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Song N, Mei S, Wang X, Hu G, Lu M. Focusing on mitochondria in the brain: from biology to therapeutics. Transl Neurodegener 2024; 13:23. [PMID: 38632601 PMCID: PMC11022390 DOI: 10.1186/s40035-024-00409-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
Mitochondria have multiple functions such as supplying energy, regulating the redox status, and producing proteins encoded by an independent genome. They are closely related to the physiology and pathology of many organs and tissues, among which the brain is particularly prominent. The brain demands 20% of the resting metabolic rate and holds highly active mitochondrial activities. Considerable research shows that mitochondria are closely related to brain function, while mitochondrial defects induce or exacerbate pathology in the brain. In this review, we provide comprehensive research advances of mitochondrial biology involved in brain functions, as well as the mitochondria-dependent cellular events in brain physiology and pathology. Furthermore, various perspectives are explored to better identify the mitochondrial roles in neurological diseases and the neurophenotypes of mitochondrial diseases. Finally, mitochondrial therapies are discussed. Mitochondrial-targeting therapeutics are showing great potentials in the treatment of brain diseases.
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Affiliation(s)
- Nanshan Song
- Department of Pharmacology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Shuyuan Mei
- The First Clinical Medical College, Nanjing Medical University, Nanjing, 211166, China
| | - Xiangxu Wang
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Neuroprotective Drug Discovery Key Laboratory, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
| | - Gang Hu
- Department of Pharmacology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Neuroprotective Drug Discovery Key Laboratory, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China.
| | - Ming Lu
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Neuroprotective Drug Discovery Key Laboratory, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China.
- Changzhou Second People's Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, 213000, China.
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2
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Kong L, Chen Y, Shen Y, Zhang D, Wei C, Lai J, Hu S. Progress and Implications from Genetic Studies of Bipolar Disorder. Neurosci Bull 2024:10.1007/s12264-023-01169-9. [PMID: 38206551 DOI: 10.1007/s12264-023-01169-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 10/05/2023] [Indexed: 01/12/2024] Open
Abstract
With the advancements in gene sequencing technologies, including genome-wide association studies, polygenetic risk scores, and high-throughput sequencing, there has been a tremendous advantage in mapping a detailed blueprint for the genetic model of bipolar disorder (BD). To date, intriguing genetic clues have been identified to explain the development of BD, as well as the genetic association that might be applied for the development of susceptibility prediction and pharmacogenetic intervention. Risk genes of BD, such as CACNA1C, ANK3, TRANK1, and CLOCK, have been found to be involved in various pathophysiological processes correlated with BD. Although the specific roles of these genes have yet to be determined, genetic research on BD will help improve the prevention, therapeutics, and prognosis in clinical practice. The latest preclinical and clinical studies, and reviews of the genetics of BD, are analyzed in this review, aiming to summarize the progress in this intriguing field and to provide perspectives for individualized, precise, and effective clinical practice.
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Affiliation(s)
- Lingzhuo Kong
- Department of Psychiatry, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yiqing Chen
- Department of Psychiatry, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yuting Shen
- Department of Psychiatry, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Danhua Zhang
- Department of Psychiatry, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Chen Wei
- Department of Psychiatry, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jianbo Lai
- Department of Psychiatry, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
- The Key Laboratory of Mental Disorder Management in Zhejiang Province, Hangzhou, 310003, China.
- Brain Research Institute of Zhejiang University, Hangzhou, 310003, China.
- Zhejiang Engineering Center for Mathematical Mental Health, Hangzhou, 310003, China.
- Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brian Medicine, and MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University School of Medicine, Hangzhou, 310003, China.
| | - Shaohua Hu
- Department of Psychiatry, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
- The Key Laboratory of Mental Disorder Management in Zhejiang Province, Hangzhou, 310003, China.
- Brain Research Institute of Zhejiang University, Hangzhou, 310003, China.
- Zhejiang Engineering Center for Mathematical Mental Health, Hangzhou, 310003, China.
- Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brian Medicine, and MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University School of Medicine, Hangzhou, 310003, China.
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3
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Chen R, Routh BN, Gaudet AD, Fonken LK. Circadian Regulation of the Neuroimmune Environment Across the Lifespan: From Brain Development to Aging. J Biol Rhythms 2023; 38:419-446. [PMID: 37357738 PMCID: PMC10475217 DOI: 10.1177/07487304231178950] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
Circadian clocks confer 24-h periodicity to biological systems, to ultimately maximize energy efficiency and promote survival in a world with regular environmental light cycles. In mammals, circadian rhythms regulate myriad physiological functions, including the immune, endocrine, and central nervous systems. Within the central nervous system, specialized glial cells such as astrocytes and microglia survey and maintain the neuroimmune environment. The contributions of these neuroimmune cells to both homeostatic and pathogenic demands vary greatly across the day. Moreover, the function of these cells changes across the lifespan. In this review, we discuss circadian regulation of the neuroimmune environment across the lifespan, with a focus on microglia and astrocytes. Circadian rhythms emerge in early life concurrent with neuroimmune sculpting of brain circuits and wane late in life alongside increasing immunosenescence and neurodegeneration. Importantly, circadian dysregulation can alter immune function, which may contribute to susceptibility to neurodevelopmental and neurodegenerative diseases. In this review, we highlight circadian neuroimmune interactions across the lifespan and share evidence that circadian dysregulation within the neuroimmune system may be a critical component in human neurodevelopmental and neurodegenerative diseases.
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Affiliation(s)
- Ruizhuo Chen
- Division of Pharmacology & Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, Texas
| | - Brandy N. Routh
- Division of Pharmacology & Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, Texas
- Institute for Neuroscience, The University of Texas at Austin, Austin, Texas
| | - Andrew D. Gaudet
- Institute for Neuroscience, The University of Texas at Austin, Austin, Texas
- Department of Psychology, The University of Texas at Austin, Austin, Texas
- Department of Neurology, Dell Medical School, The University of Texas at Austin, Austin, Texas
| | - Laura K. Fonken
- Division of Pharmacology & Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, Texas
- Institute for Neuroscience, The University of Texas at Austin, Austin, Texas
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4
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Sun C, Shen Y, Liu P, Shen Y, Hu Y, Li P, Zhang Y, Miao F, Zhang J. NLRC5 Deficiency Reduces LPS-Induced Microglial Activation via Inhibition of NF-κB Signaling and Ameliorates Mice's Depressive-like Behavior. Int J Mol Sci 2023; 24:13265. [PMID: 37686068 PMCID: PMC10487775 DOI: 10.3390/ijms241713265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/09/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Microglia are believed to be the key immune effectors of the central immune microenvironment, and their dysregulation is associated with neuroinflammation and mood disorders. Nucleotide-binding oligomerization domain-like receptor family caspase recruitment domain-containing five (NLRC5) is a new member of the Nod-like receptor family. Recently, NLRC5 has been reported to be expressed by microglia. Nonetheless, the exact roles of NLRC5 in microglial activation and its function in depression have not been investigated yet. Herein, we found that reducing NLRC5 decreased lipopolysaccharide (LPS)-induced secretion of pro-inflammatory cytokines (IL-1β, IL-6, and TNF-α) in primary cultured microglia and microglial cell lines but not in bone marrow-derived macrophages (BMDMs). In more detail, reducing NLRC5 diminished the secretion of LPS-induced cytokines by attenuating IKKα/β phosphorylation and inhibiting NF-κB signaling. Moreover, the expression of Nlrc5 in the hippocampus of LPS- or chronic unpredictable mild stress (CUMS)-induced depressive mice was increased. In line with the in vitro findings, Nlrc5 deficiency inhibited microglial activation in the mouse hippocampus and improved LPS- or CUMS-induced depressive-like behaviors. In summary, we demonstrated the critical role of NLRC5 in LPS-induced microglial activation and LPS- or CUMS-induced depressive mouse models.
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Affiliation(s)
- Chen Sun
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Microbiology and Immunology, School of Medicine, Southeast University, Nanjing 210009, China; (C.S.); (Y.S.); (Y.Z.)
| | - Yuqing Shen
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Microbiology and Immunology, School of Medicine, Southeast University, Nanjing 210009, China; (C.S.); (Y.S.); (Y.Z.)
| | - Piaopiao Liu
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing 210009, China; (P.L.); (Y.S.); (Y.H.); (P.L.); (F.M.)
| | - Yi Shen
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing 210009, China; (P.L.); (Y.S.); (Y.H.); (P.L.); (F.M.)
| | - Yue Hu
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing 210009, China; (P.L.); (Y.S.); (Y.H.); (P.L.); (F.M.)
| | - Ping Li
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing 210009, China; (P.L.); (Y.S.); (Y.H.); (P.L.); (F.M.)
| | - Ying Zhang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Microbiology and Immunology, School of Medicine, Southeast University, Nanjing 210009, China; (C.S.); (Y.S.); (Y.Z.)
| | - Fengqin Miao
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing 210009, China; (P.L.); (Y.S.); (Y.H.); (P.L.); (F.M.)
| | - Jianqiong Zhang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Microbiology and Immunology, School of Medicine, Southeast University, Nanjing 210009, China; (C.S.); (Y.S.); (Y.Z.)
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing 210009, China; (P.L.); (Y.S.); (Y.H.); (P.L.); (F.M.)
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5
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Terra Machado D, Bernardes Brustolini OJ, Côrtes Martins Y, Grivet Mattoso Maia MA, Ribeiro de Vasconcelos AT. Inference of differentially expressed genes using generalized linear mixed models in a pairwise fashion. PeerJ 2023; 11:e15145. [PMID: 37033732 PMCID: PMC10078460 DOI: 10.7717/peerj.15145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/09/2023] [Indexed: 04/05/2023] Open
Abstract
Background
Technological advances involving RNA-Seq and Bioinformatics allow quantifying the transcriptional levels of genes in cells, tissues, and cell lines, permitting the identification of Differentially Expressed Genes (DEGs). DESeq2 and edgeR are well-established computational tools used for this purpose and they are based upon generalized linear models (GLMs) that consider only fixed effects in modeling. However, the inclusion of random effects reduces the risk of missing potential DEGs that may be essential in the context of the biological phenomenon under investigation. The generalized linear mixed models (GLMM) can be used to include both effects.
Methods
We present DEGRE (Differentially Expressed Genes with Random Effects), a user-friendly tool capable of inferring DEGs where fixed and random effects on individuals are considered in the experimental design of RNA-Seq research. DEGRE preprocesses the raw matrices before fitting GLMMs on the genes and the derived regression coefficients are analyzed using the Wald statistical test. DEGRE offers the Benjamini-Hochberg or Bonferroni techniques for P-value adjustment.
Results
The datasets used for DEGRE assessment were simulated with known identification of DEGs. These have fixed effects, and the random effects were estimated and inserted to measure the impact of experimental designs with high biological variability. For DEGs’ inference, preprocessing effectively prepares the data and retains overdispersed genes. The biological coefficient of variation is inferred from the counting matrices to assess variability before and after the preprocessing. The DEGRE is computationally validated through its performance by the simulation of counting matrices, which have biological variability related to fixed and random effects. DEGRE also provides improved assessment measures for detecting DEGs in cases with higher biological variability. We show that the preprocessing established here effectively removes technical variation from those matrices. This tool also detects new potential candidate DEGs in the transcriptome data of patients with bipolar disorder, presenting a promising tool to detect more relevant genes.
Conclusions
DEGRE provides data preprocessing and applies GLMMs for DEGs’ inference. The preprocessing allows efficient remotion of genes that could impact the inference. Also, the computational and biological validation of DEGRE has shown to be promising in identifying possible DEGs in experiments derived from complex experimental designs. This tool may help handle random effects on individuals in the inference of DEGs and presents a potential for discovering new interesting DEGs for further biological investigation.
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Affiliation(s)
- Douglas Terra Machado
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | | | - Yasmmin Côrtes Martins
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
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6
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Sudre G, Gildea DE, Shastri GG, Sharp W, Jung B, Xu Q, Auluck PK, Elnitski L, Baxevanis AD, Marenco S, Shaw P. Mapping the cortico-striatal transcriptome in attention deficit hyperactivity disorder. Mol Psychiatry 2023; 28:792-800. [PMID: 36380233 PMCID: PMC9918667 DOI: 10.1038/s41380-022-01844-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 10/05/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022]
Abstract
Despite advances in identifying rare and common genetic variants conferring risk for ADHD, the lack of a transcriptomic understanding of cortico-striatal brain circuitry has stymied a molecular mechanistic understanding of this disorder. To address this gap, we mapped the transcriptome of the caudate nucleus and anterior cingulate cortex in post-mortem tissue from 60 individuals with and without ADHD. Significant differential expression of genes was found in the anterior cingulate cortex and, to a lesser extent, the caudate. Significant downregulation emerged of neurotransmitter gene pathways, particularly glutamatergic, in keeping with models that implicate these neurotransmitters in ADHD. Consistent with the genetic overlap between mental disorders, correlations were found between the cortico-striatal transcriptomic changes seen in ADHD and those seen in other neurodevelopmental and mood disorders. This transcriptomic evidence points to cortico-striatal neurotransmitter anomalies in the pathogenesis of ADHD, consistent with current models of the disorder.
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Affiliation(s)
- Gustavo Sudre
- Social and Behavioral Research Branch, Division of Intramural Research, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Derek E Gildea
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Gauri G Shastri
- Office of the Scientific Director, Division of Intramural Research, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA
| | - Wendy Sharp
- Office of the Scientific Director, Division of Intramural Research, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA
| | - Benjamin Jung
- Social and Behavioral Research Branch, Division of Intramural Research, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Qing Xu
- Human Brain Collection Core, Division of Intramural Research, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA
| | - Pavan K Auluck
- Human Brain Collection Core, Division of Intramural Research, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA
| | - Laura Elnitski
- Translational and Functional Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Andreas D Baxevanis
- Computational and Statistical Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Stefano Marenco
- Human Brain Collection Core, Division of Intramural Research, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA
| | - Philip Shaw
- Social and Behavioral Research Branch, Division of Intramural Research, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA.
- Office of the Scientific Director, Division of Intramural Research, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA.
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7
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Fu Q, Hu T, Yang Y, Zhao M. Transcriptome analysis reveals phenanthrene degradation strategy of Pseudomonas stutzeri LH-42. 3 Biotech 2023; 13:65. [PMID: 36718409 PMCID: PMC9883372 DOI: 10.1007/s13205-023-03473-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 01/02/2023] [Indexed: 01/28/2023] Open
Abstract
Toxic polycyclic aromatic hydrocarbons (PAHs) are often released into the environment during the combustion and processing of fossil fuels and are capable of causing significant pollution to people and the environment. One of the representative substances of PAHs is phenanthrene, which is often studied as a model compound for PAHs treatment. In this study, we compared the results of transcriptome analysis of Pseudomonas stutzeri LH-42 in two different culture conditions under phenanthrene-induced culture (test group) and glucose-induced culture (control group), and analysed the key enzymatic mechanisms of Pseudomonas stutzeri LH-42 in the biodegradation of phenanthrene. In our experiments, the transcriptome results showed that a total of 380 genes were more than twofold differentially expressed in the test group, of which 187 genes were significantly up-regulated in expression under Phenanthrene induction. Among the 380 differentially expressed genes, 90 genes were involved in Phenanthrene biodegradation, mainly including genes involved in biometabolism, cellular chemotaxis, substrate transport, signal induction and other related processes. Based on the transcriptome sequence analysis of Pseudomonas stutzeri LH-42 at the time of phenanthrene induction, a total of 25 dioxygenase genes were identified, and the related genes were mainly concentrated in two relatively concentrated clusters of PAHs biodegradation genes. The transcriptome analysis resulted in a complete set of enzyme genes related to the phenanthrene biodegradation pathway. The analysis of key enzymes led to the inference of a possible phenanthrene biodegradation pathway: the salicylic acid degradation pathway. The results of this study provide a theoretical basis for in situ remediation of PAHs-contaminated environments using Pseudomonas stutzeri LH-42. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03473-7.
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Affiliation(s)
- Qiang Fu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083 Hunan China
| | - Tingting Hu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083 Hunan China
| | - Yu Yang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083 Hunan China
| | - Mengshi Zhao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083 Hunan China
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8
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Webster MJ. Infections, Inflammation, and Psychiatric Illness: Review of Postmortem Evidence. Curr Top Behav Neurosci 2023; 61:35-48. [PMID: 35505055 DOI: 10.1007/7854_2022_362] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
While there is an abundance of epidemiological evidence implicating infectious agents in the etiology of severe mental illnesses, postmortem studies have not yet detected an increased incidence of microbial nucleic acid or proteins in the brains of people with mental illness. Nevertheless, abnormally expressed immune and inflammatory markers have consistently been found in the postmortem brain of patients with schizophrenia and mood disorders. Some of these abnormalities may be the result of an infection in utero or early in life that not only impacted the developing immune system but also the developing neurons of the brain. Some of the immune markers that are consistently found to be upregulated in schizophrenia implicate a possible viral infection and the blood brain barrier in the etiology and neuropathology of the disorder.
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9
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Li Z, Sun Y, Ding L, Yang J, Huang J, Cheng M, Wu L, Zhuang Z, Chen C, Huang Y, Zhu Z, Jiang S, Huang F, Wang C, Liu S, Liu L, Lei Y. Deciphering the distinct transcriptomic and gene regulatory map in adult macaque basal ganglia cells. Gigascience 2022; 12:giad095. [PMID: 38091510 PMCID: PMC10716911 DOI: 10.1093/gigascience/giad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 08/09/2023] [Accepted: 10/10/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND The basal ganglia are a complex of interconnected subcortical structures located beneath the mammalian cerebral cortex. The degeneration of dopaminergic neurons in the basal ganglia is the primary pathological feature of Parkinson's disease. Due to a lack of integrated analysis of multiomics datasets across multiple basal ganglia brain regions, very little is known about the regulatory mechanisms of this area. FINDINGS We utilized high-throughput transcriptomic and epigenomic analysis to profile over 270,000 single-nucleus cells to create a cellular atlas of the basal ganglia, characterizing the cellular composition of 4 regions of basal ganglia in adult macaque brain, including the striatum, substantia nigra (SN), globus pallidum, and amygdala. We found a distinct epigenetic regulation on gene expression of neuronal and nonneuronal cells across regions in basal ganglia. We identified a cluster of SN-specific astrocytes associated with neurodegenerative diseases and further explored the conserved and primate-specific transcriptomics in SN cell types across human, macaque, and mouse. Finally, we integrated our epigenetic landscape of basal ganglia cells with human disease heritability and identified a regulatory module consisting of candidate cis-regulatory elements that are specific to medium spiny neurons and associated with schizophrenia. CONCLUSIONS In general, our macaque basal ganglia atlas provides valuable insights into the comprehensive transcriptome and epigenome of the most important and populous cell populations in the macaque basal ganglia. We have identified 49 cell types based on transcriptomic profiles and 47 cell types based on epigenomic profiles, some of which exhibit region specificity, and characterized the molecular relationships underlying these brain regions.
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Affiliation(s)
- Zihao Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310030, China
| | - Yunong Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310030, China
| | | | - Jing Yang
- BGI Research, Hangzhou 310030, China
| | | | | | - Liang Wu
- BGI Research, Shenzhen 518083, China
| | | | - Cheng Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310030, China
| | - Yunqi Huang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310030, China
| | - Zhiyong Zhu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310030, China
| | - Siyuan Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310030, China
| | - Fubaoqian Huang
- BGI Research, Hangzhou 310030, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Chunqing Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Shenzhen 518083, China
| | - Shiping Liu
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Longqi Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Hangzhou 310030, China
- BGI Research, Shenzhen 518083, China
| | - Ying Lei
- BGI Research, Shenzhen 518083, China
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10
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Vedunova M, Turubanova V, Vershinina O, Savyuk M, Efimova I, Mishchenko T, Raedt R, Vral A, Vanhove C, Korsakova D, Bachert C, Coppieters F, Agostinis P, Garg AD, Ivanchenko M, Krysko O, Krysko DV. DC vaccines loaded with glioma cells killed by photodynamic therapy induce Th17 anti-tumor immunity and provide a four-gene signature for glioma prognosis. Cell Death Dis 2022; 13:1062. [PMID: 36539408 PMCID: PMC9767932 DOI: 10.1038/s41419-022-05514-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Gliomas, the most frequent type of primary tumor of the central nervous system in adults, results in significant morbidity and mortality. Despite the development of novel, complex, multidisciplinary, and targeted therapies, glioma therapy has not progressed much over the last decades. Therefore, there is an urgent need to develop novel patient-adjusted immunotherapies that actively stimulate antitumor T cells, generate long-term memory, and result in significant clinical benefits. This work aimed to investigate the efficacy and molecular mechanism of dendritic cell (DC) vaccines loaded with glioma cells undergoing immunogenic cell death (ICD) induced by photosens-based photodynamic therapy (PS-PDT) and to identify reliable prognostic gene signatures for predicting the overall survival of patients. Analysis of the transcriptional program of the ICD-based DC vaccine led to the identification of robust induction of Th17 signature when used as a vaccine. These DCs demonstrate retinoic acid receptor-related orphan receptor-γt dependent efficacy in an orthotopic mouse model. Moreover, comparative analysis of the transcriptome program of the ICD-based DC vaccine with transcriptome data from the TCGA-LGG dataset identified a four-gene signature (CFH, GALNT3, SMC4, VAV3) associated with overall survival of glioma patients. This model was validated on overall survival of CGGA-LGG, TCGA-GBM, and CGGA-GBM datasets to determine whether it has a similar prognostic value. To that end, the sensitivity and specificity of the prognostic model for predicting overall survival were evaluated by calculating the area under the curve of the time-dependent receiver operating characteristic curve. The values of area under the curve for TCGA-LGG, CGGA-LGG, TCGA-GBM, and CGGA-GBM for predicting five-year survival rates were, respectively, 0.75, 0.73, 0.9, and 0.69. These data open attractive prospects for improving glioma therapy by employing ICD and PS-PDT-based DC vaccines to induce Th17 immunity and to use this prognostic model to predict the overall survival of glioma patients.
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Affiliation(s)
- Maria Vedunova
- grid.28171.3d0000 0001 0344 908XInstitute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Victoria Turubanova
- grid.28171.3d0000 0001 0344 908XInstitute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia ,grid.5342.00000 0001 2069 7798Cell Death Investigation and Therapy (CDIT) Laboratory, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Olga Vershinina
- grid.28171.3d0000 0001 0344 908XInstitute of Information Technology, Mathematics and Mechanics, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Maria Savyuk
- grid.28171.3d0000 0001 0344 908XInstitute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia ,grid.5342.00000 0001 2069 7798Cell Death Investigation and Therapy (CDIT) Laboratory, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Iuliia Efimova
- grid.5342.00000 0001 2069 7798Cell Death Investigation and Therapy (CDIT) Laboratory, Department of Human Structure and Repair, Ghent University, Ghent, Belgium ,grid.510942.bCancer Research Institute Ghent, Ghent, Belgium
| | - Tatiana Mishchenko
- grid.28171.3d0000 0001 0344 908XInstitute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Robrecht Raedt
- grid.5342.00000 0001 2069 77984Brain Team, Department of Head and Skin, Ghent University, Ghent, Belgium
| | - Anne Vral
- grid.5342.00000 0001 2069 7798Radiobiology Research Group, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Christian Vanhove
- grid.5342.00000 0001 2069 7798IBiTech-MEDISIP-Infinity Laboratory, Department of Electronics and Information Systems, Ghent University, Ghent, Belgium
| | - Daria Korsakova
- grid.28171.3d0000 0001 0344 908XInstitute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Claus Bachert
- grid.5342.00000 0001 2069 7798Upper Airways Research Laboratory, Department of Head and Skin, Ghent University, Ghent, Belgium
| | - Frauke Coppieters
- grid.5342.00000 0001 2069 7798Center for Medical Genetics Ghent (CMGG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Patrizia Agostinis
- grid.5596.f0000 0001 0668 7884Laboratory of Cell Death Research & Therapy, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium ,grid.511459.dVIB Center for Cancer Biology Research, Leuven, Belgium
| | - Abhishek D. Garg
- grid.5596.f0000 0001 0668 7884Laboratory of Cell Stress & Immunity (CSI), Department of Cellular & Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Mikhail Ivanchenko
- grid.28171.3d0000 0001 0344 908XInstitute of Information Technology, Mathematics and Mechanics, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Olga Krysko
- grid.5342.00000 0001 2069 7798Cell Death Investigation and Therapy (CDIT) Laboratory, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Dmitri V. Krysko
- grid.28171.3d0000 0001 0344 908XInstitute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia ,grid.5342.00000 0001 2069 7798Cell Death Investigation and Therapy (CDIT) Laboratory, Department of Human Structure and Repair, Ghent University, Ghent, Belgium ,grid.510942.bCancer Research Institute Ghent, Ghent, Belgium
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11
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Transcriptomic analysis reveals an association of FCGBP with Parkinson’s disease. NPJ Parkinsons Dis 2022; 8:157. [DOI: 10.1038/s41531-022-00415-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 10/19/2022] [Indexed: 11/13/2022] Open
Abstract
AbstractTranscriptomics in Parkinson’s disease (PD) offers new insights into the molecular mechanism of PD pathogenesis. Several pathways, such as inflammation and protein degradation, have been identified by differential gene expression analysis. Our aim was to identify gene expression differences underlying the disease etiology and the discovery of pre-symptomatic risk biomarkers for PD from a multicenter study in the context of the PROPAG-AGEING project. We performed RNA sequencing from 47 patients with de novo PD, 10 centenarians, and 65 healthy controls. Using identified differentially expressed genes, functional annotations were assigned using gene ontology to unveil significant enriched biological processes. The expression of 16 selected genes was validated using OpenArray® assays and samples from independent cohorts of 201 patients with advanced PD, 340 healthy siblings of PD patients, and 177 healthy controls. Differential gene expression analysis identified higher FCGBP expression in patients with de novo PD compared with healthy controls and compared with centenarians. Furthermore, FCGBP showed no differences in terms of population origin or aging process. The increased FCGBP expression was validated in patients with advanced PD and their siblings. Thus, we provided evidence for an upregulation of FCGBP mRNA levels not only in patients with PD but also in individuals at putative higher risk of PD, suggesting that it could be important in gut–brain PD interaction, mediating the connection between microbiota and intestinal inflammatory processes, as well as neuroinflammation and neurodegeneration.
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12
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Zhu Y, Owens SJ, Murphy CE, Ajulu K, Rothmond D, Purves-Tyson T, Middleton F, Webster MJ, Weickert CS. Inflammation-related transcripts define "high" and "low" subgroups of individuals with schizophrenia and bipolar disorder in the midbrain. Brain Behav Immun 2022; 105:149-159. [PMID: 35764269 DOI: 10.1016/j.bbi.2022.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/10/2022] [Accepted: 06/23/2022] [Indexed: 01/08/2023] Open
Abstract
Dopamine dysregulation in schizophrenia may be associated with midbrain inflammation. Previously, we found elevated levels of pro-inflammatory cytokine mRNAs in the post-mortem midbrain of people with schizophrenia (46%) but not from unaffected controls (0%) using a brain cohort from Sydney, Australia. Here, we measured cytokine mRNAs and proteins in the midbrain in the Stanley Medical Research Institute (SMRI) array cohort (N = 105). We tested if the proportions of individuals with schizophrenia and with high inflammation can be replicated, and if individuals with bipolar disorder with elevated midbrain cytokines can be identified. mRNA levels of 7 immune transcripts from post-mortem midbrain tissue were measured via RT-PCR and two-step recursive clustering analysis was performed using 4 immune transcripts to define "high and low" inflammatory subgroups. The clustering predictors used were identical to our earlier midbrain study, and included: IL1B, IL6, TNF, and SERPINA3 mRNA levels. 46% of schizophrenia cases (16/35 SCZ), 6% of controls (2/33 CTRL), and 29% of bipolar disorder cases (10/35 BPD) were identified as belonging to the high inflammation (HI) subgroups [χ2 (2) = 13.54, p < 0.001]. When comparing inflammatory subgroups, all four mRNAs were significantly increased in SCZ-HI and BPD-HI compared to low inflammation controls (CTRL-LI) (p < 0.05). Additionally, protein levels of IL-1β, IL-6, and IL-18 were elevated in SCZ-HI and BPD-HI compared to all other low inflammatory subgroups (all p < 0.05). Surprisingly, TNF-α protein levels were unchanged according to subgroups. In conclusion, we determined that almost half of the individuals with schizophrenia were defined as having high inflammation in the midbrain, replicating our previous findings. Further, we detected close to one-third of those with bipolar disorder to be classified as having high inflammation. Elevations in some pro-inflammatory cytokine mRNAs (IL-1β and IL-6) were also found at the protein level, whereas TNF mRNA and protein levels were not concordant.
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Affiliation(s)
- Yunting Zhu
- Department of Neuroscience & Physiology, Upstate Medical University, Syracuse, NY 13210, USA
| | - Samantha J Owens
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Randwick, NSW 2031, Australia
| | - Caitlin E Murphy
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Randwick, NSW 2031, Australia
| | - Kachikwulu Ajulu
- Department of Neuroscience & Physiology, Upstate Medical University, Syracuse, NY 13210, USA
| | - Debora Rothmond
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Randwick, NSW 2031, Australia
| | - Tertia Purves-Tyson
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Randwick, NSW 2031, Australia
| | - Frank Middleton
- Department of Neuroscience & Physiology, Upstate Medical University, Syracuse, NY 13210, USA
| | - Maree J Webster
- Laboratory of Brain Research, Stanley Medical Research Institute, 9800 Medical Center Drive, Rockville, MD, USA
| | - Cynthia Shannon Weickert
- Department of Neuroscience & Physiology, Upstate Medical University, Syracuse, NY 13210, USA; Schizophrenia Research Laboratory, Neuroscience Research Australia, Randwick, NSW 2031, Australia; School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia.
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13
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Hu Y, Shen Y, Wu X, Ba R, Xu H, Lu K, Shao Y, Sun C, Zhang Y, Miao F, Shen Y, Zhang J. Expression pattern of NLRC5 in the postnatal mouse brain. Acta Histochem 2022; 124:151939. [PMID: 35952483 DOI: 10.1016/j.acthis.2022.151939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 07/31/2022] [Accepted: 08/01/2022] [Indexed: 12/01/2022]
Abstract
Nucleotide oligomerization domain-like receptors (NLRs), belonging to a large family of pattern recognition receptors, participate in the host's first line of defense against invading pathogens. Caspase recruitment domain containing 5 (NLRC5), the largest member in the NLR family, is demonstrated to be involved in the innate immune response and inflammatory diseases far and wide. Recent studies report that NLRC5 is associated with some central nervous system (CNS) diseases. Besides, NLRC5 is a mastery regulator for the expression of MHC class I both in the immune system and the CNS, while MHC class I is expressed and exerts its function in the brain. Therefore, it is necessary to investigate the expression pattern of NLRC5 in the developing and adult CNS. In our study, postnatal brain sections of C57BL/6 J mice are analyzed for the expression of NLRC5 protein by immunofluorescence. In the postnatal stages of developing telencephalon, NLRC5 exhibits a spatial and temporal expression pattern. NLRC5 is time-specifically expressed in subfields of hippocampus and different layers of prefrontal cortex. Moreover, it is shown that NLRC5 is highly cell type specific. It can be expressed in large quantities by neurons and microglia, but rarely expressed by astrocytes. Taken together, our research is important for further understanding the biological characteristics of NLRC5 and its function in the CNS.
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Affiliation(s)
- Yue Hu
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing, China
| | - Yi Shen
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing, China
| | - Xiaojing Wu
- Department of Critical Care Medicine, Zhongda Hospital, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
| | - Ru Ba
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing, China
| | - Hongwei Xu
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing, China
| | - Keze Lu
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing, China
| | - Yong Shao
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing, China
| | - Chen Sun
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, China
| | - Ying Zhang
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, China
| | - Fengqin Miao
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, China
| | - Yuqing Shen
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, China; Department of Critical Care Medicine, Zhongda Hospital, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, China
| | - Jianqiong Zhang
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing, China; Jiangsu Key Laboratory of Molecular and Functional Imaging, Zhongda Hospital, Medical School, Southeast University, Nanjing, China
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14
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Prognostic and therapeutic prediction by screening signature combinations from transcriptome-methylome interactions in oral squamous cell carcinoma. Sci Rep 2022; 12:11400. [PMID: 35794182 PMCID: PMC9259703 DOI: 10.1038/s41598-022-15534-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/24/2022] [Indexed: 02/05/2023] Open
Abstract
DNA methylation pattern in oral squamous cell carcinoma (OSCC) remains poorly described. This study aimed to perform a genome-wide integrated analysis of the transcriptome and methylome and assess the efficacy of their prognostic signature model in patients with OSCC. We analyzed transcriptome and methylome data from 391 OSCC samples and 41 adjacent normal samples. A total of 8074 differentially expressed genes (DEGs) and 10,084 differentially expressed CpGs (DMCpGs) were identified. Then 241 DEGs with DMCpGs were identified. According to the prognostic analysis, the prognostic signature of methylation-related differentially expressed genes (mrDEGPS) was established. mrDEGPS consisted of seven prognostic methylation-related genes, including ESRRG, CCNA1, SLC20A1, COL6A6, FCGBP, CDKN2A, and ZNF43. mrDEGPS was a significant stratification factor of survival (P < 0.00001) irrespective of the clinical stage. The immune effector components, including B cells, CD4+ T cells, and CD8+ T cells, were decreased in the tumor environment of patients with high mrDEGPS. Immune checkpoint expressions, including CTLA-4, PD-1, LAG3, LGALS9, HAVCR2, and TIGHT, were comprehensively elevated (P < 0.001). The estimated half-maximal inhibitory concentration difference between low- and high-risk patients was inconsistent among chemotherapeutic drugs. In conclusion, the transcriptome–methylome interaction pattern in OSCC is complex. mrDEGPS can predict patient survival and responses to immunotherapy and chemotherapy and facilitate clinical decision-making in patients with OSCC.
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15
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Park SW, Seo MK, Webster MJ, Lee JG, Kim S. Differential expression of gene co-expression networks related to the mTOR signaling pathway in bipolar disorder. Transl Psychiatry 2022; 12:184. [PMID: 35508467 PMCID: PMC9067344 DOI: 10.1038/s41398-022-01944-8] [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: 12/07/2020] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/09/2022] Open
Abstract
Bipolar disorder (BPD) is a severe mental illness characterized by episodes of depression and mania. To investigate the molecular mechanisms underlying the pathophysiology of bipolar disorder, we performed transcriptome studies using RNA-seq data from the prefrontal cortex (PFC) of individuals with BPD and matched controls, as well as data from cell culture and animal model studies. We found 879 differentially expressed genes that were also replicated in an independent cohort of post-mortem samples. Genes involving the mechanistic target of rapamycine (mTOR) pathway were down-regulated, while genes interrelated with the mTOR pathway such as Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway were up-regulated. Gene co-expression network analyses identified a module related to the mTOR pathway that was up-regulated in BPD and also enriched for markers of endothelial cells. We also found a down-regulated co-expression module enriched for genes involved in mTOR signalling and in mTOR related pathways and enriched with neuronal markers. The mTOR related modules were also replicated in the independent cohort of samples. To investigate whether the expression of the modules related to mTOR signalling pathway could be differentially regulated in different cell types we performed comparative network analyses in experimental models. We found both up-regulated modules in the PFC significantly overlapped with an up-regulated module in the brain endothelial cells from mice treated with lipopolysaccharides (LPS) and mTOR related pathways such as JAK-STAT, PI3K-Akt and ribosome were enriched in the common genes. In addition, the down-regulated module in the PFC significantly overlapped with a down-regulated module from neurons treated with the mTOR inhibitor, Torin1 and mTOR signalling, autophagy, and synaptic vesicle cycles were significantly enriched in the common genes. These results suggest that co-expression networks related to mTOR signalling pathways may be up- or down-regulated in different cell types in the PFC of BPD. These results provide novel insights into the molecular mechanisms underlying the pathophysiology of BPD.
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Affiliation(s)
- Sung Woo Park
- grid.411612.10000 0004 0470 5112Department of Convergence Biomedical Science, College of Medicine, Inje University, 75 Bokji-ro, Busnajin-gu, Busan, 47392 Republic of Korea ,grid.411612.10000 0004 0470 5112Paik Institute for Clinical Research, Inje University, 75 Bokji-ro, Busnajin-gu, Busan, 47392 Republic of Korea
| | - Mi Kyoung Seo
- grid.411612.10000 0004 0470 5112Paik Institute for Clinical Research, Inje University, 75 Bokji-ro, Busnajin-gu, Busan, 47392 Republic of Korea
| | - Maree J. Webster
- grid.453353.70000 0004 0473 2858Stanley Brain Research Laboratory, Stanley Medical Research Institute, 9800 Medical Center Drive, Rockville, MD 20850 USA
| | - Jung Goo Lee
- Paik Institute for Clinical Research, Inje University, 75 Bokji-ro, Busnajin-gu, Busan, 47392, Republic of Korea. .,Department of Psychiatry, College of Medicine, Haeundae Paik Hospital, Inje University, 875 Haeun-daero, Haeundae-gu, Busan, 47227, Republic of Korea.
| | - Sanghyeon Kim
- Stanley Brain Research Laboratory, Stanley Medical Research Institute, 9800 Medical Center Drive, Rockville, MD, 20850, USA.
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16
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Zandi PP, Jaffe AE, Goes FS, Burke EE, Collado-Torres L, Huuki-Myers L, Seyedian A, Lin Y, Seifuddin F, Pirooznia M, Ross CA, Kleinman JE, Weinberger DR, Hyde TM. Amygdala and anterior cingulate transcriptomes from individuals with bipolar disorder reveal downregulated neuroimmune and synaptic pathways. Nat Neurosci 2022; 25:381-389. [PMID: 35260864 PMCID: PMC8915427 DOI: 10.1038/s41593-022-01024-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 01/26/2022] [Indexed: 12/12/2022]
Abstract
Recent genetic studies have identified variants associated with bipolar disorder (BD), but it remains unclear how brain gene expression is altered in BD and how genetic risk for BD may contribute to these alterations. Here, we obtained transcriptomes from subgenual anterior cingulate cortex and amygdala samples from post-mortem brains of individuals with BD and neurotypical controls, including 511 total samples from 295 unique donors. We examined differential gene expression between cases and controls and the transcriptional effects of BD-associated genetic variants. We found two coexpressed modules that were associated with transcriptional changes in BD: one enriched for immune and inflammatory genes and the other with genes related to the postsynaptic membrane. Over 50% of BD genome-wide significant loci contained significant expression quantitative trait loci (QTL) (eQTL), and these data converged on several individual genes, including SCN2A and GRIN2A. Thus, these data implicate specific genes and pathways that may contribute to the pathology of BP.
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Affiliation(s)
- Peter P Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA. .,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Andrew E Jaffe
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,The Lieber Institute for Brain Development, Baltimore, MD, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Emily E Burke
- The Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Leonardo Collado-Torres
- The Lieber Institute for Brain Development, Baltimore, MD, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | | | - Arta Seyedian
- The Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Yian Lin
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Fayaz Seifuddin
- The National Heart, Lung and Blood Institute, the National Institute of Health, Bethesda, MD, USA
| | - Mehdi Pirooznia
- The National Heart, Lung and Blood Institute, the National Institute of Health, Bethesda, MD, USA
| | - Christopher A Ross
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Joel E Kleinman
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.,The Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Daniel R Weinberger
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.,The Lieber Institute for Brain Development, Baltimore, MD, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thomas M Hyde
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA. .,The Lieber Institute for Brain Development, Baltimore, MD, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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17
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Sadeghi I, Gispert JD, Palumbo E, Muñoz-Aguirre M, Wucher V, D'Argenio V, Santpere G, Navarro A, Guigo R, Vilor-Tejedor N. Brain transcriptomic profiling reveals common alterations across neurodegenerative and psychiatric disorders. Comput Struct Biotechnol J 2022; 20:4549-4561. [PMID: 36090817 PMCID: PMC9428860 DOI: 10.1016/j.csbj.2022.08.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
Neurodegenerative and neuropsychiatric disorders (ND-NPs) are multifactorial, polygenic and complex behavioral phenotypes caused by brain abnormalities. Large-scale collaborative efforts have tried to identify the genetic architecture of these conditions. However, the specific and shared underlying molecular pathobiology of brain illnesses is not clear. Here, we examine transcriptome-wide characterization of eight conditions, using a total of 2,633 post-mortem brain samples from patients with Alzheimer’s disease (AD), Parkinson’s disease (PD), Progressive Supranuclear Palsy (PSP), Pathological Aging (PA), Autism Spectrum Disorder (ASD), Schizophrenia (Scz), Major Depressive Disorder (MDD), and Bipolar Disorder (BP)–in comparison with 2,078 brain samples from matched control subjects. Similar transcriptome alterations were observed between NDs and NPs with the top correlations obtained between Scz-BP, ASD-PD, AD-PD, and Scz-ASD. Region-specific comparisons also revealed shared transcriptome alterations in frontal and temporal lobes across NPs and NDs. Co-expression network analysis identified coordinated dysregulations of cell-type-specific modules across NDs and NPs. This study provides a transcriptomic framework to understand the molecular alterations of NPs and NDs through their shared- and specific gene expression in the brain.
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18
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Batchu S. Transcriptomic Deconvolution of Dorsal Striata Reveals Increased Monocyte Fractions in Bipolar Disorder. Complex Psychiatry 2021; 6:83-88. [PMID: 34883498 DOI: 10.1159/000511887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/30/2020] [Indexed: 12/21/2022] Open
Abstract
Introduction Accumulating evidence suggests a relationship between the immune system, neuroinflammation, and mood disorders such as bipolar disorder (BD). However, the immunological landscape of critical brain structures implicated with BD, such as the dorsal striatum, has yet to be characterized. This study sought to investigate the immunological composition of dorsal striata in patients with BD. Methods CIBERSORTx, an established RNA deconvolution algorithm, was applied on RNA-sequencing data developed from dorsal striata of 18 BD patients and 17 controls. A validated gene signature matrix for 22 human hematopoietic cell subsets was used to infer the relative proportions of immune cells that were present in the original brain tissue. Results Deconvolution of the bulk gene expression data showed that dorsal striata from BD subjects had a significantly greater relative abundance of monocytes compared to control samples. Conclusion Monocytes may play a role in the pathogenesis of BD in dorsal striata. Further studies are warranted to confirm the computational results presented herein.
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Affiliation(s)
- Sai Batchu
- Cooper Medical School of Rowan University, Camden, New Jersey, USA
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19
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Zhang L, Jiao C, Liu L, Wang A, Tang L, Ren Y, Huang P, Xu J, Mao D, Liu L. NLRC5: A Potential Target for Central Nervous System Disorders. Front Immunol 2021; 12:704989. [PMID: 34220868 PMCID: PMC8250149 DOI: 10.3389/fimmu.2021.704989] [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: 05/04/2021] [Accepted: 06/07/2021] [Indexed: 12/22/2022] Open
Abstract
Nucleotide oligomerization domain-like receptors (NLRs), a class of pattern recognition receptors, participate in the host’s first line of defense against invading pathogenic microorganisms. NLR family caspase recruitment domain containing 5 (NLRC5) is the largest member of the NLR family and has been shown to play an important role in inflammatory processes, angiogenesis, immunity, and apoptosis by regulating the nuclear factor-κB, type I interferon, and inflammasome signaling pathways, as well as the expression of major histocompatibility complex I genes. Recent studies have found that NLRC5 is also associated with neuronal development and central nervous system (CNS) diseases, such as CNS infection, cerebral ischemia/reperfusion injury, glioma, multiple sclerosis, and epilepsy. This review summarizes the research progress in the structure, expression, and biological characteristics of NLRC5 and its relationship with the CNS.
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Affiliation(s)
- Lu Zhang
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Children's Brain Development and Brain Injury Research Office, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Cui Jiao
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Children's Brain Development and Brain Injury Research Office, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Lingjuan Liu
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Children's Brain Development and Brain Injury Research Office, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Aiping Wang
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Children's Brain Development and Brain Injury Research Office, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Li Tang
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Children's Brain Development and Brain Injury Research Office, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yi Ren
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Children's Brain Development and Brain Injury Research Office, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Peng Huang
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Children's Brain Development and Brain Injury Research Office, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jie Xu
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Children's Brain Development and Brain Injury Research Office, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Dingan Mao
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Children's Brain Development and Brain Injury Research Office, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Liqun Liu
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Children's Brain Development and Brain Injury Research Office, The Second Xiangya Hospital, Central South University, Changsha, China
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20
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Shin D, Rhee SJ, Lee J, Yeo I, Do M, Joo EJ, Jung HY, Roh S, Lee SH, Kim H, Bang M, Lee KY, Kwon JS, Ha K, Ahn YM, Kim Y. Quantitative Proteomic Approach for Discriminating Major Depressive Disorder and Bipolar Disorder by Multiple Reaction Monitoring-Mass Spectrometry. J Proteome Res 2021; 20:3188-3203. [PMID: 33960196 DOI: 10.1021/acs.jproteome.1c00058] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Because major depressive disorder (MDD) and bipolar disorder (BD) manifest with similar symptoms, misdiagnosis is a persistent issue, necessitating their differentiation through objective methods. This study was aimed to differentiate between these disorders using a targeted proteomic approach. Multiple reaction monitoring-mass spectrometry (MRM-MS) analysis was performed to quantify protein targets regarding the two disorders in plasma samples of 270 individuals (90 MDD, 90 BD, and 90 healthy controls (HCs)). In the training set (72 MDD and 72 BD), a generalizable model comprising nine proteins was developed. The model was evaluated in the test set (18 MDD and 18 BD). The model demonstrated a good performance (area under the curve (AUC) >0.8) in discriminating MDD from BD in the training (AUC = 0.84) and test sets (AUC = 0.81) and in distinguishing MDD from BD without current hypomanic/manic/mixed symptoms (90 MDD and 75 BD) (AUC = 0.83). Subsequently, the model demonstrated excellent performance for drug-free MDD versus BD (11 MDD and 10 BD) (AUC = 0.96) and good performance for MDD versus HC (AUC = 0.87) and BD versus HC (AUC = 0.86). Furthermore, the nine proteins were associated with neuro, oxidative/nitrosative stress, and immunity/inflammation-related biological functions. This proof-of-concept study introduces a potential model for distinguishing between the two disorders.
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Affiliation(s)
| | - Sang Jin Rhee
- Department of Psychiatry, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.,Department of Neuropsychiatry, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | | | | | | | - Eun-Jeong Joo
- Department of Neuropsychiatry, School of Medicine, Eulji University, Daejeon 34824, Republic of Korea.,Department of Psychiatry, Nowon Eulji Medical Center, Eulji University, Seoul 01830, Republic of Korea
| | - Hee Yeon Jung
- Department of Psychiatry, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.,Department of Psychiatry, SMG-SNU Boramae Medical Center, Seoul 07061, Republic of Korea.,Institute of Human Behavioral Medicine, Seoul National University Medical Research Center, 101 Daehakro, Seoul 30380, Republic of Korea
| | - Sungwon Roh
- Department of Psychiatry, Hanyang University Hospital, Seoul 04763, Republic of Korea.,Department of Psychiatry, Hanyang University College of Medicine, Seoul 04763, Republic of Korea
| | - Sang-Hyuk Lee
- Department of Psychiatry, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam 13496, Republic of Korea
| | - Hyeyoung Kim
- Department of Psychiatry, Inha University Hospital, Incheon 22332, Republic of Korea
| | - Minji Bang
- Department of Psychiatry, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam 13496, Republic of Korea
| | - Kyu Young Lee
- Department of Neuropsychiatry, School of Medicine, Eulji University, Daejeon 34824, Republic of Korea.,Department of Psychiatry, Nowon Eulji Medical Center, Eulji University, Seoul 01830, Republic of Korea
| | - Jun Soo Kwon
- Department of Psychiatry, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.,Department of Neuropsychiatry, Seoul National University Hospital, Seoul 03080, Republic of Korea.,Institute of Human Behavioral Medicine, Seoul National University Medical Research Center, 101 Daehakro, Seoul 30380, Republic of Korea
| | - Kyooseob Ha
- Department of Psychiatry, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.,Department of Neuropsychiatry, Seoul National University Hospital, Seoul 03080, Republic of Korea.,Institute of Human Behavioral Medicine, Seoul National University Medical Research Center, 101 Daehakro, Seoul 30380, Republic of Korea
| | - Yong Min Ahn
- Department of Psychiatry, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.,Department of Neuropsychiatry, Seoul National University Hospital, Seoul 03080, Republic of Korea.,Institute of Human Behavioral Medicine, Seoul National University Medical Research Center, 101 Daehakro, Seoul 30380, Republic of Korea
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21
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Arasappan D, Eickhoff SB, Nemeroff CB, Hofmann HA, Jabbi M. Transcription Factor Motifs Associated with Anterior Insula Gene Expression Underlying Mood Disorder Phenotypes. Mol Neurobiol 2021; 58:1978-1989. [PMID: 33411239 DOI: 10.1007/s12035-020-02195-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/30/2020] [Indexed: 10/22/2022]
Abstract
Mood disorders represent a major cause of morbidity and mortality worldwide but the brain-related molecular pathophysiology in mood disorders remains largely undefined. Because the anterior insula is reduced in volume in patients with mood disorders, RNA was extracted from the anterior insula postmortem anterior insula of mood disorder samples and compared with unaffected controls for RNA-sequencing identification of differentially expressed genes (DEGs) in (a) bipolar disorder (BD; n = 37) versus (vs.) controls (n = 33), and (b) major depressive disorder (MDD n = 30) vs. controls, and (c) low vs. high axis I comorbidity (a measure of cumulative psychiatric disease burden). Given the regulatory role of transcription factors (TFs) in gene expression via specific-DNA-binding domains (motifs), we used JASPAR TF binding database to identify TF-motifs. We found that DEGs in BD vs. controls, MDD vs. controls, and high vs. low axis I comorbidity were associated with TF-motifs that are known to regulate expression of toll-like receptor genes, cellular homeostatic-control genes, and genes involved in embryonic, cellular/organ, and brain development. Robust imaging-guided transcriptomics by using meta-analytic imaging results to guide independent postmortem dissection for RNA-sequencing was applied by targeting the gray matter volume reduction in the anterior insula in mood disorders, to guide independent postmortem identification of TF motifs regulating DEG. Our findings of TF-motifs that regulate the expression of immune, cellular homeostatic-control, and developmental genes provide novel information about the hierarchical relationship between gene regulatory networks, the TFs that control them, and proximate underlying neuroanatomical phenotypes in mood disorders.
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Affiliation(s)
- Dhivya Arasappan
- Center for Biomedical Research Support, University of Texas at Austin, Austin, TX, USA
| | - Simon B Eickhoff
- Institute of Systems Neuroscience, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Neuroscience and Medicine (INM-7), Research Centre Jülich, Jülich, Germany
| | - Charles B Nemeroff
- Department of Psychiatry, Dell Medical School, University of Texas at Austin, Austin, TX, USA
- The Mulva Clinic for Neurosciences, Dell Medical School, University of Texas at Austin, Austin, TX, USA
- Institute of Early Life Adversity Research, Austin, TX, USA
| | - Hans A Hofmann
- Institute for Neuroscience, University of Texas at Austin, Austin, TX, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Mbemba Jabbi
- Department of Psychiatry, Dell Medical School, University of Texas at Austin, Austin, TX, USA.
- The Mulva Clinic for Neurosciences, Dell Medical School, University of Texas at Austin, Austin, TX, USA.
- Institute for Neuroscience, University of Texas at Austin, Austin, TX, USA.
- Department of Psychology, University of Texas at Austin, Austin, TX, USA.
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22
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Pu X, Li J, Ma X, Yang S, Wang L. The functional polymorphisms linked with interleukin-1β gene expression are associated with bipolar disorder. Psychiatr Genet 2021; 31:72-78. [PMID: 33707400 DOI: 10.1097/ypg.0000000000000272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Bipolar disorder (BD) is a severe psychiatric illness attributable to multifactorial risk components (e.g. environmental stimuli, neuroinflammation, etc.), and genetic variations affecting these risk components are considered pivotal predisposing factors. The interleukin-1β (IL-1β) gene and its protein product have been repeatedly highlighted in the pathogenesis of BD. As functional polymorphisms and haplotypes linked with IL-1β mRNA expression have been reported, whether they are correlated with the risk of developing BD remains to be tested. METHODS To examine whether variations in the IL-1β gene locus confer genetic risk of BD, we recruited 930 BD patients and 912 healthy controls for the current study. All subjects were Han Chinese, and were age- and gender-matched. We tested seven functional single nucleotide polymorphisms (SNPs) spanning the IL-1β gene and one haplotype composed of three SNPs for their associations with risk of BD. RESULTS We found that the functional SNPs in the promoter region of IL-1β gene were significantly associated with risk of BD. The haplotype analyses further supported the involvement of IL-1β promoter SNPs in BD. The BD risk SNPs in our study have been previously reported to predict higher IL-1β levels in the brain and peripheral blood, which is consistent with the clinical observation of elevated IL-1β levels in the lymphocytes or peripheral blood of patients with BD compared with healthy subjects. CONCLUSION Our results support the contention that IL-1β is likely a risk gene for BD, and further investigations on this gene may promote our understanding and clinical management of this illness.
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Affiliation(s)
- Xingfu Pu
- The Second People's Hospital of Yuxi City, Yuxi, Yunnan, China
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23
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Afridi R, Seol S, Kang HJ, Suk K. Brain-immune interactions in neuropsychiatric disorders: Lessons from transcriptome studies for molecular targeting. Biochem Pharmacol 2021; 188:114532. [PMID: 33773976 DOI: 10.1016/j.bcp.2021.114532] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022]
Abstract
Understanding the pathophysiological mechanisms of neuropsychiatric disorders has been a challenging quest for neurobiologists. Recent years have witnessed enormous technological advances in the field of neuroimmunology, blurring boundaries between the central nervous system and the periphery. Consequently, the discipline has expanded to cover interactions between the nervous and immune systems in health and diseases. The complex interplay between the peripheral and central immune pathways in neuropsychiatric disorders has recently been documented in various studies, but the genetic determinants remain elusive. Recent transcriptome studies have identified dysregulated genes involved in peripheral immune cell activation, blood-brain barrier integrity, glial cell activation, and synaptic plasticity in major depressive disorder, bipolar disorder, autism spectrum disorder, and schizophrenia. Herein, the key transcriptomic techniques applied in investigating differentially expressed genes and pathways responsible for altered brain-immune interactions in neuropsychiatric disorders are discussed. The application of transcriptomics that can aid in identifying molecular targets in various neuropsychiatric disorders is highlighted.
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Affiliation(s)
- Ruqayya Afridi
- Department of Pharmacology, Brain Science & Engineering Institute, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Sihwan Seol
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hyo Jung Kang
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea.
| | - Kyoungho Suk
- Department of Pharmacology, Brain Science & Engineering Institute, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
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24
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Abstract
The human striatum can be subdivided into the caudate, putamen, and nucleus accumbens (NAc). Each of these structures have some overlapping and some distinct functions related to motor control, cognitive processing, motivation, and reward. Previously, we used a "time-of-death" approach to identify diurnal rhythms in RNA transcripts in human cortical regions. Here, we identify molecular rhythms across the three striatal subregions collected from postmortem human brain tissue in subjects without psychiatric or neurological disorders. Core circadian clock genes are rhythmic across all three regions and show strong phase concordance across regions. However, the putamen contains a much larger number of significantly rhythmic transcripts than the other two regions. Moreover, there are many differences in pathways that are rhythmic across regions. Strikingly, the top rhythmic transcripts in NAc (but not the other regions) are predominantly small nucleolar RNAs and long noncoding RNAs, suggesting that a completely different mechanism might be used for the regulation of diurnal rhythms in translation and/or RNA processing in the NAc versus the other regions. Further, although the NAc and putamen are generally in phase with regard to timing of expression rhythms, the NAc and caudate, and caudate and putamen, have several clusters of discordant rhythmic transcripts, suggesting a temporal wave of specific cellular processes across the striatum. Taken together, these studies reveal distinct transcriptome rhythms across the human striatum and are an important step in helping to understand the normal function of diurnal rhythms in these regions and how disruption could lead to pathology.
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25
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Tseng HH, Chang HH, Wei SY, Lu TH, Hsieh YT, Yang YK, Chen PS. Peripheral inflammation is associated with dysfunctional corticostriatal circuitry and executive dysfunction in bipolar disorder patients. Brain Behav Immun 2021; 91:695-702. [PMID: 32950621 DOI: 10.1016/j.bbi.2020.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/08/2020] [Accepted: 09/12/2020] [Indexed: 01/20/2023] Open
Abstract
Bipolar disorder (BD) has been linked to abnormal frontal and striatal function, and elevated inflammatory responses. However, the impact of peripheral inflammation on the corticostriatal functional connectivity (FC) remains obscure in BD. The current study aimed to explore the association between peripheral inflammation and corticostriatal connectivity in euthymic BD. We recruited 25 euthymic BD patients and 43 healthy controls (HCs) from the community. Resting state functional images were obtained using 3T magnetic resonance imaging (fMRI), and striatal seed-based whole-brain functional connectivity analyses were performed, with the fasting plasma high-sensitivity C-reactive protein (hs-CRP) level entered as a regressor of interest. The participants also completed the Wisconsin Card-Sorting Test (WCST) and the Continuous Performance Test (CPT). The euthymic BD group had a similar hs-CRP level to the HC group, but a significantly poorer cognitive performance. Compared with the HC group, a higher connectivity between the right dorsal caudal putamen (dcP) and the ventral lateral prefrontal cortex (vlPFC) in the BD group was significantly correlated with a higher hs-CRP level. Stronger dcP-vlPFC connectivity was correlated with a lower CPT unmasked d' in the BD group. BD patients might be particularly sensitive to the effects of inflammation on corticostriatal connectivity. The potentially greater sensitivity of BD patients to peripheral inflammation may differentially modulate the cognitive and reward related corticostriatal circuitry, which may contribute to the pathophysiology of cognitive-affective dysregulation in the euthymic state. Anti-inflammatory or other circuit-specific treatment is warranted for individualized treatment in BD.
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Affiliation(s)
- Huai-Hsuan Tseng
- Department of Psychiatry, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Institute of Behavioral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hui Hua Chang
- Institute of Clinical Pharmacy and Pharmaceutical Sciences, National Cheng Kung University, Tainan, Taiwan; School of Pharmacy, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Pharmacy, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Pharmacy, National Cheng Kung University Hospital, Dou-Liou Branch, Yunlin, Taiwan
| | - Shyh-Yuh Wei
- Department of Psychiatry, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tsung-Hua Lu
- Department of Psychiatry, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Ting Hsieh
- Department of Psychiatry, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yen Kuang Yang
- Department of Psychiatry, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Institute of Behavioral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Psychiatry, Tainan Hospital, Ministry of Health and Welfare, Tainan, Taiwan
| | - Po See Chen
- Department of Psychiatry, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Institute of Behavioral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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26
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Hernandez LM, Kim M, Hoftman GD, Haney JR, de la Torre-Ubieta L, Pasaniuc B, Gandal MJ. Transcriptomic Insight Into the Polygenic Mechanisms Underlying Psychiatric Disorders. Biol Psychiatry 2021; 89:54-64. [PMID: 32792264 PMCID: PMC7718368 DOI: 10.1016/j.biopsych.2020.06.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/15/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022]
Abstract
Over the past decade, large-scale genetic studies have successfully identified hundreds of genetic variants robustly associated with risk for psychiatric disorders. However, mechanistic insight and clinical translation continue to lag the pace of risk variant identification, hindered by the sheer number of targets and their predominant noncoding localization, as well as pervasive pleiotropy and incomplete penetrance. Successful next steps require identification of "causal" genetic variants and their proximal biological consequences; placing variants within biologically defined functional contexts, reflecting specific molecular pathways, cell types, circuits, and developmental windows; and characterizing the downstream, convergent neurobiological impact of polygenicity within an individual. Here, we discuss opportunities and challenges of high-throughput transcriptomic profiling in the human brain, and how transcriptomic approaches can help pinpoint mechanisms underlying genetic risk for psychiatric disorders at a scale necessary to tackle daunting levels of polygenicity. These include transcriptome-wide association studies for risk gene prioritization through integration of genome-wide association studies with expression quantitative trait loci. We outline transcriptomic results that inform our understanding of the brain-level molecular pathology of psychiatric disorders, including autism spectrum disorder, bipolar disorder, major depressive disorder, and schizophrenia. Finally, we discuss systems-level approaches for integration of distinct genetic, genomic, and phenotypic levels, including combining spatially resolved gene expression and human neuroimaging maps. Results highlight the importance of understanding gene expression (dys)regulation across human brain development as a major contributor to psychiatric disease pathogenesis, from common variants acting as expression quantitative trait loci to rare variants enriched for gene expression regulatory pathways.
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Affiliation(s)
- Leanna M Hernandez
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Minsoo Kim
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Gil D Hoftman
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Jillian R Haney
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Luis de la Torre-Ubieta
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Bogdan Pasaniuc
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Michael J Gandal
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California.
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27
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Krebs CE, Ori APS, Vreeker A, Wu T, Cantor RM, Boks MPM, Kahn RS, Olde Loohuis LM, Ophoff RA. Whole blood transcriptome analysis in bipolar disorder reveals strong lithium effect. Psychol Med 2020; 50:2575-2586. [PMID: 31589133 DOI: 10.1017/s0033291719002745] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND Bipolar disorder (BD) is a highly heritable mood disorder with complex genetic architecture and poorly understood etiology. Previous transcriptomic BD studies have had inconsistent findings due to issues such as small sample sizes and difficulty in adequately accounting for confounders like medication use. METHODS We performed a differential expression analysis in a well-characterized BD case-control sample (Nsubjects = 480) by RNA sequencing of whole blood. We further performed co-expression network analysis, functional enrichment, and cell type decomposition, and integrated differentially expressed genes with genetic risk. RESULTS While we observed widespread differential gene expression patterns between affected and unaffected individuals, these effects were largely linked to lithium treatment at the time of blood draw (FDR < 0.05, Ngenes = 976) rather than BD diagnosis itself (FDR < 0.05, Ngenes = 6). These lithium-associated genes were enriched for cell signaling and immune response functional annotations, among others, and were associated with neutrophil cell-type proportions, which were elevated in lithium users. Neither genes with altered expression in cases nor in lithium users were enriched for BD, schizophrenia, and depression genetic risk based on information from genome-wide association studies, nor was gene expression associated with polygenic risk scores for BD. CONCLUSIONS These findings suggest that BD is associated with minimal changes in whole blood gene expression independent of medication use but emphasize the importance of accounting for medication use and cell type heterogeneity in psychiatric transcriptomic studies. The results of this study add to mounting evidence of lithium's cell signaling and immune-related mechanisms.
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Affiliation(s)
- Catharine E Krebs
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University California Los Angeles, Los Angeles, CA, USA
| | - Anil P S Ori
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, CA, USA
| | - Annabel Vreeker
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, CA, USA
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Timothy Wu
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, CA, USA
| | - Rita M Cantor
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University California Los Angeles, Los Angeles, CA, USA
| | - Marco P M Boks
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, Netherlands
| | - Rene S Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Loes M Olde Loohuis
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, CA, USA
| | - Roel A Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University California Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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28
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Qi X, Wu C, Du Y, Cheng S, Wen Y, Ma M, Liang C, Liu L, Cheng B, Zhang L, Li P, Zhang F. Comparing GWAS and Brain Structure-Specific Gene Expression Profiles Identifies Psychiatric Disorder-Related Brain Structures at Different Developmental Stages. Neurosci Bull 2020; 36:1046-1050. [PMID: 32474855 DOI: 10.1007/s12264-020-00521-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 03/14/2020] [Indexed: 11/27/2022] Open
Affiliation(s)
- Xin Qi
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Cuiyan Wu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yanan Du
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Mei Ma
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Chujun Liang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Lu Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Ping Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China.
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29
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Hess JL, Tylee DS, Barve R, de Jong S, Ophoff RA, Kumarasinghe N, Tooney P, Schall U, Gardiner E, Beveridge NJ, Scott RJ, Yasawardene S, Perera A, Mendis J, Carr V, Kelly B, Cairns M, Tsuang MT, Glatt SJ. Transcriptomic abnormalities in peripheral blood in bipolar disorder, and discrimination of the major psychoses. Schizophr Res 2020; 217:124-135. [PMID: 31391148 PMCID: PMC6997041 DOI: 10.1016/j.schres.2019.07.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 07/20/2019] [Accepted: 07/23/2019] [Indexed: 02/07/2023]
Abstract
We performed a transcriptome-wide meta-analysis and gene co-expression network analysis to identify genes and gene networks dysregulated in the peripheral blood of bipolar disorder (BD) cases relative to unaffected comparison subjects, and determined the specificity of the transcriptomic signatures of BD and schizophrenia (SZ). Nineteen genes and 4 gene modules were significantly differentially expressed in BD cases. Thirteen gene modules were shown to be differentially expressed in a combined case-group of BD and SZ subjects called "major psychosis", including genes biologically linked to apoptosis, reactive oxygen, chromatin remodeling, and immune signaling. No modules were differentially expressed between BD and SZ cases. Machine-learning classifiers trained to separate diagnostic classes based solely on gene expression profiles could distinguish BD cases from unaffected comparison subjects with an area under the curve (AUC) of 0.724, as well as BD cases from SZ cases with AUC = 0.677 in withheld test samples. We introduced a novel and straightforward method called "polytranscript risk scoring" that could distinguish BD cases from unaffected subjects (AUC = 0.672) and SZ cases (AUC = 0.607) significantly better than expected by chance. Taken together, our results highlighted gene expression alterations common to BD and SZ that involve biological processes of inflammation, oxidative stress, apoptosis, and chromatin regulation, and highlight disorder-specific changes in gene expression that discriminate the major psychoses.
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Affiliation(s)
- Jonathan L. Hess
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Daniel S. Tylee
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Rahul Barve
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Simone de Jong
- MRC Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, UK
| | - Roel A. Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Behavior, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California, U.S.A.,Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nishantha Kumarasinghe
- School of Medicine & Public Health, The University of Newcastle, Callaghan, Newcastle, Australia.,Department of Anatomy, Faculty of Medical Sciences, University of Sri Jayawardenepura, Nugegoda, Sri Lanka,Faculty of Medicine, Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
| | - Paul Tooney
- School of Biomedical Sciences & Pharmacy, Faculty of Health, The University of Newcastle, New South Wales, Australia,Hunter Medical Research Institute, Newcastle, Australia
| | - Ulrich Schall
- School of Medicine & Public Health, The University of Newcastle, Callaghan, Newcastle, Australia.,Priority Centre for Brain & Mental Health Research, The University of Newcastle, Callaghan, Newcastle, Australia
| | - Erin Gardiner
- School of Biomedical Sciences & Pharmacy, Faculty of Health, The University of Newcastle, New South Wales, Australia,Priority Centre for Brain & Mental Health Research, The University of Newcastle, Callaghan, Newcastle, Australia
| | - Natalie Jane Beveridge
- School of Medicine & Public Health, The University of Newcastle, Callaghan, Newcastle, Australia.,Hunter Medical Research Institute, Newcastle, Australia,Priority Centre for Brain & Mental Health Research, The University of Newcastle, Callaghan, Newcastle, Australia
| | - Rodney J. Scott
- School of Biomedical Sciences & Pharmacy, Faculty of Health, The University of Newcastle, New South Wales, Australia,Hunter Medical Research Institute, Newcastle, Australia
| | - Surangi Yasawardene
- Department of Anatomy, Faculty of Medical Sciences, University of Sri Jayawardenepura, Nugegoda, Sri Lanka
| | - Antionette Perera
- Department of Anatomy, Faculty of Medical Sciences, University of Sri Jayawardenepura, Nugegoda, Sri Lanka
| | - Jayan Mendis
- Department of Anatomy, Faculty of Medical Sciences, University of Sri Jayawardenepura, Nugegoda, Sri Lanka
| | - Vaughan Carr
- School of Psychiatry, University of New South Wales, Kensington, New South Wales, Australia
| | - Brian Kelly
- School of Medicine & Public Health, The University of Newcastle, Callaghan, Newcastle, Australia.,Hunter Medical Research Institute, Newcastle, Australia,Priority Centre for Brain & Mental Health Research, The University of Newcastle, Callaghan, Newcastle, Australia
| | - Murray Cairns
- School of Biomedical Sciences & Pharmacy, Faculty of Health, The University of Newcastle, New South Wales, Australia,Hunter Medical Research Institute, Newcastle, Australia,Priority Centre for Brain & Mental Health Research, The University of Newcastle, Callaghan, Newcastle, Australia
| | | | - Ming T. Tsuang
- Center for Behavioral Genomics, Department of Psychiatry, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA; Harvard Institute of Psychiatric Epidemiology and Genetics, Boston, USA
| | - Stephen J. Glatt
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A.,Please address correspondence to: Dr. Stephen J. Glatt, 3710 Neuroscience Research Building, Institute for Human Performance, 505 Irving Avenue, Syracuse, NY 13202, , Phone: 1 (315) 464-7742
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Gordovez FJA, McMahon FJ. The genetics of bipolar disorder. Mol Psychiatry 2020; 25:544-559. [PMID: 31907381 DOI: 10.1038/s41380-019-0634-7] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 11/22/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022]
Abstract
Bipolar disorder (BD) is one of the most heritable mental illnesses, but the elucidation of its genetic basis has proven to be a very challenging endeavor. Genome-Wide Association Studies (GWAS) have transformed our understanding of BD, providing the first reproducible evidence of specific genetic markers and a highly polygenic architecture that overlaps with that of schizophrenia, major depression, and other disorders. Individual GWAS markers appear to confer little risk, but common variants together account for about 25% of the heritability of BD. A few higher-risk associations have also been identified, such as a rare copy number variant on chromosome 16p11.2. Large scale next-generation sequencing studies are actively searching for other alleles that confer substantial risk. As our understanding of the genetics of BD improves, there is growing optimism that some clear biological pathways will emerge, providing a basis for future studies aimed at molecular diagnosis and novel therapeutics.
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Affiliation(s)
- Francis James A Gordovez
- Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Department of Health and Human Services, National Institutes of Health, Bethesda, MD, USA.,College of Medicine, University of the Philippines Manila, 1000, Ermita, Manila, Philippines
| | - Francis J McMahon
- Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Department of Health and Human Services, National Institutes of Health, Bethesda, MD, USA.
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Tian F, Diao W, Yang X, Wang X, Roberts N, Feng C, Jia Z. Failure of activation of striatum during the performance of executive function tasks in adult patients with bipolar disorder. Psychol Med 2020; 50:653-665. [PMID: 30935439 DOI: 10.1017/s0033291719000473] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Although numerous studies have used functional neuroimaging to identify executive dysfunction in patients with bipolar disorder (BD), the findings are not consistent. The aim of this meta-analysis is to identify the most reliable functional anomalies in BD patients during performance of Executive Function (EF) tasks. METHODS A web-based search was performed on publication databases to identify functional magnetic resonance imaging studies of BD patients performing EF tasks and a voxel-based meta-analytic method known as anisotropic Effect Size Signed Differential Mapping (ES-SDM) was used to identify brain regions which showed anomalous activity in BD patients compared with healthy controls (HC). RESULTS Twenty datasets consisting of 463 BD patients and 484 HC were included. Compared with HC, BD patients showed significant hypo-activation or failure of activation in the left striatum (p = 0.00007), supplementary motor area (BA 6, p = 0.00037), precentral gyrus (BA 6, p = 0.0014) and cerebellum (BA 37, p = 0.0019), and hyper-activation in the left gyrus rectus (BA 11, p ≈ 0) and right middle temporal gyrus (BA 22, p = 0.00031) during performance of EF tasks. Sensitivity and subgroup analyses showed that the anomaly of left striatum is consistent across studies and present in both euthymic and BD I patients. CONCLUSIONS Patients with BD consistently showed abnormal activation in the cortico-striatal system during performance of EF tasks compared with HC. Failure of activation of the striatum may be a reliable marker for impairment in performance of especially inhibition tasks by patients with BD.
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Affiliation(s)
- Fangfang Tian
- Department of Nuclear Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Wei Diao
- Department of Nuclear Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Xun Yang
- School of Public Affairs, Chongqing University, Chongqing400044, China
| | - Xiuli Wang
- Department of Clinical Psychology, the Fourth People's Hospital of Chengdu, Chengdu, China
| | - Neil Roberts
- Edinburgh Imaging Facility, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Can Feng
- Department of Clinical Psychology, the Fourth People's Hospital of Chengdu, Chengdu, China
| | - Zhiyun Jia
- Department of Nuclear Medicine, West China Hospital of Sichuan University, Chengdu, China
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Missig G, Robbins JO, Mokler EL, McCullough KM, Bilbo SD, McDougle CJ, Carlezon WA. Sex-dependent neurobiological features of prenatal immune activation via TLR7. Mol Psychiatry 2020; 25:2330-2341. [PMID: 30610201 PMCID: PMC7515834 DOI: 10.1038/s41380-018-0346-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/16/2018] [Accepted: 12/10/2018] [Indexed: 12/30/2022]
Abstract
Immune activation during pregnancy via infection or autoimmune disease is a risk factor for neuropsychiatric illness. Mouse models of prenatal immune activation often involve maternal administration of agents that activate toll-like receptors (TLRs), a class of pattern recognition receptors that initiate innate immune responses. Such studies have focused primarily on activating the TLR3 or TLR4 subtypes, to mimic immune responses to viral or bacterial infections, respectively. Here, we characterize the effects of prenatal activation of TLR7, which is implicated in the pathogenesis of autoimmune disease. Prenatal TLR7 activation via administration of the selective agonist imiquimod (5.0 mg/kg) induces a phenotype in offspring characterized by reduced anxiety-like behavior, fragmented social behavior, and altered ultrasonic vocalization patterns at 6-12 weeks of age. The characteristics of this phenotype are readily distinguishable from-and in some ways opposite to-those seen following prenatal activation of TLR3 and/or TLR4. Prenatal TLR7-activated mice have normal baseline locomotor activity, but are hyperresponsive to stimuli including social partners, circadian cues, and gonadal hormone fluctuations. These alterations are accompanied by decreases in microglia density but increases in ramifications. RNA-sequencing of dorsal striatum, a region showing profound changes in microglial markers, indicates that prenatal TLR7 activation induces differential expression of hundreds of genes at 13 weeks of age, with virtually no overlap in differentially expressed genes between males and females. Our findings demonstrate that prenatal immune activation can promote a wide range of developmental trajectories, depending on the type and/or pattern of TLR activation and the sex of the offspring.
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Affiliation(s)
- Galen Missig
- grid.240206.20000 0000 8795 072XBasic Neuroscience Division, Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA USA
| | - James O. Robbins
- grid.240206.20000 0000 8795 072XBasic Neuroscience Division, Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA USA
| | - Emery L. Mokler
- grid.240206.20000 0000 8795 072XBasic Neuroscience Division, Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA USA
| | - Kenneth M. McCullough
- grid.240206.20000 0000 8795 072XBasic Neuroscience Division, Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA USA
| | - Staci D. Bilbo
- grid.32224.350000 0004 0386 9924Lurie Center for Autism, Massachusetts General Hospital, Lexington, MA USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Lexington, MA USA
| | - Christopher J. McDougle
- grid.32224.350000 0004 0386 9924Lurie Center for Autism, Massachusetts General Hospital, Lexington, MA USA ,grid.38142.3c000000041936754XDepartment of Psychiatry, Harvard Medical School, Lexington, MA USA
| | - William A. Carlezon
- grid.240206.20000 0000 8795 072XBasic Neuroscience Division, Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA USA
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Postmortem evidence of brain inflammatory markers in bipolar disorder: a systematic review. Mol Psychiatry 2020; 25:94-113. [PMID: 31249382 DOI: 10.1038/s41380-019-0448-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 03/08/2019] [Accepted: 03/18/2019] [Indexed: 12/16/2022]
Abstract
Bipolar disorder (BD) is a chronic affective disorder with extreme mood swings that include mania or hypomania and depression. Though the exact mechanism of BD is unknown, neuroinflammation is one of the numerous investigated etiopathophysiological causes of BD. This article presents a systematic review of the data regarding brain inflammation evaluating microglia, astrocytes, cytokines, chemokines, adhesion molecules, and other inflammatory markers in postmortem BD brain samples. This systematic review was performed according to PRISMA recommendations, and relevant studies were identified by searching the PubMed/MEDLINE, PsycINFO, EMBASE, LILACS, IBECS, and Web of Science databases for peer-reviewed journal articles published by March 2019. Quality of included studies appraised using the QUADAS-2 tool. Among the 1814 articles included in the primary screening, 51 articles measured inflammatory markers in postmortem BD brain samples. A number of studies have shown evidence of inflammation in BD postmortem brain samples. However, an absolute statement cannot be concluded whether neuroinflammation is present in BD due to the large number of studies did not evaluate the presence of infiltrating peripheral immune cells in the central nervous system (CNS) parenchyma, cytokines levels, and microglia activation in the same postmortem brain sample. For example, out of 15 studies that evaluated microglia cells markers, 8 studies found no effect of BD on these cells. Similarly, 17 out of 51 studies evaluating astrocytes markers, 9 studies did not find any effect of BD on astrocyte cells, whereas 8 studies found a decrease and 2 studies presented both increase and decrease in different brain regions. In addition, multiple factors account for the variability across the studies, including postmortem interval, brain area studied, age at diagnosis, undergoing treatment, and others. Future analyses should rectify these potential sources of heterogeneity and reach a consensus regarding the inflammatory markers in postmortem BD brain samples.
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Xu S, Liu Y, Pu J, Gui S, Zhong X, Tian L, Song X, Qi X, Wang H, Xie P. Chronic Stress in a Rat Model of Depression Disturbs the Glutamine-Glutamate-GABA Cycle in the Striatum, Hippocampus, and Cerebellum. Neuropsychiatr Dis Treat 2020; 16:557-570. [PMID: 32158215 PMCID: PMC7047974 DOI: 10.2147/ndt.s245282] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 02/17/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Major depressive disorder (MDD) is a complex psychiatric illness involving multiple brain regions. Increasing evidence indicates that the striatum is involved in depression, but the molecular mechanisms remain unclear. METHODS In this study, we performed a gas chromatography-mass spectrometer (GC/MS)-based metabolomic analysis in the striatum of depressed rats induced by chronic unpredictable mild stress (CUMS). We then compared striatal data with our previous data from the hippocampus and cerebellum to systematically investigate the potential pathogenesis of depression. RESULTS We identified 22 differential metabolites in the striatum between the CUMS and control groups; these altered metabolites were mainly involved in amino acid, carbohydrate, and nucleotide metabolism. Pathway analysis revealed that the shared metabolic pathways of the striatum, hippocampus, and cerebellum were mainly involved in the glutamine-glutamate metabolic system. Four genes in the striatum (GS, GLS2, GLT1, and SSADH), six genes in the hippocampus (GS, SNAT1, GAD1, SSADH, VGAT, and ABAT), and five genes in the cerebellum (GS, ABAT, SNAT1, VGAT, and GDH) were found to be significantly altered using RT-qPCR. Correlation analysis indicated that these differential genes were strongly correlated. CONCLUSION These results suggest that chronic stress might induce depressive behaviors by disturbing the glutamine-glutamate-GABA cycle in the striatum, hippocampus, and cerebellum, and that the glutamine-glutamate-GABA cycle among these three brain regions might generate cooperative action in response to chronic stress.
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Affiliation(s)
- Shaohua Xu
- Department of Neurology, Yongchuan Hospital, Chongqing Medical University, Chongqing 402160, People's Republic of China.,NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Chongqing Key Laboratory of Neurobiology, Chongqing 400016, People's Republic of China
| | - Yiyun Liu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Chongqing Key Laboratory of Neurobiology, Chongqing 400016, People's Republic of China
| | - Juncai Pu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Chongqing Key Laboratory of Neurobiology, Chongqing 400016, People's Republic of China
| | - Siwen Gui
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Chongqing Key Laboratory of Neurobiology, Chongqing 400016, People's Republic of China.,College of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Xiaogang Zhong
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Chongqing Key Laboratory of Neurobiology, Chongqing 400016, People's Republic of China
| | - Lu Tian
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Chongqing Key Laboratory of Neurobiology, Chongqing 400016, People's Republic of China
| | - Xuemian Song
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Chongqing Key Laboratory of Neurobiology, Chongqing 400016, People's Republic of China.,College of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Xunzhong Qi
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Chongqing Key Laboratory of Neurobiology, Chongqing 400016, People's Republic of China
| | - Haiyang Wang
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Chongqing Key Laboratory of Neurobiology, Chongqing 400016, People's Republic of China
| | - Peng Xie
- Department of Neurology, Yongchuan Hospital, Chongqing Medical University, Chongqing 402160, People's Republic of China.,NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Chongqing Key Laboratory of Neurobiology, Chongqing 400016, People's Republic of China.,Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
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Wang JQ, Liu YR, Xia Q, Chen RN, Liang J, Xia QR, Li J. Emerging Roles for NLRC5 in Immune Diseases. Front Pharmacol 2019; 10:1352. [PMID: 31824312 PMCID: PMC6880621 DOI: 10.3389/fphar.2019.01352] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/25/2019] [Indexed: 12/15/2022] Open
Abstract
Innate immunity activates the corresponding immune response relying on multiple pattern recognition receptors (PRRs) that includes pattern recognition receptors (PRRs), like NOD-like receptors (NLRs), RIG-I-like receptors (RLRs), and C-type lectin receptors (CLRs), which could accurately recognize invasive pathogens. In particular, NLRs belong to a large protein family of pattern recognition receptors in the cytoplasm, where they are highly correlated with activation of inflammatory response system followed by rapid clearance of invasive pathogens. Among the NLRs family, NLRC5, also known as NOD4 or NOD27, accounts for a large proportion and involves in immune responses far and wide. Notably, in the above response case of inflammation, the expression of NLRC5 remarkably increased in immune cells and immune-related tissues. However, the evidence for higher expression of NLRC5 in immune disease still remains controversial. It is noted that the growing evidence further accounts for the participation of NLRC5 in the innate immune response and inflammatory diseases. Moreover, NLRC5 has also been confirmed to exert a critical role in the control of regulatory diverse signaling pathways. Together with its broad participation in the occurrence and development of immune diseases, NLRC5 can be consequently treated as a potential therapeutic target. Nevertheless, the paucity of absolute understanding of intrinsic characteristics and underlying mechanisms of NLRC5 still make it hard to develop targeting drugs. Therefore, current summary about NLRC5 information is indispensable. Herein, current knowledge of NLRC5 is summarized, and research advances in terms of NLRC5 in characteristics, biological function, and regulatory mechanisms are reviewed.
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Affiliation(s)
- Jie-Quan Wang
- Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, China.,Department of Pharmacy, Anhui Mental Health Center, Hefei, China.,Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, China.,School of Pharmacy, Anhui Medical University, Ministry of Education, Hefei, China
| | - Ya-Ru Liu
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Quan Xia
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ruo-Nan Chen
- School of Pharmacy, Anhui Medical University, Ministry of Education, Hefei, China.,Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jun Liang
- Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, China.,Department of Pharmacy, Anhui Mental Health Center, Hefei, China.,Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, China
| | - Qing-Rong Xia
- Department of Pharmacy, Hefei Fourth People's Hospital, Hefei, China.,Department of Pharmacy, Anhui Mental Health Center, Hefei, China.,Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, China
| | - Jun Li
- School of Pharmacy, Anhui Medical University, Ministry of Education, Hefei, China
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Luykx JJ, Giuliani F, Giuliani G, Veldink J. Coding and Non-Coding RNA Abnormalities in Bipolar Disorder. Genes (Basel) 2019; 10:E946. [PMID: 31752442 PMCID: PMC6895892 DOI: 10.3390/genes10110946] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/05/2019] [Accepted: 11/15/2019] [Indexed: 12/12/2022] Open
Abstract
The molecular mechanisms underlying bipolar disorder (BPD) have remained largely unknown. Postmortem brain tissue studies comparing BPD patients with healthy controls have produced a heterogeneous array of potentially implicated protein-coding RNAs. We hypothesized that dysregulation of not only coding, but multiple classes of RNA (coding RNA, long non-coding (lnc) RNA, circular (circ) RNA, and/or alternative splicing) underlie the pathogenesis of BPD. Using non-polyadenylated libraries we performed RNA sequencing in postmortem human medial frontal gyrus tissue from BPD patients and healthy controls. Twenty genes, some of which not previously implicated in BPD, were differentially expressed (DE). PCR validation and replication confirmed the implication of these DE genes. Functional in silico analyses identified enrichment of angiogenesis, vascular system development and histone H3-K4 demethylation. In addition, ten lncRNA transcripts were differentially expressed. Furthermore, an overall increased number of alternative splicing events in BPD was detected, as well as an increase in the number of genes carrying alternative splicing events. Finally, a large reservoir of circRNAs populating brain tissue not affected by BPD is described, while in BPD altered levels of two circular transcripts, cNEBL and cEPHA3, are reported. cEPHA3, hitherto unlinked to BPD, is implicated in developmental processes in the central nervous system. Although we did not perform replication analyses of non-coding RNA findings, our findings hint that RNA dysregulation in BPD is not limited to coding regions, opening avenues for future pharmacological investigations and biomarker research.
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Affiliation(s)
- Jurjen J. Luykx
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands; (F.G.); (G.G.); (J.V.)
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht (UMCU), Utrecht University, 3584 CX Utrecht, The Netherlands
- GGNet Mental Health, 7328 JE Apeldoorn, The Netherlands
| | - Fabrizio Giuliani
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands; (F.G.); (G.G.); (J.V.)
| | - Giuliano Giuliani
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands; (F.G.); (G.G.); (J.V.)
| | - Jan Veldink
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands; (F.G.); (G.G.); (J.V.)
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht (UMCU), Utrecht University, 3584 CX Utrecht, The Netherlands
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Saffari A, Arno M, Nasser E, Ronald A, Wong CCY, Schalkwyk LC, Mill J, Dudbridge F, Meaburn EL. RNA sequencing of identical twins discordant for autism reveals blood-based signatures implicating immune and transcriptional dysregulation. Mol Autism 2019; 10:38. [PMID: 31719968 PMCID: PMC6839145 DOI: 10.1186/s13229-019-0285-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/01/2019] [Indexed: 11/13/2022] Open
Abstract
Background A gap exists in our mechanistic understanding of how genetic and environmental risk factors converge at the molecular level to result in the emergence of autism symptoms. We compared blood-based gene expression signatures in identical twins concordant and discordant for autism spectrum condition (ASC) to differentiate genetic and environmentally driven transcription differences, and establish convergent evidence for biological mechanisms involved in ASC. Methods Genome-wide gene expression data were generated using RNA-seq on whole blood samples taken from 16 pairs of monozygotic (MZ) twins and seven twin pair members (39 individuals in total), who had been assessed for ASC and autism traits at age 12. Differential expression (DE) analyses were performed between (a) affected and unaffected subjects (N = 36) and (b) within discordant ASC MZ twin pairs (total N = 11) to identify environmental-driven DE. Gene set enrichment and pathway testing was performed on DE gene lists. Finally, an integrative analysis using DNA methylation data aimed to identify genes with consistent evidence for altered regulation in cis. Results In the discordant twin analysis, three genes showed evidence for DE at FDR < 10%: IGHG4, EVI2A and SNORD15B. In the case-control analysis, four DE genes were identified at FDR < 10% including IGHG4, PRR13P5, DEPDC1B, and ZNF501. We find enrichment for DE of genes curated in the SFARI human gene database. Pathways showing evidence of enrichment included those related to immune cell signalling and immune response, transcriptional control and cell cycle/proliferation. Integrative methylomic and transcriptomic analysis identified a number of genes showing suggestive evidence for cis dysregulation. Limitations Identical twins stably discordant for ASC are rare, and as such the sample size was limited and constrained to the use of peripheral blood tissue for transcriptomic and methylomic profiling. Given these primary limitations, we focused on transcript-level analysis. Conclusions Using a cohort of ASC discordant and concordant MZ twins, we add to the growing body of transcriptomic-based evidence for an immune-based component in the molecular aetiology of ASC. Whilst the sample size was limited, the study demonstrates the utility of the discordant MZ twin design combined with multi-omics integration for maximising the potential to identify disease-associated molecular signals.
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Affiliation(s)
- Ayden Saffari
- 1Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- 2Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck, University of London, London, UK
| | - Matt Arno
- 3Edinburgh Genomics, University of Edinburgh, Edinburgh, Scotland UK
- 4King's Genomics Centre, King's College London, London, UK
| | - Eric Nasser
- 4King's Genomics Centre, King's College London, London, UK
| | - Angelica Ronald
- 2Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck, University of London, London, UK
| | - Chloe C Y Wong
- 5Social Genetic and Developmental Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | | | - Jonathan Mill
- 7University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Frank Dudbridge
- 1Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- 8Department of Health Sciences, University of Leicester, Leicester, UK
| | - Emma L Meaburn
- 2Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck, University of London, London, UK
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Sneeboer MAM, Snijders GJLJ, Berdowski WM, Fernández-Andreu A, van Mierlo HC, Berdenis van Berlekom A, Litjens M, Kahn RS, Hol EM, de Witte LD. Microglia in post-mortem brain tissue of patients with bipolar disorder are not immune activated. Transl Psychiatry 2019; 9:153. [PMID: 31127084 PMCID: PMC6534632 DOI: 10.1038/s41398-019-0490-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 04/10/2019] [Accepted: 04/29/2019] [Indexed: 12/22/2022] Open
Abstract
Genetic, epidemiological, and biomarker studies suggest that the immune system is involved in the pathogenesis of bipolar disorder (BD). It has therefore been hypothesized that immune activation of microglia, the resident immune cells of the brain, is associated with the disease. Only a few studies have addressed the involvement of microglia in BD so far and a more detailed immune profiling of microglial activation is lacking. Here, we applied a multi-level approach to determine the activation state of microglia in BD post-mortem brain tissue. We did not find differences in microglial density, and mRNA expression of microglial markers in the medial frontal gyrus (MFG) of patients with BD. Furthermore, we performed in-depth characterization of human primary microglia isolated from fresh brain tissue of the MFG, superior temporal gyrus (STG), and thalamus (THA). Similarly, these ex vivo isolated microglia did not show elevated expression of inflammatory markers. Finally, challenging the isolated microglia with LPS did not result in an increased immune response in patients with BD compared to controls. In conclusion, our study shows that microglia in post-mortem brain tissue of patients with BD are not immune activated.
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Affiliation(s)
- Marjolein A M Sneeboer
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University (BCRM-UMCU-UU), 3584 CG, Utrecht, The Netherlands.
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University (BCRM-UMCU-UU), 3584 CG, Utrecht, The Netherlands.
| | - Gijsje J L J Snijders
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University (BCRM-UMCU-UU), 3584 CG, Utrecht, The Netherlands
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University (BCRM-UMCU-UU), 3584 CG, Utrecht, The Netherlands
| | - Woutje M Berdowski
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University (BCRM-UMCU-UU), 3584 CG, Utrecht, The Netherlands
| | - Alba Fernández-Andreu
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University (BCRM-UMCU-UU), 3584 CG, Utrecht, The Netherlands
| | - Hans C van Mierlo
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University (BCRM-UMCU-UU), 3584 CG, Utrecht, The Netherlands
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University (BCRM-UMCU-UU), 3584 CG, Utrecht, The Netherlands
| | - Amber Berdenis van Berlekom
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University (BCRM-UMCU-UU), 3584 CG, Utrecht, The Netherlands
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University (BCRM-UMCU-UU), 3584 CG, Utrecht, The Netherlands
| | - Manja Litjens
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University (BCRM-UMCU-UU), 3584 CG, Utrecht, The Netherlands
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University (BCRM-UMCU-UU), 3584 CG, Utrecht, The Netherlands
| | - René S Kahn
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University (BCRM-UMCU-UU), 3584 CG, Utrecht, The Netherlands
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education and Clinical Center (MIRECC), James J Peters VA Medical Center, Bronx, NY, USA
| | - Elly M Hol
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University (BCRM-UMCU-UU), 3584 CG, Utrecht, The Netherlands
- Neuroimmunology, Netherlands Institute for Neuroscience, an Institute of The Royal Academy of Arts and Sciences, 1105 BA, Amsterdam, The Netherlands
| | - Lot D de Witte
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University (BCRM-UMCU-UU), 3584 CG, Utrecht, The Netherlands
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education and Clinical Center (MIRECC), James J Peters VA Medical Center, Bronx, NY, USA
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Holper L, Ben-Shachar D, Mann JJ. Multivariate meta-analyses of mitochondrial complex I and IV in major depressive disorder, bipolar disorder, schizophrenia, Alzheimer disease, and Parkinson disease. Neuropsychopharmacology 2019; 44:837-849. [PMID: 29855563 PMCID: PMC6461987 DOI: 10.1038/s41386-018-0090-0] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/26/2018] [Accepted: 05/07/2018] [Indexed: 12/17/2022]
Abstract
Complex I (NADH dehydrogenase, NDU) and complex IV (cytochrome-c-oxidase, COX) of the mitochondrial electron transport chain have been implicated in the pathophysiology of major psychiatric disorders, such as major depressive disorder (MDD), bipolar disorder (BD), and schizophrenia (SZ), as well as in neurodegenerative disorders, such as Alzheimer disease (AD) and Parkinson disease (PD). We conducted meta-analyses comparing complex I and IV in each disorder MDD, BD, SZ, AD, and PD, as well as in normal aging. The electronic databases Pubmed, EMBASE, CENTRAL, and Google Scholar, were searched for studies published between 1980 and 2018. Of 2049 screened studies, 125 articles were eligible for the meta-analyses. Complex I and IV were assessed in peripheral blood, muscle biopsy, or postmortem brain at the level of enzyme activity or subunits. Separate meta-analyses of mood disorder studies, MDD and BD, revealed moderate effect sizes for similar abnormality patterns in the expression of complex I with SZ in frontal cortex, cerebellum and striatum, whereas evidence for complex IV alterations was low. By contrast, the neurodegenerative disorders, AD and PD, showed strong effect sizes for shared deficits in complex I and IV, such as in peripheral blood, frontal cortex, cerebellum, and substantia nigra. Beyond the diseased state, there was an age-related robust decline in both complexes I and IV. In summary, the strongest support for a role for complex I and/or IV deficits, is in the pathophysiology of PD and AD, and evidence is less robust for MDD, BD, or SZ.
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Affiliation(s)
- L Holper
- Division of Molecular Imaging and Neuropathology, Columbia University and New York State Psychiatric Institute, New York, NY, USA.
| | - D Ben-Shachar
- Laboratory of Psychobiology, Department of Psychiatry, Rambam Health Care Campus, Rappaport Faculty of Medicine, Technion IIT, Haifa, Israel
| | - J J Mann
- Division of Molecular Imaging and Neuropathology, Columbia University and New York State Psychiatric Institute, New York, NY, USA
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Kim W, Won SY, Yoon BJ. CRMP2 mediates GSK3β actions in the striatum on regulating neuronal structure and mania-like behavior. J Affect Disord 2019; 245:1079-1088. [PMID: 30699850 DOI: 10.1016/j.jad.2018.10.371] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/29/2018] [Accepted: 10/05/2018] [Indexed: 11/20/2022]
Abstract
BACKGROUND Genetic and physiological studies have implicated the striatum in bipolar disorder (BD). Although Glycogen synthase kinase 3 beta (GSK3β) has been suggested to play a role in the pathophysiology of BD since it is inhibited by lithium, it remains unknown how GSK3β activity might be involved. Therefore we examined the functional roles of GSK3β and one of its substrates, CRMP2, within the striatum. METHODS Using CRISPR-Cas9 system, we specifically ablated GSK3β in the striatal neurons in vivo and in vitro. Sholl analysis was performed for the structural studies of medium spiny neurons (MSNs) and amphetamine-induced hyperlocomotion was measured to investigate the effects of gene ablations on the mania-like symptom of BD. RESULTS GSK3β deficiency in cultured neurons and in neurons of adult mouse brain caused opposite patterns of neurite changes. Furthermore, specific knockout of GSK3β in the MSNs of the indirect pathway significantly suppressed amphetamine-induced hyperlocomotion. We demonstrated that these phenotypes of GSK3β ablation were mediated by CRMP2, a major substrate of GSK3β. LIMITATIONS Amphetamine-induced hyperlocomotion only partially recapitulate the symptoms of BD. It requires further study to examine whether abnormality in GSK3β or CRMP2 is also involved in depression phase of BD. Additionally, we could not confirm whether the behavioral changes observed in GSK3β-ablated mice were indeed caused by the cellular structural changes observed in the striatal neurons. CONCLUSION Our results demonstrate that GSK3β and its substrate CRMP2 critically regulate the neurite structure of MSNs and their functions specifically within the indirect pathway of the basal ganglia network play a critical role in manifesting mania-like behavior of BD. Moreover, our data also suggest lithium may exert its effect on BD through a GSK3β-independent mechanism, in addition to the GSK3β inhibition-mediated mechanism.
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Affiliation(s)
- Wonju Kim
- Division of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Anam-ro 145, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Seong-Yeon Won
- Division of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Anam-ro 145, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Bong-June Yoon
- Division of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Anam-ro 145, Seongbuk-gu, Seoul 02841, Republic of Korea.
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Gandal MJ, Zhang P, Hadjimichael E, Walker RL, Chen C, Liu S, Won H, van Bakel H, Varghese M, Wang Y, Shieh AW, Haney J, Parhami S, Belmont J, Kim M, Losada PM, Khan Z, Mleczko J, Xia Y, Dai R, Wang D, Yang YT, Xu M, Fish K, Hof PR, Warrell J, Fitzgerald D, White K, Jaffe AE, Peters MA, Gerstein M, Liu C, Iakoucheva LM, Pinto D, Geschwind DH. Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder. Science 2018; 362:eaat8127. [PMID: 30545856 PMCID: PMC6443102 DOI: 10.1126/science.aat8127] [Citation(s) in RCA: 675] [Impact Index Per Article: 112.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 11/13/2018] [Indexed: 12/12/2022]
Abstract
Most genetic risk for psychiatric disease lies in regulatory regions, implicating pathogenic dysregulation of gene expression and splicing. However, comprehensive assessments of transcriptomic organization in diseased brains are limited. In this work, we integrated genotypes and RNA sequencing in brain samples from 1695 individuals with autism spectrum disorder (ASD), schizophrenia, and bipolar disorder, as well as controls. More than 25% of the transcriptome exhibits differential splicing or expression, with isoform-level changes capturing the largest disease effects and genetic enrichments. Coexpression networks isolate disease-specific neuronal alterations, as well as microglial, astrocyte, and interferon-response modules defining previously unidentified neural-immune mechanisms. We integrated genetic and genomic data to perform a transcriptome-wide association study, prioritizing disease loci likely mediated by cis effects on brain expression. This transcriptome-wide characterization of the molecular pathology across three major psychiatric disorders provides a comprehensive resource for mechanistic insight and therapeutic development.
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Affiliation(s)
- Michael J. Gandal
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Pan Zhang
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Evi Hadjimichael
- Department of Psychiatry, and Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rebecca L. Walker
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chao Chen
- The School of Life Science, Central South University, Changsha, Hunan 410078, China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, Hunan, China
| | - Shuang Liu
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA
| | - Hyejung Won
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Merina Varghese
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Fishberg Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongjun Wang
- The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Annie W. Shieh
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Jillian Haney
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Sepideh Parhami
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Judson Belmont
- Department of Psychiatry, and Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Minsoo Kim
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Patricia Moran Losada
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Zenab Khan
- Department of Genetics and Genomic Sciences, and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Justyna Mleczko
- Departments of Medicine and Cardiology, Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yan Xia
- The School of Life Science, Central South University, Changsha, Hunan 410078, China
| | - Rujia Dai
- The School of Life Science, Central South University, Changsha, Hunan 410078, China
| | - Daifeng Wang
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Yucheng T. Yang
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA
| | - Min Xu
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA
| | - Kenneth Fish
- Departments of Medicine and Cardiology, Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patrick R. Hof
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Fishberg Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan Warrell
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA
| | - Dominic Fitzgerald
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Kevin White
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago IL 60637
- Tempus Labs, Inc. Chicago IL 60654
| | - Andrew E. Jaffe
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Mette A. Peters
- CNS Data Coordination group, Sage Bionetworks, Seattle, WA 98109, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA
| | - Chunyu Liu
- The School of Life Science, Central South University, Changsha, Hunan 410078, China
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Lilia M. Iakoucheva
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Dalila Pinto
- Department of Psychiatry, and Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel H. Geschwind
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Zhao L, Chang H, Zhou DS, Cai J, Fan W, Tang W, Tang W, Li X, Liu W, Liu F, He Y, Bai Y, Sun Y, Dai J, Li L, Xiao X, Zhang C, Li M. Replicated associations of FADS1, MAD1L1, and a rare variant at 10q26.13 with bipolar disorder in Chinese population. Transl Psychiatry 2018; 8:270. [PMID: 30531795 PMCID: PMC6286364 DOI: 10.1038/s41398-018-0337-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/07/2018] [Accepted: 11/13/2018] [Indexed: 12/12/2022] Open
Abstract
Genetic analyses of psychiatric illnesses, such as bipolar disorder (BPD), have revealed essential information regarding the underlying pathological mechanisms. While such studies in populations of European ancestry have achieved prominent success, understanding the genetic risk factors of these illnesses (especially BPD) in Chinese population remains an urgent task. Given the lack of genome-wide association study (GWAS) of BPD in Chinese population from Mainland China, replicating the previously reported GWAS hits in distinct populations will provide valuable information for future GWAS analysis in Han Chinese. In the present study, we have recruited 1146 BPD cases and 1956 controls from Mainland China for genetic analyses, as well as 65 Han Chinese brain amygdala tissues for mRNA expression analyses. Using this clinical sample, one of the largest Han Chinese BPD samples till now, we have conducted replication analyses of 21 single nucleotide polymorphisms (SNPs) extracted from previous GWAS of distinct populations. Among the 21 tested SNPs, 16 showed the same direction of allelic effects in our samples compared with previous studies; 6 SNPs achieved nominal significance (p < 0.05) at one-tailed test, and 2 additional SNPs showed marginal significance (p < 0.10). Aside from replicating previously reported BPD risk SNPs, we herein also report several intriguing findings: (1) the SNP rs174576 was associated with BPD in our Chinese sample and in the overall global meta-analysis, and was significantly correlated with FADS1 mRNA in diverse public RNA-seq datasets as well as our in house collected Chinese amygdala samples; (2) two (partially) independent SNPs in MAD1L1 were both significantly associated with BPD in our Chinese sample, which was also supported by haplotype analysis; (3) a rare SNP rs78089757 in 10q26.13 region was a genome-wide significant variant for BPD in East Asians, and this SNP was near monomorphic in Europeans. In sum, these results confirmed several significant BPD risk genes. We hope this Chinese BPD case-control sample and the current brain amygdala tissues (with continuous increasing sample size in the near future) will provide helpful resources in elucidating the genetic and molecular basis of BPD in this major world population.
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Affiliation(s)
- Lijuan Zhao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 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, Kunming, Yunnan, China
| | - Dong-Sheng Zhou
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Jun Cai
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weixing Fan
- Jinhua Second Hospital, Jinhua, Zhejiang, China
| | - Wei Tang
- Wenzhou Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wenxin Tang
- Hangzhou Seventh People's Hospital, Hangzhou, Zhejiang, China
| | - Xingxing Li
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Weiqing Liu
- Department of Psychiatry, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Fang Liu
- Department of Psychiatry, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yuanfang He
- Department of Psychiatry, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yan Bai
- Department of Psychiatry, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yan Sun
- Wuhan Institute for Neuroscience and Neuroengineering, South-Central University for Nationalities, Wuhan, Hubei, China
- Chinese Brain Bank Center, Wuhan, Hubei, China
| | - Jiapei Dai
- Wuhan Institute for Neuroscience and Neuroengineering, South-Central University for Nationalities, Wuhan, Hubei, China
- Chinese Brain Bank Center, Wuhan, Hubei, China
| | - Lingyi Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 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, Kunming, Yunnan, China.
| | - Chen Zhang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 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, Kunming, Yunnan, China.
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
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Shaffer JJ, Johnson CP, Fiedorowicz JG, Christensen GE, Wemmie JA, Magnotta VA. Impaired sensory processing measured by functional MRI in Bipolar disorder manic and depressed mood states. Brain Imaging Behav 2018; 12:837-847. [PMID: 28674759 PMCID: PMC5752628 DOI: 10.1007/s11682-017-9741-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bipolar disorder is characterized by recurring episodes of depression and mania. Defining differences in brain function during these states is an important goal of bipolar disorder research. However, few imaging studies have directly compared brain activity between bipolar mood states. Herein, we compare functional magnetic resonance imaging (fMRI) responses during a flashing checkerboard stimulus between bipolar participants across mood states (euthymia, depression, and mania) in order to identify functional differences between these states. 40 participants with bipolar I disorder and 33 healthy controls underwent fMRI during the presentation of the stimulus. A total of 23 euthymic-state, 16 manic-state, 15 depressed-state, and 32 healthy control imaging sessions were analyzed in order to compare functional activation during the stimulus between mood states and with healthy controls. A reduced response was identified in the visual cortex in both the depressed and manic groups compared to euthymic and healthy participants. Functional differences between bipolar mood states were also observed in the cerebellum, thalamus, striatum, and hippocampus. Functional differences between mood states occurred in several brain regions involved in visual and other sensory processing. These differences suggest that altered visual processing may be a feature of mood states in bipolar disorder. The key limitations of this study are modest mood-state group size and the limited temporal resolution of fMRI which prevents the segregation of primary visual activity from regulatory feedback mechanisms.
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Affiliation(s)
- Joseph J Shaffer
- Department of Radiology, University of Iowa, Iowa City, IA, USA.
- , PBDB L420, 169 Newton Rd., Iowa City, IA, 52242, USA.
| | - Casey P Johnson
- Department of Radiology, University of Iowa, Iowa City, IA, USA
| | - Jess G Fiedorowicz
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
- Department of Epidemiology, University of Iowa, Iowa City, IA, USA
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
- Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA, USA
| | - Gary E Christensen
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA, USA
- Department of Radiation Oncology, University of Iowa, Iowa City, IA, USA
| | - John A Wemmie
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
- Department of Veterans Affairs Medical Center, Iowa City, IA, USA
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
- Department of Neurosurgery, University of Iowa, Iowa City, IA, USA
- Pappajohn Biomedical Institute, University of Iowa, Iowa City, IA, USA
| | - Vincent A Magnotta
- Department of Radiology, University of Iowa, Iowa City, IA, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA
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Wu C, Bendriem RM, Garamszegi SP, Song L, Lee CT. RNA sequencing in post-mortem human brains of neuropsychiatric disorders. Psychiatry Clin Neurosci 2017; 71:663-672. [PMID: 28675555 DOI: 10.1111/pcn.12550] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/30/2017] [Accepted: 06/27/2017] [Indexed: 12/28/2022]
Abstract
RNA sequencing (RNA-Seq), a revolutionary tool for transcriptome profiling, is becoming increasingly important for neuroscientists in studying the transcriptional landscape of the human brain. Studies using this next-generation sequencing technique have already revealed novel insights into the complexity of neurons in the human brain and pathogenesis of complex neurological diseases. In clinical neuroscience, RNA-Seq provides exciting opportunities for improving diagnosis and treatment of neurological diseases by facilitating the development of pharmacotherapies able to modulate gene expression. Furthermore, integrative whole genome sequencing and transcriptome sequencing can provide additional information for the functional role of mutated genes, prioritization of variants, and intron/exon splicing. This review describes the current state of RNA-Seq studies in neuropsychiatric disorders using post-mortem human brains, a brief survey of best practices for experimental design and sequencing data analysis, and the challenges associated with its application in the human brain.
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Affiliation(s)
- Chun Wu
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, USA
| | - Raphael M Bendriem
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, USA
| | - Susanna P Garamszegi
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, USA
| | - Lei Song
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, USA
| | - Chun-Ting Lee
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, USA
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