1
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Gerra MC, Dallabona C, Cecchi R. Epigenetic analyses in forensic medicine: future and challenges. Int J Legal Med 2024; 138:701-719. [PMID: 38242965 PMCID: PMC11003920 DOI: 10.1007/s00414-024-03165-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 01/09/2024] [Indexed: 01/21/2024]
Abstract
The possibility of using epigenetics in forensic investigation has gradually risen over the last few years. Epigenetic changes with their dynamic nature can either be inherited or accumulated throughout a lifetime and be reversible, prompting investigation of their use across various fields. In forensic sciences, multiple applications have been proposed, such as the discrimination of monozygotic twins, identifying the source of a biological trace left at a crime scene, age prediction, determination of body fluids and tissues, human behavior association, wound healing progression, and determination of the post-mortem interval (PMI). Despite all these applications, not all the studies considered the impact of PMI and post-sampling effects on the epigenetic modifications and the tissue-specificity of the epigenetic marks.This review aims to highlight the substantial forensic significance that epigenetics could support in various forensic investigations. First, basic concepts in epigenetics, describing the main epigenetic modifications and their functions, in particular, DNA methylation, histone modifications, and non-coding RNA, with a particular focus on forensic applications, were covered. For each epigenetic marker, post-mortem stability and tissue-specificity, factors that should be carefully considered in the study of epigenetic biomarkers in the forensic context, have been discussed. The advantages and limitations of using post-mortem tissues have been also addressed, proposing directions for these innovative strategies to analyze forensic specimens.
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Affiliation(s)
- Maria Carla Gerra
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11a, Viale Delle Scienze 11a, 43124, Parma, PR, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11a, Viale Delle Scienze 11a, 43124, Parma, PR, Italy.
| | - Rossana Cecchi
- Department of Medicine and Surgery, University of Parma, Via Antonio Gramsci 14, 43126, Parma, PR, Italy
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2
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Żarczyńska M, Żarczyński P, Tomsia M. Nucleic Acids Persistence-Benefits and Limitations in Forensic Genetics. Genes (Basel) 2023; 14:1643. [PMID: 37628694 PMCID: PMC10454188 DOI: 10.3390/genes14081643] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The analysis of genetic material may be the only way to identify an unknown person or solve a criminal case. Often, the conditions in which the genetic material was found determine the choice of the analytical method. Hence, it is extremely important to understand the influence of various factors, both external and internal, on genetic material. The review presents information on DNA and RNA persistence, depending on the chemical and physical factors affecting the genetic material integrity. One of the factors taken into account is the time elapsing to genetic material recovery. Temperature can both preserve the genetic material or lead to its rapid degradation. Radiation, aquatic environments, and various types of chemical and physical factors also affect the genetic material quality. The substances used during the forensic process, i.e., for biological trace visualization or maceration, are also discussed. Proper analysis of genetic material degradation can help determine the post-mortem interval (PMI) or time since deposition (TsD), which may play a key role in criminal cases.
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Affiliation(s)
- Małgorzata Żarczyńska
- School of Medicine in Katowice, Medical University of Silesia, 18 Medyków Street, 40-752 Katowice, Poland; (M.Ż.); (P.Ż.)
| | - Piotr Żarczyński
- School of Medicine in Katowice, Medical University of Silesia, 18 Medyków Street, 40-752 Katowice, Poland; (M.Ż.); (P.Ż.)
| | - Marcin Tomsia
- Department of Forensic Medicine and Forensic Toxicology, Medical University of Silesia, 18 Medyków Street, 40-752 Katowice, Poland
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3
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Recommendations for the successful identification of altered human remains using standard and emerging technologies: Results of a systematic approach. Forensic Sci Int Genet 2023; 62:102790. [PMID: 36272213 DOI: 10.1016/j.fsigen.2022.102790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/07/2022]
Abstract
Successful DNA-based identification of altered human remains relies on the condition of the corpses and varies between tissue types. Therefore, the aim of this prospective multicenter study was to generate evidence-based recommendations for the successful identification of altered remains. For this, 19 commonly used soft and hard tissues from 102 altered human bodies were investigated. The corpses' condition was categorized into three anatomical regions using a practical scoring system. Besides other data, DNA yields, degradation indices, and short tandem repeat (STR) profile completeness were determined in 949 tissue samples. Additionally, varying degrees of alteration and tissue-specific differences were evaluated using the Next Generation Sequencing (NGS) platform MiSeq FGx™. Selected challenging samples were sequenced in parallel with the Ion S5™ platform to assess platform-specific performances in the prediction of the deceased's phenotype and the biogeographic ancestry. Differences between tissue types and DNA extraction methods were found, revealing, for example, the lowest degradation for vertebral disc samples from corpses with initiating, advanced and high degrees of decomposition. With respect to STR profile completeness, blood samples outperformed all other tissues including even profoundly degraded corpses. NGS results revealed higher profile completeness compared to standard capillary electrophoresis (CE) genotyping. Per sample, material and degradation degree, a probability for its genotyping success, including the "extended" European Standard Set (eESS) loci, was provided for the forensic community. Based on the observations, recommendations for the alteration-specific optimal tissue types were made to improve the first-attempt identification success of altered human remains for forensic casework.
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Reshetnikov VV, Kisaretova PE, Ershov NI, Merkulova TI, Bondar NP. Social defeat stress in adult mice causes alterations in gene expression, alternative splicing, and the epigenetic landscape of H3K4me3 in the prefrontal cortex: An impact of early-life stress. Prog Neuropsychopharmacol Biol Psychiatry 2021; 106:110068. [PMID: 32810572 DOI: 10.1016/j.pnpbp.2020.110068] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/30/2020] [Accepted: 08/07/2020] [Indexed: 12/24/2022]
Abstract
Chronic stress is the leading risk factor of a broad range of severe psychopathologies. Nonetheless, the molecular mechanisms triggering these pathological processes are not well understood. In our study, we investigated the effects of 15-day social defeat stress (SDS) on the genome-wide landscape of trimethylation at the 4th lysine residue of histone H3 (H3K4me3) and on the transcriptome in the prefrontal cortex of mice that were reared normally (group SDS) or subjected to maternal separation early in life (group MS+SDS). The mice with the history of stress early in life showed increased susceptibility to SDS in adulthood and demonstrated long-lasting genome-wide alterations in gene expression and splicing as well as in the H3K4me3 epigenetic landscape in the prefrontal cortex. Thus, the high-throughput techniques applied here allowed us to simultaneously detect, for the first time, genome-wide epigenetic and transcriptional changes in the murine prefrontal cortex that are associated with both chronic SDS and increased susceptibility to this stressor.
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Affiliation(s)
- V V Reshetnikov
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia.
| | - P E Kisaretova
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - N I Ershov
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - T I Merkulova
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - N P Bondar
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia
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5
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Reshetnikov V, Kisaretova P, Ershov N, Merkulova T, Bondar N. Data of correlation analysis between the density of H3K4me3 in promoters of genes and gene expression: Data from RNA-seq and ChIP-seq analyses of the murine prefrontal cortex. Data Brief 2020; 33:106365. [PMID: 33102649 PMCID: PMC7575808 DOI: 10.1016/j.dib.2020.106365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 11/30/2022] Open
Abstract
H3K4me3 is typically found in the promoter region of genes and is a mark associated with an open chromatin state and active gene transcription. Nonetheless, the role of H3K4me3 in the regulation of transcription is still debated. To improve the understanding of the connection between H3K4me3 density in promoters and gene expression, we assessed the correlation between these two parameters. We utilized genome-wide high-throughput RNA sequencing (RNA-seq) data and H3K4me3-based chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq), carried out on the same samples of the prefrontal cortex from 10 male C57Bl6 mice with different stress experience [Social defeat stress in adult mice causes alterations in gene expression, alternative splicing, and the epigenetic landscape of H3K4me3 in the prefrontal cortex: an impact of early-life stress, 1]. In addition, we assessed the correlation between H3K4me3 density and gene expression in datasets of cell-specific genes. Altogether, the results are useful for the elucidation of H3K4me3 involvement in the regulation of transcription in the murine prefrontal cortex.
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Affiliation(s)
- V.V. Reshetnikov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
- Corresponding author. @VasiliyReshetn2
| | - P.E. Kisaretova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - N.I. Ershov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - T.I. Merkulova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - N.P. Bondar
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
- National Research Novosibirsk State University, Novosibirsk, Russia
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6
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Rajarajan P, Akbarian S. Use of the epigenetic toolbox
to contextualize common variants associated with schizophrenia risk
. DIALOGUES IN CLINICAL NEUROSCIENCE 2020; 21:407-416. [PMID: 31949408 PMCID: PMC6952750 DOI: 10.31887/dcns.2019.21.4/sakbarian] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Schizophrenia is a debilitating psychiatric disorder with a complex genetic architecture and limited understanding of its neuropathology, reflected by the lack of diagnostic measures and effective pharmacological treatments. Geneticists have recently identified more than 145 risk loci comprising hundreds of common variants of small effect sizes, most of which lie in noncoding genomic regions. This review will discuss how the epigenetic toolbox can be applied to contextualize genetic findings in schizophrenia. Progress in next-generation sequencing, along with increasing methodological complexity, has led to the compilation of genome-wide maps of DNA methylation, histone modifications, RNA expression, and more. Integration of chromatin conformation datasets is one of the latest efforts in deciphering schizophrenia risk, allowing the identification of genes in contact with regulatory variants across 100s of kilobases. Large-scale multiomics studies will facilitate the prioritization of putative causal risk variants and gene networks that contribute to schizophrenia etiology, informing clinical diagnostics and treatment downstream.
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Affiliation(s)
- Prashanth Rajarajan
- Graduate School of Biomedical Sciences; Department of Psychiatry; Friedman Brain Institute; Icahn School of Medicine at Mount Sinai, New York, NY, US
| | - Schahram Akbarian
- Department of Psychiatry; Friedman Brain Institute; Icahn School of Medicine at Mount Sinai, New York, NY, US
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7
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Jarmasz JS, Stirton H, Davie JR, Del Bigio MR. DNA methylation and histone post-translational modification stability in post-mortem brain tissue. Clin Epigenetics 2019; 11:5. [PMID: 30635019 PMCID: PMC6330433 DOI: 10.1186/s13148-018-0596-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 12/10/2018] [Indexed: 12/11/2022] Open
Abstract
Background Epigenetic (including DNA and histone) modifications occur in a variety of neurological disorders. If epigenetic features of brain autopsy material are to be studied, it is critical to understand the post-mortem stability of the modifications. Methods Pig and mouse brain tissue were formalin-fixed and paraffin-embedded, or frozen after post-mortem delays of 0, 24, 48, and 72 h. Epigenetic modifications frequently reported in the literature were studied by DNA agarose gel electrophoresis, DNA methylation enzyme-linked immunosorbent assays, Western blotting, and immunohistochemistry. We constructed a tissue microarray of human neocortex samples with devitalization or death to fixation times ranging from < 60 min to 5 days. Results In pig and mouse brain tissue, we found that DNA cytosine modifications (5mC, 5hmC, 5fC, and 5caC) were stable for ≥ 72 h post-mortem. Histone methylation was generally stable for ≥ 48 h (H3K9me2/K9me3, H3K27me2, H3K36me3) or ≥ 72 h post-mortem (H3K4me3, H3K27me3). Histone acetylation was generally less stable. The levels of H3K9ac, H3K27ac, H4K5ac, H4K12ac, and H4K16ac declined as early as ≤ 24 h post-mortem, while the levels of H3K14ac did not change at ≥ 48 h. Immunohistochemistry showed that histone acetylation loss occurred primarily in the nuclei of large neurons, while immunoreactivity in glial cell nuclei was relatively unchanged. In the human brain tissue array, immunoreactivity for DNA cytosine modifications and histone methylation was stable, while subtle changes were apparent in histone acetylation at 4 to 5 days post-mortem. Conclusion We conclude that global epigenetic studies on human post-mortem brain tissue are feasible, but great caution is needed for selection of post-mortem delay matched controls if histone acetylation is of interest. Electronic supplementary material The online version of this article (10.1186/s13148-018-0596-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessica S Jarmasz
- Department of Human Anatomy and Cell Science, University of Manitoba, Room 674 JBRC - 727 McDermot Avenue, Winnipeg, MB, R3E 3P4, Canada
| | - Hannah Stirton
- Max Rady College of Medicine, University of Manitoba, Room 260 Brodie Centre - 727 McDermot Avenue, Winnipeg, MB, R3E 3P5, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Room 333A BMSB, 745 McDermot Avenue, Winnipeg, MB, R3E 0J9, Canada
| | - Marc R Del Bigio
- Department of Pathology, University of Manitoba, Room 401 Brodie Centre - 727 McDermot Avenue, Winnipeg, MB, R3E 3P5, Canada.
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8
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Li Y, Pan X, Roberts ML, Liu P, Kotchen TA, Cowley AW, Mattson DL, Liu Y, Liang M, Kidambi S. Stability of global methylation profiles of whole blood and extracted DNA under different storage durations and conditions. Epigenomics 2018; 10:797-811. [PMID: 29683333 DOI: 10.2217/epi-2018-0025] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To test whether DNA samples stored for a prolonged period (20 years) under various storage conditions could be used for comparative methylation studies using reduced representation bisulfite sequencing. PATIENTS & METHODS Five groups of human blood DNA samples (n = 5-6/group) were compared. The groupings were based on the anticoagulant used and storage temperature and duration. RESULTS Methylation profiles of defined genomic regions in the DNA or blood samples archived for 20 years were similar across all storage temperatures, including 4°C. The level of intersample similarity in archived samples was not significantly different than that in recently collected samples. CONCLUSION Archived samples, including DNA stored at 4°C for 20 years, are suitable for comparative studies of DNA methylation.
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Affiliation(s)
- Yingchuan Li
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.,Department of Critical Care Medicine, Shanghai JiaoTong University affiliated The Sixth People's Hospital, Shanghai, China
| | - Xiaoqing Pan
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michelle L Roberts
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Pengyuan Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.,Department of Respiratory Medicine, Sir Run Run Shaw Hospital & Institute of Translational Medicine, Zhejiang University, Zhejiang, China
| | - Theodore A Kotchen
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Allen W Cowley
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - David L Mattson
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Yong Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Srividya Kidambi
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
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9
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Nativio R, Donahue G, Berson A, Lan Y, Amlie-Wolf A, Tuzer F, Toledo JB, Gosai SJ, Gregory BD, Torres C, Trojanowski JQ, Wang LS, Johnson FB, Bonini NM, Berger SL. Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease. Nat Neurosci 2018; 21:497-505. [PMID: 29507413 PMCID: PMC6124498 DOI: 10.1038/s41593-018-0101-9] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/11/2017] [Indexed: 12/21/2022]
Abstract
Aging is the strongest risk factor for Alzheimer's disease (AD), although the underlying mechanisms remain unclear. The chromatin state, in particular through the mark H4K16ac, has been implicated in aging and thus may play a pivotal role in age-associated neurodegeneration. Here we compare the genome-wide enrichment of H4K16ac in the lateral temporal lobe of AD individuals against both younger and elderly cognitively normal controls. We found that while normal aging leads to H4K16ac enrichment, AD entails dramatic losses of H4K16ac in the proximity of genes linked to aging and AD. Our analysis highlights the presence of three classes of AD-related changes with distinctive functional roles. Furthermore, we discovered an association between the genomic locations of significant H4K16ac changes with genetic variants identified in prior AD genome-wide association studies and with expression quantitative trait loci. Our results establish the basis for an epigenetic link between aging and AD.
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Affiliation(s)
- Raffaella Nativio
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Greg Donahue
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amit Berson
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Yemin Lan
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexandre Amlie-Wolf
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ferit Tuzer
- Department of Pathology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Jon B Toledo
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sager J Gosai
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Claudio Torres
- Department of Pathology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - John Q Trojanowski
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Li-San Wang
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - F Brad Johnson
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Nancy M Bonini
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Shelley L Berger
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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10
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Ershov NI, Bondar NP, Lepeshko AA, Reshetnikov VV, Ryabushkina JA, Merkulova TI. Consequences of early life stress on genomic landscape of H3K4me3 in prefrontal cortex of adult mice. BMC Genomics 2018; 19:93. [PMID: 29504911 PMCID: PMC5836825 DOI: 10.1186/s12864-018-4479-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Maternal separation models in rodents are widely used to establish molecular mechanisms underlying prolonged effects of early life adversity on neurobiological and behavioral outcomes in adulthood. However, global epigenetic signatures following early life stress in these models remain unclear. Results In this study, we carried out a ChIP-seq analysis of H3K4 trimethylation profile in the prefrontal cortex of adult male mice with a history of early life stress. Two types of stress were used: prolonged separation of pups from their mothers (for 3 h once a day, maternal separation, MS) and brief separation (for 15 min once a day, handling, HD). Adult offspring in the MS group demonstrated reduced locomotor activity in the open field test accompanied by reduced exploratory activity, while the HD group showed decreased anxiety-like behavior only. In a group of maternal separation, we have found a small number (45) of slightly up-regulated peaks, corresponding to promoters of 70 genes, while no changes were observed in a group of handling. Among the genes whose promoters have differential enrichment of H3K4me3, the most relevant ones participate in gene expression regulation, modulation of chromatin structure and mRNA processing. For two genes, Ddias and Pip4k2a, increased H3K4me3 levels were associated with the increased mRNA expression in MS group. Conclusion The distribution of H3K4me3 in prefrontal cortex showed relatively low variability across all individuals, and only some subtle changes were revealed in mice with a history of early life stress. It is possible that the observed long-lasting behavioral alterations induced by maternal separation are mediated by other epigenetic mechanisms, or other brain structures are responsible for these effects. Electronic supplementary material The online version of this article (10.1186/s12864-018-4479-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nikita I Ershov
- Laboratory of Gene Expression Regulation, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Prospect Lavrentyeva, 630090, Novosibirsk, Russia
| | - Natalya P Bondar
- Laboratory of Gene Expression Regulation, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Prospect Lavrentyeva, 630090, Novosibirsk, Russia. .,Novosibirsk National Research State University, 2 Pirogov Street, 630090, Novosibirsk, Russia.
| | - Arina A Lepeshko
- Laboratory of Gene Expression Regulation, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Prospect Lavrentyeva, 630090, Novosibirsk, Russia.,Novosibirsk National Research State University, 2 Pirogov Street, 630090, Novosibirsk, Russia
| | - Vasiliy V Reshetnikov
- Laboratory of Gene Expression Regulation, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Prospect Lavrentyeva, 630090, Novosibirsk, Russia
| | - Julia A Ryabushkina
- Novosibirsk National Research State University, 2 Pirogov Street, 630090, Novosibirsk, Russia
| | - Tatiana I Merkulova
- Laboratory of Gene Expression Regulation, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Prospect Lavrentyeva, 630090, Novosibirsk, Russia.,Novosibirsk National Research State University, 2 Pirogov Street, 630090, Novosibirsk, Russia
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11
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Maurya SK, Mishra R. Pax6 Binds to Promoter Sequence Elements Associated with Immunological Surveillance and Energy Homeostasis in Brain of Aging Mice. Ann Neurosci 2017; 24:20-25. [PMID: 28588354 DOI: 10.1159/000464419] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/21/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Patients having mutations of Pax6 bear phenotypes that match age-associated neurological disorders. Mutations affect most cellular functions such as cell division, growth, differentiation, and cell death in brain, eyes, pituitary, pineal, and pancreas. The progressive reduction in the level of Pax6 during aging has also been observed. However, information about downstream targets of Pax6 in brain is unclear. Therefore, it is presumed that age-dependent alterations of Pax6 may also affect cascades of promoter sequence recognition in brain during aging. PURPOSE This study is aimed at studying the interaction of Pax6 with DNA sequence elements to explore alteration in gene targets and transcription networks of Pax6 in brain during aging. METHODS Chromatin immunoprecipitation with anti-Pax6 using tissue extracts of brain from newborn, young, adult, and old mice was done. Pulled DNA from brain was analysed by gene-specific polymerase chain reaction (PCR). Amplified PCR products were sequenced and analyzed. RESULTS Age-associated alterations in binding to genetic sequence elements by Pax6 were observed. Promoter analysis predicts genes involved in neuronal survival (Bdnf, Sparc), specificity of astrocyte (S100β, Gfap), cell-proliferation (Pcna), inflammation and immune response (interferon-γ, tumour necrosis factor-α), management of oxidative stress (Sod, Cat), and hypoxia (Ldh). CONCLUSION The Pax6 either directly or indirectly binds to promoter sequences of genes essential for immunological surveillance and energy metabolism in brain that alters during aging.
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Affiliation(s)
- Shashank Kumar Maurya
- Department of Zoology, Biochemistry and Molecular Biology Laboratory, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Rajnikant Mishra
- Department of Zoology, Biochemistry and Molecular Biology Laboratory, Institute of Science, Banaras Hindu University, Varanasi, India
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12
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Xiao X, Chang H, Li M. Molecular mechanisms underlying noncoding risk variations in psychiatric genetic studies. Mol Psychiatry 2017; 22:497-511. [PMID: 28044063 PMCID: PMC5378805 DOI: 10.1038/mp.2016.241] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/08/2016] [Accepted: 11/14/2016] [Indexed: 12/18/2022]
Abstract
Recent large-scale genetic approaches such as genome-wide association studies have allowed the identification of common genetic variations that contribute to risk architectures of psychiatric disorders. However, most of these susceptibility variants are located in noncoding genomic regions that usually span multiple genes. As a result, pinpointing the precise variant(s) and biological mechanisms accounting for the risk remains challenging. By reviewing recent progresses in genetics, functional genomics and neurobiology of psychiatric disorders, as well as gene expression analyses of brain tissues, here we propose a roadmap to characterize the roles of noncoding risk loci in the pathogenesis of psychiatric illnesses (that is, identifying the underlying molecular mechanisms explaining the genetic risk conferred by those genomic loci, and recognizing putative functional causative variants). This roadmap involves integration of transcriptomic data, epidemiological and bioinformatic methods, as well as in vitro and in vivo experimental approaches. These tools will promote the translation of genetic discoveries to physiological mechanisms, and ultimately guide the development of preventive, therapeutic and prognostic measures for psychiatric disorders.
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Affiliation(s)
- X Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - H Chang
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - M Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
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13
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Differences in 5-HT2A and mGlu2 Receptor Expression Levels and Repressive Epigenetic Modifications at the 5-HT2A Promoter Region in the Roman Low- (RLA-I) and High- (RHA-I) Avoidance Rat Strains. Mol Neurobiol 2017; 55:1998-2012. [PMID: 28265857 DOI: 10.1007/s12035-017-0457-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/13/2017] [Indexed: 01/12/2023]
Abstract
The serotonin 2A (5-HT2A) and metabotropic glutamate 2 (mGlu2) receptors regulate each other and are associated with schizophrenia. The Roman high- (RHA-I) and the Roman low- (RLA-I) avoidance rat strains present well-differentiated behavioral profiles, with the RHA-I strain emerging as a putative genetic rat model of schizophrenia-related features. The RHA-I strain shows increased 5-HT2A and decreased mGlu2 receptor binding levels in prefrontal cortex (PFC). Here, we looked for differences in gene expression and transcriptional regulation of these receptors. The striatum (STR) was included in the analysis. 5-HT2A, 5-HT1A, and mGlu2 mRNA and [3H]ketanserin binding levels were measured in brain homogenates. As expected, 5-HT2A binding was significantly increased in PFC in the RHA-I rats, while no difference in binding was observed in STR. Surprisingly, 5-HT2A gene expression was unchanged in PFC but significantly decreased in STR. mGlu2 receptor gene expression was significantly decreased in both PFC and STR. No differences were observed for the 5-HT1A receptor. Chromatin immunoprecipitation assay revealed increased trimethylation of histone 3 at lysine 27 (H3K27me3) at the promoter region of the HTR2A gene in the STR. We further looked at the Akt/GSK3 signaling pathway, a downstream point of convergence of the serotonin and glutamate system, and found increased phosphorylation levels of GSK3β at tyrosine 216 and increased β-catenin levels in the PFC of the RHA-I rats. These results reveal region-specific regulation of the 5-HT2A receptor in the RHA-I rats probably due to absence of mGlu2 receptor that may result in differential regulation of downstream pathways.
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14
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Kundakovic M, Jiang Y, Kavanagh DH, Dincer A, Brown L, Pothula V, Zharovsky E, Park R, Jacobov R, Magro I, Kassim B, Wiseman J, Dang K, Sieberts SK, Roussos P, Fromer M, Harris B, Lipska BK, Peters MA, Sklar P, Akbarian S. Practical Guidelines for High-Resolution Epigenomic Profiling of Nucleosomal Histones in Postmortem Human Brain Tissue. Biol Psychiatry 2017; 81:162-170. [PMID: 27113501 PMCID: PMC5017897 DOI: 10.1016/j.biopsych.2016.03.1048] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/28/2016] [Accepted: 03/01/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND The nervous system may include more than 100 residue-specific posttranslational modifications of histones forming the nucleosome core that are often regulated in cell-type-specific manner. On a genome-wide scale, some of the histone posttranslational modification landscapes show significant overlap with the genetic risk architecture for several psychiatric disorders, fueling PsychENCODE and other large-scale efforts to comprehensively map neuronal and nonneuronal epigenomes in hundreds of specimens. However, practical guidelines for efficient generation of histone chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) datasets from postmortem brains are needed. METHODS Protocols and quality controls are given for the following: 1) extraction, purification, and NeuN neuronal marker immunotagging of nuclei from adult human cerebral cortex; 2) fluorescence-activated nuclei sorting; 3) preparation of chromatin by micrococcal nuclease digest; 4) ChIP for open chromatin-associated histone methylation and acetylation; and 5) generation and sequencing of ChIP-seq libraries. RESULTS We present a ChIP-seq pipeline for epigenome mapping in the neuronal and nonneuronal nuclei from the postmortem brain. This includes a stepwise system of quality controls and user-friendly data presentation platforms. CONCLUSIONS Our practical guidelines will be useful for projects aimed at histone posttranslational modification mapping in chromatin extracted from hundreds of postmortem brain samples in cell-type-specific manner.
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Affiliation(s)
- Marija Kundakovic
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yan Jiang
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - David H Kavanagh
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Aslihan Dincer
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Leanne Brown
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Venu Pothula
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elizabeth Zharovsky
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Royce Park
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rivka Jacobov
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Isabelle Magro
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bibi Kassim
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jennifer Wiseman
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | - Panos Roussos
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Menachem Fromer
- Friedman Brain Institute, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Brent Harris
- Department of Neurology, Georgetown University Medical Center, Washington, DC; Human Brain Collection Core, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland
| | - Barbara K Lipska
- Human Brain Collection Core, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland
| | | | - Pamela Sklar
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Schahram Akbarian
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.
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15
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Fullard JF, Halene TB, Giambartolomei C, Haroutunian V, Akbarian S, Roussos P. Understanding the genetic liability to schizophrenia through the neuroepigenome. Schizophr Res 2016; 177:115-124. [PMID: 26827128 PMCID: PMC4963306 DOI: 10.1016/j.schres.2016.01.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/14/2016] [Accepted: 01/18/2016] [Indexed: 12/17/2022]
Abstract
The Psychiatric Genomics Consortium-Schizophrenia Workgroup (PGC-SCZ) recently identified 108 loci associated with increased risk for schizophrenia (SCZ). The vast majority of these variants reside within non-coding sequences of the genome and are predicted to exert their effects by affecting the mechanism of action of cis regulatory elements (CREs), such as promoters and enhancers. Although a number of large-scale collaborative efforts (e.g. ENCODE) have achieved a comprehensive mapping of CREs in human cell lines or tissue homogenates, it is becoming increasingly evident that many risk-associated variants are enriched for expression Quantitative Trait Loci (eQTLs) and CREs in specific tissues or cells. As such, data derived from previous research endeavors may not capture fully cell-type and/or region specific changes associated with brain diseases. Coupling recent technological advances in genomics with cell-type specific methodologies, we are presented with an unprecedented opportunity to better understand the genetics of normal brain development and function and, in turn, the molecular basis of neuropsychiatric disorders. In this review, we will outline ongoing efforts towards this goal and will discuss approaches with the potential to shed light on the mechanism(s) of action of cell-type specific cis regulatory elements and their putative roles in disease, with particular emphasis on understanding the manner in which the epigenome and CREs influence the etiology of SCZ.
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Affiliation(s)
- John F. Fullard
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tobias B. Halene
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Mental Illness Research, Education, and Clinical Center (VISN 3), James J. Peters VA Medical Center, Bronx, NY, USA
| | | | - Vahram Haroutunian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Mental Illness Research, Education, and Clinical Center (VISN 3), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mental Illness Research, Education, and Clinical Center (VISN 3), James J. Peters VA Medical Center, Bronx, NY, USA.
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16
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Gross JA, Nagy C, Lin L, Bonneil É, Maheu M, Thibault P, Mechawar N, Jin P, Turecki G. WITHDRAWN: Global and site-specific changes in 5-methylcytosine and 5-hydroxymethylcytosine after extended post-mortem interval. Exp Mol Pathol 2016:S0014-4800(16)30042-9. [PMID: 27746278 DOI: 10.1016/j.yexmp.2016.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 08/16/2016] [Accepted: 10/11/2016] [Indexed: 11/28/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Jeffrey A Gross
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Corina Nagy
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Li Lin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Éric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Marissa Maheu
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Naguib Mechawar
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada.
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17
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Li M, Weinberger DR. RETRACTION: Illuminating the dark road from schizophrenia genetic associations to disease mechanisms. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Abstract
Recent large-scale genome-wide association studies (GWAS) have enabled the discovery of common genetic variations contributing to risk architectures of schizophrenia in human populations; however, the majority of GWAS-identified variants are located in large genomic regions spanning multiple genes, and recognizing the precise targets and mechanisms of these clinical associations is now the major challenge. Here, we review recent progress in schizophrenia genetics, functional genomics and related neuroscience research, and propose a functional pipeline to translate schizophrenia GWAS risk loci into disease biology and information for drug discovery. The pipeline includes identification of underlying molecular mechanisms using transcriptomic data in human brain, prioritization of putative functional causative variants by the integration of genetic epidemiological and bioinformatics methods as well as molecular approaches, and in vitro and in vivo experimental characterizations of the identified targeted species and causative variants to dissect the relevant disease biology. These approaches will accelerate progress from schizophrenia genetic studies to biological mechanisms and ultimately guide the development of prognostic, preventive and therapeutic measures.
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Affiliation(s)
- Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, 21205, USA
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, 21205, USA
- McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205, USA
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18
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Gross JA, Nagy C, Lin L, Bonneil É, Maheu M, Thibault P, Mechawar N, Jin P, Turecki G. Global and Site-Specific Changes in 5-Methylcytosine and 5-Hydroxymethylcytosine after Extended Post-mortem Interval. Front Genet 2016; 7:120. [PMID: 27446202 PMCID: PMC4917525 DOI: 10.3389/fgene.2016.00120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/11/2016] [Indexed: 02/04/2023] Open
Abstract
There has been a growing interest in the study of epigenetic mechanisms to elucidate the molecular bases of human brain-related diseases and disorders. Frequently, researchers utilize post-mortem tissue with the assumption that post-mortem tissue decay has little or no effect on epigenetic marks. Although previous studies show no effect of post-mortem interval on certain epigenetic marks, no such research has been performed on cytosine modifications. In this study, we use DNA from the brains of adult Sprague Dawley rats subjected to post-mortem intervals at room temperature, ranging from 0 to 96 h, to assess the stability of cytosine modifications, namely 5-methycytosine and 5-hydroxymethylcytosine. Our results indicate that neither global nor site-specific levels of 5-methycytosine and 5-hydroxymethylcytosine are affected by the post-mortem intervals we studied. As such, the use of post-mortem tissue to study cytosine modifications in the context of neurological or neuropsychiatric disorders is appropriate.
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Affiliation(s)
- Jeffrey A Gross
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal QC, Canada
| | - Corina Nagy
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal QC, Canada
| | - Li Lin
- Department of Human Genetics, Emory University School of Medicine, Atlanta GA, USA
| | - Éric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal QC, Canada
| | - Marissa Maheu
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal QC, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal QC, Canada
| | - Naguib Mechawar
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal QC, Canada
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta GA, USA
| | - Gustavo Turecki
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal QC, Canada
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19
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Cittaro D, Lampis V, Luchetti A, Coccurello R, Guffanti A, Felsani A, Moles A, Stupka E, D' Amato FR, Battaglia M. Histone Modifications in a Mouse Model of Early Adversities and Panic Disorder: Role for Asic1 and Neurodevelopmental Genes. Sci Rep 2016; 6:25131. [PMID: 27121911 PMCID: PMC4848503 DOI: 10.1038/srep25131] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 04/12/2016] [Indexed: 11/20/2022] Open
Abstract
Hyperventilation following transient, CO2-induced acidosis is ubiquitous in mammals and heritable. In humans, respiratory and emotional hypersensitivity to CO2 marks separation anxiety and panic disorders, and is enhanced by early-life adversities. Mice exposed to the repeated cross-fostering paradigm (RCF) of interference with maternal environment show heightened separation anxiety and hyperventilation to 6% CO2-enriched air. Gene-environment interactions affect CO2 hypersensitivity in both humans and mice. We therefore hypothesised that epigenetic modifications and increased expression of genes involved in pH-detection could explain these relationships. Medullae oblongata of RCF- and normally-reared female outbred mice were assessed by ChIP-seq for H3Ac, H3K4me3, H3K27me3 histone modifications, and by SAGE for differential gene expression. Integration of multiple experiments by network analysis revealed an active component of 148 genes pointing to the mTOR signalling pathway and nociception. Among these genes, Asic1 showed heightened mRNA expression, coherent with RCF-mice’s respiratory hypersensitivity to CO2 and altered nociception. Functional enrichment and mRNA transcript analyses yielded a consistent picture of enhancement for several genes affecting chemoception, neurodevelopment, and emotionality. Particularly, results with Asic1 support recent human findings with panic and CO2 responses, and provide new perspectives on how early adversities and genes interplay to affect key components of panic and related disorders.
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Affiliation(s)
- Davide Cittaro
- Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy
| | - Valentina Lampis
- Developmental Psychopathology Unit, Vita-Salute San Raffaele University, Milan, Italy
| | - Alessandra Luchetti
- Institute of Cell Biology and Neurobiology, National Research Council/Fondazione Santa Lucia, Rome, Italy
| | - Roberto Coccurello
- Institute of Cell Biology and Neurobiology, National Research Council/Fondazione Santa Lucia, Rome, Italy
| | - Alessandro Guffanti
- Laboratory of Molecular Neuroscience, Department of Biological Chemistry, The Edmond and Lily Safra Center of Brain Science, The Hebrew University of Jerusalem, Jerusalem, Israel.,Genomnia srl, Lainate, Italy
| | - Armando Felsani
- Institute of Cell Biology and Neurobiology, National Research Council/Fondazione Santa Lucia, Rome, Italy.,Genomnia srl, Lainate, Italy
| | - Anna Moles
- Institute of Cell Biology and Neurobiology, National Research Council/Fondazione Santa Lucia, Rome, Italy.,Genomnia srl, Lainate, Italy
| | - Elia Stupka
- Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy
| | - Francesca R D' Amato
- Institute of Cell Biology and Neurobiology, National Research Council/Fondazione Santa Lucia, Rome, Italy
| | - Marco Battaglia
- Department of Psychiatry, University Of Toronto, Toronto, Canada.,Division of Child and Youth Mental Health, Centre for Addiction and Mental Health, Toronto, Canada
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20
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Williams T, Soni S, White J, Can G, Javan GT. Evaluation of DNA degradation using flow cytometry: promising tool for postmortem interval determination. Am J Forensic Med Pathol 2016; 36:104-10. [PMID: 25893913 DOI: 10.1097/paf.0000000000000146] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Over the years, there have been numerous formulas proposed for use in determining the postmortem interval (PMI); however, no method is all encompassing and absolute. Even so, very little research has been undertaken to determine if there is a viable correlation between the rate of DNA degradation and PMI, which can be calculated from analysis by flow cytometry. In this study, we analyzed the rate of DNA degradation of spleen and brain tissues from 15 cadavers over a 96-hour period of time at 2 temperature conditions, that is, 21°C (room temperature) and 4°C (refrigerator) to mimic summer and winter weather, respectively. The resulting data were used to form a pattern that correlates DNA degradation to cell death occurrence. Statistical analyses were performed to determine the significance of the relationship between PMI and DNA degradation. Moreover, in search of alternative reliable organs of interest for PMI estimation, the results demonstrate that the brain has lesser DNA degradation as compared with the spleen. Thus, the current study suggests that the brain can be an organ of choice for PMI studies, but more research is underway in this aspect.
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21
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Gillio-Meina C, Zielke HR, Fraser DD. Translational Research in Pediatrics IV: Solid Tissue Collection and Processing. Pediatrics 2016; 137:peds.2015-0490. [PMID: 26659457 DOI: 10.1542/peds.2015-0490] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/05/2015] [Indexed: 11/24/2022] Open
Abstract
Solid tissues are critical for child-health research. Specimens are commonly obtained at the time of biopsy/surgery or postmortem. Research tissues can also be obtained at the time of organ retrieval for donation or from tissue that would otherwise have been discarded. Navigating the ethics of solid tissue collection from children is challenging, and optimal handling practices are imperative to maximize tissue quality. Fresh biopsy/surgical specimens can be affected by a variety of factors, including age, gender, BMI, relative humidity, freeze/thaw steps, and tissue fixation solutions. Postmortem tissues are also vulnerable to agonal factors, body storage temperature, and postmortem intervals. Nonoptimal tissue handling practices result in nucleotide degradation, decreased protein stability, artificial posttranslational protein modifications, and altered lipid concentrations. Tissue pH and tryptophan levels are 2 methods to judge the quality of solid tissue collected for research purposes; however, the RNA integrity number, together with analyses of housekeeping genes, is the new standard. A comprehensive clinical data set accompanying all tissue samples is imperative. In this review, we examined: the ethical standards relating to solid tissue procurement from children; potential sources of solid tissues; optimal practices for solid tissue processing, handling, and storage; and reliable markers of solid tissue quality.
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Affiliation(s)
- Carolina Gillio-Meina
- Translational Research Centre, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada
| | | | - Douglas D Fraser
- Translational Research Centre, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada; Centre for Critical Illness Research, Critical Care Medicine and Pediatrics, Clinical Neurologic Sciences, and Physiology and Pharmacology, Western University, London, Ontario, Canada
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22
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Wisnieski F, Calcagno DQ, Leal MF, Santos LC, Gigek CO, Chen ES, Demachki S, Artigiani R, Assumpção PP, Lourenço LG, Burbano RR, Smith MC. CDKN1A histone acetylation and gene expression relationship in gastric adenocarcinomas. Clin Exp Med 2015; 17:121-129. [PMID: 26567008 DOI: 10.1007/s10238-015-0400-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/26/2015] [Indexed: 12/13/2022]
Abstract
CDKN1A is a tumor suppressor gene involved in gastric carcinogenesis and is a potential target for histone deacetylase inhibitor-based therapies. Upregulation of CDKN1A is generally observed in several cell lines after histone deacetylase inhibitor treatment; however, little is known about the histone acetylation status associated with this gene in clinical samples, including gastric tumor tissue samples. Therefore, our goal was to quantify the H3K9 and H4K16 acetylation levels associated with three CDKN1A regions in 21 matched pairs of gastric adenocarcinoma and corresponding adjacent non-tumor samples by chromatin immunoprecipitation and to correlate these data with the gene expression. Our results demonstrated that the -402, -20, and +182 CDKN1A regions showed a significantly increased acetylation level in at least one of the histones evaluated (p < 0.05, for all comparisons), and these levels were positively correlated in gastric tumors. However, an inverse correlation was detected between both H3K9 and H4K16 acetylation at the -402 CDKN1A region and mRNA levels in gastric tumors (r = -0.51, p = 0.02; r = -0.60, p < 0.01, respectively). Furthermore, increased H4K16 acetylation at the -20 CDKN1A region was associated with gastric tumors of patients without lymph node metastasis (p = 0.04). These results highlight the complexity of these processes in gastric adenocarcinoma and contribute to a better understanding of CDKN1A regulation in carcinogenesis.
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Affiliation(s)
- Fernanda Wisnieski
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, Rua Botucatu, 740, São Paulo, 04023900, Brazil.
| | - Danielle Queiroz Calcagno
- Núcleo de Pesquisas em Oncologia, Hospital João de Barros Barreto, Universidade Federal do Pará, Avenida Mundurucus, 4487, Belém, 66073000, Brazil
| | - Mariana Ferreira Leal
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, Rua Botucatu, 740, São Paulo, 04023900, Brazil
- Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo, Rua Borges Lagoa, 783, São Paulo, 04038032, Brazil
| | - Leonardo Caires Santos
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, Rua Botucatu, 740, São Paulo, 04023900, Brazil
| | - Carolina Oliveira Gigek
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, Rua Botucatu, 740, São Paulo, 04023900, Brazil
| | - Elizabeth Suchi Chen
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, Rua Botucatu, 740, São Paulo, 04023900, Brazil
| | - Sâmia Demachki
- Núcleo de Pesquisas em Oncologia, Hospital João de Barros Barreto, Universidade Federal do Pará, Avenida Mundurucus, 4487, Belém, 66073000, Brazil
| | - Ricardo Artigiani
- Departamento de Patologia, Universidade Federal de São Paulo, Rua Botucatu, 740, São Paulo, 04023000, Brazil
| | - Paulo Pimentel Assumpção
- Núcleo de Pesquisas em Oncologia, Hospital João de Barros Barreto, Universidade Federal do Pará, Avenida Mundurucus, 4487, Belém, 66073000, Brazil
| | - Laércio Gomes Lourenço
- Disciplina de Gastroenterologia Cirúrgica, Departamento de Cirurgia, Universidade Federal de São Paulo, Rua Napoleão de Barros, 715, São Paulo, 04024002, Brazil
| | - Rommel Rodríguez Burbano
- Laboratório de Citogenética Humana, Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Correia, 01, Belém, 66075110, Brazil
| | - Marília Cardoso Smith
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, Rua Botucatu, 740, São Paulo, 04023900, Brazil
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23
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Transcriptional regulation of GAD1 GABA synthesis gene in the prefrontal cortex of subjects with schizophrenia. Schizophr Res 2015; 167:28-34. [PMID: 25458568 PMCID: PMC4417100 DOI: 10.1016/j.schres.2014.10.020] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 10/08/2014] [Accepted: 10/13/2014] [Indexed: 12/20/2022]
Abstract
Expression of GAD1 GABA synthesis enzyme is highly regulated by neuronal activity and reaches mature levels in the prefrontal cortex not before adolescence. A significant portion of cases diagnosed with schizophrenia show deficits in GAD1 RNA and protein levels in multiple areas of adult cerebral cortex, possibly reflecting molecular or cellular defects in subtypes of GABAergic interneurons essential for network synchronization and cognition. Here, we review 20years of progress towards a better understanding of disease-related regulation of GAD1 gene expression. For example, deficits in cortical GAD1 RNA in some cases of schizophrenia are associated with changes in the epigenetic architecture of the promoter, affecting DNA methylation patterns and nucleosomal histone modifications. These localized chromatin defects at the 5' end of GAD1 are superimposed by disordered locus-specific chromosomal conformations, including weakening of long-range promoter-enhancer loopings and physical disconnection of GAD1 core promoter sequences from cis-regulatory elements positioned 50 kilobases further upstream. Studies on the 3-dimensional architecture of the GAD1 locus in neurons, including developmentally regulated higher order chromatin compromised by the disease process, together with exploration of locus-specific epigenetic interventions in animal models, could pave the way for future treatments of psychosis and schizophrenia.
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Abstract
Postmortem brain research is invaluable to the study of neurologic and neuropsychiatric disorders, including Alzheimer disease, schizophrenia, and major depression. A major confounder in molecular studies using human brain tissue is postmortem interval (i.e. the amount of time between a subject's death and processing of tissue). We examined the integrity of biomolecules that were of interest to molecular studies of neurologic disorders, including RNA, microRNA, histone modifications, and proteins, at various postmortem intervals in an animal model to assess their robustness and suitability for experimentation. Sprague-Dawley rats were selected as model and subjected to 2 conditions: a variable postmortem interval at room temperature and a fixed time of 24 hours at 4°C, which simulates the period commonly spent in the morgue before brain collection. Eight time points were investigated. MicroRNA was impressively resistant to postmortem intervals; methylated histone modifications showed a threshold between 72 and 96 hours, mirroring results from histone proteins at 72 hours. RNA degradation was transcript-specific, with housekeeping genes being more robust than genes with lower expression. Our results suggest that molecules commonly investigated in genetic and epigenetic studies were highly stable through the postmortem intervals investigated. These results support the continued use of postmortem tissue for neuropsychiatric research.
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The workflow from post-mortem human brain sampling to cell microdissection: a Brain Net Europe study. J Neural Transm (Vienna) 2015; 122:975-91. [DOI: 10.1007/s00702-015-1378-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/04/2015] [Indexed: 11/25/2022]
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Bai G, Cheung I, Shulha HP, Coelho JE, Li P, Dong X, Jakovcevski M, Wang Y, Grigorenko A, Jiang Y, Hoss A, Patel K, Zheng M, Rogaev E, Myers RH, Weng Z, Akbarian S, Chen JF. Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains. Hum Mol Genet 2014; 24:1441-56. [PMID: 25480889 DOI: 10.1093/hmg/ddu561] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
To investigate epigenetic contributions to Huntington's disease (HD) pathogenesis, we carried out genome-wide mapping of the transcriptional mark, trimethyl-histone H3-lysine 4 (H3K4me3) in neuronal nuclei extracted from prefrontal cortex of HD cases and controls using chromatin immunoprecipitation followed by deep-sequencing. Neuron-specific mapping of the genome-wide distribution of H3K4me3 revealed 136 differentially enriched loci associated with genes implicated in neuronal development and neurodegeneration, including GPR3, TMEM106B, PDIA6 and the Notch signaling genes hairy and enhancer of split 4 (HES4) and JAGGED2, supporting the view that the neuronal epigenome is affected in HD. Importantly, loss of H3K4me3 at CpG-rich sequences on the HES4 promoter was associated with excessive DNA methylation, reduced binding of nuclear proteins to the methylated region and altered expression of HES4 and HES4 targeted genes MASH1 and P21 involved in striatal development. Moreover, hypermethylation of HES4 promoter sequences was strikingly correlated with measures of striatal degeneration and age-of-onset in a cohort of 25 HD brains (r = 0.56, P = 0.006). Lastly, shRNA knockdown of HES4 in human neuroblastoma cells altered MASH1 and P21 mRNA expression and markedly increased mutated HTT-induced aggregates and cell death. These findings, taken together, suggest that epigenetic dysregulation of HES4 could play a critical role in modifying HD disease pathogenesis and severity.
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Affiliation(s)
- Guang Bai
- Department of Neural and Pain Sciences, University of Maryland Dental School, Baltimore, MD 21201, USA
| | - Iris Cheung
- Brudnick Neuropsychiatric Research Institute
| | - Hennady P Shulha
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Joana E Coelho
- Department of Neurology, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118, USA
| | - Ping Li
- Department of Neurology, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118, USA
| | - Xianjun Dong
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | | | - Yumei Wang
- Department of Neurology, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118, USA
| | | | - Yan Jiang
- Friedman Brain Institute, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Andrew Hoss
- Department of Neurology, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118, USA
| | - Krupal Patel
- Department of Neural and Pain Sciences, University of Maryland Dental School, Baltimore, MD 21201, USA
| | - Ming Zheng
- Department of Neural and Pain Sciences, University of Maryland Dental School, Baltimore, MD 21201, USA
| | | | - Richard H Myers
- Department of Neurology, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118, USA, Genome Science Institute, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Schahram Akbarian
- Brudnick Neuropsychiatric Research Institute, Friedman Brain Institute, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Jiang-Fan Chen
- Department of Neurology, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118, USA,
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Shen EY, Ahern TH, Cheung I, Straubhaar J, Dincer A, Houston I, de Vries GJ, Akbarian S, Forger NG. Epigenetics and sex differences in the brain: A genome-wide comparison of histone-3 lysine-4 trimethylation (H3K4me3) in male and female mice. Exp Neurol 2014; 268:21-9. [PMID: 25131640 DOI: 10.1016/j.expneurol.2014.08.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 07/30/2014] [Accepted: 08/05/2014] [Indexed: 12/11/2022]
Abstract
Many neurological and psychiatric disorders exhibit gender disparities, and sex differences in the brain likely explain some of these effects. Recent work in rodents points to a role for epigenetics in the development or maintenance of neural sex differences, although genome-wide studies have so far been lacking. Here we review the existing literature on epigenetics and brain sexual differentiation and present preliminary analyses on the genome-wide distribution of histone-3 lysine-4 trimethylation in a sexually dimorphic brain region in male and female mice. H3K4me3 is a histone mark primarily organized as 'peaks' surrounding the transcription start site of active genes. We microdissected the bed nucleus of the stria terminalis and preoptic area (BNST/POA) in adult male and female mice and used ChIP-Seq to compare the distribution of H3K4me3 throughout the genome. We found 248 genes and loci with a significant sex difference in H3K4me3. Of these, the majority (71%) had larger H3K4me3 peaks in females. Comparisons with existing databases indicate that genes and loci with increased H3K4me3 in females are associated with synaptic function and with expression atlases from related brain areas. Based on RT-PCR, only a minority of genes with a sex difference in H3K4me3 has detectable sex differences in expression at baseline conditions. Together with previous findings, our data suggest that there may be sex biases in the use of epigenetic marks. Such biases could underlie sex differences in vulnerabilities to drugs or diseases that disrupt specific epigenetic processes.
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Affiliation(s)
- Erica Y Shen
- Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Todd H Ahern
- Center for Behavioral Neuroscience, Department of Psychology, Quinnipiac University, Hamden, CT 06518, USA
| | - Iris Cheung
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Juerg Straubhaar
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Aslihan Dincer
- Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomics Science, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Isaac Houston
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Geert J de Vries
- Neuroscience Institute, Georgia State University, Atlanta, GA 30302, USA
| | - Schahram Akbarian
- Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nancy G Forger
- Neuroscience Institute, Georgia State University, Atlanta, GA 30302, USA.
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Mitchell AC, Bharadwaj R, Whittle C, Krueger W, Mirnics K, Hurd Y, Rasmussen T, Akbarian S. The genome in three dimensions: a new frontier in human brain research. Biol Psychiatry 2014; 75:961-9. [PMID: 23958183 PMCID: PMC3925763 DOI: 10.1016/j.biopsych.2013.07.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 06/16/2013] [Accepted: 07/10/2013] [Indexed: 12/21/2022]
Abstract
Less than 1.5% of the human genome encodes protein. However, vast portions of the human genome are subject to transcriptional and epigenetic regulation, and many noncoding regulatory DNA elements are thought to regulate the spatial organization of interphase chromosomes. For example, chromosomal "loopings" are pivotal for the orderly process of gene expression, by enabling distal regulatory enhancer or silencer elements to directly interact with proximal promoter and transcription start sites, potentially bypassing hundreds of kilobases of interspersed sequence on the linear genome. To date, however, epigenetic studies in the human brain are mostly limited to the exploration of DNA methylation and posttranslational modifications of the nucleosome core histones. In contrast, very little is known about the regulation of supranucleosomal structures. Here, we show that chromosome conformation capture, a widely used approach to study higher-order chromatin, is applicable to tissue collected postmortem, thereby informing about genome organization in the human brain. We introduce chromosome conformation capture protocols for brain and compare higher-order chromatin structures at the chromosome 6p22.2-22.1 schizophrenia and bipolar disorder susceptibility locus, and additional neurodevelopmental risk genes, (DPP10, MCPH1) in adult prefrontal cortex and various cell culture systems, including neurons derived from reprogrammed skin cells. We predict that the exploration of three-dimensional genome architectures and function will open up new frontiers in human brain research and psychiatric genetics and provide novel insights into the epigenetic risk architectures of regulatory noncoding DNA.
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Affiliation(s)
- Amanda C. Mitchell
- Departments of Psychiatry and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Rahul Bharadwaj
- Departments of Psychiatry and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY,Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester MA
| | - Catheryne Whittle
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester MA
| | - Winfried Krueger
- Center for Regenerative Biology and Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT
| | - Karoly Mirnics
- Department of Psychiatry, Vanderbilt University, Nashville, TN
| | - Yasmin Hurd
- Departments of Psychiatry and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Theodore Rasmussen
- Center for Regenerative Biology and Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT
| | - Schahram Akbarian
- Departments of Psychiatry and Neuroscience , Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Brudnick Neuropsychiatric Research Institute , University of Massachusetts Medical School, Worcester, Massachusetts.
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Increased striatal adenosine A2A receptor levels is an early event in Parkinson's disease-related pathology and it is potentially regulated by miR-34b. Neurobiol Dis 2014; 69:206-14. [PMID: 24892887 DOI: 10.1016/j.nbd.2014.05.030] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 05/01/2014] [Accepted: 05/22/2014] [Indexed: 12/20/2022] Open
Abstract
Adenosine A2A receptor (A2AR) is a G-protein coupled receptor that stimulates adenylyl cyclase activity. In the brain, A2ARs are found highly enriched in striatal GABAergic medium spiny neurons, related to the control of voluntary movement. Pharmacological modulation of A2ARs is particularly useful in Parkinson's disease (PD) due to their property of antagonizing dopamine D2 receptor activity. Increases in A2AR levels have been described in PD patients showing an important loss of dopaminergic denervation markers, but no data have been reported about A2AR levels in incidental PD brains. In the present report, we show that increased A2ARs protein levels were also detected in the putamen of incidental PD cases (Braak PD stages 1-2) with respect to age-matched controls. By contrast, A2ARs mRNA levels remained unchanged, suggesting that posttranslational mechanisms could be involved in the regulation of A2ARs. It has been described how miR-34b/c downregulation is an early event in PD cases. We found that miR-34b levels are also significantly reduced in the putamen of incidental PD cases and along disease progression. Given that 3'UTR of A2AR contains a predicted target site for miR-34b, the potential role of this miRNA in protein A2AR levels was assessed. In vitro studies revealed that endogenous A2AR protein levels increased when miR-34b function was blocked using a specific anti-miR-34b. Moreover, using a luciferase reporter assay with point mutations in a miR-34b predicted binding site within the 3'UTR region of A2AR mRNA abolished the effect of the miRNA using a miR-34b mimic. In addition, we showed a reduced percentage of DNA methylation in the 5'UTR region of ADORA2A in advanced PD cases. Overall, these findings reveal that increased A2AR protein levels occur in asymptomatic PD patients and provide new insights into the molecular mechanisms underlying A2AR expression levels along the progression of this neurodegenerative disease.
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Felsani A, Gudmundsson B, Nanni S, Brini E, Moles A, Thormar HG, Estibeiro P, Gaetano C, Capogrossi M, Farsetti A, Jonsson JJ, Guffanti A. Impact of different ChIP-Seq protocols on DNA integrity and quality of bioinformatics analysis results. Brief Funct Genomics 2014; 14:156-62. [DOI: 10.1093/bfgp/elu001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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McCullumsmith RE, Hammond JH, Shan D, Meador-Woodruff JH. Postmortem brain: an underutilized substrate for studying severe mental illness. Neuropsychopharmacology 2014; 39:65-87. [PMID: 24091486 PMCID: PMC3857666 DOI: 10.1038/npp.2013.239] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 07/30/2013] [Accepted: 08/02/2013] [Indexed: 02/08/2023]
Abstract
We propose that postmortem tissue is an underutilized substrate that may be used to translate genetic and/or preclinical studies, particularly for neuropsychiatric illnesses with complex etiologies. Postmortem brain tissues from subjects with schizophrenia have been extensively studied, and thus serve as a useful vehicle for illustrating the challenges associated with this biological substrate. Schizophrenia is likely caused by a combination of genetic risk and environmental factors that combine to create a disease phenotype that is typically not apparent until late adolescence. The complexity of this illness creates challenges for hypothesis testing aimed at understanding the pathophysiology of the illness, as postmortem brain tissues collected from individuals with schizophrenia reflect neuroplastic changes from a lifetime of severe mental illness, as well as treatment with antipsychotic medications. While there are significant challenges with studying postmortem brain, such as the postmortem interval, it confers a translational element that is difficult to recapitulate in animal models. On the other hand, data derived from animal models typically provide specific mechanistic and behavioral measures that cannot be generated using human subjects. Convergence of these two approaches has led to important insights for understanding molecular deficits and their causes in this illness. In this review, we discuss the problem of schizophrenia, review the common challenges related to postmortem studies, discuss the application of biochemical approaches to this substrate, and present examples of postmortem schizophrenia studies that illustrate the role of the postmortem approach for generating important new leads for understanding the pathophysiology of severe mental illness.
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Affiliation(s)
| | - John H Hammond
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama-Birmingham, Birmingham, AL, USA
| | - Dan Shan
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama-Birmingham, Birmingham, AL, USA
| | - James H Meador-Woodruff
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama-Birmingham, Birmingham, AL, USA
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Wockner LF, Noble EP, Lawford BR, Young RM, Morris CP, Whitehall VLJ, Voisey J. Genome-wide DNA methylation analysis of human brain tissue from schizophrenia patients. Transl Psychiatry 2014; 4:e339. [PMID: 24399042 PMCID: PMC3905221 DOI: 10.1038/tp.2013.111] [Citation(s) in RCA: 224] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 10/29/2013] [Indexed: 01/08/2023] Open
Abstract
Recent studies suggest that genetic and environmental factors do not account for all the schizophrenia risk, and epigenetics also has a role in disease susceptibility. DNA methylation is a heritable epigenetic modification that can regulate gene expression. Genome-wide DNA methylation analysis was performed on post-mortem human brain tissue from 24 patients with schizophrenia and 24 unaffected controls. DNA methylation was assessed at over 485,000 CpG sites using the Illumina Infinium HumanMethylation450 Bead Chip. After adjusting for age and post-mortem interval, 4641 probes corresponding to 2929 unique genes were found to be differentially methylated. Of those genes, 1291 were located in a CpG island and 817 were in a promoter region. These include NOS1, AKT1, DTNBP1, DNMT1, PPP3CC and SOX10, which have previously been associated with schizophrenia. More than 100 of these genes overlap with a previous DNA methylation study of peripheral blood from schizophrenia patients in which 27,000 CpG sites were analysed. Unsupervised clustering analysis of the top 3000 most variable probes revealed two distinct groups with significantly more people with schizophrenia in cluster one compared with controls (P=1.74 × 10(-4)). The first cluster composed of 88% of patients with schizophrenia and only 12% controls, whereas the second cluster composed of 27% of patients with schizophrenia and 73% controls. These results strongly suggest that differential DNA methylation is important in schizophrenia etiology and add support for the use of DNA methylation profiles as a future prognostic indicator of schizophrenia.
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Affiliation(s)
- L F Wockner
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - E P Noble
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - B R Lawford
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia,Alcohol and Drug Service, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - R McD Young
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - C P Morris
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - V L J Whitehall
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - J Voisey
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia,Institute of Health and Biomedical Innovation, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000, Australia. E-mail:
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Mitchell A, Roussos P, Peter C, Tsankova N, Akbarian S. The future of neuroepigenetics in the human brain. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 128:199-228. [PMID: 25410546 DOI: 10.1016/b978-0-12-800977-2.00008-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Complex mechanisms shape the genome of brain cells into transcriptional units, clusters of condensed chromatin, and many other features that distinguish between various cell types and developmental stages sharing the same genetic material. Only a few years ago, the field's focus was almost entirely on a single mark, CpG methylation; the emerging complexity of neuronal and glial epigenomes now includes multiple types of DNA cytosine methylation, more than 100 residue-specific posttranslational histone modifications and histone variants, all of which superimposed by a dynamic and highly regulated three-dimensional organization of the chromosomal material inside the cell nucleus. Here, we provide an update on the most innovative approaches in neuroepigenetics and their potential contributions to approach cognitive functions and disorders unique to human. We propose that comprehensive, cell type-specific mappings of DNA and histone modifications, chromatin-associated RNAs, and chromosomal "loopings" and other determinants of three-dimensional genome organization will critically advance insight into the pathophysiology of the disease. For example, superimposing the epigenetic landscapes of neuronal and glial genomes onto genetic maps for complex disorders, ranging from Alzheimer's disease to schizophrenia, could provide important clues about neurological function for some of the risk-associated noncoding sequences in the human genome.
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Affiliation(s)
- Amanda Mitchell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Cyril Peter
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Nadejda Tsankova
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
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Vilahur N, Baccarelli AA, Bustamante M, Agramunt S, Byun HM, Fernandez MF, Sunyer J, Estivill X. Storage conditions and stability of global DNA methylation in placental tissue. Epigenomics 2013; 5:341-8. [PMID: 23750648 DOI: 10.2217/epi.13.29] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
AIM The placenta is an informative and easily available tissue for many epidemiological studies. We analyzed the extent to which storage delay affects DNA methylation. MATERIAL & METHODS Biopsies from two placentas were sequentially stored at -80°C after standing at room temperature for 30 min, 1 h, 2 h, 6 h and 24 h. Global DNA methylation was measured by bisulfite pyrosequencing of repetitive elements and the luminometric methylation assay. RESULTS Small changes in global DNA methylation in relation to time-to-storage were observed by pyrosequencing, with a coefficient of variation (COV) of 2.49% (placenta 1) and 2.86% (placenta 2), similar to the mean technical variation observed for pyrosequencing (COV: 1.91 and 1.51%, respectively). A luminometric methylation assay yielded more variable results in the two placentas analyzed, both among time points (COV: 9.13 and 10.35%, respectively) and technical replicates (COV: 11.60 and 9.80%, respectively). CONCLUSION Global DNA methylation is stable at room temperature. However, some techniques to measure methylation might be confounded by DNA degradation caused by a delay in storage.
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Affiliation(s)
- Nadia Vilahur
- Center for Research in Environmental Epidemiology CREAL, Barcelona, Catalonia, Spain.
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Wang JH, Gouda-Vossos A, Dzamko N, Halliday G, Huang Y. DNA extraction from fresh-frozen and formalin-fixed, paraffin-embedded human brain tissue. Neurosci Bull 2013; 29:649-54. [PMID: 23996594 DOI: 10.1007/s12264-013-1379-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 06/07/2013] [Indexed: 11/25/2022] Open
Abstract
Both fresh-frozen and formalin-fixed, paraffin-embedded (FFPE) human brain tissues are invaluable resources for molecular genetic studies of central nervous system diseases, especially neurodegenerative disorders. To identify the optimal method for DNA extraction from human brain tissue, we compared methods on differently-processed tissues. Fragments of LRRK2 and MAPT (257 bp and 483 bp/245 bp) were amplified for evaluation. We found that for FFPE samples, the success rate of DNA extraction was greater when using a commercial kit than a laboratory-based method (successful DNA extraction from 76% versus 33% of samples). PCR amplicon size and storage period were key factors influencing the success rate of DNA extraction from FFPE samples. In the fresh-frozen samples, the DNA extraction success rate was 100% using either a commercial kit (QIAamp DNA Micro) or a laboratory-based method (sample boiling in 0.1 mol/L NaOH, followed by proteinase K digestion, and then DNA extraction using Chelex-100) regardless of PCR amplicon length or tissue storage time. Although the present results demonstrate that PCR-amplifiable genomic DNA can be extracted from both fresh-frozen and FFPE samples, fresh brain tissue is recommended for DNA extraction in future neuropathological studies.
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Affiliation(s)
- Jian-Hua Wang
- Neuroscience Research Australia and the University of New South Wales, Sydney, 2031, Australia,
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Schroeder FA, Lewis MC, Fass DM, Wagner FF, Zhang YL, Hennig KM, Gale J, Zhao WN, Reis S, Barker DD, Berry-Scott E, Kim SW, Clore EL, Hooker JM, Holson EB, Haggarty SJ, Petryshen TL. A selective HDAC 1/2 inhibitor modulates chromatin and gene expression in brain and alters mouse behavior in two mood-related tests. PLoS One 2013; 8:e71323. [PMID: 23967191 PMCID: PMC3743770 DOI: 10.1371/journal.pone.0071323] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 06/27/2013] [Indexed: 12/31/2022] Open
Abstract
Psychiatric diseases, including schizophrenia, bipolar disorder and major depression, are projected to lead global disease burden within the next decade. Pharmacotherapy, the primary – albeit often ineffective – treatment method, has remained largely unchanged over the past 50 years, highlighting the need for novel target discovery and improved mechanism-based treatments. Here, we examined in wild type mice the impact of chronic, systemic treatment with Compound 60 (Cpd-60), a slow-binding, benzamide-based inhibitor of the class I histone deacetylase (HDAC) family members, HDAC1 and HDAC2, in mood-related behavioral assays responsive to clinically effective drugs. Cpd-60 treatment for one week was associated with attenuated locomotor activity following acute amphetamine challenge. Further, treated mice demonstrated decreased immobility in the forced swim test. These changes are consistent with established effects of clinical mood stabilizers and antidepressants, respectively. Whole-genome expression profiling of specific brain regions (prefrontal cortex, nucleus accumbens, hippocampus) from mice treated with Cpd-60 identified gene expression changes, including a small subset of transcripts that significantly overlapped those previously reported in lithium-treated mice. HDAC inhibition in brain was confirmed by increased histone acetylation both globally and, using chromatin immunoprecipitation, at the promoter regions of upregulated transcripts, a finding consistent with in vivo engagement of HDAC targets. In contrast, treatment with suberoylanilide hydroxamic acid (SAHA), a non-selective fast-binding, hydroxamic acid HDAC 1/2/3/6 inhibitor, was sufficient to increase histone acetylation in brain, but did not alter mood-related behaviors and had dissimilar transcriptional regulatory effects compared to Cpd-60. These results provide evidence that selective inhibition of HDAC1 and HDAC2 in brain may provide an epigenetic-based target for developing improved treatments for mood disorders and other brain disorders with altered chromatin-mediated neuroplasticity.
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Affiliation(s)
- Frederick A. Schroeder
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Psychiatry, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Department of Radiology, Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Michael C. Lewis
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Daniel M. Fass
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Florence F. Wagner
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Yan-Ling Zhang
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Krista M. Hennig
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Jennifer Gale
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Wen-Ning Zhao
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Surya Reis
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Douglas D. Barker
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Erin Berry-Scott
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Sung Won Kim
- Medical Department, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Elizabeth L. Clore
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Jacob M. Hooker
- Department of Radiology, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Department of Radiology, Harvard Medical School, Charlestown, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Edward B. Holson
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Stephen J. Haggarty
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Psychiatry, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- * E-mail: (SJH); (TLP)
| | - Tracey L. Petryshen
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Psychiatry, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- * E-mail: (SJH); (TLP)
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Shulha HP, Cheung I, Guo Y, Akbarian S, Weng Z. Coordinated cell type-specific epigenetic remodeling in prefrontal cortex begins before birth and continues into early adulthood. PLoS Genet 2013; 9:e1003433. [PMID: 23593028 PMCID: PMC3623761 DOI: 10.1371/journal.pgen.1003433] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 02/20/2013] [Indexed: 11/21/2022] Open
Abstract
Development of prefrontal and other higher-order association cortices is associated with widespread changes in the cortical transcriptome, particularly during the transitions from prenatal to postnatal development, and from early infancy to later stages of childhood and early adulthood. However, the timing and longitudinal trajectories of neuronal gene expression programs during these periods remain unclear in part because of confounding effects of concomitantly occurring shifts in neuron-to-glia ratios. Here, we used cell type–specific chromatin sorting techniques for genome-wide profiling of a histone mark associated with transcriptional regulation—H3 with trimethylated lysine 4 (H3K4me3)—in neuronal chromatin from 31 subjects from the late gestational period to 80 years of age. H3K4me3 landscapes of prefrontal neurons were developmentally regulated at 1,157 loci, including 768 loci that were proximal to transcription start sites. Multiple algorithms consistently revealed that the overwhelming majority and perhaps all of developmentally regulated H3K4me3 peaks were on a unidirectional trajectory defined by either rapid gain or loss of histone methylation during the late prenatal period and the first year after birth, followed by similar changes but with progressively slower kinetics during early and later childhood and only minimal changes later in life. Developmentally downregulated H3K4me3 peaks in prefrontal neurons were enriched for Paired box (Pax) and multiple Signal Transducer and Activator of Transcription (STAT) motifs, which are known to promote glial differentiation. In contrast, H3K4me3 peaks subject to a progressive increase in maturing prefrontal neurons were enriched for activating protein-1 (AP-1) recognition elements that are commonly associated with activity-dependent regulation of neuronal gene expression. We uncovered a developmental program governing the remodeling of neuronal histone methylation landscapes in the prefrontal cortex from the late prenatal period to early adolescence, which is linked to cis-regulatory sequences around transcription start sites. Prolonged maturation of the human cerebral cortex, which extends into the third decade of life, is critical for proper development of executive functions such as higher-order problem-solving and complex cognition. Little is known about changes of post-mitotic neurons during this prolonged maturation period, including changes in epigenetic regulation, and more broadly, in genome organization and function. Such knowledge is critical for a deeper understanding of human development, cognitive abilities, and psychiatric diseases. Here, we identify 1,157 genomic loci in neuronal cells from the prefrontal cortex that show developmental changes in a chromatin mark, histone H3 trimethylated at lysine 4 (H3K4me3), which has been associated with regulation of gene expression. Interestingly, the overwhelming majority of these developmentally regulated H3K4me3 peaks were defined by rapid gain or loss of histone methylation during the late prenatal period and the first year after birth, followed by slower changes during early and later childhood and minimal changes thereafter. The genomic sequences showing these dynamic changes in H3K4me3 were enriched with distinct transcription factor motifs. Our findings suggest that there is highly regulated, pre-programmed remodeling of neuronal histone methylation landscapes in the human brain that begins before birth and continues into adolescence.
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Affiliation(s)
- Hennady P. Shulha
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Iris Cheung
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Yin Guo
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Schahram Akbarian
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Departments of Psychiatry and Neuroscience, Mount Sinai School of Medicine, New York, New York, United States of America
- * E-mail: (SA); (ZW)
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail: (SA); (ZW)
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Villar-Menéndez I, Blanch M, Tyebji S, Pereira-Veiga T, Albasanz JL, Martín M, Ferrer I, Pérez-Navarro E, Barrachina M. Increased 5-Methylcytosine and Decreased 5-Hydroxymethylcytosine Levels are Associated with Reduced Striatal A2AR Levels in Huntington’s Disease. Neuromolecular Med 2013; 15:295-309. [DOI: 10.1007/s12017-013-8219-0] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 01/24/2013] [Indexed: 12/22/2022]
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Abstract
Many cellular constituents in the human brain permanently exit from the cell cycle during pre- or early postnatal development, but little is known about epigenetic regulation of neuronal and glial epigenomes during maturation and aging, including changes in mood and psychosis spectrum disorders and other cognitive or emotional disease. Here, we summarize the current knowledge base as it pertains to genome organization in the human brain, including the regulation of DNA cytosine methylation and hydroxymethylation, and a subset of (altogether >100) residue-specific histone modifications associated with gene expression, and silencing and various other functional chromatin states. We propose that high-resolution mapping of epigenetic markings in postmortem brain tissue or neural cultures derived from induced pluripotent cells (iPS), in conjunction with transcriptome profiling and whole-genome sequencing, will increasingly be used to define the molecular pathology of specific cases diagnosed with depression, schizophrenia, autism, or other major psychiatric disease. We predict that these highly integrative explorations of genome organization and function will provide an important alternative to conventional approaches in human brain studies, which mainly are aimed at uncovering group effects by diagnosis but generally face limitations because of cohort size.
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Shulha HP, Crisci JL, Reshetov D, Tushir JS, Cheung I, Bharadwaj R, Chou HJ, Houston IB, Peter CJ, Mitchell AC, Yao WD, Myers RH, Chen JF, Preuss TM, Rogaev EI, Jensen JD, Weng Z, Akbarian S. Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. PLoS Biol 2012; 10:e1001427. [PMID: 23185133 PMCID: PMC3502543 DOI: 10.1371/journal.pbio.1001427] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 10/12/2012] [Indexed: 11/18/2022] Open
Abstract
Cognitive abilities and disorders unique to humans are thought to result from adaptively driven changes in brain transcriptomes, but little is known about the role of cis-regulatory changes affecting transcription start sites (TSS). Here, we mapped in human, chimpanzee, and macaque prefrontal cortex the genome-wide distribution of histone H3 trimethylated at lysine 4 (H3K4me3), an epigenetic mark sharply regulated at TSS, and identified 471 sequences with human-specific enrichment or depletion. Among these were 33 loci selectively methylated in neuronal but not non-neuronal chromatin from children and adults, including TSS at DPP10 (2q14.1), CNTN4 and CHL1 (3p26.3), and other neuropsychiatric susceptibility genes. Regulatory sequences at DPP10 and additional loci carried a strong footprint of hominid adaptation, including elevated nucleotide substitution rates and regulatory motifs absent in other primates (including archaic hominins), with evidence for selective pressures during more recent evolution and adaptive fixations in modern populations. Chromosome conformation capture at two neurodevelopmental disease loci, 2q14.1 and 16p11.2, revealed higher order chromatin structures resulting in physical contact of multiple human-specific H3K4me3 peaks spaced 0.5-1 Mb apart, in conjunction with a novel cis-bound antisense RNA linked to Polycomb repressor proteins and downregulated DPP10 expression. Therefore, coordinated epigenetic regulation via newly derived TSS chromatin could play an important role in the emergence of human-specific gene expression networks in brain that contribute to cognitive functions and neurological disease susceptibility in modern day humans.
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Affiliation(s)
- Hennady P. Shulha
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jessica L. Crisci
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Denis Reshetov
- Department of Human Genetics and Genomics, Vavilov Institute of General Genetics, Moscow, Russian Federation
| | - Jogender S. Tushir
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Iris Cheung
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Rahul Bharadwaj
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Hsin-Jung Chou
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Isaac B. Houston
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Cyril J. Peter
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Amanda C. Mitchell
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Wei-Dong Yao
- New England Primate Center, Southboro, Massachusetts, United States of America
| | - Richard H. Myers
- Department of Neurology, Boston University, Boston, Massachusetts, United States of America
| | - Jiang-fan Chen
- Department of Neurology, Boston University, Boston, Massachusetts, United States of America
| | - Todd M. Preuss
- Yerkes National Primate Research Center/Emory University, Atlanta, Georgia, United States of America
| | - Evgeny I. Rogaev
- Department of Human Genetics and Genomics, Vavilov Institute of General Genetics, Moscow, Russian Federation
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow, Russian Federation
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation
| | - Jeffrey D. Jensen
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Schahram Akbarian
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Departments of Psychiatry and Neuroscience, Friedman Brain Institute, Mount Sinai School of Medicine, New York, New York, United States of America
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Effects of histone modifications on increased expression of polyamine biosynthetic genes in suicide. Int J Neuropsychopharmacol 2012; 15:1161-6. [PMID: 22008221 DOI: 10.1017/s1461145711001520] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Altered polyamine metabolism has been consistently observed as underlying the suicide process. We recently performed a global analysis of polyamine gene expression across the brains of suicide completers, and identified up-regulation of four genes, arginase II (ARG2), S-adenosylmethionine decarboxylase (AMD1), and antizymes 1 and 2 (OAZ1 and OAZ2), which play essential roles in polyamine biosynthesis. To determine if a shared epigenetic mechanism is involved in their overexpression in the prefrontal cortex, we measured promoter levels of tri-methyl modified histone-3-lysine-4 (H3K4me3), a marker of open chromatin, and assessed its association with suicide and gene expression. We identified increased H3K4me3 in the promoter region of OAZ1 in suicide, and found that H3K4me3 was correlated with the expression of OAZ1 and ARG2. Overall, our findings indicate that the H3K4me3 modification plays an important role in the regulation of polyamine biosynthesis, and that this mechanism may be involved in the neurobiology of suicide.
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Labrie V, Pai S, Petronis A. Epigenetics of major psychosis: progress, problems and perspectives. Trends Genet 2012; 28:427-35. [PMID: 22622229 PMCID: PMC3422438 DOI: 10.1016/j.tig.2012.04.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 04/03/2012] [Accepted: 04/23/2012] [Indexed: 01/26/2023]
Abstract
Understanding the origins of normal and pathological behavior is one of the most exciting opportunities in contemporary biomedical research. There is increasing evidence that, in addition to DNA sequence and the environment, epigenetic modifications of DNA and histone proteins may contribute to complex phenotypes. Inherited and/or acquired epigenetic factors are partially stable and have regulatory roles in numerous genomic activities, thus making epigenetics a promising research path in etiological studies of psychiatric disease. In this article, we review recent epigenetic studies examining the brain and other tissues, including those from individuals with schizophrenia (SCZ) and bipolar disorder (BPD). We also highlight heuristic aspects of the epigenetic theory of psychiatric disease and discuss the future directions of psychiatric epigenetics.
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Affiliation(s)
- Viviane Labrie
- The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, 250 College Street, Toronto, ONT, M5T 1R8, Canada
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Kurita M, Holloway T, García-Bea A, Kozlenkov A, Friedman AK, Moreno JL, Heshmati M, Golden SA, Kennedy PJ, Takahashi N, Dietz DM, Mocci G, Gabilondo AM, Hanks J, Umali A, Callado LF, Gallitano AL, Neve RL, Shen L, Buxbaum JD, Han MH, Nestler EJ, Meana JJ, Russo SJ, González-Maeso J. HDAC2 regulates atypical antipsychotic responses through the modulation of mGlu2 promoter activity. Nat Neurosci 2012; 15:1245-54. [PMID: 22864611 PMCID: PMC3431440 DOI: 10.1038/nn.3181] [Citation(s) in RCA: 213] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 07/05/2012] [Indexed: 02/08/2023]
Abstract
Histone deacetylases (HDACs) compact chromatin structure and repress gene transcription. In schizophrenia, clinical studies demonstrate that HDAC inhibitors are efficacious when given in combination with atypical antipsychotics. However, the molecular mechanism that integrates a better response to antipsychotics with changes in chromatin structure remains unknown. Here we found that chronic atypical antipsychotics downregulated the transcription of metabotropic glutamate 2 receptor (mGlu2, also known as Grm2), an effect that was associated with decreased histone acetylation at its promoter in mouse and human frontal cortex. This epigenetic change occurred in concert with a serotonin 5-HT(2A) receptor-dependent upregulation and increased binding of HDAC2 to the mGlu2 promoter. Virally mediated overexpression of HDAC2 in frontal cortex decreased mGlu2 transcription and its electrophysiological properties, thereby increasing psychosis-like behavior. Conversely, HDAC inhibitors prevented the repressive histone modifications induced at the mGlu2 promoter by atypical antipsychotics, and augmented their therapeutic-like effects. These observations support the view of HDAC2 as a promising new target for schizophrenia treatment.
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Affiliation(s)
- Mitsumasa Kurita
- Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, USA
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Gavin DP, Akbarian S. Epigenetic and post-transcriptional dysregulation of gene expression in schizophrenia and related disease. Neurobiol Dis 2012; 46:255-62. [DOI: 10.1016/j.nbd.2011.12.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 11/10/2011] [Accepted: 12/04/2011] [Indexed: 12/22/2022] Open
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Barrachina M, Moreno J, Villar-Menéndez I, Juvés S, Ferrer I. Histone tail acetylation in brain occurs in an unpredictable fashion after death. Cell Tissue Bank 2011; 13:597-606. [PMID: 21922206 DOI: 10.1007/s10561-011-9278-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Accepted: 09/08/2011] [Indexed: 10/17/2022]
Abstract
Histone acetylation plays a role in the regulation of gene transcription. Yet it is not known whether post-mortem brain tissue is suitable for the analysis of histone acetylation. To examine this question, nucleosomes were isolated from frontal cortex of nine subjects which were obtained at short times after death and immediately frozen at -80°C or maintained at room temperature from 3 h up to 50 h after death and then frozen at -80°C to mimic variable post-mortem delay in tissue processing as currently occurs in normal practice. Chromatin immunoprecipitation assays were performed for two lysine residues, H3K9ac and H3K27ac. Four gene loci were amplified by SyBrGreen PCR: Adenosine A(2A) receptor, UCHL1, α-synuclein and β-globin. Results showed variability in the histone acetylation level along the post-mortem times and an increase in the acetylation level at an unpredictable time from one case to another and from one gene to another within the first 24 h of post-mortem delay. Similar results were found with three rat brains used to exclude the effects of agonal state and to normalize the start-point as real time zero. Therefore, the present observations show that human post-mortem brain is probably not suitable for comparative studies of histone acetylation.
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Affiliation(s)
- Marta Barrachina
- Institute of Neuropathology, [Bellvitge Biomedical Research Institute-] IDIBELL, Bellvitge University Hospital-ICS, c/Feixa Llarga s/n, 08908 L'Hospitalet de Llobregat, Spain.
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Fiori LM, Turecki G. Epigenetic regulation of spermidine/spermine N1-acetyltransferase (SAT1) in suicide. J Psychiatr Res 2011; 45:1229-35. [PMID: 21501848 DOI: 10.1016/j.jpsychires.2011.03.015] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 03/02/2011] [Accepted: 03/24/2011] [Indexed: 02/04/2023]
Abstract
We have recently shown that the expression of spermidine/spermine N1-acetyltransferase (SAT1) is downregulated across the brains of suicide completers, and that its expression is influenced by genetic variations in the promoter. Several promoter polymorphisms in SAT1, including rs6526342, have been associated with suicide and other psychiatric disorders, and display haplotype-specific effects on expression. However, these effects cannot explain total variability in SAT1 expression, and other regulatory mechanisms, such as epigenetic factors, may also be at play. In this study, we assessed the involvement of epigenetic factors in controlling SAT1 expression in the prefrontal cortex of suicide completers by mapping CpG methylation across a 1880-bp region of the SAT1 promoter, and measuring levels of tri-methylated histone-3-lysine 27 (H3K27me3) at the promoter in suicide completers and controls. Our results demonstrated that CpG methylation was significantly negatively correlated with SAT1 expression. Although overall or site-specific CpG methylation was not associated with suicide or SAT1 expression, we observed high levels of methylation at the polymorphic CpG site created by rs6526342, indicating a relationship between promoter haplotypes and methylation. There was no association between H3K27me3 and suicide, nor was this modification associated with SAT1 expression. Overall, our results indicate that epigenetic factors in the promoter region of SAT1 influence gene expression levels, and may provide a mechanism for both our previous findings of haplotype-specific effects of promoter variations on SAT1 expression, as well as the widespread downregulation of SAT1 expression observed in the brains of suicide completers.
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Affiliation(s)
- Laura M Fiori
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada
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48
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Jiang Y, Matevossian A, Guo Y, Akbarian S. Setdb1-mediated histone H3K9 hypermethylation in neurons worsens the neurological phenotype of Mecp2-deficient mice. Neuropharmacology 2011; 60:1088-97. [PMID: 20869373 PMCID: PMC3025056 DOI: 10.1016/j.neuropharm.2010.09.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 09/03/2010] [Accepted: 09/16/2010] [Indexed: 12/26/2022]
Abstract
Rett syndrome (RTT, OMIM # 312750), a neurodevelopmental disorder of early childhood, is primarily caused by mutations in the gene encoding methyl-CpG-binding protein 2 (MECP2). Various molecular functions have been ascribed to MECP2, including the regulation of histone modifications associated with repressive chromatin remodeling, but the role of these mechanisms for the pathophysiology of RTT remains unclear. Here, we explore whether or not neuronal expression of the histone H3-lysine 9 specific methyl-transferase, Setdb1 (Set domain, bifurcated 1)/Eset/Kmt1e, which is normally present only at low levels in differentiated neurons, rescues the RTT-like phenotype of Mecp2-deficient mice. A myc-tagged Setdb1 cDNA was expressed through the tau locus for ubiquitous expression in CNS neurons, or under control of the calcium/calmodulin-dependent protein kinase II (CK) promoter to selectively target postmitotic neurons in forebrain. However, the CK-Setdb1 transgene lead to an enhanced neurological deficit, and the tauSetdb1 allele further shortened life span of mice with a brain-wide deletion of Mecp2 during prenatal development. In contrast, no neurological deficits or premature death was observed in CK-Setdb1 and tauSetdb1 mice expressing wildtype Mecp2. However, levels of trimethylated H3K9 at pericentromeric repeats were fully maintained in differentiated neurons from symptomatic Mecp2 null mutant mice. Based on these results, we draw two conclusions: First, neuronal chromatin in RTT brain is not affected by a generalized deficit in H3K9 trimethylation. Second, artificial up-regulation of this repressive chromatin mark via Setdb1 gene delivery specifically to neurons is harmful for the Mecp2-deficient brain. This article is part of a Special Issue entitled 'Trends in neuropharmacology: in memory of Erminio Costa'.
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Affiliation(s)
- Yan Jiang
- Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester MA
- Graduate School of Biomedical Sciences, University of Massachusetts Medical School, Worcester MA
| | - Anouch Matevossian
- Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester MA
| | - Yin Guo
- Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester MA
| | - Schahram Akbarian
- Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester MA
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Yuferov V, Nielsen DA, Levran O, Randesi M, Hamon S, Ho A, Morgello S, Kreek MJ. Tissue-specific DNA methylation of the human prodynorphin gene in post-mortem brain tissues and PBMCs. Pharmacogenet Genomics 2011; 21:185-96. [PMID: 20808262 PMCID: PMC3017726 DOI: 10.1097/fpc.0b013e32833eecbc] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Dynorphins, the endogenous ligands for the κ opioid receptor, are implicated in neuropsychiatric disorders through modulation of basal and stimuli-induced dopaminergic, glutamatergic, and serotonergic tones. Expression of the prodynorphin gene (PDYN) is critical for rewarding properties of drugs of abuse and stress-induced responses. Epigenetic factors, such as DNA methylation, play an important role in modulation of gene expression. METHODS We analyzed DNA methylation patterns of three CpG-rich regions of PDYN, a CpG island, and cluster A in the proximal promoter, and cluster B in coding exon 4, by bisulfite sequencing of DNA from the caudate and anterior cingulate cortex from post-mortem brain of 35 individuals (22 HIV seropositive), and in peripheral blood mononuclear cells from 21 of these individuals. RESULTS We found remarkably similar patterns of methylation across CpG sites in these tissues. However, there were tissue-specific differences in methylation levels (P=0.000001) of the CpG island: higher levels in peripheral blood mononuclear cells (82%) than in the brain tissues, the caudate (62%), and the anterior cingulate cortex (44%). But there was higher PDYN expression in the caudate than in the anterior cingulate cortex. In contrast, cluster A near the transcription start site is hypomethylated. CONCLUSION This DNA methylation profile of the PDYN gene is typical for primary responsive genes with regulatory elements for both basal and tissue-specific transcription. Our findings provide a rationale for further studies of the role of other epigenetic factors in the regulation of PDYN expression in individuals with psychiatric and neurological disorders.
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Affiliation(s)
- Vadim Yuferov
- The Laboratory of the Biology of Addictive Diseases, The Rockefeller University, Box 171, 1230 York Avenue, New York, NY 10065, USA.
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The epigenetic effects of antidepressant treatment on human prefrontal cortex BDNF expression. Int J Neuropsychopharmacol 2011; 14:427-9. [PMID: 21134314 DOI: 10.1017/s1461145710001422] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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