101
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An integrative model of pathway convergence in genetically heterogeneous blast crisis chronic myeloid leukemia. Blood 2021; 135:2337-2353. [PMID: 32157296 DOI: 10.1182/blood.2020004834] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 02/17/2020] [Indexed: 12/20/2022] Open
Abstract
Targeted therapies against the BCR-ABL1 kinase have revolutionized treatment of chronic phase (CP) chronic myeloid leukemia (CML). In contrast, management of blast crisis (BC) CML remains challenging because BC cells acquire complex molecular alterations that confer stemness features to progenitor populations and resistance to BCR-ABL1 tyrosine kinase inhibitors. Comprehensive models of BC transformation have proved elusive because of the rarity and genetic heterogeneity of BC, but are important for developing biomarkers predicting BC progression and effective therapies. To better understand BC, we performed an integrated multiomics analysis of 74 CP and BC samples using whole-genome and exome sequencing, transcriptome and methylome profiling, and chromatin immunoprecipitation followed by high-throughput sequencing. Employing pathway-based analysis, we found the BC genome was significantly enriched for mutations affecting components of the polycomb repressive complex (PRC) pathway. While transcriptomically, BC progenitors were enriched and depleted for PRC1- and PRC2-related gene sets respectively. By integrating our data sets, we determined that BC progenitors undergo PRC-driven epigenetic reprogramming toward a convergent transcriptomic state. Specifically, PRC2 directs BC DNA hypermethylation, which in turn silences key genes involved in myeloid differentiation and tumor suppressor function via so-called epigenetic switching, whereas PRC1 represses an overlapping and distinct set of genes, including novel BC tumor suppressors. On the basis of these observations, we developed an integrated model of BC that facilitated the identification of combinatorial therapies capable of reversing BC reprogramming (decitabine+PRC1 inhibitors), novel PRC-silenced tumor suppressor genes (NR4A2), and gene expression signatures predictive of disease progression and drug resistance in CP.
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102
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Corbett RJ, Luttman AM, Wurtz KE, Siegford JM, Raney NE, Ford LM, Ernst CW. Weaning Induces Stress-Dependent DNA Methylation and Transcriptional Changes in Piglet PBMCs. Front Genet 2021; 12:633564. [PMID: 33613645 PMCID: PMC7893110 DOI: 10.3389/fgene.2021.633564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/14/2021] [Indexed: 11/19/2022] Open
Abstract
Changes to the epigenome, including those to DNA methylation, have been proposed as mechanisms by which stress can induce long-term physiological changes in livestock species. Pig weaning is associated with dietary and social stress, both of which elicit an immune response and changes to the hypothalamic–pituitary–adrenal (HPA) axis. While differential methylation following stress has been assessed in model organisms, it remains poorly understood how the pig methylome is altered by stressors in production settings. We quantified changes in CpG methylation and transcript abundance in piglet peripheral blood mononuclear cells (PBMCs) following weaning and also assessed differential patterns in pigs exhibiting high and low stress response as measured by cortisol concentration and lesion scores. Blood was collected from nine gilt piglets 24 h before and after weaning, and whole-genome bisulfite sequencing (WGBS) and RNA-sequencing were performed on six and nine animals, respectively, at both time points. We identified 2,674 differentially methylated regions (DMRs) that were enriched within promoters of genes associated with lymphocyte stimulation and transcriptional regulation. Stress groups displayed unique differential methylation and expression patterns associated with activation and suppression of T cell immunity in low and high stress animals, respectively. Differential methylation was strongly associated with differential expression; specifically, upregulated genes were enriched among hypomethylated genes. We observed post-weaning hypermethylation of the glucocorticoid receptor (NR3C1) promoter and a significant decrease in NR3C1 expression (n = 9, p = 6.1 × 10–3). Our results indicate that weaning-associated stress elicits genome-wide methylation changes associated with differential gene expression, reduced T cell activation, and an altered HPA axis response.
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Affiliation(s)
- Ryan J Corbett
- Genetics and Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, United States
| | - Andrea M Luttman
- Genetics and Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, United States
| | - Kaitlin E Wurtz
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Janice M Siegford
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Nancy E Raney
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Laura M Ford
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
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103
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Milad M, Olbricht GR. Testing differentially methylated regions through functional principal component analysis. J Appl Stat 2021; 49:1677-1691. [DOI: 10.1080/02664763.2021.1877636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Mohamed Milad
- Department of Mathematics and Statistics, Arkansas State University, Jonesboro, AR, USA
| | - Gayla R. Olbricht
- Department of Mathematics and Statistics, Missouri University of Science and Technology, Rolla, MO, USA
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104
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Yu Y, Yang G, Huang H, Fu Z, Cao Z, Zheng L, You L, Zhang T. Preclinical models of pancreatic ductal adenocarcinoma: challenges and opportunities in the era of precision medicine. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:8. [PMID: 33402215 PMCID: PMC7783994 DOI: 10.1186/s13046-020-01787-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/23/2020] [Indexed: 12/16/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an extremely lethal malignancy, with an average 5-year survival rate of 9% (Siegel RL, Miller KD, Jemal A. Ca Cancer J Clin. 2019;69(1):7-34). The steady increase in mortality rate indicates limited efficacy of the conventional regimen. The heterogeneity of PDAC calls for personalized treatment in clinical practice, which requires the construction of a preclinical system for generating patient-derived models. Currently, the lack of high-quality preclinical models results in ineffective translation of novel targeted therapeutics. This review summarizes applications of commonly used models, discusses major difficulties in PDAC model construction and provides recommendations for integrating workflows for precision medicine.
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Affiliation(s)
- Yiqi Yu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Gang Yang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Hua Huang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Ziyao Fu
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Zhe Cao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Lianfang Zheng
- Department of Nuclear Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Lei You
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Taiping Zhang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China. .,Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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105
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Schenning KJ, Holden S, Davis BA, Mulford A, Nevonen KA, Quinn JF, Raber J, Carbone L, Alkayed NJ. Gene-Specific DNA Methylation Linked to Postoperative Cognitive Dysfunction in Apolipoprotein E3 and E4 Mice. J Alzheimers Dis 2021; 83:1251-1268. [PMID: 34420963 PMCID: PMC8801332 DOI: 10.3233/jad-210499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Geriatric surgical patients are at higher risk of developing postoperative neurocognitive disorders (NCD) than younger patients. The specific mechanisms underlying postoperative NCD remain unknown, but they have been linked to genetic risk factors, such as the presence of APOE4, compared to APOE3, and epigenetic modifications caused by exposure to anesthesia and surgery. OBJECTIVE To test the hypothesis that compared to E3 mice, E4 mice exhibit a more pronounced postoperative cognitive impairment associated with differential DNA methylation in brain regions linked to learning and memory. METHODS 16-month-old humanized apolipoprotein-E targeted replacement mice bearing E3 or E4 were subjected to surgery (laparotomy) under general isoflurane anesthesia or sham. Postoperative behavioral testing and genome-wide DNA methylation were performed. RESULTS Exposure to surgery and anesthesia impaired cognition in aged E3, but not E4 mice, likely due to the already lower cognitive performance of E4 prior to surgery. Cognitive impairment in E3 mice was associated with hypermethylation of specific genes, including genes in the Ephrin pathway implicated in synaptic plasticity and learning in adults and has been linked to Alzheimer's disease. Other genes, such as the Scratch Family Transcriptional Repressor 2, were altered after surgery and anesthesia in both the E3 and E4 mice. CONCLUSION Our findings suggest that the neurocognitive and behavioral effects of surgery and anesthesia depend on baseline neurocognitive status and are associated with APOE isoform-dependent epigenetic modifications of specific genes and pathways involved in memory and learning.
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Affiliation(s)
- Katie J. Schenning
- Department of Anesthesiology & Perioperative Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Sarah Holden
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - Brett A. Davis
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA
| | - Amelia Mulford
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - Kimberly A. Nevonen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA
| | - Joseph F. Quinn
- Department of Neurology, Oregon Health & Science University, Portland, OR, USA
| | - Jacob Raber
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
- Department of Neurology, Oregon Health & Science University, Portland, OR, USA
- Department of Radiation Medicine, Division of Neuroscience, ONPRC, Portland, OR, USA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Genetics, Oregon National Primate Research Center, Portland, OR, USA
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Nabil J. Alkayed
- Department of Anesthesiology & Perioperative Medicine, Oregon Health & Science University, Portland, OR, USA
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA
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106
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Kikuchi M, Nakazawa T, Kinoshita M, Yamamori H, Yasuda Y, Fujimoto M, Hashimoto R, Numata S. Methylation Analysis in Monozygotic Twins With Treatment-Resistant Schizophrenia and Discordant Responses to Clozapine. Front Psychiatry 2021; 12:734606. [PMID: 34616320 PMCID: PMC8488120 DOI: 10.3389/fpsyt.2021.734606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/24/2021] [Indexed: 01/04/2023] Open
Abstract
Schizophrenia is a mental illness that involves both genetic and environmental factors. Clozapine, an atypical antipsychotic, is a well-established therapy for treatment-resistant schizophrenia. In this study, we focused on a set of monozygotic twins with treatment-resistant schizophrenia in which one twin effectively responded to clozapine treatment and the other did not. Our previous study generated neurons from induced pluripotent stem (iPS) cells derived from these patients and compared the transcriptome profiles between mock- and clozapine-treated neurons. In this study, we performed genome-wide DNA methylation profiling to investigate the mechanisms underlying gene expression changes. First, we extracted the differentially methylated sites from each twin based on statistical analysis. Then, we combined the DNA methylation profiling with transcriptome profiling from our previous RNA-seq data. Among the genes with altered methylation and expression, we found the different proportions of the genes related to neuronal and synaptic functions between the clozapine responder and non-responder (35.7 and 6.7%, respectively). This trend was observed even when the basal differences between the responder and non-responder was excluded. These results suggest that effective clozapine action may correct the abnormalities of neuronal and synapse functions in schizophrenia via changes in methylation.
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Affiliation(s)
- Masataka Kikuchi
- Department of Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Takanobu Nakazawa
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Makoto Kinoshita
- Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Hidenaga Yamamori
- Department of Pathology of Mental Diseases, National Center of Neurology and Psychiatry, National Institute of Mental Health, Tokyo, Japan.,Department of Psychiatry, Graduate School of Medicine, Osaka University, Osaka, Japan.,Japan Community Health Care Organization Osaka Hospital, Osaka, Japan
| | - Yuka Yasuda
- Department of Pathology of Mental Diseases, National Center of Neurology and Psychiatry, National Institute of Mental Health, Tokyo, Japan.,Medical Corporation Foster, Osaka, Japan
| | - Michiko Fujimoto
- Department of Pathology of Mental Diseases, National Center of Neurology and Psychiatry, National Institute of Mental Health, Tokyo, Japan.,Department of Psychiatry, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Center of Neurology and Psychiatry, National Institute of Mental Health, Tokyo, Japan
| | - Shusuke Numata
- Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
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107
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Madrid A, Borth LE, Hogan KJ, Hariharan N, Papale LA, Alisch RS, Iskandar BJ. DNA methylation and hydroxymethylation have distinct genome-wide profiles related to axonal regeneration. Epigenetics 2021; 16:64-78. [PMID: 32633672 PMCID: PMC7889172 DOI: 10.1080/15592294.2020.1786320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/04/2020] [Accepted: 05/28/2020] [Indexed: 12/23/2022] Open
Abstract
Alterations in environmentally sensitive epigenetic mechanisms (e.g., DNA methylation) influence axonal regeneration in the spinal cord following sharp injury. Conventional DNA methylation detection methods using sodium bisulphite treatment do not distinguish between methylated and hydroxymethylated forms of cytosine, meaning that past studies report a composite of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). To identify the distinct contributions of DNA methylation modifications to axonal regeneration, we collected spinal cord tissue after sharp injury from untreated adult F3 male rats with enhanced regeneration of injured spinal axons or controls, derived from folate- or water-treated F0 lineages, respectively. Genomic DNA was profiled for genome-wide 5hmC levels, revealing 658 differentially hydroxymethylated regions (DhMRs). Genomic profiling with whole genome bisulphite sequencing disclosed regeneration-related alterations in composite 5mC + 5hmC DNA methylation levels at 2,260 differentially methylated regions (DMRs). While pathway analyses revealed that differentially hydroxymethylated and methylated genes are linked to biologically relevant axon developmental pathways, only 22 genes harbour both DhMR and DMRs. Since these differential modifications were more than 60 kilobases on average away from each other, the large majority of differential hydroxymethylated and methylated regions are unique with distinct functions in the axonal regeneration phenotype. These data highlight the importance of distinguishing independent contributions of 5mC and 5hmC levels in the central nervous system, and denote discrete roles for DNA methylation modifications in spinal cord injury and regeneration in the context of transgenerational inheritance.
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Affiliation(s)
- Andy Madrid
- Department of Neurological Surgery, University of Wisconsin – Madison, Madison, WI, USA
- Neuroscience Training Program, University of Wisconsin – Madison, Madison, WI, USA
| | - Laura E. Borth
- Department of Neurological Surgery, University of Wisconsin – Madison, Madison, WI, USA
- Interdepartmental Graduate Program in Nutritional Science, University of Wisconsin – Madison, Madison, WI, USA
| | - Kirk J. Hogan
- Department of Anesthesiology, University of Wisconsin – Madison, Madison, WI, USA
| | - Nithya Hariharan
- Department of Neurological Surgery, University of Wisconsin – Madison, Madison, WI, USA
| | - Ligia A. Papale
- Department of Neurological Surgery, University of Wisconsin – Madison, Madison, WI, USA
| | - Reid S. Alisch
- Department of Neurological Surgery, University of Wisconsin – Madison, Madison, WI, USA
| | - Bermans J. Iskandar
- Department of Neurological Surgery, University of Wisconsin – Madison, Madison, WI, USA
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108
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Sharma NK, Comeau ME, Montoya D, Pellegrini M, Howard TD, Langefeld CD, Das SK. Integrative Analysis of Glucometabolic Traits, Adipose Tissue DNA Methylation, and Gene Expression Identifies Epigenetic Regulatory Mechanisms of Insulin Resistance and Obesity in African Americans. Diabetes 2020; 69:2779-2793. [PMID: 32928872 PMCID: PMC7679782 DOI: 10.2337/db20-0117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 08/28/2020] [Indexed: 12/13/2022]
Abstract
Decline in insulin sensitivity due to dysfunction of adipose tissue (AT) is one of the earliest pathogenic events in type 2 diabetes. We hypothesize that differential DNA methylation (DNAm) controls insulin sensitivity and obesity by modulating transcript expression in AT. Integrating AT DNAm profiles with transcript profile data measured in a cohort of 230 African Americans (AAs) from the African American Genetics of Metabolism and Expression cohort, we performed cis-expression quantitative trait methylation (cis-eQTM) analysis to identify epigenetic regulatory loci for glucometabolic trait-associated transcripts. We identified significantly associated cytosine-guanine dinucleotide regions for 82 transcripts (false discovery rate [FDR]-P < 0.05). The strongest eQTM locus was observed for the proopiomelanocortin (POMC; ρ = -0.632, P = 4.70 × 10-27) gene. Epigenome-wide association studies (EWAS) further identified 155, 46, and 168 cytosine-guanine dinucleotide regions associated (FDR-P < 0.05) with the Matsuda index, SI, and BMI, respectively. Intersection of EWAS, transcript level to trait association, and eQTM results, followed by causal inference test identified significant eQTM loci for 23 genes that were also associated with Matsuda index, SI, and/or BMI in EWAS. These associated genes include FERMT3, ITGAM, ITGAX, and POMC In summary, applying an integrative multiomics approach, our study provides evidence for DNAm-mediated regulation of gene expression at both previously identified and novel loci for many key AT transcripts influencing insulin resistance and obesity.
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Affiliation(s)
- Neeraj K Sharma
- Department of Internal Medicine, Section of Endocrinology and Metabolism, Wake Forest School of Medicine, Winston-Salem, NC
| | - Mary E Comeau
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Dennis Montoya
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA
| | - Timothy D Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Swapan K Das
- Department of Internal Medicine, Section of Endocrinology and Metabolism, Wake Forest School of Medicine, Winston-Salem, NC
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109
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Schmidt M, Maié T, Dahl E, Costa IG, Wagner W. Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites. BMC Biol 2020; 18:178. [PMID: 33234153 PMCID: PMC7687708 DOI: 10.1186/s12915-020-00910-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Background The complex composition of different cell types within a tissue can be estimated by deconvolution of bulk gene expression profiles or with various single-cell sequencing approaches. Alternatively, DNA methylation (DNAm) profiles have been used to establish an atlas for multiple human tissues and cell types. DNAm is particularly suitable for deconvolution of cell types because each CG dinucleotide (CpG site) has only two states per DNA strand—methylated or non-methylated—and these epigenetic modifications are very consistent during cellular differentiation. So far, deconvolution of DNAm profiles implies complex signatures of many CpGs that are often measured by genome-wide analysis with Illumina BeadChip microarrays. In this study, we investigated if the characterization of cell types in tissue is also feasible with individual cell type-specific CpG sites, which can be addressed by targeted analysis, such as pyrosequencing. Results We compiled and curated 579 Illumina 450k BeadChip DNAm profiles of 14 different non-malignant human cell types. A training and validation strategy was applied to identify and test for cell type-specific CpGs. We initially focused on estimating the relative amount of fibroblasts using two CpGs that were either hypermethylated or hypomethylated in fibroblasts. The combination of these two DNAm levels into a “FibroScore” correlated with the state of fibrosis and was associated with overall survival in various types of cancer. Furthermore, we identified hypomethylated CpGs for leukocytes, endothelial cells, epithelial cells, hepatocytes, glia, neurons, fibroblasts, and induced pluripotent stem cells. The accuracy of this eight CpG signature was tested in additional BeadChip datasets of defined cell mixtures and the results were comparable to previously published signatures based on several thousand CpGs. Finally, we established and validated pyrosequencing assays for the relevant CpGs that can be utilized for classification and deconvolution of cell types. Conclusion This proof of concept study demonstrates that DNAm analysis at individual CpGs reflects the cellular composition of cellular mixtures and different tissues. Targeted analysis of these genomic regions facilitates robust methods for application in basic research and clinical settings.
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Affiliation(s)
- Marco Schmidt
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, 52074, Aachen, Germany
| | - Tiago Maié
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, 52074, Aachen, Germany
| | - Edgar Dahl
- RWTH centralized Biomaterial Bank (RWTH cBMB), Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, 52074, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, 52074, Aachen, Germany. .,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, 52074, Aachen, Germany.
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110
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Dratwa M, Wysoczańska B, Łacina P, Kubik T, Bogunia-Kubik K. TERT-Regulation and Roles in Cancer Formation. Front Immunol 2020; 11:589929. [PMID: 33329574 PMCID: PMC7717964 DOI: 10.3389/fimmu.2020.589929] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/16/2020] [Indexed: 12/16/2022] Open
Abstract
Telomerase reverse transcriptase (TERT) is a catalytic subunit of telomerase. Telomerase complex plays a key role in cancer formation by telomere dependent or independent mechanisms. Telomere maintenance mechanisms include complex TERT changes such as gene amplifications, TERT structural variants, TERT promoter germline and somatic mutations, TERT epigenetic changes, and alternative lengthening of telomere. All of them are cancer specific at tissue histotype and at single cell level. TERT expression is regulated in tumors via multiple genetic and epigenetic alterations which affect telomerase activity. Telomerase activity via TERT expression has an impact on telomere length and can be a useful marker in diagnosis and prognosis of various cancers and a new therapy approach. In this review we want to highlight the main roles of TERT in different mechanisms of cancer development and regulation.
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Affiliation(s)
- Marta Dratwa
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Barbara Wysoczańska
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Piotr Łacina
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Tomasz Kubik
- Department of Computer Engineering, Faculty of Electronics, Wrocław University of Science and Technology, Wroclaw, Poland
| | - Katarzyna Bogunia-Kubik
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
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111
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Olsson Lindvall M, Angerfors A, Andersson B, Nilsson S, Davila Lopez M, Hansson L, Stanne TM, Jern C. Comparison of DNA Methylation Profiles of Hemostatic Genes between Liver Tissue and Peripheral Blood within Individuals. Thromb Haemost 2020; 121:573-583. [PMID: 33202445 PMCID: PMC8116175 DOI: 10.1055/s-0040-1720980] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
DNA methylation has become increasingly recognized in the etiology of complex diseases, including thrombotic disorders. Blood is often collected in epidemiological studies for genotyping and has recently also been used to examine DNA methylation in epigenome-wide association studies. DNA methylation patterns are often tissue-specific, thus, peripheral blood may not accurately reflect the methylation pattern in the tissue of relevance. Here, we collected paired liver and blood samples concurrently from 27 individuals undergoing liver surgery. We performed targeted bisulfite sequencing for a set of 35 hemostatic genes primarily expressed in liver to analyze DNA methylation levels of >10,000 cytosine-phosphate-guanine (CpG) dinucleotides. We evaluated whether DNA methylation in blood could serve as a proxy for DNA methylation in liver at individual CpGs. Approximately 30% of CpGs were nonvariable and were predominantly hypo- (<25%) or hypermethylated (>70%) in both tissues. While blood can serve as a proxy for liver at these CpGs, the low variability renders these unlikely to explain phenotypic differences. We therefore focused on CpG sites with variable methylation levels in liver. The level of blood-liver tissue correlation varied widely across these variable CpGs; moderate correlations (0.5 ≤ r < 0.75) were detected for 6% and strong correlations (r ≥ 0.75) for a further 4%. Our findings indicate that it is essential to study the concordance of DNA methylation between blood and liver at individual CpGs. This paired blood-liver dataset is intended as a resource to aid interpretation of blood-based DNA methylation results.
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Affiliation(s)
- Martina Olsson Lindvall
- Department of Laboratory Medicine, Institute of Biomedicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Annelie Angerfors
- Department of Laboratory Medicine, Institute of Biomedicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Bioinformatics Core Facility, University of Gothenburg, Gothenburg, Sweden
| | - Björn Andersson
- Bioinformatics Core Facility, University of Gothenburg, Gothenburg, Sweden
| | - Staffan Nilsson
- Department of Laboratory Medicine, Institute of Biomedicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | | | | | - Tara M Stanne
- Department of Laboratory Medicine, Institute of Biomedicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Christina Jern
- Department of Laboratory Medicine, Institute of Biomedicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
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112
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Roubroeks JAY, Smith AR, Smith RG, Pishva E, Ibrahim Z, Sattlecker M, Hannon EJ, Kłoszewska I, Mecocci P, Soininen H, Tsolaki M, Vellas B, Wahlund LO, Aarsland D, Proitsi P, Hodges A, Lovestone S, Newhouse SJ, Dobson RJB, Mill J, van den Hove DLA, Lunnon K. An epigenome-wide association study of Alzheimer's disease blood highlights robust DNA hypermethylation in the HOXB6 gene. Neurobiol Aging 2020; 95:26-45. [PMID: 32745807 PMCID: PMC7649340 DOI: 10.1016/j.neurobiolaging.2020.06.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/27/2020] [Accepted: 06/27/2020] [Indexed: 12/21/2022]
Abstract
A growing number of epigenome-wide association studies have demonstrated a role for DNA methylation in the brain in Alzheimer's disease. With the aim of exploring peripheral biomarker potential, we have examined DNA methylation patterns in whole blood collected from 284 individuals in the AddNeuroMed study, which included 89 nondemented controls, 86 patients with Alzheimer's disease, and 109 individuals with mild cognitive impairment, including 38 individuals who progressed to Alzheimer's disease within 1 year. We identified significant differentially methylated regions, including 12 adjacent hypermethylated probes in the HOXB6 gene in Alzheimer's disease, which we validated using pyrosequencing. Using weighted gene correlation network analysis, we identified comethylated modules of genes that were associated with key variables such as APOE genotype and diagnosis. In summary, this study represents the first large-scale epigenome-wide association study of Alzheimer's disease and mild cognitive impairment using blood. We highlight the differences in various loci and pathways in early disease, suggesting that these patterns relate to cognitive decline at an early stage.
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Affiliation(s)
| | - Adam R Smith
- College of Medicine and Health, University of Exeter, Exeter, UK
| | - Rebecca G Smith
- College of Medicine and Health, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- College of Medicine and Health, University of Exeter, Exeter, UK; School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands
| | - Zina Ibrahim
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience (IOPPN), King's College London, London, UK; Farr Institute of Health Informatics Research, University College London, London, UK
| | - Martina Sattlecker
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience (IOPPN), King's College London, London, UK
| | - Eilis J Hannon
- College of Medicine and Health, University of Exeter, Exeter, UK
| | | | - Patrizia Mecocci
- Institute of Gerontology and Geriatrics, University of Perugia, Perugia, Italy
| | - Hilkka Soininen
- Institute of Clinical Medicine, Neurology, University of Eastern Finland, Kuopio, Finland; Neurocenter, Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Magda Tsolaki
- 1st Department of Neurology, Memory and Dementia Unit, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Bruno Vellas
- INSERM U 558, University of Toulouse, Toulouse, France
| | - Lars-Olof Wahlund
- NVS Department, Section for Clinical Geriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Dag Aarsland
- King's Health Partners Centre for Neurodegeneration Research, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; Centre for Age-Related Diseases, Stavanger University Hospital, Stavanger, Norway
| | - Petroula Proitsi
- King's Health Partners Centre for Neurodegeneration Research, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; NIHR Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, King's College London, London, UK
| | - Angela Hodges
- King's Health Partners Centre for Neurodegeneration Research, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Simon Lovestone
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, UK; Current Affiliation at Janssen-Cilag UK
| | - Stephen J Newhouse
- King's Health Partners Centre for Neurodegeneration Research, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; NIHR Biomedical Research Centre for Mental Health at South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, King's College London, London, UK
| | - Richard J B Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience (IOPPN), King's College London, London, UK; Farr Institute of Health Informatics Research, University College London, London, UK
| | - Jonathan Mill
- College of Medicine and Health, University of Exeter, Exeter, UK
| | - Daniël L A van den Hove
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Katie Lunnon
- College of Medicine and Health, University of Exeter, Exeter, UK.
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113
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Hypoxia and Oxygen-Sensing Signaling in Gene Regulation and Cancer Progression. Int J Mol Sci 2020; 21:ijms21218162. [PMID: 33142830 PMCID: PMC7663541 DOI: 10.3390/ijms21218162] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/19/2022] Open
Abstract
Oxygen homeostasis regulation is the most fundamental cellular process for adjusting physiological oxygen variations, and its irregularity leads to various human diseases, including cancer. Hypoxia is closely associated with cancer development, and hypoxia/oxygen-sensing signaling plays critical roles in the modulation of cancer progression. The key molecules of the hypoxia/oxygen-sensing signaling include the transcriptional regulator hypoxia-inducible factor (HIF) which widely controls oxygen responsive genes, the central members of the 2-oxoglutarate (2-OG)-dependent dioxygenases, such as prolyl hydroxylase (PHD or EglN), and an E3 ubiquitin ligase component for HIF degeneration called von Hippel–Lindau (encoding protein pVHL). In this review, we summarize the current knowledge about the canonical hypoxia signaling, HIF transcription factors, and pVHL. In addition, the role of 2-OG-dependent enzymes, such as DNA/RNA-modifying enzymes, JmjC domain-containing enzymes, and prolyl hydroxylases, in gene regulation of cancer progression, is specifically reviewed. We also discuss the therapeutic advancement of targeting hypoxia and oxygen sensing pathways in cancer.
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114
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Corbett RJ, Te Pas MFW, van den Brand H, Groenen MAM, Crooijmans RPMA, Ernst CW, Madsen O. Genome-Wide Assessment of DNA Methylation in Chicken Cardiac Tissue Exposed to Different Incubation Temperatures and CO 2 Levels. Front Genet 2020; 11:558189. [PMID: 33193638 PMCID: PMC7655987 DOI: 10.3389/fgene.2020.558189] [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: 05/01/2020] [Accepted: 09/30/2020] [Indexed: 12/26/2022] Open
Abstract
Temperature and CO2 concentration during incubation have profound effects on broiler chick development, and numerous studies have identified significant effects on hatch heart weight (HW) as a result of differences in these parameters. Early life environment has also been shown to affect broiler performance later in life; it has thus been suggested that epigenetic mechanisms may mediate long-term physiological changes induced by environmental stimuli. DNA methylation is an epigenetic modification that can confer heritable changes in gene expression. Using reduced-representation bisulfite sequencing (RRBS), we assessed DNA methylation patterns in cardiac tissue of 84 broiler hatchlings incubated at two egg shell temperatures (EST; 37.8°C and 38.9°C) and three CO2 concentrations (0.1%, 0.4%, and 0.8%) from day 8 of incubation onward. We assessed differential methylation between EST treatments and identified 2,175 differentially methylated (DM) CpGs (1,121 hypermethylated, 1,054 hypomethylated at 38.9° vs. 37.8°) in 269 gene promoters and 949 intragenic regions. DM genes (DMGs) were associated with heart developmental processes, including cardiomyocyte proliferation and differentiation. We identified enriched binding motifs among DM loci, including those for transcription factors associated with cell proliferation and heart development among hypomethylated CpGs that suggest increased binding ability at higher EST. We identified 9,823 DM CpGs between at least two CO2 treatments, with the greatest difference observed between 0.8 and 0.1% CO2 that disproportionately impacted genes involved in cardiac muscle development and response to low oxygen levels. Using HW measurements from the same chicks, we performed an epigenome-wide association study (EWAS) for HW, and identified 23 significantly associated CpGs, nine of which were also DM between ESTs. We found corresponding differences in transcript abundance between ESTs in three DMGs (ABLIM2, PITX2, and THRSP). Hypomethylation of an exonic CpG in PITX2 at 38.9°C was associated with increased expression, and suggests increased cell proliferation in broiler hatchlings incubated at higher temperatures. Overall, these results identified numerous epigenetic associations between chick incubation factors and heart development that may manifest in long-term differences in animal performance.
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Affiliation(s)
- Ryan J Corbett
- Genetics and Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, United States
| | - Marinus F W Te Pas
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | - Henry van den Brand
- Adaptation Physiology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | | | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
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115
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Miller BF, Pisanic Ii TR, Margolin G, Petrykowska HM, Athamanolap P, Goncearenco A, Osei-Tutu A, Annunziata CM, Wang TH, Elnitski L. Leveraging locus-specific epigenetic heterogeneity to improve the performance of blood-based DNA methylation biomarkers. Clin Epigenetics 2020; 12:154. [PMID: 33081832 PMCID: PMC7574234 DOI: 10.1186/s13148-020-00939-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 09/21/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Variation in intercellular methylation patterns can complicate the use of methylation biomarkers for clinical diagnostic applications such as blood-based cancer testing. Here, we describe development and validation of a methylation density binary classification method called EpiClass (available for download at https://github.com/Elnitskilab/EpiClass ) that can be used to predict and optimize the performance of methylation biomarkers, particularly in challenging, heterogeneous samples such as liquid biopsies. This approach is based upon leveraging statistical differences in single-molecule sample methylation density distributions to identify ideal thresholds for sample classification. RESULTS We developed and tested the classifier using reduced representation bisulfite sequencing (RRBS) data derived from ovarian carcinoma tissue DNA and controls. We used these data to perform in silico simulations using methylation density profiles from individual epiallelic copies of ZNF154, a genomic locus known to be recurrently methylated in numerous cancer types. From these profiles, we predicted the performance of the classifier in liquid biopsies for the detection of epithelial ovarian carcinomas (EOC). In silico analysis indicated that EpiClass could be leveraged to better identify cancer-positive liquid biopsy samples by implementing precise thresholds with respect to methylation density profiles derived from circulating cell-free DNA (cfDNA) analysis. These predictions were confirmed experimentally using DREAMing to perform digital methylation density analysis on a cohort of low volume (1-ml) plasma samples obtained from 26 EOC-positive and 41 cancer-free women. EpiClass performance was then validated in an independent cohort of 24 plasma specimens, derived from a longitudinal study of 8 EOC-positive women, and 12 plasma specimens derived from 12 healthy women, respectively, attaining a sensitivity/specificity of 91.7%/100.0%. Direct comparison of CA-125 measurements with EpiClass demonstrated that EpiClass was able to better identify EOC-positive women than standard CA-125 assessment. Finally, we used independent whole genome bisulfite sequencing (WGBS) datasets to demonstrate that EpiClass can also identify other cancer types as well or better than alternative methylation-based classifiers. CONCLUSIONS Our results indicate that assessment of intramolecular methylation density distributions calculated from cfDNA facilitates the use of methylation biomarkers for diagnostic applications. Furthermore, we demonstrated that EpiClass analysis of ZNF154 methylation was able to outperform CA-125 in the detection of etiologically diverse ovarian carcinomas, indicating broad utility of ZNF154 for use as a biomarker of ovarian cancer.
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Affiliation(s)
- Brendan F Miller
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Thomas R Pisanic Ii
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Gennady Margolin
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hanna M Petrykowska
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Pornpat Athamanolap
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Alexander Goncearenco
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Akosua Osei-Tutu
- Women's Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christina M Annunziata
- Women's Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tza-Huei Wang
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Laura Elnitski
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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116
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Chhatbar K, Cholewa-Waclaw J, Shah R, Bird A, Sanguinetti G. Quantitative analysis questions the role of MeCP2 as a global regulator of alternative splicing. PLoS Genet 2020; 16:e1009087. [PMID: 33048927 PMCID: PMC7584252 DOI: 10.1371/journal.pgen.1009087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/23/2020] [Accepted: 08/28/2020] [Indexed: 11/19/2022] Open
Abstract
MeCP2 is an abundant protein in mature nerve cells, where it binds to DNA sequences containing methylated cytosine. Mutations in the MECP2 gene cause the severe neurological disorder Rett syndrome (RTT), provoking intensive study of the underlying molecular mechanisms. Multiple functions have been proposed, one of which involves a regulatory role in splicing. Here we leverage the recent availability of high-quality transcriptomic data sets to probe quantitatively the potential influence of MeCP2 on alternative splicing. Using a variety of machine learning approaches that can capture both linear and non-linear associations, we show that widely different levels of MeCP2 have a minimal effect on alternative splicing in three different systems. Alternative splicing was also apparently indifferent to developmental changes in DNA methylation levels. Our results suggest that regulation of splicing is not a major function of MeCP2. They also highlight the importance of multi-variate quantitative analyses in the formulation of biological hypotheses.
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Affiliation(s)
- Kashyap Chhatbar
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Justyna Cholewa-Waclaw
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Ruth Shah
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Adrian Bird
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Guido Sanguinetti
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
- International School for Advanced Studies (SISSA), Trieste, Italy
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117
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Chung RH, Kang CY. pWGBSSimla: a profile-based whole-genome bisulfite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions. Bioinformatics 2020; 36:660-665. [PMID: 31397839 DOI: 10.1093/bioinformatics/btz635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/05/2019] [Accepted: 08/08/2019] [Indexed: 12/19/2022] Open
Abstract
MOTIVATION DNA methylation plays an important role in regulating gene expression. DNA methylation is commonly analyzed using bisulfite sequencing (BS-seq)-based designs, such as whole-genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS) and oxidative bisulfite sequencing (oxBS-seq). Furthermore, there has been growing interest in investigating the roles that genetic variants play in changing the methylation levels (i.e. methylation quantitative trait loci or meQTLs), how methylation regulates the imprinting of gene expression (i.e. allele-specific methylation or ASM) and the differentially methylated regions (DMRs) among different cell types. However, none of the current simulation tools can generate different BS-seq data types (e.g. WGBS, RRBS and oxBS-seq) while modeling meQTLs, ASM and DMRs. RESULTS We developed profile-based whole-genome bisulfite sequencing data simulator (pWGBSSimla), a profile-based bisulfite sequencing data simulator, which simulates WGBS, RRBS and oxBS-seq data for different cell types based on real data. meQTLs and ASM are modeled based on the block structures of the methylation status at CpGs, whereas the simulation of DMRs is based on observations of methylation rates in real data. We demonstrated that pWGBSSimla adequately simulates data and allows performance comparisons among different methylation analysis methods. AVAILABILITY AND IMPLEMENTATION pWGBSSimla is available at https://omicssimla.sourceforge.io. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ren-Hua Chung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350, Taiwan
| | - Chen-Yu Kang
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350, Taiwan
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118
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A Unique Epigenomic Landscape Defines Human Erythropoiesis. Cell Rep 2020; 28:2996-3009.e7. [PMID: 31509757 PMCID: PMC6863094 DOI: 10.1016/j.celrep.2019.08.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/28/2019] [Accepted: 08/02/2019] [Indexed: 12/15/2022] Open
Abstract
Mammalian erythropoiesis yields a highly specialized cell type, the mature erythrocyte, evolved to meet the organismal needs of increased oxygen-carrying capacity. To better understand the regulation of erythropoiesis, we performed genome-wide studies of chromatin accessibility, DNA methylation, and transcriptomics using a recently developed strategy to obtain highly purified populations of primary human erythroid cells. The integration of gene expression, DNA methylation, and chromatin state dynamics reveals that stage-specific gene regulation during erythropoiesis is a stepwise and hierarchical process involving many cis-regulatory elements. Erythroid-specific, nonpromoter sites of chromatin accessibility are linked to erythroid cell phenotypic variation and inherited disease. Comparative analyses of stage-specific chromatin accessibility indicate that there is limited early chromatin priming of erythroid genes during hematopoiesis. The epigenome of terminally differentiating erythroid cells defines a distinct subset of highly specialized cells that are vastly dissimilar from other hematopoietic and nonhematopoietic cell types. These epigenomic and transcriptome data are powerful tools to study human erythropoiesis. Schulz et al. use genome-wide studies of chromatin accessibility, DNA methylation, and transcriptomes in primary human erythroid cells to reveal important characteristics of erythropoiesis. Chromatin accessibility of terminal erythroid differentiation is markedly dissimilar from other hematopoietic cell types. Epigenomic changes are linked to erythroid cell traits and disease genes.
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119
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Carter JL, Halmai JANM, Fink KD. The iNs and Outs of Direct Reprogramming to Induced Neurons. Front Genome Ed 2020; 2:7. [PMID: 34713216 PMCID: PMC8525349 DOI: 10.3389/fgeed.2020.00007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding of cell-type specific transcription factors has promoted progress in methods for cellular reprogramming, such as directly reprogramming somatic cells to induced neurons (iN). Methods for direct reprogramming require neuronal-fate determining gene activation via neuron-specific microRNAs, chemical modulation of key neuronal signaling pathways or overexpression via viral vectors, with some reprogramming strategies requiring a combination of these methods to induce the neuronal-cell fate. These methods have been employed in a multitude of cell types, including fibroblasts, hepatocytes, peripheral blood mononuclear, and T cells. The ability to create iN from skin biopsies and blood samples coupled with recent advancements in artificially inducing age- and disease-associated phenotypes are accelerating the development of disease models for late-onset neurodegenerative disorders. Here, we review how activation of the neuronal transcriptome alters the epigenetic landscape of the donor cell to facilitate reprogramming to neurons. We also discuss the advantages of using DNA binding domains such as CRISPR/dCas9 to overcome epigenetic barriers to induce neuronal-cell fate by activating endogenous neuronal cell-fate determining genes.
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120
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Smith AR, Wheildon G, Lunnon K. Invited Review – A 5‐year update on epigenome‐wide association studies of DNA modifications in Alzheimer’s disease: progress, practicalities and promise. Neuropathol Appl Neurobiol 2020; 46:641-653. [DOI: 10.1111/nan.12650] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 07/10/2020] [Accepted: 07/12/2020] [Indexed: 12/12/2022]
Affiliation(s)
- A. R. Smith
- University of Exeter Medical School College of Medicine and Health Exeter University Exeter UK
| | - G. Wheildon
- University of Exeter Medical School College of Medicine and Health Exeter University Exeter UK
| | - K. Lunnon
- University of Exeter Medical School College of Medicine and Health Exeter University Exeter UK
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121
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Guarnieri G, Sarchielli E, Comeglio P, Herrera-Puerta E, Piaceri I, Nacmias B, Benelli M, Kelsey G, Maggi M, Gallina P, Vannelli GB, Morelli A. Tumor Necrosis Factor α Influences Phenotypic Plasticity and Promotes Epigenetic Changes in Human Basal Forebrain Cholinergic Neuroblasts. Int J Mol Sci 2020; 21:E6128. [PMID: 32854421 PMCID: PMC7504606 DOI: 10.3390/ijms21176128] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 01/08/2023] Open
Abstract
TNFα is the main proinflammatory cytokine implicated in the pathogenesis of neurodegenerative disorders, but it also modulates physiological functions in both the developing and adult brain. In this study, we investigated a potential direct role of TNFα in determining phenotypic changes of a recently established cellular model of human basal forebrain cholinergic neuroblasts isolated from the nucleus basalis of Meynert (hfNBMs). Exposing hfNBMs to TNFα reduced the expression of immature markers, such as nestin and β-tubulin III, and inhibited primary cilium formation. On the contrary, TNFα increased the expression of TNFα receptor TNFR2 and the mature neuron marker MAP2, also promoting neurite elongation. Moreover, TNFα affected nerve growth factor receptor expression. We also found that TNFα induced the expression of DNA-methylation enzymes and, accordingly, downregulated genes involved in neuronal development through epigenetic mechanisms, as demonstrated by methylome analysis. In summary, TNFα showed a dual role on hfNBMs phenotypic plasticity, exerting a negative influence on neurogenesis despite a positive effect on differentiation, through mechanisms that remain to be elucidated. Our results help to clarify the complexity of TNFα effects in human neurons and suggest that manipulation of TNFα signaling could provide a potential therapeutic approach against neurodegenerative disorders.
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Affiliation(s)
- Giulia Guarnieri
- Section of Human Anatomy and Histology, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (E.S.); (G.B.V.)
| | - Erica Sarchielli
- Section of Human Anatomy and Histology, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (E.S.); (G.B.V.)
| | - Paolo Comeglio
- Sexual Medicine and Andrology Unit, Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy;
| | | | - Irene Piaceri
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, 50134 Florence, Italy; (I.P.); (B.N.)
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, 50134 Florence, Italy; (I.P.); (B.N.)
| | - Matteo Benelli
- Bioinformatics Unit, Hospital of Prato, Azienda USL Toscana Centro, 50122 Prato, Italy;
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK;
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 1TN, UK
| | - Mario Maggi
- Endocrinology Unit, Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy;
| | - Pasquale Gallina
- Neurosurgical Unit, Department of Neurosciences, Psychology, Drug Research and Child Health, University of Florence, 50134 Florence, Italy;
| | - Gabriella Barbara Vannelli
- Section of Human Anatomy and Histology, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (E.S.); (G.B.V.)
| | - Annamaria Morelli
- Section of Human Anatomy and Histology, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy; (E.S.); (G.B.V.)
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122
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Conway ME, McDaniel JM, Graham JM, Guillen KP, Oliver PG, Parker SL, Yue P, Turkson J, Buchsbaum DJ, Welm BE, Myers RM, Varley KE. STAT3 and GR Cooperate to Drive Gene Expression and Growth of Basal-Like Triple-Negative Breast Cancer. Cancer Res 2020; 80:4355-4370. [PMID: 32816914 DOI: 10.1158/0008-5472.can-20-1379] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/17/2020] [Accepted: 08/13/2020] [Indexed: 11/16/2022]
Abstract
Breast cancers are divided into subtypes with different prognoses and treatment responses based on global differences in gene expression. Luminal breast cancer gene expression and proliferation are driven by estrogen receptor alpha, and targeting this transcription factor is the most effective therapy for this subtype. By contrast, it remains unclear which transcription factors drive the gene expression signature that defines basal-like triple-negative breast cancer, and there are no targeted therapies approved to treat this aggressive subtype. In this study, we utilized integrated genomic analysis of DNA methylation, chromatin accessibility, transcription factor binding, and gene expression in large collections of breast cancer cell lines and patient tumors to identify transcription factors responsible for the basal-like gene expression program. Glucocorticoid receptor (GR) and STAT3 bind to the same genomic regulatory regions, which were specifically open and unmethylated in basal-like breast cancer. These transcription factors cooperated to regulate expression of hundreds of genes in the basal-like gene expression signature, which were associated with poor prognosis. Combination treatment with small-molecule inhibitors of both transcription factors resulted in synergistic decreases in cell growth in cell lines and patient-derived organoid models. This study demonstrates that GR and STAT3 cooperate to regulate the basal-like breast cancer gene expression program and provides the basis for improved therapy for basal-like triple-negative breast cancer through rational combination of STAT3 and GR inhibitors. SIGNIFICANCE: This study demonstrates that GR and STAT3 cooperate to activate the canonical gene expression signature of basal-like triple-negative breast cancer and that combination treatment with STAT3 and GR inhibitors could provide synergistic therapeutic efficacy.
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Affiliation(s)
- Megan E Conway
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Joy M McDaniel
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - James M Graham
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Katrin P Guillen
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Patsy G Oliver
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Peibin Yue
- Department of Medicine and Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - James Turkson
- Department of Medicine and Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Donald J Buchsbaum
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Bryan E Welm
- Department of Surgery, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - Katherine E Varley
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.
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Correlative study of epigenetic regulation of tumor microenvironment in spindle cell melanomas and cutaneous malignant peripheral nerve sheath tumors. Sci Rep 2020; 10:12996. [PMID: 32747660 PMCID: PMC7398924 DOI: 10.1038/s41598-020-69787-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/10/2020] [Indexed: 12/15/2022] Open
Abstract
The tumor microenvironment (TME) plays critical roles in tumor growth and progression, however key regulators of gene expression in the TME of cutaneous malignant peripheral nerve sheath tumor (C-MPNST) and spindle cell melanoma (SCM) have not been well elucidated. Herein, we investigate the epigenetic regulation of promoters and gene bodies and their effect on the TME composition of C-MPNSTs and SCMs. A cohort of 30 patients was analyzed using differential gene expression (DGE) and gene set enrichment analysis (GSEA) using the Nanostring platform. Methylation analysis was carried out utilizing an Infinium Methylation EPIC array targeting 866,562 methylation site (CpG) islands. DGE revealed overexpression of genes related to mast cells in the TME of SCMs, and a predominance of exhausted CD8+ T cells and macrophages in the TME of C-MPNSTs. Interestingly, we further observed promoter hypermethylation in key overexpressed genes and corresponding gene body hypomethylation. Analysis using ENCODE ChIP-sequencing data identified CTCF as the common transcription factor at the site of the hypomethylated probe. These findings support that the TME composition of C-MPNSTs and SCMs is at least partially independent on promoter methylation status, suggesting a possible relationship between gene body enhancers and expression of key TME genes in both entities.
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124
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Lee D, Choi YH, Seo J, Kim JK, Lee SB. Discovery of new epigenomics-based biomarkers and the early diagnosis of neurodegenerative diseases. Ageing Res Rev 2020; 61:101069. [PMID: 32416267 DOI: 10.1016/j.arr.2020.101069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 03/02/2020] [Accepted: 04/06/2020] [Indexed: 12/12/2022]
Abstract
Treatment options for many neurodegenerative diseases are limited due to the lack of early diagnostic procedures that allow timely delivery of therapeutic agents to affected neurons prior to cell death. While notable advances have been made in neurodegenerative disease biomarkers, whether or not the biomarkers discovered to date are useful for early diagnosis remains an open question. Additionally, the reliability of these biomarkers has been disappointing, due in part to the large dissimilarities between the tissues traditionally used to source biomarkers and primarily diseased neurons. In this article, we review the potential viability of atypical epigenetic and/or consequent transcriptional alterations (ETAs) as biomarkers of early-stage neurodegenerative disease, and present our perspectives on the discovery and practical use of such biomarkers in patient-derived neural samples using single-cell level analyses, thereby greatly enhancing the reliability of biomarker application.
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125
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Fiches GN, Zhou D, Kong W, Biswas A, Ahmed EH, Baiocchi RA, Zhu J, Santoso N. Profiling of immune related genes silenced in EBV-positive gastric carcinoma identified novel restriction factors of human gammaherpesviruses. PLoS Pathog 2020; 16:e1008778. [PMID: 32841292 PMCID: PMC7473590 DOI: 10.1371/journal.ppat.1008778] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 09/04/2020] [Accepted: 07/05/2020] [Indexed: 12/24/2022] Open
Abstract
EBV-associated gastric cancer (EBVaGC) is characterized by high frequency of DNA methylation. In this study, we investigated how epigenetic alteration of host genome contributes to pathogenesis of EBVaGC through the analysis of transcriptomic and epigenomic datasets from NIH TCGA (The Cancer Genome Atlas) consortium. We identified that immune related genes (IRGs) is a group of host genes preferentially silenced in EBV-positive gastric cancers through DNA hypermethylation. Further functional characterizations of selected IRGs reveal their novel antiviral activity against not only EBV but also KSHV. In particular, we showed that metallothionein-1 (MT1) and homeobox A (HOXA) gene clusters are down-regulated via EBV-driven DNA hypermethylation. Several MT1 isoforms suppress EBV lytic replication and release of progeny virions as well as KSHV lytic reactivation, suggesting functional redundancy of these genes. In addition, single HOXA10 isoform exerts antiviral activity against both EBV and KSHV. We also confirmed the antiviral effect of other dysregulated IRGs, such as IRAK2 and MAL, in scenario of EBV and KSHV lytic reactivation. Collectively, our results demonstrated that epigenetic silencing of IRGs is a viral strategy to escape immune surveillance and promote viral propagation, which is overall beneficial to viral oncogenesis of human gamma-herpesviruses (EBV and KSHV), considering that these IRGs possess antiviral activities against these oncoviruses.
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Affiliation(s)
- Guillaume N. Fiches
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Dawei Zhou
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Weili Kong
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
| | - Ayan Biswas
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Elshafa H. Ahmed
- Division of Hematology, Department of Internal Medicine, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Robert A. Baiocchi
- Division of Hematology, Department of Internal Medicine, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Jian Zhu
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Netty Santoso
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
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Xiao C, Beitler JJ, Higgins KA, Chico CE, Withycombe JS, Zhu Y, Zhao H, Lin IH, Li F, Jeon S, Irwin M, Bruner DW, Miller AH, Gary R. Pilot study of combined aerobic and resistance exercise on fatigue for patients with head and neck cancer: Inflammatory and epigenetic changes. Brain Behav Immun 2020; 88:184-192. [PMID: 32330594 PMCID: PMC7415514 DOI: 10.1016/j.bbi.2020.04.044] [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: 10/17/2019] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 12/29/2022] Open
Abstract
This pilot study examined whether a combined aerobic resistance exercise program reduced fatigue and the potential inflammatory and epigenetic mechanisms in patients with head and neck cancer (HNC) receiving intensity-modulated radiotherapy. The exercise group (N = 12) received a 3-month supervised aerobic resistance exercise intervention that was initiated before a 6-week radiotherapy regimen; the control group (N = 14) received standard care. Fatigue was measured using Multidimensional Fatigue Inventory-20; physical function measures included a 6-minute walk distance (6MWD), chair stands, bicep curls, and hand grip strength. Inflammatory markers and DNA methylation data were acquired using standardized protocol. Patients were mostly white (93%) and male (81%) with a mean age of 57 years. At the end of the intervention, the exercise group had a marginal decrease in fatigue compared with the control (-5.0 vs. 4.9; P = 0.10). The exercise group had a significantly greater improvement in 6MWD (29.8 vs. -55.5 m; P = 0.04), and a marginally smaller decline in hand grip (-0.3 vs. -5.8 lbs; P = 0.05) at the end of the intervention than the control. No significant difference in inflammatory markers was observed between groups. Lower plasma interleukin (IL) 6, IL1 receptor antagonist, tumor necrosis factor α (TNFα), soluble TNF receptor II and C-reactive protein were significantly associated with increased 6MWD, chair stand, and bicep curl at the end of the intervention (p < 0.05). Among the 1152 differentially methylated sites (DMS) after intervention (p < 0.001), 163 DMS were located in gene promoter regions. Enrichment analysis suggested that the top 10 upstream regulators were associated with tumor (HNF4A, RPP38, HOXA9, SAHM1, CDK7, NDN, RPS15) and inflammation (IRF7, CRKL, ONECUT1). The top 5 diseases or functions annotations of the 62 hypermethylated DMS indicated anti-tumor and anti-inflammatory effects that might be linked to exercise. These findings suggest that exercise may improve physical performance and reduce fatigue, which could be further linked to decreased inflammation, during active radiotherapy for HNC patients. Larger studies are warranted.
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Affiliation(s)
- Canhua Xiao
- School of Nursing, Yale University, 400 West Campus Drive, Orange 06477, United States.
| | - Jonathan J Beitler
- Department of Radiation, School of Medicine, Emory University, 1520 Clifton Road NE, Atlanta 30322, United States
| | - Kristin A Higgins
- Department of Radiation, School of Medicine, Emory University, 1520 Clifton Road NE, Atlanta 30322, United States
| | - Cynthia E Chico
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Emory University, 1365-B Clifton Road, Atlanta, GA 30322, United States
| | - Janice S Withycombe
- School of Nursing, Clemson University, 508 Edward's, Clemson, SC 29634, United States
| | - Ying Zhu
- State Key Laboratory of Medical Neurobiology and MOE Frontier Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200433, China
| | - Hongyu Zhao
- Department of Epidemiology and Public Health, School of Medicine, Yale University, 300 George Street, New Haven, CT 06510, United States
| | - I-Hsin Lin
- Yale Center for Analytical Sciences, School of Public Health, Yale University, 300 George Street, New Haven, CT 06510, United States
| | - Fangyong Li
- School of Public Health, Yale University, 60 College St, New Haven, CT 06510, United States
| | - Sangchoon Jeon
- School of Nursing, Yale University, 400 West Campus Drive, Orange 06477, United States
| | - Melinda Irwin
- School of Public Health, Yale University, 60 College St, New Haven, CT 06510, United States
| | - Deborah W Bruner
- School of Nursing, Emory University, 1520 Clifton Road NE, Atlanta 30322, United States
| | - Andrew H Miller
- Department of Psychiatry and Behavioral Sciences, School of Medicine, Emory University, 1365-B Clifton Road, Atlanta, GA 30322, United States
| | - Rebecca Gary
- School of Nursing, Emory University, 1520 Clifton Road NE, Atlanta 30322, United States
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127
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Zhou Y, Liu S, Hu Y, Fang L, Gao Y, Xia H, Schroeder SG, Rosen BD, Connor EE, Li CJ, Baldwin RL, Cole JB, Van Tassell CP, Yang L, Ma L, Liu GE. Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns. BMC Biol 2020; 18:85. [PMID: 32631327 PMCID: PMC7339546 DOI: 10.1186/s12915-020-00793-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/12/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Efforts to improve animal health, and understand genetic bases for production, may benefit from a comprehensive analysis of animal genomes and epigenomes. Although DNA methylation has been well studied in humans and other model species, its distribution patterns and regulatory impacts in cattle are still largely unknown. Here, we present the largest collection of cattle DNA methylation epigenomic data to date. RESULTS Using Holstein cattle, we generated 29 whole genome bisulfite sequencing (WGBS) datasets for 16 tissues, 47 corresponding RNA-seq datasets, and 2 whole genome sequencing datasets. We did read mapping and DNA methylation calling based on two different cattle assemblies, demonstrating the high quality of the long-read-based assembly markedly improved DNA methylation results. We observed large differences across cattle tissues in the methylation patterns of global CpG sites, partially methylated domains (PMDs), hypomethylated regions (HMRs), CG islands (CGIs), and common repeats. We detected that each tissue had a distinct set of PMDs, which showed tissue-specific patterns. Similar to human PMD, cattle PMDs were often linked to a general decrease of gene expression and a decrease in active histone marks and related to long-range chromatin organizations, like topologically associated domains (TADs). We tested a classification of the HMRs based on their distributions relative to transcription start sites (TSSs) and detected tissue-specific TSS-HMRs and genes that showed strong tissue effects. When performing cross-species comparisons of paired genes (two opposite strand genes with their TSS located in the same HMR), we found out they were more consistently co-expressed among human, mouse, sheep, goat, yak, pig, and chicken, but showed lower consistent ratios in more divergent species. We further used these WGBS data to detect 50,023 experimentally supported CGIs across bovine tissues and found that they might function as a guard against C-to-T mutations for TSS-HMRs. Although common repeats were often heavily methylated, some young Bov-A2 repeats were hypomethylated in sperm and could affect the promoter structures by exposing potential transcription factor binding sites. CONCLUSIONS This study provides a comprehensive resource for bovine epigenomic research and enables new discoveries about DNA methylation and its role in complex traits.
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Affiliation(s)
- Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Yan Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Lingzhao Fang
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Han Xia
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Steven G. Schroeder
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Erin E. Connor
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716 USA
| | - Cong-jun Li
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Ransom L. Baldwin
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
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128
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Connelly JC, Cholewa-Waclaw J, Webb S, Steccanella V, Waclaw B, Bird A. Absence of MeCP2 binding to non-methylated GT-rich sequences in vivo. Nucleic Acids Res 2020; 48:3542-3552. [PMID: 32064528 PMCID: PMC7144902 DOI: 10.1093/nar/gkaa102] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/18/2020] [Accepted: 02/13/2020] [Indexed: 12/16/2022] Open
Abstract
MeCP2 is a nuclear protein that binds to sites of cytosine methylation in the genome. While most evidence confirms this epigenetic mark as the primary determinant of DNA binding, MeCP2 is also reported to have an affinity for non-methylated DNA sequences. Here we investigated the molecular basis and in vivo significance of its reported affinity for non-methylated GT-rich sequences. We confirmed this interaction with isolated domains of MeCP2 in vitro and defined a minimal target DNA sequence. Binding depends on pyrimidine 5′ methyl groups provided by thymine and requires adjacent guanines and a correctly orientated A/T-rich flanking sequence. Unexpectedly, full-length MeCP2 protein failed to bind GT-rich sequences in vitro. To test for MeCP2 binding to these motifs in vivo, we analysed human neuronal cells using ChIP-seq and ATAC-seq technologies. While both methods robustly detected DNA methylation-dependent binding of MeCP2 to mCG and mCAC, neither showed evidence of MeCP2 binding to GT-rich motifs. The data suggest that GT binding is an in vitro phenomenon without in vivo relevance. Our findings argue that MeCP2 does not read unadorned DNA sequence and therefore support the notion that its primary role is to interpret epigenetic modifications of DNA.
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Affiliation(s)
- John C Connelly
- The Wellcome Centre for Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, UK
| | | | - Shaun Webb
- The Wellcome Centre for Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, UK
| | - Verdiana Steccanella
- The Wellcome Centre for Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, UK
| | - Bartlomiej Waclaw
- School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | - Adrian Bird
- The Wellcome Centre for Cell Biology, University of Edinburgh, EH9 3BF Edinburgh, UK
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129
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Interplay between Metabolism, Nutrition and Epigenetics in Shaping Brain DNA Methylation, Neural Function and Behavior. Genes (Basel) 2020; 11:genes11070742. [PMID: 32635190 PMCID: PMC7397264 DOI: 10.3390/genes11070742] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/25/2020] [Accepted: 07/02/2020] [Indexed: 12/14/2022] Open
Abstract
Gene expression in the brain is dramatically regulated by a variety of stimuli. While the role of neural activity has been extensively studied, less is known about the effects of metabolism and nutrition on transcriptional control mechanisms in the brain. Extracellular signals are integrated at the chromatin level through dynamic modifications of epigenetic marks, which in turn fine-tune gene transcription. In the last twenty years, it has become clear that epigenetics plays a crucial role in modulating central nervous system functions and finally behavior. Here, we will focus on the effect of metabolic signals in shaping brain DNA methylation, both during development and adulthood. We will provide an overview of maternal nutrition effects on brain methylation and behavior in offspring. In addition, the impact of different diet challenges on cytosine methylation dynamics in the adult brain will be discussed. Finally, the possible role played by the metabolic status in modulating DNA hydroxymethylation, which is particularly abundant in neural tissue, will be considered.
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130
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Marples B, Kerns S. Oncology Scan: Radiation Biology and Genomic Predictors of Response. Int J Radiat Oncol Biol Phys 2020; 107:393-397. [PMID: 32531379 DOI: 10.1016/j.ijrobp.2020.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Brian Marples
- Department of Radiation Oncology, University of Rochester Medical Center, Rochester, New York.
| | - Sarah Kerns
- Department of Radiation Oncology, University of Rochester Medical Center, Rochester, New York
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131
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Salvadores M, Fuster-Tormo F, Supek F. Matching cell lines with cancer type and subtype of origin via mutational, epigenomic, and transcriptomic patterns. SCIENCE ADVANCES 2020; 6:6/27/eaba1862. [PMID: 32937430 PMCID: PMC7458440 DOI: 10.1126/sciadv.aba1862] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 05/01/2020] [Indexed: 05/04/2023]
Abstract
Cell lines are commonly used as cancer models. The tissue of origin provides context for understanding biological mechanisms and predicting therapy response. We therefore systematically examined whether cancer cell lines exhibit features matching the presumed cancer type of origin. Gene expression and DNA methylation classifiers trained on ~9000 tumors identified 35 (of 614 examined) cell lines that better matched a different tissue or cell type than the one originally assigned. Mutational patterns further supported most reassignments. For instance, cell lines identified as originating from the skin often exhibited a UV mutational signature. We cataloged 366 "golden set" cell lines in which transcriptomic and epigenomic profiles strongly resemble the cancer type of origin, further proposing their assignments to subtypes. Accounting for the uncertain tissue of origin in cell line panels can change the interpretation of drug screening and genetic screening data, revealing previously unknown genomic determinants of sensitivity or resistance.
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Affiliation(s)
- Marina Salvadores
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francisco Fuster-Tormo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- MDS Research Group, Institut de Recerca Contra la Leucèmia Josep Carreras, Institut Català d'Oncologia-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Fran Supek
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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132
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Ma X, Sun P, Gong M. An integrative framework of heterogeneous genomic data for cancer dynamic modules based on matrix decomposition. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 19:305-316. [PMID: 32750874 DOI: 10.1109/tcbb.2020.3004808] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cancer progression is dynamic, and tracking dynamic modules is promising for cancer diagnosis and therapy. Accumulated genomic data provide us an opportunity to investigate the underlying mechanisms of cancers. However, as far as we know, no algorithm has been designed for dynamic modules by integrating heterogeneous omics data. To address this issue, we propose an integrative framework for dynamic module detection based on regularized nonnegative matrix factorization method (DrNMF) by integrating the gene expression and protein interaction network. To remove the heterogeneity of genomic data, we divide the samples of expression profiles into groups to construct gene co-expression networks. To characterize the dynamics of modules, the temporal smoothness framework is adopted, in which the gene co-expression network at the previous stage and protein interaction network are incorporated into the objective function of DrNMF via regularization. The experimental results demonstrate that DrNMF is superior to state-of-the-art methods in terms of accuracy. For breast cancer data, the obtained dynamic modules are more enriched by the known pathways, and can be used to predict the stages of cancers and survival time of patients. The proposed model and algorithm provide an effective integrative analysis of heterogeneous genomic data for cancer progression.
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133
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Emerging Precision Oncology Applications of Liquid Biopsy using Circulating Tumour DNA and Methylome Profiling. Clin Oncol (R Coll Radiol) 2020; 32:626-631. [PMID: 32586654 DOI: 10.1016/j.clon.2020.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/13/2020] [Accepted: 05/29/2020] [Indexed: 01/13/2023]
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134
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Sachdeva A, Gouge J, Kontovounisios C, Nikolaou S, Ashworth A, Lim K, Chong I. Klotho and the Treatment of Human Malignancies. Cancers (Basel) 2020; 12:cancers12061665. [PMID: 32585905 PMCID: PMC7352559 DOI: 10.3390/cancers12061665] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/16/2020] [Indexed: 12/24/2022] Open
Abstract
Klotho was first discovered as an anti-ageing protein linked to a number of age-related disease processes, including cardiovascular, renal, musculoskeletal, and neurodegenerative conditions. Emerging research has also demonstrated a potential therapeutic role for Klotho in cancer biology, which is perhaps unsurprising given that cancer and ageing share similar molecular hallmarks. In addition to functioning as a tumour suppressor in numerous solid tumours and haematological malignancies, Klotho represents a candidate therapeutic target for patients with these diseases, the majority of whom have limited treatment options. Here, we examine contemporary evidence evaluating the anti-neoplastic effects of Klotho and describe the modulation of downstream oncogenic signalling pathways, including Wnt/β-catenin, FGF, IGF1, PIK3K/AKT, TGFβ, and the Unfolded Protein Response. We also discuss possible approaches to developing therapeutic Klotho and consider technological advances that may facilitate the delivery of Klotho through gene therapy.
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Affiliation(s)
- Aishani Sachdeva
- The Royal Marsden NHS Foundation Trust, London SW6 6JJ, UK; (A.S.); (C.K.)
- Department of Surgery and Cancer, Chelsea and Westminster Hospital, London SW10 9NH, UK;
| | - Jerome Gouge
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK;
| | - Christos Kontovounisios
- The Royal Marsden NHS Foundation Trust, London SW6 6JJ, UK; (A.S.); (C.K.)
- Department of Surgery and Cancer, Chelsea and Westminster Hospital, London SW10 9NH, UK;
| | - Stella Nikolaou
- Department of Surgery and Cancer, Chelsea and Westminster Hospital, London SW10 9NH, UK;
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA;
| | - Kenneth Lim
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202-5181, USA;
| | - Irene Chong
- The Royal Marsden NHS Foundation Trust, London SW6 6JJ, UK; (A.S.); (C.K.)
- The Institute of Cancer Research, London SW3 6JB, UK
- Correspondence:
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135
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Chokeshaiusaha K, Puthier D, Sananmuang T, Olanratmanee EO, Nguyen C, Kedkovid R. Differential DNA methylation analysis across the promoter regions using methylated DNA immunoprecipitation sequencing profiling of porcine loin muscle. Vet World 2020; 13:1113-1125. [PMID: 32801562 PMCID: PMC7396332 DOI: 10.14202/vetworld.2020.1113-1125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/05/2020] [Indexed: 12/15/2022] Open
Abstract
Background and Aim: Pork leanness and marbling are among the essential traits of consumer preference. To acquire knowledge about universal epigenetic regulations for improving breed selection, a meta-analysis of methylated DNA immunoprecipitation sequencing (MeDIP-seq) profiling data of mixed loin muscle types was performed in this study. Materials and Methods: MeDIP-seq profiling datasets of longissimus dorsi muscle and psoas major muscles from male and female pigs of Landrace and Tibetan breeds were preprocessed and aligned to the porcine genome. Analysis of differential methylated DNA regions (DMRs) between the breeds was performed by focusing on transcription start sites (TSSs) of known genes (−20,000-3000 bases from TSS). All associated genes were further reviewed for their functions and predicted for transcription factors (TF) possibly associated with their TSSs. Results: When the methylation levels of DMRs in TSS regions of Landrace breed were compared to those of Tibetan breed, 10 DMRs were hypomethylated (Landrace < Tibetan), and 19 DMRs were hypermethylated (Landrace > Tibetan), accordingly (p≤0.001). According to the reviews about gene functions, all associated genes were pieces of evidence for their roles in a variety of muscle and lipid metabolisms. Prediction of the binding TFs revealed the six most abundant binding TFs to such DMRs-associated TSS (p≤0.0001) as follows: ZNF384, Foxd3, IRF1, KLF9, EWSR1-FLI1, HES5, and TFAP2A. Conclusion: Common DMRs-associated TSS between the lean-type and the marbled-type loin muscles were identified in this study. Interestingly, the genes associated with such regions were strongly evidenced for their possible roles on the muscle trait characteristics by which further novel research topics could be focused on them in the future.
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Affiliation(s)
- Kaj Chokeshaiusaha
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chon Buri, Thailand
| | - Denis Puthier
- Aix-Marseille University, INSERM UMR 1090, TAGC, Marseille, France
| | - Thanida Sananmuang
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chon Buri, Thailand
| | - Em-On Olanratmanee
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chon Buri, Thailand
| | - Catherine Nguyen
- Aix-Marseille University, INSERM UMR 1090, TAGC, Marseille, France
| | - Roongtham Kedkovid
- Department of Veterinary Medicine, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Swine Reproduction Research Unit, Chulalongkorn University, Bangkok, Thailand
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136
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Handl L, Jalali A, Scherer M, Eggeling R, Pfeifer N. Weighted elastic net for unsupervised domain adaptation with application to age prediction from DNA methylation data. Bioinformatics 2020; 35:i154-i163. [PMID: 31510704 PMCID: PMC6612879 DOI: 10.1093/bioinformatics/btz338] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
MOTIVATION Predictive models are a powerful tool for solving complex problems in computational biology. They are typically designed to predict or classify data coming from the same unknown distribution as the training data. In many real-world settings, however, uncontrolled biological or technical factors can lead to a distribution mismatch between datasets acquired at different times, causing model performance to deteriorate on new data. A common additional obstacle in computational biology is scarce data with many more features than samples. To address these problems, we propose a method for unsupervised domain adaptation that is based on a weighted elastic net. The key idea of our approach is to compare dependencies between inputs in training and test data and to increase the cost of differently behaving features in the elastic net regularization term. In doing so, we encourage the model to assign a higher importance to features that are robust and behave similarly across domains. RESULTS We evaluate our method both on simulated data with varying degrees of distribution mismatch and on real data, considering the problem of age prediction based on DNA methylation data across multiple tissues. Compared with a non-adaptive standard model, our approach substantially reduces errors on samples with a mismatched distribution. On real data, we achieve far lower errors on cerebellum samples, a tissue which is not part of the training data and poorly predicted by standard models. Our results demonstrate that unsupervised domain adaptation is possible for applications in computational biology, even with many more features than samples. AVAILABILITY AND IMPLEMENTATION Source code is available at https://github.com/PfeiferLabTue/wenda. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lisa Handl
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany.,Department of Computer Science, University of Tübingen, Tübingen, Germany.,Institute for Biomedical Informatics, University of Tübingen, Tübingen, Germany
| | - Adrin Jalali
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Michael Scherer
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Ralf Eggeling
- Department of Computer Science, University of Tübingen, Tübingen, Germany.,Institute for Biomedical Informatics, University of Tübingen, Tübingen, Germany
| | - Nico Pfeifer
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany.,Department of Computer Science, University of Tübingen, Tübingen, Germany.,Institute for Biomedical Informatics, University of Tübingen, Tübingen, Germany
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137
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Lee D, Lee S, Kim S. PRISM: methylation pattern-based, reference-free inference of subclonal makeup. Bioinformatics 2020; 35:i520-i529. [PMID: 31510697 PMCID: PMC6612819 DOI: 10.1093/bioinformatics/btz327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Motivation Characterizing cancer subclones is crucial for the ultimate conquest of cancer. Thus, a number of bioinformatic tools have been developed to infer heterogeneous tumor populations based on genomic signatures such as mutations and copy number variations. Despite accumulating evidence for the significance of global DNA methylation reprogramming in certain cancer types including myeloid malignancies, none of the bioinformatic tools are designed to exploit subclonally reprogrammed methylation patterns to reveal constituent populations of a tumor. In accordance with the notion of global methylation reprogramming, our preliminary observations on acute myeloid leukemia (AML) samples implied the existence of subclonally occurring focal methylation aberrance throughout the genome. Results We present PRISM, a tool for inferring the composition of epigenetically distinct subclones of a tumor solely from methylation patterns obtained by reduced representation bisulfite sequencing. PRISM adopts DNA methyltransferase 1-like hidden Markov model-based in silico proofreading for the correction of erroneous methylation patterns. With error-corrected methylation patterns, PRISM focuses on a short individual genomic region harboring dichotomous patterns that can be split into fully methylated and unmethylated patterns. Frequencies of such two patterns form a sufficient statistic for subclonal abundance. A set of statistics collected from each genomic region is modeled with a beta-binomial mixture. Fitting the mixture with expectation-maximization algorithm finally provides inferred composition of subclones. Applying PRISM for two AML samples, we demonstrate that PRISM could infer the evolutionary history of malignant samples from an epigenetic point of view. Availability and implementation PRISM is freely available on GitHub (https://github.com/dohlee/prism). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dohoon Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea
| | - Sangseon Lee
- Department of Computer Science and Engineering, Seoul National University, Seoul, Korea
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea.,Department of Computer Science and Engineering, Seoul National University, Seoul, Korea.,Bioinformatics Institute, Seoul National University, Seoul, Korea
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138
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Choi J, Zhang T, Vu A, Ablain J, Makowski MM, Colli LM, Xu M, Hennessey RC, Yin J, Rothschild H, Gräwe C, Kovacs MA, Funderburk KM, Brossard M, Taylor J, Pasaniuc B, Chari R, Chanock SJ, Hoggart CJ, Demenais F, Barrett JH, Law MH, Iles MM, Yu K, Vermeulen M, Zon LI, Brown KM. Massively parallel reporter assays of melanoma risk variants identify MX2 as a gene promoting melanoma. Nat Commun 2020; 11:2718. [PMID: 32483191 PMCID: PMC7264232 DOI: 10.1038/s41467-020-16590-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 05/12/2020] [Indexed: 02/07/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified ~20 melanoma susceptibility loci, most of which are not functionally characterized. Here we report an approach integrating massively-parallel reporter assays (MPRA) with cell-type-specific epigenome and expression quantitative trait loci (eQTL) to identify susceptibility genes/variants from multiple GWAS loci. From 832 high-LD variants, we identify 39 candidate functional variants from 14 loci displaying allelic transcriptional activity, a subset of which corroborates four colocalizing melanocyte cis-eQTL genes. Among these, we further characterize the locus encompassing the HIV-1 restriction gene, MX2 (Chr21q22.3), and validate a functional intronic variant, rs398206. rs398206 mediates the binding of the transcription factor, YY1, to increase MX2 levels, consistent with the cis-eQTL of MX2 in primary human melanocytes. Melanocyte-specific expression of human MX2 in a zebrafish model demonstrates accelerated melanoma formation in a BRAFV600E background. Our integrative approach streamlines GWAS follow-up studies and highlights a pleiotropic function of MX2 in melanoma susceptibility. There are more than 20 known melanoma susceptibility genes. Here, using a massively parallel reporter assay, the authors identify risk-associated variants that alter gene transcription, and demonstrate that expression of one such gene, MX2, leads to the promotion of melanoma in a zebrafish model.
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Affiliation(s)
- Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Andrew Vu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Julien Ablain
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Matthew M Makowski
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 XZ, Nijmegen, The Netherlands
| | - Leandro M Colli
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Mai Xu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Rebecca C Hennessey
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Jinhu Yin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Harriet Rothschild
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Cathrin Gräwe
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 XZ, Nijmegen, The Netherlands
| | - Michael A Kovacs
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Karen M Funderburk
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Myriam Brossard
- Université de Paris, UMRS-1124, Institut National de la Santé et de la Recherche Médicale (INSERM), F-75006, Paris, France
| | - John Taylor
- Leeds Institute for Data Analytics, School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90024, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Lab for Cancer Research, National Cancer Institute, Frederick, MD, 21701, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Clive J Hoggart
- Department of Medicine, Imperial College London, London, SW7 2BU, UK
| | - Florence Demenais
- Université de Paris, UMRS-1124, Institut National de la Santé et de la Recherche Médicale (INSERM), F-75006, Paris, France
| | - Jennifer H Barrett
- Leeds Institute for Data Analytics, School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Mark M Iles
- Leeds Institute for Data Analytics, School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 XZ, Nijmegen, The Netherlands
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA.
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139
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Pan MS, Cao J, Fan YZ. Insight into norcantharidin, a small-molecule synthetic compound with potential multi-target anticancer activities. Chin Med 2020; 15:55. [PMID: 32514288 PMCID: PMC7260769 DOI: 10.1186/s13020-020-00338-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 05/25/2020] [Indexed: 02/07/2023] Open
Abstract
Norcantharidin (NCTD) is a demethylated derivative of cantharidin, which is an anticancer active ingredient of traditional Chinese medicine, and is currently used clinically as a routine anti-cancer drug in China. Clarifying the anticancer effect and molecular mechanism of NCTD is critical for its clinical application. Here, we summarized the physiological, chemical, pharmacokinetic characteristics and clinical applications of NCTD. Besides, we mainly focus on its potential multi-target anticancer activities and underlying mechanisms, and discuss the problems existing in clinical application and scientific research of NCTD, so as to provide a potential anticancer therapeutic agent for human malignant tumors.
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Affiliation(s)
- Mu-Su Pan
- Department of Surgery, Tongji Hospital, Tongji University School of Medicine, Tongji University, 389 Xincun Road, Shanghai, 200065 People’s Republic of China
| | - Jin Cao
- Department of Surgery, Tongji Hospital, Tongji University School of Medicine, Tongji University, 389 Xincun Road, Shanghai, 200065 People’s Republic of China
| | - Yue-Zu Fan
- Department of Surgery, Tongji Hospital, Tongji University School of Medicine, Tongji University, 389 Xincun Road, Shanghai, 200065 People’s Republic of China
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140
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Li Y, Shan Y, Kilaru GK, Berto S, Wang GZ, Cox KH, Yoo SH, Yang S, Konopka G, Takahashi JS. Epigenetic inheritance of circadian period in clonal cells. eLife 2020; 9:54186. [PMID: 32459177 PMCID: PMC7289596 DOI: 10.7554/elife.54186] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 05/26/2020] [Indexed: 12/22/2022] Open
Abstract
Circadian oscillations are generated via transcriptional-translational negative feedback loops. However, individual cells from fibroblast cell lines have heterogeneous rhythms, oscillating independently and with different period lengths. Here we showed that heterogeneity in circadian period is heritable and used a multi-omics approach to investigate underlying mechanisms. By examining large-scale phenotype-associated gene expression profiles in hundreds of mouse clonal cell lines, we identified and validated multiple novel candidate genes involved in circadian period determination in the absence of significant genomic variants. We also discovered differentially co-expressed gene networks that were functionally associated with period length. We further demonstrated that global differential DNA methylation bidirectionally regulated these same gene networks. Interestingly, we found that depletion of DNMT1 and DNMT3A had opposite effects on circadian period, suggesting non-redundant roles in circadian gene regulation. Together, our findings identify novel gene candidates involved in periodicity, and reveal DNA methylation as an important regulator of circadian periodicity.
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Affiliation(s)
- Yan Li
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Yongli Shan
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Gokhul Krishna Kilaru
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Stefano Berto
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Guang-Zhong Wang
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Kimberly H Cox
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Seung-Hee Yoo
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Shuzhang Yang
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Genevieve Konopka
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
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141
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Senner CE, Chrysanthou S, Burge S, Lin HY, Branco MR, Hemberger M. TET1 and 5-Hydroxymethylation Preserve the Stem Cell State of Mouse Trophoblast. Stem Cell Reports 2020; 15:1301-1316. [PMID: 32442533 PMCID: PMC7724466 DOI: 10.1016/j.stemcr.2020.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023] Open
Abstract
The ten-eleven translocation factor TET1 and its conferred epigenetic modification 5-hydroxymethylcytosine (5hmC) have important roles in maintaining the pluripotent state of embryonic stem cells (ESCs). We previously showed that TET1 is also essential to maintain the stem cell state of trophoblast stem cells (TSCs). Here, we establish an integrated panel of absolute 5hmC levels, genome-wide DNA methylation and hydroxymethylation patterns, transcriptomes, and TET1 chromatin occupancy in TSCs and differentiated trophoblast cells. We show that the combined presence of 5-methylcytosine (5mC) and 5hmC correlates with transcriptional activity of associated genes. Hypoxia can slow down the global loss of 5hmC that occurs upon differentiation of TSCs. Notably, unlike in ESCs and epiblast cells, most TET1-bound regions overlap with active chromatin marks and TFAP2C binding sites and demarcate putative trophoblast enhancer regions. These chromatin modification and occupancy patterns are highly informative to identify novel candidate regulators of the TSC state. 5hmC to 5mC ratios correlate with gene activity in TS cells TS cell differentiation-associated loss of 5hmC is slowed down in hypoxia TET1 binding in TS cells forms long-range interactions with key trophoblast genes Intergenic TET1 binding sites in TS cells demarcate putative trophoblast enhancers
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Affiliation(s)
- Claire E Senner
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK.
| | - Stephanie Chrysanthou
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Sarah Burge
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Hai-Yan Lin
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Miguel R Branco
- Blizard Institute, Barts and the London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Myriam Hemberger
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK; Departments of Biochemistry & Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta, T2N 4N1, Canada.
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142
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Elshaer M, ElManawy AI, Hammad A, Namani A, Wang XJ, Tang X. Integrated data analysis reveals significant associations of KEAP1 mutations with DNA methylation alterations in lung adenocarcinomas. Aging (Albany NY) 2020; 12:7183-7206. [PMID: 32327612 PMCID: PMC7202502 DOI: 10.18632/aging.103068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/29/2020] [Indexed: 12/17/2022]
Abstract
KEAP1 regulates the cytoprotection induced by NRF2 and has been reported to be a candidate tumor suppressor. Recent evidence has shown that mutations in several driver genes cause aberrant DNA methylation patterns, a hallmark of cancer. However, the correlation between KEAP1 mutations and DNA methylation in lung cancer has still not been investigated. In this study, we systematically carried out an integrated multi-omics analysis to explore the correlation between KEAP1 mutations and DNA methylation and its effect on gene expression in lung adenocarcinoma (LUAD). We found that most of the DNA aberrations associated with KEAP1 mutations in LAUD were hypomethylation. Surprisingly, we found several NRF2-regulated genes among the genes that showed differential DNA methylation. Moreover, we identified an 8-gene signature with altered DNA methylation pattern and elevated gene expression levels in LUAD patients with mutated KEAP1, and evaluated the prognostic value of this signature in various clinical datasets. These results establish that KEAP1 mutations are associated with DNA methylation changes capable of shaping regulatory network functions. Combining both epigenomic and transcriptomic changes along with KEAP1 mutations may provide a better understanding of the molecular mechanisms associated with the progression of lung cancer and may help to provide better therapeutic approaches.
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Affiliation(s)
- Mohamed Elshaer
- Department of Biochemistry and Department of Thoracic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, PR China
- Labeled Compounds Department, Hot Labs Center, Egyptian Atomic Energy Authority, Cairo 13759, Egypt
| | - Ahmed Islam ElManawy
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China
- Agricultural Engineering Department, Faculty of Agriculture, Suez Canal University, Ismailia 41522, Egypt
| | - Ahmed Hammad
- Department of Biochemistry and Department of Thoracic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, PR China
- Radiation Biology Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo 13759, Egypt
| | - Akhileshwar Namani
- Department of Biochemistry and Department of Thoracic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, PR China
| | - Xiu Jun Wang
- Department of Pharmacology and Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, PR China
| | - Xiuwen Tang
- Department of Biochemistry and Department of Thoracic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, PR China
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143
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Tissue-specific epigenetic inheritance after paternal heat exposure in male wild guinea pigs. Mamm Genome 2020; 31:157-169. [PMID: 32285146 PMCID: PMC7369130 DOI: 10.1007/s00335-020-09832-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/19/2020] [Indexed: 12/28/2022]
Abstract
External temperature change has been shown to modify epigenetic patterns, such as DNA methylation, which regulates gene expression. DNA methylation is heritable, and as such provides a mechanism to convey environmental information to subsequent generations. Studies on epigenetic response to temperature increase are still scarce in wild mammals, even more so studies that compare tissue-specific epigenetic responses. Here, we aim to address differential epigenetic responses on a gene and gene pathway level in two organs, liver and testis. We chose these organs, because the liver is the main metabolic and thermoregulation organ, and epigenetic modifications in testis are potentially transmitted to the F2 generation. We focused on the transmission of DNA methylation changes to naive male offspring after paternal exposure to an ambient temperature increase of 10 °C, and investigated differential methylated regions of sons sired before and after the paternal exposure using Reduced Representation Bisulfite Sequencing. We detected both a highly tissue-specific epigenetic response, reflected in genes involved in organ-specific metabolic pathways, and a more general regulation of single genes epigenetically modified in both organs. We conclude that genomes are context-specifically differentially epigenetically regulated in response to temperature increase. These findings emphasize the epigenetic relevance in cell differentiation, which is essential for the specific function(s) of complex organs, and is represented in a diverse molecular regulation of genes and gene pathways. The results also emphasize the paternal contribution to adaptive processes.
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144
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Huang W, Hu H, Zhang Q, Wang N, Yang X, Guo AY. Genome-Wide DNA Methylation Enhances Stemness in the Mechanical Selection of Tumor-Repopulating Cells. Front Bioeng Biotechnol 2020; 8:88. [PMID: 32258002 PMCID: PMC7090028 DOI: 10.3389/fbioe.2020.00088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/29/2020] [Indexed: 12/31/2022] Open
Abstract
Background DNA methylation plays essential roles in tumor occurrence and stemness maintenance. Tumor-repopulating cells (TRCs) are cancer stem cell (CSC)-like cells with highly tumorigenic and self-renewing abilities, which were selected from tumor cells in soft three-dimensional (3D) fibrin gels. Methods Here, we presented a genome-wide map of methylated cytosines for time-series samples in TRC selection, in a 3D culture using whole-genome bisulfite sequencing (WGBS). Results A comparative analysis revealed that the methylation degrees of many differentially methylated genes (DMGs) were increased by the mechanical environment and changed from 2D rigid to 3D soft. DMGs were significantly enriched in stemness-related terms. In 1-day, TRCs had the highest non-CG methylation rate indicating its strong stemness. We found that genes with continuously increasing or decreasing methylation like CREB5/ADAMTS6/LMX1A may also affect the TRC screening process. Furthermore, results showed that stage-specific/common CSCs markers were biased toward changing their methylation in non-CG (CHG and CHH, where H corresponds to A, T, or C) methylation and enriched in gene body region. Conclusions WGBS provides DNA methylome in TRC screening. It was confirmed that non-CG DNA methylation plays an important role in TRC selection, which indicates that it is more sensitive to mechanical microenvironments and affects TRCs by regulating the expression of stemness genes in tumor cells.
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Affiliation(s)
- Wei Huang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Hu
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qiong Zhang
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Ning Wang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Department of Mechanical Science and Engineering, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Xiangliang Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - An-Yuan Guo
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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145
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Klenke S, Specking C, Stegen M, Engler A, Peters J. Methylation in HT22 cells and primary hippocampal neurons with and without isoflurane exposurewhether isoflurane causes. BMC Anesthesiol 2020; 20:66. [PMID: 32171245 PMCID: PMC7071644 DOI: 10.1186/s12871-020-00981-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 03/05/2020] [Indexed: 12/25/2022] Open
Abstract
Background Epigenetic modulation may play a role in anesthesia related phenotypes, such as cognitive impairment or memory loss, especially with exposure to anesthetics in the vulnerable phase of brain development. While isoflurane anesthesia can evoke neuroinflammation and neuroapoptosis in young animals, we investigated in a permanent hippocampal cell line (HT22) and in primary hippocampal neurons in an a priori in vitro analysis, whether isoflurane exposure 1) evokes DNA methylation changes in genes involved in apoptosis and inflammation, and 2) results observed in a permanent hippocampal cell line are comparable to primary hippocampal neurons. In case of methylation changes in specific genes, (3) mRNA analysis was performed to assess possible effects on gene expression. Methods HT22 cells and primary mouse hippocampal neurons were exposed to 3% isoflurane for 4 h and DNA (each 6 single experiments) and RNA (3 single independent experiments) were extracted. Methylation analysis (EpiTect Methyl II PCR Array Systems, Qiagen) included the methylation status of 66 genes involved in apoptosis, cytokine production, inflammatory response, and autoimmunity. Quantitative Real-Time PCR was performed using the Quantitect SYBR Green Kit on a Step One Plus. Results Methylation status was markedly different between immortalized HT22 cells and cultured primary hippocampal neurons without isoflurane exposure. Of 66 genes investigated, 29 were methylated to a significantly greater degree in HT22 cells compared to primary hippocampal neurons. In cultured primary hippocampal neurons, in contrast, there was a greater methylation in several genes involved in inflammation, accompanied with significant downregulation of C-X-C motif chemokine 12 with isoflurane exposure (p = 0.023). Conclusions We demonstrate marked differences in gene methylation between HT22 cells and cultured primary hippocampal neurons without isoflurane exposure, with a greater methylation of several genes involved in inflammation upon isoflurane exposure and significant downregulation of Cxcl12 mRNA expression in primary hippocampal neurons. Accordingly, further investigations of anesthesia related DNA methylation should be performed with special consideration being given to the choice of cells targeted for such investigations.
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Affiliation(s)
- Stefanie Klenke
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Hufelandstr. 55, D-45122, Essen, Germany.
| | - Christian Specking
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Hufelandstr. 55, D-45122, Essen, Germany
| | - Maike Stegen
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Hufelandstr. 55, D-45122, Essen, Germany
| | - Andrea Engler
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Hufelandstr. 55, D-45122, Essen, Germany
| | - Jürgen Peters
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Hufelandstr. 55, D-45122, Essen, Germany
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146
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Tillotson R, Bird A. The Molecular Basis of MeCP2 Function in the Brain. J Mol Biol 2020; 432:1602-1623. [PMID: 31629770 DOI: 10.1016/j.jmb.2019.10.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 12/14/2022]
Abstract
MeCP2 is a reader of the DNA methylome that occupies a large proportion of the genome due to its high abundance and the frequency of its target sites. It has been the subject of extensive study because of its link with 'MECP2-related disorders', of which Rett syndrome is the most prevalent. This review integrates evidence from patient mutation data with results of experimental studies using mouse models, cell lines and in vitro systems to critically evaluate our understanding of MeCP2 protein function. Recent evidence challenges the idea that MeCP2 is a multifunctional hub that integrates diverse processes to underpin neuronal function, suggesting instead that its primary role is to recruit the NCoR1/2 co-repressor complex to methylated sites in the genome, leading to dampening of gene expression.
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Affiliation(s)
- Rebekah Tillotson
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada; Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK
| | - Adrian Bird
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK.
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147
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Stoffel M, Gardini E, Ehrenthal J, Abbruzzese E, Ditzen B. Evaluation of Stress Management and Stress Prevention Using Epigenetic Markers. VERHALTENSTHERAPIE 2020. [DOI: 10.1159/000506323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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148
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Luo X, Wang F, Wang G, Zhao Y. Identification of methylation states of DNA regions for Illumina methylation BeadChip. BMC Genomics 2020; 21:672. [PMID: 32138668 PMCID: PMC7057447 DOI: 10.1186/s12864-019-6019-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/07/2019] [Indexed: 12/24/2022] Open
Abstract
Background Methylation of cytosine bases in DNA is a critical epigenetic mark in many eukaryotes and has also been implicated in the development and progression of normal and diseased cells. Therefore, profiling DNA methylation across the genome is vital to understanding the effects of epigenetic. In recent years the Illumina HumanMethylation450 (HM450K) and MethylationEPIC (EPIC) BeadChip have been widely used to profile DNA methylation in human samples. The methods to predict the methylation states of DNA regions based on microarray methylation datasets are critical to enable genome-wide analyses. Result We report a computational approach based on the two layers two-state hidden Markov model (HMM) to identify methylation states of single CpG site and DNA regions in HM450K and EPIC BeadChip. Using this mothed, all CpGs detected by HM450K and EPIC in H1-hESC and GM12878 cell lines are identified as un-methylated, middle-methylated and full-methylated states. A large number of DNA regions are segmented into three methylation states as well. Comparing the identified regions with the result from the whole genome bisulfite sequencing (WGBS) datasets segmented by MethySeekR, our method is verified. Genome-wide maps of chromatin states show that methylation state is inversely correlated with active histone marks. Genes regulated by un-methylated regions are expressed and regulated by full-methylated regions are repressed. Our method is illustrated to be useful and robust. Conclusion Our method is valuable for DNA methylation genome-wide analyses. It is focusing on identification of DNA methylation states on microarray methylation datasets. For the features of array datasets, using two layers two-state HMM to identify to methylation states on CpG sites and regions creatively, our method which takes into account the distribution of genome-wide methylation levels is more reasonable than segmentation with a fixed threshold. Electronic supplementary material The online version of this article (10.1186/s12864-019-6019-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ximei Luo
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Fang Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Guohua Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China.
| | - Yuming Zhao
- Information and Computer Engineering College, Northeast Forestry University, Harbin, China.
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149
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Liu S, Cheng K, Zhang H, Kong R, Wang S, Mao C, Liu S. Methylation Status of the Nanog Promoter Determines the Switch between Cancer Cells and Cancer Stem Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903035. [PMID: 32154082 PMCID: PMC7055559 DOI: 10.1002/advs.201903035] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 12/19/2019] [Indexed: 05/12/2023]
Abstract
Cancer stem cells (CSCs) are the main cause of tumor development, metastasis, and relapse. CSCs are thus considered promising targets for cancer therapy. However, it is hard to eradicate CSCs due to their inherent plasticity and heterogeneity, and the underlying mechanism of the switch between non-CSCs and CSCs remains unclear. Here, it is shown that miR-135a combined with SMYD4 activates Nanog expression and induces the switch of non-CSCs into CSCs. The miR-135a level, once elevated, lowers the methylation level of the CG5 site in the Nanog promoter by directly targeting DNMT1. SMYD4 binds to the unmethylated Nanog promoter to activate Nanog expression in Nanog-negative tumor cells. The in vivo regulation of miR-135a levels could significantly affect both the CSCs proportion and tumor progression. These findings indicate that DNA methylation of the Nanog promoter modulates the switch of non-CSCs into CSCs under the control of the miRNA-135 level. In addition, the related pathways, miR-135a/DNMT1 and SMYD4, involved in these processes are potential targets for CSC-targeted therapy.
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Affiliation(s)
- Shupeng Liu
- Department of Obstetrics and GynecologyShanghai Tenth People's HospitalTongji UniversityShanghai200072China
- Department of Laboratory DiagnosticsChanghai HospitalSecond Military Medical UniversityShanghai200433China
| | - Kai Cheng
- Department of Laboratory DiagnosticsChanghai HospitalSecond Military Medical UniversityShanghai200433China
| | - Hui Zhang
- Department of Laboratory DiagnosticsChanghai HospitalSecond Military Medical UniversityShanghai200433China
| | - Ruijiao Kong
- Department of Laboratory DiagnosticsShanghai Fourth People's HospitalAffiliated to Tongji University School of MedicineShanghai200081China
| | - Shuo Wang
- Department of Laboratory DiagnosticsChanghai HospitalSecond Military Medical UniversityShanghai200433China
| | - Chuanbin Mao
- Department of Chemistry and BiochemistryStephenson Life Sciences Research CenterUniversity of Oklahoma101 Stephenson ParkwayNormanOK73019‐5300USA
| | - Shanrong Liu
- Department of Laboratory DiagnosticsChanghai HospitalSecond Military Medical UniversityShanghai200433China
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150
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Abstract
Epigenetic mechanisms govern the transcription of the genome. Research with model systems reveals that environmental conditions can directly influence epigenetic mechanisms that are associated with interindividual differences in gene expression in brain and neural function. In this review, we provide a brief overview of epigenetic mechanisms and research with relevant rodent models. We emphasize more recent translational research programs in epigenetics as well as the challenges inherent in the integration of epigenetics into developmental and clinical psychology. Our objectives are to present an update with respect to the translational relevance of epigenetics for the study of psychopathology and to consider the state of current research with respect to its potential importance for clinical research and practice in mental health.
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Affiliation(s)
- Kieran J O'Donnell
- Department of Psychiatry and Sackler Program for Epigenetics and Psychobiology, McGill University, Montreal, Quebec H4H 1R3, Canada; .,Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Quebec H3H 1R4, Canada.,Child and Brain Development Program, CIFAR, Toronto, Ontario M5G 1M1, Canada
| | - Michael J Meaney
- Department of Psychiatry and Sackler Program for Epigenetics and Psychobiology, McGill University, Montreal, Quebec H4H 1R3, Canada; .,Child and Brain Development Program, CIFAR, Toronto, Ontario M5G 1M1, Canada.,Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), 117609 Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 119228 Singapore
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