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Shi Z, Das S, Morabito S, Miyoshi E, Stocksdale J, Emerson N, Srinivasan SS, Shahin A, Rahimzadeh N, Cao Z, Silva J, Castaneda AA, Head E, Thompson L, Swarup V. Single-nucleus multi-omics identifies shared and distinct pathways in Pick's and Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.06.611761. [PMID: 39282421 PMCID: PMC11398495 DOI: 10.1101/2024.09.06.611761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
The study of neurodegenerative diseases, particularly tauopathies like Pick's disease (PiD) and Alzheimer's disease (AD), offers insights into the underlying regulatory mechanisms. By investigating epigenomic variations in these conditions, we identified critical regulatory changes driving disease progression, revealing potential therapeutic targets. Our comparative analyses uncovered disease-enriched non-coding regions and genome-wide transcription factor (TF) binding differences, linking them to target genes. Notably, we identified a distal human-gained enhancer (HGE) associated with E3 ubiquitin ligase (UBE3A), highlighting disease-specific regulatory alterations. Additionally, fine-mapping of AD risk genes uncovered loci enriched in microglial enhancers and accessible in other cell types. Shared and distinct TF binding patterns were observed in neurons and glial cells across PiD and AD. We validated our findings using CRISPR to excise a predicted enhancer region in UBE3A and developed an interactive database (http://swaruplab.bio.uci.edu/scROAD) to visualize predicted single-cell TF occupancy and regulatory networks.
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Affiliation(s)
- Zechuan Shi
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
| | - Sudeshna Das
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
| | - Samuel Morabito
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
- Mathematical, Computational and Systems Biology Program, University of California, Irvine, CA 92697, USA
| | - Emily Miyoshi
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
| | - Jennifer Stocksdale
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Nora Emerson
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
| | - Shushrruth Sai Srinivasan
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
- Mathematical, Computational and Systems Biology Program, University of California, Irvine, CA 92697, USA
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Arshi Shahin
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Negin Rahimzadeh
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Mathematical, Computational and Systems Biology Program, University of California, Irvine, CA 92697, USA
| | - Zhenkun Cao
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Justine Silva
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Andres Alonso Castaneda
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Elizabeth Head
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Leslie Thompson
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697, USA
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA 92697, USA
- Mathematical, Computational and Systems Biology Program, University of California, Irvine, CA 92697, USA
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Camerini L, Zurchimitten G, Bock B, Xavier J, Bastos CR, Martins E, Ardais AP, Dos Santos Motta JV, Pires AJ, de Matos MB, de Ávila Quevedo L, Pinheiro RT, Ghisleni G. Genetic Variations in Elements of the Oxytocinergic Pathway are Associated with Attention/Hyperactivity Problems and Anxiety Problems in Childhood. Child Psychiatry Hum Dev 2024; 55:552-563. [PMID: 36087156 DOI: 10.1007/s10578-022-01419-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/03/2022] [Accepted: 08/17/2022] [Indexed: 11/28/2022]
Abstract
Genetic alterations related to oxytocin system seem to influence the neurobiology of attention-deficit hyperactivity disorder and anxiety problems leading to greater functional, social and emotional impairment. Here, we analyzed the association of OXTR rs2254298 and CD38 rs6449182 variants with attention/hyperactivity problems and anxiety problems in children. The study enrolled 292 children and adjusted regression model revealed OXTR rs2254298 AA genotype as a risk factor for attention deficit/hyperactivity problems (PR: 2.37; PadjFDR = 0.006), attention problems (PR: 2.71; PadjFDR = 0.003) and anxiety problems (PR: 1.92; PadjFDR = 0.018). CD38 rs6449182 G allele showed as a risk factor for attention deficit/hyperactivity problems (PR: 1.56; PadjFDR = 0.028). Moreover, in silico approach for regulatory roles found markers that influence chromatin accessibility and transcription capacity. Together, these data provide genetic information of oxytocin in developmental and behavioral disorders opening a range of opportunities for future studies that clarify their neurobiology in childhood.
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Affiliation(s)
- Laísa Camerini
- Postgraduate Program in Health and Behavior, Catholic University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Gabriel Zurchimitten
- Postgraduate Program in Health and Behavior, Catholic University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Bertha Bock
- Postgraduate Program in Health and Behavior, Catholic University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Janaína Xavier
- Postgraduate Program in Health and Behavior, Catholic University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Clarissa Ribeiro Bastos
- Department of Neurosciences, Federal University of Santa Catarina, Florianopolis, Santa Catarina, Brazil
| | - Evânia Martins
- Postgraduate Program in Health and Behavior, Catholic University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Ana Paula Ardais
- Postgraduate Program in Health and Behavior, Catholic University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | | | - Andressa Jacondino Pires
- Postgraduate Program in Health and Behavior, Catholic University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Mariana Bonati de Matos
- Postgraduate Program in Health and Behavior, Catholic University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Luciana de Ávila Quevedo
- Postgraduate Program in Health and Behavior, Catholic University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Ricardo Tavares Pinheiro
- Postgraduate Program in Health and Behavior, Catholic University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Gabriele Ghisleni
- Postgraduate Program in Health and Behavior, Catholic University of Pelotas, Pelotas, Rio Grande do Sul, Brazil.
- Post-Graduation Program of Health and Behavior, Laboratory of Clinical Neuroscience, Catholic University of Pelotas - UCPel, Center of Health Science, Rua Gonçalves Chaves 373, sala 324, CEP 96010-280, Pelotas, RS, Brasil.
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Huang M, Wang J, Liu W, Zhou H. Advances in the role of the GADD45 family in neurodevelopmental, neurodegenerative, and neuropsychiatric disorders. Front Neurosci 2024; 18:1349409. [PMID: 38332860 PMCID: PMC10850240 DOI: 10.3389/fnins.2024.1349409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024] Open
Abstract
The growth arrest and DNA damage inducible protein 45 (GADD45) family comprises stress-induced nuclear proteins that interact with DNA demethylases to facilitate DNA demethylation, thereby regulating diverse cellular processes including oxidative stress, DNA damage repair, apoptosis, proliferation, differentiation, inflammation, and neuroplasticity by modulating the expression patterns of specific genes. Widely expressed in the central nervous system, the GADD45 family plays a pivotal role in various neurological disorders, rendering it a potential therapeutic target for central nervous system diseases. This review presented a comprehensive overview of the expression patterns and potential mechanisms of action associated with each member of GADD45 family (GADD45α, GADD45β, and GADD45γ) in neurodevelopmental, neurodegenerative, and neuropsychiatric disorders, while also explored strategies to harness these mechanisms for intervention and treatment. Future research should prioritize the development of effective modulators targeting the GADD45 family for clinical trials aimed at treating central nervous system diseases.
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Affiliation(s)
| | | | | | - Hongyan Zhou
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
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Tooley KB, Chucair-Elliott AJ, Ocañas SR, Machalinski AH, Pham KD, Hoolehan W, Kulpa AM, Stanford DR, Freeman WM. Differential usage of DNA modifications in neurons, astrocytes, and microglia. Epigenetics Chromatin 2023; 16:45. [PMID: 37953264 PMCID: PMC10642035 DOI: 10.1186/s13072-023-00522-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Cellular identity is determined partly by cell type-specific epigenomic profiles that regulate gene expression. In neuroscience, there is a pressing need to isolate and characterize the epigenomes of specific CNS cell types in health and disease. In this study, we developed an in vivo tagging mouse model (Camk2a-NuTRAP) for paired isolation of neuronal DNA and RNA without cell sorting and then used this model to assess epigenomic regulation, DNA modifications in particular, of gene expression between neurons and glia. RESULTS After validating the cell-specificity of the Camk2a-NuTRAP model, we performed TRAP-RNA-Seq and INTACT-whole genome oxidative bisulfite sequencing (WGoxBS) to assess the neuronal translatome and epigenome in the hippocampus of young mice (4 months old). WGoxBS findings were validated with enzymatic methyl-Seq (EM-Seq) and nanopore sequencing. Comparing neuronal data to microglial and astrocytic data from NuTRAP models, microglia had the highest global mCG levels followed by astrocytes and then neurons, with the opposite pattern observed for hmCG and mCH. Differentially modified regions between cell types were predominantly found within gene bodies and distal intergenic regions, rather than proximal promoters. Across cell types there was a negative correlation between DNA modifications (mCG, mCH, hmCG) and gene expression at proximal promoters. In contrast, a negative correlation of gene body mCG and a positive relationship between distal promoter and gene body hmCG with gene expression was observed. Furthermore, we identified a neuron-specific inverse relationship between mCH and gene expression across promoter and gene body regions. CONCLUSIONS Neurons, astrocytes, and microglia demonstrate different genome-wide levels of mCG, hmCG, and mCH that are reproducible across analytical methods. However, modification-gene expression relationships are conserved across cell types. Enrichment of differential modifications across cell types in gene bodies and distal regulatory elements, but not proximal promoters, highlights epigenomic patterning in these regions as potentially greater determinants of cell identity. These findings also demonstrate the importance of differentiating between mC and hmC in neuroepigenomic analyses, as up to 30% of what is conventionally interpreted as mCG can be hmCG, which often has a different relationship to gene expression than mCG.
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Affiliation(s)
- Kyla B Tooley
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Ana J Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Sarah R Ocañas
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Adeline H Machalinski
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Kevin D Pham
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Walker Hoolehan
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - Adam M Kulpa
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK, 73104, USA
| | - David R Stanford
- Center for Biomedical Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Willard M Freeman
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA.
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Tooley KB, Chucair-Elliott AJ, Ocañas SR, Machalinski AH, Pham KD, Stanford DR, Freeman WM. Differential usage of DNA modifications in neurons, astrocytes, and microglia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543497. [PMID: 37333391 PMCID: PMC10274634 DOI: 10.1101/2023.06.05.543497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Background Cellular identity is determined partly by cell type-specific epigenomic profiles that regulate gene expression. In neuroscience, there is a pressing need to isolate and characterize the epigenomes of specific CNS cell types in health and disease. This is especially true as for DNA modifications where most data are derived from bisulfite sequencing that cannot differentiate between DNA methylation and hydroxymethylation. In this study, we developed an in vivo tagging mouse model (Camk2a-NuTRAP) for paired isolation of neuronal DNA and RNA without cell sorting and then used this model to assess epigenomic regulation of gene expression between neurons and glia. Results After validating the cell-specificity of the Camk2a-NuTRAP model, we performed TRAP-RNA-Seq and INTACT whole genome oxidative bisulfite sequencing to assess the neuronal translatome and epigenome in the hippocampus of young mice (3 months old). These data were then compared to microglial and astrocytic data from NuTRAP models. When comparing the different cell types, microglia had the highest global mCG levels followed by astrocytes and then neurons, with the opposite pattern observed for hmCG and mCH. Differentially modified regions between cell types were predominantly found within gene bodies and distal intergenic regions, with limited differences occurring within proximal promoters. Across cell types there was a negative correlation between DNA modifications (mCG, mCH, hmCG) and gene expression at proximal promoters. In contrast, a negative correlation of mCG with gene expression within the gene body while a positive relationship between distal promoter and gene body hmCG and gene expression was observed. Furthermore, we identified a neuron-specific inverse relationship between mCH and gene expression across promoter and gene body regions. Conclusions In this study, we identified differential usage of DNA modifications across CNS cell types, and assessed the relationship between DNA modifications and gene expression in neurons and glia. Despite having different global levels, the general modification-gene expression relationship was conserved across cell types. The enrichment of differential modifications in gene bodies and distal regulatory elements, but not proximal promoters, across cell types highlights epigenomic patterning in these regions as potentially greater determinants of cell identity.
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Affiliation(s)
- Kyla B. Tooley
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Ana J. Chucair-Elliott
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Sarah R. Ocañas
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Adeline H. Machalinski
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Kevin D. Pham
- Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - David R. Stanford
- Center for Biomedical Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
| | - Willard M. Freeman
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
- Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK USA
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Choi YJ, Cho J, Hong YC, Lee DW, Moon S, Park SJ, Lee KS, Shin CH, Lee YA, Kim BN, Kaminsky Z, Kim JI, Lim YH. DNA methylation is associated with prenatal exposure to sulfur dioxide and childhood attention-deficit hyperactivity disorder symptoms. Sci Rep 2023; 13:3501. [PMID: 36859453 PMCID: PMC9977725 DOI: 10.1038/s41598-023-29843-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 02/10/2023] [Indexed: 03/03/2023] Open
Abstract
Epigenetic influence plays a role in the association between exposure to air pollution and attention deficit hyperactivity disorder (ADHD); however, research regarding sulfur dioxide (SO2) is scarce. Herein, we investigate the associations between prenatal SO2 exposure and ADHD rating scale (ARS) at ages 4, 6 and 8 years repeatedly in a mother-child cohort (n = 329). Whole blood samples were obtained at ages 2 and 6 years, and genome-wide DNA methylation (DNAm) was analyzed for 51 children using the Illumina Infinium HumanMethylation BeadChip. We analyzed the associations between prenatal SO2 exposure and DNAm levels at ages 2 and 6, and further investigated the association between the DNAm and ARS at ages 4, 6 and 8. Prenatal SO2 exposure was associated with ADHD symptoms. From candidate gene analysis, DNAm levels at the 6 CpGs at age 2 were associated with prenatal SO2 exposure levels. Of the 6 CpGs, cg07583420 (INS-IGF2) was persistently linked with ARS at ages 4, 6 and 8. Epigenome-wide analysis showed that DNAm at 6733 CpG sites were associated with prenatal SO2 exposure, of which 58 CpGs involved in Notch signalling pathway were further associated with ARS at age 4, 6 and 8 years, persistently. DNAm at age 6 was not associated with prenatal SO2 exposure. Changes in DNAm levels associated with prenatal SO2 exposure during early childhood are associated with increases in ARS in later childhood.
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Affiliation(s)
- Yoon-Jung Choi
- National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea.,Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Environmental Health Center, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jinwoo Cho
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Environmental Health Center, Seoul National University College of Medicine, Seoul, Republic of Korea.,Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Dong-Wook Lee
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Environmental Health Center, Seoul National University College of Medicine, Seoul, Republic of Korea.,Public Healthcare Center, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sungji Moon
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Soo Jin Park
- Department of Surgery, Wonkwang University Sanbon Hospital, Gunpo, Republic of Korea
| | - Kyung-Shin Lee
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Environmental Health Center, Seoul National University College of Medicine, Seoul, Republic of Korea.,Public Health Research Institute, National Medical Center, Seoul, Republic of Korea
| | - Choong Ho Shin
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Young Ah Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Bung-Nyun Kim
- Division of Children and Adolescent Psychiatry, Department of Psychiatry, Seoul National University Hospital, Seoul, Republic of Korea
| | - Zachary Kaminsky
- Institute of Mental Health Research, University of Ottawa, Ottawa, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Johanna Inhyang Kim
- Department of Psychiatry, Hanyang University Medical Center, 222-1 Wangsimni-Ro, Seongdong-Gu, Seoul, 04763, Republic of Korea.
| | - Youn-Hee Lim
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea. .,Section of Environmental Epidemiology, Department of Public Health, University of Copenhagen, Østerster Farimagsgade 5, 1014, København K, Copenhagen, Denmark.
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The role of DNA methylation in progression of neurological disorders and neurodegenerative diseases as well as the prospect of using DNA methylation inhibitors as therapeutic agents for such disorders. IBRO Neurosci Rep 2022; 14:28-37. [PMID: 36590248 PMCID: PMC9794904 DOI: 10.1016/j.ibneur.2022.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/23/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Genome-wide studies related to neurological disorders and neurodegenerative diseases have pointed to the role of epigenetic changes such as DNA methylation, histone modification, and noncoding RNAs. DNA methylation machinery controls the dynamic regulation of methylation patterns in discrete brain regions. Objective This review aims to describe the role of DNA methylation in inhibiting and progressing neurological and neurodegenerative disorders and therapeutic approaches. Methods A Systematic search of PubMed, Web of Science, and Cochrane Library was conducted for all qualified studies from 2000 to 2022. Results For the current need of time, we have focused on the DNA methylation role in neurological and neurodegenerative diseases and the expression of genes involved in neurodegeneration such as Alzheimer's, Depression, and Rett Syndrome. Finally, it appears that the various epigenetic changes do not occur separately and that DNA methylation and histone modification changes occur side by side and affect each other. We focused on the role of modification of DNA methylation in several genes associated with depression (NR3C1, NR3C2, CRHR1, SLC6A4, BDNF, and FKBP5), Rett syndrome (MECP2), Alzheimer's, depression (APP, BACE1, BIN1 or ANK1) and Parkinson's disease (SNCA), as well as the co-occurring modifications to histones and expression of non-coding RNAs. Understanding these epigenetic changes and their interactions will lead to better treatment strategies. Conclusion This review captures the state of understanding of the epigenetics of neurological and neurodegenerative diseases. With new epigenetic mechanisms and targets undoubtedly on the horizon, pharmacological modulation and regulation of epigenetic processes in the brain holds great promise for therapy.
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Wagner A, Schosserer M. The epitranscriptome in ageing and stress resistance: A systematic review. Ageing Res Rev 2022; 81:101700. [PMID: 35908668 DOI: 10.1016/j.arr.2022.101700] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 01/31/2023]
Abstract
Modifications of RNA, collectively called the "epitranscriptome", might provide novel biomarkers and innovative targets for interventions in geroscience but are just beginning to be studied in the context of ageing and stress resistance. RNA modifications modulate gene expression by affecting translation initiation and speed, miRNA binding, RNA stability, and RNA degradation. Nonetheless, the precise underlying molecular mechanisms and physiological consequences of most alterations of the epitranscriptome are still only poorly understood. We here systematically review different types of modifications of rRNA, tRNA and mRNA, the methodology to analyze them, current challenges in the field, and human disease associations. Furthermore, we compiled evidence for a connection between individual enzymes, which install RNA modifications, and lifespan in yeast, worm and fly. We also included resistance to different stressors and competitive fitness as search criteria for genes potentially relevant to ageing. Promising candidates identified by this approach include RCM1/NSUN5, RRP8, and F33A8.4/ZCCHC4 that introduce base methylations in rRNA, the methyltransferases DNMT2 and TRM9/ALKBH8, as well as factors involved in the thiolation or A to I editing in tRNA, and finally the m6A machinery for mRNA.
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Affiliation(s)
- Anja Wagner
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Schosserer
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria; Austrian Cluster for Tissue Regeneration, Vienna, Austria.
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Kessi M, Duan H, Xiong J, Chen B, He F, Yang L, Ma Y, Bamgbade OA, Peng J, Yin F. Attention-deficit/hyperactive disorder updates. Front Mol Neurosci 2022; 15:925049. [PMID: 36211978 PMCID: PMC9532551 DOI: 10.3389/fnmol.2022.925049] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/26/2022] [Indexed: 11/15/2022] Open
Abstract
Background Attention-deficit/hyperactive disorder (ADHD) is a neurodevelopmental disorder that commonly occurs in children with a prevalence ranging from 3.4 to 7.2%. It profoundly affects academic achievement, well-being, and social interactions. As a result, this disorder is of high cost to both individuals and society. Despite the availability of knowledge regarding the mechanisms of ADHD, the pathogenesis is not clear, hence, the existence of many challenges especially in making correct early diagnosis and provision of accurate management. Objectives We aimed to review the pathogenic pathways of ADHD in children. The major focus was to provide an update on the reported etiologies in humans, animal models, modulators, therapies, mechanisms, epigenetic changes, and the interaction between genetic and environmental factors. Methods References for this review were identified through a systematic search in PubMed by using special keywords for all years until January 2022. Results Several genes have been reported to associate with ADHD: DRD1, DRD2, DRD4, DAT1, TPH2, HTR1A, HTR1B, SLC6A4, HTR2A, DBH, NET1, ADRA2A, ADRA2C, CHRNA4, CHRNA7, GAD1, GRM1, GRM5, GRM7, GRM8, TARBP1, ADGRL3, FGF1, MAOA, BDNF, SNAP25, STX1A, ATXN7, and SORCS2. Some of these genes have evidence both from human beings and animal models, while others have evidence in either humans or animal models only. Notably, most of these animal models are knockout and do not generate the genetic alteration of the patients. Besides, some of the gene polymorphisms reported differ according to the ethnic groups. The majority of the available animal models are related to the dopaminergic pathway. Epigenetic changes including SUMOylation, methylation, and acetylation have been reported in genes related to the dopaminergic pathway. Conclusion The dopaminergic pathway remains to be crucial in the pathogenesis of ADHD. It can be affected by environmental factors and other pathways. Nevertheless, it is still unclear how environmental factors relate to all neurotransmitter pathways; thus, more studies are needed. Although several genes have been related to ADHD, there are few animal model studies on the majority of the genes, and they do not generate the genetic alteration of the patients. More animal models and epigenetic studies are required.
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Affiliation(s)
- Miriam Kessi
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Haolin Duan
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Juan Xiong
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Baiyu Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fang He
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Lifen Yang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Yanli Ma
- Department of Neurology, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Olumuyiwa A. Bamgbade
- Department of Anesthesiology and Pharmacology, University of British Columbia, Vancouver, BC, Canada
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
- Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
- *Correspondence: Fei Yin,
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10
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Silk T, Dipnall L, Wong YT, Craig JM. Epigenetics and ADHD. Curr Top Behav Neurosci 2022; 57:269-289. [PMID: 35505060 DOI: 10.1007/7854_2022_339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
There is robust evidence of genetic susceptibility to Attention-Deficit Hyperactivity Disorder (ADHD); however, there still remains significant variability that is not attributable to genetic factors. The emerging field of epigenetics is beginning to reveal how genotypic expression can be mediated by an array of variables including external environmental exposure, inter-individual developmental variation, and by the genome itself. Epigenetic modification plays a central role in neurobiological and developmental processes, and disturbances to these processes can have implications for a range of mental health problems. Although the field is still in its early days, this chapter will discuss the current standing of epigenetic research into ADHD. Firstly, key relevant epigenetic processes will be discussed. This will be followed by an overview of the key findings to date investigating the role of epigenetics in ADHD. Human studies have included the theory-driven approach of candidate-gene studies (CGS), as well as the increasingly popular exploratory approach of epigenome-wide association studies (EWAS). Overall, the findings are heterogeneous. However, it is possible that with more longitudinal studies and better characterised cohorts, both predictive and protective links between epigenetic processes and ADHD will be revealed.
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Affiliation(s)
- Timothy Silk
- Centre for Social and Early Emotional Development and School of Psychology, Deakin University, Geelong, VIC, Australia. .,Murdoch Children's Research Institute, Parkville, VIC, Australia.
| | - Lillian Dipnall
- Centre for Social and Early Emotional Development and School of Psychology, Deakin University, Geelong, VIC, Australia
| | - Yen Ting Wong
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Jeffrey M Craig
- Murdoch Children's Research Institute, Parkville, VIC, Australia.,Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, VIC, Australia
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11
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Peedicayil J. The Role of Epigenetics in the Pathogenesis and Potential Treatment of Attention Deficit Hyperactivity Disorder. Curr Neuropharmacol 2022; 20:1642-1650. [PMID: 34544344 PMCID: PMC9881064 DOI: 10.2174/1570159x19666210920091036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 11/22/2022] Open
Abstract
There is increasing evidence that dysregulated epigenetic mechanisms of gene expression are involved in the pathogenesis of attention deficit hyperactivity disorder (ADHD). This review presents a comprehensive summary of the current state of research on the role of epigenetics in the pathogenesis of ADHD. The potential role of epigenetic drugs in the treatment of ADHD is also reviewed. Several studies suggest that there are epigenetic abnormalities in preclinical models of ADHD and in ADHD patients. Regarding DNA methylation, many studies have reported DNA hypermethylation. There is evidence that there is increased histone deacetylation in ADHD patients. Abnormalities in the expression of microRNAs (miRNAs) in ADHD patients have also been found. Some currently used drugs for treating ADHD, in addition to their more well-established mechanisms of action, have been shown to alter epigenetic mechanisms of gene expression. Clinical trials of epigenetic drugs in patients with ADHD report favorable results. These data suggest that abnormal epigenetic mechanisms of gene expression may be involved in the pathogenesis of ADHD. Drugs acting on epigenetic mechanisms may be a potential new class of drugs for treating ADHD.
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Affiliation(s)
- Jacob Peedicayil
- Department of Pharmacology and Clinical Pharmacology, Christian Medical College, Vellore, India,Address correspondence to this author at the Department of Pharmacology and Clinical Pharmacology, Christian Medical College, Vellore, India;Tel: 91-0416-2284237; E-mail:
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