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Markiewicz R, Markiewicz-Gospodarek A, Borowski B, Trubalski M, Łoza B. Reelin Signaling and Synaptic Plasticity in Schizophrenia. Brain Sci 2023; 13:1704. [PMID: 38137152 PMCID: PMC10741648 DOI: 10.3390/brainsci13121704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Recent research emphasizes the significance of studying the quality of life of schizophrenia patients, considering the complex nature of the illness. Identifying neuronal markers for early diagnosis and treatment is crucial. Reelin (RELN) stands out among these markers, with genetic studies highlighting its role in mental health. Suppression of RELN expression may contribute to cognitive deficits by limiting dendritic proliferation, affecting neurogenesis, and leading to improper neuronal circuits. Although the physiological function of reelin is not fully understood, it plays a vital role in hippocampal cell stratification and neuroglia formation. This analysis explores reelin's importance in the nervous system, shedding light on its impact on mental disorders such as schizophrenia, paving the way for innovative therapeutic approaches, and at the same time, raises the following conclusions: increased methylation levels of the RELN gene in patients with a diagnosis of schizophrenia results in a multiple decrease in the expression of reelin, and monitoring of this indicator, i.e., methylation levels, can be used to monitor the severity of symptoms in the course of schizophrenia.
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Affiliation(s)
- Renata Markiewicz
- Occupational Therapy Laboratory, Chair of Nursing Development, Medical University of Lublin, 4 Staszica St., 20-081 Lublin, Poland;
| | | | - Bartosz Borowski
- Students Scientific Association, Department of Normal, Clinical and Imaging Anatomy, Medical University of Lublin, 20-090 Lublin, Poland; (B.B.); (M.T.)
| | - Mateusz Trubalski
- Students Scientific Association, Department of Normal, Clinical and Imaging Anatomy, Medical University of Lublin, 20-090 Lublin, Poland; (B.B.); (M.T.)
| | - Bartosz Łoza
- Department of Psychiatry, Medical University of Warsaw, 02-091 Warsaw, Poland;
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2
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Li P, Tian Y, Shang Q, Tang C, Hou Z, Li Y, Cao L, Xue S, Bian J, Luo C, Wu D, Li Z, Ding H. Discovery of a highly potent NPAS3 heterodimer inhibitor by covalently modifying ARNT. Bioorg Chem 2023; 139:106676. [PMID: 37352720 DOI: 10.1016/j.bioorg.2023.106676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/01/2023] [Accepted: 06/09/2023] [Indexed: 06/25/2023]
Abstract
Neuronal PAS domain protein 3 (NPAS3), a basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) family member, is a pivotal transcription factor in neuronal regeneration, development, and related diseases, regulating the expression of downstream genes. Despite several modulators of certain bHLH-PAS family proteins being identified, the NPAS3-targeted compound has yet to be reported. Herein, we discovered a hit compound BI-78D3 that directly blocks the NPAS3-ARNT heterodimer formation by covalently binding to the aryl hydrocarbon receptor nuclear translocator (ARNT) subunit. Further optimization based on the hit scaffold yielded a highly potent Compound 6 with a biochemical EC50 value of 282 ± 61 nM and uncovered the 5-nitrothiazole-2-sulfydryl as a cysteine-targeting covalent warhead. Compound 6 effectively down-regulated NPAS3's transcriptional function by disrupting the interface of NPAS3-ARNT complexes at cellular level. In conclusion, our study identifies the 5-nitrothiazole-2-sulfydryl as a cysteine-modified warhead and provides a strategy that blocks the NPAS3-ARNT heterodimerization by covalently conjugating ARNT Cys336 residue. Compound 6 may serve as a promising chemical probe for exploring NPAS3-related physiological functions.
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Affiliation(s)
- Peizhuo Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yucheng Tian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qinghong Shang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Cailing Tang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zeng Hou
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310053, China
| | - Yuanqing Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Liyuan Cao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Shengyu Xue
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jinlei Bian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Cheng Luo
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Dalei Wu
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Zhiyu Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Hong Ding
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
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3
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Ochneva A, Zorkina Y, Abramova O, Pavlova O, Ushakova V, Morozova A, Zubkov E, Pavlov K, Gurina O, Chekhonin V. Protein Misfolding and Aggregation in the Brain: Common Pathogenetic Pathways in Neurodegenerative and Mental Disorders. Int J Mol Sci 2022; 23:ijms232214498. [PMID: 36430976 PMCID: PMC9695177 DOI: 10.3390/ijms232214498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/07/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022] Open
Abstract
Mental disorders represent common brain diseases characterized by substantial impairments of social and cognitive functions. The neurobiological causes and mechanisms of psychopathologies still have not been definitively determined. Various forms of brain proteinopathies, which include a disruption of protein conformations and the formation of protein aggregates in brain tissues, may be a possible cause behind the development of psychiatric disorders. Proteinopathies are known to be the main cause of neurodegeneration, but much less attention is given to the role of protein impairments in psychiatric disorders' pathogenesis, such as depression and schizophrenia. For this reason, the aim of this review was to discuss the potential contribution of protein illnesses in the development of psychopathologies. The first part of the review describes the possible mechanisms of disruption to protein folding and aggregation in the cell: endoplasmic reticulum stress, dysfunction of chaperone proteins, altered mitochondrial function, and impaired autophagy processes. The second part of the review addresses the known proteins whose aggregation in brain tissue has been observed in psychiatric disorders (amyloid, tau protein, α-synuclein, DISC-1, disbindin-1, CRMP1, SNAP25, TRIOBP, NPAS3, GluA1, FABP, and ankyrin-G).
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Affiliation(s)
- Aleksandra Ochneva
- Department Basic and Applied Neurobiology, V.P. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia
- Healthcare Department, Mental-Health Clinic No. 1 Named after N.A. Alexeev of Moscow, 117152 Moscow, Russia
- Correspondence: ; Tel.: +7-915-670-39-35
| | - Yana Zorkina
- Department Basic and Applied Neurobiology, V.P. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia
- Healthcare Department, Mental-Health Clinic No. 1 Named after N.A. Alexeev of Moscow, 117152 Moscow, Russia
| | - Olga Abramova
- Department Basic and Applied Neurobiology, V.P. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia
- Healthcare Department, Mental-Health Clinic No. 1 Named after N.A. Alexeev of Moscow, 117152 Moscow, Russia
| | - Olga Pavlova
- Department Basic and Applied Neurobiology, V.P. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia
| | - Valeriya Ushakova
- Department Basic and Applied Neurobiology, V.P. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia
- Healthcare Department, Mental-Health Clinic No. 1 Named after N.A. Alexeev of Moscow, 117152 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Anna Morozova
- Department Basic and Applied Neurobiology, V.P. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia
- Healthcare Department, Mental-Health Clinic No. 1 Named after N.A. Alexeev of Moscow, 117152 Moscow, Russia
| | - Eugene Zubkov
- Department Basic and Applied Neurobiology, V.P. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia
| | - Konstantin Pavlov
- Department Basic and Applied Neurobiology, V.P. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia
- Healthcare Department, Mental-Health Clinic No. 1 Named after N.A. Alexeev of Moscow, 117152 Moscow, Russia
| | - Olga Gurina
- Department Basic and Applied Neurobiology, V.P. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia
| | - Vladimir Chekhonin
- Department Basic and Applied Neurobiology, V.P. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia
- Department of Medical Nanobiotechnology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- National University of Science and Technology “MISiS”, Leninskiy Avenue 4, 119049 Moscow, Russia
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Liu JW, Li H, Zhang Y. Npas3 regulates stemness maintenance of radial glial cells and neuronal migration in the developing mouse cerebral cortex. Front Cell Neurosci 2022; 16:865681. [PMID: 36313621 PMCID: PMC9608153 DOI: 10.3389/fncel.2022.865681] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
The neuronal PAS domain 3 (NPAS3) is a member of the basic helix-loop-helix (bHLH) PAS family of transcription factors and is implicated in psychiatric and neurodevelopmental disorders. NPAS3 is robustly expressed in the cortical ventricle zone (VZ), a transient proliferative zone containing progenitor cells, mainly radial glial cells, destined to give rise to cortical excitatory neurons. However, the role of NPAS3 in corticogenesis remains largely unknown. In this study, we knocked down Npas3 expression in the neural progenitor cells residing in the cortical VZ to investigate the role of Npas3 in cerebral cortical development in mice. We demonstrated that Npas3 knockdown profoundly impaired neuronal radial migration and changed the laminar cell fate of the cells detained in the deep cortical layers. Furthermore, the downregulation of Npas3 led to the stemness maintenance of radial glial cells and increased the proliferation rate of neural progenitor cells residing in the VZ/subventricular zone (SVZ). These findings underline the function of Npas3 in the development of the cerebral cortex and may shed light on the etiology of NPAS3-related disorders.
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Gorina YV, Salmina AB, Erofeev AI, Gerasimov EI, Bolshakova AV, Balaban PM, Bezprozvanny IB, Vlasova OL. Astrocyte Activation Markers. Biochemistry (Mosc) 2022; 87:851-870. [PMID: 36180985 DOI: 10.1134/s0006297922090012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 06/16/2023]
Abstract
Astrocytes are the most common type of glial cells that provide homeostasis and protection of the central nervous system. Important specific characteristic of astrocytes is manifestation of morphological heterogeneity, which is directly dependent on localization in a particular area of the brain. Astrocytes can integrate into neural networks and keep neurons active in various areas of the brain. Moreover, astrocytes express a variety of receptors, channels, and membrane transporters, which underlie their peculiar metabolic activity, and, hence, determine plasticity of the central nervous system during development and aging. Such complex structural and functional organization of astrocytes requires the use of modern methods for their identification and analysis. Considering the important fact that determining the most appropriate marker for polymorphic and multiple subgroups of astrocytes is of decisive importance for studying their multifunctionality, this review presents markers, modern imaging techniques, and identification of astrocytes, which comprise a valuable resource for studying structural and functional properties of astrocytes, as well as facilitate better understanding of the extent to which astrocytes contribute to neuronal activity.
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Affiliation(s)
- Yana V Gorina
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 194091, Russia.
- Research Institute of Molecular Medicine and Pathobiochemistry, Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russia
| | - Alla B Salmina
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 194091, Russia
- Research Institute of Molecular Medicine and Pathobiochemistry, Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russia
- Laboratory of Neurobiology and Tissue Engineering, Brain Institute, Research Center of Neurology, Moscow, 105064, Russia
| | - Alexander I Erofeev
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 194091, Russia
| | - Evgeniy I Gerasimov
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 194091, Russia
| | - Anastasia V Bolshakova
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 194091, Russia
| | - Pavel M Balaban
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 194091, Russia
- Laboratory of Cellular Neurobiology of Learning, Institute of Higher Nervous Activity, Moscow, 117485, Russia
| | - Ilya B Bezprozvanny
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 194091, Russia
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Olga L Vlasova
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 194091, Russia
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Li Y, Fan T, Li X, Liu L, Mao F, Li Y, Miao Z, Zeng C, Song W, Pan J, Zhou S, Wang H, Wang Y, Sun ZS. Npas3 deficiency impairs cortical astrogenesis and induces autistic-like behaviors. Cell Rep 2022; 40:111289. [PMID: 36044858 DOI: 10.1016/j.celrep.2022.111289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 06/13/2022] [Accepted: 08/08/2022] [Indexed: 11/22/2022] Open
Abstract
Transcription factors with basic-helix-loop-helix (bHLH) motifs can control neural progenitor fate determination to neurons and oligodendrocytes. How bHLH transcription factors regulate astrogenesis remains largely unknown. Here, we report that NPAS3, a bHLH transcription factor, is a critical regulator of astrogenesis. Npas3 deficiency impairs cortical astrogenesis, correlating with abnormal brain development and autistic-like behaviors. Single-cell transcriptomes reveal that Npas3 knockout induces abnormal transition states in the differentiation trajectories from radial glia to astrocytes. Analysis of chromatin immunoprecipitation sequencing data in primary cortical astrocytes shows that NPAS3 binding targets are involved in functions of brain development and synapse organization. Co-culture assay further indicates that NPAS3-impaired astrogenesis induces synaptic deficits in wild-type neurons. Astrocyte-specific knockdown of NPAS3 in wild-type cortex causes synaptic and behavioral abnormalities associated with the core symptoms in autism. Together, our findings suggest that transcription factor NPAS3 regulates astrogenesis and its subsequent consequences for brain development and behavior.
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Samardžija B, Pavešić Radonja A, Zaharija B, Bergman M, Renner É, Palkovits M, Rubeša G, Bradshaw NJ. Protein Aggregation of NPAS3, Implicated in Mental Illness, Is Not Limited to the V304I Mutation. J Pers Med 2021; 11:1070. [PMID: 34834422 DOI: 10.3390/jpm11111070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 01/01/2023] Open
Abstract
An emerging phenomenon in our understanding of the pathophysiology of mental illness is the idea that specific proteins may form insoluble aggregates in the brains of patients, in partial analogy to similar proteinopathies in neurodegenerative diseases. Several proteins have now been detected as forming such aggregates in the brains of patients, including DISC1, dysbindin-1 and TRIOBP-1. Recently, neuronal PAS domain protein 3 (NPAS3), a known genetic risk factor for schizophrenia, was implicated through a V304I point mutation in a family with major mental illness. Investigation of the mutation revealed that it may lead to aggregation of NPAS3. Here we investigated NPAS3 aggregation in insular cortex samples from 40 individuals, by purifying the insoluble fraction of these samples and testing them by Western blotting. Strikingly, full-length NPAS3 was found in the insoluble fraction of 70% of these samples, implying that aggregation is far more widely spread than can be accounted for by this rare mutation. We investigated the possible mechanism of aggregation further in neuroblastoma cells, finding that oxidative stress plays a larger role than the V304I mutation. Finally, we tested to see if NPAS3 aggregation could also be seen in blood serum, as a more accessible tissue than the human brain for future diagnosis. While no indication of NPAS3 aggregation was seen in the serum, soluble NPAS3 was detected, and was more prevalent in patients with schizophrenia than in those with major depressive disorder or controls. Aggregation of NPAS3 therefore appears to be a widespread and multifactorial phenomenon. Further research is now needed to determine whether it is specifically enhanced in schizophrenia or other mental illnesses.
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Pisanu C, Congiu D, Severino G, Ardau R, Chillotti C, Del Zompo M, Baune BT, Squassina A. Investigation of genetic loci shared between bipolar disorder and risk-taking propensity: potential implications for pharmacological interventions. Neuropsychopharmacology 2021; 46:1680-1692. [PMID: 34035470 PMCID: PMC8280111 DOI: 10.1038/s41386-021-01045-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 11/09/2022]
Abstract
Patients with bipolar disorder (BD) often show increased risk-taking propensity, which may contribute to poor clinical outcome. While these two phenotypes are genetically correlated, there is scarce knowledge on the shared genetic determinants. Using GWAS datasets on BD (41,917 BD cases and 371,549 controls) and risk-taking (n = 466,571), we dissected shared genetic determinants using conjunctional false discovery rate (conjFDR) and local genetic covariance analysis. We investigated specificity of identified targets using GWAS datasets on schizophrenia (SCZ) and attention-deficit hyperactivity disorder (ADHD). The putative functional role of identified targets was evaluated using different tools and GTEx v. 8. Target druggability was evaluated using DGIdb and enrichment for drug targets with genome for REPositioning drugs (GREP). Among 102 loci shared between BD and risk-taking, 87% showed the same direction of effect. Sixty-two were specifically shared between risk-taking propensity and BD, while the others were also shared between risk-taking propensity and either SCZ or ADHD. By leveraging pleiotropic enrichment, we reported 15 novel and specific loci associated with BD and 22 with risk-taking. Among cross-disorder genes, CACNA1C (a known target of calcium channel blockers) was significantly associated with risk-taking propensity and both BD and SCZ using conjFDR (p = 0.001 for both) as well as local genetic covariance analysis, and predicted to be differentially expressed in the cerebellar hemisphere in an eQTL-informed gene-based analysis (BD, Z = 7.48, p = 3.8E-14; risk-taking: Z = 4.66, p = 1.6E-06). We reported for the first time shared genetic determinants between BD and risk-taking propensity. Further investigation into calcium channel blockers or development of innovative ligands of calcium channels might form the basis for innovative pharmacotherapy in patients with BD with increased risk-taking propensity.
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Affiliation(s)
- Claudia Pisanu
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - Donatella Congiu
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - Giovanni Severino
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - Raffaella Ardau
- Unit of Clinical Pharmacology of the University Hospital of Cagliari, Cagliari, Italy
| | - Caterina Chillotti
- Unit of Clinical Pharmacology of the University Hospital of Cagliari, Cagliari, Italy
| | - Maria Del Zompo
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
- Unit of Clinical Pharmacology of the University Hospital of Cagliari, Cagliari, Italy
| | - Bernhard T Baune
- Department of Psychiatry, University of Münster, Münster, Germany
- Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Alessio Squassina
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy.
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Rossi JJ, Rosenfeld JA, Chan KM, Streff H, Nankivell V, Peet DJ, Whitelaw ML, Bersten DC. Molecular characterisation of rare loss-of-function NPAS3 and NPAS4 variants identified in individuals with neurodevelopmental disorders. Sci Rep 2021; 11:6602. [PMID: 33758288 PMCID: PMC7987981 DOI: 10.1038/s41598-021-86041-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/01/2021] [Indexed: 01/01/2023] Open
Abstract
Aberrations in the excitatory/inhibitory balance within the brain have been associated with both intellectual disability (ID) and schizophrenia (SZ). The bHLH-PAS transcription factors NPAS3 and NPAS4 have been implicated in controlling the excitatory/inhibitory balance, and targeted disruption of either gene in mice results in a phenotype resembling ID and SZ. However, there are few human variants in NPAS3 and none in NPAS4 that have been associated with schizophrenia or neurodevelopmental disorders. From a clinical exome sequencing database we identified three NPAS3 variants and four NPAS4 variants that could potentially disrupt protein function in individuals with either developmental delay or ID. The transcriptional activity of the variants when partnered with either ARNT or ARNT2 was assessed by reporter gene activity and it was found that variants which truncated the NPAS3/4 protein resulted in a complete loss of transcriptional activity. The ability of loss-of-function variants to heterodimerise with neuronally enriched partner protein ARNT2 was then determined by co-immunoprecipitation experiments. It was determined that the mechanism for the observed loss of function was the inability of the truncated NPAS3/4 protein to heterodimerise with ARNT2. This further establishes NPAS3 and NPAS4 as candidate neurodevelopmental disorder genes.
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Affiliation(s)
- Joseph J Rossi
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, 5005, Australia
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Clinical Genomics, Baylor Genetics Laboratory, Houston, TX, 77030, USA
| | - Katie M Chan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Victoria Nankivell
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, 5005, Australia
| | - Daniel J Peet
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, 5005, Australia
| | - Murray L Whitelaw
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, 5005, Australia
| | - David C Bersten
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, 5005, Australia.
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Tarczewska A, Greb-Markiewicz B. The Significance of the Intrinsically Disordered Regions for the Functions of the bHLH Transcription Factors. Int J Mol Sci 2019; 20:E5306. [PMID: 31653121 PMCID: PMC6862971 DOI: 10.3390/ijms20215306] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/22/2019] [Accepted: 10/22/2019] [Indexed: 11/17/2022] Open
Abstract
The bHLH proteins are a family of eukaryotic transcription factors regulating expression of a wide range of genes involved in cell differentiation and development. They contain the Helix-Loop-Helix (HLH) domain, preceded by a stretch of basic residues, which are responsible for dimerization and binding to E-box sequences. In addition to the well-preserved DNA-binding bHLH domain, these proteins may contain various additional domains determining the specificity of performed transcriptional regulation. According to this, the family has been divided into distinct classes. Our aim was to emphasize the significance of existing disordered regions within the bHLH transcription factors for their functionality. Flexible, intrinsically disordered regions containing various motives and specific sequences allow for multiple interactions with transcription co-regulators. Also, based on in silico analysis and previous studies, we hypothesize that the bHLH proteins have a general ability to undergo spontaneous phase separation, forming or participating into liquid condensates which constitute functional centers involved in transcription regulation. We shortly introduce recent findings on the crucial role of the thermodynamically liquid-liquid driven phase separation in transcription regulation by disordered regions of regulatory proteins. We believe that further experimental studies should be performed in this field for better understanding of the mechanism of gene expression regulation (among others regarding oncogenes) by important and linked to many diseases the bHLH transcription factors.
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Affiliation(s)
- Aneta Tarczewska
- Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Beata Greb-Markiewicz
- Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
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11
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Greb-Markiewicz B, Kolonko M. Subcellular Localization Signals of bHLH-PAS Proteins: Their Significance, Current State of Knowledge and Future Perspectives. Int J Mol Sci 2019; 20:E4746. [PMID: 31554340 DOI: 10.3390/ijms20194746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/22/2019] [Accepted: 09/23/2019] [Indexed: 12/14/2022] Open
Abstract
The bHLH-PAS (basic helix-loop-helix/ Period-ARNT-Single minded) proteins are a family of transcriptional regulators commonly occurring in living organisms. bHLH-PAS members act as intracellular and extracellular "signals" sensors, initiating response to endo- and exogenous signals, including toxins, redox potential, and light. The activity of these proteins as transcription factors depends on nucleocytoplasmic shuttling: the signal received in the cytoplasm has to be transduced, via translocation, to the nucleus. It leads to the activation of transcription of particular genes and determines the cell response to different stimuli. In this review, we aim to present the current state of knowledge concerning signals that affect shuttling of bHLH-PAS transcription factors. We summarize experimentally verified and published nuclear localization signals/nuclear export signals (NLSs/NESs) in the context of performed in silico predictions. We have used most of the available NLS/NES predictors. Importantly, all our results confirm the existence of a complex system responsible for protein localization regulation that involves many localization signals, which activity has to be precisely controlled. We conclude that the current stage of knowledge in this area is still not complete and for most of bHLH-PAS proteins an experimental verification of the activity of further NLS/NES is needed.
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Bradshaw NJ, Korth C. Protein misassembly and aggregation as potential convergence points for non-genetic causes of chronic mental illness. Mol Psychiatry 2019; 24:936-51. [PMID: 30089789 DOI: 10.1038/s41380-018-0133-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/10/2018] [Accepted: 06/18/2018] [Indexed: 12/13/2022]
Abstract
Chronic mental illnesses (CMI), such as schizophrenia or recurrent affective disorders, are complex conditions with both genetic and non-genetic elements. In many other chronic brain conditions, including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and frontotemporal dementia, sporadic instances of the disease are more common than gene-driven familial cases. Yet, the pathology of these conditions can be characterized by the presence of aberrant protein homeostasis, proteostasis, resulting in misfolded or aggregated proteins in the brains of patients that predominantly do not derive from genetic mutations. While visible deposits of aggregated protein have not yet been detected in CMI patients, we propose the existence of more subtle protein misassembly in these conditions, which form a continuum with the psychiatric phenotypes found in the early stages of many neurodegenerative conditions. Such proteinopathies need not rely on genetic variation. In a similar manner to the established aberrant neurotransmitter homeostasis in CMI, aberrant homeostasis of proteins is a functional statement that can only partially be explained by, but is certainly complementary to, genetic approaches. Here, we review evidence for aberrant proteostasis signatures from post mortem human cases, in vivo animal work, and in vitro analysis of candidate proteins misassembled in CMI. The five best-characterized proteins in this respect are currently DISC1, dysbindin-1, CRMP1, TRIOBP-1, and NPAS3. Misassembly of these proteins with inherently unstructured domains is triggered by extracellular stressors and thus provides a converging point for non-genetic causes of CMI.
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Abstract
Understanding the biological basis for human-specific cognitive traits presents both immense challenges and unique opportunities. Although the question of what makes us human has been investigated with several different methods, the rise of comparative genomics, epigenomics, and medical genetics has provided tools to help narrow down and functionally assess the regions of the genome that seem evolutionarily relevant along the human lineage. In this review, we focus on how medical genetic cases have provided compelling functional evidence for genes and loci that appear to have interesting evolutionary signatures in humans. Furthermore, we examine a special class of noncoding regions, human accelerated regions (HARs), that have been suggested to show human-lineage-specific divergence, and how the use of clinical and population data has started to provide functional information to examine these regions. Finally, we outline methods that provide new insights into functional noncoding sequences in evolution.
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Affiliation(s)
- Ryan N Doan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Taehwan Shin
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Departments of Pediatrics and Neurology, Harvard Medical School, Boston, Massachusetts 02138, USA
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Wang AW, Avramopoulos D, Lori A, Mulle J, Conneely K, Powers A, Duncan E, Almli L, Massa N, McGrath J, Schwartz AC, Goes FS, Weng L, Wang R, Yolken R, Ruczinski I, Gillespie CF, Jovanovic T, Ressler K, Pulver AE, Pearce BD. Genome-wide association study in two populations to determine genetic variants associated with Toxoplasma gondii infection and relationship to schizophrenia risk. Prog Neuropsychopharmacol Biol Psychiatry 2019; 92:133-147. [PMID: 30610941 DOI: 10.1016/j.pnpbp.2018.12.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/20/2018] [Accepted: 12/30/2018] [Indexed: 01/10/2023]
Abstract
T. gondii (TOXO) infects over one billion people worldwide, yet the literature lacks a Genome Wide Association Study (GWAS) focused on genetic variants controlling the persistence of TOXO infection. To identify putative T. gondii susceptibility genes, we performed a GWAS using IgG seropositivity as the outcome variable in a discovery sample (n = 790) from an Ashkenazi dataset, and a second sample of predominately African Americans (The Grady Trauma Project, n = 285). We also performed a meta-analyses of the 2 cohorts. None of the SNPs in these analyses was statistically significant after Bonferroni correction for multiple comparisons. In the Ashkenazi population, the gene region of CHIA (chitinase) showed the most nominally significant association with TOXO. Prior studies have shown that the production of chitinase by macrophages in the brain responding to TOXO infection is crucial for controlling the burden of T. gondii cysts. We found a surprising number of genes involved in neurodevelopment and psychiatric disorders among our top hits even though our outcome variable was TOXO infection. In the meta-analysis combining the Ashkenazi and Grady Trauma Project samples, there was enrichment for genes implicated in schizophrenia spectrum disorders (p < .05). Upon limiting our sample to those without mental illness, two schizophrenia related genes (CNTNAP2, GABAR2) still had significant TOXO-associated variants at the p < .05 level, but did not pass the genome wide significance threshold after correction for multiple comparisons. Using Ingenuity Systems molecular network analysis, we identified molecular nodes suggesting that while different genetic variants associated with TOXO in the two population samples, the molecular pathways for TOXO susceptibility nevertheless converged on common pathways. Molecular nodes in these common pathways included NOTCH1, CD44, and RXRA. Prior studies show that CD44 participates in TOXO-induced immunopathology and that RXRA is instrumental in regulating T-helper immune responses. These data provide new insights into the pathophysiology of this common neurotropic parasite.
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Affiliation(s)
- Alex W Wang
- Department of Epidemiology, Rollins School of Public Health, 1518 Clifton Rd., Atlanta, GA 30322, United States
| | - Dimitrios Avramopoulos
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Adriana Lori
- Department of Human Genetics, Emory University, Atlanta, GA, United States
| | - Jennifer Mulle
- Department of Human Genetics, Emory University, Atlanta, GA, United States
| | - Karen Conneely
- Department of Human Genetics, Emory University, Atlanta, GA, United States
| | - Abigail Powers
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, United States
| | - Erica Duncan
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, United States; Atlanta Veterans Affairs Medical Center, 1670 Clairmont Rd, Decatur, GA 30033, United States
| | - Lynn Almli
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, United States
| | - Nicholas Massa
- Department of Epidemiology, Rollins School of Public Health, 1518 Clifton Rd., Atlanta, GA 30322, United States; Atlanta Veterans Affairs Medical Center, 1670 Clairmont Rd, Decatur, GA 30033, United States
| | - John McGrath
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ann C Schwartz
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, United States
| | - Fernando S Goes
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lei Weng
- Department of Epidemiology, Rollins School of Public Health, 1518 Clifton Rd., Atlanta, GA 30322, United States
| | - Ruihua Wang
- McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Robert Yolken
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ingo Ruczinski
- Bloomberg School of Public Heath, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Charles F Gillespie
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, United States
| | - Tanja Jovanovic
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, United States
| | - Kerry Ressler
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, United States; Department of Psychiatry, Harvard School of Medicine, 25 Shattuck St, Boston, MA 02115, United States
| | - Ann E Pulver
- Bloomberg School of Public Heath, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Brad D Pearce
- Department of Epidemiology, Rollins School of Public Health, 1518 Clifton Rd., Atlanta, GA 30322, United States.
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15
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Pearl JR, Colantuoni C, Bergey DE, Funk CC, Shannon P, Basu B, Casella AM, Oshone RT, Hood L, Price ND, Ament SA. Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders. Cell Syst 2019; 8:122-135.e7. [DOI: 10.1016/j.cels.2019.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 10/19/2018] [Accepted: 01/14/2019] [Indexed: 12/23/2022]
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Abstract
Background NPAS3 encodes a transcription factor which has been associated with multiple human psychiatric and neurodevelopmental disorders. In mice, deletion of Npas3 was found to cause alterations in neurodevelopment, as well as a marked reduction in neurogenesis in the adult mouse hippocampus. This neurogenic deficit, alongside the reduction in cortical interneuron number, likely contributes to the behavioral and cognitive alterations observed in Npas3 knockout mice. Although loss of Npas3 has been found to affect proliferation and apoptosis, the molecular function of NPAS3 is largely uncharacterized outside of predictions based on its high homology to bHLH–PAS transcription factors. Here we set out to characterize NPAS3 as a transcription factor, and to confirm whether NPAS3 acts as predicted for a Class 1 bHLH–PAS family member. Results Through these studies we have experimentally demonstrated that NPAS3 behaves as a true transcription factor, capable of gene regulation through direct association with DNA. NPAS3 and ARNT are confirmed to directly interact in human cells through both bHLH and PAS dimerization domains. The C-terminus of NPAS3 was found to contain a functional transactivation domain. Further, the NPAS3::ARNT heterodimer was shown to directly regulate the expression of VGF and TXNIP through binding of their proximal promoters. Finally, we assessed the effects of three human variants of NPAS3 on gene regulatory function and do not observe significant deficits. Conclusions NPAS3 is a true transcription factor capable of regulating expression of target genes through their promoters by directly cooperating with ARNT. The tested human variants of NPAS3 require further characterization to identify their effects on NPAS3 expression and function in the individuals that carry them. These data enhance our understanding of the molecular function of NPAS3 and the mechanism by which it contributes to normal and abnormal neurodevelopment and neural function. Electronic supplementary material The online version of this article (10.1186/s12867-018-0117-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Leiah M Luoma
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Fred B Berry
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada. .,Department of Surgery, 3002D Li Ka Shing Centre, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
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Luoma LM, Macintyre G, Tibbo PG, Wild TC, Colman I, Purdon SE. NPAS3 exonic SNP genotype is linked to working memory performance in healthy young adults. Psychiatry Res 2018; 265:263-264. [PMID: 29763846 DOI: 10.1016/j.psychres.2018.04.063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 03/28/2018] [Accepted: 04/26/2018] [Indexed: 11/15/2022]
Affiliation(s)
- Leiah M Luoma
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Georgina Macintyre
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Philip G Tibbo
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada
| | - T Cameron Wild
- School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Ian Colman
- School of Epidemiology, Public Health and Preventative Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Scot E Purdon
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada; Neuropsychology Service, Alberta Hospital Edmonton, Edmonton, AB, Canada.
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Fahim A, Rehman Z, Bhatti MF, Ali A, Virk N, Rashid A, Paracha RZ. Structural insights and characterization of human Npas4 protein. PeerJ 2018; 6:e4978. [PMID: 29915698 PMCID: PMC6004298 DOI: 10.7717/peerj.4978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 05/15/2018] [Indexed: 12/25/2022] Open
Abstract
Npas4 is an activity dependent transcription factor which is responsible for gearing the expression of target genes involved in neuro-transmission. Despite the importance of Npas4 in many neuronal diseases, the tertiary structure of Npas4 protein along with its physico-chemical properties is limited. In the current study, first we perfomed the phylogenetic analysis of Npas4 and determined the content of hydrophobic, flexible and order-disorder promoting amino acids. The protein binding regions, post-translational modifications and crystallization propensity of Npas4 were predicted through different in-silico methods. The three dimensional model of Npas4 was predicted through LOMET, SPARSKS-X, I-Tasser, RaptorX, MUSTER and Pyhre and the best model was selected on the basis of Ramachandran plot, PROSA, and Qmean scores. The best model was then subjected to further refinement though MODREFINER. Finally the interacting partners of Npas4 were identified through STRING database. The phylogenetic analysis showed the human Npas4 gene to be closely related to other primates such as chimpanzees, monkey, gibbon. The physiochemical properties of Npas4 showed that it is an intrinsically disordered protein with N-terminal ordered region. The post-translational modification analyses indicated absence of acetylation and mannosylation sites. Three potential phosphorylation sites (S108, T130 and T136) were found in PAS A domain whilst a single phosphorylation site (S273) was present in PAS B domain. The predicted tertiary structure of Npas4 showed that bHLH domain and PAS domain possess tertiary structures while the rest of the protein exhibited disorder property. Protein-protein interaction analysis revealed NPas4 interaction with various proteins which are mainly involved in nuclear trafficking of proteins to cytoplasm, activity regulated gene transcription and neurodevelopmental disorders. Moreover the analysis also highlighted the direct relation to proteins involved in promoting neuronal survival, plasticity and cAMP responsive element binding protein proteins. The current study helps in understanding the physicochemical properties and reveals the neuro-modulatory role of Npas4 in crucial pathways involved in neuronal survival and neural signalling hemostasis.
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Affiliation(s)
- Ammad Fahim
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Zaira Rehman
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Nasar Virk
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Amir Rashid
- Army Medical College, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Rehan Zafar Paracha
- Research Center for Modeling and Simulation (RCMS), National University of Sciences & Technology (NUST), Islamabad, Pakistan
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Halgren C, Nielsen NM, Nazaryan-Petersen L, Silahtaroglu A, Collins RL, Lowther C, Kjaergaard S, Frisch M, Kirchhoff M, Brøndum-Nielsen K, Lind-Thomsen A, Mang Y, El-Schich Z, Boring CA, Mehrjouy MM, Jensen PK, Fagerberg C, Krogh LN, Hansen J, Bryndorf T, Hansen C, Talkowski ME, Bak M, Tommerup N, Bache I. Risks and Recommendations in Prenatally Detected De Novo Balanced Chromosomal Rearrangements from Assessment of Long-Term Outcomes. Am J Hum Genet 2018; 102:1090-1103. [PMID: 29805044 DOI: 10.1016/j.ajhg.2018.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/06/2018] [Indexed: 12/20/2022] Open
Abstract
The 6%-9% risk of an untoward outcome previously established by Warburton for prenatally detected de novo balanced chromosomal rearrangements (BCRs) does not account for long-term morbidity. We performed long-term follow-up (mean 17 years) of a registry-based nationwide cohort of 41 individuals carrying a prenatally detected de novo BCR with normal first trimester screening/ultrasound scan. We observed a significantly higher frequency of neurodevelopmental and/or neuropsychiatric disorders than in a matched control group (19.5% versus 8.3%, p = 0.04), which was increased to 26.8% upon clinical follow-up. Chromosomal microarray of 32 carriers revealed no pathogenic imbalances, illustrating a low prognostic value when fetal ultrasound scan is normal. In contrast, mate-pair sequencing revealed disrupted genes (ARID1B, NPAS3, CELF4), regulatory domains of known developmental genes (ZEB2, HOXC), and complex BCRs associated with adverse outcomes. Seven unmappable autosomal-autosomal BCRs with breakpoints involving pericentromeric/heterochromatic regions may represent a low-risk group. We performed independent phenotype-aware and blinded interpretation, which accurately predicted benign outcomes (specificity = 100%) but demonstrated relatively low sensitivity for prediction of the clinical outcome in affected carriers (sensitivity = 45%-55%). This sensitivity emphasizes the challenges associated with prenatal risk prediction for long-term morbidity in the absence of phenotypic data given the still immature annotation of the morbidity genome and poorly understood long-range regulatory mechanisms. In conclusion, we upwardly revise the previous estimates of Warburton to a morbidity risk of 27% and recommend sequencing of the chromosomal breakpoints as the first-tier diagnostic test in pregnancies with a de novo BCR.
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Levchenko A, Kanapin A, Samsonova A, Gainetdinov RR. Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development. Genome Biol Evol 2018; 10:166-188. [PMID: 29149249 PMCID: PMC5767953 DOI: 10.1093/gbe/evx240] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2017] [Indexed: 12/24/2022] Open
Abstract
The review discusses, in a format of a timeline, the studies of different types of genetic variants, present in Homo sapiens, but absent in all other primate, mammalian, or vertebrate species, tested so far. The main characteristic of these variants is that they are found in regions of high evolutionary conservation. These sequence variations include single nucleotide substitutions (called human accelerated regions), deletions, and segmental duplications. The rationale for finding such variations in the human genome is that they could be responsible for traits, specific to our species, of which the human brain is the most remarkable. As became obvious, the vast majority of human-specific single nucleotide substitutions are found in noncoding, likely regulatory regions. A number of genes, associated with these human-specific alleles, often through novel enhancer activity, were in fact shown to be implicated in human-specific development of certain brain areas, including the prefrontal cortex. Human-specific deletions may remove regulatory sequences, such as enhancers. Segmental duplications, because of their large size, create new coding sequences, like new functional paralogs. Further functional study of these variants will shed light on evolution of our species, as well as on the etiology of neurodevelopmental disorders.
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Affiliation(s)
- Anastasia Levchenko
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
| | - Alexander Kanapin
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
- Department of Oncology, University of Oxford, United Kingdom
| | - Anastasia Samsonova
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
- Department of Oncology, University of Oxford, United Kingdom
| | - Raul R Gainetdinov
- Institute of Translational Biomedicine, Saint Petersburg State University, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia
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22
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Michaelson JJ, Shin MK, Koh JY, Brueggeman L, Zhang A, Katzman A, McDaniel L, Fang M, Pufall M, Pieper AA. Neuronal PAS Domain Proteins 1 and 3 Are Master Regulators of Neuropsychiatric Risk Genes. Biol Psychiatry 2017; 82:213-223. [PMID: 28499489 PMCID: PMC6901278 DOI: 10.1016/j.biopsych.2017.03.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND NPAS3 has been established as a robust genetic risk factor in major mental illness. In mice, loss of neuronal PAS domain protein 3 (NPAS3) impairs postnatal hippocampal neurogenesis, while loss of the related protein NPAS1 promotes it. These and other findings suggest a critical role for NPAS proteins in neuropsychiatric functioning, prompting interest in the molecular pathways under their control. METHODS We used RNA sequencing coupled with chromatin immunoprecipitation sequencing to identify genes directly regulated by NPAS1 and NPAS3 in the hippocampus of wild-type, Npas1-/-, and Npas3-/- mice. Computational integration with human genetic and expression data revealed the disease relevance of NPAS-regulated genes and pathways. Specific findings were confirmed at the protein level by Western blot. RESULTS This is the first in vivo, transcriptome-scale investigation of genes regulated by NPAS1 and NPAS3. These transcription factors control an ensemble of genes that are themselves also major regulators of neuropsychiatric function. Specifically, Fmr1 (fragile X syndrome) and Ube3a (Angelman syndrome) are transcriptionally regulated by NPAS3, as is the neurogenesis regulator Notch. Dysregulation of these pathways was confirmed at the protein level. Furthermore, NPAS1/3 targets show increased human genetic burden for schizophrenia and intellectual disability. CONCLUSIONS Together, these data provide a clear, unbiased view of the full spectrum of genes regulated by NPAS1 and NPAS3 and show that these transcription factors are master regulators of neuropsychiatric function. These findings expose the molecular pathophysiology of NPAS1/3 mutations and provide a striking example of the shared, combinatorial nature of molecular pathways that underlie diagnostically distinct neuropsychiatric conditions.
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Affiliation(s)
- Jacob J Michaelson
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa; Department of Biomedical Engineering, University of Iowa College of Engineering, University of Iowa, Iowa City, Iowa; Department of Communication Sciences and Disorders, University of Iowa College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa; Iowa Institute of Human Genetics, University of Iowa, Iowa City, Iowa; Genetics Cluster Initiative, University of Iowa, Iowa City, Iowa; The DeLTA Center, University of Iowa, Iowa City, Iowa; University of Iowa Informatics Initiative, University of Iowa, Iowa City, Iowa.
| | - Min-Kyoo Shin
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Jin-Young Koh
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Leo Brueggeman
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Angela Zhang
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Aaron Katzman
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Latisha McDaniel
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Mimi Fang
- Department of Biochemistry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Miles Pufall
- Department of Biochemistry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Andrew A Pieper
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa; Department of Neurology, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa; Free Radical and Radiation Biology Program, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa; Department of Veterans Affairs, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa; Pappajohn Biomedical Institute, University of Iowa, Iowa City, Iowa; Weill Cornell Autism Research Program, Weill Cornell Medicine, Cornell University, New York, New York
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Moen MJ, Adams HH, Brandsma JH, Dekkers DH, Akinci U, Karkampouna S, Quevedo M, Kockx CE, Ozgür Z, van IJcken WF, Demmers J, Poot RA. An interaction network of mental disorder proteins in neural stem cells. Transl Psychiatry 2017; 7:e1082. [PMID: 28375211 DOI: 10.1038/tp.2017.52] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 02/06/2017] [Accepted: 02/13/2017] [Indexed: 12/22/2022] Open
Abstract
Mental disorders (MDs) such as intellectual disability (ID), autism spectrum disorders (ASD) and schizophrenia have a strong genetic component. Recently, many gene mutations associated with ID, ASD or schizophrenia have been identified by high-throughput sequencing. A substantial fraction of these mutations are in genes encoding transcriptional regulators. Transcriptional regulators associated with different MDs but acting in the same gene regulatory network provide information on the molecular relation between MDs. Physical interaction between transcriptional regulators is a strong predictor for their cooperation in gene regulation. Here, we biochemically purified transcriptional regulators from neural stem cells, identified their interaction partners by mass spectrometry and assembled a protein interaction network containing 206 proteins, including 68 proteins mutated in MD patients and 52 proteins significantly lacking coding variation in humans. Our network shows molecular connections between established MD proteins and provides a discovery tool for novel MD genes. Network proteins preferentially co-localize on the genome and cooperate in disease-relevant gene regulation. Our results suggest that the observed transcriptional regulators associated with ID, ASD or schizophrenia are part of a transcriptional network in neural stem cells. We find that more severe mutations in network proteins are associated with MDs that include lower intelligence quotient (IQ), suggesting that the level of disruption of a shared transcriptional network correlates with cognitive dysfunction.
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Yang D, Zhang W, Padhiar A, Yue Y, Shi Y, Zheng T, Davis K, Zhang Y, Huang M, Li Y, Sha L. NPAS3 Regulates Transcription and Expression of VGF: Implications for Neurogenesis and Psychiatric Disorders. Front Mol Neurosci 2016; 9:109. [PMID: 27877109 PMCID: PMC5099284 DOI: 10.3389/fnmol.2016.00109] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/12/2016] [Indexed: 01/01/2023] Open
Abstract
Neuronal PAS domain protein 3 (NPAS3) and VGF (VGF Nerve Growth Factor (NGF) Inducible) are important for neurogenesis and psychiatric disorders. Previously, we have demonstrated that NPAS3 regulates VGF at the transcriptional level. In this study, VGF (non-acronymic) was found regulated by NPAS3 in neuronal stem cells. However, the underlying mechanism of this regulation remains unclear. The aim of this study was to explore the correlation of NPAS3 and VGF, and their roles in neural cell proliferation, in the context of psychiatric illnesses. First, we focused on the structure of NPAS3, to identify the functional domain of NPAS3. Truncated NPAS3 lacking transactivation domain was also found to activate VGF, which suggested that not only transactivation domain but other structural motifs were also involved in the regulation. Second, Mutated enhancer box (E-box) of VGF promoter showed a significant response to this basic helix-loop-helix (bHLH) transcription factor, which suggested an indirect regulatory mechanism for controlling VGF expression by NPAS3. κB site within VGF promoter was identified for VGF activation induced by NPAS3, apart from direct binding to E-box. Furthermore, ectopically expressed NPAS3 in PC12 cells produced parallel responses for nuclear factor kappa-light-chain-enhancer of activated B cells [NF-κB (P65)] expression, which specifies that NPAS3 regulates VGF through the NF-κB signaling pathway. Over-expression of NPAS3 also enhances the cell proliferation, which can be blocked by knockdown of VGF. Finally, NPAS3 was found to influence proliferation of neural cells through VGF. Therefore, downstream signaling pathways that are responsible for NPAS3-VGF induced proliferation via glutamate receptors were explored. Combining this work and published literature, a potential network composed by NPAS3, NF-κB, Brain-Derived Neurotrophic Factor (BDNF), NGF and VGF, was proposed. This network collectively detailed how NPAS3 connects with VGF and intersected neural cell proliferation, synaptic activity and psychiatric disorders.
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Affiliation(s)
- Dongxue Yang
- College of Basic Medicine, Dalian Medical University Dalian, China
| | - Wenbo Zhang
- College of Basic Medicine, Dalian Medical University Dalian, China
| | - Arshad Padhiar
- College of Basic Medicine, Dalian Medical University Dalian, China
| | - Yao Yue
- College of Basic Medicine, Dalian Medical University Dalian, China
| | - Yonghui Shi
- College of Basic Medicine, Dalian Medical University Dalian, China
| | - Tiezheng Zheng
- College of Basic Medicine, Dalian Medical University Dalian, China
| | - Kaspar Davis
- Department of Physical Education, Dalian University of Technology Dalian, China
| | - Yu Zhang
- Department of Physical Education, Dalian University of Technology Dalian, China
| | - Min Huang
- College of Basic Medicine, Dalian Medical University Dalian, China
| | - Yuyuan Li
- College of Basic Medicine, Dalian Medical University Dalian, China
| | - Li Sha
- College of Basic Medicine, Dalian Medical University Dalian, China
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Wu D, Su X, Potluri N, Kim Y, Rastinejad F. NPAS1-ARNT and NPAS3-ARNT crystal structures implicate the bHLH-PAS family as multi-ligand binding transcription factors. eLife 2016; 5. [PMID: 27782878 PMCID: PMC5111884 DOI: 10.7554/elife.18790] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/25/2016] [Indexed: 02/07/2023] Open
Abstract
The neuronal PAS domain proteins NPAS1 and NPAS3 are members of the basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) family, and their genetic deficiencies are linked to a variety of human psychiatric disorders including schizophrenia, autism spectrum disorders and bipolar disease. NPAS1 and NPAS3 must each heterodimerize with the aryl hydrocarbon receptor nuclear translocator (ARNT), to form functional transcription complexes capable of DNA binding and gene regulation. Here we examined the crystal structures of multi-domain NPAS1-ARNT and NPAS3-ARNT-DNA complexes, discovering each to contain four putative ligand-binding pockets. Through expanded architectural comparisons between these complexes and HIF-1α-ARNT, HIF-2α-ARNT and CLOCK-BMAL1, we show the wider mammalian bHLH-PAS family is capable of multi-ligand-binding and presents as an ideal class of transcription factors for direct targeting by small-molecule drugs. DOI:http://dx.doi.org/10.7554/eLife.18790.001 Transcription factors are proteins that can bind to DNA to regulate the activity of genes. One family of transcription factors in mammals is known as the bHLH-PAS family, which consists of sixteen members including NPAS1 and NPAS3. These two proteins are both found in nerve cells, and genetic mutations that affect NPAS1 or NPAS3 have been linked to psychiatric conditions in humans. Therefore, researchers would like to discover new drugs that can bind to these proteins and control their activities in nerve cells. Understanding the three-dimensional structure of a protein can aid the discovery of small molecules that can bind to these proteins and act as drugs. Proteins in the bHLH-PAS family have to form pairs in order to bind to DNA: NPAS1 and NPAS3 both interact with another bHLH-PAS protein called ARNT, but it is not clear exactly how this works. In 2015, a team of researchers described the shapes that ARNT adopts when it forms pairs with two other bHLH-PAS proteins that are important for sensing when oxygen levels drop in cells. Here, Wu et al. – including many of the researchers involved in the earlier work – have used a technique called X-ray crystallography to determine the three-dimensional shapes of NPAS1 when it is bound to ARNT, and NPAS3 when it is bound to both ARNT and DNA. The experiments show that each of these structures contains four distinct pockets that certain small molecules might be able to bind to. The NPAS1 and NPAS3 structures are similar to each other and to the previously discovered bHLH-PAS structures involved in oxygen sensing. Further analysis of other bHLH-PAS proteins suggests that all the members of this protein family are likely to be able to bind to small molecules and should therefore be considered as potential drug targets. The next step following on from this work is to identify small molecules that bind to bHLH-PAS proteins, which will help to reveal the genes that are regulated by this family. In the future, these small molecules may have the potential to be developed into new drugs to treat psychiatric conditions and other diseases in humans. DOI:http://dx.doi.org/10.7554/eLife.18790.002
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Affiliation(s)
- Dalei Wu
- Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, United States
| | - Xiaoyu Su
- Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, United States
| | - Nalini Potluri
- Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, United States
| | - Youngchang Kim
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, United States
| | - Fraydoon Rastinejad
- Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, United States
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Wu D, Rastinejad F. Structural characterization of mammalian bHLH-PAS transcription factors. Curr Opin Struct Biol 2016; 43:1-9. [PMID: 27721191 DOI: 10.1016/j.sbi.2016.09.011] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/06/2016] [Accepted: 09/21/2016] [Indexed: 11/28/2022]
Abstract
The mammalian basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) transcription factors share common architectural features that include a bHLH DNA-binding domain and tandemly positioned PAS domains. The sixteen members of this family include the hypoxia-inducible factors (HIF-1α and HIF-2α), ARNT (also known as HIF-1β), CLOCK and BMAL1. Most bHLH-PAS proteins have been genetically linked to variety of diseases in humans, including cancers, metabolic syndromes and psychiatric conditions. To function as transcription factors, the bHLH-PAS proteins must form heterodimeric complexes. Recent crystallographic studies of HIF-α-ARNT and CLOCK-BMAL1 complexes have unveiled the organization of their multi-domain bHLH-PAS-A-PAS-B segments, revealing how these architectures can give rise to unique patterns of heterodimerization. As our structural understanding becomes better integrated with ligand-discovery and target gene identification, a more comprehensive picture of their architectural and functional properties will emerge.
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Affiliation(s)
- Dalei Wu
- Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827, USA; State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Fraydoon Rastinejad
- Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827, USA.
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Abstract
Psychiatric disorders continue to be among the most challenging disorders to diagnose and treat because there is no single genetic or anatomical locus that is causative for the disease. Current treatments are often blunt tools used to ameliorate the most severe symptoms, at the risk of disrupting functional neural systems. There is a critical need to develop new therapeutic strategies that can target circumscribed functional or anatomical domains of pathology. Adult hippocampal neurogenesis may be one such domain. Here, we review the evidence suggesting that adult hippocampal neurogenesis plays a role in emotional regulation and forms of learning and memory that include temporal and spatial memory encoding and context discrimination, and that its dysregulation is associated with psychiatric disorders, such as affective disorders, schizophrenia, and drug addiction. Further, adult neurogenesis has proven to be an effective model to investigate basic processes of neuronal development and converging evidence suggests that aberrant neural development may be an etiological factor, even in late-onset diseases. Constitutive neurogenesis in the hippocampus of the mature brain reflects large-scale plasticity unique to this region and could be a potential hub for modulation of a subset of cognitive and affective behaviors that are affected by multiple psychiatric disorders.
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Affiliation(s)
- Eunchai Kang
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Zhexing Wen
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Hongjun Song
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Kimberly M Christian
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Guo-Li Ming
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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Nucifora LG, Wu YC, Lee BJ, Sha L, Margolis RL, Ross CA, Sawa A, Nucifora FC. A Mutation in NPAS3 That Segregates with Schizophrenia in a Small Family Leads to Protein Aggregation. Mol Neuropsychiatry 2016; 2:133-144. [PMID: 27867938 DOI: 10.1159/000447358] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/31/2016] [Indexed: 12/21/2022]
Abstract
Schizophrenia and other major mental illnesses result from a complex interplay of genetic and environmental factors. We previously identified a mutation in NPAS3 that results in a valine to isoleucine (V304I) amino acid substitution segregating with schizophrenia in a small family. The amino acid change occurs in a potentially critical region for protein function. Furthermore, the same amino acid substitution in proteins related to familial Alzheimer's disease and transthyretin amyloidosis has been associated with protein aggregation. In this study, we demonstrate that NPAS3 is prone to aggregation, and that the V304I mutation in NPAS3 increases this propensity in both bacterial and mammalian expression systems. We also show that NPAS3-V304I reduces soluble endogenous NPAS3, and increases insoluble endogenous NPAS3 and leads to alteration of transcriptional activity. These results suggest that protein aggregation, potentially leading to cell dysfunction via a loss of protein function through sequestration, may contribute to the pathogenesis of schizophrenia and other forms of mental illness. Further exploration of the mechanisms leading to abnormal protein quality control could lead to new therapeutic targets.
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Affiliation(s)
- Leslie G Nucifora
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, Md., USA
| | - YeeWen Candace Wu
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, Md., USA
| | - Brian J Lee
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, Md., USA
| | - Li Sha
- Department of Biotechnology, Dalian Medical University, Dalian, China
| | - Russell L Margolis
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, Md., USA
| | - Christopher A Ross
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, Md., USA
| | - Akira Sawa
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, Md., USA
| | - Frederick C Nucifora
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, Md., USA
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González-Peñas J, Arrojo M, Paz E, Brenlla J, Páramo M, Costas J. Cumulative role of rare and common putative functional genetic variants at NPAS3 in schizophrenia susceptibility. Am J Med Genet B Neuropsychiatr Genet 2015; 168:528-35. [PMID: 25982957 DOI: 10.1002/ajmg.b.32324] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 05/04/2015] [Indexed: 11/07/2022]
Abstract
Schizophrenia may be considered a human-specific disorder arisen as a maladaptive by-product of human-specific brain evolution. Therefore, genetic variants involved in susceptibility to schizophrenia may be identified among those genes related to acquisition of human-specific traits. NPAS3, a transcription factor involved in central nervous system development and neurogenesis, seems to be implicated in the evolution of human brain, as it is the human gene with most human-specific accelerated elements (HAEs), i.e., .mammalian conserved regulatory sequences with accelerated evolution in the lineage leading to humans after human-chimpanzee split. We hypothesize that any nucleotide variant at the NPAS3 HAEs may lead to altered susceptibility to schizophrenia. Twenty-one variants at these HAEs detected by the 1000 genomes Project, as well as five additional variants taken from psychiatric genome-wide association studies, were genotyped in 538 schizophrenic patients and 539 controls from Galicia. Analyses at the haplotype level or based on the cumulative role of the variants assuming different susceptibility models did not find any significant association in spite of enough power under several plausible scenarios regarding direction of effect and the specific role of rare and common variants. These results suggest that, contrary to our hypothesis, the special evolution of the NPAS3 HAEs in Homo relaxed the strong constraint on sequence that characterized these regions during mammalian evolution, allowing some sequence changes without any effect on schizophrenia risk.
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Affiliation(s)
- Javier González-Peñas
- Instituto de investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Manuel Arrojo
- Instituto de investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain.,Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Eduardo Paz
- Instituto de investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain.,Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Julio Brenlla
- Instituto de investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain.,Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Mario Páramo
- Instituto de investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain.,Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Javier Costas
- Instituto de investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
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Abstract
Carbazoles represent an important class of heterocycles. These have been reported to exhibit diverse biological activities such as antimicrobial, antitumor, antiepileptic, antihistaminic, antioxidative, anti-inflammatory, antidiarrhoeal, analgesic, neuroprotective and pancreatic lipase inhibition properties. A series of carbazole derivatives such as N-substituted carbazoles, benzocarbazoles, furocarbazoles, pyrrolocarbazoles, indolocarbazoles, imidazocarbazoles, etc. have been synthesized. The N-substituted derivatives have gained the attention of researchers due to their therapeutic potential against neurological disorders and cell proliferation. Herein an attempt is made to review the medicinal importance of recently synthesized N-substituted carbazoles.
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Pereira-Terra P, Kholdebarin R, Higgins M, Iwasiow BM, Correia-Pinto J, Keijzer R. Lower NPAS3 expression during the later stages of abnormal lung development in rat congenital diaphragmatic hernia. Pediatr Surg Int 2015; 31:659-63. [PMID: 25862168 DOI: 10.1007/s00383-015-3703-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
Abstract
PURPOSE Congenital diaphragmatic hernia (CDH) is characterized by a developmental defect in the diaphragm, pulmonary hypoplasia and pulmonary hypertension. NPAS3 is a PAS domain transcription factor regulating Drosophila tracheogenesis. NPAS3 null mice develop pulmonary hypoplasia in utero and die after birth due to respiratory failure. We aimed to evaluate NPAS3 expression during normal and abnormal lung development due to CDH. METHODS CDH was induced by administering 100 mg/ml nitrofen to time-pregnant dams on embryonic day (E) 9 of gestation. Lungs were isolated on E15, E18 and E21 and NPAS3 localization was determined by immunohistochemistry and quantified using Western blotting. RESULTS We found that only E21 hypoplastic CDH lungs have reduced expression of NPAS3 in the terminal saccules. Western blotting confirmed the down-regulation of NPAS3 protein in the nitrofen-induced hypoplastic lungs. CONCLUSIONS We demonstrate for the first time that nitrofen-induced hypoplastic CDH lungs have reduced NPAS3 expression in the terminal saccules during the later stages of abnormal lung development. Our findings suggest that NPAS3 is associated with pulmonary hypoplasia in CDH.
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Mei H, Li L, Liu S, Jiang F, Griswold M, Mosley T. The uniform-score gene set analysis for identifying common pathways associated with different diabetes traits. BMC Genomics 2015; 16:336. [PMID: 25898945 PMCID: PMC4415316 DOI: 10.1186/s12864-015-1515-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 04/09/2015] [Indexed: 02/07/2023] Open
Abstract
Background Genetic heritability and expression study have shown that different diabetes traits have common genetic components and pathways. A computationally efficient pathway analysis of GWAS results will benefit post-GWAS study of SNP associations and identification of common genetic pathways from diabetes GWAS can help to improve understanding of the disease pathogenesis. Results We proposed a uniform-score gene-set analysis (USGSA) with implemented package to unify different gene measures by a uniform score for identifying pathways from GWAS data, and use a pre-generated permutation distribution table to quickly obtain multiple-testing adjusted p-value. Simulation studies of uniform score for four gene measures (minP, 2ndP, simP and fishP) have shown that USGSA has strictly controlled family-wise error rate. The power depends on types of gene measure. USGSA with a two-stage study strategy was applied to identify common pathways associated with diabetes traits based on public dbGaP GWAS results. The study identified 7 gene sets that contain binding motifs at promoter region of component genes for 5 transcription factors (TFs) of FOXO4, TCF3, NFAT, VSX1 and POU2F1, and 1 microRNA of mir-218. These gene sets include 25 common genes that are among top 5% of the gene associations over genome for all GWAS. Previous evidences showed that nearly all of these genes are mainly expressed in the brain. Conclusions USGSA is a computationally efficient approach for pathway analysis of GWAS data with promoted interpretability and comparability. The pathway analysis suggested that different diabetes traits share common pathways and component genes are potentially regulated by common TFs and microRNA. The result also indicated that the central nervous system has a critical role in diabetes pathogenesis. The findings will be important in formulating novel hypotheses for guiding follow-up studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1515-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Mei
- Center of Biostatistics & Bioinformatics, University of Mississippi Medical Center, Jackson, MS, USA. .,Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Lianna Li
- Department of Biology, Tougaloo College, Jackson, MS, USA.
| | - Shijian Liu
- Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Fan Jiang
- Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Michael Griswold
- Center of Biostatistics & Bioinformatics, University of Mississippi Medical Center, Jackson, MS, USA.
| | - Thomas Mosley
- Department of Neurology, University of Mississippi Medical Center, Jackson, MS, USA.
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Chen J, Lin M, Hrabovsky A, Pedrosa E, Dean J, Jain S, Zheng D, Lachman HM. ZNF804A Transcriptional Networks in Differentiating Neurons Derived from Induced Pluripotent Stem Cells of Human Origin. PLoS One 2015; 10:e0124597. [PMID: 25905630 PMCID: PMC4408091 DOI: 10.1371/journal.pone.0124597] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 03/16/2015] [Indexed: 12/23/2022] Open
Abstract
ZNF804A (Zinc Finger Protein 804A) has been identified as a candidate gene for schizophrenia (SZ), autism spectrum disorders (ASD), and bipolar disorder (BD) in replicated genome wide association studies (GWAS) and by copy number variation (CNV) analysis. Although its function has not been well-characterized, ZNF804A contains a C2H2-type zinc-finger domain, suggesting that it has DNA binding properties, and consequently, a role in regulating gene expression. To further explore the role of ZNF804A on gene expression and its downstream targets, we used a gene knockdown (KD) approach to reduce its expression in neural progenitor cells (NPCs) derived from induced pluripotent stem cells (iPSCs). KD was accomplished by RNA interference (RNAi) using lentiviral particles containing shRNAs that target ZNF804A mRNA. Stable transduced NPC lines were generated after puromycin selection. A control cell line expressing a random (scrambled) shRNA was also generated. Neuronal differentiation was induced, RNA was harvested after 14 days and transcriptome analysis was carried out using RNA-seq. 1815 genes were found to be differentially expressed at a nominally significant level (p<0.05); 809 decreased in expression in the KD samples, while 1106 increased. Of these, 370 achieved genome wide significance (FDR<0.05); 125 were lower in the KD samples, 245 were higher. Pathway analysis showed that genes involved in interferon-signaling were enriched among those that were down-regulated in the KD samples. Correspondingly, ZNF804A KD was found to affect interferon-alpha 2 (IFNA2)-mediated gene expression. The findings suggest that ZNF804A may affect a differentiating neuron’s response to inflammatory cytokines, which is consistent with models of SZ and ASD that support a role for infectious disease, and/or autoimmunity in a subgroup of patients.
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Affiliation(s)
- Jian Chen
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Mingyan Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Anastasia Hrabovsky
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Jason Dean
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Swati Jain
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Dominick Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (DZ); (HML)
| | - Herbert M. Lachman
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Dominick Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (DZ); (HML)
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Davies G, Armstrong N, Bis JC, Bressler J, Chouraki V, Giddaluru S, Hofer E, Ibrahim-Verbaas CA, Kirin M, Lahti J, van der Lee SJ, Le Hellard S, Liu T, Marioni RE, Oldmeadow C, Postmus I, Smith AV, Smith JA, Thalamuthu A, Thomson R, Vitart V, Wang J, Yu L, Zgaga L, Zhao W, Boxall R, Harris SE, Hill WD, Liewald DC, Luciano M, Adams H, Ames D, Amin N, Amouyel P, Assareh AA, Au R, Becker JT, Beiser A, Berr C, Bertram L, Boerwinkle E, Buckley BM, Campbell H, Corley J, De Jager PL, Dufouil C, Eriksson JG, Espeseth T, Faul JD, Ford I, Scotland G, Gottesman RF, Griswold ME, Gudnason V, Harris TB, Heiss G, Hofman A, Holliday EG, Huffman J, Kardia SLR, Kochan N, Knopman DS, Kwok JB, Lambert JC, Lee T, Li G, Li SC, Loitfelder M, Lopez OL, Lundervold AJ, Lundqvist A, Mather KA, Mirza SS, Nyberg L, Oostra BA, Palotie A, Papenberg G, Pattie A, Petrovic K, Polasek O, Psaty BM, Redmond P, Reppermund S, Rotter JI, Schmidt H, Schuur M, Schofield PW, Scott RJ, Steen VM, Stott DJ, van Swieten JC, Taylor KD, Trollor J, Trompet S, Uitterlinden AG, Weinstein G, Widen E, Windham BG, Jukema JW, Wright AF, Wright MJ, Yang Q, Amieva H, Attia JR, Bennett DA, Brodaty H, de Craen AJM, Hayward C, Ikram MA, Lindenberger U, Nilsson LG, Porteous DJ, Räikkönen K, Reinvang I, Rudan I, Sachdev PS, Schmidt R, Schofield PR, Srikanth V, Starr JM, Turner ST, Weir DR, Wilson JF, van Duijn C, Launer L, Fitzpatrick AL, Seshadri S, Mosley TH, Deary IJ. Genetic contributions to variation in general cognitive function: a meta-analysis of genome-wide association studies in the CHARGE consortium (N=53949). Mol Psychiatry 2015; 20:183-92. [PMID: 25644384 PMCID: PMC4356746 DOI: 10.1038/mp.2014.188] [Citation(s) in RCA: 260] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 11/11/2014] [Accepted: 11/24/2014] [Indexed: 01/14/2023]
Abstract
General cognitive function is substantially heritable across the human life course from adolescence to old age. We investigated the genetic contribution to variation in this important, health- and well-being-related trait in middle-aged and older adults. We conducted a meta-analysis of genome-wide association studies of 31 cohorts (N=53,949) in which the participants had undertaken multiple, diverse cognitive tests. A general cognitive function phenotype was tested for, and created in each cohort by principal component analysis. We report 13 genome-wide significant single-nucleotide polymorphism (SNP) associations in three genomic regions, 6q16.1, 14q12 and 19q13.32 (best SNP and closest gene, respectively: rs10457441, P=3.93 × 10(-9), MIR2113; rs17522122, P=2.55 × 10(-8), AKAP6; rs10119, P=5.67 × 10(-9), APOE/TOMM40). We report one gene-based significant association with the HMGN1 gene located on chromosome 21 (P=1 × 10(-6)). These genes have previously been associated with neuropsychiatric phenotypes. Meta-analysis results are consistent with a polygenic model of inheritance. To estimate SNP-based heritability, the genome-wide complex trait analysis procedure was applied to two large cohorts, the Atherosclerosis Risk in Communities Study (N=6617) and the Health and Retirement Study (N=5976). The proportion of phenotypic variation accounted for by all genotyped common SNPs was 29% (s.e.=5%) and 28% (s.e.=7%), respectively. Using polygenic prediction analysis, ~1.2% of the variance in general cognitive function was predicted in the Generation Scotland cohort (N=5487; P=1.5 × 10(-17)). In hypothesis-driven tests, there was significant association between general cognitive function and four genes previously associated with Alzheimer's disease: TOMM40, APOE, ABCG1 and MEF2C.
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Affiliation(s)
- G Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - N Armstrong
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW, Australia
| | - J C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - J Bressler
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - V Chouraki
- Inserm-UMR744, Institut Pasteur de Lille, Unité d'Epidémiologie et de Santé Publique, Lille, France,Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - S Giddaluru
- K.G. Jebsen Centre for Psychosis Research and the Norwegian Centre for Mental Disorders Research (NORMENT), Department of Clinical Science, University of Bergen, Bergen, Norway,Dr Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - E Hofer
- Department of Neurology, Medical University of Graz, Graz, Austria,Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - C A Ibrahim-Verbaas
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands,Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - M Kirin
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - J Lahti
- Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland,Folkhälsan Research Centre, Helsinki, Finland
| | - S J van der Lee
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - S Le Hellard
- K.G. Jebsen Centre for Psychosis Research and the Norwegian Centre for Mental Disorders Research (NORMENT), Department of Clinical Science, University of Bergen, Bergen, Norway,Dr Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - T Liu
- Max Planck Institute for Human Development, Berlin, Germany,Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - R E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Medical Genetics Section, University of Edinburgh Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK,Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - C Oldmeadow
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW, Australia
| | - I Postmus
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - A V Smith
- Icelandic Heart Association, Kopavogur, Iceland,University of Iceland, Reykjavik, Iceland
| | - J A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - A Thalamuthu
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - R Thomson
- Menzies Research Institute, Hobart, Tasmania
| | - V Vitart
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - J Wang
- Framingham Heart Study, Framingham, MA, USA,Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - L Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - L Zgaga
- Department of Public Health and Primary Care, Trinity College Dublin, Dublin, Ireland,Andrija Stampar School of Public Health, Medical School, University of Zagreb, Zagreb, Croatia
| | - W Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - R Boxall
- Medical Genetics Section, University of Edinburgh Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - S E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Medical Genetics Section, University of Edinburgh Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - W D Hill
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - D C Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - M Luciano
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - H Adams
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - D Ames
- National Ageing Research Institute, Royal Melbourne Hospital, Melbourne, VIC, Australia,Academic Unit for Psychiatry of Old Age, St George's Hospital, University of Melbourne, Kew, Australia
| | - N Amin
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - P Amouyel
- Inserm-UMR744, Institut Pasteur de Lille, Unité d'Epidémiologie et de Santé Publique, Lille, France
| | - A A Assareh
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - R Au
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA,Framingham Heart Study, Framingham, MA, USA
| | - J T Becker
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA,Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA,Department of Psychology, University of Pittsburgh, Pittsburgh, PA, USA
| | - A Beiser
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA,Framingham Heart Study, Framingham, MA, USA
| | - C Berr
- Inserm, U106, Montpellier, France,Université Montpellier I, Montpellier, France
| | - L Bertram
- Max Planck Institute for Molecular Genetics, Berlin, Germany,Faculty of Medicine, School of Public Health, Imperial College, London, UK
| | - E Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA,Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, University of Texas Health Science Center at Houston, Houston, TX, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - B M Buckley
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland
| | - H Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - J Corley
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - P L De Jager
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - C Dufouil
- Inserm U708, Neuroepidemiology, Paris, France,Inserm U897, Université Bordeaux Segalen, Bordeaux, France
| | - J G Eriksson
- Folkhälsan Research Centre, Helsinki, Finland,National Institute for Health and Welfare, Helsinki, Finland,Department of General Practice and Primary health Care, University of Helsinki, Helsinki, Finland,Unit of General Practice, Helsinki University Central Hospital, Helsinki, Finland
| | - T Espeseth
- K.G. Jebsen Centre for Psychosis Research, Norwegian Centre For Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Department of Psychology, University of Oslo, Oslo, Norway
| | - J D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - I Ford
- Robertson Center for Biostatistics, Glasgow, UK
| | - Generation Scotland
- Generation Scotland, University of Edinburgh Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - R F Gottesman
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - M E Griswold
- Center of Biostatistics and Bioinformatics, University of Mississippi Medical Center, Jackson, MS, USA
| | - V Gudnason
- Icelandic Heart Association, Kopavogur, Iceland,University of Iceland, Reykjavik, Iceland
| | - T B Harris
- Intramural Research Program National Institutes on Aging, National Institutes of Health, Bethesda, MD, USA
| | - G Heiss
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - A Hofman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - E G Holliday
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW, Australia
| | - J Huffman
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - S L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - N Kochan
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia,Neuropsychiatric Institute, Prince of Wales Hospital, Sydney, NSW, Australia
| | - D S Knopman
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - J B Kwok
- Neuroscience Research Australia, Randwick, NSW, Australia,School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - J-C Lambert
- Inserm-UMR744, Institut Pasteur de Lille, Unité d'Epidémiologie et de Santé Publique, Lille, France
| | - T Lee
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia,Neuropsychiatric Institute, Prince of Wales Hospital, Sydney, NSW, Australia
| | - G Li
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - S-C Li
- Max Planck Institute for Human Development, Berlin, Germany,Technische Universität Dresden, Dresden, Germany
| | - M Loitfelder
- Department of Neurology, Medical University of Graz, Graz, Austria
| | - O L Lopez
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - A J Lundervold
- Department of Biological and Medical Psychology, University of Bergen, Bergen, Norway,Kavli Research Centre for Aging and Dementia, Haraldsplass Deaconess Hospital, Bergen, Norway,K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - A Lundqvist
- Umeå Center for Functional Brain Imaging (UFBI), Umeå University, Umeå, Sweden
| | - K A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - S S Mirza
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - L Nyberg
- Umeå Center for Functional Brain Imaging (UFBI), Umeå University, Umeå, Sweden,Department of Radiation Sciences, Umeå University, Umeå, Sweden,Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - B A Oostra
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - A Palotie
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland,Department of Medical Genetics, University of Helsinki and University Central Hospital, Helsinki, Finland
| | - G Papenberg
- Max Planck Institute for Human Development, Berlin, Germany,Karolinska Institutet, Aging Research Center, Stockholm University, Stockholm, Sweden
| | - A Pattie
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - K Petrovic
- Department of Neurology, Medical University of Graz, Graz, Austria
| | - O Polasek
- Faculty of Medicine, Department of Public Health, University of Split, Split, Croatia
| | - B M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA,Deparment of Epidemiology, University of Washington, Seattle, WA, USA,Deparment of Health Services, University of Washington, Seattle, WA, USA,Group Health Research Unit, Group Health Cooperative, Seattle, WA, USA
| | - P Redmond
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - S Reppermund
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - J I Rotter
- Institute for Translational Genomics and Population Sciences Los Angeles BioMedical Research Institute, Harbor-UCLA Medical Center, Los Angeles, CA, USA,Division of Genetic Outcomes, Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles, CA, USA
| | - H Schmidt
- Department of Neurology, Medical University of Graz, Graz, Austria,Centre for Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - M Schuur
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands,Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - P W Schofield
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, Australia
| | - R J Scott
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW, Australia
| | - V M Steen
- K.G. Jebsen Centre for Psychosis Research and the Norwegian Centre for Mental Disorders Research (NORMENT), Department of Clinical Science, University of Bergen, Bergen, Norway,Dr Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - D J Stott
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - J C van Swieten
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - K D Taylor
- Institute for Translational Genomics and Population Sciences Los Angeles BioMedical Research Institute, Harbor-UCLA Medical Center, Los Angeles, CA, USA,Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles, CA, USA
| | - J Trollor
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia,Department of Developmental Disability Neuropsychiatry, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - S Trompet
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands,Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - A G Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands,Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - G Weinstein
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA,Framingham Heart Study, Framingham, MA, USA
| | - E Widen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - B G Windham
- Division of Geriatrics, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - J W Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands,Durrer Center for Cardiogenetic Research, Amsterdam, The Netherlands,Interuniversity Cardiology Institute of the Netherlands, Utrecht, The Netherlands
| | - A F Wright
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - M J Wright
- Neuroimaging Genetics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Q Yang
- Framingham Heart Study, Framingham, MA, USA,Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - H Amieva
- Inserm U897, Université Bordeaux Segalen, Bordeaux, France
| | - J R Attia
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW, Australia
| | - D A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - H Brodaty
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia,Dementia Collaborative Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - A J M de Craen
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - C Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - M A Ikram
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands,Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands,Department of Radiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - U Lindenberger
- Max Planck Institute for Human Development, Berlin, Germany
| | - L-G Nilsson
- ARC, Karolinska Institutet, Stockholm and UFBI, Umeå University, Umeå, Sweden
| | - D J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Medical Genetics Section, University of Edinburgh Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK,Generation Scotland, University of Edinburgh Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - K Räikkönen
- Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland
| | - I Reinvang
- Department of Psychology, University of Oslo, Oslo, Norway
| | - I Rudan
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - P S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia,Neuropsychiatric Institute, Prince of Wales Hospital, Sydney, NSW, Australia
| | - R Schmidt
- Department of Neurology, Medical University of Graz, Graz, Austria
| | - P R Schofield
- Neuroscience Research Australia, Sydney, NSW, Australia,Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - V Srikanth
- Menzies Research Institute, Hobart, Tasmania,Stroke and Ageing Research, Medicine, Southern Clinical School, Monash University, Melbourne, VIC, Australia
| | - J M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - S T Turner
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - D R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - J F Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - C van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - L Launer
- Intramural Research Program National Institutes on Aging, National Institutes of Health, Bethesda, MD, USA
| | - A L Fitzpatrick
- Deparment of Epidemiology, University of Washington, Seattle, WA, USA,Department of Global Health, University of Washington, Seattle, WA, USA
| | - S Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA,Framingham Heart Study, Framingham, MA, USA
| | - T H Mosley
- Division of Geriatrics, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - I J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Department of Psychology, University of Edinburgh, Edinburgh, UK,Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ, Scotland, UK. E-mail:
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Wang HW, Sun HJ, Chang TY, Lo HH, Cheng WC, Tseng GC, Lin CT, Chang SJ, Pal N, Chung IF. Discovering monotonic stemness marker genes from time-series stem cell microarray data. BMC Genomics 2015; 16 Suppl 2:S2. [PMID: 25708300 PMCID: PMC4331716 DOI: 10.1186/1471-2164-16-s2-s2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Identification of genes with ascending or descending monotonic expression patterns over time or stages of stem cells is an important issue in time-series microarray data analysis. We propose a method named Monotonic Feature Selector (MFSelector) based on a concept of total discriminating error (DEtotal) to identify monotonic genes. MFSelector considers various time stages in stage order (i.e., Stage One vs. other stages, Stages One and Two vs. remaining stages and so on) and computes DEtotal of each gene. MFSelector can successfully identify genes with monotonic characteristics. Results We have demonstrated the effectiveness of MFSelector on two synthetic data sets and two stem cell differentiation data sets: embryonic stem cell neurogenesis (ESCN) and embryonic stem cell vasculogenesis (ESCV) data sets. We have also performed extensive quantitative comparisons of the three monotonic gene selection approaches. Some of the monotonic marker genes such as OCT4, NANOG, BLBP, discovered from the ESCN dataset exhibit consistent behavior with that reported in other studies. The role of monotonic genes found by MFSelector in either stemness or differentiation is validated using information obtained from Gene Ontology analysis and other literature. We justify and demonstrate that descending genes are involved in the proliferation or self-renewal activity of stem cells, while ascending genes are involved in differentiation of stem cells into variant cell lineages. Conclusions We have developed a novel system, easy to use even with no pre-existing knowledge, to identify gene sets with monotonic expression patterns in multi-stage as well as in time-series genomics matrices. The case studies on ESCN and ESCV have helped to get a better understanding of stemness and differentiation. The novel monotonic marker genes discovered from a data set are found to exhibit consistent behavior in another independent data set, demonstrating the utility of the proposed method. The MFSelector R function and data sets can be downloaded from: http://microarray.ym.edu.tw/tools/MFSelector/.
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Abstract
Several lines of evidence suggest that adult neurogenesis, the production of new neurons in adulthood, may play a role in psychiatric disorders, including depression, anxiety, and schizophrenia. Medications and other treatments for mental disorders often promote the proliferation of new neurons; the time course for maturation and integration of new neurons in circuitry parallels the delayed efficacy of psychiatric therapies; adverse and beneficial experiences similarly affect development of mental illness and neurogenesis; and ablation of new neurons in adulthood alters the behavioral impact of drugs in animal models. At present, the links between adult neurogenesis and depression seem stronger than those suggesting a relationship between new neurons and anxiety or schizophrenia. Yet, even in the case of depression there is currently no direct evidence for a causative role. This article reviews the data relating adult neurogenesis to mental illness and discusses where research needs to head in the future.
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Affiliation(s)
- Timothy J Schoenfeld
- Section on Neuroplasticity, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Heather A Cameron
- Section on Neuroplasticity, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA,Section on Neuroplasticity, NIMH, 35 Convent Drive, Building 35/3C915, Bethesda, MD 20892-3718, USA, Tel: +1 301 496 3814, Fax: +1 301 480 4564, E-mail:
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Stanco A, Pla R, Vogt D, Chen Y, Mandal S, Walker J, Hunt RF, Lindtner S, Erdman CA, Pieper AA, Hamilton SP, Xu D, Baraban SC, Rubenstein JLR. NPAS1 represses the generation of specific subtypes of cortical interneurons. Neuron 2014; 84:940-53. [PMID: 25467980 DOI: 10.1016/j.neuron.2014.10.040] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2014] [Indexed: 11/29/2022]
Abstract
Little is known about genetic mechanisms that regulate the ratio of cortical excitatory and inhibitory neurons. We show that NPAS1 and NPAS3 transcription factors (TFs) are expressed in progenitor domains of the mouse basal ganglia (subpallium, MGE, and CGE). NPAS1(-/-) mutants had increased proliferation, ERK signaling, and expression of Arx in the MGE and CGE. NPAS1(-/-) mutants also had increased neocortical inhibition (sIPSC and mIPSC) and generated an excess of somatostatin(+) (SST) (MGE-derived) and vasoactive intestinal polypeptide(+) (VIP) (CGE-derived) neocortical interneurons, but had a normal density of parvalbumin(+) (PV) (MGE-derived) interneurons. In contrast, NPAS3(-/-) mutants showed decreased proliferation and ERK signaling in progenitors of the ganglionic eminences and had fewer SST(+) and VIP(+) interneurons. NPAS1 repressed activity of an Arx enhancer, and Arx overexpression resulted in increased proliferation of CGE progenitors. These results provide insights into genetic regulation of cortical interneuron numbers and cortical inhibitory tone.
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Affiliation(s)
- Amelia Stanco
- Department of Psychiatry, Neuroscience Program, and the Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA 94158-2324, USA.
| | - Ramón Pla
- Department of Psychiatry, Neuroscience Program, and the Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA 94158-2324, USA
| | - Daniel Vogt
- Department of Psychiatry, Neuroscience Program, and the Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA 94158-2324, USA
| | - Yiran Chen
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Shyamali Mandal
- Department of Psychiatry, Neuroscience Program, and the Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA 94158-2324, USA
| | - Jamie Walker
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Robert F Hunt
- Department of Neurological Surgery, Neuroscience Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Susan Lindtner
- Department of Psychiatry, Neuroscience Program, and the Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA 94158-2324, USA
| | - Carolyn A Erdman
- Department of Psychiatry, Neuroscience Program, and the Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA 94158-2324, USA
| | - Andrew A Pieper
- Department of Psychiatry and Neurology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Steven P Hamilton
- Department of Psychiatry, Neuroscience Program, and the Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA 94158-2324, USA
| | - Duan Xu
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Scott C Baraban
- Department of Neurological Surgery, Neuroscience Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John L R Rubenstein
- Department of Psychiatry, Neuroscience Program, and the Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA 94158-2324, USA.
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Bernier D, Macintyre G, Bartha R, Hanstock CC, McAllindon D, Cox D, Purdon S, Aitchison KJ, Rusak B, Tibbo PG. NPAS3 variants in schizophrenia: a neuroimaging study. BMC Med Genet 2014; 15:37. [PMID: 24674381 PMCID: PMC3986669 DOI: 10.1186/1471-2350-15-37] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 03/21/2014] [Indexed: 11/10/2022]
Abstract
Background This research is a one-site neuroimaging component of a two-site genetic study involving patients with schizophrenia at early and later stages of illness. Studies support a role for the neuronal Per-Arnt-Sim 3 (NPAS3) gene in processes that are essential for normal brain development. Specific NPAS3 variants have been observed at an increased frequency in schizophrenia. In humans, NPAS3 protein was detected in the hippocampus from the first trimester of gestation. In addition, NPAS3 protein levels were reduced in the dorsolateral prefrontal cortex of some patients with schizophrenia. Npas3 knockout mice display behavioural, neuroanatomical and structural changes with associated severe reductions in neural precursor cell proliferation in the hippocampal dentate gyrus. This study will evaluate the hypothesis that the severe reductions in neural precursor cell proliferation in the dentate gyrus will be present to some degree in patients carrying schizophrenia-associated NPAS3 variants and less so in other patients. Methods/Design Patients enrolled in the larger genetic study (n = 150) will be invited to participate in this neuroimaging arm. The genetic data will be used to ensure a sample size of 45 participants in each genetic subgroup of patients (with and without NPAS3 variants). In addition, we will recruit 60 healthy controls for acquisition of normative data. The following neuroimaging measures will be acquired from the medial temporal region: a) an index of the microcellular environment; b) a macro-structural volumetric measure of the hippocampus; and c) concentration levels of N-acetylaspartate, a marker of neuronal health. Discussion This study will help to establish the contribution of the NPAS3 gene and its variants to brain tissue abnormalities in schizophrenia. Given the genetic and phenotypic heterogeneity of the disorder and the large variation in outcomes, the identification of biological subgroups may in future support tailoring of treatment approaches in order to optimize recovery.
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Affiliation(s)
- Denise Bernier
- Department of Psychiatry, Dalhousie University, Halifax, Canada.
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Yu L, Arbez N, Nucifora LG, Sell GL, Delisi LE, Ross CA, Margolis RL, Nucifora FC Jr. A mutation in NPAS3 segregates with mental illness in a small family. Mol Psychiatry 2014; 19:7-8. [PMID: 23337948 DOI: 10.1038/mp.2012.192] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Ruan L, Lau BWM, Wang J, Huang L, Zhuge Q, Wang B, Jin K, So KF. Neurogenesis in neurological and psychiatric diseases and brain injury: from bench to bedside. Prog Neurobiol 2013; 115:116-37. [PMID: 24384539 DOI: 10.1016/j.pneurobio.2013.12.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 12/08/2013] [Accepted: 12/12/2013] [Indexed: 02/08/2023]
Abstract
Researchers who have uncovered the presence of stem cells in an adult's central nervous system have not only challenged the dogma that new neurons cannot be generated during adulthood, but also shed light on the etiology and disease mechanisms underlying many neurological and psychiatric disorders. Brain trauma, neurodegenerative diseases, and psychiatric disorders pose enormous burdens at both personal and societal levels. Although medications for these disorders are widely used, the treatment mechanisms underlying the illnesses remain largely elusive. In the past decade, an increasing amount of evidence indicate that adult neurogenesis (i.e. generating new CNS neurons during adulthood) may be involved in the pathology of different CNS disorders, and thus neurogenesis may be a potential target area for treatments. Although new neurons were shown to be a major player in mediating treatment efficacy of neurological and psychotropic drugs on cognitive functions, it is still debatable if the altered production of new neurons can cause the disorders. This review hence seeks to discuss pre and current clinical studies that demonstrate the functional impact adult neurogenesis have on neurological and psychiatric illnesses while examining the related underlying disease mechanisms.
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Affiliation(s)
- Linhui Ruan
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China; Department of Pharmacology and Neuroscience, University of North Texas Health Science Center at Fort Worth, TX 76107, USA.
| | - Benson Wui-Man Lau
- Department of Rehabilitation Science, The Hong Kong Polytechnic University, Hong Kong, PR China
| | - Jixian Wang
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center at Fort Worth, TX 76107, USA
| | - Lijie Huang
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China; Department of Pharmacology and Neuroscience, University of North Texas Health Science Center at Fort Worth, TX 76107, USA
| | - Qichuan Zhuge
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Brian Wang
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center at Fort Worth, TX 76107, USA
| | - Kunlin Jin
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China; Department of Pharmacology and Neuroscience, University of North Texas Health Science Center at Fort Worth, TX 76107, USA.
| | - Kwok-Fai So
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China; The State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China; Research Centre of Heart, Brain, Hormone and Healthy Aging, Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, PR China; GMH Institute of CNS Regeneration, Jinan University, Guangzhou, PR China.
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41
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Kamm GB, López-Leal R, Lorenzo JR, Franchini LF. A fast-evolving human NPAS3 enhancer gained reporter expression in the developing forebrain of transgenic mice. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130019. [PMID: 24218632 DOI: 10.1098/rstb.2013.0019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The developmental brain gene NPAS3 stands out as a hot spot in human evolution because it contains the largest number of human-specific, fast-evolving, conserved, non-coding elements. In this paper we studied 2xHAR142, one of these elements that is located in the fifth intron of NPAS3. Using transgenic mice, we show that the mouse and chimp 2xHAR142 orthologues behave as transcriptional enhancers driving expression of the reporter gene lacZ to a similar NPAS3 expression subdomain in the mouse central nervous system. Interestingly, the human 2xHAR142 orthologue drives lacZ expression to an extended expression pattern in the nervous system. Thus, molecular evolution of 2xHAR142 provides the first documented example of human-specific heterotopy in the forebrain promoted by a transcriptional enhancer and suggests that it may have contributed to assemble the unique properties of the human brain.
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Affiliation(s)
- Gretel B Kamm
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), , Buenos Aires, Argentina
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42
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Shin J, Kim J. Novel alternative splice variants of chicken NPAS3 are expressed in the developing central nervous system. Gene 2013; 530:222-8. [PMID: 23962688 DOI: 10.1016/j.gene.2013.08.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 08/07/2013] [Accepted: 08/09/2013] [Indexed: 11/20/2022]
Abstract
We report isolation of novel splice variants of chicken Neuronal Per-Arnt-Sim domain protein 3 (cNPAS3) gene distinct from the previously predicted cNPAS3 at the 5' end. Newly identified cNPAS3 splice variants feature N-terminus coding sequences with high degrees of homology to human NPAS3 (hNAPS3). We also show that the alternative splicing pattern of NPAS3 is conserved between chicken and human. RNA in situ hybridization indicated that the expression of cNPAS3 in the developing central nervous system (CNS) is limited to the ventricular zone and only partially overlaps with that of chicken Reelin (cReelin), the only known regulatory target gene of NPAS3 in the adult brain. Overexpression of cNPAS3 by in ovo electroporation had little effect on the expression of Sox2, a marker for neural precursors, or of Isl1/2, a marker for early differentiating motor neurons. Taken together with the little effect of cNPAS3 overexpression on cReelin, it is noted that the function of NPAS3 in the developing CNS remains to be determined. Still, identification of proper cDNA sequences for cNPAS3 should represent a solid beginning of the understanding process.
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Affiliation(s)
- Jiheon Shin
- Department of Life Sciences and Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Korea
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44
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Wong J, Duncan CE, Beveridge NJ, Webster MJ, Cairns MJ, Shannon Weickert C. Expression of NPAS3 in the human cortex and evidence of its posttranscriptional regulation by miR-17 during development, with implications for schizophrenia. Schizophr Bull 2013; 39:396-406. [PMID: 22228753 PMCID: PMC3576160 DOI: 10.1093/schbul/sbr177] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
NPAS3 is a developmentally important transcription factor that has been associated with psychiatric illness. Our aim is to better define the regulation of NPAS3 mRNA (messenger RNA) levels during normal human prefrontal cortical development and in schizophrenia. Utilizing postmortem tissue from 134 human brains, we assessed: 60 normal brains ranging in age from birth to adulthood, 37 chronic individuals with schizophrenia, and 37 matched controls. mRNA and microRNA (miRNA) expressions were measured by microarray and quantitative real-time PCR. Protein expression was measured by Western blotting. During human postnatal cortical development (neonate to adult), we found decreased NPAS3 mRNA yet increased NPAS3 protein expression, suggesting the involvement of posttranscriptional regulation. Through screening, we identified one NPAS-targeted miRNA (miR-17) that changed in a pattern consistent with the developmental regulation of NPAS3. Using luciferase reporter assays, we assessed the impact of miR-17 on NPAS3 translation and demonstrated that miR-17 alters NPAS3 biosynthesis by binding to the NPAS3 3'untranslated region (UTR). In schizophrenia prefrontal cortex, we found significant elevations in miR-17 expression. While NPAS3 mRNA was unaltered, reduced NPAS3 protein expression was detected in a subpopulation of people with schizophrenia. The reciprocal expression of NPAS3 mRNA and protein during postnatal development mediated by a schizophrenia-associated change in miR-17 suggests that there is complex control over NPAS3 synthesis in the human prefrontal cortex and that if NPAS3 is dysregulated in schizophrenia, it is not evident by large changes in NPAS3 expression. Further studies into how changes in NPAS3 or its miRNA regulator may influence the development of schizophrenia are warranted.
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Affiliation(s)
- Jenny Wong
- All 3 authors made equal contributions to the article
| | - Carlotta E. Duncan
- Schizophrenia Research Institute, Sydney, Australia,Neuroscience Research Australia, Randwick, New South Wales, Australia,All 3 authors made equal contributions to the article
| | - Natalie J. Beveridge
- Schizophrenia Research Institute, Sydney, Australia,School of Biomedical Sciences and Pharmacy, Faculty of Health, Centre for Brain and Mental Health Research and Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia,All 3 authors made equal contributions to the article
| | | | - Murray J. Cairns
- Schizophrenia Research Institute, Sydney, Australia,School of Biomedical Sciences and Pharmacy, Faculty of Health, Centre for Brain and Mental Health Research and Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia
| | - Cynthia Shannon Weickert
- Schizophrenia Research Institute, Sydney, Australia,Neuroscience Research Australia, Randwick, New South Wales, Australia,School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia,All 3 authors made equal contributions to the article
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45
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Kamm GB, Pisciottano F, Kliger R, Franchini LF. The developmental brain gene NPAS3 contains the largest number of accelerated regulatory sequences in the human genome. Mol Biol Evol 2013; 30:1088-102. [PMID: 23408798 PMCID: PMC3670734 DOI: 10.1093/molbev/mst023] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
To identify the evolutionary genetic novelties that contributed to shape human-specific traits such as the use of a complex language, long-term planning and exceptional learning abilities is one of the ultimate frontiers of modern biology. Evolutionary signatures of functional shifts could be detected by comparing noncoding regions that are highly conserved across mammals or primates and rapidly accumulated nucleotide substitutions only in the lineage leading to humans. As gene loci densely populated with human-accelerated elements (HAEs) are more likely to have contributed to human-specific novelties, we sought to identify the transcriptional units and genomic 1 Mb intervals of the entire human genome carrying the highest number of HAEs. To this end, we took advantage of four available data sets of human genomic accelerated regions obtained through different comparisons and algorithms and performed a meta-analysis of the combined data. We found that the brain developmental transcription factor neuronal PAS domain-containing protein 3 (NPAS3) contains the largest cluster of noncoding-accelerated regions in the human genome with up to 14 elements that are highly conserved in mammals, including primates, but carry human-specific nucleotide substitutions. We then tested the ability of the 14 HAEs identified at the NPAS3 locus to act as transcriptional regulatory sequences in a reporter expression assay performed in transgenic zebrafish. We found that 11 out of the 14 HAEs present in NPAS3 act as transcriptional enhancers during development, particularly within the nervous system. As NPAS3 is known to play a crucial role during mammalian brain development, our results indicate that the high density of HAEs present in the human NPAS3 locus could have modified the spatiotemporal expression pattern of NPAS3 in the developing human brain and, therefore, contributed to human brain evolution.
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Affiliation(s)
- Gretel B Kamm
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, INGEBI, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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Stachowiak MK, Kucinski A, Curl R, Syposs C, Yang Y, Narla S, Terranova C, Prokop D, Klejbor I, Bencherif M, Birkaya B, Corso T, Parikh A, Tzanakakis ES, Wersinger S, Stachowiak EK. Schizophrenia: a neurodevelopmental disorder--integrative genomic hypothesis and therapeutic implications from a transgenic mouse model. Schizophr Res 2013; 143:367-76. [PMID: 23231877 DOI: 10.1016/j.schres.2012.11.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 11/02/2012] [Accepted: 11/06/2012] [Indexed: 12/14/2022]
Abstract
Schizophrenia is a neurodevelopmental disorder featuring complex aberrations in the structure, wiring, and chemistry of multiple neuronal systems. The abnormal developmental trajectory of the brain appears to be established during gestation, long before clinical symptoms of the disease appear in early adult life. Many genes are associated with schizophrenia, however, altered expression of no one gene has been shown to be present in a majority of schizophrenia patients. How does altered expression of such a variety of genes lead to the complex set of abnormalities observed in the schizophrenic brain? We hypothesize that the protein products of these genes converge on common neurodevelopmental pathways that affect the development of multiple neural circuits and neurotransmitter systems. One such neurodevelopmental pathway is Integrative Nuclear FGFR1 Signaling (INFS). INFS integrates diverse neurogenic signals that direct the postmitotic development of embryonic stem cells, neural progenitors and immature neurons, by direct gene reprogramming. Additionally, FGFR1 and its partner proteins link multiple upstream pathways in which schizophrenia-linked genes are known to function and interact directly with those genes. A th-fgfr1(tk-) transgenic mouse with impaired FGF receptor signaling establishes a number of important characteristics that mimic human schizophrenia - a neurodevelopmental origin, anatomical abnormalities at birth, a delayed onset of behavioral symptoms, deficits across multiple domains of the disorder and symptom improvement with typical and atypical antipsychotics, 5-HT antagonists, and nicotinic receptor agonists. Our research suggests that altered FGF receptor signaling plays a central role in the developmental abnormalities underlying schizophrenia and that nicotinic agonists are an effective class of compounds for the treatment of schizophrenia.
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Affiliation(s)
- M K Stachowiak
- Molecular and Structural Neurobiology & Gene Therapy Program, Department of Pathology and Anatomical Sciences, Western New York Stem Cell Culture and Analysis Center, SUNY, Buffalo, NY, USA.
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Abstract
In psychiatric disorders, the effect of genetic and environmental factors may converge on molecular pathways and brain circuits related to growth factor functioning. In this review, we describe how disturbances in fibroblast growth factors (FGFs) and their receptors influence behavior by affecting brain development. Recently, several studies reported associations of members of the FGF family with psychiatric disorders. FGFs are key candidates to modulate the impact of environmental factors, such as stress. Mutant mice for FGF receptor 1 show schizophrenia-like behaviors that are related to general loss of neurons and postnatal glia dysfunction. Mice lacking FGF2, a FGFR1 ligand, show similar reductions in brain volume and hyperactivity, as well as increased anxiety behaviors. FGFR2 and FGF17 are involved in the development of frontal brain regions and impairments in cognitive and social behaviors, respectively. Moreover, treatment with FGF2 was beneficial for depressive and cognitive measures in several animal studies and one human study. These findings indicate the importance of the FGF system with respect to developing novel etiology-directed treatments for psychopathology.
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Jun H, Mohammed Qasim Hussaini S, Rigby MJ, Jang MH. Functional role of adult hippocampal neurogenesis as a therapeutic strategy for mental disorders. Neural Plast 2012; 2012:854285. [PMID: 23346419 DOI: 10.1155/2012/854285] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 11/30/2012] [Accepted: 11/30/2012] [Indexed: 02/07/2023] Open
Abstract
Adult neurogenesis, the process of generating new neurons from neural stem cells, plays significant roles in synaptic plasticity, memory, and mood regulation. In the mammalian brain, it continues to occur well into adulthood in discrete regions, namely, the hippocampus and olfactory bulb. During the past decade, significant progress has been made in understanding the mechanisms regulating adult hippocampal neurogenesis and its role in the etiology of mental disorders. In addition, adult hippocampal neurogenesis is highly correlated with the remission of the antidepressant effect. In this paper, we discuss three major psychiatric disorders, depression, schizophrenia, and drug addiction, in light of preclinical evidence used in establishing the neurobiological significance of adult neurogenesis. We interpret the significance of these results and pose questions that remain unanswered. Potential treatments which include electroconvulsive therapy, deep brain stimulation, chemical antidepressants, and exercise therapy are discussed. While consensus lacks on specific mechanisms, we highlight evidence which indicates that these treatments may function via an increase in neural progenitor proliferation and changes to the hippocampal circuitry. Establishing a significant role of adult neurogenesis in the pathogenicity of psychiatric disorders may hold the key to potential strategies toward effective treatment.
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49
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Floor K, Barøy T, Misceo D, Kanavin OJ, Fannemel M, Frengen E. A 1 Mb de novo deletion within 11q13.1q13.2 in a boy with mild intellectual disability and minor dysmorphic features. Eur J Med Genet 2012; 55:695-9. [PMID: 22986108 DOI: 10.1016/j.ejmg.2012.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 08/03/2012] [Indexed: 11/30/2022]
Abstract
We report a 11 year old male patient ascertained for mild intellectual disability and minor dysmorphic features, carrying a 1 Mb de novo deletion on chromosome 11q13.1q13.2 detected by aCGH. This is the first report of a deletion in this region in a patient presenting with intellectual impairment and mild dysmorphic traits. The 1 Mb deleted area encompasses 47 RefSeq genes, including Cornichon homologue 2 (CNIH2), Cofilin-1 (CFL1) and neuronal PAS domain-containing protein 4 (NPAS4), which are highly expressed in the central nervous system. Knockout of the CNIH2 and CFL1 orthologues in animals results in migration disturbances, while low or no expression of Npas4 in mice results in impairment of memory and learning. These three genes have previously been suggested as candidate genes for neurological disorders.
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Affiliation(s)
- Karijn Floor
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo, Norway.
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Piccione M, Serra G, Consiglio V, Di Fiore A, Cavani S, Grasso M, Malacarne M, Pierluigi M, Viaggi C, Corsello G. 14q13.1-21.1 deletion encompassing the HPE8 locus in an adolescent with intellectual disability and bilateral microphthalmia, but without holoprosencephaly. Am J Med Genet A 2012; 158A:1427-33. [PMID: 22581785 DOI: 10.1002/ajmg.a.35334] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 01/12/2012] [Indexed: 11/08/2022]
Abstract
Interstitial deletions involving 14q13.1q21.1 are rare. In the literature at least 10 cases involving this region have been described and all patients showed a phenotype within the holoprosencephaly (HPE) spectrum. Previous studies suggested the HPE8 region as a candidate locus for HPE at 14q13. We report an adolescent with a 14q13.1q21.1 deletion encompassing the HPE8 region associated with intellectual disability (ID), bilateral microphthalmia, and coloboma, without cerebral anomalies typical of HPE. Except for ocular defects (i.e., microphthalmia, coloboma) consistent with HPE-type anomalies, the minor facial dysmorphia was not suggestive for HPE and the absence of cerebral anomalies should rule out this diagnosis. The deletion of the potential HPE candidate genes NPAS3, EAPP, SNX6, and TULIP1, raises doubts about their pathologic role in determining HPE. It is likely that deletions of HPE genes are not sufficient to cause HPE, and that multiple genetic, chromosomal, and environmental factors interact to determine the variable clinical expression of HPE. This is the first case of a 14q deletion encompassing the HPE8 locus with the only features consistent with HPE-type anomalies affecting the ocular system (i.e., microphthalmia, coloboma), and without cerebral anomalies specific for HPE. The inclusion of potential HPE candidate genes in the deletion raises the question whether this patient is affected by a less severe form of HPE (HPE microform), or whether he has a new ID/MCA deletion syndrome.
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Affiliation(s)
- Maria Piccione
- Centro di Riferimento Regionale per la Sindrome di Down e le Altre Patologie Cromosomiche e Genetiche-Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy.
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