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Mostafavi Abdolmaleky H, Alam R, Nohesara S, Deth RC, Zhou JR. iPSC-Derived Astrocytes and Neurons Replicate Brain Gene Expression, Epigenetic, Cell Morphology and Connectivity Alterations Found in Autism. Cells 2024; 13:1095. [PMID: 38994948 PMCID: PMC11240613 DOI: 10.3390/cells13131095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/04/2024] [Accepted: 06/19/2024] [Indexed: 07/13/2024] Open
Abstract
Excessive inflammatory reactions and oxidative stress are well-recognized molecular findings in autism and these processes can affect or be affected by the epigenetic landscape. Nonetheless, adequate therapeutics are unavailable, as patient-specific brain molecular markers for individualized therapies remain challenging. METHODS We used iPSC-derived neurons and astrocytes of patients with autism vs. controls (5/group) to examine whether they replicate the postmortem brain expression/epigenetic alterations of autism. Additionally, DNA methylation of 10 postmortem brain samples (5/group) was analyzed for genes affected in PSC-derived cells. RESULTS We found hyperexpression of TGFB1, TGFB2, IL6 and IFI16 and decreased expression of HAP1, SIRT1, NURR1, RELN, GPX1, EN2, SLC1A2 and SLC1A3 in the astrocytes of patients with autism, along with DNA hypomethylation of TGFB2, IL6, TNFA and EN2 gene promoters and a decrease in HAP1 promoter 5-hydroxymethylation in the astrocytes of patients with autism. In neurons, HAP1 and IL6 expression trended alike. While HAP1 promoter was hypermethylated in neurons, IFI16 and SLC1A3 promoters were hypomethylated and TGFB2 exhibited increased promoter 5-hydroxymethlation. We also found a reduction in neuronal arborization, spine size, growth rate, and migration, but increased astrocyte size and a reduced growth rate in autism. In postmortem brain samples, we found DNA hypomethylation of TGFB2 and IFI16 promoter regions, but DNA hypermethylation of HAP1 and SLC1A2 promoters in autism. CONCLUSION Autism-associated expression/epigenetic alterations in iPSC-derived cells replicated those reported in the literature, making them appropriate surrogates to study disease pathogenesis or patient-specific therapeutics.
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Affiliation(s)
- Hamid Mostafavi Abdolmaleky
- Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Reza Alam
- Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Shabnam Nohesara
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Richard C Deth
- Department of Pharmaceutical Sciences, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Jin-Rong Zhou
- Nutrition/Metabolism Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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Sugawara H, Date A, Fuke S, Nakachi Y, Kato T, Narita M, Bundo M, Iwamoto K. Quantification of cytosine modifications in the aged mouse brain. Neuropsychopharmacol Rep 2024; 44:250-255. [PMID: 38058257 PMCID: PMC10932792 DOI: 10.1002/npr2.12396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 12/08/2023] Open
Abstract
Quantifying cytosine modifications in various brain regions provides important insights into the gene expression regulation and pathophysiology of neuropsychiatric disorders. In this study, we quantified 5-methylcytosine (5-mC), 5-hydroxymethylation (5-hmC), and 5-formylcytosine (5-fC) levels in five brain regions (the frontal lobe, cerebral cortical region without frontal lobe, hippocampus, basal ganglia, and the cerebellum) and the heart at three developmental periods (12, 48, and 101 weeks). We observed significant regional variations in cytosine modification. Notably, regional variations were generally maintained throughout development, suggesting that epigenetic regulation is unique to each brain region and remains relatively stable with age. The 5-mC and 5-hmC levels were positively correlated, although the extent of the correlations seemed to differ in different brain regions. On the contrary, 5-fC levels did not correlate with 5-mC or 5-hmC levels. Additionally, we observed an age-dependent decrease in 5-fC levels in the basal ganglia, suggesting a unique epigenetic regulation mechanism. Further high-resolution studies using animal models of neuropsychiatric disorders as well as postmortem brain evaluation are warranted.
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Affiliation(s)
- Hiroko Sugawara
- Department of Psychiatry, Faculty of MedicineFukuoka UniversityFukuokaJapan
- Department of PsychiatryKansai Rosai HospitalAmagasakiJapan
- Department of Psychiatry, Graduate School of MedicineOsaka UniversityOsakaJapan
| | - Akitoshi Date
- Department of PharmacologyHoshi University School of Pharmacy and Pharmaceutical SciencesTokyoJapan
| | - Satoshi Fuke
- Lab for Molecular Dynamics of Mental DisordersRIKEN Center for Brain ScienceWakoJapan
- Research Unit/NeuroscienceSohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma CorporationYokohamaJapan
| | - Yutaka Nakachi
- Department of Molecular Brain Science, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Tadafumi Kato
- Lab for Molecular Dynamics of Mental DisordersRIKEN Center for Brain ScienceWakoJapan
- Department of Psychiatry and Behavior Science, Graduate School of MedicineJuntendo UniversityTokyoJapan
| | - Minoru Narita
- Department of PharmacologyHoshi University School of Pharmacy and Pharmaceutical SciencesTokyoJapan
| | - Miki Bundo
- Lab for Molecular Dynamics of Mental DisordersRIKEN Center for Brain ScienceWakoJapan
- Department of Molecular Brain Science, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Kazuya Iwamoto
- Lab for Molecular Dynamics of Mental DisordersRIKEN Center for Brain ScienceWakoJapan
- Department of Molecular Brain Science, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
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Hino M, Kunii Y, Shishido R, Nagaoka A, Matsumoto J, Akatsu H, Hashizume Y, Hayashi H, Kakita A, Tomita H, Yabe H. Marked alteration of phosphoinositide signaling-associated molecules in postmortem prefrontal cortex with bipolar disorder. Neuropsychopharmacol Rep 2024; 44:121-128. [PMID: 38253804 PMCID: PMC10932789 DOI: 10.1002/npr2.12409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 01/24/2024] Open
Abstract
AIM The etiology of bipolar disorder (BD) remains unknown; however, lipid abnormalities in BD have received increasing attention in recent years. In this study, we examined the expression levels of enzyme proteins associated with the metabolic pathway of phosphoinositides (PIs) and their downstream effectors, protein kinase B (Akt1) and glycogen synthase kinase 3β (GSK3β), which have been assumed to be the targets of mood stabilizers such as lithium, in the postmortem brains of patients with BD. METHODS The protein expression levels of phosphatidylinositol 4-phosphate 5-kinase type-1 gamma (PIP5K1C), phosphatidylinositol 4-kinase alpha (PIK4CA), phosphatase and tensin homolog deleted from chromosome 10 (PTEN), Akt1, and GSK3β were measured using enzyme-linked immunosorbent assays and multiplex fluorescent bead-based immunoassays in the prefrontal cortex (PFC). Specifically, PTEN, Akt1, GSK3β, and PIP5K1C were measured in seven BD patients and 48 controls. Additionally, PIK4CA was analyzed in 10 cases and 34 controls. RESULTS PTEN expression levels were markedly decreased in the PFCs of patients with BD, whereas those of Akt and GSK3β were prominently elevated. Moreover, patients medicated with lithium exhibited higher Akt1 expression levels and lower PTEN expression levels in comparison with the untreated group. CONCLUSION Our results suggest that the expression levels of Akt1/GSK3β and its upstream regulator PTEN are considerably altered.
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Affiliation(s)
- Mizuki Hino
- Department of Disaster Psychiatry, International Research Institute of Disaster ScienceTohoku UniversitySendaiJapan
- Department of Neuropsychiatry, School of MedicineFukushima Medical UniversityFukushimaJapan
| | - Yasuto Kunii
- Department of Disaster Psychiatry, International Research Institute of Disaster ScienceTohoku UniversitySendaiJapan
- Department of Neuropsychiatry, School of MedicineFukushima Medical UniversityFukushimaJapan
| | - Risa Shishido
- Department of Neuropsychiatry, School of MedicineFukushima Medical UniversityFukushimaJapan
| | - Atsuko Nagaoka
- Department of Neuropsychiatry, School of MedicineFukushima Medical UniversityFukushimaJapan
| | - Junya Matsumoto
- Department of Neuropsychiatry, School of MedicineFukushima Medical UniversityFukushimaJapan
| | - Hiroyasu Akatsu
- Department of Community‐Based Medical Education/Department of Community‐Based MedicineNagoya City University Graduate School of Medical ScienceNagoyaAichiJapan
- Choju Medical Institute, Fukushimura HospitalToyohashiAichiJapan
| | - Yoshio Hashizume
- Choju Medical Institute, Fukushimura HospitalToyohashiAichiJapan
| | - Hideki Hayashi
- Department of Pathology, Brain Research InstituteNiigata UniversityNiigataJapan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research InstituteNiigata UniversityNiigataJapan
| | - Hiroaki Tomita
- Department of Psychiatry, Graduate School of MedicineTohoku UniversitySendaiMiyagiJapan
| | - Hirooki Yabe
- Department of Disaster Psychiatry, International Research Institute of Disaster ScienceTohoku UniversitySendaiJapan
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Ohi K, Shimada M, Soda M, Nishizawa D, Fujikane D, Takai K, Kuramitsu A, Muto Y, Sugiyama S, Hasegawa J, Kitaichi K, Ikeda K, Shioiri T. Genome-wide DNA methylation risk scores for schizophrenia derived from blood and brain tissues further explain the genetic risk in patients stratified by polygenic risk scores for schizophrenia and bipolar disorder. BMJ MENTAL HEALTH 2024; 27:e300936. [PMID: 38216218 PMCID: PMC10806921 DOI: 10.1136/bmjment-2023-300936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/14/2023] [Indexed: 01/14/2024]
Abstract
BACKGROUND Genetic and environmental factors contribute to the pathogenesis of schizophrenia (SZ) and bipolar disorder (BD). Among genetic risk groups stratified by combinations of Polygenic Risk Score (PRS) deciles for SZ, BD and SZ versus BD, genetic SZ risk groups had high SZ risk and prominent cognitive impairments. Furthermore, epigenetic alterations are implicated in these disorders. However, it was unclear whether DNA Methylation Risk Scores (MRSs) for SZ risk derived from blood and brain tissues were associated with SZ risk, particularly the PRS-stratified genetic SZ risk group. METHODS Epigenome-wide association studies (EWASs) of SZ risk in whole blood were preliminarily conducted between 66 SZ patients and 30 healthy controls (HCs) and among genetic risk groups (individuals with low genetic risk for SZ and BD in HCs (n=30) and in SZ patients (n=11), genetic BD risk in SZ patients (n=25) and genetic SZ risk in SZ patients (n=30)) stratified by combinations of PRSs for SZ, BD and SZ versus BD. Next, differences in MRSs based on independent EWASs of SZ risk in whole blood, postmortem frontal cortex (FC) and superior temporal gyrus (STG) were investigated among our case‒control and PRS-stratified genetic risk status groups. RESULTS Among case‒control and genetic risk status groups, 33 and 351 genome-wide significant differentially methylated positions (DMPs) associated with SZ were identified, respectively, many of which were hypermethylated. Compared with the low genetic risk in HCs group, the genetic SZ risk in SZ group had 39 genome-wide significant DMPs, while the genetic BD risk in SZ group had only six genome-wide significant DMPs. The MRSs for SZ risk derived from whole blood, FC and STG were higher in our SZ patients than in HCs in whole blood and were particularly higher in the genetic SZ risk in SZ group than in the low genetic risk in HCs and genetic BD risk in SZ groups. Conversely, the MRSs for SZ risk based on our whole-blood EWASs among genetic risk groups were also associated with SZ in the FC and STG. There were no correlations between the MRSs and PRSs. CONCLUSIONS These findings suggest that the MRS is a potential genetic marker in understanding SZ, particularly in patients with a genetic SZ risk.
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Affiliation(s)
- Kazutaka Ohi
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
- Department of General Internal Medicine, Kanazawa Medical University, Ishikawa, Japan
| | - Mihoko Shimada
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Midori Soda
- Laboratory of Pharmaceutics, Department of Biomedical Pharmaceutics, Gifu Pharmaceutical University, Gifu, Japan
| | - Daisuke Nishizawa
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Daisuke Fujikane
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Kentaro Takai
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Ayumi Kuramitsu
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yukimasa Muto
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Shunsuke Sugiyama
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Junko Hasegawa
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kiyoyuki Kitaichi
- Laboratory of Pharmaceutics, Department of Biomedical Pharmaceutics, Gifu Pharmaceutical University, Gifu, Japan
| | - Kazutaka Ikeda
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Toshiki Shioiri
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
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Zhu W, Yuan N, Wan C, Huang M, Fang S, Chen M, Chen J, Ma Q, Chen J. Mapping the scientific research on bipolar disorder: A scientometric study of hotspots, bursts, and trends. J Affect Disord 2023; 340:626-638. [PMID: 37595897 DOI: 10.1016/j.jad.2023.08.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
Bipolar disorder (BD) is a severe psychiatric illness with an increasing prevalence worldwide. Although the pathological mechanism of and pharmacological interventions for BD have been extensively investigated in preclinical and clinical studies, a scientometric analysis of the developmental trends, interdisciplinary frontiers, and research hotspots in this field has not yet been conducted. Therefore, we performed a comprehensive scientometric review of 55,358 published studies on BD over the past two decades (2002-2021) to identify the most frequently used keywords and explore research hotspots and trajectories. The present findings revealed the main distribution, knowledge structure, topic evolution, and emerging topics of BD research. Analysing the risk factors, pathogenesis, key brain regions, comorbid conditions, and treatment strategies for BD contributed to understanding of the aetiology, progression, and treatment of this disorder. These findings provided substantial support for continued research in this area.
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Affiliation(s)
- Wenjun Zhu
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou 510632, PR China
| | - Naijun Yuan
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou 510632, PR China; Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Shenzhen, Guangdong 518020, PR China; Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou 510632, PR China
| | - Chunmiao Wan
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou 510632, PR China
| | - Minyi Huang
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou 510632, PR China
| | - Shaoyi Fang
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou 510632, PR China
| | - Man Chen
- College of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, Hubei 430065, PR China
| | - Jianbei Chen
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, PR China
| | - Qingyu Ma
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou 510632, PR China.
| | - Jiaxu Chen
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou 510632, PR China; School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, PR China.
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Watanabe R, Nakachi Y, Matsubara H, Ueda J, Ishii T, Ukai W, Hashimoto E, Kasai K, Simizu S, Kato T, Bundo M, Iwamoto K. Identification of epigenetically active L1 promoters in the human brain and their relationship with psychiatric disorders. Neurosci Res 2023; 195:37-51. [PMID: 37141946 DOI: 10.1016/j.neures.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/09/2023] [Accepted: 05/01/2023] [Indexed: 05/06/2023]
Abstract
Long interspersed nuclear element-1 (LINE-1, L1) affects the transcriptome landscape in multiple ways. Promoter activity within its 5'UTR plays a critical role in regulating diverse L1 activities. However, the epigenetic status of L1 promoters in adult brain cells and their relationship with psychiatric disorders remain poorly understood. Here, we examined DNA methylation and hydroxymethylation of the full-length L1s in neurons and nonneurons and identified "epigenetically active" L1s. Notably, some of epigenetically active L1s were retrotransposition competent, which even had chimeric transcripts from the antisense promoters at their 5'UTRs. We also identified differentially methylated L1s in the prefrontal cortices of patients with psychiatric disorders. In nonneurons of bipolar disorder patients, one L1 was significantly hypomethylated and showed an inverse correlation with the expression level of the overlapping gene NREP. Finally, we observed that altered DNA methylation levels of L1 in patients with psychiatric disorders were not affected by the surrounding genomic regions but originated from the L1 sequences. These results suggested that altered epigenetic regulation of the L1 5'UTR in the brain was involved in the pathophysiology of psychiatric disorders.
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Affiliation(s)
- Risa Watanabe
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yutaka Nakachi
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hikari Matsubara
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Junko Ueda
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takao Ishii
- Department of Occupational Therapy, Sapporo Medical University School of Health Sciences, Sapporo, Japan
| | - Wataru Ukai
- Department of Neuropsychiatry, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Eri Hashimoto
- Department of Neuropsychiatry, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; The International Research Center for Neurointelligence (WPI-IRCN), University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, Tokyo, Japan; University of Tokyo Institute for Diversity and Adaptation of Human Mind (UTIDAHM), The University of Tokyo, Tokyo, Japan; UTokyo Center for Integrative Science of Human Behaviour (CiSHuB), The University of Tokyo, Tokyo, Japan
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Tadafumi Kato
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan.
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan.
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Zakaria WNA, Wijaya A, Al-Rahbi B, Ahmad AH, Zakaria R, Othman Z. Emerging trends in gene and bipolar disorder research: a bibliometric analysis and network visualisation. Psychiatr Genet 2023; 33:102-112. [PMID: 36825833 DOI: 10.1097/ypg.0000000000000338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
This study aims to use a bibliometric technique to evaluate the scientific output of gene and bipolar disorder research. The search query related to gene and bipolar disorder from the Scopus database identified 1848 documents from 1951 to 2020. The growth in the publications increased since early 1990, peaked in 2011, and started to decline thereafter. High occurrence in author keywords suggests that some research topics, such as "polymorphism", "linkage" and "association study" have waned over time, whereas others, such as "DNA methylation," "circadian rhythm," "" and "meta-analysis," are now the emerging trends in gene and bipolar disorder research. The USA was the country with the highest production followed by the UK, Canada, Italy and Germany. The leading institutions were Cardiff University in the UK, the National Institute of Mental Health (NIMH) in the USA, King's College London in the UK and the University of California, San Diego in the USA. The leading journals publishing gene and bipolar literature were the American Journal of Medical Genetics Neuropsychiatric Genetics, Molecular Psychiatry and Psychiatric Genetics. The top authors in the number of publications were Craddock N, Serretti A and Rietschel M. According to the co-authorship network analysis of authors, the majority of the authors in the same clusters were closely linked together and originated from the same or neighbouring country. The findings of this study may be useful in identifying emerging topics for future research and promoting research collaboration in the field of genetic studies related to bipolar disorder.
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Affiliation(s)
- Wan Nur Amalina Zakaria
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia Health Campus, Kubang Kerian, Kelantan, Malaysia
| | - Adi Wijaya
- Department of Health Information Management, Universitas Indonesia Maju, Jakarta, Indonesia
| | | | | | | | - Zahiruddin Othman
- Department of Psychiatry, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
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Kumar A, Kos MZ, Roybal D, Carless MA. A pilot investigation of differential hydroxymethylation levels in patient-derived neural stem cells implicates altered cortical development in bipolar disorder. Front Psychiatry 2023; 14:1077415. [PMID: 37139321 PMCID: PMC10150707 DOI: 10.3389/fpsyt.2023.1077415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/24/2023] [Indexed: 05/05/2023] Open
Abstract
Introduction Bipolar disorder (BD) is a chronic mental illness characterized by recurrent episodes of mania and depression and associated with social and cognitive disturbances. Environmental factors, such as maternal smoking and childhood trauma, are believed to modulate risk genotypes and contribute to the pathogenesis of BD, suggesting a key role in epigenetic regulation during neurodevelopment. 5-hydroxymethylcytosine (5hmC) is an epigenetic variant of particular interest, as it is highly expressed in the brain and is implicated in neurodevelopment, and psychiatric and neurological disorders. Methods Induced pluripotent stem cells (iPSCs) were generated from the white blood cells of two adolescent patients with bipolar disorder and their same-sex age-matched unaffected siblings (n = 4). Further, iPSCs were differentiated into neuronal stem cells (NSCs) and characterized for purity using immuno-fluorescence. We used reduced representation hydroxymethylation profiling (RRHP) to perform genome-wide 5hmC profiling of iPSCs and NSCs, to model 5hmC changes during neuronal differentiation and assess their impact on BD risk. Functional annotation and enrichment testing of genes harboring differentiated 5hmC loci were performed with the online tool DAVID. Results Approximately 2 million sites were mapped and quantified, with the majority (68.8%) located in genic regions, with elevated 5hmC levels per site observed for 3' UTRs, exons, and 2-kb shorelines of CpG islands. Paired t-tests of normalized 5hmC counts between iPSC and NSC cell lines revealed global hypo-hydroxymethylation in NSCs and enrichment of differentially hydroxymethylated sites within genes associated with plasma membrane (FDR = 9.1 × 10-12) and axon guidance (FDR = 2.1 × 10-6), among other neuronal processes. The most significant difference was observed for a transcription factor binding site for the KCNK9 gene (p = 8.8 × 10-6), encoding a potassium channel protein involved in neuronal activity and migration. Protein-protein-interaction (PPI) networking showed significant connectivity (p = 3.2 × 10-10) between proteins encoded by genes harboring highly differentiated 5hmC sites, with genes involved in axon guidance and ion transmembrane transport forming distinct sub-clusters. Comparison of NSCs of BD cases and unaffected siblings revealed additional patterns of differentiation in hydroxymethylation levels, including sites in genes with functions related to synapse formation and regulation, such as CUX2 (p = 2.4 × 10-5) and DOK-7 (p = 3.6 × 10-3), as well as an enrichment of genes involved in the extracellular matrix (FDR = 1.0 × 10-8). Discussion Together, these preliminary results lend evidence toward a potential role for 5hmC in both early neuronal differentiation and BD risk, with validation and more comprehensive characterization to be achieved through follow-up study.
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Affiliation(s)
- Ashish Kumar
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Mark Z. Kos
- South Texas Diabetes and Obesity Institute, Department of Human Genetics, The University of Texas Rio Grande Valley School of Medicine, San Antonio, TX, United States
| | - Donna Roybal
- Traditions Behavioral Health, Larkspur, CA, United States
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Melanie A. Carless
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- Brain Health Consortium, The University of Texas at San Antonio, San Antonio, TX, United States
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Cheng Y, Song H, Ming GL, Weng YL. Epigenetic and epitranscriptomic regulation of axon regeneration. Mol Psychiatry 2023; 28:1440-1450. [PMID: 36922674 PMCID: PMC10650481 DOI: 10.1038/s41380-023-02028-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/18/2023]
Abstract
Effective axonal regeneration in the adult mammalian nervous system requires coordination of elevated intrinsic growth capacity and decreased responses to the inhibitory environment. Intrinsic regenerative capacity largely depends on the gene regulatory network and protein translation machinery. A failure to activate these pathways upon injury is underlying a lack of robust axon regeneration in the mature mammalian central nervous system. Epigenetics and epitranscriptomics are key regulatory mechanisms that shape gene expression and protein translation. Here, we provide an overview of different types of modifications on DNA, histones, and RNA, underpinning the regenerative competence of axons in the mature mammalian peripheral and central nervous systems. We highlight other non-neuronal cells and their epigenetic changes in determining the microenvironment for tissue repair and axon regeneration. We also address advancements of single-cell technology in charting transcriptomic and epigenetic landscapes that may further facilitate the mechanistic understanding of differential regenerative capacity in neuronal subtypes. Finally, as epigenetic and epitranscriptomic processes are commonly affected by brain injuries and psychiatric disorders, understanding their alterations upon brain injury would provide unprecedented mechanistic insights into etiology of injury-associated-psychiatric disorders and facilitate the development of therapeutic interventions to restore brain function.
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Affiliation(s)
- Yating Cheng
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX, 77030, USA
- Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Hongjun Song
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Yi-Lan Weng
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX, 77030, USA.
- Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, 77030, USA.
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10
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Huang J, Song Z, Wei B, Li Q, Lin P, Li H, Dong K. Immunological evaluation of patients with Alzheimer's disease based on mitogen-stimulated cytokine productions and mitochondrial DNA indicators. BMC Psychiatry 2023; 23:145. [PMID: 36890488 PMCID: PMC9993804 DOI: 10.1186/s12888-023-04634-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/27/2023] [Indexed: 03/10/2023] Open
Abstract
BACKGROUND Based on its objective characteristics, laboratory markers have always been the research direction of clinical diagnosis and assessment of mental disorders including Alzheimer's disease. METHODS MTT Colorimetric Assay, ELISA, and quantitative PCR were used to investigate the responsiveness of peripheral blood mononuclear cells (PBMCs) to mitogen Lipopolysaccharides (LPS) and Phytohemagglutinin (PHA), PBMCs genomic methylation and hydroxymethylation levels, nuclear DNA and mitochondrial DNA damage, respiratory chain enzyme activities, and circulating cell-free mitochondrial DNA levels were detected in 90 patients with Alzheimer's disease. RESULTS In the Alzheimer's disease group, LPS stimulated PBMCs viability, TNF-α secretion, PHA stimulated IL-10 secretion, genomic DNA methylation levels, circulating cell-free mitochondrial DNA copies, citrate synthase activity were reduced compared to the control; while the LPS stimulated PBMCs IL-1α secretion, PHA stimulated IL-1α and IFN-γ secretion, plasma IL-6 and TNF-α, mitochondrial DNA damages were increased compared to the control. CONCLUSIONS The reactivity of peripheral blood mononuclear cells to mitogens, mitochondrial DNA integrity characteristics, and cell-free mitochondrial DNA copies may be used as candidate laboratory biomarkers to help clinical management of Alzheimer's disease.
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Affiliation(s)
- Jiewen Huang
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China
| | - Zhen Song
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Beiwen Wei
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingtian Li
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping Lin
- Department of Clinical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Hui Li
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Ke Dong
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China.
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11
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Does treatment with autophagy-enhancers and/or ROS-scavengers alleviate behavioral and neurochemical consequences of low-dose rotenone-induced mild mitochondrial dysfunction in mice? Mol Psychiatry 2023; 28:1667-1678. [PMID: 36690794 DOI: 10.1038/s41380-023-01955-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/24/2023]
Abstract
Bipolar-disorder's pathophysiology and the mechanism by which medications exert their beneficial effect is yet unknown, but others' and our data implicate patients' brain mitochondrial-dysfunction and its amendment by mood-stabilizers. We recently designed a novel mouse bipolar-disorder-like model using chronic administration of a low-dose of the oxidative-phosphorylation complex I inhibitor, rotenone. Four and eight weeks rotenone treatment induced manic- and depressive-like behavior, respectively, accompanied by mood-related neurochemical changes. Here we aimed to investigate whether each of the autophagy-enhancers lithium (a mood-stabilizer), trehalose and resveratrol and/or each of the reactive oxygen species (ROS)-scavengers, resveratrol and N-acetylcystein and/or the combinations lithium+resveratrol or trehalose+N-acetylcystein, can ameliorate behavioral and neurochemical consequences of neuronal mild mitochondrial-dysfunction. We observed that lithium, trehalose and N-acetylcystein reversed rotenone-induced manic-like behavior as well as deviations in protein levels of mitochondrial complexes and the autophagy marker LC3-II. This raises the possibility that mild mitochondrial-dysfunction accompanied by impaired autophagy and a very mild increase in ROS levels are related to predisposition to manic-like behavior. On the other hand, although, as expected, most of the drugs tested eliminated the eight weeks rotenone-induced increase in protein levels of all hippocampal mitochondrial complexes, only lithium ubiquitously ameliorated the depressive-like behaviors. We cautiously deduce that aberrant autophagy and/or elevated ROS levels are not involved in predisposition to the depressive phase of bipolar-like behavior. Rather, that amending the depressive-like characteristics requires different mitochondria-related interventions. The latter might be antagonizing N-methyl-D-aspartate receptors (NMDARs), thus protecting from disruption of mitochondrial calcium homeostasis and its detrimental consequences. In conclusion, our findings suggest that by-and-large, among the autophagy-enhancers and ROS-scavengers tested, lithium is the most effective in counteracting rotenone-induced changes. Trehalose and N-acetylcystein may also be effective in attenuating manic-like behavior.
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Micale V, Di Bartolomeo M, Di Martino S, Stark T, Dell'Osso B, Drago F, D'Addario C. Are the epigenetic changes predictive of therapeutic efficacy for psychiatric disorders? A translational approach towards novel drug targets. Pharmacol Ther 2023; 241:108279. [PMID: 36103902 DOI: 10.1016/j.pharmthera.2022.108279] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 02/06/2023]
Abstract
The etiopathogenesis of mental disorders is not fully understood and accumulating evidence support that clinical symptomatology cannot be assigned to a single gene mutation, but it involves several genetic factors. More specifically, a tight association between genes and environmental risk factors, which could be mediated by epigenetic mechanisms, may play a role in the development of mental disorders. Several data suggest that epigenetic modifications such as DNA methylation, post-translational histone modification and interference of microRNA (miRNA) or long non-coding RNA (lncRNA) may modify the severity of the disease and the outcome of the therapy. Indeed, the study of these mechanisms may help to identify patients particularly vulnerable to mental disorders and may have potential utility as biomarkers to facilitate diagnosis and treatment of psychiatric disorders. This article summarizes the most relevant preclinical and human data showing how epigenetic modifications can be central to the therapeutic efficacy of antidepressant and/or antipsychotic agents, as possible predictor of drugs response.
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Affiliation(s)
- Vincenzo Micale
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy.
| | - Martina Di Bartolomeo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Serena Di Martino
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy
| | - Tibor Stark
- Department of Pharmacology, Faculty of Medicine, Masaryk University, Brno, Czech Republic; Scientific Core Unit Neuroimaging, Max Planck Institute of Psychiatry, Munich, Germany
| | - Bernardo Dell'Osso
- Department of Biomedical and Clinical Sciences 'Luigi Sacco', University of Milan, Milan, Italy, Department of Mental Health, ASST Fatebenefratelli-Sacco, Milan, Italy; "Aldo Ravelli" Research Center for Neurotechnology and Experimental Brain Therapeutics, Department of Health Sciences, University of Milan Medical School, Milan, Italy; Department of Psychiatry and Behavioral Sciences, Stanford University, CA, USA
| | - Filippo Drago
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy.
| | - Claudio D'Addario
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy; Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
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Kho SH, Yee JY, Puang SJ, Han L, Chiang C, Rapisarda A, Goh WWB, Lee J, Sng JCG. DNA methylation levels of RELN promoter region in ultra-high risk, first episode and chronic schizophrenia cohorts of schizophrenia. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2022; 8:81. [PMID: 36216926 PMCID: PMC9550813 DOI: 10.1038/s41537-022-00278-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
The essential role of the Reelin gene (RELN) during brain development makes it a prominent candidate in human epigenetic studies of Schizophrenia. Previous literature has reported differing levels of DNA methylation (DNAm) in patients with psychosis. Therefore, this study aimed to (1) examine and compare RELN DNAm levels in subjects at different stages of psychosis cross-sectionally, (2) analyse the effect of antipsychotics (AP) on DNAm, and (3) evaluate the effectiveness and applicability of RELN promoter DNAm as a possible biological-based marker for symptom severity in psychosis.. The study cohort consisted of 56 healthy controls, 87 ultra-high risk (UHR) individuals, 26 first-episode (FE) psychosis individuals and 30 chronic schizophrenia (CS) individuals. The Positive and Negative Syndrome Scale (PANSS) was used to assess Schizophrenia severity. After pyrosequencing selected CpG sites of peripheral blood, the Average mean DNAm levels were compared amongst the 4 subgroups. Our results showed differing levels of DNAm, with UHR having the lowest (7.72 ± 0.19) while the CS had the highest levels (HC: 8.78 ± 0.35; FE: 7.75 ± 0.37; CS: 8.82 ± 0.48). Significantly higher Average mean DNAm levels were found in CS subjects on AP (9.12 ± 0.61) compared to UHR without medication (UHR(-)) (7.39 ± 0.18). A significant association was also observed between the Average mean DNAm of FE and PANSS Negative symptom factor (R2 = 0.237, ß = -0.401, *p = 0.033). In conclusion, our findings suggested different levels of DNAm for subjects at different stages of psychosis. Those subjects that took AP have different DNAm levels. There were significant associations between FE DNAm and Negative PANSS scores. With more future experiments and on larger cohorts, there may be potential use of DNAm of the RELN gene as one of the genes for the biological-based marker for symptom severity in psychosis.
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Affiliation(s)
- Sok-Hong Kho
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
| | - Jie Yin Yee
- Research Division, Institute of Mental Health, Singapore, Singapore
| | - Shu Juan Puang
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Luke Han
- Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Christine Chiang
- Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Attilio Rapisarda
- Research Division, Institute of Mental Health, Singapore, Singapore
- Neuroscience and Behavioural Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Wilson Wen Bin Goh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jimmy Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Research Division, Institute of Mental Health, Singapore, Singapore
- Department of Psychosis, Institute of Mental Health, Singapore, Singapore
| | - Judy Chia Ghee Sng
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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14
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Kushima I, Nakatochi M, Aleksic B, Okada T, Kimura H, Kato H, Morikawa M, Inada T, Ishizuka K, Torii Y, Nakamura Y, Tanaka S, Imaeda M, Takahashi N, Yamamoto M, Iwamoto K, Nawa Y, Ogawa N, Iritani S, Hayashi Y, Lo T, Otgonbayar G, Furuta S, Iwata N, Ikeda M, Saito T, Ninomiya K, Okochi T, Hashimoto R, Yamamori H, Yasuda Y, Fujimoto M, Miura K, Itokawa M, Arai M, Miyashita M, Toriumi K, Ohi K, Shioiri T, Kitaichi K, Someya T, Watanabe Y, Egawa J, Takahashi T, Suzuki M, Sasaki T, Tochigi M, Nishimura F, Yamasue H, Kuwabara H, Wakuda T, Kato TA, Kanba S, Horikawa H, Usami M, Kodaira M, Watanabe K, Yoshikawa T, Toyota T, Yokoyama S, Munesue T, Kimura R, Funabiki Y, Kosaka H, Jung M, Kasai K, Ikegame T, Jinde S, Numata S, Kinoshita M, Kato T, Kakiuchi C, Yamakawa K, Suzuki T, Hashimoto N, Ishikawa S, Yamagata B, Nio S, Murai T, Son S, Kunii Y, Yabe H, Inagaki M, Goto YI, Okumura Y, Ito T, Arioka Y, Mori D, Ozaki N. Cross-Disorder Analysis of Genic and Regulatory Copy Number Variations in Bipolar Disorder, Schizophrenia, and Autism Spectrum Disorder. Biol Psychiatry 2022; 92:362-374. [PMID: 35667888 DOI: 10.1016/j.biopsych.2022.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND We aimed to determine the similarities and differences in the roles of genic and regulatory copy number variations (CNVs) in bipolar disorder (BD), schizophrenia (SCZ), and autism spectrum disorder (ASD). METHODS Based on high-resolution CNV data from 8708 Japanese samples, we performed to our knowledge the largest cross-disorder analysis of genic and regulatory CNVs in BD, SCZ, and ASD. RESULTS In genic CNVs, we found an increased burden of smaller (<100 kb) exonic deletions in BD, which contrasted with the highest burden of larger (>500 kb) exonic CNVs in SCZ/ASD. Pathogenic CNVs linked to neurodevelopmental disorders were significantly associated with the risk for each disorder, but BD and SCZ/ASD differed in terms of the effect size (smaller in BD) and subtype distribution of CNVs linked to neurodevelopmental disorders. We identified 3 synaptic genes (DLG2, PCDH15, and ASTN2) as risk factors for BD. Whereas gene set analysis showed that BD-associated pathways were restricted to chromatin biology, SCZ and ASD involved more extensive and similar pathways. Nevertheless, a correlation analysis of gene set results indicated weak but significant pathway similarities between BD and SCZ or ASD (r = 0.25-0.31). In SCZ and ASD, but not BD, CNVs were significantly enriched in enhancers and promoters in brain tissue. CONCLUSIONS BD and SCZ/ASD differ in terms of CNV burden, characteristics of CNVs linked to neurodevelopmental disorders, and regulatory CNVs. On the other hand, they have shared molecular mechanisms, including chromatin biology. The BD risk genes identified here could provide insight into the pathogenesis of BD.
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Affiliation(s)
- Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan; Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan.
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takashi Okada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan; Department of Developmental Disorders, National Institute of Mental Health National Center of Neurology and Psychiatry, Nagoya, Japan
| | - Hiroki Kimura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hidekazu Kato
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mako Morikawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshiya Inada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kanako Ishizuka
- Health Support Center, Nagoya Institute of Technology, Nagoya, Japan
| | - Youta Torii
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yukako Nakamura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoshi Tanaka
- National Hospital Organization Higashi Owari National Hospital, National Hospital Organization Nagoya Medical Center, Nagoya, Japan; Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Miho Imaeda
- Department of Clinical Oncology and Chemotherapy, Nagoya University Hospital, Nagoya, Japan
| | - Nagahide Takahashi
- Department of Integrated Health Sciences, Department of Child and Adolescent Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Maeri Yamamoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kunihiro Iwamoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshihiro Nawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nanayo Ogawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shuji Iritani
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan; Okehazama Hospital Brain Research Institute, Fujita Health University School of Medicine, Toyoake, Japan
| | - Yu Hayashi
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tzuyao Lo
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Gantsooj Otgonbayar
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sho Furuta
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nakao Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - Masashi Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - Takeo Saito
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - Kohei Ninomiya
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tomo Okochi
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Hidenaga Yamamori
- Department of Pathology of Mental Diseases, National Institute of Mental Health National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan; Japan Community Health Care Organization Osaka Hospital, Osaka, Japan
| | - Yuka Yasuda
- Department of Pathology of Mental Diseases, National Institute of Mental Health National Center of Neurology and Psychiatry, Tokyo, Japan; Medical Corporation Foster, Osaka, Japan
| | - Michiko Fujimoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kenichiro Miura
- Department of Pathology of Mental Diseases, National Institute of Mental Health National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Masanari Itokawa
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Tokyo, Japan
| | - Makoto Arai
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Mitsuhiro Miyashita
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Tokyo, Japan; Department of Psychiatry, Takatsuki Hospital, Tokyo, Japan
| | - Kazuya Toriumi
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kazutaka Ohi
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan; Department of General Internal Medicine, Kanazawa Medical University, Ishikawa, Japan
| | - Toshiki Shioiri
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Kiyoyuki Kitaichi
- Laboratory of Pharmaceutics, Department of Biomedical Pharmaceutics, Gifu Pharmaceutical University, Gifu, Japan
| | - Toshiyuki Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yuichiro Watanabe
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Jun Egawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tsutomu Takahashi
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan; Research Center for Idling Brain Science, University of Toyama, Toyama, Japan
| | - Michio Suzuki
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan; Research Center for Idling Brain Science, University of Toyama, Toyama, Japan
| | - Tsukasa Sasaki
- Laboratory of Health Education, Graduate School of Education, University of Tokyo, Tokyo, Japan
| | - Mamoru Tochigi
- Department of Neuropsychiatry, Teikyo University School of Medicine, Tokyo, Japan
| | - Fumichika Nishimura
- Center for Research on Counseling and Support Services, University of Tokyo, Tokyo, Japan
| | - Hidenori Yamasue
- Department of Psychiatry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hitoshi Kuwabara
- Department of Psychiatry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tomoyasu Wakuda
- Department of Psychiatry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takahiro A Kato
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shigenobu Kanba
- Japan Depression Center, Tokyo, Japan; Kyushu University, Fukuoka, Japan
| | - Hideki Horikawa
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Horikawa Hospital, Kurume, Japan
| | - Masahide Usami
- Department of Child and Adolescent Psychiatry, Kohnodai Hospital, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Masaki Kodaira
- Department of Child and Adolescent Mental Health, Aiiku Clinic, Tokyo, Japan
| | - Kyota Watanabe
- Hiroshima City Center for Children's Health and Development, Hiroshima, Japan
| | - Takeo Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Japan
| | - Tomoko Toyota
- Laboratory for Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Japan
| | - Shigeru Yokoyama
- Research Center for Child Mental Development, Kanazawa University, Ishikawa, Japan
| | - Toshio Munesue
- Research Center for Child Mental Development, Kanazawa University, Ishikawa, Japan
| | - Ryo Kimura
- Department of Anatomy and Developmental Biology, Kyoto University, Kyoto, Japan
| | - Yasuko Funabiki
- Department of Cognitive and Behavioral Science, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Hirotaka Kosaka
- Department of Neuropsychiatry, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Minyoung Jung
- Department of Neuropsychiatry, Faculty of Medical Sciences, University of Fukui, Fukui, Japan; Cognitive Science Group, Korea Brain Research Institute, Daegu, South Korea
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, University of Tokyo, Tokyo, Japan; International Research Center for Neurointelligence at University of Tokyo Institutes for Advanced Study, Tokyo, Japan
| | - Tempei Ikegame
- Department of Neuropsychiatry, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Seiichiro Jinde
- Department of Neuropsychiatry, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Shusuke Numata
- Department of Psychiatry, Graduate School of Biomedical Science, Tokushima University, Tokushima, Japan
| | - Makoto Kinoshita
- Department of Psychiatry, Graduate School of Biomedical Science, Tokushima University, Tokushima, Japan
| | - Tadafumi Kato
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Chihiro Kakiuchi
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kazuhiro Yamakawa
- Department of Neurodevelopmental Disorder Genetics, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Toshimitsu Suzuki
- Department of Neurodevelopmental Disorder Genetics, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Naoki Hashimoto
- Department of Psychiatry, Hokkaido University Graduate School of Medicine, Hokkaido, Japan
| | - Shuhei Ishikawa
- Department of Psychiatry, Hokkaido University Hospital, Hokkaido, Japan
| | - Bun Yamagata
- Department of Neuropsychiatry, Keio University School of Medicine, Tokyo, Japan
| | - Shintaro Nio
- Department of Psychiatry, Saiseikai Central Hospital, Tokyo, Japan
| | - Toshiya Murai
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shuraku Son
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuto Kunii
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan; Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hirooki Yabe
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Masumi Inagaki
- Department of Pediatrics, Tottori Prefecture Rehabilitation Center, Tottori, Japan
| | - Yu-Ichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Yuto Okumura
- Public Health Informatics Unit, Nagoya University Graduate School of Medicine, Nagoya, Japan; Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Tomoya Ito
- Public Health Informatics Unit, Nagoya University Graduate School of Medicine, Nagoya, Japan; Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Yuko Arioka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan; Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Daisuke Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan; Brain and Mind Research Center, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan; Institute for Glyco-core Research, Nagoya University, Nagoya, Japan.
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15
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Michel N, Young HMR, Atkin ND, Arshad U, Al-Humadi R, Singh S, Manukyan A, Gore L, Burbulis IE, Wang YH, McConnell MJ. Transcription-associated DNA DSBs activate p53 during hiPSC-based neurogenesis. Sci Rep 2022; 12:12156. [PMID: 35840793 PMCID: PMC9287420 DOI: 10.1038/s41598-022-16516-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Neurons are overproduced during cerebral cortical development. Neural progenitor cells (NPCs) divide rapidly and incur frequent DNA double-strand breaks (DSBs) throughout cortical neurogenesis. Although half of the neurons born during neurodevelopment die, many neurons with inaccurate DNA repair survive leading to brain somatic mosaicism. Recurrent DNA DSBs during neurodevelopment are associated with both gene expression level and gene length. We used imaging flow cytometry and a genome-wide DNA DSB capture approach to quantify and map DNA DSBs during human induced pluripotent stem cell (hiPSC)-based neurogenesis. Reduced p53 signaling was brought about by knockdown (p53KD); p53KD led to elevated DNA DSB burden in neurons that was associated with gene expression level but not gene length in neural progenitor cells (NPCs). Furthermore, DNA DSBs incurred from transcriptional, but not replicative, stress lead to p53 activation in neurotypical NPCs. In p53KD NPCs, DNA DSBs accumulate at transcription start sites of genes that are associated with neurological and psychiatric disorders. These findings add to a growing understanding of how neuronal genome dynamics are engaged by high transcriptional or replicative burden during neurodevelopment.
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Affiliation(s)
- Nadine Michel
- Neuroscience Graduate Program, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Heather M Raimer Young
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Naomi D Atkin
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Umar Arshad
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Reem Al-Humadi
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Sandeep Singh
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Arkadi Manukyan
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Lana Gore
- Lieber Institute for Brain Development, 855 N. Wolfe St., Ste. 300, Baltimore, MD, 21205, USA
| | - Ian E Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
- Sede de la Patagonia, Facultad de Medicina y Ciencias, Universidad San Sebastián, Puerto Montt, Chile
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Michael J McConnell
- Lieber Institute for Brain Development, 855 N. Wolfe St., Ste. 300, Baltimore, MD, 21205, USA.
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16
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Soheili M, Alinaghipour A, Salami M. Good bacteria, oxidative stress and neurological disorders: Possible therapeutical considerations. Life Sci 2022; 301:120605. [DOI: 10.1016/j.lfs.2022.120605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 12/11/2022]
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17
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Kushima I, Lo T, Aleksic B, Ozaki N. Case report of a female with bipolar disorder and MBD5 deletion. Psychiatry Clin Neurosci 2022; 76:127-128. [PMID: 35088487 DOI: 10.1111/pcn.13329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/13/2021] [Accepted: 12/29/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Tzuyao Lo
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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18
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Algothmi K, Alqurashi A, Alrofaidi A, Alharbi M, Farsi R, Alburae N, Ganash M, Azhari S, Basingab F, Almuhammadi A, Alqosaibi A, Alkhatabi H, Elaimi A, Jan M, Aldhalaan H, Alrafiah A, Alhazmi S. DNA Methylation Level of Transcription Factor Binding Site in the Promoter Region of Acyl-CoA Synthetase Family Member 3 ( ACSF3) in Saudi Autistic Children. Pharmgenomics Pers Med 2022; 15:131-142. [PMID: 35221709 PMCID: PMC8865760 DOI: 10.2147/pgpm.s346187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/24/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND DNA methylation (DNAm) is one of the main epigenetic mechanisms that affects gene expression without changing the underlying DNA sequence. Aberrant DNAm has an implication in different human diseases such as cancer, schizophrenia, and autism spectrum disorder (ASD). ASD is a neurodevelopmental disorder that affects behavior, learning, and communication skills. Acyl-CoA synthetase family member 3 (ACSF3) encodes malonyl-CoA synthetase that is involved in the synthesis and oxidation of fatty acids. The dysregulation in such gene has been reported in combined malonic and methylmalonic aciduria associated with neurological symptoms such as memory problems, psychiatric diseases, and/or cognitive decline. This research aims to study DNAm in the transcription factor (TF) binding site of ACSF3 in Saudi autistic children. To determine whether the DNAm of the TF-binding site is a cause or a consequence of transcription regulation of ACSF3. METHODS RT-qPCR and DNA methylight qPCR were used to determine the expression and DNAm level in the promoter region of ACSF3, respectively. DNA and RNA were extracted from 19 cases of ASD children and 18 control samples from their healthy siblings. RESULTS The results showed a significant correlation between the gene expression of ACSF3 and specificity protein 1 (SP1) in 17 samples of ASD patients, where both genes were upregulated in 9 samples and downregulated in 8 samples. CONCLUSION Although this study found no DNAm in the binding site of SP1 within the ACSF3 promoter, the indicated correlation highlights a possible role of ACSF3 and SP1 in ASD patients.
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Affiliation(s)
- Khloud Algothmi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amal Alqurashi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aisha Alrofaidi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mona Alharbi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem Farsi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Najla Alburae
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Magdah Ganash
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sheren Azhari
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fatemah Basingab
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asma Almuhammadi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amany Alqosaibi
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Heba Alkhatabi
- King Abdulaziz University, Centre of Excellence in Genomic Medicine Research, Jeddah, Saudi Arabia,Medical LaboratorySciencesDepartment,Faculty of Applied Medical Sciences, Jeddah, Saudi Arabia
| | - Aisha Elaimi
- King Abdulaziz University, Centre of Excellence in Genomic Medicine Research, Jeddah, Saudi Arabia,Medical LaboratorySciencesDepartment,Faculty of Applied Medical Sciences, Jeddah, Saudi Arabia
| | - Mohammed Jan
- College of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hesham Aldhalaan
- Center for Autism Research at King Faisal Specialist Hospital & Research Center (KFSH & RC), Riyadh, Saudi Arabia
| | - Aziza Alrafiah
- Medical LaboratorySciencesDepartment,Faculty of Applied Medical Sciences, Jeddah, Saudi Arabia,Correspondence: Aziza Alrafiah, P.O Box 80200, Jeddah, 21589, Saudi Arabia, Tel +966 126401000 Ext. 23495, Fax +966 126401000 Ext. 21686, Email
| | - Safiah Alhazmi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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19
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Sugawara H, Bundo M, Kasahara T, Nakachi Y, Ueda J, Kubota-Sakashita M, Iwamoto K, Kato T. Cell-type-specific DNA methylation analysis of the frontal cortices of mutant Polg1 transgenic mice with neuronal accumulation of deleted mitochondrial DNA. Mol Brain 2022; 15:9. [PMID: 34991677 PMCID: PMC8740475 DOI: 10.1186/s13041-021-00894-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/25/2021] [Indexed: 11/15/2022] Open
Abstract
Bipolar disorder (BD) is a severe psychiatric disorder characterized by repeated conflicting manic and depressive states. In addition to genetic factors, complex gene–environment interactions, which alter the epigenetic status in the brain, contribute to the etiology and pathophysiology of BD. Here, we performed a promoter-wide DNA methylation analysis of neurons and nonneurons derived from the frontal cortices of mutant Polg1 transgenic (n = 6) and wild-type mice (n = 6). The mutant mice expressed a proofreading-deficient mitochondrial DNA (mtDNA) polymerase under the neuron-specific CamK2a promoter and showed BD-like behavioral abnormalities, such as activity changes and altered circadian rhythms. We identified a total of 469 differentially methylated regions (DMRs), consisting of 267 neuronal and 202 nonneuronal DMRs. Gene ontology analysis of DMR-associated genes showed that cell cycle-, cell division-, and inhibition of peptide activity-related genes were enriched in neurons, whereas synapse- and GABA-related genes were enriched in nonneurons. Among the DMR-associated genes, Trim2 and Lrpprc showed an inverse relationship between DNA methylation and gene expression status. In addition, we observed that mutant Polg1 transgenic mice shared several features of DNA methylation changes in postmortem brains of patients with BD, such as dominant hypomethylation changes in neurons, which include hypomethylation of the molecular motor gene and altered DNA methylation of synapse-related genes in nonneurons. Taken together, the DMRs identified in this study will contribute to understanding the pathophysiology of BD from an epigenetic perspective.
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Affiliation(s)
- Hiroko Sugawara
- Department of Psychiatry, Kansai Rosai Hospital, Amagasaki, Japan.,Department of Psychiatry, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto-shi, Kumamoto, 860-8556, Japan
| | - Takaoki Kasahara
- Career Development Program, RIKEN Center for Brain Science, Saitama, Japan
| | - Yutaka Nakachi
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto-shi, Kumamoto, 860-8556, Japan
| | - Junko Ueda
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto-shi, Kumamoto, 860-8556, Japan
| | - Mie Kubota-Sakashita
- Department of Psychiatry and Behavior Science, Graduate School of Medicine, Juntendo University, 3-1-3 Hongo, Bunkyo-ku, Tokyo, 113-8431, Japan
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto-shi, Kumamoto, 860-8556, Japan.
| | - Tadafumi Kato
- Department of Psychiatry and Behavior Science, Graduate School of Medicine, Juntendo University, 3-1-3 Hongo, Bunkyo-ku, Tokyo, 113-8431, Japan.
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20
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Du J, Nakachi Y, Kiyono T, Fujii S, Kasai K, Bundo M, Iwamoto K. Comprehensive DNA Methylation Analysis of Human Neuroblastoma Cells Treated With Haloperidol and Risperidone. Front Mol Neurosci 2021; 14:792874. [PMID: 34938161 PMCID: PMC8687450 DOI: 10.3389/fnmol.2021.792874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/02/2021] [Indexed: 11/13/2022] Open
Abstract
Accumulating evidence suggests that the epigenetic alterations induced by antipsychotics contribute to the therapeutic efficacy. However, global and site-specific epigenetic changes by antipsychotics and those shared by different classes of antipsychotics remain poorly understood. We conducted a comprehensive DNA methylation analysis of human neuroblastoma cells cultured with antipsychotics. The cells were cultured with low and high concentrations of haloperidol or risperidone for 8 days. DNA methylation assay was performed with the Illumina HumanMethylation450 BeadChip. We found that both haloperidol and risperidone tended to cause hypermethylation changes and showed similar DNA methylation changes closely related to neuronal functions. A total of 294 differentially methylated probes (DMPs), including 197 hypermethylated and 97 hypomethylated DMPs, were identified with both haloperidol and risperidone treatment. Gene ontology analysis of the hypermethylated probe-associated genes showed enrichment of genes related to the regulation of neurotransmitter receptor activity and lipoprotein lipase activity. Pathway analysis identified that among the DMP-associated genes, SHANK1 and SHANK2 were the major genes in the neuropsychiatric disorder-related pathways. Our data would be valuable for understanding the mechanisms of action of antipsychotics from an epigenetic viewpoint.
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Affiliation(s)
- Jianbin Du
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yutaka Nakachi
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Tomoki Kiyono
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shinya Fujii
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,The International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), Tokyo, Japan.,University of Tokyo Center for Integrative Science of Human Behavior (CiSHuB), Tokyo, Japan
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
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21
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Ueda J, Bundo M, Nakachi Y, Kasai K, Kato T, Iwamoto K. Cell type-specific DNA methylation analysis of the prefrontal cortex of patients with schizophrenia. Psychiatry Clin Neurosci 2021; 75:297-299. [PMID: 34164871 PMCID: PMC8457163 DOI: 10.1111/pcn.13282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/28/2021] [Accepted: 06/18/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Junko Ueda
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.,Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yutaka Nakachi
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,The International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), Tokyo, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan.,Department of Psychiatry and Behavioral Science, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
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