, 53 drug-naïve patients with first-episode schizophrenia and 56 healthy controls were enrolled. For the genetic study, a total of 823 schizophrenia patients and 859 controls were recruited. Among them, 239 drug-naïve patients with first-episode schizophrenia were enrolled for clinical evaluation. There is no significant difference in NLRP3 mRNA levels between patients with schizophrenia and healthy controls (p = 0.07). We did not observe any significant differences in allele and genotype frequencies of rs10754558 polymorphism between the schizophrenia and control groups. We noticed significant differences in the scores of RBANS attention and total scores between the patients with different genotypes of rs10754558 polymorphism (p = 0.001 and p < 0.01, respectively). Further eQTL analysis presented a significant association between the rs10754558 polymorphism and NLRP3 in frontal cortex (p = 0.0028, p = 0.028 after Bonferroni correction). Although our findings did not support NLRP3 confer susceptibility to schizophrenia, NLRP3 may be a risk factor for cognitive impairment, especially attention deficit in this disorder.
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Affiliation(s)
- Ruimei Liu
- Schizophrenia Program, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Tang
- Department of Psychiatry, The Affiliated Kangning Hospital of Wenzhou Medical University, Wenzhou, China
| | - Weiping Wang
- Department of Psychiatry, Jinhua Second Hospital, Jinhua, China
| | - Feikang Xu
- Schizophrenia Program, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weixing Fan
- Department of Psychiatry, Jinhua Second Hospital, Jinhua, China
| | - Yi Zhang
- Schizophrenia Program, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chen Zhang
- Schizophrenia Program, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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18
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Gao Y, Li Y, Li S, Liang X, Ren Z, Yang X, Zhang B, Hu Y, Yang X. Systematic discovery of signaling pathways linking immune activation to schizophrenia. iScience 2021; 24:103209. [PMID: 34746692 PMCID: PMC8551081 DOI: 10.1016/j.isci.2021.103209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/21/2021] [Accepted: 09/29/2021] [Indexed: 11/06/2022] Open
Abstract
Immune activation has been shown to play a critical role in the development of schizophrenia; however its underlying mechanism remains unknown. Our report demonstrates a high-quality protein interaction network for schizophrenia (SCZ Network), constructed using our “neighborhood walk” approach in combination with “random walk with restart”. The spatiotemporal expression pattern of the genes in this disease network revealed two developmental stages sensitive to perturbation by immune activation: mid-to late gestation, and adolescence. Furthermore, we induced immune activation at these stages in mice, carried out transcriptome sequencing on the mouse brains, and illustrated clear potential molecular pathways and key regulators correlating maternal immune activation during gestation and an increased risk for schizophrenia after a second immune activation at puberty. This work provides not only valuable resources for the study on molecular mechanisms underlying schizophrenia, but also a systematic strategy for the discovery of molecular pathways of complex mental disorders. A high-quality molecular network for schizophrenia (SCZ Network) A landscape of molecular pathways linking immune activation and schizophrenia The spatiotemporal network dynamics revealing stages susceptible to immune activation Identification of the molecular pathways and regulators in the immune-activated brain
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Affiliation(s)
- Yue Gao
- Center for Genetics and Developmental Systems Biology, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence and Guangdong Key Laboratory of Psychiatric Disorders, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yanjun Li
- Center for Genetics and Developmental Systems Biology, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence and Guangdong Key Laboratory of Psychiatric Disorders, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - ShuangYan Li
- Department of Psychiatry, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xiaozhen Liang
- Center for Genetics and Developmental Systems Biology, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Zhonglu Ren
- Center for Genetics and Developmental Systems Biology, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xiaoxue Yang
- Center for Genetics and Developmental Systems Biology, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Bin Zhang
- Department of Psychiatry, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Xinping Yang
- Center for Genetics and Developmental Systems Biology, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence and Guangdong Key Laboratory of Psychiatric Disorders, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
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19
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Kyrousi C, O’Neill AC, Brazovskaja A, He Z, Kielkowski P, Coquand L, Di Giaimo R, D’ Andrea P, Belka A, Forero Echeverry A, Mei D, Lenge M, Cruceanu C, Buchsbaum IY, Khattak S, Fabien G, Binder E, Elmslie F, Guerrini R, Baffet AD, Sieber SA, Treutlein B, Robertson SP, Cappello S. Extracellular LGALS3BP regulates neural progenitor position and relates to human cortical complexity. Nat Commun 2021; 12:6298. [PMID: 34728600 PMCID: PMC8564519 DOI: 10.1038/s41467-021-26447-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 09/26/2021] [Indexed: 12/15/2022] Open
Abstract
Basal progenitors (BPs), including intermediate progenitors and basal radial glia, are generated from apical radial glia and are enriched in gyrencephalic species like humans, contributing to neuronal expansion. Shortly after generation, BPs delaminate towards the subventricular zone, where they further proliferate before differentiation. Gene expression alterations involved in BP delamination and function in humans are poorly understood. Here, we study the role of LGALS3BP, so far known as a cancer biomarker, which is a secreted protein enriched in human neural progenitors (NPCs). We show that individuals with LGALS3BP de novo variants exhibit altered local gyrification, sulcal depth, surface area and thickness in their cortex. Additionally, using cerebral organoids, human fetal tissues and mice, we show that LGALS3BP regulates the position of NPCs. Single-cell RNA-sequencing and proteomics reveal that LGALS3BP-mediated mechanisms involve the extracellular matrix in NPCs' anchoring and migration within the human brain. We propose that its temporal expression influences NPCs' delamination, corticogenesis and gyrification extrinsically.
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Affiliation(s)
- Christina Kyrousi
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany ,grid.5216.00000 0001 2155 0800Present Address: First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, Greece and University Mental Health, Neurosciences and Precision Medicine Research Institute “Costas Stefanis”, Athens, Greece
| | - Adam C. O’Neill
- grid.29980.3a0000 0004 1936 7830Department of Women’s and Children’s Health, University of Otago, 9054 Dunedin, New Zealand
| | - Agnieska Brazovskaja
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Zhisong He
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany ,grid.5801.c0000 0001 2156 2780ETH Zurich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
| | - Pavel Kielkowski
- grid.6936.a0000000123222966Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching, Germany ,grid.5252.00000 0004 1936 973XPresent Address: Department Chemie Ludwig-Maximilians-Universität München Butenandtstr. 5-13, 81377 München, Germany
| | - Laure Coquand
- grid.4444.00000 0001 2112 9282Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d’Ulm, F-75005 Paris, France
| | - Rossella Di Giaimo
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany ,grid.4691.a0000 0001 0790 385XDepartment of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Pierpaolo D’ Andrea
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Alexander Belka
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | | | - Davide Mei
- grid.413181.e0000 0004 1757 8562Neuroscience Department, Children’s Hospital A. Meyer-University of Florence, 50139 Florence, Italy
| | - Matteo Lenge
- grid.413181.e0000 0004 1757 8562Neuroscience Department, Children’s Hospital A. Meyer-University of Florence, 50139 Florence, Italy
| | - Cristiana Cruceanu
- grid.419548.50000 0000 9497 5095Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Isabel Y. Buchsbaum
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany ,grid.5252.00000 0004 1936 973XGraduate School of Systemic Neurosciences, Ludwig-Maximilians-University, 82152 Munich Planegg, Germany
| | - Shahryar Khattak
- grid.4488.00000 0001 2111 7257DFG-Research Center and Cluster of Excellence for Regenerative Therapies (CRTD), School of Medicine, Technical University Dresden, 01307 Dresden, Germany ,grid.4912.e0000 0004 0488 7120Present Address: Royal College of Surgeons Ireland (RCSI) in Bahrain, Adliya, Kingdom of Bahrain
| | - Guimiot Fabien
- grid.50550.350000 0001 2175 4109Unité de Foetopathologie, Assistance Publique-Hôpitaux de Paris, CHU Robert Debré, F-75019 Paris, France
| | - Elisabeth Binder
- grid.419548.50000 0000 9497 5095Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Frances Elmslie
- grid.4464.20000 0001 2161 2573South West Thames Regional Genetics Service, St George’s, University of London, London, SW17 0RE UK
| | - Renzo Guerrini
- grid.413181.e0000 0004 1757 8562Neuroscience Department, Children’s Hospital A. Meyer-University of Florence, 50139 Florence, Italy
| | - Alexandre D. Baffet
- grid.4444.00000 0001 2112 9282Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d’Ulm, F-75005 Paris, France
| | - Stephan A. Sieber
- grid.6936.a0000000123222966Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching, Germany
| | - Barbara Treutlein
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany ,grid.5801.c0000 0001 2156 2780ETH Zurich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
| | - Stephen P. Robertson
- grid.29980.3a0000 0004 1936 7830Department of Women’s and Children’s Health, University of Otago, 9054 Dunedin, New Zealand
| | - Silvia Cappello
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany
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20
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Mahadevan V, Mitra A, Zhang Y, Yuan X, Peltekian A, Chittajallu R, Esnault C, Maric D, Rhodes C, Pelkey KA, Dale R, Petros TJ, McBain CJ. NMDARs Drive the Expression of Neuropsychiatric Disorder Risk Genes Within GABAergic Interneuron Subtypes in the Juvenile Brain. Front Mol Neurosci 2021; 14:712609. [PMID: 34630033 PMCID: PMC8500094 DOI: 10.3389/fnmol.2021.712609] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
Medial ganglionic eminence (MGE)-derived parvalbumin (PV)+, somatostatin (SST)+and Neurogliaform (NGFC)-type cortical and hippocampal interneurons, have distinct molecular, anatomical, and physiological properties. However, the molecular mechanisms regulating their maturation remain poorly understood. Here, via single-cell transcriptomics, we show that the obligate NMDA-type glutamate receptor (NMDAR) subunit gene Grin1 mediates transcriptional regulation of gene expression in specific subtypes of MGE-derived interneurons, leading to altered subtype abundances. Notably, MGE-specific early developmental Grin1 loss results in a broad downregulation of diverse transcriptional, synaptogenic and membrane excitability regulatory programs in the juvenile brain. These widespread gene expression abnormalities mirror aberrations that are typically associated with neurodevelopmental disorders. Our study hence provides a road map for the systematic examination of NMDAR signaling in interneuron subtypes, revealing potential MGE-specific genetic targets that could instruct future therapies of psychiatric disorders.
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Affiliation(s)
- Vivek Mahadevan
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Bethesda, MD, United States
| | - Apratim Mitra
- Bioinformatics and Scientific Programming Core, NICHD, Bethesda, MD, United States
| | - Yajun Zhang
- Unit on Cellular and Molecular Neurodevelopment, NICHD, Bethesda, MD, United States
| | - Xiaoqing Yuan
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Bethesda, MD, United States
| | - Areg Peltekian
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Bethesda, MD, United States
| | - Ramesh Chittajallu
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Bethesda, MD, United States
| | - Caroline Esnault
- Bioinformatics and Scientific Programming Core, NICHD, Bethesda, MD, United States
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, United States
| | - Christopher Rhodes
- Unit on Cellular and Molecular Neurodevelopment, NICHD, Bethesda, MD, United States
| | - Kenneth A Pelkey
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Bethesda, MD, United States
| | - Ryan Dale
- Bioinformatics and Scientific Programming Core, NICHD, Bethesda, MD, United States
| | - Timothy J Petros
- Unit on Cellular and Molecular Neurodevelopment, NICHD, Bethesda, MD, United States
| | - Chris J McBain
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Bethesda, MD, United States
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21
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Analysis of Molecular Networks in the Cerebellum in Chronic Schizophrenia: Modulation by Early Postnatal Life Stressors in Murine Models. Int J Mol Sci 2021; 22:ijms221810076. [PMID: 34576238 PMCID: PMC8469990 DOI: 10.3390/ijms221810076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 01/17/2023] Open
Abstract
Despite the growing importance of the cerebellum as a region highly vulnerable to accumulating molecular errors in schizophrenia, limited information is available regarding altered molecular networks with potential therapeutic targets. To identify altered networks, we conducted one-shot liquid chromatography–tandem mass spectrometry in postmortem cerebellar cortex in schizophrenia and healthy individuals followed by bioinformatic analysis (PXD024937 identifier in ProteomeXchange repository). A total of 108 up-regulated proteins were enriched in stress-related proteins, half of which were also enriched in axonal cytoskeletal organization and vesicle-mediated transport. A total of 142 down-regulated proteins showed an enrichment in proteins involved in mitochondrial disease, most of which were also enriched in energy-related biological functions. Network analysis identified a mixed module of mainly axonal-related pathways for up-regulated proteins with a high number of interactions for stress-related proteins. Energy metabolism and neutrophil degranulation modules were found for down-regulated proteins. Further, two double-hit postnatal stress murine models based on maternal deprivation combined with social isolation or chronic restraint stress were used to investigate the most robust candidates of generated networks. CLASP1 from the axonal module in the model of maternal deprivation was combined with social isolation, while YWHAZ was not altered in either model. METTL7A from the degranulation pathway was reduced in both models and was identified as altered also in previous gene expression studies, while NDUFB9 from the energy network was reduced only in the model of maternal deprivation combined with social isolation. This work provides altered stress- and mitochondrial disease-related proteins involved in energy, immune and axonal networks in the cerebellum in schizophrenia as possible novel targets for therapeutic interventions and suggests that METTL7A is a possible relevant altered stress-related protein in this context.
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22
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Ding C, Zhang C, Kopp R, Kuney L, Meng Q, Wang L, Xia Y, Jiang Y, Dai R, Min S, Yao WD, Wong ML, Ruan H, Liu C, Chen C. Transcription factor POU3F2 regulates TRIM8 expression contributing to cellular functions implicated in schizophrenia. Mol Psychiatry 2021; 26:3444-3460. [PMID: 32929213 PMCID: PMC7956165 DOI: 10.1038/s41380-020-00877-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 01/17/2023]
Abstract
Schizophrenia (SCZ) is a neuropsychiatric disorder with aberrant expression of multiple genes. However, identifying its exact causal genes remains a considerable challenge. The brain-specific transcription factor POU3F2 (POU domain, class 3, transcription factor 2) has been recognized as a risk factor for SCZ, but our understanding of its target genes and pathogenic mechanisms are still limited. Here we report that POU3F2 regulates 42 SCZ-related genes in knockdown and RNA-sequencing experiments of human neural progenitor cells (NPCs). Among those SCZ-related genes, TRIM8 (Tripartite motif containing 8) is located in SCZ-associated genetic locus and is aberrantly expressed in patients with SCZ. Luciferase reporter and electrophoretic mobility shift assays (EMSA) showed that POU3F2 induces TRIM8 expression by binding to the SCZ-associated SNP (single nucleotide polymorphism) rs5011218, which affects POU3F2-binding efficiency at the promoter region of TRIM8. We investigated the cellular functions of POU3F2 and TRIM8 as they co-regulate several pathways related to neural development and synaptic function. Knocking down either POU3F2 or TRIM8 promoted the proliferation of NPCs, inhibited their neuronal differentiation, and impaired the excitatory synaptic transmission of NPC-derived neurons. These results indicate that POU3F2 regulates TRIM8 expression through the SCZ-associated SNP rs5011218, and both genes may be involved in the etiology of SCZ by regulating neural development and synaptic function.
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Affiliation(s)
- Chaodong Ding
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China,Department of Psychiatry, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Chunling Zhang
- Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Richard Kopp
- Department of Psychiatry, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Liz Kuney
- Department of Psychiatry, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Qingtuan Meng
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China,Guangxi Clinical Research Center for Neurological Diseases, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China,Guangxi Key Laboratory of Brain and Cognitive Neuroscience, Guilin Medical University, Guilin, Guangxi, China
| | - Le Wang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China,Child Health Institute of New Jersey, Department of Neuroscience and Cell Biology, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Yan Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China,Department of Psychiatry, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Yi Jiang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Rujia Dai
- Department of Psychiatry, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Shishi Min
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China,Department of Psychiatry, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Wei-Dong Yao
- Department of Psychiatry, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Ma-Li Wong
- Department of Psychiatry, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Hongyu Ruan
- Department of Psychiatry, State University of New York Upstate Medical University, Syracuse, NY, USA.
| | - Chunyu Liu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China. .,Department of Psychiatry, State University of New York Upstate Medical University, Syracuse, NY, USA. .,School of Psychology, Shaanxi Normal University, Xi'an, Shaanxi, China.
| | - Chao Chen
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, the Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan, China. .,Hunan Key Laboratory of Molecular Precision Medicine, Central South University, Changsha, Hunan, China.
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23
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Integrative genomics analysis identifies five promising genes implicated in insomnia risk based on multiple omics datasets. Biosci Rep 2021; 40:226183. [PMID: 32830860 PMCID: PMC7468094 DOI: 10.1042/bsr20201084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 08/15/2020] [Accepted: 08/21/2020] [Indexed: 12/27/2022] Open
Abstract
In recent decades, many genome-wide association studies on insomnia have reported numerous genes harboring multiple risk variants. Nevertheless, the molecular functions of these risk variants conveying risk to insomnia are still ill-studied. In the present study, we integrated GWAS summary statistics (N=386,533) with two independent brain expression quantitative trait loci (eQTL) datasets (N=329) to determine whether expression-associated SNPs convey risk to insomnia. Furthermore, we applied numerous bioinformatics analyses to highlight promising genes associated with insomnia risk. By using Sherlock integrative analysis, we detected 449 significant insomnia-associated genes in the discovery stage. These identified genes were significantly overrepresented in six biological pathways including Huntington’s disease (P=5.58 × 10−5), Alzheimer’s disease (P=5.58 × 10−5), Parkinson’s disease (P=6.34 × 10−5), spliceosome (P=1.17 × 10−4), oxidative phosphorylation (P=1.09 × 10−4), and wnt signaling pathways (P=2.07 × 10−4). Further, five of these identified genes were replicated in an independent brain eQTL dataset. Through a PPI network analysis, we found that there existed highly functional interactions among these five identified genes. Three genes of LDHA (P=0.044), DALRD3 (P=5.0 × 10−5), and HEBP2 (P=0.032) showed significantly lower expression level in brain tissues of insomnic patients than that in controls. In addition, the expression levels of these five genes showed prominently dynamic changes across different time points between behavioral states of sleep and sleep deprivation in mice brain cortex. Together, the evidence of the present study strongly suggested that these five identified genes may represent candidate genes and contributed risk to the etiology of insomnia.
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24
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Liu Y, Qu HQ, Chang X, Tian L, Qu J, Glessner J, Sleiman PMA, Hakonarson H. Machine Learning Reduced Gene/Non-Coding RNA Features That Classify Schizophrenia Patients Accurately and Highlight Insightful Gene Clusters. Int J Mol Sci 2021; 22:3364. [PMID: 33805976 PMCID: PMC8037538 DOI: 10.3390/ijms22073364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/20/2021] [Accepted: 03/23/2021] [Indexed: 12/28/2022] Open
Abstract
RNA-seq has been a powerful method to detect the differentially expressed genes/long non-coding RNAs (lncRNAs) in schizophrenia (SCZ) patients; however, due to overfitting problems differentially expressed targets (DETs) cannot be used properly as biomarkers. This study used machine learning to reduce gene/non-coding RNA features. Dorsolateral prefrontal cortex (dlpfc) RNA-seq data from 254 individuals was obtained from the CommonMind consortium. The average predictive accuracy for SCZ patients was 67% based on coding genes, and 96% based on long non-coding RNAs (lncRNAs). Machine learning is a powerful algorithm to reduce functional biomarkers in SCZ patients. The lncRNAs capture the characteristics of SCZ tissue more accurately than mRNA as the former regulate every level of gene expression, not limited to mRNA levels.
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Affiliation(s)
- Yichuan Liu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (H.-Q.Q.); (X.C.); (L.T.); (J.Q.); (J.G.); (P.M.A.S.)
| | - Hui-Qi Qu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (H.-Q.Q.); (X.C.); (L.T.); (J.Q.); (J.G.); (P.M.A.S.)
| | - Xiao Chang
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (H.-Q.Q.); (X.C.); (L.T.); (J.Q.); (J.G.); (P.M.A.S.)
| | - Lifeng Tian
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (H.-Q.Q.); (X.C.); (L.T.); (J.Q.); (J.G.); (P.M.A.S.)
| | - Jingchun Qu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (H.-Q.Q.); (X.C.); (L.T.); (J.Q.); (J.G.); (P.M.A.S.)
| | - Joseph Glessner
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (H.-Q.Q.); (X.C.); (L.T.); (J.Q.); (J.G.); (P.M.A.S.)
| | - Patrick M. A. Sleiman
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (H.-Q.Q.); (X.C.); (L.T.); (J.Q.); (J.G.); (P.M.A.S.)
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; (Y.L.); (H.-Q.Q.); (X.C.); (L.T.); (J.Q.); (J.G.); (P.M.A.S.)
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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Ren Z, Gao Y, Gao Y, Liang G, Chen Q, Jiang S, Yang X, Fan C, Wang H, Wang J, Shi YW, Xiao C, Zhong M, Yang X. Distinct placental molecular processes associated with early-onset and late-onset preeclampsia. Am J Cancer Res 2021; 11:5028-5044. [PMID: 33754042 PMCID: PMC7978310 DOI: 10.7150/thno.56141] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/29/2021] [Indexed: 12/13/2022] Open
Abstract
Background: Patients with preeclampsia display a spectrum of onset time and severity of clinical presentation, yet the underlying molecular bases for the early-onset and late-onset clinical subtypes are not known. Although several transcriptome studies have been done on placentae from PE patients, only a small number of differentially expressed genes have been identified due to very small sample sizes and no distinguishing of clinical subtypes. Methods: We carried out RNA-seq on 65 high-quality placenta samples, including 33 from 30 patients and 32 from 30 control subjects, to search for dysregulated genes and the molecular network and pathways they are involved in. Results: We identified two functionally distinct sets of dysregulated genes in the two major subtypes: 2,977 differentially expressed genes in early-onset severe preeclampsia, which are enriched with metabolism-related pathways, notably transporter functions; and 375 differentially expressed genes in late-onset severe preeclampsia, which are enriched with immune-related pathways. We also identified some key transcription factors, which may drive the widespread gene dysregulation in both early-onset and late-onset patients. Conclusion: These results suggest that early-onset and late-onset severe preeclampsia have different molecular mechanisms, whereas the late-onset mild preeclampsia may have no placenta-specific causal factors. A few regulators may be the key drivers of the dysregulated molecular pathways.
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Hertzberg L, Zohar AH, Yitzhaky A. Gene Expression Meta-Analysis of Cerebellum Samples Supports the FKBP5 Gene-Environment Interaction Model for Schizophrenia. Life (Basel) 2021; 11:190. [PMID: 33673722 PMCID: PMC7997256 DOI: 10.3390/life11030190] [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: 02/01/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND One of the most studied molecular models of gene-environment interactions is that of FKBP5, which has been shown to interact with childhood adversity to increase the risk of psychiatric disorders, and has been implicated in schizophrenia. While the model predicts up-regulation of FKBP5, previous brain samples gene expression studies yielded inconsistent results. METHODS We performed a systematic gene expression meta-analysis of FKBP5 and NR3C1, a glucocorticoid receptor inhibited by FKBP5, in cerebellum samples of patients with schizophrenia. The gene expression databases GEO, SMRI and those of NIMH were searched, and out of six screened datasets, three were eligible for the meta-analysis (overall 69 with schizophrenia and 78 controls). RESULTS We detected up-regulation of FKBP5 and down-regulation of NR3C1 in schizophrenia, and a negative correlation between their expression patterns. Correlation analysis suggested that the detected differential expression did not result from potential confounding factors. CONCLUSIONS Our results give significant support to the FKBP5 gene-environment interaction model for schizophrenia, which provides a molecular mechanism by which childhood adversity is involved in the development of the disorder. To explore FKBP5's potential as a therapeutic target, a mapping of its differential expression patterns in different brain regions of schizophrenia patients is needed.
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Affiliation(s)
- Libi Hertzberg
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel;
- Shalvata Mental Health Center, Affiliated with the Sackler School of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Ada H. Zohar
- Department of Behavioral Sciences, Ruppin Academic Center, Hefer Valley 40250, Israel;
| | - Assif Yitzhaky
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel;
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27
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He Y, Yu Y, Li Y, Duan W, Sun Z, Yang J, Kastin AJ, Pan W, Zhang Y, Wang K. Phenotypic Resemblance to Neuropsychiatric Disorder and Altered mRNA Profiles in Cortex and Hippocampus Underlying IL15Rα Knockout. Front Neurosci 2021; 14:582279. [PMID: 33613171 PMCID: PMC7887313 DOI: 10.3389/fnins.2020.582279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 12/23/2020] [Indexed: 01/05/2023] Open
Abstract
Background Previous studies of the functions of IL15Rα have been limited to immune activities and skeletal muscle development. Immunological factors have been identified as one of the multiple causes of psychosis, and neurological symptoms have been described in IL15Rα knockout (KO) mice. Seeking to explore possible mechanisms for this in the IL15Rα-/- mouse brain, we analyzed gene expression patterns in the cortex and hippocampus using the RNA-seq technique. Methods IL15Rα KO mice were generated and littermate wildtype (WT) mice were used as a control group. A Y-maze was used to assess behavior differences between the two groups. The cortex and hippocampus of 3-month-old male mice were prepared and RNA-seq and transcriptome analysis were performed by gene set enrichment analysis (GSEA). Results Compared with the WT group, IL15Rα KO animals showed higher speed in the novel arm and more entrance frequency in the old arm in the Y-maze experiment. GSEA indicated that 18 pathways were downregulated and 13 pathways upregulated in both cortex and hippocampus from the GO, KEGG, and Hallmark gene sets. The downregulated pathways formed three clusters: respiratory chain and electron transport, regulation of steroid process, and skeletal muscle development. Conclusion IL15Rα KO mice exhibit altered expression of multiple pathways, which could affect many functions of the brain. Lipid biosynthesis and metabolism in the central nervous system (CNS) should be investigated to provide insights into the effect of IL15Rα on psychosis in this murine model.
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Affiliation(s)
- Yi He
- The National Clinical Research Center for Mental Disorders, Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China.,Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China
| | - Yuxin Yu
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanan Li
- Department of Gastrointestinal Surgery, Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Weicheng Duan
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zuoli Sun
- The National Clinical Research Center for Mental Disorders, Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China.,Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China
| | - Jian Yang
- The National Clinical Research Center for Mental Disorders, Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China.,Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China
| | - Abba J Kastin
- Pennington Biomedical Research Center, Baton Rouge, LA, United States
| | - Weihong Pan
- BioPotentials Consult, Sedona, AZ, United States
| | - Yan Zhang
- Department of Clinical Laboratory, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kang Wang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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28
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Novel CTSF Indel in a patient with Kufs disease and resistant schizophrenia: A case report. Schizophr Res 2021; 228:435-437. [PMID: 33578366 DOI: 10.1016/j.schres.2021.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/20/2021] [Accepted: 01/24/2021] [Indexed: 11/21/2022]
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Guan J, Lin Y, Wang Y, Gao J, Ji G. An analytical method for the identification of cell type-specific disease gene modules. J Transl Med 2021; 19:20. [PMID: 33407556 PMCID: PMC7788893 DOI: 10.1186/s12967-020-02690-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/22/2020] [Indexed: 12/13/2022] Open
Abstract
Background Genome-wide association studies have identified genetic variants associated with the risk of brain-related diseases, such as neurological and psychiatric disorders, while the causal variants and the specific vulnerable cell types are often needed to be studied. Many disease-associated genes are expressed in multiple cell types of human brains, while the pathologic variants affect primarily specific cell types. We hypothesize a model in which what determines the manifestation of a disease in a cell type is the presence of disease module comprised of disease-associated genes, instead of individual genes. Therefore, it is essential to identify the presence/absence of disease gene modules in cells. Methods To characterize the cell type-specificity of brain-related diseases, we construct human brain cell type-specific gene interaction networks integrating human brain nucleus gene expression data with a referenced tissue-specific gene interaction network. Then from the cell type-specific gene interaction networks, we identify significant cell type-specific disease gene modules by performing statistical tests. Results Between neurons and glia cells, the constructed cell type-specific gene networks and their gene functions are distinct. Then we identify cell type-specific disease gene modules associated with autism spectrum disorder and find that different gene modules are formed and distinct gene functions may be dysregulated in different cells. We also study the similarity and dissimilarity in cell type-specific disease gene modules among autism spectrum disorder, schizophrenia and bipolar disorder. The functions of neurons-specific disease gene modules are associated with synapse for all three diseases, while those in glia cells are different. To facilitate the use of our method, we develop an R package, CtsDGM, for the identification of cell type-specific disease gene modules. Conclusions The results support our hypothesis that a disease manifests itself in a cell type through forming a statistically significant disease gene module. The identification of cell type-specific disease gene modules can promote the development of more targeted biomarkers and treatments for the disease. Our method can be applied for depicting the cell type heterogeneity of a given disease, and also for studying the similarity and dissimilarity between different disorders, providing new insights into the molecular mechanisms underlying the pathogenesis and progression of diseases.
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Affiliation(s)
- Jinting Guan
- Department of Automation, Xiamen University, Xiamen, China. .,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.
| | - Yiping Lin
- Department of Automation, Xiamen University, Xiamen, China
| | - Yang Wang
- Department of Automation, Xiamen University, Xiamen, China
| | - Junchao Gao
- Department of Instrumental and Electrical Engineering, Xiamen University, Xiamen, China
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
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Nesbit N, Wallace R, Harihar S, Zhou M, Jung JY, Silberstein M, Lee PH. Genomewide alteration of histone H3K4 methylation underlies genetic vulnerability to psychopathology. J Genet 2021; 100:44. [PMID: 34282735 PMCID: PMC8459212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Dysregulated histone methylation has emerged as a recurring theme in multiple neuropsychiatric disorders. However, it is yet unclear whether the altered histone methylation is associated with aetiologic mechanisms or an outcome of disease manifestation. In this study, we examined the genomewide association studies datasets of three major psychiatric disorders, schizophrenia (SCZ), bipolar disorder (BIP), and major depression disorder (MDD), which represents a total of 231,783 cases and 425,444 controls, to clarify the relationship. Our gene-set enrichment analysis results identified statistically significant association of genes involved in three histone methylation biological processes with the three adult-onset psychiatric disorders, which is mainly driven by the histone H3K4 methylation pathway (GO: 0051568). Further analysis of histone H3K4 methylation pathway genes revealed a widespread role of the genes in brain function and disease; 29 (52%) and 41 genes (73.2%) were associated with at least one brain-related trait or brain disorder, respectively. Spatiotemporal gene expression analysis suggests that these pathway genes play a critical role during the prenatal period and are consistent regulators in the cerebral cortex throughout an individual's life. AUTS2, DNMT1 and TET2 are genes of particular interest due to their pervasive role in various aspects of brain function. Our findings support a critical aetiologic role of H3K4 methylation genes shared across SCZ, BIP and MDD, providing new direction for the development of epigenetically-focussed drugs targeting common causal factors of these devastating disorders.
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Affiliation(s)
- Nicholas Nesbit
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
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Hong JK, Lee JB, Ramayo-Caldas Y, Kim SD, Cho ES, Kim YS, Cho KH, Lee DH, Park HB. Single-step genome-wide association study for social genetic effects and direct genetic effects on growth in Landrace pigs. Sci Rep 2020; 10:14958. [PMID: 32917921 PMCID: PMC7486944 DOI: 10.1038/s41598-020-71647-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/03/2020] [Indexed: 02/08/2023] Open
Abstract
In livestock social interactions, social genetic effects (SGE) represent associations between phenotype of one individual and genotype of another. Such associations occur when the trait of interest is affected by transmissible phenotypes of social partners. The aim of this study was to estimate SGE and direct genetic effects (DGE, genetic effects of an individual on its own phenotype) on average daily gain (ADG) in Landrace pigs, and to conduct single-step genome-wide association study using SGE and DGE as dependent variables to identify quantitative trait loci (QTLs) and their positional candidate genes. A total of 1,041 Landrace pigs were genotyped using the Porcine SNP 60K BeadChip. Estimates of the two effects were obtained using an extended animal model. The SGE contributed 16% of the total heritable variation of ADG. The total heritability estimated by the extended animal model including both SGE and DGE was 0.52. The single-step genome-wide association study identified a total of 23 QTL windows for the SGE on ADG distributed across three chromosomes (i.e., SSC1, SSC2, and SSC6). Positional candidate genes within these QTL regions included PRDM13, MAP3K7, CNR1, HTR1E, IL4, IL5, IL13, KIF3A, EFHD2, SLC38A7, mTOR, CNOT1, PLCB2, GABRR1, and GABRR2, which have biological roles in neuropsychiatric processes. The results of biological pathway and gene network analyses also support the association of the neuropsychiatric processes with SGE on ADG in pigs. Additionally, a total of 11 QTL windows for DGE on ADG in SSC2, 3, 6, 9, 10, 12, 14, 16, and 17 were detected with positional candidate genes such as ARL15. We found a putative pleotropic QTL for both SGE and DGE on ADG on SSC6. Our results in this study provide important insights that can help facilitate a better understanding of the molecular basis of SGE for socially affected traits.
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Affiliation(s)
- Joon-Ki Hong
- National Institute of Animal Science, Rural Development Administration, Cheonan, 31000, Republic of Korea
| | - Jae-Bong Lee
- Korea Zoonosis Research Institute, Chonbuk National University, 54531, Iksan, Republic of Korea
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Spain
| | - Si-Dong Kim
- National Institute of Animal Science, Rural Development Administration, Cheonan, 31000, Republic of Korea
| | - Eun-Seok Cho
- National Institute of Animal Science, Rural Development Administration, Cheonan, 31000, Republic of Korea
| | - Young-Sin Kim
- National Institute of Animal Science, Rural Development Administration, Cheonan, 31000, Republic of Korea
| | - Kyu-Ho Cho
- National Institute of Animal Science, Rural Development Administration, Cheonan, 31000, Republic of Korea
| | - Deuk-Hwan Lee
- Department of Animal Life Resources, Hankyong National University, Anseong, 17579, Republic of Korea
| | - Hee-Bok Park
- Department of Animal Resources Science, Kongju National University, Yesan, 32439, Republic of Korea.
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Wang D, Tang W, Zhao J, Fan W, Zhang Y, Zhang C. A Comprehensive Analysis of the Effect of SIRT1 Variation on the Risk of Schizophrenia and Depressive Symptoms. Front Genet 2020; 11:832. [PMID: 32849821 PMCID: PMC7413929 DOI: 10.3389/fgene.2020.00832] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/09/2020] [Indexed: 12/22/2022] Open
Abstract
Depressive symptoms could be considered a mutual manifestation of major depressive disorder and schizophrenia. Rs3758391 is a functional locus of Sirtuin (SIRT1) involving depression etiology. In this study, we hypothesized that the SIRT1 SNP rs3758391 might be a hazard for schizophrenia pathogenesis, especially related to the appearance of depressive symptoms. We recruited 723 healthy controls and 715 schizophrenia patients, the occurrence of psychotic and depressive symptoms was evaluated by Calgary Depression Scale (CDSS) and PANSS. Meanwhile, qt-PCR was used to detect the mRNA levels of SIRT1 in peripheral blood of 197 olanzapine monotherapy schizophrenia patients. 45.6% of schizophrenia patients had depressive symptoms. In the patient group, mRNA levels of patients with depressive symptoms were significantly lower than those without depressive symptoms (P < 0.01). CDSS scores of schizophrenia patients with different rs3758391 genotypes were significantly different (P < 0.01). Post hoc comparisons indicated that the CDSS scores of rs3758391 C/C and C/T carriers were higher than those of T/T carriers (Ps < 0.01). In the occipital cortex, our eQTL analysis showed that there was a clear correlation between rs3758391 and the SIRT1 mRNA levels. Our preliminary findings provide suggestive evidence that SIRT1 makes schizophrenia patients more prone to depressive symptoms. This SNP might be a biomarker of depression in schizophrenia.
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Affiliation(s)
- Dandan Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Tang
- Department of Psychiatry, The Affiliated Kangning Hospital of Wenzhou Medical University, Wenzhou, China
| | - Junxiong Zhao
- Department of Psychiatry, Jinhua Second Hospital, Jinhua, China
| | - Weixing Fan
- Department of Psychiatry, Jinhua Second Hospital, Jinhua, China
| | - Yi Zhang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chen Zhang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Zhou J, Ma C, Wang K, Li X, Jian X, Zhang H, Yuan J, Yin J, Chen J, Shi Y. Identification of rare and common variants in BNIP3L: a schizophrenia susceptibility gene. Hum Genomics 2020; 14:16. [PMID: 32393399 PMCID: PMC7212671 DOI: 10.1186/s40246-020-00266-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/24/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Schizophrenia is a chronic and severe mental disorder, and it has been predicted to be highly polygenic. Common SNPs located in or near BNIP3L were found to be genome-wide significantly associated with schizophrenia in recent genome-wide association studies. The purpose of our study is to investigate potential causal variants in BNIP3L gene. RESULTS We performed targeted sequencing for all exons and un-translated regions of BNIP3L gene among 1806 patients with schizophrenia and 998 healthy controls of Han Chinese origin. Three rare nonsynonymous mutations, BNIP3L (NM_004331): c.52A>G, c.167G>A and c.313A>T, were identified in schizophrenia cases, and two of them were newly reported. The frequencies of these rare nonsynonymous mutations were significantly different between schizophrenia cases and healthy controls. For the common variants, rs147389989 achieved significance in both allelic and genotypic distributions with schizophrenia. Rs1042992 and rs17310286 were significantly associated with schizophrenia in meta-analyses using PGC, CLOZUK, and our new datasets in this study. CONCLUSIONS Our findings provided further evidence that BNIP3L gene is a susceptibility gene of schizophrenia and revealed functional and potential causal mutations in BNIP3L. However, more functional validations are suggested to better understand the role of BNIP3L in the etiology of schizophrenia.
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Affiliation(s)
- Juan Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Chuanchuan Ma
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Ke Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Xiuli Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Xuemin Jian
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Han Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Jianmin Yuan
- Brain Science Basic Laboratory, The Affiliated Wuxi Mental Health Center With Nanjing Medical University, Wuxi, 214151, Jiangsu Province, People's Republic of China
| | - Jiajun Yin
- Brain Science Basic Laboratory, The Affiliated Wuxi Mental Health Center With Nanjing Medical University, Wuxi, 214151, Jiangsu Province, People's Republic of China
| | - Jianhua Chen
- Shanghai Clinical Research Center for Mental Health, Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, People's Republic of China. .,Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China.
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Wu Y, Li X, Liu J, Luo XJ, Yao YG. SZDB2.0: an updated comprehensive resource for schizophrenia research. Hum Genet 2020; 139:1285-1297. [DOI: 10.1007/s00439-020-02171-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 04/25/2020] [Indexed: 12/11/2022]
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Zhou J, Ma C, Wang K, Li X, Zhang H, Chen J, Li Z, Shi Y. Rare and common variants analysis of the EMB gene in patients with schizophrenia. BMC Psychiatry 2020; 20:135. [PMID: 32213169 PMCID: PMC7093976 DOI: 10.1186/s12888-020-02513-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/24/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent genome-wide association study showed rs10940346 locus near EMB gene was significantly associated with schizophrenia and suggested that EMB gene is one of the potentially causal genes for schizophrenia, but no causal variant has been identified. Our study aims to further verify EMB gene is a susceptibility gene for schizophrenia and to identify potentially causal variants in EMB gene that lead to schizophrenia. METHODS Targeted sequencing for the un-translated region and all exons of EMB gene was performed among 1803 patients with schizophrenia and 997 healthy controls recruited from Chinese Han population. RESULTS A total of 58 high-quality variants were identified in case and control groups. Seven of them are nonsynonymous rare variations, EMB: p.(Ala52Thr), p.(Glu66Gly), p.(Ser93Cys), p.(Ala118Val), p.(Ile131Met), p.(Gly163Arg) and p.(Arg238Tyr), but none of them reached statistical significance. Among them, p.(Ile131Met), p.(Gly163Arg) and p.(Arg238Tyr), were predicted to be deleterious variants. In addition, a common variant, rs3933097 located in 3'-UTR of EMB gene, achieved allelic and genotypic significance with schizophrenia (Pallele = 3.82 × 10- 6, Pgenotype = 3.18 × 10- 5). CONCLUSIONS Our research first presented a comprehensive mutation spectrum of exons and un-translated region in EMB gene for schizophrenia and provided additional evidence of EMB gene being a susceptibility gene for schizophrenia. However, further functional validations are necessary to reveal its role in the etiology of schizophrenia.
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Affiliation(s)
- Juan Zhou
- grid.16821.3c0000 0004 0368 8293Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Chuanchuan Ma
- grid.16821.3c0000 0004 0368 8293Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Ke Wang
- grid.16821.3c0000 0004 0368 8293Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuli Li
- grid.16821.3c0000 0004 0368 8293Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Han Zhang
- grid.16821.3c0000 0004 0368 8293Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Jianhua Chen
- grid.16821.3c0000 0004 0368 8293Shanghai Clinical Research Center for Mental Health, Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030 People’s Republic of China
| | - Zhiqiang Li
- grid.410645.20000 0001 0455 0905The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute, Qingdao University, Qingdao, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China. .,Shanghai Clinical Research Center for Mental Health, Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, People's Republic of China. .,The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute, Qingdao University, Qingdao, China.
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36
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Liang W, Yu H, Su Y, Lu T, Yan H, Yue W, Zhang D. Variants of GRM7 as risk factor and response to antipsychotic therapy in schizophrenia. Transl Psychiatry 2020; 10:83. [PMID: 32127521 PMCID: PMC7054263 DOI: 10.1038/s41398-020-0763-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/07/2020] [Accepted: 02/12/2020] [Indexed: 11/09/2022] Open
Abstract
Genome-wide association study (GWAS) has determined the metabotropic glutamate receptor 7 (GRM7) gene as potential locus for schizophrenia risk variants; However, the relationship between the GRM7 variants and the risk of schizophrenia is still uncertain, and there are significant individual variations in response to the antipsychotic drugs. In order to identify susceptible gene and drug-response-related markers, 2413 subjects in our research were chosen for determining drug-response-related markers in schizophrenia. The rs1516569 variant (OR = 0.95, P < 3.47 × 10-4) was a significant risk factor, and a single-nucleotide polymorphism of GRM7 gene- rs9883258 (OR = 0.84, P = 2.18 × 10-3) has been determined as potential biomarkers for therapeutic responses of seven commonly used antipsychotic drugs (aripiprazole, haloperidol, olanzapine, perphenazine, quetiapine, risperidone and ziprasidone) in Chinese Han population; Significant associations with treatment response for several single-nucleotide polymorphisms in every antipsychotic drugs, such as rs779746 (OR = 1.39, P = 0.03), rs480409 (OR = 0.73, P = 0.04), rs78137319 (OR = 3.09, P = 0.04), rs1154370 (OR = 1.51, P = 0.006) have been identified in our study. Hence our research elucidates that GRM7 variants play the critical role of predicting the risk of schizophrenia and antipsychotic effect of seven common drugs.
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Affiliation(s)
- Wei Liang
- grid.459847.30000 0004 1798 0615Institute of Mental Health, Peking University Sixth Hospital, 100191 Beijing, China ,grid.453135.50000 0004 1769 3691NHC Key Laboratory of Mental Health, National Clinical Research Center for Mental Disorders and Key Laboratory of Mental Health, Ministry of Health (Peking University Sixth Hospital), 100191 Beijing, China
| | - Hao Yu
- grid.449428.70000 0004 1797 7280Shandong Collaborative Innovation Center for Diagnosis, Treatment and Behavioral Interventions of Mental Disorders, Department of Psychiatry, Jining Medical University, 272067 Jining, Shandong China
| | - Yi Su
- grid.459847.30000 0004 1798 0615Institute of Mental Health, Peking University Sixth Hospital, 100191 Beijing, China ,grid.453135.50000 0004 1769 3691NHC Key Laboratory of Mental Health, National Clinical Research Center for Mental Disorders and Key Laboratory of Mental Health, Ministry of Health (Peking University Sixth Hospital), 100191 Beijing, China
| | - Tianlan Lu
- grid.459847.30000 0004 1798 0615Institute of Mental Health, Peking University Sixth Hospital, 100191 Beijing, China ,grid.453135.50000 0004 1769 3691NHC Key Laboratory of Mental Health, National Clinical Research Center for Mental Disorders and Key Laboratory of Mental Health, Ministry of Health (Peking University Sixth Hospital), 100191 Beijing, China
| | - Hao Yan
- grid.459847.30000 0004 1798 0615Institute of Mental Health, Peking University Sixth Hospital, 100191 Beijing, China ,grid.453135.50000 0004 1769 3691NHC Key Laboratory of Mental Health, National Clinical Research Center for Mental Disorders and Key Laboratory of Mental Health, Ministry of Health (Peking University Sixth Hospital), 100191 Beijing, China
| | - Weihua Yue
- Institute of Mental Health, Peking University Sixth Hospital, 100191, Beijing, China. .,NHC Key Laboratory of Mental Health, National Clinical Research Center for Mental Disorders and Key Laboratory of Mental Health, Ministry of Health (Peking University Sixth Hospital), 100191, Beijing, China. .,PKU-IDG/McGovern Institute for Brain Research, Peking University, 100871, Beijing, China. .,Chinese Academy of Medical Sciences Research Unit (No. 2018RU006), Peking University, 100191, Beijing, China.
| | - Dai Zhang
- Institute of Mental Health, Peking University Sixth Hospital, 100191, Beijing, China. .,NHC Key Laboratory of Mental Health, National Clinical Research Center for Mental Disorders and Key Laboratory of Mental Health, Ministry of Health (Peking University Sixth Hospital), 100191, Beijing, China. .,PKU-IDG/McGovern Institute for Brain Research, Peking University, 100871, Beijing, China.
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37
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Yang ZH, Cai X, Qu N, Zhao LJ, Zhong BL, Zhang SF, Chen J, Xia B, Jiang HY, Zhou DY, Liu WP, Chang H, Xiao X, Li Y, Li M. Identification of a functional 339 bp Alu insertion polymorphism in the schizophrenia-associated locus at 10q24.32. Zool Res 2020; 41:84-89. [PMID: 31840948 PMCID: PMC6956716 DOI: 10.24272/j.issn.2095-8137.2020.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Zhi-Hui Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Xin Cai
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Na Qu
- Affiliated Wuhan Mental Health Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430012, China.,Research Center for Psychological and Health Sciences, China University of Geosciences, Wuhan, Hubei 430012, China
| | - Li-Juan Zhao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Bao-Liang Zhong
- Affiliated Wuhan Mental Health Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430012, China.,Research Center for Psychological and Health Sciences, China University of Geosciences, Wuhan, Hubei 430012, China
| | - Shu-Fang Zhang
- Affiliated Wuhan Mental Health Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430012, China.,Research Center for Psychological and Health Sciences, China University of Geosciences, Wuhan, Hubei 430012, China
| | - Jing Chen
- Affiliated Wuhan Mental Health Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430012, China.,Research Center for Psychological and Health Sciences, China University of Geosciences, Wuhan, Hubei 430012, China
| | - Bin Xia
- Affiliated Wuhan Mental Health Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430012, China.,Research Center for Psychological and Health Sciences, China University of Geosciences, Wuhan, Hubei 430012, China
| | - Hong-Yan Jiang
- Department of Psychiatry, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China
| | - Dan-Yang Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wei-Peng Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Hong Chang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yi Li
- Affiliated Wuhan Mental Health Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430012, China.,Research Center for Psychological and Health Sciences, China University of Geosciences, Wuhan, Hubei 430012, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China. E-mail:
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Yu Q, He Z, Zubkov D, Huang S, Kurochkin I, Yang X, Halene T, Willmitzer L, Giavalisco P, Akbarian S, Khaitovich P. Lipidome alterations in human prefrontal cortex during development, aging, and cognitive disorders. Mol Psychiatry 2020; 25:2952-2969. [PMID: 30089790 PMCID: PMC7577858 DOI: 10.1038/s41380-018-0200-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/26/2018] [Accepted: 06/11/2018] [Indexed: 12/27/2022]
Abstract
Lipids are essential to brain functions, yet they remain largely unexplored. Here we investigated the lipidome composition of prefrontal cortex gray matter in 396 cognitively healthy individuals with ages spanning 100 years, as well as 67 adult individuals diagnosed with autism (ASD), schizophrenia (SZ), and Down syndrome (DS). Of the 5024 detected lipids, 95% showed significant age-dependent concentration differences clustering into four temporal stages, and resulting in a gradual increase in membrane fluidity in individuals ranging from newborn to nonagenarian. Aging affects 14% of the brain lipidome with late-life changes starting predominantly at 50-55 years of age-a period of general metabolic transition. All three diseases alter the brain lipidome composition, leading-among other things-to a concentration decrease in glycerophospholipid metabolism and endocannabinoid signaling pathways. Lipid concentration decreases in SZ were further linked to genetic variants associated with disease, indicating the relevance of the lipidome changes to disease progression.
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Affiliation(s)
- Qianhui Yu
- grid.9227.e0000000119573309Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China ,grid.419092.70000 0004 0467 2285CAS Key Laboratory of Compstudy has been deposited in the National Omics Datautational Biology, CAS-MPG Partner Institute for Computational Biology, SIBS, CAS, Shanghai, 200031 China
| | - Zhisong He
- grid.419092.70000 0004 0467 2285CAS Key Laboratory of Compstudy has been deposited in the National Omics Datautational Biology, CAS-MPG Partner Institute for Computational Biology, SIBS, CAS, Shanghai, 200031 China ,grid.454320.40000 0004 0555 3608Skolkovo Institute of Science and Technology, Moscow, 143028 Russia
| | - Dmitry Zubkov
- grid.454320.40000 0004 0555 3608Skolkovo Institute of Science and Technology, Moscow, 143028 Russia
| | - Shuyun Huang
- grid.419092.70000 0004 0467 2285CAS Key Laboratory of Compstudy has been deposited in the National Omics Datautational Biology, CAS-MPG Partner Institute for Computational Biology, SIBS, CAS, Shanghai, 200031 China ,grid.440637.20000 0004 4657 8879ShanghaiTech University, Shanghai, 200031 China
| | - Ilia Kurochkin
- grid.454320.40000 0004 0555 3608Skolkovo Institute of Science and Technology, Moscow, 143028 Russia
| | - Xiaode Yang
- grid.9227.e0000000119573309Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031 China ,grid.419092.70000 0004 0467 2285CAS Key Laboratory of Compstudy has been deposited in the National Omics Datautational Biology, CAS-MPG Partner Institute for Computational Biology, SIBS, CAS, Shanghai, 200031 China
| | - Tobias Halene
- grid.59734.3c0000 0001 0670 2351Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Lothar Willmitzer
- grid.418390.70000 0004 0491 976XMax Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, Potsdam, 14476 Germany
| | - Patrick Giavalisco
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, Potsdam, 14476, Germany.
| | - Schahram Akbarian
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia. .,ShanghaiTech University, Shanghai, 200031, China. .,Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany. .,Comparative Biology Group, CAS-MPG Partner Institute for Computational Biology, SIBS, CAS, Shanghai, 200031, China.
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Mohammadi S, Davila-Velderrain J, Kellis M. Reconstruction of Cell-type-Specific Interactomes at Single-Cell Resolution. Cell Syst 2019; 9:559-568.e4. [PMID: 31786210 PMCID: PMC6943823 DOI: 10.1016/j.cels.2019.10.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/13/2019] [Accepted: 10/22/2019] [Indexed: 01/03/2023]
Abstract
The human interactome is instrumental in the systems-level study of the cell and the contextualization of disease-associated gene perturbations. However, reference organismal interactomes do not capture the cell-type-specific context in which proteins and modules preferentially act. Here, we introduce SCINET, a computational framework that reconstructs an ensemble of cell-type-specific interactomes by integrating a global, context-independent reference interactome with a single-cell gene-expression profile. SCINET addresses technical challenges of single-cell data by robustly imputing, transforming, and normalizing the initially noisy and sparse expression of data. Inferred cell-level gene interaction probabilities and group-level interaction strengths define cell-type-specific interactomes. We use SCINET to reconstruct and analyze interactomes of the major human brain and immune cell types, revealing specificity and modularity of perturbations associated with neurodegenerative, neuropsychiatric, and autoimmune disorders. We report cell-type interactomes for brain and immune cell types, together with the SCINET package.
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Affiliation(s)
- Shahin Mohammadi
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Jose Davila-Velderrain
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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40
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The Eminence of Co-Expressed Ties in Schizophrenia Network Communities. DATA 2019. [DOI: 10.3390/data4040149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Exploring gene networks is crucial for identifying significant biological interactions occurring in a disease condition. These interactions can be acknowledged by modeling the tie structure of networks. Such tie orientations are often detected within embedded community structures. However, most of the prevailing community detection modules are intended to capture information from nodes and its attributes, usually ignoring the ties. In this study, a modularity maximization algorithm is proposed based on nonlinear representation of local tangent space alignment (LTSA). Initially, the tangent coordinates are computed locally to identify k-nearest neighbors across the genes. These local neighbors are further optimized by generating a nonlinear network embedding function for detecting gene communities based on eigenvector decomposition. Experimental results suggest that this algorithm detects gene modules with a better modularity index of 0.9256, compared to other traditional community detection algorithms. Furthermore, co-expressed genes across these communities are identified by discovering the characteristic tie structures. These detected ties are known to have substantial biological influence in the progression of schizophrenia, thereby signifying the influence of tie patterns in biological networks. This technique can be extended logically on other diseases networks for detecting substantial gene “hotspots”.
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Chromatin profiling of cortical neurons identifies individual epigenetic signatures in schizophrenia. Transl Psychiatry 2019; 9:256. [PMID: 31624234 PMCID: PMC6797775 DOI: 10.1038/s41398-019-0596-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 09/09/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022] Open
Abstract
Both heritability and environment contribute to risk for schizophrenia. However, the molecular mechanisms of interactions between genetic and non-genetic factors remain unclear. Epigenetic regulation of neuronal genome may be a presumable mechanism in pathogenesis of schizophrenia. Here, we performed analysis of open chromatin landscape of gene promoters in prefrontal cortical (PFC) neurons from schizophrenic patients. We cataloged cell-type-based epigenetic signals of transcriptional start sites (TSS) marked by histone H3-K4 trimethylation (H3K4me3) across the genome in PFC from multiple schizophrenia subjects and age-matched control individuals. One of the top-ranked chromatin alterations was found in the major histocompatibility (MHC) locus on chromosome 6 highlighting the overlap between genetic and epigenetic risk factors in schizophrenia. The chromosome conformation capture (3C) analysis in human brain cells revealed the architecture of multipoint chromatin interactions between the schizophrenia-associated genetic and epigenetic polymorphic sites and distantly located HLA-DRB5 and BTNL2 genes. In addition, schizophrenia-specific chromatin modifications in neurons were particularly prominent for non-coding RNA genes, including an uncharacterized LINC01115 gene and recently identified BNRNA_052780. Notably, protein-coding genes with altered epigenetic state in schizophrenia are enriched for oxidative stress and cell motility pathways. Our results imply the rare individual epigenetic alterations in brain neurons are involved in the pathogenesis of schizophrenia.
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42
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Loftis JM, Lasarev M, Shi X, Lapidus J, Janowsky A, Hoffman WF, Huckans M. Trace amine-associated receptor gene polymorphism increases drug craving in individuals with methamphetamine dependence. PLoS One 2019; 14:e0220270. [PMID: 31600226 PMCID: PMC6786581 DOI: 10.1371/journal.pone.0220270] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/27/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Methamphetamine (MA) is a potent agonist at the trace amine-associated receptor 1 (TAAR1). This study evaluated a common variant (CV) in the human TAAR1 gene, synonymous single nucleotide polymorphism (SNP) V288V, to determine the involvement of TAAR1 in MA dependence. METHODS Participants (n = 106) with active MA dependence (MA-ACT), in remission from MA dependence (MA-REM), with active polysubstance dependence, in remission from polysubstance dependence, and with no history of substance dependence completed neuropsychiatric symptom questionnaires and provided blood samples. In vitro expression and function of CV and wild type TAAR1 receptors were also measured. RESULTS The V288V polymorphism demonstrated a 40% increase in TAAR1 protein expression in cell culture, but message sequence and protein function were unchanged, suggesting an increase in translation efficiency. Principal components analysis resolved neuropsychiatric symptoms into four components, PC1 (depression, anxiety, memory, and fatigue), PC2 (pain), PC3 (drug and alcohol craving), and PC4 (sleep disturbances). Analyses of study group and TAAR1 genotype revealed a significant interaction for PC3 (craving response) (p = 0.003). The control group showed no difference in PC3 associated with TAAR1, while adjusted mean craving for the MA-ACT and MA-REM groups, among those with at least one copy of V288V, was estimated to be, respectively, 1.55 (p = 0.036) and 1.77 (p = 0.071) times the adjusted mean craving for those without the TAAR1 SNP. CONCLUSIONS Neuroadaptation to chronic MA use may be altered by TAAR1 genotype and result in increased dopamine signaling and craving in individuals with the V288V genotype.
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Affiliation(s)
- Jennifer M. Loftis
- Research & Development Service, VA Portland Health Care System, Portland, OR, United States of America
- Department of Psychiatry, Oregon Health & Science University, Portland, OR, United States of America
- Methamphetamine Abuse Research Center, Oregon Health & Science University, Portland, OR, United States of America
| | - Michael Lasarev
- Methamphetamine Abuse Research Center, Oregon Health & Science University, Portland, OR, United States of America
- Oregon Health & Science University and Portland State University School of Public Health, Portland, OR, United States of America
| | - Xiao Shi
- Research & Development Service, VA Portland Health Care System, Portland, OR, United States of America
- Methamphetamine Abuse Research Center, Oregon Health & Science University, Portland, OR, United States of America
| | - Jodi Lapidus
- Methamphetamine Abuse Research Center, Oregon Health & Science University, Portland, OR, United States of America
- Oregon Health & Science University and Portland State University School of Public Health, Portland, OR, United States of America
| | - Aaron Janowsky
- Research & Development Service, VA Portland Health Care System, Portland, OR, United States of America
- Department of Psychiatry, Oregon Health & Science University, Portland, OR, United States of America
- Methamphetamine Abuse Research Center, Oregon Health & Science University, Portland, OR, United States of America
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, United States of America
| | - William F. Hoffman
- Research & Development Service, VA Portland Health Care System, Portland, OR, United States of America
- Department of Psychiatry, Oregon Health & Science University, Portland, OR, United States of America
- Methamphetamine Abuse Research Center, Oregon Health & Science University, Portland, OR, United States of America
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, United States of America
- Mental Health and Clinical Neurosciences Division, VA Portland Health Care System, Portland, OR, United States of America
| | - Marilyn Huckans
- Research & Development Service, VA Portland Health Care System, Portland, OR, United States of America
- Department of Psychiatry, Oregon Health & Science University, Portland, OR, United States of America
- Methamphetamine Abuse Research Center, Oregon Health & Science University, Portland, OR, United States of America
- Mental Health and Clinical Neurosciences Division, VA Portland Health Care System, Portland, OR, United States of America
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Jian X, Chen J, Li Z, Song Z, Zhou J, Xu W, Liu Y, Shen J, Wang Y, Yi Q, Shi Y. SLC39A8 is a risk factor for schizophrenia in Uygur Chinese: a case-control study. BMC Psychiatry 2019; 19:293. [PMID: 31533672 PMCID: PMC6751796 DOI: 10.1186/s12888-019-2240-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 08/15/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Schizophrenia is a severe mental disease with high morbidity and heritability. The SLC39A8 gene is located in 4q24 and encodes a protein that transports many metal ions. Multiple previous studies found that one of the most pleiotropic single nucleotide polymorphisms (SNPs) in SLC39A8, rs13107325, is associated with schizophrenia in the European population. However, the polymorphism of this locus is rare in other populations. In China, the Han Chinese and the Uygur Chinese are two ethnic populations that originate from different races. METHODS A case-control study was conducted with 983 schizophrenia cases and 1230 healthy controls of the Chinese Uygur population. To validate the most promising SNP, meta-analyses were conducted with the Han Chinese and the European PGC2 data sets reported previously. RESULTS A susceptible locus, rs10014145 (pallele = 0.014, pallele = 0.098 after correction; pgenotype = 0.004, pgenotype = 0.032 after correction) was identified in case-control study of the Chinese Uygur population. Further, the association between rs10014145 and schizophrenia was supported by a meta-analysis of Han and Uygur Chinese samples (pooled OR [95% CI] =1.10 [1.03-1.17], Z = 2.73, p = 0.006). The association between rs10014145 and schizophrenia was not significant in a meta-analysis of combined Chinese and European samples (pooled OR [95% CI] =1.07 [1.00-1.14], Z = 1.88, and p = 0.06). In addition, the "CCAC" haplotype of rs4698844-rs233814-rs13114343-rs151394 was significantly associated with schizophrenia in Uygur Chinese (P = 0.003, corrected p = 0.012). CONCLUSIONS The results of this study support that SLC39A8 is a susceptible gene for schizophrenia in the populations of Han Chinese and Uygur Chinese in China, further studies are suggested to validate the association.
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Affiliation(s)
- Xuemin Jian
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Jianhua Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, People's Republic of China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, Shandong, 266003, People's Republic of China
| | - Zhijian Song
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Juan Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Wei Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Yahui Liu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Jiawei Shen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Yonggang Wang
- Department of Neurology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, 200127, People's Republic of China.
| | - Qizhong Yi
- Psychological Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, People's Republic of China.
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China.
- Shanghai key laboratory of Sleep Disordered Breathing, Shanghai Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, People's Republic of China.
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, Shandong, 266003, People's Republic of China.
- Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China.
- Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China.
- Shanghai Changning Mental Health Center, Shanghai, 200030, People's Republic of China.
- Department of Psychiatry, First Teaching Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, People's Republic of China.
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Rivera AD, Butt AM. Astrocytes are direct cellular targets of lithium treatment: novel roles for lysyl oxidase and peroxisome-proliferator activated receptor-γ as astroglial targets of lithium. Transl Psychiatry 2019; 9:211. [PMID: 31477687 PMCID: PMC6718419 DOI: 10.1038/s41398-019-0542-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/11/2019] [Accepted: 07/07/2019] [Indexed: 12/26/2022] Open
Abstract
Astrocytes are multifunctional glial cells that play essential roles in supporting synaptic signalling and white matter-associated connectivity. There is increasing evidence that astrocyte dysfunction is involved in several brain disorders, including bipolar disorder (BD), depression and schizophrenia. The mood stabiliser lithium is a frontline treatment for BD, but the mechanisms of action remain unclear. Here, we demonstrate that astrocytes are direct targets of lithium and identify unique astroglial transcriptional networks that regulate specific molecular changes in astrocytes associated with BD and schizophrenia, together with Alzheimer's disease (AD). Using pharmacogenomic analyses, we identified novel roles for the extracellular matrix (ECM) regulatory enzyme lysyl oxidase (LOX) and peroxisome proliferator-activated receptor gamma (PPAR-γ) as profound regulators of astrocyte morphogenesis. This study unravels new pathophysiological mechanisms in astrocytes that have potential as novel biomarkers and potential therapeutic targets for regulating astroglial responses in diverse neurological disorders.
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Affiliation(s)
- Andrea D. Rivera
- 0000 0001 0728 6636grid.4701.2Institute of Biomedical and Biomolecular Sciences, School of Pharmacy and Biomedical Science, University of Portsmouth, St Michael’s Building, White Swan Road, Portsmouth, PO1 2DT UK
| | - Arthur M. Butt
- 0000 0001 0728 6636grid.4701.2Institute of Biomedical and Biomolecular Sciences, School of Pharmacy and Biomedical Science, University of Portsmouth, St Michael’s Building, White Swan Road, Portsmouth, PO1 2DT UK
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45
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Wu M, Lin Z, Ma S, Chen T, Jiang R, Wong WH. Simultaneous inference of phenotype-associated genes and relevant tissues from GWAS data via Bayesian integration of multiple tissue-specific gene networks. J Mol Cell Biol 2019; 9:436-452. [PMID: 29300920 DOI: 10.1093/jmcb/mjx059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/20/2017] [Indexed: 02/07/2023] Open
Abstract
Although genome-wide association studies (GWAS) have successfully identified thousands of genomic loci associated with hundreds of complex traits in the past decade, the debate about such problems as missing heritability and weak interpretability has been appealing for effective computational methods to facilitate the advanced analysis of the vast volume of existing and anticipated genetic data. Towards this goal, gene-level integrative GWAS analysis with the assumption that genes associated with a phenotype tend to be enriched in biological gene sets or gene networks has recently attracted much attention, due to such advantages as straightforward interpretation, less multiple testing burdens, and robustness across studies. However, existing methods in this category usually exploit non-tissue-specific gene networks and thus lack the ability to utilize informative tissue-specific characteristics. To overcome this limitation, we proposed a Bayesian approach called SIGNET (Simultaneously Inference of GeNEs and Tissues) to integrate GWAS data and multiple tissue-specific gene networks for the simultaneous inference of phenotype-associated genes and relevant tissues. Through extensive simulation studies, we showed the effectiveness of our method in finding both associated genes and relevant tissues for a phenotype. In applications to real GWAS data of 14 complex phenotypes, we demonstrated the power of our method in both deciphering genetic basis and discovering biological insights of a phenotype. With this understanding, we expect to see SIGNET as a valuable tool for integrative GWAS analysis, thereby boosting the prevention, diagnosis, and treatment of human inherited diseases and eventually facilitating precision medicine.
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Affiliation(s)
- Mengmeng Wu
- Department of Computer Science, Tsinghua University, Beijing 100084, China.,Ministry of Education Key Laboratory of Bioinformatics and Bioinformatics Division, Tsinghua National Laboratory for Information Science and Technology, Beijing 100084, China.,Department of Statistics, Stanford University, CA 94305, USA
| | - Zhixiang Lin
- Department of Statistics, Stanford University, CA 94305, USA
| | - Shining Ma
- Department of Statistics, Stanford University, CA 94305, USA
| | - Ting Chen
- Department of Computer Science, Tsinghua University, Beijing 100084, China.,Ministry of Education Key Laboratory of Bioinformatics and Bioinformatics Division, Tsinghua National Laboratory for Information Science and Technology, Beijing 100084, China
| | - Rui Jiang
- Ministry of Education Key Laboratory of Bioinformatics and Bioinformatics Division, Tsinghua National Laboratory for Information Science and Technology, Beijing 100084, China.,Department of Automation, Tsinghua University, Beijing 100084, China
| | - Wing Hung Wong
- Department of Statistics, Stanford University, CA 94305, USA
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46
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Commonality in dysregulated expression of gene sets in cortical brains of individuals with autism, schizophrenia, and bipolar disorder. Transl Psychiatry 2019; 9:152. [PMID: 31127088 PMCID: PMC6534650 DOI: 10.1038/s41398-019-0488-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 04/03/2019] [Accepted: 04/10/2019] [Indexed: 12/14/2022] Open
Abstract
Individuals affected with different neuropsychiatric disorders such as autism (AUT), schizophrenia (SCZ) and bipolar disorder (BPD), may share similar clinical manifestations, suggesting shared genetic influences and common biological mechanisms underlying these disorders. Using brain transcriptome data gathered from postmortem donors affected with AUT, SCZ and BPD, it is now possible to identify shared dysregulated gene sets, i.e., those abnormally expressed in brains of neuropsychiatric patients, compared to non-psychiatric controls. Here, we apply a novel aberrant gene expression analysis method, coupled with consensus co-expression network analysis, to identify gene sets with shared dysregulated expression in cortical brains of individuals affected with AUT, SCZ and BPD. We identify eight gene sets with dysregulated expression shared by AUT, SCZ and BPD, 23 by AUT and SCZ, four by AUT and BPD, and two by SCZ and BPD. The identified genes are enriched with functions relevant to amino acid transport, synapse, neurotransmitter release, oxidative stress, nitric oxide synthase biosynthesis, immune response, protein folding, lysophosphatidic acid-mediated signaling and glycolysis. Our method has been proven to be effective in discovering and revealing multigene sets with dysregulated expression shared by different neuropsychiatric disorders. Our findings provide new insights into the common molecular mechanisms underlying the pathogenesis and progression of AUT, SCZ and BPD, contributing to the study of etiological overlap between these neuropsychiatric disorders.
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47
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Tenenbaum JD, Bhuvaneshwar K, Gagliardi JP, Fultz Hollis K, Jia P, Ma L, Nagarajan R, Rakesh G, Subbian V, Visweswaran S, Zhao Z, Rozenblit L. Translational bioinformatics in mental health: open access data sources and computational biomarker discovery. Brief Bioinform 2019; 20:842-856. [PMID: 29186302 PMCID: PMC6585382 DOI: 10.1093/bib/bbx157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/24/2017] [Indexed: 12/12/2022] Open
Abstract
Mental illness is increasingly recognized as both a significant cost to society and a significant area of opportunity for biological breakthrough. As -omics and imaging technologies enable researchers to probe molecular and physiological underpinnings of multiple diseases, opportunities arise to explore the biological basis for behavioral health and disease. From individual investigators to large international consortia, researchers have generated rich data sets in the area of mental health, including genomic, transcriptomic, metabolomic, proteomic, clinical and imaging resources. General data repositories such as the Gene Expression Omnibus (GEO) and Database of Genotypes and Phenotypes (dbGaP) and mental health (MH)-specific initiatives, such as the Psychiatric Genomics Consortium, MH Research Network and PsychENCODE represent a wealth of information yet to be gleaned. At the same time, novel approaches to integrate and analyze data sets are enabling important discoveries in the area of mental and behavioral health. This review will discuss and catalog into an organizing framework the increasingly diverse set of MH data resources available, using schizophrenia as a focus area, and will describe novel and integrative approaches to molecular biomarker discovery that make use of mental health data.
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Affiliation(s)
- Jessica D Tenenbaum
- Department of Biostatistics and Bioinformatics at the Duke University School of Medicine
| | | | | | - Kate Fultz Hollis
- Department of Biomedical Informatics and Clinical Epidemiology at Oregon Health and Science University
| | - Peilin Jia
- University of Texas Health Science Center at Houston
| | - Liang Ma
- Bioinformatics and Systems Medicine Laboratory (BSML), Center for Precision Health, School of Biomedical Informatics, the University of Texas Health Science Center at Houston
| | | | | | - Vignesh Subbian
- Department of Biomedical Engineering and the Department of Systems and Industrial Engineering at the University of Arizona
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48
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Zhang DF, Xu M, Bi R, Yao YG. Genetic Analyses of Alzheimer's Disease in China: Achievements and Perspectives. ACS Chem Neurosci 2019; 10:890-901. [PMID: 30698408 DOI: 10.1021/acschemneuro.8b00435] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Since 2010, the Chinese have become one of the most aged populations in the world, leading to a severe burden of neurodegenerative disorders. Alzheimer's disease (AD) is the most prevalent neurodegenerative disease and has a high genetic heritability. In the past two decades, numerous genetic analyses, from linkage analyses and candidate gene studies to genome-wide association studies (GWASs) and next-generation sequencing studies, have identified dozens of AD susceptibility or causal genes. These studies have provided a comprehensive genetic view and contributed to the understanding of the pathological and molecular mechanisms of the disease. However, most of the recognized AD genetic risk factors have been reported in studies based on European populations or populations of European ancestry, and data about the genetics of AD from other populations has been very limited. As China has the largest AD population in the world and because of the remarkable genetic differences between the East and the West, deciphering the genetic basis and molecular mechanism in Chinese patients with AD may add key points to the full characterization of AD. In this review, we present an overview of the current state of AD genetic research in China, with an emphasis on genome-level studies. We also describe the challenges and opportunities for future advances, especially for in-depth collaborations, brain bank construction, and primate animal modeling. There is an urgent need to promote public awareness and increase our collaborations and data sharing.
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Affiliation(s)
- Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Min Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- Kunming Institute of Zoology−Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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49
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Huo Y, Li S, Liu J, Li X, Luo XJ. Functional genomics reveal gene regulatory mechanisms underlying schizophrenia risk. Nat Commun 2019; 10:670. [PMID: 30737407 PMCID: PMC6368563 DOI: 10.1038/s41467-019-08666-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/20/2018] [Indexed: 02/07/2023] Open
Abstract
Genome-wide association studies (GWASs) have identified over 180 independent schizophrenia risk loci. Nevertheless, how the risk variants in the reported loci confer schizophrenia susceptibility remains largely unknown. Here we systematically investigate the gene regulatory mechanisms underpinning schizophrenia risk through integrating data from functional genomics (including 30 ChIP-Seq experiments) and position weight matrix (PWM). We identify 132 risk single nucleotide polymorphisms (SNPs) that disrupt transcription factor binding and we find that 97 of the 132 TF binding-disrupting SNPs are associated with gene expression in human brain tissues. We validate the regulatory effect of some TF binding-disrupting SNPs with reporter gene assays (9 SNPs) and allele-specific expression analysis (10 SNPs). Our study reveals gene regulatory mechanisms affected by schizophrenia risk SNPs (including widespread disruption of POLR2A and CTCF binding) and identifies target genes for mechanistic studies and drug development. Our results can be accessed and visualized at SZDB database ( http://www.szdb.org/ ).
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Affiliation(s)
- Yongxia Huo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Shiwu Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Jiewei Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Xiaoyan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
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50
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Feltrin AS, Tahira AC, Simões SN, Brentani H, Martins DC. Assessment of complementarity of WGCNA and NERI results for identification of modules associated to schizophrenia spectrum disorders. PLoS One 2019; 14:e0210431. [PMID: 30645614 PMCID: PMC6333352 DOI: 10.1371/journal.pone.0210431] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 12/21/2018] [Indexed: 02/07/2023] Open
Abstract
Psychiatric disorders involve both changes in multiple genes as well different types of variations. As such, gene co-expression networks allowed the comparison of different stages and parts of the brain contributing to an integrated view of genetic variation. Two methods based on co-expression networks presents appealing results: Weighted Gene Correlation Network Analysis (WGCNA) and Network-Medicine Relative Importance (NERI). By selecting two different gene expression databases related to schizophrenia, we evaluated the biological modules selected by both WGCNA and NERI along these databases as well combining both WGCNA and NERI results (WGCNA-NERI). Also we conducted a enrichment analysis for the identification of partial biological function of each result (as well a replication analysis). To appraise the accuracy of whether both algorithms (as well our approach, WGCNA-NERI) were pointing to genes related to schizophrenia and its complex genetic architecture we conducted the MSET analysis, based on a reference gene list of schizophrenia database (SZDB) related to DNA Methylation, Exome, GWAS as well as copy number variation mutation studies. The WGCNA results were more associated with inflammatory pathways and immune system response; NERI obtained genes related with cellular regulation, embryological pathways e cellular growth factors. Only NERI were able to provide a statistical meaningful results to the MSET analysis (for Methylation and de novo mutations data). However, combining WGCNA and NERI provided a much more larger overlap in these two categories and additionally on Transcriptome database. Our study suggests that using both methods in combination is better for establishing a group of modules and pathways related to a complex disease than using each method individually. NERI is available at: https://bitbucket.org/sergionery/neri.
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Affiliation(s)
- Arthur Sant’Anna Feltrin
- Center for Mathematics, Computation and Cognition, Federal University of ABC (UFABC), Santo André, SP, Brazil
- * E-mail: (ASF); (DCMJ)
| | - Ana Carolina Tahira
- LIM23, Instituto de Psiquiatria, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Sérgio Nery Simões
- Federal Institute of Education, Science and Technology of Espírito Santo, Serra, ES, Brazil
| | - Helena Brentani
- LIM23, Instituto de Psiquiatria, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
- Instituto de Psiquiatria, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
- National Institute of Developmental Psychiatry for Children and Adolescents (INPD), São Paulo, SP, Brazil
| | - David Corrêa Martins
- Center for Mathematics, Computation and Cognition, Federal University of ABC (UFABC), Santo André, SP, Brazil
- * E-mail: (ASF); (DCMJ)
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