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Wang Z, Fu G, Ma G, Wang C, Wang Q, Lu C, Fu L, Zhang X, Cong B, Li S. The association between DNA methylation and human height and a prospective model of DNA methylation-based height prediction. Hum Genet 2024; 143:401-421. [PMID: 38507014 DOI: 10.1007/s00439-024-02659-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024]
Abstract
As a vital anthropometric characteristic, human height information not only helps to understand overall developmental status and genetic risk factors, but is also important for forensic DNA phenotyping. We utilized linear regression analysis to test the association between each CpG probe and the height phenotype. Next, we designed a methylation sequencing panel targeting 959 CpGs and subsequent height inference models were constructed for the Chinese population. A total of 11,730 height-associated sites were identified. By employing KPCA and deep neural networks, a prediction model was developed, of which the cross-validation RMSE, MAE and R2 were 5.62 cm, 4.45 cm and 0.64, respectively. Genetic factors could explain 39.4% of the methylation level variance of sites used in the height inference models. Collectively, we demonstrated an association between height and DNA methylation status through an EWAS analysis. Targeted methylation sequencing of only 959 CpGs combined with deep learning techniques could provide a model to estimate human height with higher accuracy than SNP-based prediction models.
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Affiliation(s)
- Zhonghua Wang
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Guangping Fu
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Guanju Ma
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Chunyan Wang
- Physical Examination Center of Shijiazhuang People's Hospital, Shijiazhuang, 050011, Hebei, China
| | - Qian Wang
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Chaolong Lu
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Lihong Fu
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Xiaojing Zhang
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Shujin Li
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China.
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Annunzi E, Cannito L, Bellia F, Mercante F, Vismara M, Benatti B, Di Domenico A, Palumbo R, Adriani W, Dell'Osso B, D'Addario C. Mild internet use is associated with epigenetic alterations of key neurotransmission genes in salivary DNA of young university students. Sci Rep 2023; 13:22192. [PMID: 38092954 PMCID: PMC10719329 DOI: 10.1038/s41598-023-49492-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023] Open
Abstract
The potentially problematic use of the Internet is a growing concern worldwide, which causes and consequences are not completely understood yet. The neurobiology of Internet addiction (IA) has attracted much attention in scientific research, which is now focusing on identifying measurable biological markers. Aim of this study was to investigate epigenetic and genetic regulation of oxytocin receptor (OXTR), dopamine transporter (DAT1) and serotonin transporter (SERT) genes using DNA obtained from saliva samples of young university students: the Internet Addiction Test (IAT) was administered to evaluate the potential existence and intensity of IA. Significant changes in DNA methylation levels at OXTR, DAT1 and SERT genes were observed in the 30 < IAT < 49 group (mild-risk internet users) compared to the IAT < 29 subjects (complete control of internet use) and IAT > 50 subjects (considered as moderately addicted). Moreover, epigenetic markers were significantly correlated, either directly (for OXTR and DAT1) or inversely (OXTR and DAT1 versus SERT), to the psychometric properties. Our data confirmed the association of OXTR, DAT1 and SERT genes in processes related to behavioural addictions and might be of relevance to suggest possible biological predictors of altered behaviours and the eventual vulnerability to develop an IA. Different other genetic pathways have been suggested to play a role in IA and research is ongoing to better define them, in order to help in the early diagnosis as well as in the development of new potential treatments.
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Affiliation(s)
- Eugenia Annunzi
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, 66100, Chieti, Italy
| | - Loreta Cannito
- Department of Humanities, University of Foggia, Foggia, Italy
- Center for Advanced Studies and Technology, University "G. d'Annunzio" of Chieti-Pescara, 66100, Chieti, Italy
| | - Fabio Bellia
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100, Teramo, Italy
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Francesca Mercante
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100, Teramo, Italy
| | - Matteo Vismara
- Department of Psychiatry, Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, ASST Fatebenefratelli-Sacco, 20019, Milan, Italy
| | - Beatrice Benatti
- Department of Psychiatry, Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, ASST Fatebenefratelli-Sacco, 20019, Milan, Italy
- "Aldo Ravelli" Center for Nanotechnology and Neurostimulation, University of Milan, Milan, Italy
| | - Alberto Di Domenico
- Department of Psychological, Health and Territorial Sciences, University "G. d'Annunzio" of Chieti-Pescara, 66100, Chieti, Italy
| | - Riccardo Palumbo
- Department of Neuroscience, Imaging and Clinical Sciences, University "G. d'Annunzio" of Chieti-Pescara, 66100, Chieti, Italy
- Center for Advanced Studies and Technology, University "G. d'Annunzio" of Chieti-Pescara, 66100, Chieti, Italy
| | - Walter Adriani
- Center for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy
| | - Bernardo Dell'Osso
- Department of Psychiatry, Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, ASST Fatebenefratelli-Sacco, 20019, Milan, Italy
- "Aldo Ravelli" Center for Nanotechnology and Neurostimulation, University of Milan, Milan, Italy
| | - Claudio D'Addario
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100, Teramo, Italy.
- Department of Clinical Neuroscience, Karolinska Institute, 10316, Stockholm, Sweden.
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Meijer M, Franke B, Sandi C, Klein M. Epigenome-wide DNA methylation in externalizing behaviours: A review and combined analysis. Neurosci Biobehav Rev 2023; 145:104997. [PMID: 36566803 DOI: 10.1016/j.neubiorev.2022.104997] [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: 08/08/2022] [Revised: 11/24/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
DNA methylation (DNAm) is one of the most frequently studied epigenetic mechanisms facilitating the interplay of genomic and environmental factors, which can contribute to externalizing behaviours and related psychiatric disorders. Previous epigenome-wide association studies (EWAS) for externalizing behaviours have been limited in sample size, and, therefore, candidate genes and biomarkers with robust evidence are still lacking. We 1) performed a systematic literature review of EWAS of attention-deficit/hyperactivity disorder (ADHD)- and aggression-related behaviours conducted in peripheral tissue and cord blood and 2) combined the most strongly associated DNAm sites observed in individual studies (p < 10-3) to identify candidate genes and biological systems for ADHD and aggressive behaviours. We observed enrichment for neuronal processes and neuronal cell marker genes for ADHD. Astrocyte and granulocytes cell markers among genes annotated to DNAm sites were relevant for both ADHD and aggression-related behaviours. Only 1 % of the most significant epigenetic findings for ADHD/ADHD symptoms were likely to be directly explained by genetic factors involved in ADHD. Finally, we discuss how the field would greatly benefit from larger sample sizes and harmonization of assessment instruments.
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Affiliation(s)
- Mandy Meijer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Laboratory of Behavioural Genetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Barbara Franke
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Carmen Sandi
- Laboratory of Behavioural Genetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marieke Klein
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Psychiatry, University of California, La Jolla, San Diego, CA, 92093, USA.
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4
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Song M, Bai H, Zhang P, Zhou X, Ying B. Promising applications of human-derived saliva biomarker testing in clinical diagnostics. Int J Oral Sci 2023; 15:2. [PMID: 36596771 PMCID: PMC9810734 DOI: 10.1038/s41368-022-00209-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/23/2022] [Accepted: 11/03/2022] [Indexed: 01/05/2023] Open
Abstract
Saliva testing is a vital method for clinical applications, for its noninvasive features, richness in substances, and the huge amount. Due to its direct anatomical connection with oral, digestive, and endocrine systems, clinical usage of saliva testing for these diseases is promising. Furthermore, for other diseases that seeming to have no correlations with saliva, such as neurodegenerative diseases and psychological diseases, researchers also reckon saliva informative. Tremendous papers are being produced in this field. Updated summaries of recent literature give newcomers a shortcut to have a grasp of this topic. Here, we focused on recent research about saliva biomarkers that are derived from humans, not from other organisms. The review mostly addresses the proceedings from 2016 to 2022, to shed light on the promising usage of saliva testing in clinical diagnostics. We recap the recent advances following the category of different types of biomarkers, such as intracellular DNA, RNA, proteins and intercellular exosomes, cell-free DNA, to give a comprehensive impression of saliva biomarker testing.
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Affiliation(s)
- Mengyuan Song
- grid.13291.380000 0001 0807 1581Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Bai
- grid.13291.380000 0001 0807 1581Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ping Zhang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases & Human Saliva Laboratory & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases & Human Saliva Laboratory & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.
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Dolinko AV, Schultz BM, Ghosh J, Kalliora C, Mainigi M, Coutifaris C, Sapienza C, Senapati S. Disrupted methylation patterns at birth persist in early childhood: a prospective cohort analysis. Clin Epigenetics 2022; 14:129. [PMID: 36243864 PMCID: PMC9568969 DOI: 10.1186/s13148-022-01348-x] [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: 03/08/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alterations in the epigenome are a risk factor in multiple disease states. We have demonstrated in the past that disruption of the epigenome during early pregnancy or periconception, as demonstrated by altered methylation, may be associated with both assisted reproductive technology and undesirable clinical outcomes at birth, such as low birth weight. We have previously defined this altered methylation, calculated based on statistical upper and lower limits of outlier CpGs compared to the population, as an 'outlier methylation phenotype' (OMP). Our aim in this study was to determine whether children thus identified as possessing an OMP at birth by DNA methylation in cord blood persist as outliers in early childhood based on salivary DNA methylation. RESULTS A total of 31 children were included in the analysis. Among 24 children for whom both cord blood DNA and salivary DNA were available, DNA methylation patterns, analyzed using the Illumina Infinium MethylationEPIC BeadChip (850 K), between cord blood at birth and saliva in childhood at age 6-12 years remain stable (R2 range 0.89-0.97). At birth, three out of 28 children demonstrated an OMP in multiple cord blood datasets and hierarchical clustering. Overall DNA methylation among all three OMP children identified as outliers at birth was remarkably stable (individual R2 0.908, 0.92, 0.915), even when only outlier CpG sites were considered (R2 0.694, 0.738, 0.828). CONCLUSIONS DNA methylation signatures in cord blood remain stable over time as demonstrated by a strong correlation with epigenetic salivary signatures in childhood. Future work is planned to identify whether a clinical phenotype is associated with OMP and, if so, could undesirable clinical outcomes in childhood and adulthood be predicted at birth.
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Affiliation(s)
- Andrey V Dolinko
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Bryant M Schultz
- Fels Cancer Institute for Personalized Medicine, Temple University, Philadelphia, PA, USA
| | - Jayashri Ghosh
- Fels Cancer Institute for Personalized Medicine, Temple University, Philadelphia, PA, USA
| | - Charikleia Kalliora
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Monica Mainigi
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Christos Coutifaris
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Carmen Sapienza
- Fels Cancer Institute for Personalized Medicine, Temple University, Philadelphia, PA, USA
| | - Suneeta Senapati
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA.
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León I, Herrero Roldán S, Rodrigo MJ, López Rodríguez M, Fisher J, Mitchell C, Lage-Castellanos A. The shared mother-child epigenetic signature of neglect is related to maternal adverse events. Front Physiol 2022; 13:966740. [PMID: 36091392 PMCID: PMC9448913 DOI: 10.3389/fphys.2022.966740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Studies of DNA methylation have revealed the biological mechanisms by which life adversity confers risk for later physical and mental health problems. What remains unknown is the “biologically embedding” of maternal adverse experiences resulting in maladaptive parenting and whether these epigenetic effects are transmitted to the next generation. This study focuses on neglectful mothering indexed by a severe disregard for the basic and psychological needs of the child. Using the Illumina Human Methylation EPIC BeadChip in saliva samples, we identified genes with differentially methylated regions (DMRs) in those mothers with (n = 51), versus those without (n = 87), neglectful behavior that present similar DMRs patterns in their children being neglected versus non-neglected (n = 40 vs. 75). Mothers reported the emotional intensity of adverse life events. After covariate adjustment and multiple testing corrections, we identified 69 DMRs in the mother epigenome and 42 DMRs in the child epigenome that were simultaneously above the α = 0.01 threshold. The common set of nine DMRs contained genes related to childhood adversity, neonatal and infant diabetes, child neurobehavioral development and other health problems such as obesity, hypertension, cancer, posttraumatic stress, and the Alzheimer’s disease; four of the genes were associated with maternal life adversity. Identifying a shared epigenetic signature of neglect linked to maternal life adversity is an essential step in breaking the intergenerational transmission of one of the most common forms of childhood maltreatment.
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Affiliation(s)
- Inmaculada León
- Instituto Universitario de Neurociencia, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
| | - Silvia Herrero Roldán
- Instituto Universitario de Neurociencia, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
- *Correspondence: Silvia Herrero Roldán,
| | - María José Rodrigo
- Instituto Universitario de Neurociencia, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
- Facultad de Psicología, Universidad de La Laguna, San Cristóbal de la Laguna, Spain
| | - Maykel López Rodríguez
- Department of Pathology and Experimental Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, United States
| | - Jonah Fisher
- Institute for Social Research, University of Michigan, Ann Abor, MI, United States
| | - Colter Mitchell
- Institute for Social Research, University of Michigan, Ann Abor, MI, United States
| | - Agustín Lage-Castellanos
- Department of NeuroInformatics, Cuban Center for Neuroscience, Havana, Cuba
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands
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D'Addario C, Pucci M, Bellia F, Girella A, Sabatucci A, Fanti F, Vismara M, Benatti B, Ferrara L, Fasciana F, Celebre L, Viganò C, Elli L, Sergi M, Maccarrone M, Buzzelli V, Trezza V, Dell'Osso B. Regulation of oxytocin receptor gene expression in obsessive-compulsive disorder: a possible role for the microbiota-host epigenetic axis. Clin Epigenetics 2022; 14:47. [PMID: 35361281 PMCID: PMC8973787 DOI: 10.1186/s13148-022-01264-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Obsessive-compulsive disorder (OCD) is a prevalent and severe clinical condition. Robust evidence suggests a gene-environment interplay in its etiopathogenesis, yet the underlying molecular clues remain only partially understood. In order to further deepen our understanding of OCD, it is essential to ascertain how genes interact with environmental risk factors, a cross-talk that is thought to be mediated by epigenetic mechanisms. The human microbiota may be a key player, because bacterial metabolites can act as epigenetic modulators. We analyzed, in the blood and saliva of OCD subjects and healthy controls, the transcriptional regulation of the oxytocin receptor gene and, in saliva, also the different levels of major phyla. We also investigated the same molecular mechanisms in specific brain regions of socially isolated rats showing stereotyped behaviors reminiscent of OCD as well as short chain fatty acid levels in the feces of rats. RESULTS Higher levels of oxytocin receptor gene DNA methylation, inversely correlated with gene expression, were observed in the blood as well as saliva of OCD subjects when compared to controls. Moreover, Actinobacteria also resulted higher in OCD and directly correlated with oxytocin receptor gene epigenetic alterations. The same pattern of changes was present in the prefrontal cortex of socially-isolated rats, where also altered levels of fecal butyrate were observed at the beginning of the isolation procedure. CONCLUSIONS This is the first demonstration of an interplay between microbiota modulation and epigenetic regulation of gene expression in OCD, opening new avenues for the understanding of disease trajectories and for the development of new therapeutic strategies.
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Affiliation(s)
- Claudio D'Addario
- Faculty of Bioscience, University of Teramo, Teramo, Italy. .,Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden. .,Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via Renato Balzarini, 1, 64100, Teramo, Italy.
| | | | - Fabio Bellia
- Faculty of Bioscience, University of Teramo, Teramo, Italy
| | | | | | - Federico Fanti
- Faculty of Bioscience, University of Teramo, Teramo, Italy
| | - Matteo Vismara
- Department of Mental Health, Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milano, Milano, Italy
| | - Beatrice Benatti
- Department of Mental Health, Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milano, Milano, Italy
| | - Luca Ferrara
- Department of Mental Health, Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milano, Milano, Italy
| | - Federica Fasciana
- Department of Mental Health, Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milano, Milano, Italy
| | - Laura Celebre
- Department of Mental Health, Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milano, Milano, Italy
| | - Caterina Viganò
- Department of Mental Health, Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milano, Milano, Italy
| | - Luca Elli
- Department of Mental Health, Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milano, Milano, Italy
| | - Manuel Sergi
- Faculty of Bioscience, University of Teramo, Teramo, Italy
| | - Mauro Maccarrone
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy.,European Center for Brain Research/Santa Lucia Foundation IRCCS, Rome, Italy
| | | | | | - Bernardo Dell'Osso
- Department of Mental Health, Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milano, Milano, Italy. .,Department of Psychiatry, Department of Biomedical and Clinical Sciences "Luigi Sacco", Psychiatry Unit 2, ASST Sacco-Fatebenefratelli, Via G.B. Grassi, 74, 20157, Milan, Italy.
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Epigenome-wide association study of posttraumatic stress disorder identifies novel loci in U.S. military veterans. Transl Psychiatry 2022; 12:65. [PMID: 35177594 PMCID: PMC8854688 DOI: 10.1038/s41398-022-01822-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/26/2021] [Accepted: 01/14/2022] [Indexed: 01/23/2023] Open
Abstract
Posttraumatic stress disorder (PTSD) is a chronic and disabling psychiatric disorder prevalent in military veterans. Epigenetic mechanisms have been implicated in the etiology of PTSD, with DNA methylation being the most studied to identify novel molecular biomarkers associated with this disorder. We performed one of the largest single-sample epigenome-wide association studies (EWAS) of PTSD to date. Our sample included 1135 male European-American U.S. veterans who participated in the National Health and Resilience in Veterans Study (NHRVS). DNA was collected from saliva samples and the Illumina HumanMethylation EPIC BeadChip was used for the methylation analysis. PTSD was assessed using the PTSD Checklist. An EWAS was conducted using linear regression adjusted for age, cell-type proportions, first 10 principal components, and smoking status. After Bonferroni correction, we identified six genome-wide significant (GWS) CpG sites associated with past-month PTSD and three CpGs with lifetime PTSD (prange = 10-10-10-8). These CpG sites map to genes involved in immune function, transcription regulation, axonal guidance, cell signaling, and protein binding. Among these, SENP7, which is involved in transcription regulation and has been linked to risk-taking behavior and alcohol consumption in genome-wide association studies, replicated in an independent veteran cohort and was downregulated in medial orbitofrontal cortex of PTSD postmortem brain tissue. These findings suggest potential epigenetic biomarkers of PTSD that may help inform the pathophysiology of this disorder in veterans and other trauma-affected populations.
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D'Addario C, Macellaro M, Bellia F, Benatti B, Annunzi E, Palumbo R, Conti D, Fasciana F, Vismara M, Varinelli A, Ferrara L, Celebre L, Viganò C, Dell'Osso B. In Search for Biomarkers in Obsessive-Compulsive Disorder: New Evidence on Saliva as a Practical Source of DNA to Assess Epigenetic Regulation. Curr Med Chem 2021; 29:5782-5791. [PMID: 34879796 DOI: 10.2174/0929867328666211208115536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/08/2021] [Accepted: 10/18/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Brain-Derived Neurotrophic Factor (BDNF) is a promising candidate biomarker in both the development and aetiology of different neuropsychiatric conditions, including obsessive-compulsive disorder (OCD). Most of the studies in the field have been carried out in blood cells, including peripheral blood mononucleated cells (PBMCs), although DNA of high quality can be easily isolated from saliva. OBJECTIVE The objective of this study was to evaluate the epigenetic regulation of the BDNF gene in the saliva of a clinical sample of OCD patients in order to assess this source as an alternative to blood. METHODS We first analyzed DNA methylation levels at BDNF in the saliva of subjects suffering from OCD (n= 50) and healthy controls (n=50). Then, we compared these data with the results previously obtained for the same genomic region in blood samples from the same patients and controls (CTRL). RESULTS Our preliminary data showed a significant reduction of 5mC levels at BDNF gene (OCD: 1.23 ± 0.45; CTRL: 1.85 ± 0.64; p < 0.0001) and a significant correlation between DNA methylation in PBMCs and saliva (Spearman r = 0.2788). CONCLUSION We support the perspective that saliva could be a possible, reliable source, and a substitute for blood, in search of epigenetic biomarkers in OCD.
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Affiliation(s)
| | - Monica Macellaro
- University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milano. Italy
| | | | - Beatrice Benatti
- University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milano. Italy
| | | | - Riccardo Palumbo
- Department of Neuroscience, Imaging and Clinical Sciences, Gabriele D'Annunzio University, Chieti. Italy
| | - Dario Conti
- University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milano. 0
| | - Federica Fasciana
- University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milano. 0
| | - Matteo Vismara
- University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milano. 0
| | - Alberto Varinelli
- University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milano. Italy
| | - Luca Ferrara
- University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milano. Italy
| | - Laura Celebre
- University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milano. Italy
| | - Caterina Viganò
- University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milano. Italy
| | - Bernardo Dell'Osso
- University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milano. Italy
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Methylmercury and Polycyclic Aromatic Hydrocarbons in Mediterranean Seafood: A Molecular Anthropological Perspective. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app112311179] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Eating seafood has numerous health benefits; however, it constitutes one of the main sources of exposure to several harmful environmental pollutants, both of anthropogenic and natural origin. Among these, methylmercury and polycyclic aromatic hydrocarbons give rise to concerns related to their possible effects on human biology. In the present review, we summarize the results of epidemiological investigations on the genetic component of individual susceptibility to methylmercury and polycyclic aromatic hydrocarbons exposure in humans, and on the effects that these two pollutants have on human epigenetic profiles (DNA methylation). Then, we provide evidence that Mediterranean coastal communities represent an informative case study to investigate the potential impact of methylmercury and polycyclic aromatic hydrocarbons on the human genome and epigenome, since they are characterized by a traditionally high local seafood consumption, and given the characteristics that render the Mediterranean Sea particularly polluted. Finally, we discuss the challenges of a molecular anthropological approach to this topic.
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Herrero-Roldán S, Rodrigo MJ, Hernández-Cabrera JA, Mitchell C, López M, Alcoba-Florez J, Fisher J, Espinosa F, León I. Reduction in Epigenetic Age Acceleration Is Related to Empathy in Mothers with Neglectful Caregiving. Brain Sci 2021; 11:brainsci11111376. [PMID: 34827375 PMCID: PMC8615407 DOI: 10.3390/brainsci11111376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/01/2021] [Accepted: 10/18/2021] [Indexed: 11/16/2022] Open
Abstract
DNA methylation clocks are used as molecular estimators of epigenetic age, but with little evidence in mothers and none in neglectful mothering. We investigated differences in epigenetic age acceleration (EAA) and the role of empathy using the PhenoAge clock. We collected saliva samples from mothers with extreme disregard for their child's needs (50 in the neglect group, NG) and mothers with non-neglectful caregiving (87 in the control group, CG). Mothers completed an empathy scale, along with questionnaires of their own childhood maltreatment, adverse life events and psychiatric disorders. Sociodemographic variables potentially affecting EAA were also measured. The ANCOVA solution showed a significant increase in EAA in the NG compared to the CG, after adjustment for maternal age, number of pregnancies, financial assistance, adverse events, childhood maltreatment and psychiatric disorder. The group interaction effects showed a reduction in EAA for greater empathic concern and for a higher education level both as positive factors, and an increment in EAA for mothers living in a two-parent family as a risk factor, all in the NG. Our findings open the search for protective factors of EAA associated with caregiver behavior to reduce health vulnerabilities and poor social functioning, especially for mothers at risk of maladaptive caregiving.
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Affiliation(s)
- Silvia Herrero-Roldán
- Instituto Universitario de Neurociencia, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain; (S.H.-R.); (M.J.R.); (J.A.H.-C.); (F.E.)
- Facultad de Psicología, Universidad de La Laguna, 38071 San Cristóbal de La Laguna, Spain
| | - María José Rodrigo
- Instituto Universitario de Neurociencia, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain; (S.H.-R.); (M.J.R.); (J.A.H.-C.); (F.E.)
- Facultad de Psicología, Universidad de La Laguna, 38071 San Cristóbal de La Laguna, Spain
| | - Juan A. Hernández-Cabrera
- Instituto Universitario de Neurociencia, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain; (S.H.-R.); (M.J.R.); (J.A.H.-C.); (F.E.)
- Facultad de Psicología, Universidad de La Laguna, 38071 San Cristóbal de La Laguna, Spain
| | - Colter Mitchell
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48109, USA; (C.M.); (J.F.)
- Population Studies Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maykel López
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland;
| | - Julia Alcoba-Florez
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, 38010 San Cristóbal de La Laguna, Spain;
| | - Jonah Fisher
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48109, USA; (C.M.); (J.F.)
| | - Fernanda Espinosa
- Instituto Universitario de Neurociencia, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain; (S.H.-R.); (M.J.R.); (J.A.H.-C.); (F.E.)
- Facultad de Psicología, Universidad de La Laguna, 38071 San Cristóbal de La Laguna, Spain
| | - Inmaculada León
- Instituto Universitario de Neurociencia, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain; (S.H.-R.); (M.J.R.); (J.A.H.-C.); (F.E.)
- Facultad de Psicología, Universidad de La Laguna, 38071 San Cristóbal de La Laguna, Spain
- Correspondence: ; Tel.: +34-9223-17506
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Saadatmand F, Gurdziel K, Jackson L, Kwabi-Addo B, Ruden DM. DNA methylation and exposure to violence among African American young adult males. Brain Behav Immun Health 2021; 14:100247. [PMID: 34589758 PMCID: PMC8474503 DOI: 10.1016/j.bbih.2021.100247] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 02/02/2023] Open
Abstract
Exposure to violence (ETV) has been linked to epigenomics mechanisms such as DNA methylation (DNAm). We used epigenetic profiling of blood collected from 32 African American young adult males who lived in Washington DC to determine if changes in DNAm at CpG sites affiliated with nervous and immune system were associated with exposure to violence. Pathway analysis of differentially methylated regions comparing high and low ETV groups revealed an enrichment of gene sets annotated to nervous system and immune ontologies. Many of these genes are known to interact with each other which suggests DNAm alters gene function in the nervous and immune system in response to ETV. Using data from a unique age group, young African American adult males, we provide evidence that lifetime ETV could impact DNA methylation in genes impacted at Central Nervous System and Immune Function sites. METHOD Methylation analysis was performed on DNA collected from the blood of participants classified with either high or low lifetime ETV. Illumina®MethylationEPIC Beadchips (~850k CpG sites) were processed on the iScan System to examine whole-genome methylation differences. Differentially methylated CpG-sites between high (n = 19) and low (n = 13) groups were identified using linear regression with violence and substance abuse as model covariates. Gene ontology analysis was used to identify enrichment categories from probes annotated to the nearest gene. RESULTS A total of 595 probes (279 hypermethylated; 316 hypomethylated) annotated to 383 genes were considered differentially methylated in association with ETV. Males with high ETV showed elevated methylation in several signaling pathways but were most impacted at Central Nervous System and Immune Function affiliated sites. Eight candidate genes were identified that play important biological roles in stress response to violence with HDAC4 (10%), NR4A3 (11%), NR4A2 (12%), DSCAML1(12%), and ELAVL3 (13%) exhibiting higher levels in the low ETV group and DLGAP1 (10%), SHANK2 (10%), and NRG1(11%) having increased methylation in the high ETV group. These findings suggest that individuals subjected to high ETV may be at risk for poor health outcomes that have not been reported previously.
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Affiliation(s)
- Forough Saadatmand
- Department of Pediatrics, College of Medicine, Howard University, Washington, DC, USA
| | - Katherine Gurdziel
- Office of the Vice President of Research, Wayne State University, Detroit, MI, USA
| | - Latifa Jackson
- Department of Pediatrics, College of Medicine, Howard University, Washington, DC, USA
- W. Montague Cobb Research Laboratory, College of Arts and Sciences, Howard University, Washington, DC, USA
| | - Bernard Kwabi-Addo
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington, DC, USA
| | - Douglas M. Ruden
- Department of Ob/Gyn, CS Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI, USA
- Institutes for Environmental Health Science, Wayne State University School of Medicine, Detroit, MI, USA
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13
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Parade SH, Huffhines L, Daniels TE, Stroud LR, Nugent NR, Tyrka AR. A systematic review of childhood maltreatment and DNA methylation: candidate gene and epigenome-wide approaches. Transl Psychiatry 2021; 11:134. [PMID: 33608499 PMCID: PMC7896059 DOI: 10.1038/s41398-021-01207-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/18/2020] [Accepted: 01/07/2021] [Indexed: 01/31/2023] Open
Abstract
Childhood maltreatment is a major risk factor for chronic and severe mental and physical health problems across the lifespan. Increasing evidence supports the hypothesis that maltreatment is associated with epigenetic changes that may subsequently serve as mechanisms of disease. The current review uses a systematic approach to identify and summarize the literature related to childhood maltreatment and alterations in DNA methylation in humans. A total of 100 empirical articles were identified in our systematic review of research published prior to or during March 2020, including studies that focused on candidate genes and studies that leveraged epigenome-wide data in both children and adults. Themes arising from the literature, including consistent and inconsistent patterns of results, are presented. Several directions for future research, including important methodological considerations for future study design, are discussed. Taken together, the literature on childhood maltreatment and DNA methylation underscores the complexity of transactions between the environment and biology across development.
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Affiliation(s)
- Stephanie H Parade
- Initiative on Stress, Trauma, and Resilience, Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA.
- Bradley/Hasbro Children's Research Center, E. P. Bradley Hospital, East Providence, RI, USA.
| | - Lindsay Huffhines
- Initiative on Stress, Trauma, and Resilience, Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA
- Bradley/Hasbro Children's Research Center, E. P. Bradley Hospital, East Providence, RI, USA
| | - Teresa E Daniels
- Initiative on Stress, Trauma, and Resilience, Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA
- Laboratory for Clinical and Translational Neuroscience, Butler Hospital, Providence, RI, USA
| | - Laura R Stroud
- Initiative on Stress, Trauma, and Resilience, Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA
- Center for Behavioral and Preventive Medicine, The Miriam Hospital, Providence, RI, USA
| | - Nicole R Nugent
- Initiative on Stress, Trauma, and Resilience, Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Audrey R Tyrka
- Initiative on Stress, Trauma, and Resilience, Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA
- Laboratory for Clinical and Translational Neuroscience, Butler Hospital, Providence, RI, USA
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Murata Y, Fujii A, Kanata S, Fujikawa S, Ikegame T, Nakachi Y, Zhao Z, Jinde S, Kasai K, Bundo M, Iwamoto K. Evaluation of the usefulness of saliva for DNA methylation analysis in cohort studies. Neuropsychopharmacol Rep 2019; 39:301-305. [PMID: 31393092 PMCID: PMC7292296 DOI: 10.1002/npr2.12075] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/25/2019] [Accepted: 07/01/2019] [Indexed: 12/15/2022] Open
Abstract
Introduction Epigenetic information such as DNA methylation is a useful biomarker that reflects complex gene‐environmental interaction. Peripheral tissues such as blood and saliva are commonly collected as the source of genomic DNA in cohort studies. Epigenetic studies mainly use blood, while a few studies have addressed the epigenetic characteristics of saliva. Methods The effects of methods for DNA extraction and purification from saliva on DNA methylation were surveyed using Illumina Infinium HumanMethylation450 BeadChip. Using 386 661 probes, DNA methylation differences between blood and saliva from 22 healthy volunteers, and their functional and structural characteristics were examined. CpG sites with DNA methylation levels showing large interindividual variations in blood were evaluated using saliva DNA methylation profiles. Results Genomic DNA prepared by simplified protocol from saliva showed a similar quality DNA methylation profile to that derived from the manufacturer provided protocol. Consistent with previous studies, the DNA methylation profiles of blood and saliva showed high correlations. Blood showed 1,514 hypomethylated and 2099 hypermethylated probes, suggesting source‐dependent DNA methylation patterns. CpG sites with large methylation difference between the two sources were underrepresented in the promoter regions and enriched within gene bodies. CpG sites with large interindividual methylation variations in blood also showed considerable variations in saliva. Conclusion In addition to high correlation in DNA methylation profiles, CpG sites showing large interindividual DNA methylation differences were similar between blood and saliva, ensuring saliva could be a suitable alternative source for genomic DNA in cohort studies. Consideration of source‐dependent DNA methylation differences will, however, be necessary. We compared quality of saliva methylome data collected by several DNA purification protocols and examined the characteristics of saliva methylome. Optimized protocol and identified characteristics such as common informative CpG sites to blood and unique epigenetic changes in saliva will contribute to promote the use of saliva for epigenetic studies in clinical settings and epidemiological cohort studies.![]()
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Affiliation(s)
- Yui Murata
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Ayaka Fujii
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Sho Kanata
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Psychiatry, Teikyo University School of Medicine, Tokyo, Japan
| | - Shinya Fujikawa
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tempei Ikegame
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yutaka Nakachi
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Zhilei Zhao
- 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
| | - Seiichiro Jinde
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, 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
| | - 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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