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Tsang E, Han VX, Flutter C, Alshammery S, Keating BA, Williams T, Gloss BS, Graham ME, Aryamanesh N, Pang I, Wong M, Winlaw D, Cardamone M, Mohammad S, Gold W, Patel S, Dale RC. Ketogenic diet modifies ribosomal protein dysregulation in KMT2D Kabuki syndrome. EBioMedicine 2024; 104:105156. [PMID: 38768529 PMCID: PMC11134553 DOI: 10.1016/j.ebiom.2024.105156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Kabuki syndrome (KS) is a genetic disorder caused by DNA mutations in KMT2D, a lysine methyltransferase that methylates histones and other proteins, and therefore modifies chromatin structure and subsequent gene expression. Ketones, derived from the ketogenic diet, are histone deacetylase inhibitors that can 'open' chromatin and encourage gene expression. Preclinical studies have shown that the ketogenic diet rescues hippocampal memory neurogenesis in mice with KS via the epigenetic effects of ketones. METHODS Single-cell RNA sequencing and mass spectrometry-based proteomics were used to explore molecular mechanisms of disease in individuals with KS (n = 4) versus controls (n = 4). FINDINGS Pathway enrichment analysis indicated that loss of function mutations in KMT2D are associated with ribosomal protein dysregulation at an RNA and protein level in individuals with KS (FDR <0.05). Cellular proteomics also identified immune dysregulation and increased abundance of other lysine modification and histone binding proteins, representing a potential compensatory mechanism. A 12-year-old boy with KS, suffering from recurrent episodes of cognitive decline, exhibited improved cognitive function and neuropsychological assessment performance after 12 months on the ketogenic diet, with concomitant improvement in transcriptomic ribosomal protein dysregulation. INTERPRETATION Our data reveals that lysine methyltransferase deficiency is associated with ribosomal protein dysfunction, with secondary immune dysregulation. Diet and the production of bioactive molecules such as ketone bodies serve as a significant environmental factor that can induce epigenetic changes and improve clinical outcomes. Integrating transcriptomic, proteomic, and clinical data can define mechanisms of disease and treatment effects in individuals with neurodevelopmental disorders. FUNDING This study was supported by the Dale NHMRC Investigator Grant (APP1193648) (R.D), Petre Foundation (R.D), and The Sydney Children's Hospital Foundation/Kids Research Early and Mid-Career Researcher Grant (E.T).
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Affiliation(s)
- Erica Tsang
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Velda X Han
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore; Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chloe Flutter
- The Kabuki Syndrome Foundation - Volunteer, Northbrook, IL, USA
| | - Sarah Alshammery
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Brooke A Keating
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Tracey Williams
- Kids Rehab, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Brian S Gloss
- Westmead Research Hub, Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Mark E Graham
- Biomedical Proteomics, Children's Medical Research Institute, The University of Sydney, Australia
| | - Nader Aryamanesh
- Bioinformatics Group, Children's Medical Research Institute, Westmead, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Ignatius Pang
- Bioinformatics Group, Children's Medical Research Institute, Westmead, Sydney, NSW, Australia
| | - Melanie Wong
- The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - David Winlaw
- Heart Centre, Ann and Robert H. Lurie Children's Hospital of Chicago and Feinberg School of Medicine, Northwestern University, USA
| | - Michael Cardamone
- Sydney Children's Hospital, Randwick, NSW, Australia; School of Clinical Medicine, University of New South Wales, NSW, Australia
| | - Shekeeb Mohammad
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Wendy Gold
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW, Australia; Molecular Neurobiology Research Laboratory, Kids Research, The Children's Hospital at Westmead & the Children's Medical Research Institute, NSW, Australia
| | - Shrujna Patel
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Russell C Dale
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; The Brain and Mind Centre, The University of Sydney, Sydney, NSW, Australia.
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Zhu B, Ainsworth RI, Wang Z, Liu Z, Sierra S, Deng C, Callado LF, Meana JJ, Wang W, Lu C, González-Maeso J. Antipsychotic-induced epigenomic reorganization in frontal cortex of individuals with schizophrenia. eLife 2024; 12:RP92393. [PMID: 38648100 PMCID: PMC11034945 DOI: 10.7554/elife.92393] [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] [Indexed: 04/25/2024] Open
Abstract
Genome-wide association studies have revealed >270 loci associated with schizophrenia risk, yet these genetic factors do not seem to be sufficient to fully explain the molecular determinants behind this psychiatric condition. Epigenetic marks such as post-translational histone modifications remain largely plastic during development and adulthood, allowing a dynamic impact of environmental factors, including antipsychotic medications, on access to genes and regulatory elements. However, few studies so far have profiled cell-specific genome-wide histone modifications in postmortem brain samples from schizophrenia subjects, or the effect of antipsychotic treatment on such epigenetic marks. Here, we conducted ChIP-seq analyses focusing on histone marks indicative of active enhancers (H3K27ac) and active promoters (H3K4me3), alongside RNA-seq, using frontal cortex samples from antipsychotic-free (AF) and antipsychotic-treated (AT) individuals with schizophrenia, as well as individually matched controls (n=58). Schizophrenia subjects exhibited thousands of neuronal and non-neuronal epigenetic differences at regions that included several susceptibility genetic loci, such as NRG1, DISC1, and DRD3. By analyzing the AF and AT cohorts separately, we identified schizophrenia-associated alterations in specific transcription factors, their regulatees, and epigenomic and transcriptomic features that were reversed by antipsychotic treatment; as well as those that represented a consequence of antipsychotic medication rather than a hallmark of schizophrenia in postmortem human brain samples. Notably, we also found that the effect of age on epigenomic landscapes was more pronounced in frontal cortex of AT-schizophrenics, as compared to AF-schizophrenics and controls. Together, these data provide important evidence of epigenetic alterations in the frontal cortex of individuals with schizophrenia, and remark for the first time on the impact of age and antipsychotic treatment on chromatin organization.
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Affiliation(s)
- Bohan Zhu
- Department of Chemical Engineering, Virginia TechBlacksburgUnited States
| | - Richard I Ainsworth
- Department of Chemistry and Biochemistry, University of California, San DiegoLa JollaUnited States
| | - Zengmiao Wang
- Department of Chemistry and Biochemistry, University of California, San DiegoLa JollaUnited States
| | - Zhengzhi Liu
- Department of Biomedical Engineering and Mechanics, Virginia TechBlacksburgUnited States
| | - Salvador Sierra
- Department of Physiology and Biophysics, Virginia Commonwealth University School of MedicineRichmondUnited States
| | - Chengyu Deng
- Department of Chemical Engineering, Virginia TechBlacksburgUnited States
| | - Luis F Callado
- Department of Pharmacology, University of the Basque Country UPV/EHU, CIBERSAM, Biocruces Health Research InstituteBizkaiaSpain
| | - J Javier Meana
- Department of Pharmacology, University of the Basque Country UPV/EHU, CIBERSAM, Biocruces Health Research InstituteBizkaiaSpain
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San DiegoLa JollaUnited States
- Department of Cellular and Molecular Medicine, University of California, San DiegoLa JollaUnited States
| | - Chang Lu
- Department of Chemical Engineering, Virginia TechBlacksburgUnited States
| | - Javier González-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University School of MedicineRichmondUnited States
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Lee BK, Salamah J, Cheeran E, Adu-Gyamfi EA. Dynamic and distinct histone modifications facilitate human trophoblast lineage differentiation. Sci Rep 2024; 14:4505. [PMID: 38402275 PMCID: PMC10894295 DOI: 10.1038/s41598-024-55189-0] [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: 12/08/2023] [Accepted: 02/21/2024] [Indexed: 02/26/2024] Open
Abstract
The placenta serves as an essential organ for fetal growth throughout pregnancy. Histone modification is a crucial regulatory mechanism involved in numerous biological processes and development. Nevertheless, there remains a significant gap in our understanding regarding the epigenetic regulations that influence trophoblast lineage differentiation, a fundamental aspect of placental development. Here, through comprehensive mapping of H3K4me3, H3K27me3, H3K9me3, and H3K27ac loci during the differentiation of trophoblast stem cells (TSCs) into syncytiotrophoblasts (STs) and extravillous trophoblasts (EVTs), we reveal dynamic reconfiguration in H3K4me3 and H3K27ac patterns that establish an epigenetic landscape conducive to proper trophoblast lineage differentiation. We observe that broad H3K4me3 domains are associated with trophoblast lineage-specific gene expression. Unlike embryonic stem cells, TSCs lack robust bivalent domains. Notably, the repression of ST- and EVT-active genes in TSCs is primarily attributed to the weak H3K4me3 signal rather than bivalent domains. We also unveil the inactivation of TSC enhancers precedes the activation of ST enhancers during ST formation. Our results provide a comprehensive global map of diverse histone modifications, elucidating the dynamic histone modifications during trophoblast lineage differentiation.
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Affiliation(s)
- Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, 12144, USA.
| | - Joudi Salamah
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, 12144, USA
| | - Elisha Cheeran
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, 12144, USA
| | - Enoch Appiah Adu-Gyamfi
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, 12144, USA
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4
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Kent D, Marchetti L, Mikulasova A, Russell LJ, Rico D. Broad H3K4me3 domains: Maintaining cellular identity and their implication in super-enhancer hijacking. Bioessays 2023; 45:e2200239. [PMID: 37350339 DOI: 10.1002/bies.202200239] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023]
Abstract
The human and mouse genomes are complex from a genomic standpoint. Each cell has the same genomic sequence, yet a wide array of cell types exists due to the presence of a plethora of regulatory elements in the non-coding genome. Recent advances in epigenomic profiling have uncovered non-coding gene proximal promoters and distal enhancers of transcription genome-wide. Extension of promoter-associated H3K4me3 histone mark across the gene body, known as a broad H3K4me3 domain (H3K4me3-BD), is a signature of constitutive expression of cell-type-specific regulation and of tumour suppressor genes in healthy cells. Recently, it has been discovered that the presence of H3K4me3-BDs over oncogenes is a cancer-specific feature associated with their dysregulated gene expression and tumourigenesis. Moreover, it has been shown that the hijacking of clusters of enhancers, known as super-enhancers (SE), by proto-oncogenes results in the presence of H3K4me3-BDs over the gene body. Therefore, H3K4me3-BDs and SE crosstalk in healthy and cancer cells therefore represents an important mechanism to identify future treatments for patients with SE driven cancers.
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Affiliation(s)
- Daniel Kent
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Letizia Marchetti
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Aneta Mikulasova
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Lisa J Russell
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel Rico
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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5
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Patel PJ, Ren Y, Yan Z. Epigenomic analysis of Alzheimer's disease brains reveals diminished CTCF binding on genes involved in synaptic organization. Neurobiol Dis 2023; 184:106192. [PMID: 37302762 PMCID: PMC10519202 DOI: 10.1016/j.nbd.2023.106192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/13/2023] Open
Abstract
Epigenetic aberrations are suggested to play an important role in transcriptional alterations in Alzheimer's disease (AD). One of the key mechanisms of epigenetic regulation of gene expression is through the dynamic organization of chromatin structure via the master genome architecture protein, CCCTC-binding factor (CTCF). By forming chromatin loops, CTCF can influence gene transcription in a complex manner. To find out whether genome-wide DNA binding sites for CTCF are altered in AD, we compared CTCF chromatin immunoprecipitation sequencing (ChIP-Seq) data from frontal cortex of human AD patients and normal controls (n = 9 pairs, all females). We have revealed that CTCF-binding affinity on many genes is significantly reduced in AD patients, and these genes are enriched in synaptic organization, cell adhesion, and actin cytoskeleton, including synaptic scaffolding molecules and receptors, such as SHANK2, HOMER1, NRXN1, CNTNAP2 and GRIN2A, and protocadherin (PCDH) and cadherin (CDH) family members. By comparing transcriptomic data from AD patients, we have discovered that many of the synaptic and adhesion genes with reduced CTCF binding in AD are significantly reduced in their mRNA expression. Moreover, a significant overlap of genes with the diminished CTCF binding and the reduced H3K27ac is identified in AD, with the common genes enriched in synaptic organization. These data suggest that the CTCF-controlled 3D chromatin organization is perturbed in AD, which may be linked to the diminished expression of target genes, probably through changes in histone modification.
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Affiliation(s)
- Prachetas J Patel
- Department of Physiology and Biophysics, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Yong Ren
- Department of Physiology and Biophysics, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Zhen Yan
- Department of Physiology and Biophysics, State University of New York at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA.
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Chow JC, Hormozdiari F. Prediction of Neurodevelopmental Disorders Based on De Novo Coding Variation. J Autism Dev Disord 2023; 53:963-976. [PMID: 35596027 PMCID: PMC9986216 DOI: 10.1007/s10803-022-05586-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2022] [Indexed: 11/27/2022]
Abstract
The early detection of neurodevelopmental disorders (NDDs) can significantly improve patient outcomes. The differential burden of non-synonymous de novo mutation among NDD cases and controls indicates that de novo coding variation can be used to identify a subset of samples that will likely display an NDD phenotype. Thus, we have developed an approach for the accurate prediction of NDDs with very low false positive rate (FPR) using de novo coding variation for a small subset of cases. We use a shallow neural network that integrates de novo likely gene-disruptive and missense variants, measures of gene constraint, and conservation information to predict a small subset of NDD cases at very low FPR and prioritizes NDD risk genes for future clinical study.
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Affiliation(s)
- Julie C Chow
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
| | - Fereydoun Hormozdiari
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA.
- MIND Institute, University of California, Davis, 95817, USA.
- Biochemistry and Molecular Medicine, University of California, Davis, 95616, USA.
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Yang Z, Jia Y, Wang S, Zhang Y, Fan W, Wang X, He L, Shen X, Yang X, Zhang Y, Yang H. Retinoblastoma-Binding Protein 5 Regulates H3K4 Methylation Modification to Inhibit the Proliferation of Melanoma Cells by Inactivating the Wnt/ β-Catenin and Epithelial-Mesenchymal Transition Pathways. JOURNAL OF ONCOLOGY 2023; 2023:5093941. [PMID: 36866240 PMCID: PMC9974310 DOI: 10.1155/2023/5093941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/29/2022] [Accepted: 01/20/2023] [Indexed: 02/25/2023]
Abstract
Histone 3 lysine 4 methylation (H3K4me), especially histone 3 lysine 4 trimethylation (H3K4me3), is one of the most extensively studied patterns of histone modification and plays crucial roles in many biological processes. However, as a part of H3K4 methyltransferase that participates in H3K4 methylation and transcriptional regulation, retinoblastoma-binding protein 5 (RBBP5) has not been well studied in melanoma. The present study sought to explore RBBP5-mediated H3K4 histone modification and the potential mechanisms in melanoma. RBBP5 expression in melanoma and nevi specimens was detected by immunohistochemistry. Western blotting was performed for three pairs of melanoma cancer tissues and nevi tissues. In vitro and in vivo assays were used to investigate the function of RBBP5. The molecular mechanism was determined using RT-qPCR, western blotting, ChIP assays, and Co-IP assays. Our study showed that RBBP5 was significantly downregulated in melanoma tissue and cells compared with nevi tissues and normal epithelia cells (P < 0.05). Reducing RBBP5 in human melanoma cells leads to H3K4me3 downregulation and promotes cell proliferation, migration, and invasion. On the one hand, we verified that WSB2 was an upstream gene of RBBP5-mediated H3K4 modification, which could directly bind to RBBP5 and negatively regulate its expression. On the other hand, we also confirmed that p16 (a cancer suppressor gene) was a downstream target of H3K4me3, the promoter of which can directly bind to H3K4me3. Mechanistically, our data revealed that RBBP5 inactivated the Wnt/β-catenin and epithelial-mesenchymal transition (EMT) pathways (P < 0.05), leading to melanoma suppression. Histone methylation is rising as an important factor affecting tumorigenicity and tumor progression. Our findings verified the significance of RBBP5-mediated H3K4 modification in melanoma and the potential regulatory mechanisms of melanoma proliferation and growth, suggesting that RBBP5 is a potential therapeutic target for the treatment of melanoma.
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Affiliation(s)
- Zhiqin Yang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
- 2Departments of Gynecology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - Yue Jia
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Shaojia Wang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Yongjun Zhang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Wen Fan
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
- 3Departments of Reproduction, The Second Affiliated Hospital of Kunming Medical University, Kunming 650106, China
| | - Xin Wang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Liang He
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Xiaoyu Shen
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Xiangqun Yang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Yi Zhang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Hongying Yang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
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8
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Li Z, Zhou P, Kwon E, Fitzgerald KA, Weng Z, Zhou C. Flnc: Machine Learning Improves the Identification of Novel Long Noncoding RNAs from Stand-Alone RNA-Seq Data. Noncoding RNA 2022; 8:70. [PMID: 36287122 PMCID: PMC9607125 DOI: 10.3390/ncrna8050070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/01/2022] [Accepted: 10/06/2022] [Indexed: 01/16/2025] Open
Abstract
Long noncoding RNAs (lncRNAs) play critical regulatory roles in human development and disease. Although there are over 100,000 samples with available RNA sequencing (RNA-seq) data, many lncRNAs have yet to be annotated. The conventional approach to identifying novel lncRNAs from RNA-seq data is to find transcripts without coding potential but this approach has a false discovery rate of 30-75%. Other existing methods either identify only multi-exon lncRNAs, missing single-exon lncRNAs, or require transcriptional initiation profiling data (such as H3K4me3 ChIP-seq data), which is unavailable for many samples with RNA-seq data. Because of these limitations, current methods cannot accurately identify novel lncRNAs from existing RNA-seq data. To address this problem, we have developed software, Flnc, to accurately identify both novel and annotated full-length lncRNAs, including single-exon lncRNAs, directly from RNA-seq data without requiring transcriptional initiation profiles. Flnc integrates machine learning models built by incorporating four types of features: transcript length, promoter signature, multiple exons, and genomic location. Flnc achieves state-of-the-art prediction power with an AUROC score over 0.92. Flnc significantly improves the prediction accuracy from less than 50% using the conventional approach to over 85%. Flnc is available via GitHub platform.
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Affiliation(s)
- Zixiu Li
- Division of Biostatistics and Health Services Research, Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Peng Zhou
- Division of Biostatistics and Health Services Research, Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Euijin Kwon
- Division of Biostatistics and Health Services Research, Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Katherine A. Fitzgerald
- Program in Innate Immunity, Division of Infectious Disease and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Chan Zhou
- Division of Biostatistics and Health Services Research, Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- The RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- UMass Cancer Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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Belhocine M, Simonin M, Abad Flores JD, Cieslak A, Manosalva I, Pradel L, Smith C, Mathieu EL, Charbonnier G, Martens JHA, Stunnenberg HG, Maqbool MA, Mikulasova A, Russell LJ, Rico D, Puthier D, Ferrier P, Asnafi V, Spicuglia S. Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes. Genome Res 2022; 32:1328-1342. [PMID: 34162697 PMCID: PMC9341507 DOI: 10.1101/gr.266924.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 05/05/2021] [Indexed: 01/03/2023]
Abstract
Broad domains of H3K4 methylation have been associated with consistent expression of tissue-specific, cell identity, and tumor suppressor genes. Here, we identified broad domain-associated genes in healthy human thymic T cell populations and a collection of T cell acute lymphoblastic leukemia (T-ALL) primary samples and cell lines. We found that broad domains are highly dynamic throughout T cell differentiation, and their varying breadth allows the distinction between normal and neoplastic cells. Although broad domains preferentially associate with cell identity and tumor suppressor genes in normal thymocytes, they flag key oncogenes in T-ALL samples. Moreover, the expression of broad domain-associated genes, both coding and noncoding, is frequently deregulated in T-ALL. Using two distinct leukemic models, we showed that the ectopic expression of T-ALL oncogenic transcription factor preferentially impacts the expression of broad domain-associated genes in preleukemic cells. Finally, an H3K4me3 demethylase inhibitor differentially targets T-ALL cell lines depending on the extent and number of broad domains. Our results show that the regulation of broad H3K4me3 domains is associated with leukemogenesis, and suggest that the presence of these structures might be used for epigenetic prioritization of cancer-relevant genes, including long noncoding RNAs.
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Affiliation(s)
- Mohamed Belhocine
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
- Molecular Biology and Genetics Laboratory, Dubai, United Arab Emirates
| | - Mathieu Simonin
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - José David Abad Flores
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Agata Cieslak
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Iris Manosalva
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Lydie Pradel
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Charlotte Smith
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Eve-Lyne Mathieu
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Guillaume Charbonnier
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Joost H A Martens
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands
| | - Muhammad Ahmad Maqbool
- CRUK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Aderley Park, Macclesfield SK104TG, United Kingdom
| | - Aneta Mikulasova
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Lisa J Russell
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Daniel Rico
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Denis Puthier
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Pierre Ferrier
- Aix Marseille University, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, 13288 Marseille, France
| | - Vahid Asnafi
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
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10
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Peng Y, Kang H, Luo J, Zhang Y. A Comparative Analysis of Super-Enhancers and Broad H3K4me3 Domains in Pig, Human, and Mouse Tissues. Front Genet 2021; 12:701049. [PMID: 34899824 PMCID: PMC8652260 DOI: 10.3389/fgene.2021.701049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Super-enhancers (SEs) and broad H3K4me3 domains (BDs) are crucial regulators in the control of tissue identity in human and mouse. However, their features in pig remain largely unknown. In this study, by integrative computational analyses of epigenomic and transcriptomic data, we have characterized SEs and BDs in six pig tissues and analyzed their conservation in comparison with human and mouse tissues. Similar to human and mouse, pig SEs and BDs display higher tissue specificity than their typical counterparts. Genes proximal to SEs and BDs are associated with tissue identity in most tissues. About 55-182 SEs (5-17% in total) and 99-309 BDs (8-16% in total) across pig tissues are considered as functionally conserved elements because they have orthologous SEs and BDs in human and mouse. However, these elements do not necessarily exhibit sequence conservation. The functionally conserved SEs are correlated to tissue identity in majority of pig tissues, while those conserved BDs are linked to tissue identity in a few tissues. Our study provides resources for future gene regulatory studies in pig. It highlights that SEs are more effective in defining tissue identity than BDs, which is contrasting to a previous study. It also provides novel insights on understanding the sequence features of functionally conserved elements.
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Affiliation(s)
- Yanling Peng
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Huifang Kang
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jing Luo
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yubo Zhang
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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11
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Beacon TH, Delcuve GP, López C, Nardocci G, Kovalchuk I, van Wijnen AJ, Davie JR. The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes. Clin Epigenetics 2021; 13:138. [PMID: 34238359 PMCID: PMC8264473 DOI: 10.1186/s13148-021-01126-1] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/30/2021] [Indexed: 02/06/2023] Open
Abstract
Transcriptionally active chromatin is marked by tri-methylation of histone H3 at lysine 4 (H3K4me3) located after first exons and around transcription start sites. This epigenetic mark is typically restricted to narrow regions at the 5`end of the gene body, though a small subset of genes have a broad H3K4me3 domain which extensively covers the coding region. Although most studies focus on the H3K4me3 mark, the broad H3K4me3 domain is associated with a plethora of histone modifications (e.g., H3 acetylated at K27) and is therein termed broad epigenetic domain. Genes marked with the broad epigenetic domain are involved in cell identity and essential cell functions and have clinical potential as biomarkers for patient stratification. Reducing expression of genes with the broad epigenetic domain may increase the metastatic potential of cancer cells. Enhancers and super-enhancers interact with the broad epigenetic domain marked genes forming a hub of interactions involving nucleosome-depleted regions. Together, the regulatory elements coalesce with transcription factors, chromatin modifying/remodeling enzymes, coactivators, and the Mediator and/or Integrator complex into a transcription factory which may be analogous to a liquid–liquid phase-separated condensate. The broad epigenetic domain has a dynamic chromatin structure which supports frequent transcription bursts. In this review, we present the current knowledge of broad epigenetic domains.
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Affiliation(s)
- Tasnim H Beacon
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Geneviève P Delcuve
- Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Camila López
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Gino Nardocci
- Faculty of Medicine, Universidad de Los Andes, Santiago, Chile.,Molecular Biology and Bioinformatics Lab, Program in Molecular Biology and Bioinformatics, Center for Biomedical Research and Innovation (CIIB), Universidad de Los Andes, Santiago, Chile
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Andre J van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - James R Davie
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada. .,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada.
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12
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Hsu CL, Lo YC, Kao CF. H3K4 Methylation in Aging and Metabolism. EPIGENOMES 2021; 5:14. [PMID: 34968301 PMCID: PMC8594702 DOI: 10.3390/epigenomes5020014] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/15/2021] [Indexed: 02/03/2023] Open
Abstract
During the process of aging, extensive epigenetic alterations are made in response to both exogenous and endogenous stimuli. Here, we summarize the current state of knowledge regarding one such alteration, H3K4 methylation (H3K4me), as it relates to aging in different species. We especially highlight emerging evidence that links this modification with metabolic pathways, which may provide a mechanistic link to explain its role in aging. H3K4me is a widely recognized marker of active transcription, and it appears to play an evolutionarily conserved role in determining organism longevity, though its influence is context specific and requires further clarification. Interestingly, the modulation of H3K4me dynamics may occur as a result of nutritional status, such as methionine restriction. Methionine status appears to influence H3K4me via changes in the level of S-adenosyl methionine (SAM, the universal methyl donor) or the regulation of H3K4-modifying enzyme activities. Since methionine restriction is widely known to extend lifespan, the mechanistic link between methionine metabolic flux, the sensing of methionine concentrations and H3K4me status may provide a cogent explanation for several seemingly disparate observations in aging organisms, including age-dependent H3K4me dynamics, gene expression changes, and physiological aberrations. These connections are not yet entirely understood, especially at a molecular level, and will require further elucidation. To conclude, we discuss some potential H3K4me-mediated molecular mechanisms that may link metabolic status to the aging process.
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Affiliation(s)
- Chia-Ling Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Yi-Chen Lo
- Graduate Institute of Food Science and Technology, National Taiwan University, Taipei 10617, Taiwan;
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
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13
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Abstract
Epigenetic modifications have been implicated to mediate several complications of diabetes mellitus (DM), especially nephropathy and retinopathy. Our aim was to ascertain whether epigenetic alterations in whole blood discriminate among patients with DM with normal, delayed, and rapid gastric emptying (GE).
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14
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Inhibiting MLL1-WDR5 interaction ameliorates neuropathic allodynia by attenuating histone H3 lysine 4 trimethylation-dependent spinal mGluR5 transcription. Pain 2021; 161:1995-2009. [PMID: 32345914 DOI: 10.1097/j.pain.0000000000001898] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 04/20/2020] [Indexed: 01/24/2023]
Abstract
ABSTRACT Mixed lineage leukemia 1 (MLL1)-mediated histone H3 lysine 4 trimethylation (H3K4me3) of a subset of genes has been linked to the transcriptional activation critical for synaptic plasticity, but its potential contribution to neuropathic allodynia development remains poorly explored. Here, we show that MLL1, which is induced in dorsal horn neuron after spinal nerve ligation (SNL), is responsible for mechanical allodynia and increased H3K4me3 at metabotropic glutamate receptor subtype 5 (mGluR5) promoter. Moreover, SNL induced WD (Trp-Asp) repeat domain 5 subunit (WDR5) expression as well as the MLL1-WDR5 interaction accompany with H3K4me3 enrichment and transcription of mGluR5 gene in the dorsal horn in neuropathic allodynia progression. Conversely, WDR5-0103, a novel inhibitor of the MLL1-WDR5 interaction, reversed SNL-induced allodynia and inhibited SNL-enhanced mGluR5 transcription/expression as well as MLL1, WDR5, and H3K4me3 at the mGluR5 promoter in the dorsal horn. Furthermore, disrupting the expression of MLL1 or WDR5 using small interfering RNA attenuated mechanical allodynia and reversed protein transcription/expression and complex localizing at mGluR5 promoter in the dorsal horn induced by SNL. This finding revealed that MLL1-WDR5 complex integrity regulates MLL1 and WDR5 recruitment to H3K4me3 enrichment at mGluR5 promoter in the dorsal horn underlying neuropathic allodynia. Collectively, our findings indicated that SNL enhances the MLL1-WDR5 complex, which facilitates MLL1 and WDR5 recruitment to H3K4me3 enrichment at mGluR5 promoter in spinal plasticity contributing to neuropathic allodynia pathogenesis.
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15
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Yokotsuka-Ishida S, Nakamura M, Tomiyasu Y, Nagai M, Kato Y, Tomiyasu A, Umehara H, Hayashi T, Sasaki N, Ueno SI, Sano A. Positional cloning and comprehensive mutation analysis identified a novel KDM2B mutation in a Japanese family with minor malformations, intellectual disability, and schizophrenia. J Hum Genet 2021; 66:597-606. [PMID: 33402700 DOI: 10.1038/s10038-020-00889-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/25/2020] [Accepted: 11/29/2020] [Indexed: 11/09/2022]
Abstract
The importance of epigenetic control in the development of the central nervous system has recently been attracting attention. Methylation patterns of lysine 4 and lysine 36 in histone H3 (H3K4 and H3K36) in the central nervous system are highly conserved among species. Numerous complications of body malformations and neuropsychiatric disorders are due to abnormal histone H3 methylation modifiers. In this study, we analyzed a Japanese family with a dominant inheritance of symptoms including Marfan syndrome-like minor physical anomalies (MPAs), intellectual disability, and schizophrenia (SCZ). We performed positional cloning for this family using a single nucleotide polymorphism (SNP) array and whole-exome sequencing, which revealed a missense coding strand mutation (rs1555289644, NM_032590.4: c.2173G>A, p.A725T) in exon 15 on the plant homeodomain of the KDM2B gene as a possible cause of the disease in the family. The exome sequencing revealed that within the coding region, only a point mutation in KDM2B was present in the region with the highest logarithm of odds score of 2.41 resulting from whole genome linkage analysis. Haplotype analysis revealed co-segregation with four affected family members (IV-9, III-4, IV-5, and IV-8). Lymphoblastoid cell lines from the proband with this mutation showed approximately halved KDM2B expression in comparison with healthy controls. KDM2B acts as an H3K4 and H3K36 histone demethylase. Our findings suggest that haploinsufficiency of KDM2B in the process of development, like other H3K4 and H3K36 methylation modifiers, may have caused MPAs, intellectual disability, and SCZ in this Japanese family.
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Affiliation(s)
- Saeko Yokotsuka-Ishida
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Masayuki Nakamura
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.
| | - Yoko Tomiyasu
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Mio Nagai
- Division of Psychiatry, Matsuyama Red Cross Hospital, Matsuyama, Japan
| | - Yuko Kato
- Division of Psychiatry, Jiundo Hospital, Tokyo, Japan
| | - Akiyuki Tomiyasu
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hiromi Umehara
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Takehiro Hayashi
- Department of Social Welfare, The International University of Kagoshima, Kagoshima, Japan
| | - Natsuki Sasaki
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Shu-Ichi Ueno
- Department of Neuropsychiatry, Ehime University Graduate School of Medicine Toon, Kagoshima, Japan
| | - Akira Sano
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
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16
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Powell SK, O'Shea C, Brennand KJ, Akbarian S. Parsing the Functional Impact of Noncoding Genetic Variants in the Brain Epigenome. Biol Psychiatry 2021; 89:65-75. [PMID: 33131715 PMCID: PMC7718420 DOI: 10.1016/j.biopsych.2020.06.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 12/31/2022]
Abstract
The heritability of common psychiatric disorders has motivated global efforts to identify risk-associated genetic variants and elucidate molecular pathways connecting DNA sequence to disease-associated brain dysfunction. The overrepresentation of risk variants among gene regulatory loci instead of protein-coding loci, however, poses a unique challenge in discerning which among the many thousands of variants identified contribute functionally to disease etiology. Defined broadly, psychiatric epigenomics seeks to understand the effects of disease-associated genetic variation on functional readouts of chromatin in an effort to prioritize variants in terms of their impact on gene expression in the brain. Here, we provide an overview of epigenomic mapping in the human brain and highlight findings of particular relevance to psychiatric genetics. Computational methods, including convolutional neuronal networks, and other machine learning approaches hold great promise for elucidating the functional impact of both common and rare genetic variants, thereby refining the epigenomic architecture of psychiatric disorders and enabling integrative analyses of regulatory noncoding variants in the context of large population-level genome and phenome databases.
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Affiliation(s)
- Samuel K Powell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Callan O'Shea
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York.
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17
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Wei J, Ma L, Ju P, Yang B, Wang YX, Chen J. Involvement of Oxytocin Receptor/Erk/MAPK Signaling in the mPFC in Early Life Stress-Induced Autistic-Like Behaviors. Front Cell Dev Biol 2020; 8:564485. [PMID: 33134294 PMCID: PMC7561716 DOI: 10.3389/fcell.2020.564485] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/10/2020] [Indexed: 12/13/2022] Open
Abstract
The neonatal or infant period is a critical stage for the development of brain neuroplasticity. Early life stresses in the neonatal period, including neonatal maternal separation (NMS), have adverse effects on an increased risk of psychiatric disorders in juveniles and adults. However, the underlying molecular mechanisms are not largely understood. Here, we found that juvenile rats subjected to 4 h daily NMS during postnatal days 1 to 20 exhibited autistic-like behavioral deficits without impairments in learning and memory functions. Molecular mechanism studies showed that oxytocin receptor (OXTR) in the medial prefrontal cortex of NMS rats was evidently downregulated when compared with control pups, especially in neurons. Erk/MAPK signaling, the downstream coupling signaling of OTXR, was also inhibited in NMS juvenile rats. Treatment with oxytocin could relieve NMS-induced social deficit behaviors and activated phosphorylation of Erk/MAPK signaling. Furthermore, medication with the inhibitor of H3K4 demethylase alleviated the abnormal behaviors in NMS rats and increased the expression of OXTR in the medial prefrontal cortex, which showed an epigenetic mechanism underlying social deficits induced by NMS. Taken together, these findings identified a molecular mechanism by which disruptions of mother-infant interactions influenced later displays of typical social behaviors and suggested the potential for NMS-driven epigenetic tuning of OXTR expression.
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Affiliation(s)
- Jinbao Wei
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,King's Lab, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.,Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Institute of Wudang Traditional Chinese Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Le Ma
- King's Lab, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Peijun Ju
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Beibei Yang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yong-Xiang Wang
- King's Lab, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Jinghong Chen
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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18
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Exposure to low doses of inorganic arsenic induces transgenerational changes on behavioral and epigenetic markers in zebrafish (Danio rerio). Toxicol Appl Pharmacol 2020; 396:115002. [PMID: 32277946 DOI: 10.1016/j.taap.2020.115002] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/26/2020] [Accepted: 04/07/2020] [Indexed: 02/06/2023]
Abstract
The ability of environmental pollutants to alter the epigenome with resultant development of behavioral alterations has received more attention in recent years. These alterations can be transmitted and affect later generations that have not been directly in contact with the contaminant. Arsenic (As) is a neurotoxicant and potent epigenetic disruptor that is widespread in the environment; however, the precise potential of As to produce transgenerational effects is unknown. Our study focused on the possible transgenerational effects on behavior by ancestral exposure to doses relevant to the environment of As, and the epigenetic mechanisms that could be involved. Embryos of F0 (ancestral generation) were directly exposed to 50 or 500 ppb of As for 150 days. F0 adults were raised to produce the F1 generation (intergeneration) and subsequently the F2 generation (transgeneration). We evaluated motor and cognitive behavior, neurodevelopment-related genes, and epigenetic markers on the F0 and F2 generation. As proposed in our hypothesis, ancestral arsenic exposure altered motor activity through the development and increased anxiety-like behaviors which were transmitted to the F2 generation. Additionally, we found a reduction in brain-derived neurotrophic factor expression between the F0 and F2 generation, and an increase in methylation on histone H3K4me3 in the nervous system.
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19
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Park S, Kim GW, Kwon SH, Lee JS. Broad domains of histone H3 lysine 4 trimethylation in transcriptional regulation and disease. FEBS J 2020; 287:2891-2902. [PMID: 31967712 DOI: 10.1111/febs.15219] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/23/2019] [Accepted: 01/17/2020] [Indexed: 12/11/2022]
Abstract
Histone modifications affect transcription by changing the chromatin structure. In particular, histone H3 lysine 4 trimethylation (H3K4me3) is one of the most recognized epigenetic marks of active transcription. While many studies have provided evidence of the correlation between H3K4me3 and active transcription, details regarding the mechanism involved remain unclear. The first study on the broad H3K4me3 domain was reported in 2014; subsequently, the function of this domain has been studied in various cell types. In this review, we summarized the recent studies on the role of the broad H3K4me3 domain in transcription, development, memory formation, and several diseases, including cancer and autoimmune diseases. The broadest H3K4me3 domains are associated with increased transcriptional precision of cell-type-specific genes related to cell identity and other essential functions. The broad H3K4me3 domain regulates maternal zygotic activation in early mammalian development. In systemic autoimmune diseases, high expression of immune-responsive genes requires the presence of the broad H3K4me3 domain in the promoter-proximal regions. Transcriptional repression of tumor-suppressor genes is associated with the shortening of the broad H3K4me3 domains in cancer cells. Additionally, the broad H3K4me3 domain interacts with the super-enhancer to regulate cancer-associated genes. During memory formation, H3K4me3 breadth is regulated in the hippocampus CA1 neurons. Taken together, these findings indicate that H3K4me3 breadth is essential for the regulation of the transcriptional output across multiple cell types.
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Affiliation(s)
- Shinae Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, Korea.,Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, Korea
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Korea
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Korea.,Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul, Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, Korea.,Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, Korea
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20
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Harmanci A, Harmanci AS, Swaminathan J, Gopalakrishnan V. EpiSAFARI: sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements. Bioinformatics 2019; 36:1014-1021. [PMID: 31501853 PMCID: PMC7703766 DOI: 10.1093/bioinformatics/btz702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/22/2019] [Accepted: 09/05/2019] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION Functional genomics experiments generate genomewide signal profiles that are dense information sources for annotating the regulatory elements. These profiles measure epigenetic activity at the nucleotide resolution and they exhibit distinctive patterns as they fluctuate along the genome. Most notable of these patterns are the valley patterns that are prevalently observed in assays such as ChIP Sequencing and bisulfite sequencing. The genomic positions of valleys pinpoint locations of cis-regulatory elements such as enhancers and insulators. Systematic identification of the valleys provides novel information for delineating the annotation of regulatory elements. Nevertheless, the valleys are not reported by majority of the analysis pipelines. RESULTS We describe EpiSAFARI, a computational method for sensitive detection of valleys from diverse types of epigenetic profiles. EpiSAFARI employs a novel smoothing method for decreasing noise in signal profiles and accounts for technical factors such as sparse signals, mappability and nucleotide content. In performance comparisons, EpiSAFARI performs favorably in terms of accuracy. The histone modification valleys detected by EpiSAFARI exhibit high conservation, transcription factor binding and they are enriched in nascent transcription. In addition, the large clusters of histone valleys are found to be enriched at the promoters of the developmentally associated genes. Differential histone valleys exhibit concordance with differential DNase signal at cell line specific valleys. DNA methylation valleys exhibit elevated conservation and high transcription factor binding. Specifically, we observed enriched binding of transcription factors associated with chromatin structure around methyl-valleys. AVAILABILITY AND IMPLEMENTATION EpiSAFARI is publicly available at https://github.com/harmancilab/EpiSAFARI. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Akdes Serin Harmanci
- School of Biomedical Informatics, Center for Systems Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | | | - Vidya Gopalakrishnan
- Department of Pediatrics, USA,Department of Molecular and Cellular Oncology, USA,Brain Tumor Center, USA,Center for Cancer Epigenetics, University of Texas, M.D. Anderson Cancer Center, Houston, TX 77030, USA,M.D. Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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21
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Abstract
The spreading of epigenetic domains has emerged as a distinguishing epigenomic phenotype for diverse cell types. In particular, clusters of H3K27ac- and H3K4me3-marked elements, referred to as super-enhancers, and broad H3K4me3 domains, respectively, have been linked to cell identity and disease states. Here, we characterized the broad domains from different pancreatic ductal adenocarcinoma (PDAC) cell lines that represent distinct histological grades. Our integrative genomic analysis found that human derived cell line models for distinct PDAC grades exhibit characteristic broad epigenetic features associated with gene expression patterns that are predictive of patient prognosis and provide insight into pancreatic cancer cell identity. In particular, we find that genes marked by overlapping Low-Grade broad domains correspond to an epithelial phenotype and hold potential as markers for patient stratification. We further utilize ChIP-seq to compare the effects of histone acetyltransferase (HAT) inhibitors to detect global changes in histone acetylation and methylation levels. We found that HAT inhibitors impact certain broad domains of pancreatic cancer cells. Overall, our results reveal potential roles for broad domains in cells from distinct PDAC grades and demonstrate the plasticity of particular broad epigenomic domains to epigenetic inhibitors.
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22
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Collins BE, Sweatt JD, Greer CB. Broad domains of histone 3 lysine 4 trimethylation are associated with transcriptional activation in CA1 neurons of the hippocampus during memory formation. Neurobiol Learn Mem 2019; 161:149-157. [PMID: 31002880 DOI: 10.1016/j.nlm.2019.04.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 12/18/2022]
Abstract
Transcriptional changes in the hippocampus are required for memory formation, and these changes are regulated by numerous post-translational modifications of chromatin-associated proteins. One of the epigenetic marks that has been implicated in memory formation is histone 3 lysine 4 trimethylation (H3K4me3), and this modification is found at the promoters of actively transcribed genes. The total levels of H3K4me3 are increased in the CA1 region of the hippocampus during memory formation, and genetic perturbation of the K4 methyltransferases and demethylases interferes with forming memories. Previous chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) analyses failed to detect changes in H3K4me3 levels at the promoters of memory-linked genes. Since the breadth of H3K4me3 marks was recently reported to be associated with the transcriptional outcome of a gene, we re-analyzed H3K4me3 ChIP-seq data sets to identify the role of H3K4me3 broad domains in CA1 neurons, as well as identify differences in breadth that occur during contextual fear conditioning. We found that, under baseline conditions, broad H3K4me3 peaks mark important learning and memory genes and are often regulated by super-enhancers. The peaks at many learning-associated genes become broader during novel environment exposure and memory formation. Furthermore, the important learning- and memory-associated lysine methyltransferases, Kmt2a and Kmt2b, are involved in maintaining H3K4me3 peak width. Our findings highlight the importance of analyzing H3K4me3 peak shape, and demonstrate that breadth of H3K4me3 marks in neurons of the hippocampus is regulated during memory formation.
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Affiliation(s)
- Bridget E Collins
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - J David Sweatt
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Celeste B Greer
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.
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23
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Gusev FE, Reshetov DA, Mitchell AC, Andreeva TV, Dincer A, Grigorenko AP, Fedonin G, Halene T, Aliseychik M, Goltsov AY, Solovyev V, Brizgalov L, Filippova E, Weng Z, Akbarian S, Rogaev EI. Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons. FASEB J 2019; 33:8161-8173. [PMID: 30970224 DOI: 10.1096/fj.201802646r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Human prefrontal cortex (PFC) is associated with broad individual variabilities in functions linked to personality, social behaviors, and cognitive functions. The phenotype variabilities associated with brain functions can be caused by genetic or epigenetic factors. The interactions between these factors in human subjects is, as of yet, poorly understood. The heterogeneity of cerebral tissue, consisting of neuronal and nonneuronal cells, complicates the comparative analysis of gene activities in brain specimens. To approach the underlying neurogenomic determinants, we performed a deep analysis of open chromatin-associated histone methylation in PFC neurons sorted from multiple human individuals in conjunction with whole-genome and transcriptome sequencing. Integrative analyses produced novel unannotated neuronal genes and revealed individual-specific chromatin "blueprints" of neurons that, in part, relate to genetic background. Surprisingly, we observed gender-dependent epigenetic signals, implying that gender may contribute to the chromatin variabilities in neurons. Finally, we found epigenetic, allele-specific activation of the testis-specific gene nucleoporin 210 like (NUP210L) in brain in some individuals, which we link to a genetic variant occurring in <3% of the human population. Recently, the NUP210L locus has been associated with intelligence and mathematics ability. Our findings highlight the significance of epigenetic-genetic footprinting for exploring neurologic function in a subject-specific manner.-Gusev, F. E., Reshetov, D. A., Mitchell, A. C., Andreeva, T. V., Dincer, A., Grigorenko, A. P., Fedonin, G., Halene, T., Aliseychik, M., Goltsov, A. Y., Solovyev, V., Brizgalov, L., Filippova, E., Weng, Z., Akbarian, S., Rogaev, E. I. Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons.
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Affiliation(s)
- Fedor E Gusev
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Denis A Reshetov
- Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Amanda C Mitchell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Tatiana V Andreeva
- Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Aslihan Dincer
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anastasia P Grigorenko
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Gennady Fedonin
- Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia
| | - Tobias Halene
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Maria Aliseychik
- Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Andrey Y Goltsov
- Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia
| | - Victor Solovyev
- Department of Cell Biology, Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Leonid Brizgalov
- Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena Filippova
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Zhiping Weng
- Department of Cell Biology, Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Schahram Akbarian
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Evgeny I Rogaev
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Center for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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24
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Collins BE, Greer CB, Coleman BC, Sweatt JD. Histone H3 lysine K4 methylation and its role in learning and memory. Epigenetics Chromatin 2019; 12:7. [PMID: 30616667 PMCID: PMC6322263 DOI: 10.1186/s13072-018-0251-8] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/19/2018] [Indexed: 01/09/2023] Open
Abstract
Epigenetic modifications such as histone methylation permit change in chromatin structure without accompanying change in the underlying genomic sequence. A number of studies in animal models have shown that dysregulation of various components of the epigenetic machinery causes cognitive deficits at the behavioral level, suggesting that proper epigenetic control is necessary for the fundamental processes of learning and memory. Histone H3 lysine K4 (H3K4) methylation comprises one component of such epigenetic control, and global levels of this mark are increased in the hippocampus during memory formation. Modifiers of H3K4 methylation are needed for memory formation, shown through animal studies, and many of the same modifiers are mutated in human cognitive diseases. Indeed, all of the known H3K4 methyltransferases and four of the known six H3K4 demethylases have been associated with impaired cognition in a neurologic or psychiatric disorder. Cognitive impairment in such patients often manifests as intellectual disability, consistent with a role for H3K4 methylation in learning and memory. As a modification quintessentially, but not exclusively, associated with transcriptional activity, H3K4 methylation provides unique insights into the regulatory complexity of writing, reading, and erasing chromatin marks within an activated neuron. The following review will discuss H3K4 methylation and connect it to transcriptional events required for learning and memory within the developed nervous system. This will include an initial discussion of the most recent advances in the developing methodology to analyze H3K4 methylation, namely mass spectrometry and deep sequencing, as well as how these methods can be applied to more deeply understand the biology of this mark in the brain. We will then introduce the core enzymatic machinery mediating addition and removal of H3K4 methylation marks and the resulting epigenetic signatures of these marks throughout the neuronal genome. We next foray into the brain, discussing changes in H3K4 methylation marks within the hippocampus during memory formation and retrieval, as well as the behavioral correlates of H3K4 methyltransferase deficiency in this region. Finally, we discuss the human cognitive diseases connected to each H3K4 methylation modulator and summarize advances in developing drugs to target them.
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Affiliation(s)
- Bridget E Collins
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA
| | - Celeste B Greer
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA
| | - Benjamin C Coleman
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA
| | - J David Sweatt
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA.
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25
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Khan A, Mathelier A, Zhang X. Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers. Epigenetics 2018; 13:910-922. [PMID: 30169995 DOI: 10.1080/15592294.2018.1514231] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Super-enhancers and stretch enhancers represent classes of transcriptional enhancers that have been shown to control the expression of cell identity genes and carry disease- and trait-associated variants. Specifically, super-enhancers are clusters of enhancers defined based on the binding occupancy of master transcription factors, chromatin regulators, or chromatin marks, while stretch enhancers are large chromatin-defined regulatory regions of at least 3,000 base pairs. Several studies have characterized these regulatory regions in numerous cell types and tissues to decipher their functional importance. However, the differences and similarities between these regulatory regions have not been fully assessed. We integrated genomic, epigenomic, and transcriptomic data from ten human cell types to perform a comparative analysis of super and stretch enhancers with respect to their chromatin profiles, cell type-specificity, and ability to control gene expression. We found that stretch enhancers are more abundant, more distal to transcription start sites, cover twice as much the genome, and are significantly less conserved than super-enhancers. In contrast, super-enhancers are significantly more enriched for active chromatin marks and cohesin complex, and more transcriptionally active than stretch enhancers. Importantly, a vast majority of super-enhancers (85%) overlap with only a small subset of stretch enhancers (13%), which are enriched for cell type-specific biological functions, and control cell identity genes. These results suggest that super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers, and importantly, most of the stretch enhancers that are distinct from super-enhancers do not show an association with cell identity genes, are less active, and more likely to be poised enhancers.
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Affiliation(s)
- Aziz Khan
- a Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership , University of Oslo , Oslo , Norway.,b Key Lab of Bioinformatics/Bioinformatics Division, BNRIST (Beijing National Research Center for Information Science and Technology), Department of Automation , Tsinghua University , Beijing , China
| | - Anthony Mathelier
- a Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership , University of Oslo , Oslo , Norway.,c Department of Cancer Genetics, Institute for Cancer Research , Oslo University Hospital Radiumhospitalet , Oslo , Norway
| | - Xuegong Zhang
- b Key Lab of Bioinformatics/Bioinformatics Division, BNRIST (Beijing National Research Center for Information Science and Technology), Department of Automation , Tsinghua University , Beijing , China.,d School of Life Sciences , Tsinghua University , Beijing , China
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26
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Song J, Baek IJ, Chun CH, Jin EJ. Dysregulation of the NUDT7-PGAM1 axis is responsible for chondrocyte death during osteoarthritis pathogenesis. Nat Commun 2018; 9:3427. [PMID: 30143643 PMCID: PMC6109082 DOI: 10.1038/s41467-018-05787-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/26/2018] [Indexed: 01/07/2023] Open
Abstract
Osteoarthritis (OA) is the most common degenerative joint disease; however, its etiopathogenesis is not completely understood. Here we show a role for NUDT7 in OA pathogenesis. Knockdown of NUDT7 in normal human chondrocytes results in the disruption of lipid homeostasis. Moreover, Nudt7-/- mice display significant accumulation of lipids via peroxisomal dysfunction, upregulation of IL-1β expression, and stimulation of apoptotic death of chondrocytes. Our genome-wide analysis reveals that NUDT7 knockout affects the glycolytic pathway, and we identify Pgam1 as a significantly altered gene. Consistent with the results obtained on the suppression of NUDT7, overexpression of PGAM1 in chondrocytes induces the accumulation of lipids, upregulation of IL-1β expression, and apoptotic cell death. Furthermore, these negative actions of PGAM1 in maintaining cartilage homeostasis are reversed by the co-introduction of NUDT7. Our results suggest that NUDT7 could be a potential therapeutic target for controlling cartilage-degrading disorders.
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Affiliation(s)
- Jinsoo Song
- Department of Biological Sciences, College of Natural Sciences, Wonkwang University, Iksan, Chunbuk, 54538, Republic of Korea
| | - In-Jeoung Baek
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Churl-Hong Chun
- Department of Orthopedic Surgery, Wonkwang University School of Medicine, Iksan, Chunbuk, 54538, Republic of Korea
| | - Eun-Jung Jin
- Department of Biological Sciences, College of Natural Sciences, Wonkwang University, Iksan, Chunbuk, 54538, Republic of Korea.
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27
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Fiziev P, Ernst J. ChromTime: modeling spatio-temporal dynamics of chromatin marks. Genome Biol 2018; 19:109. [PMID: 30097049 PMCID: PMC6085762 DOI: 10.1186/s13059-018-1485-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 07/17/2018] [Indexed: 11/17/2022] Open
Abstract
To model spatial changes of chromatin mark peaks over time we develop and apply ChromTime, a computational method that predicts peaks to be either expanding, contracting, or holding steady between time points. Predicted expanding and contracting peaks can mark regulatory regions associated with transcription factor binding and gene expression changes. Spatial dynamics of peaks provide information about gene expression changes beyond localized signal density changes. ChromTime detects asymmetric expansions and contractions, which for some marks associate with the direction of transcription. ChromTime facilitates the analysis of time course chromatin data in a range of biological systems.
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Affiliation(s)
- Petko Fiziev
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, Los Angeles, CA, USA
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA. .,Department of Biological Chemistry, University of California, Los Angeles, CA, USA. .,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, Los Angeles, CA, USA. .,Computer Science Department, University of California, Los Angeles, CA, USA. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA. .,Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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28
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Pu M, Wang M, Wang W, Velayudhan SS, Lee SS. Unique patterns of trimethylation of histone H3 lysine 4 are prone to changes during aging in Caenorhabditis elegans somatic cells. PLoS Genet 2018; 14:e1007466. [PMID: 29912876 PMCID: PMC6023244 DOI: 10.1371/journal.pgen.1007466] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 06/28/2018] [Accepted: 06/02/2018] [Indexed: 11/18/2022] Open
Abstract
Tri-methylation on histone H3 lysine 4 (H3K4me3) is associated with active gene expression but its regulatory role in transcriptional activation is unclear. Here we used Caenorhabditis elegans to investigate the connection between H3K4me3 and gene expression regulation during aging. We uncovered around 30% of H3K4me3 enriched regions to show significant and reproducible changes with age. We further showed that these age-dynamic H3K4me3 regions largely mark gene-bodies and are acquired during adult stages. We found that these adult-specific age-dynamic H3K4me3 regions are correlated with gene expression changes with age. In contrast, H3K4me3 marking established during developmental stages remained largely stable with age, even when the H3K4me3 associated genes exhibited RNA expression changes during aging. Importantly, the genes associated with changes in H3K4me3 and RNA levels with age are enriched for functional groups commonly implicated in aging biology. Therefore, our findings suggested divergent roles of H3K4me3 in gene expression regulation during aging, with important implications on aging-dependent pathophysiologies. Histone modifications, the specific chemical modifications on histone proteins, are key for regulating the packing of DNA, and thus have important influence on diverse biological processes. An intensely studied function of histone modifications is their contribution to regulating gene expression. Recent studies in diverse model organisms demonstrated that the global alterations of particular histone modifications, for instance H3K4me3, extend the lifespan of the organism. However, the underlying molecular mechanisms remain largely unclear. In this study, we monitored whether and how the genome-wide pattern of the histone modification H3K4me3 changes during aging in the somatic cells of the model organism C. elegans. We identified interesting and non-conventional patterns of H3K4me3, which span gene-bodies and are acquired during adulthood, that are particularly prone to changes with aging. This is contrasted to the well-studied H3K4me3 patterns that span transcriptional start sites and 5’ promoter regions and are established early during development, which remain stable with age. Consistent with the close association between H3K4me3 marking and active transcription, we observed that the age-dynamic H3K4me3 markings are highly correlated with corresponding RNA expression changes. Importantly, the genes that are associated with both H3K4me3 and RNA expression changes with age are over-represented for functional groups commonly implicated in aging biology. In summary, our findings revealed a lesser known pattern of H3K4me3 modification that can have important biological roles in aging.
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Affiliation(s)
- Mintie Pu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York City, United States of America
- * E-mail: (MP); (SSL)
| | - Minghui Wang
- Computational Biology Service Unit, Cornell University, Ithaca, New York City, United States of America
| | - Wenke Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York City, United States of America
| | - Satheeja Santhi Velayudhan
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York City, United States of America
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York City, United States of America
- * E-mail: (MP); (SSL)
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29
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Ma S, Hsieh YP, Ma J, Lu C. Low-input and multiplexed microfluidic assay reveals epigenomic variation across cerebellum and prefrontal cortex. SCIENCE ADVANCES 2018; 4:eaar8187. [PMID: 29675472 PMCID: PMC5906078 DOI: 10.1126/sciadv.aar8187] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/01/2018] [Indexed: 05/20/2023]
Abstract
Extensive effort is under way to survey the epigenomic landscape of primary ex vivo tissues to establish normal reference data and to discern variation associated with disease. The low abundance of some tissue types and the isolation procedure required to generate a homogenous cell population often yield a small quantity of cells for examination. This difficulty is further compounded by the need to profile a myriad of epigenetic marks. Thus, technologies that permit both ultralow input and high throughput are desired. We demonstrate a simple microfluidic technology, SurfaceChIP-seq, for profiling genome-wide histone modifications using as few as 30 to 100 cells per assay and with up to eight assays running in parallel. We applied the technology to profile epigenomes using nuclei isolated from prefrontal cortex and cerebellum of mouse brain. Our cell type-specific data revealed that neuronal and glial fractions exhibited profound epigenomic differences across the two functionally distinct brain regions.
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Affiliation(s)
- Sai Ma
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Yuan-Pang Hsieh
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
- Corresponding author.
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30
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Chromosomal Conformations and Epigenomic Regulation in Schizophrenia. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:21-40. [PMID: 29933951 DOI: 10.1016/bs.pmbts.2017.11.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chromosomal conformations, including promoter-enhancer loops, provide a critical regulatory layer for the transcriptional machinery. Therefore, schizophrenia, a common psychiatric disorder associated with broad changes in neuronal gene expression in prefrontal cortex and other brain regions implicated in psychosis, could be associated with alterations in higher-order chromatin. Here, we review early studies on spatial genome organization in the schizophrenia postmortem brain and discuss how integrative approaches using cell culture and animal model systems could gain deeper insight into the potential roles of higher-order chromatin for the neurobiology of and novel treatment avenues for common psychiatric disease.
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31
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Tansey KE, Hill MJ. Enrichment of schizophrenia heritability in both neuronal and glia cell regulatory elements. Transl Psychiatry 2018; 8:7. [PMID: 29317610 PMCID: PMC5802526 DOI: 10.1038/s41398-017-0053-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/25/2017] [Accepted: 09/29/2017] [Indexed: 01/28/2023] Open
Abstract
Genome-wide association studies have identified over 100 robust risk loci for schizophrenia with thousands of variants mediating genetic heritability, the majority of which reside in non-coding regions. Analytical approaches have shown this heritability is strongly enriched at variants within regulatory elements identified from human post-mortem brain tissue. However, bulk post-mortem brain tissue has a heterogeneous cell composition, making biological interpretations difficult. We sought to refine the cell types mediating schizophrenia heritability by separating neuronal and glial signals using data from: (1) NeuN-sorted post-mortem brain and (2) cell culture systems. Schizophrenia heritability was partitioned using linkage disequilbrium (LD) score regression. Variants within genomic regions marked by H3K4me3 (marker of active promoters) from NeuN-positive (neuronal) and NeuN-negative (non-neuronal) cells explained a significant amount of schizophrenia heritability (P = 1.38 × 10-10 and P = 7.97 × 10-10). However, variants located in H3K4me3 sites specific to NeuN-positive (neuronal) cells were enriched (P = 3.13 × 10-4), while those specific to NeuN-negative (non-neuronal) cells were not (P = 0.470). Data from cell culture systems mimicked this pattern of association. We show the previously observed enrichment of heritability from variants at brain H3K4me3 sites is mediated by both neuronal and non-neuronal brain cell types. However, only neuronal cell populations showed a unique contribution driven by cell-type specific regulatory elements. Cell culture systems recapitulate disease relevant gene-regulatory landscapes, validating them as a tool for future investigation of genetic mechanisms underlying schizophrenia. Identifying the cell types in which risk variants operate will greatly increase our understanding of schizophrenia pathobiology and aid in the development of novel model systems and therapies.
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Affiliation(s)
- Katherine E. Tansey
- 0000 0001 0807 5670grid.5600.3Core Bioinformatics and Statistics Team, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Matthew J. Hill
- 0000 0001 0807 5670grid.5600.3MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK ,0000 0001 0807 5670grid.5600.3Neuroscience and Mental Health Research Institute, School of Medicine, Cardiff University, Cardiff, UK
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32
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Early rearing history influences oxytocin receptor epigenetic regulation in rhesus macaques. Proc Natl Acad Sci U S A 2017; 114:11769-11774. [PMID: 29078292 PMCID: PMC5676889 DOI: 10.1073/pnas.1706206114] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Epigenetically programmed stress adaptation may be a conduit for informing offspring of environmental challenge. We employed ChIP-sequencing to examine effects of early environment on epigenetic regulation using hippocampal samples from macaques exposed to disruption in maternal care. We found decreased H3K4me3 binding at genes critical to behavioral stress response, the most robust being the oxytocin receptor gene (OXTR), for which we observed a corresponding decrease in RNA expression. Post hoc analysis showed that a gain-of-function OXTR SNP rescued behavioral differences in early stress-exposed subjects. Our data suggest that epigenetic down-modulation of OXTR in brain could contribute to behavioral differences observed in early stress-exposed subjects and that functional genetic variation plays a role. These could have translational implications for human psychiatric disease and personality disorders. Adaptations to stress can occur through epigenetic processes and may be a conduit for informing offspring of environmental challenge. We employed ChIP-sequencing for H3K4me3 to examine effects of early maternal deprivation (peer-rearing, PR) in archived rhesus macaque hippocampal samples (male, n = 13). Focusing on genes with roles in stress response and behavior, we assessed the effects of rearing on H3K4me3 binding by ANOVA. We found decreased H3K4me3 binding at genes critical to behavioral stress response, the most robust being the oxytocin receptor gene OXTR, for which we observed a corresponding decrease in RNA expression. Based on this finding, we performed behavioral analyses to determine whether a gain-of-function nonsynonymous OXTR SNP interacted with early stress to influence relevant behavioral stress reactivity phenotypes (n = 194), revealing that this SNP partially rescued the PR phenotype. PR infants exhibited higher levels of separation anxiety and arousal in response to social separation, but infants carrying the alternative OXTR allele did not exhibit as great a separation response. These data indicate that the oxytocin system is involved in social-separation response and suggest that epigenetic down-modulation of OXTR could contribute to behavioral differences observed in PR animals. Epigenetic changes at OXTR may represent predictive adaptive responses that could impart readiness to respond to environmental challenge or maintain proximity to a caregiver but also contribute to behavioral pathology. Our data also demonstrate that OXTR polymorphism can permit animals to partially overcome the detrimental effects of early maternal deprivation, which could have translational implications for human psychiatric disorders.
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Fabbri C, Serretti A. Role of 108 schizophrenia-associated loci in modulating psychopathological dimensions in schizophrenia and bipolar disorder. Am J Med Genet B Neuropsychiatr Genet 2017; 174:757-764. [PMID: 28786528 DOI: 10.1002/ajmg.b.32577] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 07/10/2017] [Indexed: 12/23/2022]
Abstract
The Schizophrenia Working Group of the Psychiatric Genomics Consortium (PGC) identified 108 loci associated with schizophrenia, but their role in modulating specific psychopathological dimensions of the disease is unknown. This study investigated which symptom dimensions may be affected by these loci in schizophrenia, and bipolar disorder. Positive, negative and depressive symptoms, suicidal ideation, cognition, violent behaviors, quality of life, and early onset were investigated in schizophrenia and bipolar disorder using the clinical antipsychotic trials of intervention effectiveness (CATIE) and systematic treatment enhancement program for bipolar disorder (STEP-BD) studies. Individual loci were investigated, then genes within 50 Kbp from polymorphisms with p < 0.10 were included in an enrichment analysis (Cytoscape GeneMania plugin) and used to estimate polygenic risk scores (PRS). Covariates were center, age, gender, ancestry-informative population, principal components, and for cognition, also years of education were considered. Eighty-nine polymorphisms were available, 479 and 810 white subjects were included from CATIE and STEP-BD, respectively. rs75059851 (IGSF9B gene) was associated with negative symptoms in CATIE (p = 0.00048). Genes within 50 Kbp from variants contributing to negative symptoms and suicide were enriched with GO terms involved in acetylcholine neurotransmission, cognition showed enrichment with GO terms involved in vitamin B6 and fucose metabolism while early onset with GO terms related to extracellular matrix structure. PRS showed nominal associations with violent behaviors and depressive symptoms. This study provided preliminary evidence that a schizophrenia-associated variant (rs75059851) may modulate negative symptoms. Multi-locus models may provide interesting insights about the biological mechanisms that mediate psychopathological dimensions.
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Affiliation(s)
- Chiara Fabbri
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Alessandro Serretti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
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34
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Javidfar B, Park R, Kassim BS, Bicks LK, Akbarian S. The epigenomics of schizophrenia, in the mouse. Am J Med Genet B Neuropsychiatr Genet 2017; 174:631-640. [PMID: 28699694 PMCID: PMC5573750 DOI: 10.1002/ajmg.b.32566] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 05/04/2017] [Accepted: 06/12/2017] [Indexed: 01/02/2023]
Abstract
Large-scale consortia including the Psychiatric Genomics Consortium, the Common Minds Consortium, BrainSeq and PsychENCODE, and many other studies taken together provide increasingly detailed insights into the genetic and epigenetic risk architectures of schizophrenia (SCZ) and offer vast amounts of molecular information, but with largely unexplored therapeutic potential. Here we discuss how epigenomic studies in human brain could guide animal work to test the impact of disease-associated alterations in chromatin structure and function on cognition and behavior. For example, transcription factors such as MYOCYTE-SPECIFIC ENHANCER FACTOR 2C (MEF2C), or multiple regulators of the open chromatin mark, methyl-histone H3-lysine 4, are associated with the genetic risk architectures of common psychiatric disease and alterations in chromatin structure and function in diseased brain tissue. Importantly, these molecules also affect cognition and behavior in genetically engineered mice, including virus-mediated expression changes in prefrontal cortex (PFC) and other key nodes in the circuitry underlying psychosis. Therefore, preclinical and small laboratory animal work could target genomic sequences affected by chromatin alterations in SCZ. To this end, in vivo editing of enhancer and other regulatory non-coding DNA by RNA-guided nucleases including CRISPR-Cas, and designer transcription factors, could be expected to deliver pipelines for novel therapeutic approaches aimed at improving cognitive dysfunction and other core symptoms of SCZ.
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Affiliation(s)
| | | | | | - Lucy K. Bicks
- Department of Psychiatry; Friedman Brain Institute; Icahn School of Medicine at Mount Sinai; New York New York
| | - Schahram Akbarian
- Department of Psychiatry; Friedman Brain Institute; Icahn School of Medicine at Mount Sinai; New York New York
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35
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Xie W, Nagarajan S, Baumgart SJ, Kosinsky RL, Najafova Z, Kari V, Hennion M, Indenbirken D, Bonn S, Grundhoff A, Wegwitz F, Mansouri A, Johnsen SA. RNF40 regulates gene expression in an epigenetic context-dependent manner. Genome Biol 2017; 18:32. [PMID: 28209164 PMCID: PMC5314486 DOI: 10.1186/s13059-017-1159-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/23/2017] [Indexed: 12/20/2022] Open
Abstract
Background Monoubiquitination of H2B (H2Bub1) is a largely enigmatic histone modification that has been linked to transcriptional elongation. Because of this association, it has been commonly assumed that H2Bub1 is an exclusively positively acting histone modification and that increased H2Bub1 occupancy correlates with increased gene expression. In contrast, depletion of the H2B ubiquitin ligases RNF20 or RNF40 alters the expression of only a subset of genes. Results Using conditional Rnf40 knockout mouse embryo fibroblasts, we show that genes occupied by low to moderate amounts of H2Bub1 are selectively regulated in response to Rnf40 deletion, whereas genes marked by high levels of H2Bub1 are mostly unaffected by Rnf40 loss. Furthermore, we find that decreased expression of RNF40-dependent genes is highly associated with widespread narrowing of H3K4me3 peaks. H2Bub1 promotes the broadening of H3K4me3 to increase transcriptional elongation, which together lead to increased tissue-specific gene transcription. Notably, genes upregulated following Rnf40 deletion, including Foxl2, are enriched for H3K27me3, which is decreased following Rnf40 deletion due to decreased expression of the Ezh2 gene. As a consequence, increased expression of some RNF40-“suppressed” genes is associated with enhancer activation via FOXL2. Conclusion Together these findings reveal the complexity and context-dependency whereby one histone modification can have divergent effects on gene transcription. Furthermore, we show that these effects are dependent upon the activity of other epigenetic regulatory proteins and histone modifications. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1159-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wanhua Xie
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Sankari Nagarajan
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Simon J Baumgart
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Robyn Laura Kosinsky
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Zeynab Najafova
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Vijayalakshmi Kari
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Magali Hennion
- Research Group for Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), Griesebachstraße 5, 37077, Göttingen, Germany
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251, Hamburg, Germany
| | - Stefan Bonn
- Research Group for Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), Griesebachstraße 5, 37077, Göttingen, Germany
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251, Hamburg, Germany
| | - Florian Wegwitz
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany
| | - Ahmed Mansouri
- Department of Molecular Cell Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg, 37077, Göttingen, Germany.,Department of Clinical Neurophysiology, University of Göttingen, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, Göttingen Center for Molecular Biosciences, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
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36
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Shen EY, Jiang Y, Javidfar B, Kassim B, Loh YHE, Ma Q, Mitchell AC, Pothula V, Stewart AF, Ernst P, Yao WD, Martin G, Shen L, Jakovcevski M, Akbarian S. Neuronal Deletion of Kmt2a/Mll1 Histone Methyltransferase in Ventral Striatum is Associated with Defective Spike-Timing-Dependent Striatal Synaptic Plasticity, Altered Response to Dopaminergic Drugs, and Increased Anxiety. Neuropsychopharmacology 2016; 41:3103-3113. [PMID: 27485686 PMCID: PMC5101561 DOI: 10.1038/npp.2016.144] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 07/25/2016] [Accepted: 07/27/2016] [Indexed: 12/27/2022]
Abstract
Lysine (K) methyltransferase 2a (Kmt2a) and other regulators of H3 lysine 4 methylation, a histone modification enriched at promoters and enhancers, are widely expressed throughout the brain, but molecular and cellular phenotypes in subcortical areas remain poorly explored. We report that Kmt2a conditional deletion in postnatal forebrain is associated with excessive nocturnal activity and with absent or blunted responses to stimulant and dopaminergic agonist drugs, in conjunction with near-complete loss of spike-timing-dependent long-term potentiation in medium spiny neurons (MSNs). Selective ablation of Kmt2a, but not the ortholog Kmt2b, in adult ventral striatum/nucleus accumbens neurons markedly increased anxiety scores in multiple behavioral paradigms. Striatal transcriptome sequencing in adult mutants identified 262 Kmt2a-sensitive genes, mostly downregulated in Kmt2a-deficient mice. Transcriptional repression includes the 5-Htr2a serotonin receptor, strongly associated with anxiety- and depression-related disorders in human and animal models. Consistent with the role of Kmt2a in promoting gene expression, the transcriptional regulators Bahcc1, Isl1, and Sp9 were downregulated and affected by H3K4 promoter hypomethylation. Therefore, Kmt2a regulates synaptic plasticity in striatal neurons and provides an epigenetic drug target for anxiety and dopamine-mediated behaviors.
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Affiliation(s)
| | - Yan Jiang
- Department of Psychiatry, New York, NY, USA
| | | | | | - Yong-Hwee E Loh
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, NY, USA
| | - Qi Ma
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | | | | | | | - Patricia Ernst
- University of Colorado School of Medicine, Department of Pediatrics, Aurora, CO, USA
| | - Wei-Dong Yao
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Gilles Martin
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Li Shen
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, NY, USA
| | - Mira Jakovcevski
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany,Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Kraepelinstrasse 2, 80804 Munich, Germany, Tel: +49 89 30622 643, E-mail:
| | - Schahram Akbarian
- Department of Psychiatry, New York, NY, USA,Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, Floor 9 Room 105, 1470 Madison Avenue, New York, NY 10029, USA, Tel: +1 212 824 8984, E-mail:
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37
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Broad H3K4me3 as A Novel Epigenetic Signature for Normal Development and Disease. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:262-264. [PMID: 27744060 PMCID: PMC5093773 DOI: 10.1016/j.gpb.2016.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 11/07/2022]
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38
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Bell CG. Insights in human epigenomic dynamics through comparative primate analysis. Genomics 2016; 108:115-125. [DOI: 10.1016/j.ygeno.2016.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 08/03/2016] [Accepted: 09/29/2016] [Indexed: 12/11/2022]
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39
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van de Leemput J, Hess JL, Glatt SJ, Tsuang MT. Genetics of Schizophrenia: Historical Insights and Prevailing Evidence. ADVANCES IN GENETICS 2016; 96:99-141. [PMID: 27968732 DOI: 10.1016/bs.adgen.2016.08.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Schizophrenia's (SZ's) heritability and familial transmission have been known for several decades; however, despite the clear evidence for a genetic component, it has been very difficult to pinpoint specific causative genes. Even so genetic studies have taught us a lot, even in the pregenomic era, about the molecular underpinnings and disease-relevant pathways. Recurring themes emerged revealing the involvement of neurodevelopmental processes, glutamate regulation, and immune system differential activation in SZ etiology. The recent emergence of epigenetic studies aimed at shedding light on the biological mechanisms underlying SZ has provided another layer of information in the investigation of gene and environment interactions. However, this epigenetic insight also brings forth another layer of complexity to the (epi)genomic landscape such as interactions between genetic variants, epigenetic marks-including cross-talk between DNA methylation and histone modification processes-, gene expression regulation, and environmental influences. In this review, we seek to synthesize perspectives, including limitations and obstacles yet to overcome, from genetic and epigenetic literature on SZ through a qualitative review of risk factors and prevailing hypotheses. Encouraged by the findings of both genetic and epigenetic studies to date, as well as the continued development of new technologies to collect and interpret large-scale studies, we are left with a positive outlook for the future of elucidating the molecular genetic mechanisms underlying SZ and other complex neuropsychiatric disorders.
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Affiliation(s)
- J van de Leemput
- University of California, San Diego, La Jolla, CA, United States
| | - J L Hess
- SUNY Upstate Medical University, Syracuse, NY, United States
| | - S J Glatt
- SUNY Upstate Medical University, Syracuse, NY, United States
| | - M T Tsuang
- University of California, San Diego, La Jolla, CA, United States
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40
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Abstract
Two recent reports convincingly demonstrate that the risk of schizophrenia is influenced by common variation of C4, which codes for complement component 4, and by rare, disruptive mutations of SETD1A, which codes for a histone methylase. These important results open the way for major advances in our understanding of the fundamental biological processes leading to disease.
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Affiliation(s)
- David Curtis
- David Curtis, MD, PhD, FRCPsych, UCL Genetics Institute, UCL, and Centre for Psychiatry, Barts and the London School of Medicine and Dentistry, Darwin Building, Gower Street, London WC1E 6BT, UK.
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41
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Bayarsaihan D. A central role of H3K4me3 extended chromatin domains in gene regulation. Epigenomics 2016; 8:1011-4. [PMID: 27410771 DOI: 10.2217/epi-2016-0062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Dashzeveg Bayarsaihan
- Institute for Systems Genomics, Center for Regenerative Medicine & Skeletal Development, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
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42
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Singh T, Kurki MI, Curtis D, Purcell SM, Crooks L, McRae J, Suvisaari J, Chheda H, Blackwood D, Breen G, Pietiläinen O, Gerety SS, Ayub M, Blyth M, Cole T, Collier D, Coomber EL, Craddock N, Daly MJ, Danesh J, DiForti M, Foster A, Freimer NB, Geschwind D, Johnstone M, Joss S, Kirov G, Körkkö J, Kuismin O, Holmans P, Hultman CM, Iyegbe C, Lönnqvist J, Männikkö M, McCarroll SA, McGuffin P, McIntosh AM, McQuillin A, Moilanen JS, Moore C, Murray RM, Newbury-Ecob R, Ouwehand W, Paunio T, Prigmore E, Rees E, Roberts D, Sambrook J, Sklar P, St Clair D, Veijola J, Walters JTR, Williams H, Sullivan PF, Hurles ME, O'Donovan MC, Palotie A, Owen MJ, Barrett JC. Rare loss-of-function variants in SETD1A are associated with schizophrenia and developmental disorders. Nat Neurosci 2016; 19:571-7. [PMID: 26974950 DOI: 10.1038/nn.4267] [Citation(s) in RCA: 322] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/11/2016] [Indexed: 12/17/2022]
Abstract
By analyzing the whole-exome sequences of 4,264 schizophrenia cases, 9,343 controls and 1,077 trios, we identified a genome-wide significant association between rare loss-of-function (LoF) variants in SETD1A and risk for schizophrenia (P = 3.3 × 10(-9)). We found only two heterozygous LoF variants in 45,376 exomes from individuals without a neuropsychiatric diagnosis, indicating that SETD1A is substantially depleted of LoF variants in the general population. Seven of the ten individuals with schizophrenia carrying SETD1A LoF variants also had learning difficulties. We further identified four SETD1A LoF carriers among 4,281 children with severe developmental disorders and two more carriers in an independent sample of 5,720 Finnish exomes, both with notable neuropsychiatric phenotypes. Together, our observations indicate that LoF variants in SETD1A cause a range of neurodevelopmental disorders, including schizophrenia. Combining these data with previous common variant evidence, we suggest that epigenetic dysregulation, specifically in the histone H3K4 methylation pathway, is an important mechanism in the pathogenesis of schizophrenia.
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Affiliation(s)
- Tarjinder Singh
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Mitja I Kurki
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics and Genetic Analysis Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - David Curtis
- University College London Genetics Institute, University College London, London, UK
| | - Shaun M Purcell
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lucy Crooks
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Sheffield Diagnostic Genetics Service, Sheffield Childrens' NHS Foundation Trust, Sheffield, UK
| | - Jeremy McRae
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Jaana Suvisaari
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Himanshu Chheda
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Douglas Blackwood
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Gerome Breen
- Institute of Psychiatry, Kings College London, London, UK.,NIHR BRC for Mental Health, Institute of Psychiatry and SLaM NHS Trust, King's College London, London, UK
| | - Olli Pietiläinen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Sebastian S Gerety
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Muhammad Ayub
- Division of Developmental Disabilities, Department of Psychiatry, Queen's University, Kingston, Ontario, Canada
| | - Moira Blyth
- Department of Clinical Genetics, Chapel Allerton Hospital, Chapeltown Road, Leeds, UK
| | - Trevor Cole
- Birmingham Women's Hospital, Edgbaston, Birmingham, UK
| | - David Collier
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK.,Lilly Research Laboratories, Eli Lilly &Co. Ltd., Windlesham, Surrey, UK
| | - Eve L Coomber
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Nick Craddock
- MRC Centre for Neuropsychiatric Genetics &Genomics, Institute of Psychological Medicine &Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Mark J Daly
- Program in Medical and Population Genetics and Genetic Analysis Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - John Danesh
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,INTERVAL Coordinating Centre, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Marta DiForti
- Institute of Psychiatry, Kings College London, London, UK
| | - Alison Foster
- Clinical Genetics Unit, Birmingham Women's NHS Foundation Trust, Edgbaston, Birmingham, UK
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, California, USA
| | - Daniel Geschwind
- UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - Mandy Johnstone
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Shelagh Joss
- West of Scotland Genetics Service, South Glasgow University Hospitals, Glasgow, UK
| | - Georg Kirov
- MRC Centre for Neuropsychiatric Genetics &Genomics, Institute of Psychological Medicine &Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Jarmo Körkkö
- Center for Intellectual Disability Care, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Outi Kuismin
- PEDEGO Research Unit, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics &Genomics, Institute of Psychological Medicine &Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Conrad Iyegbe
- Institute of Psychiatry, Kings College London, London, UK
| | - Jouko Lönnqvist
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Minna Männikkö
- Center for Life Course Epidemiology and Systems Medicine, University of Oulu, Oulu, Finland
| | - Steve A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Peter McGuffin
- Institute of Psychiatry, Kings College London, London, UK
| | - Andrew M McIntosh
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Andrew McQuillin
- University College London, Molecular Psychiatry Laboratory, Division of Psychiatry, London, UK
| | - Jukka S Moilanen
- PEDEGO Research Unit, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Carmel Moore
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,INTERVAL Coordinating Centre, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Robin M Murray
- Institute of Psychiatry, Kings College London, London, UK.,NIHR BRC for Mental Health, Institute of Psychiatry and SLaM NHS Trust, King's College London, London, UK
| | - Ruth Newbury-Ecob
- Department of Clinical Genetics, University Hospitals Bristol NHS Foundation Trust, St Michael's Hospital, Bristol, UK
| | - Willem Ouwehand
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,Department of Haemotology, University of Cambridge, Cambridge, UK.,NHS Blood and Transplant, Cambridge, UK
| | - Tiina Paunio
- National Institute for Health and Welfare (THL), Helsinki, Finland.,University of Helsinki, Department of Psychiatry, Helsinki, Finland
| | - Elena Prigmore
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Elliott Rees
- MRC Centre for Neuropsychiatric Genetics &Genomics, Institute of Psychological Medicine &Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - David Roberts
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,NHS Blood and Transplant Oxford Centre, John Radcliffe Hospital, Oxford, UK.,Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jennifer Sambrook
- INTERVAL Coordinating Centre, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,Department of Haemotology, University of Cambridge, Cambridge, UK
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David St Clair
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Juha Veijola
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics &Genomics, Institute of Psychological Medicine &Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Hywel Williams
- MRC Centre for Neuropsychiatric Genetics &Genomics, Institute of Psychological Medicine &Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | | | | | | | | | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics &Genomics, Institute of Psychological Medicine &Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Aarno Palotie
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics and Genetic Analysis Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael J Owen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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43
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Halene TB, Kozlenkov A, Jiang Y, Mitchell A, Javidfar B, Dincer A, Park R, Wiseman J, Croxson P, Giannaris EL, Hof PR, Roussos P, Dracheva S, Hemby SE, Akbarian S. NeuN+ neuronal nuclei in non-human primate prefrontal cortex and subcortical white matter after clozapine exposure. Schizophr Res 2016; 170:235-44. [PMID: 26776227 PMCID: PMC4740223 DOI: 10.1016/j.schres.2015.12.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/24/2015] [Accepted: 12/28/2015] [Indexed: 12/01/2022]
Abstract
Increased neuronal densities in subcortical white matter have been reported for some cases with schizophrenia. The underlying cellular and molecular mechanisms remain unresolved. We exposed 26 young adult macaque monkeys for 6 months to either clozapine, haloperidol or placebo and measured by structural MRI frontal gray and white matter volumes before and after treatment, followed by observer-independent, flow-cytometry-based quantification of neuronal and non-neuronal nuclei and molecular fingerprinting of cell-type specific transcripts. After clozapine exposure, the proportion of nuclei expressing the neuronal marker NeuN increased by approximately 50% in subcortical white matter, in conjunction with a more subtle and non-significant increase in overlying gray matter. Numbers and proportions of nuclei expressing the oligodendrocyte lineage marker, OLIG2, and cell-type specific RNA expression patterns, were maintained after antipsychotic drug exposure. Frontal lobe gray and white matter volumes remained indistinguishable between antipsychotic-drug-exposed and control groups. Chronic clozapine exposure increases the proportion of NeuN+ nuclei in frontal subcortical white matter, without alterations in frontal lobe volumes or cell type-specific gene expression. Further exploration of neurochemical plasticity in non-human primate brain exposed to antipsychotic drugs is warranted.
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Affiliation(s)
- Tobias B. Halene
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Corresponding author: Tobias B. Halene, MD PhD, Icahn School of Medicine at Mount Sinai, Department of Psychiatry, 1470 Madison Ave, Hess 9-105, New York, NY 10029, Tel: 646 627 5529, Fax: 646-537-9583,
| | - Alexey Kozlenkov
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yan Jiang
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amanda Mitchell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Behnam Javidfar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aslihan Dincer
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Royce Park
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jennifer Wiseman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paula Croxson
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eustathia Lela Giannaris
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Patrick R. Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, 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
| | - Stella Dracheva
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Scott E. Hemby
- Department of Physiology and Pharmacology, Wake Forest University, Winston-Salem, NC, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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