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Iourov IY, Vorsanova SG, Zelenova MA, Vasin KS, Kurinnaia OS, Korostelev SA, Yurov YB. [Epigenomic variations manifesting as a loss of heterozygosity affecting imprinted genes represent a molecular mechanism of autism spectrum disorders and intellectual disability in children]. Zh Nevrol Psikhiatr Im S S Korsakova 2019; 119:91-97. [PMID: 31317896 DOI: 10.17116/jnevro201911905191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AIM Long continuous stretches of homozygosity (LCSH) are regularly detected in studies using molecular karyotyping (SNP array). Despite this type of variation being able to provide meaningful data on the parents' kinship, uniparental disomy and chromosome rearrangements, LCSH are rarely considered as a possible epigenetic cause of neurodevelopmental disorders. Despite their direct relationship to imprinting, LCSH in imprinted loci have not been considered in terms of pathogenicity. The present work is aimed at studying LCSH in chromosomal regions containing imprinted genes previously associated with disease in children with idiopathic intellectual disability, autism, congenital malformations and/or epilepsy. MATERIAL AND METHODS Five hundred and four patients with autism spectrum disorders and intellectual disability were examined. RESULTS LCSH affecting imprinted loci associated with various diseases were identified in 40 (7.9%) individuals. Chromosomal region 7q21.3 was affected in twenty three cases, 15q11.2 in twelve, 11p15.5 in five, 7q32.2 in four. Four patients had 2 LCSH affecting imprinted loci. Besides one LCSH in 7q31.33q32.3 (~4 Mbp) region, all LCSH were 1-1.6 Mbp. Clinically, these cases resembled the corresponding imprinting diseases (e.g. Silver-Russell, Beckwith-Wiedemann, Prader-Willi, Angelman syndromes). Parental kinship was identified in 8 cases (1.59%), which were not affected by LCSH at imprinted loci. CONCLUSION The present study shows that LCSH affecting chromosomal regions 7q21.3, 7q32.2, 11p15.5 and 15p11.2 occur in about 7.9% of children with intellectual disability, autism, congenital malformations and/or epilepsy. Consequently, this type of epigenetic mutations is obviously common in a group of children with neurodevelopmental disorders. LCSH less than 2.5-10 Mbp are usually ignored in molecular karyotyping (SNP array) studies and, therefore, an important epigenetic cause of intellectual disability, autism or epilepsy with high probability remains without attention.
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Affiliation(s)
- I Y Iourov
- Mental Health Research Center, Moscow, Russia; Veltishchev Research Clinical Institute of Pediatric of Pirogov Russian National Research Medical University, Moscow, Russia; Russian Medical Academy for Postgraduate Continuing Education, Moscow, Russia
| | - S G Vorsanova
- Mental Health Research Center, Moscow, Russia; Veltishchev Research Clinical Institute of Pediatric of Pirogov Russian National Research Medical University, Moscow, Russia
| | - M A Zelenova
- Mental Health Research Center, Moscow, Russia; Veltishchev Research Clinical Institute of Pediatric of Pirogov Russian National Research Medical University, Moscow, Russia
| | - K S Vasin
- Mental Health Research Center, Moscow, Russia; Veltishchev Research Clinical Institute of Pediatric of Pirogov Russian National Research Medical University, Moscow, Russia
| | - O S Kurinnaia
- Mental Health Research Center, Moscow, Russia; Veltishchev Research Clinical Institute of Pediatric of Pirogov Russian National Research Medical University, Moscow, Russia
| | - S A Korostelev
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Yu B Yurov
- Mental Health Research Center, Moscow, Russia; Veltishchev Research Clinical Institute of Pediatric of Pirogov Russian National Research Medical University, Moscow, Russia
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Sriganesh R, Joseph Ponniah R. Genetics of language and its implications on language interventions. J Genet 2018; 97:1485-1491. [PMID: 30555099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Genetic variation of language genes affect neurophysiology of brain and can thus influence the way people respond to environmental language input, leading to differences in terms of their response to environmental language learning. Conversely, language learning environment too can affect gene expressions through neuroepigenetic mechanisms, leading to increasedinterindividual differences. Further, language-related cognitive processes such as learning, working memory and perception; and language-related affective factors such as stress and positive emotion involve neuroplasticity, which is also epigenetically regulated. Language intervention methods must understand the extent and the type of difficulties, and must offer personalized learning andmedical solutions. Medical intervention in terms of epigenetics and neurotransmitter regulation is proposed in addition to effectiveteaching methods to aid in effective language acquisition.
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Strafella C, Caputo V, Galota MR, Zampatti S, Marella G, Mauriello S, Cascella R, Giardina E. Application of Precision Medicine in Neurodegenerative Diseases. Front Neurol 2018; 9:701. [PMID: 30190701 PMCID: PMC6115491 DOI: 10.3389/fneur.2018.00701] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/03/2018] [Indexed: 12/24/2022] Open
Abstract
One of the main challenges for healthcare systems is the increasing prevalence of neurodegenerative pathologies together with the rapidly aging populations. The enormous progresses made in the field of biomedical research and informatics have been crucial for improving the knowledge of how genes, epigenetic modifications, aging, nutrition, drugs and microbiome impact health and disease. In fact, the availability of high technology and computational facilities for large-scale analysis enabled a deeper investigation of neurodegenerative disorders, providing a more comprehensive overview of disease and encouraging the development of a precision medicine approach for these pathologies. On this subject, the creation of collaborative networks among medical centers, research institutes and highly qualified specialists can be decisive for moving the precision medicine from the bench to the bedside. To this purpose, the present review has been thought to discuss the main components which may be part of precise and personalized treatment programs applied to neurodegenerative disorders. Parkinson Disease will be taken as an example to understand how precision medicine approach can be clinically useful and provide substantial benefit to patients. In this perspective, the realization of web-based networks can be decisive for the implementation of precision medicine strategies across different specialized centers as well as for supporting clinical/therapeutical decisions and promoting a more preventive and participative medicine for neurodegenerative disorders. These collaborative networks are essentially addressed to find innovative, sustainable and effective strategies able to provide optimal and safer therapies, discriminate at risk individuals, identify patients at preclinical or early stage of disease, set-up individualized and preventative strategies for improving prognosis and patient's quality of life.
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Affiliation(s)
- Claudia Strafella
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy.,Emotest Laboratory, Pozzuoli, Italy
| | - Valerio Caputo
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Maria R Galota
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy
| | - Stefania Zampatti
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy
| | | | | | - Raffaella Cascella
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy.,Department of Chemical-Toxicological and Pharmacological Evaluation of Drugs, Catholic University Our Lady of Good Counsel, Tirana, Albania
| | - Emiliano Giardina
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy.,Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy
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Angarica VE, Del Sol A. Bioinformatics Tools for Genome-Wide Epigenetic Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 978:489-512. [PMID: 28523562 DOI: 10.1007/978-3-319-53889-1_25] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Epigenetics play a central role in the regulation of many important cellular processes, and dysregulations at the epigenetic level could be the source of serious pathologies, such as neurological disorders affecting brain development, neurodegeneration, and intellectual disability. Despite significant technological advances for epigenetic profiling, there is still a need for a systematic understanding of how epigenetics shapes cellular circuitry, and disease pathogenesis. The development of accurate computational approaches for analyzing complex epigenetic profiles is essential for disentangling the mechanisms underlying cellular development, and the intricate interaction networks determining and sensing chromatin modifications and DNA methylation to control gene expression. In this chapter, we review the recent advances in the field of "computational epigenetics," including computational methods for processing different types of epigenetic data, prediction of chromatin states, and study of protein dynamics. We also discuss how "computational epigenetics" has complemented the fast growth in the generation of epigenetic data for uncovering the main differences and similarities at the epigenetic level between individuals and the mechanisms underlying disease onset and progression.
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Affiliation(s)
- Vladimir Espinosa Angarica
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4366 Belvaux, Luxembourg.
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4366 Belvaux, Luxembourg
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Lee PKM, Goh WWB, Sng JCG. Network-based characterization of the synaptic proteome reveals that removal of epigenetic regulator Prmt8 restricts proteins associated with synaptic maturation. J Neurochem 2017; 140:613-628. [PMID: 27935040 DOI: 10.1111/jnc.13921] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 11/30/2016] [Accepted: 12/04/2016] [Indexed: 12/13/2022]
Abstract
The brain adapts to dynamic environmental conditions by altering its epigenetic state, thereby influencing neuronal transcriptional programs. An example of an epigenetic modification is protein methylation, catalyzed by protein arginine methyltransferases (PRMT). One member, Prmt8, is selectively expressed in the central nervous system during a crucial phase of early development, but little else is known regarding its function. We hypothesize Prmt8 plays a role in synaptic maturation during development. To evaluate this, we used a proteome-wide approach to characterize the synaptic proteome of Prmt8 knockout versus wild-type mice. Through comparative network-based analyses, proteins and functional clusters related to neurite development were identified to be differentially regulated between the two genotypes. One interesting protein that was differentially regulated was tenascin-R (TNR). Chromatin immunoprecipitation demonstrated binding of PRMT8 to the tenascin-r (Tnr) promoter. TNR, a component of perineuronal nets, preserves structural integrity of synaptic connections within neuronal networks during the development of visual-somatosensory cortices. On closer inspection, Prmt8 removal increased net formation and decreased inhibitory parvalbumin-positive (PV+) puncta on pyramidal neurons, thereby hindering the maturation of circuits. Consequently, visual acuity of the knockout mice was reduced. Our results demonstrated Prmt8's involvement in synaptic maturation and its prospect as an epigenetic modulator of developmental neuroplasticity by regulating structural elements such as the perineuronal nets.
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Affiliation(s)
- Patrick Kia Ming Lee
- Integrative Neuroscience Program, Singapore Institute for Clinical Sciences, Agency for Science Technology and Research (A*STAR), Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Wilson Wen Bin Goh
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China.,Department of Computer Science, National University of Singapore, Singapore
| | - Judy Chia Ghee Sng
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Ricq EL, Hooker JM, Haggarty SJ. Toward development of epigenetic drugs for central nervous system disorders: Modulating neuroplasticity via H3K4 methylation. Psychiatry Clin Neurosci 2016; 70:536-550. [PMID: 27485392 PMCID: PMC5764164 DOI: 10.1111/pcn.12426] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/29/2016] [Indexed: 12/19/2022]
Abstract
The mammalian brain dynamically activates or silences gene programs in response to environmental input and developmental cues. This neuroplasticity is controlled by signaling pathways that modify the activity, localization, and/or expression of transcriptional-regulatory enzymes in combination with alterations in chromatin structure in the nucleus. Consistent with this key neurobiological role, disruptions in the fine-tuning of epigenetic and transcriptional regulation have emerged as a recurrent theme in studies of the genetics of neurodevelopmental and neuropsychiatric disorders. Furthermore, environmental factors have been implicated in the increased risk of heterogeneous, multifactorial, neuropsychiatric disorders via epigenetic mechanisms. Aberrant epigenetic regulation of gene expression thus provides an attractive unifying model for understanding the complex risk architecture of mental illness. Here, we review emerging genetic evidence implicating dysregulation of histone lysine methylation in neuropsychiatric disease and outline advancements in small-molecule probes targeting this chromatin modification. The emerging field of neuroepigenetic research is poised to provide insight into the biochemical basis of genetic risk for diverse neuropsychiatric disorders and to develop the highly selective chemical tools and imaging agents necessary to dissect dynamic transcriptional-regulatory mechanisms in the nervous system. On the basis of these findings, continued advances may lead to the validation of novel, disease-modifying therapeutic targets for a range of disorders with aberrant chromatin-mediated neuroplasticity.
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Affiliation(s)
- Emily L. Ricq
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
- Chemical Neurobiology Laboratory, Center for Human Genetic Research, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Jacob M. Hooker
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Stephen J. Haggarty
- Chemical Neurobiology Laboratory, Center for Human Genetic Research, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
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Pataskar A, Tiwari VK. Computational challenges in modeling gene regulatory events. Transcription 2016; 7:188-195. [PMID: 27390891 DOI: 10.1080/21541264.2016.1204491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Cellular transcriptional programs driven by genetic and epigenetic mechanisms could be better understood by integrating "omics" data and subsequently modeling the gene-regulatory events. Toward this end, computational biology should keep pace with evolving experimental procedures and data availability. This article gives an exemplified account of the current computational challenges in molecular biology.
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Affiliation(s)
| | - Vijay K Tiwari
- a Institute of Molecular Biology (IMB) , Mainz , Germany
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Yu L, Chibnik LB, Yang J, McCabe C, Xu J, Schneider JA, De Jager PL, Bennett DA. Methylation profiles in peripheral blood CD4+ lymphocytes versus brain: The relation to Alzheimer's disease pathology. Alzheimers Dement 2016; 12:942-951. [PMID: 27016692 DOI: 10.1016/j.jalz.2016.02.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 01/12/2016] [Accepted: 02/16/2016] [Indexed: 12/13/2022]
Abstract
INTRODUCTION We investigated the change in DNA methylation in peripheral blood CD4+ lymphocytes over time, examined the relation between CD4+ lymphocytes and brain methylation, and compared their associations with AD pathology. METHODS Genome-wide methylation was measured three times in 41 older persons using Illumina Infinium HumanMethylation450 array. The two CD4+ lymphocytes measures were at study baseline and proximate to death. Brain tissue came from frozen dorsolateral prefrontal cortex. RESULTS Global methylation features were conserved across tissue. At individual CpG sites, methylation level was concordant between the two CD4+ lymphocytes but more diffuse between CD4+ lymphocytes and brain. Previous associations of brain methylation with neuritic plaques at target methylation sites were not replicated in CD4+ lymphocytes. DISCUSSION There is no strong evidence of change in CD4+ lymphocytes methylation among older persons over an average of 7.5 years. Methylation associations with AD pathology found in neocortex are not directly reflected in CD4+ lymphocytes.
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Affiliation(s)
- Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA.
| | - Lori B Chibnik
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Jingyun Yang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Cristin McCabe
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Jishu Xu
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA; Department of Pathology, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
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Iourov IY, Vorsanova SG, Korostelev SA, Zelenova MA, Yurov YB. Long contiguous stretches of homozygosity spanning shortly the imprinted loci are associated with intellectual disability, autism and/or epilepsy. Mol Cytogenet 2015; 8:77. [PMID: 26478745 PMCID: PMC4608298 DOI: 10.1186/s13039-015-0182-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/27/2015] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Long contiguous stretches of homozygosity (LCSH) (regions/runs of homozygosity) are repeatedly detected by single-nucleotide polymorphism (SNP) chromosomal microarrays. Providing important clues regarding parental relatedness (consanguinity), uniparental disomy, chromosomal recombination or rearrangements, LCSH are rarely considered as a possible epigenetic cause of neurodevelopmental disorders. Additionally, despite being relevant to imprinting, LCSH at imprinted loci have not been truly addressed in terms of pathogenicity. In this study, we examined LCSH in children with unexplained intellectual disability, autism, congenital malformations and/or epilepsy focusing on chromosomal regions which harbor imprinted disease genes. RESULTS Out of 267 cases, 14 (5.2 %) were found to have LCSH at imprinted loci associated with a clinical outcome. There were 5 cases of LCSH at 15p11.2, 4 cases of LCSH at 7q31.2, 3 cases of LCSH at 11p15.5, and 2 cases of LCSH at 7q21.3. Apart from a case of LCSH at 7q31.33q32.3 (~4 Mb in size), all causative LCSH were 1-1.5 Mb in size. Clinically, these cases were characterized by a weak resemblance to corresponding imprinting diseases (i.e., Silver-Russell, Beckwith-Wiedemann, and Prader-Willi/Angelman syndromes), exhibiting distinctive intellectual disability, autistic behavior, developmental delay, seizures and/or facial dysmorphisms. Parental consanguinity was detected in 8 cases (3 %), and these cases did not exhibit LCSH at imprinted loci. CONCLUSIONS This study demonstrates that shorter LCSH at chromosomes 7q21.3, 7q31.2, 11p15.5, and 15p11.2 occur with a frequency of about 5 % in the children with intellectual disability, autism, congenital malformations and/or epilepsy. Consequently, this type of epigenetic mutations appears to be the most common one among children with neurodevelopmental diseases. Finally, since LCSH less than 2.5-10 Mb in size are generally ignored in diagnostic SNP microarray studies, one can conclude that an important epigenetic cause of intellectual disability, autism or epilepsy is actually overlooked.
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Affiliation(s)
- Ivan Y Iourov
- Mental Health Research Center, 117152 Moscow, Russia ; Separated Structural Unit "Clinical Research Institute of Pediatrics", Russian National Research Medical University named after N.I. Pirogov, Ministry of Health of Russian Federation, 125412 Moscow, Russia ; Department of Medical Genetics, Russian Medical Academy of Postgraduate Education, 123995 Moscow, Russia
| | - Svetlana G Vorsanova
- Mental Health Research Center, 117152 Moscow, Russia ; Separated Structural Unit "Clinical Research Institute of Pediatrics", Russian National Research Medical University named after N.I. Pirogov, Ministry of Health of Russian Federation, 125412 Moscow, Russia
| | | | - Maria A Zelenova
- Mental Health Research Center, 117152 Moscow, Russia ; Separated Structural Unit "Clinical Research Institute of Pediatrics", Russian National Research Medical University named after N.I. Pirogov, Ministry of Health of Russian Federation, 125412 Moscow, Russia
| | - Yuri B Yurov
- Mental Health Research Center, 117152 Moscow, Russia ; Separated Structural Unit "Clinical Research Institute of Pediatrics", Russian National Research Medical University named after N.I. Pirogov, Ministry of Health of Russian Federation, 125412 Moscow, Russia
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