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Dogan F, Forsyth NR. TERT Promoter Methylation Is Oxygen-Sensitive and Regulates Telomerase Activity. Biomolecules 2024; 14:131. [PMID: 38275760 PMCID: PMC10813121 DOI: 10.3390/biom14010131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/03/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
Telomere repeats protect linear chromosomes from degradation, and telomerase has a prominent role in their maintenance. Telomerase has telomere-independent effects on cell proliferation, DNA replication, differentiation, and tumorigenesis. TERT (telomerase reverse transcriptase enzyme), the catalytic subunit of telomerase, is required for enzyme activity. TERT promoter mutation and methylation are strongly associated with increased telomerase activation in cancer cells. TERT levels and telomerase activity are downregulated in stem cells during differentiation. The link between differentiation and telomerase can provide a valuable tool for the study of the epigenetic regulation of TERT. Oxygen levels can affect cellular behaviors including proliferation, metabolic activity, stemness, and differentiation. The role of oxygen in driving TERT promoter modifications in embryonic stem cells (ESCs) is poorly understood. We adopted a monolayer ESC differentiation model to explore the role of physiological oxygen (physoxia) in the epigenetic regulation of telomerase and TERT. We further hypothesized that DNMTs played a role in physoxia-driven epigenetic modification. ESCs were cultured in either air or a 2% O2 environment. Physoxia culture increased the proliferation rate and stemness of the ESCs and induced a slower onset of differentiation than in ambient air. As anticipated, downregulated TERT expression correlated with reduced telomerase activity during differentiation. Consistent with the slower onset of differentiation in physoxia, the TERT expression and telomerase activity were elevated in comparison to the air-oxygen-cultured ESCs. The TERT promoter methylation levels increased during differentiation in ambient air to a greater extent than in physoxia. The chemical inhibition of DNMT3B reduced TERT promoter methylation and was associated with increased TERT gene and telomerase activity during differentiation. DNMT3B ChIP (Chromatin immunoprecipitation) demonstrated that downregulated TERT expression and increased proximal promoter methylation were associated with DNMT3B promoter binding. In conclusion, we have demonstrated that DNMT3B directly associates with TERT promoter, is associated with differentiation-linked TERT downregulation, and displays oxygen sensitivity. Taken together, these findings help identify novel aspects of telomerase regulation that may play a role in better understanding developmental regulation and potential targets for therapeutic intervention.
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Affiliation(s)
- Fatma Dogan
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
- The Guy Hilton Research Laboratories, School of Pharmacy and Bioengineering, Faculty of Medicine and Health Sciences, Keele University, Stoke on Trent ST4 7QB, UK
| | - Nicholas R. Forsyth
- The Guy Hilton Research Laboratories, School of Pharmacy and Bioengineering, Faculty of Medicine and Health Sciences, Keele University, Stoke on Trent ST4 7QB, UK
- Vice Principals Office, Kings College, University of Aberdeen, Aberdeen AB24 3FX, UK
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2
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Liu Y, Chen C, Wang X, Sun Y, Zhang J, Chen J, Shi Y. An Epigenetic Role of Mitochondria in Cancer. Cells 2022; 11:cells11162518. [PMID: 36010594 PMCID: PMC9406960 DOI: 10.3390/cells11162518] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are not only the main energy supplier but are also the cell metabolic center regulating multiple key metaborates that play pivotal roles in epigenetics regulation. These metabolites include acetyl-CoA, α-ketoglutarate (α-KG), S-adenosyl methionine (SAM), NAD+, and O-linked beta-N-acetylglucosamine (O-GlcNAc), which are the main substrates for DNA methylation and histone post-translation modifications, essential for gene transcriptional regulation and cell fate determination. Tumorigenesis is attributed to many factors, including gene mutations and tumor microenvironment. Mitochondria and epigenetics play essential roles in tumor initiation, evolution, metastasis, and recurrence. Targeting mitochondrial metabolism and epigenetics are promising therapeutic strategies for tumor treatment. In this review, we summarize the roles of mitochondria in key metabolites required for epigenetics modification and in cell fate regulation and discuss the current strategy in cancer therapies via targeting epigenetic modifiers and related enzymes in metabolic regulation. This review is an important contribution to the understanding of the current metabolic-epigenetic-tumorigenesis concept.
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Affiliation(s)
- Yu’e Liu
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Chao Chen
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, China
| | - Xinye Wang
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yihong Sun
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Jin Zhang
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Juxiang Chen
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, China
- Correspondence: (J.C.); (Y.S.)
| | - Yufeng Shi
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
- Clinical Center for Brain and Spinal Cord Research, Tongji University, Shanghai 200092, China
- Correspondence: (J.C.); (Y.S.)
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3
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Lee JU, Soo Chang H, Kyung Kim M, Park SL, Kim JH, Park JS, Park CS. Genome-wide DNA methylation profile of peripheral blood lymphocytes from subjects with nonsteroidal anti-inflammatory drug-induced respiratory diseases. Pharmacogenet Genomics 2022; 32:226-234. [PMID: 35696287 DOI: 10.1097/fpc.0000000000000475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Significant changes in CpG methylation have been identified in nasal polyps, which are the main targets of nonsteroidal anti-inflammatory drug-exacerbated respiratory disease (NERD); however, these polyps are composed of various cellular components. In the present study, whole-genome CpG methylation in peripheral blood lymphocytes (PBLs) was analyzed to define the epigenetic changes in lymphocytes, which are the primary immune cells involved in NERD. MATERIALS AND METHODS Genomic DNA from peripheral blood mononuclear cells from 27 NERD and 24 aspirin-tolerant asthma (ATA) was subjected to bisulfate conversion and a methylation array. Quantitative CpG methylation, the β-values as a quantitative measure of DNA methylation, in lymphocytes were calculated after adjustments for cellular composition. RESULTS Fifty-six hypermethylated and three hypomethylated differentially methylated CpGs (DMCs) in PBLs in the NERD compared with ATA. The top 10 CpG loci predicted the methylation risk score, with a positive predictive value of 91.3%, a negative predictive value of 81.5% and an accuracy of 84.3%. As demonstrated in the nasal polyps, 30 DMCs were predicted to bind to the following 10 transcription factors, ranked in descending order: AP-2alphaA, TFII-1, STAT4, FOXP3, GR, c-Est-1, E2F-1, XBP1, ENKTF-1 and NF-1. Gene ontology analysis identified 13 categories such as regulation of T-helper 17 cell differentiation, including SMAD7 and NFKBIZ. PBLs in NERD contained no DMCs in genes associated with the prostaglandin and leukotriene pathways, which were found in ATA. CONCLUSION PBLs in NERD form a unique pattern of DNA CpG methylation, and the combined analysis may provide predictive values for NERD.
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Affiliation(s)
- Jong-Uk Lee
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital
| | - Hun Soo Chang
- Department of Anatomy and BK21 FOUR Project, College of Medicine, Soonchunhyang University, Cheonan
| | - Min Kyung Kim
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchuhyang University
| | - Seung-Lee Park
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchuhyang University
| | - Jung Hyun Kim
- Department of Internal Medicine, Korean Armed Forces Capital Hospital, Seongnam
| | - Jong-Sook Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital
| | - Choon-Sik Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital
- PulmoBioPark Co., Ltd., Soonchunhyang University Bucheon Hospital, Bucheon, Korea
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4
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Dogan F, Aljumaily RMK, Kitchen M, Forsyth NR. Physoxia Influences Global and Gene-Specific Methylation in Pluripotent Stem Cells. Int J Mol Sci 2022; 23:5854. [PMID: 35628663 PMCID: PMC9148100 DOI: 10.3390/ijms23105854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 12/10/2022] Open
Abstract
Pluripotent stem cells (PSC) possess unlimited proliferation, self-renewal, and a differentiation capacity spanning all germ layers. Appropriate culture conditions are important for the maintenance of self-renewal, pluripotency, proliferation, differentiation, and epigenetic states. Oxygen concentrations vary across different human tissues depending on precise cell location and proximity to vascularisation. The bulk of PSC culture-based research is performed in a physiologically hyperoxic, air oxygen (21% O2) environment, with numerous reports now detailing the impact of a physiologic normoxia (physoxia), low oxygen culture in the maintenance of stemness, survival, morphology, proliferation, differentiation potential, and epigenetic profiles. Epigenetic mechanisms affect multiple cellular characteristics including gene expression during development and cell-fate determination in differentiated cells. We hypothesized that epigenetic marks are responsive to a reduced oxygen microenvironment in PSCs and their differentiation progeny. Here, we evaluated the role of physoxia in PSC culture, the regulation of DNA methylation (5mC (5-methylcytosine) and 5hmC (5-hydroxymethylcytosine)), and the expression of regulatory enzyme DNMTs and TETs. Physoxia enhanced the functional profile of PSC including proliferation, metabolic activity, and stemness attributes. PSCs cultured in physoxia revealed the significant downregulation of DNMT3B, DNMT3L, TET1, and TET3 vs. air oxygen, accompanied by significantly reduced 5mC and 5hmC levels. The downregulation of DNMT3B was associated with an increase in its promoter methylation. Coupled with the above, we also noted decreased HIF1A but increased HIF2A expression in physoxia-cultured PSCs versus air oxygen. In conclusion, PSCs display oxygen-sensitive methylation patterns that correlate with the transcriptional and translational regulation of the de novo methylase DNMT3B.
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Affiliation(s)
- Fatma Dogan
- The Guy Hilton Research Laboratories, School of Pharmacy and Bioengineering, Faculty of Medicine and Health Sciences, Keele University, Stoke on Trent ST4 7QB, UK; (F.D.); (M.K.)
| | - Rakad M. Kh Aljumaily
- Department of Biology, College of Science, University of Baghdad, Baghdad 17635, Iraq;
| | - Mark Kitchen
- The Guy Hilton Research Laboratories, School of Pharmacy and Bioengineering, Faculty of Medicine and Health Sciences, Keele University, Stoke on Trent ST4 7QB, UK; (F.D.); (M.K.)
| | - Nicholas R. Forsyth
- The Guy Hilton Research Laboratories, School of Pharmacy and Bioengineering, Faculty of Medicine and Health Sciences, Keele University, Stoke on Trent ST4 7QB, UK; (F.D.); (M.K.)
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5
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Dietary Restriction and Rapamycin Affect Brain Aging in Mice by Attenuating Age-Related DNA Methylation Changes. Genes (Basel) 2022; 13:genes13040699. [PMID: 35456505 PMCID: PMC9030181 DOI: 10.3390/genes13040699] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/02/2022] [Accepted: 04/13/2022] [Indexed: 02/07/2023] Open
Abstract
The fact that dietary restriction (DR) and long-term rapamycin treatment (RALL) can ameliorate the aging process has been reported by many researchers. As the interface between external and genetic factors, epigenetic modification such as DNA methylation may have latent effects on the aging rate at the molecular level. To understand the mechanism behind the impacts of dietary restriction and rapamycin on aging, DNA methylation and gene expression changes were measured in the hippocampi of different-aged mice. Examining the single-base resolution of DNA methylation, we discovered that both dietary restriction and rapamycin treatment can maintain DNA methylation in a younger state compared to normal-aged mice. Through functional enrichment analysis of genes in which DNA methylation or gene expression can be affected by DR/RALL, we found that DR/RALL may retard aging through a relationship in which DNA methylation and gene expression work together not only in the same gene but also in the same biological process. This study is instructive for understanding the maintenance of DNA methylation by DR/RALL in the aging process, as well as the role of DR and RALL in the amelioration of aging.
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6
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Saha D, Norvil AB, Lanman NA, Gowher H. Simplified MethylRAD Sequencing to Detect Changes in DNA Methylation at Enhancer Elements in Differentiating Embryonic Stem Cells. EPIGENOMES 2020; 4:24. [PMID: 33828860 PMCID: PMC8023688 DOI: 10.3390/epigenomes4040024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/28/2020] [Indexed: 11/17/2022] Open
Abstract
Differential DNA methylation is characteristic of gene regulatory regions, such as enhancers, which mostly constitute low or intermediate CpG content in their DNA sequence. Consequently, quantification of changes in DNA methylation at these sites is challenging. Given that DNA methylation across most of the mammalian genome is maintained, the use of genome-wide bisulfite sequencing to measure fractional changes in DNA methylation at specific sites is an overexertion which is both expensive and cumbersome. Here, we developed a MethylRAD technique with an improved experimental plan and bioinformatic analysis tool to examine regional DNA methylation changes in embryonic stem cells (ESCs) during differentiation. The transcriptional silencing of pluripotency genes (PpGs) during ESC differentiation is accompanied by PpG enhancer (PpGe) silencing mediated by the demethylation of H3K4me1 by LSD1. Our MethylRAD data show that in the presence of LSD1 inhibitor, a significant fraction of LSD1-bound PpGe fails to gain DNA methylation. We further show that this effect is mostly observed in PpGes with low/intermediate CpG content. Underscoring the sensitivity and accuracy of MethylRAD sequencing, our study demonstrates that this method can detect small changes in DNA methylation in regulatory regions, including those with low/intermediate CpG content, thus asserting its use as a method of choice for diagnostic purposes.
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Affiliation(s)
- Debapriya Saha
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; (D.S.); (A.B.N.)
| | - Allison B. Norvil
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; (D.S.); (A.B.N.)
| | - Nadia A. Lanman
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA;
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; (D.S.); (A.B.N.)
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA;
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7
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Sharma S, Bhonde R. Genetic and epigenetic stability of stem cells: Epigenetic modifiers modulate the fate of mesenchymal stem cells. Genomics 2020; 112:3615-3623. [DOI: 10.1016/j.ygeno.2020.04.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/08/2020] [Accepted: 04/24/2020] [Indexed: 12/11/2022]
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8
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The ubiquitin-conjugating enzyme UBE2K determines neurogenic potential through histone H3 in human embryonic stem cells. Commun Biol 2020; 3:262. [PMID: 32451438 PMCID: PMC7248108 DOI: 10.1038/s42003-020-0984-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 05/01/2020] [Indexed: 01/05/2023] Open
Abstract
Histones modulate gene expression by chromatin compaction, regulating numerous processes such as differentiation. However, the mechanisms underlying histone degradation remain elusive. Human embryonic stem cells (hESCs) have a unique chromatin architecture characterized by low levels of trimethylated histone H3 at lysine 9 (H3K9me3), a heterochromatin-associated modification. Here we assess the link between the intrinsic epigenetic landscape and ubiquitin-proteasome system of hESCs. We find that hESCs exhibit high expression of the ubiquitin-conjugating enzyme UBE2K. Loss of UBE2K upregulates the trimethyltransferase SETDB1, resulting in H3K9 trimethylation and repression of neurogenic genes during differentiation. Besides H3K9 trimethylation, UBE2K binds histone H3 to induce its polyubiquitination and degradation by the proteasome. Notably, ubc-20, the worm orthologue of UBE2K, also regulates histone H3 levels and H3K9 trimethylation in Caenorhabditis elegans germ cells. Thus, our results indicate that UBE2K crosses evolutionary boundaries to promote histone H3 degradation and reduce H3K9me3 repressive marks in immortal cells. Azra Fatima et al. show that ubiquitin-conjugating enzyme UBE2K regulates neurogenic potential through its target histone H3 in human embryonic stem cells. This study suggests that UBE2K promotes histone H3 degradation, reducing the H3K9me3 repressive marks in immortal cells of both worms and humans.
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Dompe C, Janowicz K, Hutchings G, Moncrieff L, Jankowski M, Nawrocki MJ, Józkowiak M, Mozdziak P, Petitte J, Shibli JA, Dyszkiewicz-Konwińska M, Bruska M, Piotrowska-Kempisty H, Kempisty B, Nowicki M. Epigenetic Research in Stem Cell Bioengineering-Anti-Cancer Therapy, Regenerative and Reconstructive Medicine in Human Clinical Trials. Cancers (Basel) 2020; 12:E1016. [PMID: 32326172 PMCID: PMC7226111 DOI: 10.3390/cancers12041016] [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: 03/16/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/12/2022] Open
Abstract
The epigenome denotes all the information related to gene expression that is not contained in the DNA sequence but rather results from chemical changes to histones and DNA. Epigenetic modifications act in a cooperative way towards the regulation of gene expression, working at the transcriptional or post-transcriptional level, and play a key role in the determination of phenotypic variations in cells containing the same genotype. Epigenetic modifications are important considerations in relation to anti-cancer therapy and regenerative/reconstructive medicine. Moreover, a range of clinical trials have been performed, exploiting the potential of epigenetics in stem cell engineering towards application in disease treatments and diagnostics. Epigenetic studies will most likely be the basis of future cancer therapies, as epigenetic modifications play major roles in tumour formation, malignancy and metastasis. In fact, a large number of currently designed or tested clinical approaches, based on compounds regulating epigenetic pathways in various types of tumours, employ these mechanisms in stem cell bioengineering.
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Affiliation(s)
- Claudia Dompe
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (C.D.); (L.M.); (M.N.)
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (K.J.); (G.H.)
| | - Krzysztof Janowicz
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (K.J.); (G.H.)
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
| | - Greg Hutchings
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (K.J.); (G.H.)
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
| | - Lisa Moncrieff
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (C.D.); (L.M.); (M.N.)
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK; (K.J.); (G.H.)
| | - Maurycy Jankowski
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
| | - Mariusz J. Nawrocki
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
| | - Małgorzata Józkowiak
- Department of Toxicology, Poznan University of Medical Sciences, 61-631 Poznan, Poland; (M.J.); (H.P.-K.)
| | - Paul Mozdziak
- Physiology Graduate Program, North Carolina State University, Raleigh, NC 27695, USA;
| | - Jim Petitte
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA;
| | - Jamil A. Shibli
- Department of Periodontology and Oral Implantology, Dental Research Division, University of Guarulhos, São Paulo 07023-070, Brazil;
| | - Marta Dyszkiewicz-Konwińska
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
- Department of Biomaterials and Experimental Dentistry, Poznan University of Medical Sciences, 61 701 Poznan, Poland
| | - Małgorzata Bruska
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
| | - Hanna Piotrowska-Kempisty
- Department of Toxicology, Poznan University of Medical Sciences, 61-631 Poznan, Poland; (M.J.); (H.P.-K.)
| | - Bartosz Kempisty
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (C.D.); (L.M.); (M.N.)
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (M.J.); (M.J.N.); (M.D.-K.); (M.B.)
- Department of Obstetrics and Gynaecology, University Hospital and Masaryk University, 602 00 Brno, Czech Republic
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87 100 Torun, Poland
| | - Michał Nowicki
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland; (C.D.); (L.M.); (M.N.)
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Klatt D, Cheng E, Hoffmann D, Santilli G, Thrasher AJ, Brendel C, Schambach A. Differential Transgene Silencing of Myeloid-Specific Promoters in the AAVS1 Safe Harbor Locus of Induced Pluripotent Stem Cell-Derived Myeloid Cells. Hum Gene Ther 2020; 31:199-210. [PMID: 31773990 DOI: 10.1089/hum.2019.194] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Targeted integration into a genomic safe harbor, such as the AAVS1 locus on chromosome 19, promises predictable transgene expression and reduces the risk of insertional mutagenesis in the host genome. The application of gamma-retroviral long terminal repeat (LTR)-driven vectors, which semirandomly integrate into the genome, has previously caused severe adverse events in some clinical studies due to transactivation of neighboring proto-oncogenes. Consequently, the site-specific integration of a therapeutic transgene into a genomic safe harbor locus would allow stable genetic correction with a reduced risk of insertional mutagenesis. However, recent studies revealed that transgene silencing, especially in case of weaker cell type-specific promoters, can occur in the AAVS1 locus of human pluripotent stem cells (PSCs) and can impede transgene expression during differentiation. In this study, we aimed to correct p47phox deficiency, which is the second most common cause of chronic granulomatous disease, by insertion of a therapeutic p47phox transgene into the AAVS1 locus of human induced PSCs (iPSCs) using CRISPR-Cas9. We analyzed transgene expression and functional correction from three different myeloid-specific promoters (miR223, CatG/cFes, and myeloid-related protein 8 [MRP8]). Upon myeloid differentiation of corrected iPSC clones, we observed that the miR223 and CatG/cFes promoters achieved therapeutically relevant levels of p47phox expression and nicotinamide adenine dinucleotide phosphate oxidase activity, whereas the MRP8 promoter was less efficient. Analysis of the different promoters revealed high CpG methylation of the MRP8 promoter in differentiated cells, which correlated with the transgene expression data. In summary, we identified the miR223 and CatG/cFes promoters as cell type-specific promoters that allow stable transgene expression in the AAVS1 locus of iPSC-derived myeloid cells. Our findings further indicate that promoter silencing can occur in the AAVS1 safe harbor locus in differentiated hematopoietic cells and that a comparison of different promoters is necessary to achieve optimal transgene expression for therapeutic application of iPSC-derived cells.
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Affiliation(s)
- Denise Klatt
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Erica Cheng
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Dirk Hoffmann
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Giorgia Santilli
- Infection, Immunity and Inflammation Program, Molecular and Cellular Immunology Section, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Adrian J Thrasher
- Infection, Immunity and Inflammation Program, Molecular and Cellular Immunology Section, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Christian Brendel
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany.,Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
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11
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Stowers RS, Shcherbina A, Israeli J, Gruber JJ, Chang J, Nam S, Rabiee A, Teruel MN, Snyder MP, Kundaje A, Chaudhuri O. Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility. Nat Biomed Eng 2019; 3:1009-1019. [PMID: 31285581 PMCID: PMC6899165 DOI: 10.1038/s41551-019-0420-5] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 05/31/2019] [Indexed: 11/10/2022]
Abstract
In breast cancer, the increased stiffness of the extracellular matrix is a key driver of malignancy. Yet little is known about the epigenomic changes that underlie the tumorigenic impact of extracellular matrix mechanics. Here, we show in a three-dimensional culture model of breast cancer that stiff extracellular matrix induces a tumorigenic phenotype through changes in chromatin state. We found that increased stiffness yielded cells with more wrinkled nuclei and with increased lamina-associated chromatin, that cells cultured in stiff matrices displayed more accessible chromatin sites, which exhibited footprints of Sp1 binding, and that this transcription factor acts along with the histone deacetylases 3 and 8 to regulate the induction of stiffness-mediated tumorigenicity. Just as cell culture on soft environments or in them rather than on tissue-culture plastic better recapitulates the acinar morphology observed in mammary epithelium in vivo, mammary epithelial cells cultured on soft microenvironments or in them also more closely replicate the in vivo chromatin state. Our results emphasize the importance of culture conditions for epigenomic studies, and reveal that chromatin state is a critical mediator of mechanotransduction.
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Affiliation(s)
- Ryan S Stowers
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA
| | - Anna Shcherbina
- Department of Biological Data Science, Stanford University, Stanford, CA, USA
| | - Johnny Israeli
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Physics, Stanford University, Stanford, CA, USA
| | - Joshua J Gruber
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine, Oncology Division, Stanford University, Stanford, CA, USA
| | - Julie Chang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Sungmin Nam
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA
| | - Atefeh Rabiee
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Mary N Teruel
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ovijit Chaudhuri
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA.
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12
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Thong T, Forté CA, Hill EM, Colacino JA. Environmental exposures, stem cells, and cancer. Pharmacol Ther 2019; 204:107398. [PMID: 31376432 PMCID: PMC6881547 DOI: 10.1016/j.pharmthera.2019.107398] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/29/2019] [Indexed: 12/19/2022]
Abstract
An estimated 70-90% of all cancers are linked to exposure to environmental risk factors. In parallel, the number of stem cells in a tissue has been shown to be a strong predictor of risk of developing cancer in that tissue. Tumors themselves are characterized by an acquisition of "stem cell" characteristics, and a growing body of evidence points to tumors themselves being sustained and propagated by a stem cell-like population. Here, we review our understanding of the interplay between environmental exposures, stem cell biology, and cancer. We provide an overview of the role of stem cells in development, tissue homeostasis, and wound repair. We discuss the pathways and mechanisms governing stem cell plasticity and regulation of the stem cell state, and describe experimental methods for assessment of stem cells. We then review the current understanding of how environmental exposures impact stem cell function relevant to carcinogenesis and cancer prevention, with a focus on environmental and occupational exposures to chemical, physical, and biological hazards. We also highlight key areas for future research in this area, including defining whether the biological basis for cancer disparities is related to effects of complex exposure mixtures on stem cell biology.
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Affiliation(s)
- Tasha Thong
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Chanese A Forté
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Michigan Institute for Computational Discovery and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Evan M Hill
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
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13
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Zamani ARN, Saberianpour S, Geranmayeh MH, Bani F, Haghighi L, Rahbarghazi R. Modulatory effect of photobiomodulation on stem cell epigenetic memory: a highlight on differentiation capacity. Lasers Med Sci 2019; 35:299-306. [PMID: 31494789 DOI: 10.1007/s10103-019-02873-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/03/2019] [Indexed: 02/06/2023]
Abstract
Differentiation potential of stem cells into various lineages makes these cells as promising sources to treat multiple diseases. In this regard, the use of different strategies and protocols to increase differentiation capacity is highly demanded. Low-level laser therapy, a relatively noninvasive technique, has the capacity to accelerate the healing of numerous injuries and a portion of restorative capacity could be correlated with the stem cell activation and differentiation. Several mechanisms have been diagnosed to participate in orientation of stem cells to functional mature cells. Among them, the status of DNA methylation orchestrates the maintenance of tissue-specific gene expression during the differentiation procedure. DNA methylation is a momentous event in embryogenesis and functional maturation. This review article highlighted the potency of laser irradiation (low-level intensities) in the differentiation of stem cells by modulation of methylation. The analysis of these modalities could help us to understand the underlying mechanisms participating in the therapeutic effects of photobiomodulation.
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Affiliation(s)
| | - Shirin Saberianpour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Farhad Bani
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Haghighi
- Department of Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Reza Rahbarghazi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. .,Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
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14
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Bar S, Benvenisty N. Epigenetic aberrations in human pluripotent stem cells. EMBO J 2019; 38:embj.2018101033. [PMID: 31088843 DOI: 10.15252/embj.2018101033] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/13/2019] [Accepted: 03/15/2019] [Indexed: 12/14/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are being increasingly utilized worldwide in investigating human development, and modeling and discovering therapies for a wide range of diseases as well as a source for cellular therapy. Yet, since the first isolation of human embryonic stem cells (hESCs) 20 years ago, followed by the successful reprogramming of human-induced pluripotent stem cells (hiPSCs) 10 years later, various studies shed light on abnormalities that sometimes accumulate in these cells in vitro Whereas genetic aberrations are well documented, epigenetic alterations are not as thoroughly discussed. In this review, we highlight frequent epigenetic aberrations found in hPSCs, including alterations in DNA methylation patterns, parental imprinting, and X chromosome inactivation. We discuss the potential origins of these abnormalities in hESCs and hiPSCs, survey the different methods for detecting them, and elaborate on their potential consequences for the different utilities of hPSCs.
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Affiliation(s)
- Shiran Bar
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Nissim Benvenisty
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
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15
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Shafi A, Mitrea C, Nguyen T, Draghici S. A survey of the approaches for identifying differential methylation using bisulfite sequencing data. Brief Bioinform 2019; 19:737-753. [PMID: 28334228 DOI: 10.1093/bib/bbx013] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Indexed: 01/03/2023] Open
Abstract
DNA methylation is an important epigenetic mechanism that plays a crucial role in cellular regulatory systems. Recent advancements in sequencing technologies now enable us to generate high-throughput methylation data and to measure methylation up to single-base resolution. This wealth of data does not come without challenges, and one of the key challenges in DNA methylation studies is to identify the significant differences in the methylation levels of the base pairs across distinct biological conditions. Several computational methods have been developed to identify differential methylation using bisulfite sequencing data; however, there is no clear consensus among existing approaches. A comprehensive survey of these approaches would be of great benefit to potential users and researchers to get a complete picture of the available resources. In this article, we present a detailed survey of 22 such approaches focusing on their underlying statistical models, primary features, key advantages and major limitations. Importantly, the intrinsic drawbacks of the approaches pointed out in this survey could potentially be addressed by future research.
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Affiliation(s)
- Adib Shafi
- Department of Computer Science, Wayne State University, USA
| | | | - Tin Nguyen
- Department of Computer Science, Wayne State University, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, USA.,Department of Obstetrics and Gynecology, Wayne State University, USA
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16
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Kerr CL, Bol GM, Vesuna F, Raman V. Targeting RNA helicase DDX3 in stem cell maintenance and teratoma formation. Genes Cancer 2019; 10:11-20. [PMID: 30899416 PMCID: PMC6420792 DOI: 10.18632/genesandcancer.187] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
DDX3 is an RNA helicase that has antiapoptotic properties, and promotes proliferation and transformation. Besides the role of DDX3 in transformed cells, there is evidence to indicate that DDX3 expression is at its highest levels during early embryonic development and is also expressed in germ cells of adults. Even though there is a distinct pattern of DDX3 expression during embryonic development and in adults, very little is known regarding its role in embryonic stem cells and pluripotency. In this work, we examined the relationship between DDX3 and human embryonic stem cells and its differentiated lineages. DDX3 expression was analyzed by immunohistochemistry in human embryonic stem cells and embryonal carcinoma cells. From the data obtained, it was evident that DDX3 was overexpressed in undifferentiated stem cells compared to differentiated cells. Moreover, when DDX3 expression was abrogated in multiple stem cells, proliferation was decreased, but differentiation was facilitated. Importantly, this resulted in reduced potency to induce teratoma formation. Taken together, these findings indicate a distinct role for DDX3 in stem cell maintenance.
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Affiliation(s)
- Candace L Kerr
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guus M Bol
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, University Medical Center Utrecht Cancer Center, GA Utrecht, The Netherlands
| | - Farhad Vesuna
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, University Medical Center Utrecht Cancer Center, GA Utrecht, The Netherlands
| | - Venu Raman
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Pathology, University Medical Center Utrecht Cancer Center, GA Utrecht, The Netherlands
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17
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Transcriptome variations among human embryonic stem cell lines are associated with their differentiation propensity. PLoS One 2018; 13:e0192625. [PMID: 29444173 PMCID: PMC5812638 DOI: 10.1371/journal.pone.0192625] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/26/2018] [Indexed: 12/20/2022] Open
Abstract
Human embryonic stem cells (hESCs) have the potential to form any cell type in the body, making them attractive cell sources in drug screening, regenerative medicine, disease and developmental processes modeling. However, not all hESC lines have the equal potency to generate desired cell types in vitro. Significant variations have been observed for the differentiation efficiency of various human ESC lines. The precise underpinning molecular mechanisms are still unclear. In this work, we compared transcriptome variations of four hESC lines H7, HUES1, HUES8 and HUES9. We found that hESC lines have different gene expression profiles, and these differentially expressed genes (DEGs) are significantly enriched in developmental processes, such as ectodermal, mesodermal and endodermal development. The enrichment difference between hESC lines was consistent with its lineage bias. Among these DEGs, some pluripotency factors and genes involved in signaling transduction showed great variations as well. The pleiotropic functions of these genes in controlling hESC identity and early lineage specification, implicated that different hESC lines may utilize distinct balance mechanisms to maintain pluripotent state. When the balance is broken in a certain environment, gene expression variation between them could impact on their different lineage specification behavior.
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18
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Abstract
In the Outlook from Laptenko and Prives, the authors discuss the study published in this issue by Tovy et al. regarding the control of DNA methylation homeostasis by p53 in embryonic stem cells. Long understood as a bona fide tumor suppressor that safeguards the integrity of the genome via regulating numerous cellular outcomes, p53 may also exert its decisive and versatile functions by controlling DNA methylation. In this issue of Genes & Development, Tovy and colleagues (pp. 959–972) report that, in naïve mouse embryonic stem cells (ESCs), p53 controls DNA methylation homeostasis by regulating the expression of key counteracting components of the DNA methylation machinery. Their findings indicate that p53 may exert its “guardian of genome” duties at least in part via safeguarding the epigenome of ESCs.
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Affiliation(s)
- Oleg Laptenko
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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19
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Yan H, He J, Guan Q, Cai H, Zhang L, Zheng W, Qi L, Zhang S, Liu H, Li H, Zhao W, Yang S, Guo Z. Identifying CpG sites with different differential methylation frequencies in colorectal cancer tissues based on individualized differential methylation analysis. Oncotarget 2017; 8:47356-47364. [PMID: 28537885 PMCID: PMC5564570 DOI: 10.18632/oncotarget.17647] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 04/21/2017] [Indexed: 12/20/2022] Open
Abstract
A big challenge to clinical diagnosis and therapy of colorectal cancer (CRC) is its extreme heterogeneity, and thus it would be of special importance if we could find common biomarkers besides subtype-specific biomarkers for CRC. Here, with DNA methylation data produced by different laboratories, we firstly revealed that the relative methylation-level orderings (RMOs) of CpG sites within colorectal normal tissues are highly stable but widely disrupted in the CRC tissues. This finding provides the basis for using the RankComp algorithm to identify differentially methylated (DM) CpG sites in every individual CRC sample through comparing the RMOs within the individual sample with the stable RMOs predetermined in normal tissues. For 75 CRC samples, RankComp detected averagely 4,062 DM CpG sites per sample and reached an average precision of 91.34% in terms that the hypermethylation or hypomethylation states of the DM CpG sites detected for each cancer sample were consistent with the observed differences between this cancer sample and its paired adjacent normal sample. Finally, we applied RankComp to identify DM CpG sites for each of the 268 CRC samples from The Cancer Genome Atlas and found 26 and 143 genes whose promoter regions included CpG sites that were hypermethylated and hypomethylated, respectively, in more than 95% of the 268 CRC samples. Individualized pathway analysis identified six pathways that were significantly enriched with DM genes in more than 90% of the CRC tissues. These universal DNA methylation biomarkers could be important diagnostic makers and therapy targets for CRC.
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Affiliation(s)
- Haidan Yan
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
| | - Jun He
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
| | - Qingzhou Guan
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
| | - Hao Cai
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
| | - Lin Zhang
- Institute of Biomedical Engineering and Instrumentation, Hangzhou Dianzi University, Hangzhou, China
| | - Weicheng Zheng
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
| | - Lishuang Qi
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Suyun Zhang
- Department of Medical Oncology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Huaping Liu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
| | - Hongdong Li
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
| | - Wenyuan Zhao
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Sheng Yang
- Department of Medical Oncology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Zheng Guo
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China.,Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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20
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Byun HM, Eshaghian S, Douer D, Trent J, Garcia-Manero G, Bhatia R, Siegmund K, Yang AS. Impact of Chromosomal Rearrangement upon DNA Methylation Patterns in Leukemia. Open Med (Wars) 2017; 12:76-85. [PMID: 28730166 PMCID: PMC5444343 DOI: 10.1515/med-2017-0014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 03/22/2017] [Indexed: 12/31/2022] Open
Abstract
Genomic instability, including genetic mutations and chromosomal rearrangements, can lead to cancer development. Aberrant DNA methylation occurs commonly in cancer cells. The aim of this study is to determine the effects of a specific chromosomal lesion the BCR-ABL translocation t(9:22), in establishing DNA methylation profiles in cancer. Materials and methods We compared DNA methylation of 1,505 selected promoter CpGs in chronic myelogenous leukemia (CML), acute lymphoblastic leukemia (ALL) with and without the Philadelphia chromosome t(9:22), CD34+ hematopoietic stem cells transfected with BCR-ABL, and other tumors without BCR-ABL (acute promyelocytic leukemia (APL) and gastrointestinal stromal tumors (GIST). In this study, the DNA methylation profile of CML was more closely related to APL, another myeloid leukemia, than Ph+ ALL. Although DNA methylation profiles were consistent within a specific tumor type, overall DNA methylation profiles were no influenced by BCR-ABL gene translocation in the cancers and tissues studied. We conclude that DNA methylation profiles may reflect the cell of origin in cancers rather than the chromosomal lesions involved in leukemogenesis.
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Affiliation(s)
- Hyang-Min Byun
- Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE4 5PLUnited Kingdom
| | - Shahrooz Eshaghian
- Jane Anne Nohl Division of Hematology; University of Southern California, Los Angeles, CA, USA
| | - Dan Douer
- Jane Anne Nohl Division of Hematology; University of Southern California, Los Angeles, CA, USA
| | - Jonathen Trent
- Department of Sarcoma, University of Texas-MD Anderson Cancer Center, Houston, TX, USA
| | | | - Ravi Bhatia
- Department of Hematology, City of Hope Cancer Center, Duarte, CA, USA
| | - Kim Siegmund
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Allen S Yang
- Jane Anne Nohl Division of Hematology; University of Southern California, Los Angeles, CA, USA
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21
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Yan H, Guan Q, He J, Lin Y, Zhang J, Li H, Liu H, Gu Y, Guo Z, He F. Individualized analysis reveals CpG sites with methylation aberrations in almost all lung adenocarcinoma tissues. J Transl Med 2017; 15:26. [PMID: 28178989 PMCID: PMC5299650 DOI: 10.1186/s12967-017-1122-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/07/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Due to the heterogeneity of cancer, identifying differentially methylated (DM) CpG sites between a set of cancer samples and a set of normal samples cannot tell us which patients have methylation aberrations in a particular DM CpG site. METHODS We firstly showed that the relative methylation-level orderings (RMOs) of CpG sites within individual normal lung tissues are highly stable but widely disrupted in lung adenocarcinoma tissues. This finding provides the basis of using the RankComp algorithm, previously developed for differential gene expression analysis at the individual level, to identify DM CpG sites in each cancer tissue compared with its own normal state. Briefly, through comparing with the highly stable normal RMOs predetermined in a large collection of samples for normal lung tissues, the algorithm finds those CpG sites whose hyper- or hypo-methylations may lead to the disrupted RMOs of CpG site pairs within a disease sample based on Fisher's exact test. RESULTS Evaluated in 59 lung adenocarcinoma tissues with paired adjacent normal tissues, RankComp reached an average precision of 94.26% for individual-level DM CpG sites. Then, after identifying DM CpG sites in each of the 539 lung adenocarcinoma samples from TCGA, we found five and 44 CpG sites hypermethylated and hypomethylated in above 90% of the disease samples, respectively. These findings were validated in 140 publicly available and eight additionally measured paired cancer-normal samples. Gene expression analysis revealed that four of the five genes, HOXA9, TAL1, ATP8A2, ENG and SPARCL1, each harboring one of the five frequently hypermethylated CpG sites within its promoters, were also frequently down-regulated in lung adenocarcinoma. CONCLUSIONS The common DNA methylation aberrations in lung adenocarcinoma tissues may be important for lung adenocarcinoma diagnosis and therapy.
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Affiliation(s)
- Haidan Yan
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, 350001, China
| | - Qingzhou Guan
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, 350001, China
| | - Jun He
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, 350001, China
| | - Yunqing Lin
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, 350001, China
| | - Juan Zhang
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, 350001, China
| | - Hongdong Li
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, 350001, China
| | - Huaping Liu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, 350001, China
| | - Yunyan Gu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Zheng Guo
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China. .,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, 350001, China.
| | - Fei He
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, 350001, China.
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22
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Ling KY, Cheow LF, Quake SR, Burkholder WF, Messerschmidt DM. Single Cell Restriction Enzyme-Based Analysis of Methylation at Genomic Imprinted Regions in Preimplantation Mouse Embryos. Methods Mol Biol 2017; 1605:171-189. [PMID: 28456965 DOI: 10.1007/978-1-4939-6988-3_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The methylation of cytosines in DNA is a fundamental epigenetic regulatory mechanism. During preimplantation development, mammalian embryos undergo extensive epigenetic reprogramming, including the global erasure of germ cell-specific DNA methylation marks, to allow for the establishment of the pluripotent state of the epiblast. However, DNA methylation marks at specific regions, such as imprinted gene regions, escape this reprogramming process, as their inheritance from germline to soma is paramount for proper development. To study the dynamics of DNA methylation marks in single blastomeres of mouse preimplantation embryos, we devised a new approach-single cell restriction enzyme analysis of methylation (SCRAM). SCRAM allows for reliable, fast, and high-throughput analysis of DNA methylation states of multiple regions of interest from single cells. In the method described below, SCRAM is specifically used to address loss of DNA methylation at genomic imprints or other highly methylated regions of interest.
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Affiliation(s)
- Ka Yi Ling
- Developmental Epigenetics and Disease Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lih Feng Cheow
- Microfluidics Systems Biology Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Stephen R Quake
- Department of Bioengineering and Applied Physics, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - William F Burkholder
- Microfluidics Systems Biology Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Daniel M Messerschmidt
- Developmental Epigenetics and Disease Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
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23
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Genome-wide DNA methylation profiles of maternal peripheral blood and placentas: potential risk factors for preeclampsia and validation of GRK5. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0486-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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24
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Brenner C, Luciani J, Bizet M, Ndlovu M, Josseaux E, Dedeurwaerder S, Calonne E, Putmans P, Cartron PF, Defrance M, Fuks F, Deplus R. The interplay between the lysine demethylase KDM1A and DNA methyltransferases in cancer cells is cell cycle dependent. Oncotarget 2016; 7:58939-58952. [PMID: 27449289 PMCID: PMC5312287 DOI: 10.18632/oncotarget.10624] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 07/06/2016] [Indexed: 12/12/2022] Open
Abstract
DNA methylation and histone modifications are key epigenetic regulators of gene expression, and tight connections are known between the two. DNA methyltransferases are upregulated in several tumors and aberrant DNA methylation profiles are a cancer hallmark. On the other hand, histone demethylases are upregulated in cancer cells. Previous work on ES cells has shown that the lysine demethylase KDM1A binds to DNMT1, thereby affecting DNA methylation. In cancer cells, the occurrence of this interaction has not been explored. Here we demonstrate in several tumor cell lines an interaction between KDM1A and both DNMT1 and DNMT3B. Intriguingly and in contrast to what is observed in ES cells, KDM1A depletion in cancer cells was found not to trigger any reduction in the DNMT1 or DNMT3B protein level or any change in DNA methylation. In the S-phase, furthermore, KDM1A and DNMT1 were found, to co-localize within the heterochromatin. Using P-LISA, we revealed substantially increased binding of KDM1A to DNMT1 during the S-phase. Together, our findings propose a mechanistic link between KDM1A and DNA methyltransferases in cancer cells and suggest that the KDM1A/DNMT1 interaction may play a role during replication. Our work also strengthens the idea that DNMTs can exert functions unrelated to act on DNA methylation.
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Affiliation(s)
- Carmen Brenner
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Judith Luciani
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Matladi Ndlovu
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Eleonore Josseaux
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Sarah Dedeurwaerder
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Pierre-Francois Cartron
- Centre de Recherche en Cancérologie Nantes-Angers, INSERM, U892, Equipe Apoptose et Progression Tumorale, BP7021, 44007 Nantes, France
- Département de Recherche en Cancérologie, Faculté de Médecine, Université de Nantes, IFR26, F-4400, Nantes, France
- LaBCT, Institut de Cancérologie de l'Ouest, 44805 Nantes, Saint Herblain Cedex, France
| | - Matthieu Defrance
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
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25
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Abstract
The derivation of human embryonic stem (hES) cells heralds a new era in stem cell research, generating excitement for their therapeutic potential in regenerative medicine. Pioneering work of embryologists, developmental biologists, and reproductive medicine practitioners in in vitro fertilization clinics has facilitated hES cell research. This review summarizes current research focused on optimizing hES cell culture conditions for good manufacturing practice, directing hES cell differentiation toward trophectoderm and germ cells, and approaches used to reprogram cells for pluripotent cell derivation. The identification of germ stem cells in the testis and the recent controversy over their existence in the ovary raise the possibility of harnessing them for treating young cancer survivors. There is also the potential to harvest fetal stem cells with pluripotent cell-like properties from discarded placental tissues. The recent identification of adult stem/progenitor cell activity in the human endometrium offers a new understanding of common gynecological diseases. Discoveries resulting from research into embryonic, germ, fetal, and adult stem cells are highly relevant to human reproduction.
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Affiliation(s)
- Caroline E Gargett
- Centre for Women's Health Research, Monash Institute of Medical Research, and Monash University Department of Obstetrics and Gynaecology, Monash Medical Centre, Clayton, Victoria, Australia.
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26
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Rebuzzini P, Zuccotti M, Redi CA, Garagna S. Achilles' heel of pluripotent stem cells: genetic, genomic and epigenetic variations during prolonged culture. Cell Mol Life Sci 2016; 73:2453-66. [PMID: 26961132 PMCID: PMC11108315 DOI: 10.1007/s00018-016-2171-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/28/2016] [Accepted: 02/25/2016] [Indexed: 12/12/2022]
Abstract
Pluripotent stem cells differentiate into almost any specialized adult cell type of an organism. PSCs can be derived either from the inner cell mass of a blastocyst-giving rise to embryonic stem cells-or after reprogramming of somatic terminally differentiated cells to obtain ES-like cells, named induced pluripotent stem cells. The potential use of these cells in the clinic, for investigating in vitro early embryonic development or for screening the effects of new drugs or xenobiotics, depends on capability to maintain their genome integrity during prolonged culture and differentiation. Both human and mouse PSCs are prone to genomic and (epi)genetic instability during in vitro culture, a feature that seriously limits their real potential use. Culture-induced variations of specific chromosomes or genes, are almost all unpredictable and, as a whole, differ among independent cell lines. They may arise at different culture passages, suggesting the absence of a safe passage number maintaining genome integrity and rendering the control of genomic stability mandatory since the very early culture passages. The present review highlights the urgency for further studies on the mechanisms involved in determining (epi)genetic and chromosome instability, exploiting the knowledge acquired earlier on other cell types.
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Affiliation(s)
- Paola Rebuzzini
- Laboratorio di Biologia dello Sviluppo, Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani', Università degli Studi di Pavia, Via Ferrata 9, 27100, Pavia, Italy.
- Center for Health Technologies (C.H.T.), Università degli Studi di Pavia, Via Ferrata 1, Pavia, Italy.
| | - Maurizio Zuccotti
- Unita' di Anatomia, Istologia ed Embriologia, Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali (S.BI.BI.T.), Università degli Studi di Parma, Via Volturno 39, 43100, Parma, Italy.
| | - Carlo Alberto Redi
- Laboratorio di Biologia dello Sviluppo, Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani', Università degli Studi di Pavia, Via Ferrata 9, 27100, Pavia, Italy
- Center for Health Technologies (C.H.T.), Università degli Studi di Pavia, Via Ferrata 1, Pavia, Italy
- Fondazione I.R.C.C.S. Policlinico San Matteo, Piazzale Golgi, 19, 27100, Pavia, Italy
| | - Silvia Garagna
- Laboratorio di Biologia dello Sviluppo, Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani', Università degli Studi di Pavia, Via Ferrata 9, 27100, Pavia, Italy.
- Center for Health Technologies (C.H.T.), Università degli Studi di Pavia, Via Ferrata 1, Pavia, Italy.
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27
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Sun L, Wang J, Yin X, Sun S, Zi C, Zhu G, Wu S, Bao W. Identification of a 5-Methylcytosine Site that may Regulate C/EBPβ Binding and Determine Tissue-Specific Expression of the BPI Gene in Piglets. Sci Rep 2016; 6:28506. [PMID: 27338589 PMCID: PMC4919782 DOI: 10.1038/srep28506] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/03/2016] [Indexed: 01/19/2023] Open
Abstract
Bactericidal/permeability-increasing protein (BPI) plays an important role in innate immune defense in mammals. A previous study showed that BPI gene expression correlates to gram-negative bacteria resistance. However, this gene showed tissue-specific expression in piglets and strongly expressed only in the digestive tract. To investigate the mechanisms governing the tissue-specificity, bisulfite sequencing PCR and next generation sequencing were used for high accuracy methylation quantitation of CpG islands of BPI gene upstream in 11 different tissues from weaned Yorkshire piglets. Additionally, qPCR was used to examine mRNA levels of BPI gene as well as transcription factor. We additionally analyzed transcriptional regulation by studying key 5-methylcytosine sites and transcription factors. Results showed that BPI mRNA levels significantly correlated with the overall methylation as well as methylation at mC-15 which was non-CpG site, no significant correlation could be found between the BPI and transcription factor mRNA levels, EMSA test showed that C/EBPβ could interact with BPI wild-type promoter DNA, but not methylated DNA. So we confirmed that methylation of mC-15 residue could inhibit the ability of C/EBPβ binding to the BPI promoter and affect the expression, and this mechanism probably plays a role in the tissue specificity of BPI gene expression in weaned piglets.
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Affiliation(s)
- Li Sun
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China
| | - Jing Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China
| | - Xuemei Yin
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China
| | - Shouyong Sun
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China
| | - Chen Zi
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P. R. China
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28
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Chen DP, Lin YC, Fann CSJ. Methods for identifying differentially methylated regions for sequence- and array-based data. Brief Funct Genomics 2016; 15:485-490. [PMID: 27323952 DOI: 10.1093/bfgp/elw018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
DNA methylation is one of the most important epigenetic mechanisms, and participates in the pathogenic processes of many diseases. Differentially methylated regions (DMRs) in the genome have been reported and implicated in a number of different diseases, tissues and cell types, and are associated with gene expression levels. Therefore, identification of DMRs is one of the most critical and fundamental issues in dissecting the disease etiologies. Based on bisulfite conversion, advances in sequence- and array-based technologies have helped investigators study genome-wide DNA methylation. Many methods have been developed to detect DMRs, and they have revolutionized our understanding of DNA methylation and provided new insights into its role in diverse biological functions. According to data and region types, we discuss various methods in detecting DMRs, their utility and limitations comprehensively. We recommend using a few of the methods in the same data and region type to detect DMRs because they could be complementary to one another.
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29
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Chen J, Zheng Z, Chen Y, Li J, Qian S, Shi Y, Sun L, Han Y, Zhang S, Yu K. Histone Deacetylase Inhibitors Trichostatin A and MCP30 Relieve Benzene-Induced Hematotoxicity via Restoring Topoisomerase IIα. PLoS One 2016; 11:e0153330. [PMID: 27058040 PMCID: PMC4826000 DOI: 10.1371/journal.pone.0153330] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 03/28/2016] [Indexed: 11/28/2022] Open
Abstract
Dysfunction of histone acetylation inhibits topoisomerase IIα (Topo IIα), which is implicated in benzene-induced hematotoxicity in patients with chronic benzene exposure. Whether histone deacetylase (HDAC) inhibitors can relieve benzene-induced hematotoxicity remains unclear. Here we showed that hydroquinone, a main metabolite of benzene, increased the HDAC activity, decreased the Topo IIα expression and induced apoptosis in human bone marrow mononuclear cells in vitro, and treatment with two HDAC inhibitors, namely trichostatin A (TSA) or a mixture of ribosome-inactivating proteins MCP30, almost completely reversed these effects. We further established a benzene poisoning murine model by inhaling benzene vapor in a container and found that benzene poisoning decreased the expression and activity of Topo IIα, and impaired acetylation of histone H4 and H3. The analysis of regulatory factors of Topo IIα promoter found that benzene poisoning decreased the mRNA levels of SP1 and C-MYB, and increased the mRNA level of SP3. Both TSA and MCP30 significantly enhanced the acetylation of histone H3 and H4 in Topo IIα promoter and increased the expression and activity of Topo IIα in benzene poisoning mice, which contributed to relieve the symptoms of hematotoxicity. Thus, treatment with HDAC inhibitors represents an attractive approach to reduce benzene-induced hematotoxicity.
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Affiliation(s)
- Jingjing Chen
- Department of Hematology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Zhouyi Zheng
- Department of Hematology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Yi Chen
- Department of Hematology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Jiaqi Li
- Department of Hematology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Shanhu Qian
- Department of Hematology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Yifen Shi
- Department of Hematology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Lan Sun
- Department of Hematology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Yixiang Han
- Laboratory of Internal Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Shenghui Zhang
- Department of Hematology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
| | - Kang Yu
- Department of Hematology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, China
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30
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Abstract
Aberrant DNA methylation is considered to be one of the most common hallmarks of cancer. Several recent advances in assessing the DNA methylome provide great promise for deciphering the cancer-specific DNA methylation patterns. Herein, we present the current key technologies used to detect high-throughput genome-wide DNA methylation, and the available cancer-associated methylation databases. Additionally, we focus on the computational methods for preprocessing, analyzing and interpreting the cancer methylome data. It not only discusses the challenges of the differentially methylated region calling and the prediction model construction but also highlights the biomarker investigation for cancer diagnosis, prognosis and response to treatment. Finally, some emerging challenges in the computational analysis of cancer methylome data are summarized.
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31
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Kim JH, Park JL, Kim SY. Non-negligible Occurrence of Errors in Gender Description in Public Data Sets. Genomics Inform 2016; 14:34-40. [PMID: 27103889 PMCID: PMC4838528 DOI: 10.5808/gi.2016.14.1.34] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 12/30/2015] [Accepted: 12/30/2015] [Indexed: 11/20/2022] Open
Abstract
Due to advances in omics technologies, numerous genome-wide studies on human samples have been published, and most of the omics data with the associated clinical information are available in public repositories, such as Gene Expression Omnibus and ArrayExpress. While analyzing several public datasets, we observed that errors in gender information occur quite often in public datasets. When we analyzed the gender description and the methylation patterns of gender-specific probes (glucose-6-phosphate dehydrogenase [G6PD], ephrin-B1 [EFNB1], and testis specific protein, Y-linked 2 [TSPY2]) in 5,611 samples produced using Infinium 450K HumanMethylation arrays, we found that 19 samples from 7 datasets were erroneously described. We also analyzed 1,819 samples produced using the Affymetrix U133Plus2 array using several gender-specific genes (X (inactive)-specific transcript [XIST], eukaryotic translation initiation factor 1A, Y-linked [EIF1AY], and DEAD [Asp-Glu-Ala-Asp] box polypeptide 3, Y-linked [DDDX3Y]) and found that 40 samples from 3 datasets were erroneously described. We suggest that the users of public datasets should not expect that the data are error-free and, whenever possible, that they should check the consistency of the data.
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Affiliation(s)
- Jong Hwan Kim
- Genome Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.; Department of Functional Genomics, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Jong-Luyl Park
- Epigenome Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Seon-Young Kim
- Genome Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.; Department of Functional Genomics, University of Science and Technology (UST), Daejeon 34113, Korea
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32
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Pérez-Campo FM, Riancho JA. Epigenetic Mechanisms Regulating Mesenchymal Stem Cell Differentiation. Curr Genomics 2016; 16:368-83. [PMID: 27019612 PMCID: PMC4765524 DOI: 10.2174/1389202916666150817202559] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 03/27/2015] [Accepted: 04/07/2015] [Indexed: 12/28/2022] Open
Abstract
Human Mesenchymal Stem Cells (hMSCs) have emerged in the last few years as one of the most promising therapeutic cell sources and, in particular, as an important tool for regenerative medicine of skeletal tissues. Although they present a more restricted potency than Embryonic Stem (ES) cells, the use of hMCS in regenerative medicine avoids many of the drawbacks characteristic of ES cells or induced pluripotent stem cells. The challenge in using these cells lies into developing precise protocols for directing cellular differentiation to generate a specific cell lineage. In order to achieve this goal, it is of the upmost importance to be able to control de process of fate decision and lineage commitment. This process requires the coordinate regulation of different molecular layers at transcriptional, posttranscriptional and translational levels. At the transcriptional level, switching on and off different sets of genes is achieved not only through transcriptional regulators, but also through their interplay with epigenetic modifiers. It is now well known that epigenetic changes take place in an orderly way through development and are critical in the determination of lineage-specific differentiation. More importantly, alteration of these epigenetic changes would, in many cases, lead to disease generation and even tumour formation. Therefore, it is crucial to elucidate how epigenetic factors, through their interplay with transcriptional regulators, control lineage commitment in hMSCs.
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Affiliation(s)
- Flor M Pérez-Campo
- Department of Internal Medicine, Hospital U. Marqués de Valdecilla-IDIVAL Universidad de Cantabria, 39008 Santander, Cantabria, Spain
| | - José A Riancho
- Department of Internal Medicine, Hospital U. Marqués de Valdecilla-IDIVAL Universidad de Cantabria, 39008 Santander, Cantabria, Spain
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33
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Chen M, Baumbach J, Vandin F, Röttger R, Barbosa E, Dong M, Frost M, Christiansen L, Tan Q. Differentially Methylated Genomic Regions in Birth-Weight Discordant Twin Pairs. Ann Hum Genet 2016; 80:81-7. [DOI: 10.1111/ahg.12146] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 12/03/2015] [Accepted: 12/07/2015] [Indexed: 01/07/2023]
Affiliation(s)
- Mubo Chen
- Computational Biology Group, Department of Mathematics and Computer Science; University of Southern Denmark; Odense Denmark
- Department of Electrical and Computer Engineering, Faculty of Science and Technology; University of Macau; Macau China
| | - Jan Baumbach
- Computational Biology Group, Department of Mathematics and Computer Science; University of Southern Denmark; Odense Denmark
| | - Fabio Vandin
- Computational Biology Group, Department of Mathematics and Computer Science; University of Southern Denmark; Odense Denmark
- Department of Information Engineering; University of Padova; Padova Italy
| | - Richard Röttger
- Computational Biology Group, Department of Mathematics and Computer Science; University of Southern Denmark; Odense Denmark
| | - Eudes Barbosa
- Computational Biology Group, Department of Mathematics and Computer Science; University of Southern Denmark; Odense Denmark
| | - Mingchui Dong
- Department of Electrical and Computer Engineering, Faculty of Science and Technology; University of Macau; Macau China
| | - Morten Frost
- Department of Endocrinology; Odense University Hospital; Odense Denmark
| | - Lene Christiansen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health; University of Southern Denmark; Odense Denmark
| | - Qihua Tan
- Epidemiology, Biostatistics and Biodemography, Department of Public Health; University of Southern Denmark; Odense Denmark
- Unit of Human Genetics, Department of Clinical Research; University of Southern Denmark; Odense Denmark
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34
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Chen HC, Huang HY, Chen YL, Lee KD, Chu YR, Lin PY, Hsu CC, Chu PY, Huang THM, Hsiao SH, Leu YW. Methylation of the Tumor Suppressor Genes HIC1 and RassF1A Clusters Independently From the Methylation of Polycomb Target Genes in Colon Cancer. Ann Surg Oncol 2015; 24:578-585. [PMID: 26671036 DOI: 10.1245/s10434-015-5024-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Indexed: 12/31/2022]
Abstract
BACKGROUND Methylation changes within tumor suppressor (TS) genes or polycomb group target (PcG) genes alter cell fates. Chromatin associated with PcG targets is bivalent in stem cells, while TS genes are not normally bivalent. PcG target methylation changes have been identified in tumor stem cells, and abnormal methylation is found in TS genes in cancers. If the epigenetic states of genes influence DNA methylation, then methylation of PcG targets and TS genes may evolve differently during cancer development. More importantly, methylation changes may be part of a sequence in tumorigenesis. METHODS Chromatin and methylation states of 4 PcG targets and 2 TS genes were determined in colon cancer cells. The methylation states were also detected in 100 pairs of colon cancer samples. Principle component analysis (PCA) was used to reveal whether TS methylation or PcG methylation was the main methylation change associated with colon cancers. RESULTS Chromatin and methylation states differ in colon cancer cell lines. The methylation states within PcG targets clustered independently from the methylation states in TS genes, a finding we previously reported in liver cancers. PCA in colon cancers revealed the strongest association with methylation changes in 2 TS genes, HIC1 and RassF1A. Loss of HIC1 methylation correlated with decreased tumor migration. CONCLUSIONS PcG and TS methylation states cluster independently from each other. The deduced principle component correlated better with TS methylation than PcG methylation in colon cancer. Abnormal methylation changes may represent a sequential biomarker profile to identify developing colon cancer.
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Affiliation(s)
- Hong-Chang Chen
- Division of Colorectal Surgery, Department of Surgery, Changhua Christian Hospital, Changhua, Taiwan
| | - Hsuan-Yuan Huang
- Division of Colorectal Surgery, Department of Surgery, Changhua Christian Hospital, Changhua, Taiwan
| | - Yao-Li Chen
- Transplant Medicine & Surgery Research Centre, Changhua Christian Hospital, Changhua, Taiwan.,School of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kuan-Der Lee
- Department of Hematology and Oncology, Chang Gung Memorial Hospital, Chiayi, Chang Gung University College of Medicine, Taoyuan, Taiwan.,Chang Gung Institute of Technology, Taoyuan, Taiwan
| | - Yi-Ru Chu
- Department of Hematology and Oncology, Chang Gung Memorial Hospital, Chiayi, Chang Gung University College of Medicine, Taoyuan, Taiwan.,Chang Gung Institute of Technology, Taoyuan, Taiwan.,Department of Life Science, Human Epigenomics Center, Institute of Molecular Biology and Institute of Biomedical Science, National Chung Cheng University, Chia-Yi, Taiwan
| | - Ping-Yi Lin
- Transplant Medicine & Surgery Research Centre, Changhua Christian Hospital, Changhua, Taiwan
| | - Chia-Chen Hsu
- Department of Life Science, Human Epigenomics Center, Institute of Molecular Biology and Institute of Biomedical Science, National Chung Cheng University, Chia-Yi, Taiwan
| | - Pei-Yi Chu
- Department of Pathology, Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Tim H-M Huang
- Department of Molecular Medicine and Institute of Biotechnology, School of Medicine, Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Shu-Huei Hsiao
- Department of Life Science, Human Epigenomics Center, Institute of Molecular Biology and Institute of Biomedical Science, National Chung Cheng University, Chia-Yi, Taiwan
| | - Yu-Wei Leu
- Department of Life Science, Human Epigenomics Center, Institute of Molecular Biology and Institute of Biomedical Science, National Chung Cheng University, Chia-Yi, Taiwan.
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35
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Kozlenkov A, Wang M, Roussos P, Rudchenko S, Barbu M, Bibikova M, Klotzle B, Dwork AJ, Zhang B, Hurd YL, Koonin EV, Wegner M, Dracheva S. Substantial DNA methylation differences between two major neuronal subtypes in human brain. Nucleic Acids Res 2015; 44:2593-612. [PMID: 26612861 PMCID: PMC4824074 DOI: 10.1093/nar/gkv1304] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/09/2015] [Indexed: 12/29/2022] Open
Abstract
The brain is built from a large number of cell types which have been historically classified using location, morphology and molecular markers. Recent research suggests an important role of epigenetics in shaping and maintaining cell identity in the brain. To elucidate the role of DNA methylation in neuronal differentiation, we developed a new protocol for separation of nuclei from the two major populations of human prefrontal cortex neurons—GABAergic interneurons and glutamatergic (GLU) projection neurons. Major differences between the neuronal subtypes were revealed in CpG, non-CpG and hydroxymethylation (hCpG). A dramatically greater number of undermethylated CpG sites in GLU versus GABA neurons were identified. These differences did not directly translate into differences in gene expression and did not stem from the differences in hCpG methylation, as more hCpG methylation was detected in GLU versus GABA neurons. Notably, a comparable number of undermethylated non-CpG sites were identified in GLU and GABA neurons, and non-CpG methylation was a better predictor of subtype-specific gene expression compared to CpG methylation. Regions that are differentially methylated in GABA and GLU neurons were significantly enriched for schizophrenia risk loci. Collectively, our findings suggest that functional differences between neuronal subtypes are linked to their epigenetic specification.
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Affiliation(s)
- Alexey Kozlenkov
- James J. Peters VA Medical Center, Bronx, NY 10468, USA The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panos Roussos
- James J. Peters VA Medical Center, Bronx, NY 10468, USA The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Mihaela Barbu
- Hospital for Special Surgery, New York, NY 10021, USA
| | | | | | - Andrew J Dwork
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yasmin L Hurd
- The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Stella Dracheva
- James J. Peters VA Medical Center, Bronx, NY 10468, USA The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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36
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Hadjimichael C, Chanoumidou K, Papadopoulou N, Arampatzi P, Papamatheakis J, Kretsovali A. Common stemness regulators of embryonic and cancer stem cells. World J Stem Cells 2015; 7:1150-1184. [PMID: 26516408 PMCID: PMC4620423 DOI: 10.4252/wjsc.v7.i9.1150] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 05/30/2015] [Accepted: 10/08/2015] [Indexed: 02/06/2023] Open
Abstract
Pluripotency of embryonic stem cells (ESCs) and induced pluripotent stem cells is regulated by a well characterized gene transcription circuitry. The circuitry is assembled by ESC specific transcription factors, signal transducing molecules and epigenetic regulators. Growing understanding of stem-like cells, albeit of more complex phenotypes, present in tumors (cancer stem cells), provides a common conceptual and research framework for basic and applied stem cell biology. In this review, we highlight current results on biomarkers, gene signatures, signaling pathways and epigenetic regulators that are common in embryonic and cancer stem cells. We discuss their role in determining the cell phenotype and finally, their potential use to design next generation biological and pharmaceutical approaches for regenerative medicine and cancer therapies.
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37
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Pells S, Koutsouraki E, Morfopoulou S, Valencia-Cadavid S, Tomlinson SR, Kalathur R, Futschik ME, De Sousa PA. Novel Human Embryonic Stem Cell Regulators Identified by Conserved and Distinct CpG Island Methylation State. PLoS One 2015; 10:e0131102. [PMID: 26151932 PMCID: PMC4495055 DOI: 10.1371/journal.pone.0131102] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/27/2015] [Indexed: 12/21/2022] Open
Abstract
Human embryonic stem cells (hESCs) undergo epigenetic changes in vitro which may compromise function, so an epigenetic pluripotency “signature” would be invaluable for line validation. We assessed Cytosine-phosphate-Guanine Island (CGI) methylation in hESCs by genomic DNA hybridisation to a CGI array, and saw substantial variation in CGI methylation between lines. Comparison of hESC CGI methylation profiles to corresponding somatic tissue data and hESC mRNA expression profiles identified a conserved hESC-specific methylation pattern associated with expressed genes. Transcriptional repressors and activators were over-represented amongst genes whose associated CGIs were methylated or unmethylated specifically in hESCs, respectively. Knockdown of candidate transcriptional regulators (HMGA1, GLIS2, PFDN5) induced differentiation in hESCs, whereas ectopic expression in fibroblasts modulated iPSC colony formation. Chromatin immunoprecipitation confirmed interaction between the candidates and the core pluripotency transcription factor network. We thus identify novel pluripotency genes on the basis of a conserved and distinct epigenetic configuration in human stem cells.
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Affiliation(s)
- Steve Pells
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
- * E-mail: (PDS); (SP)
| | - Eirini Koutsouraki
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
| | - Sofia Morfopoulou
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
| | - Sara Valencia-Cadavid
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
| | - Simon R. Tomlinson
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
| | - Ravi Kalathur
- Centre for Molecular and Structural Biomedicine, University of Algarve, 8005–139, Faro, Portugal
| | - Matthias E. Futschik
- Centre for Molecular and Structural Biomedicine, University of Algarve, 8005–139, Faro, Portugal
| | - Paul A. De Sousa
- MRC Centre for Regenerative Medicine, School of Clinical Studies, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, United Kingdom
- * E-mail: (PDS); (SP)
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Martinez SR, Gay MS, Zhang L. Epigenetic mechanisms in heart development and disease. Drug Discov Today 2015; 20:799-811. [PMID: 25572405 PMCID: PMC4492921 DOI: 10.1016/j.drudis.2014.12.018] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/05/2014] [Accepted: 12/29/2014] [Indexed: 12/11/2022]
Abstract
Suboptimal intrauterine development has been linked to predisposition to cardiovascular disease in adulthood, a concept termed 'developmental origins of health and disease'. Although the exact mechanisms underlying this developmental programming are unknown, a growing body of evidence supports the involvement of epigenetic regulation. Epigenetic mechanisms such as DNA methylation, histone modifications and micro-RNA confer added levels of gene regulation without altering DNA sequences. These modifications are relatively stable signals, offering possible insight into the mechanisms underlying developmental origins of health and disease. This review will discuss the role of epigenetic mechanisms in heart development as well as aberrant epigenetic regulation contributing to cardiovascular disease. Additionally, we will address recent advances targeting epigenetic mechanisms as potential therapeutic approaches to cardiovascular disease.
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Affiliation(s)
- Shannalee R Martinez
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Maresha S Gay
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Lubo Zhang
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA.
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40
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Holland N, Lizarraga D, Huen K. Recent progress in the genetics and epigenetics of paraoxonase: why it is relevant to children's environmental health. Curr Opin Pediatr 2015; 27:240-7. [PMID: 25635583 PMCID: PMC4431624 DOI: 10.1097/mop.0000000000000192] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Children are more susceptible to exposures in utero and during early childhood that may result in developmental problems and chronic diseases. Novel discoveries in the field of molecular epidemiology that can help explain susceptibility to exposures and disease will be demonstrated using the multifunctional enzyme paraoxonase 1 (PON1) as an example. RECENT FINDINGS The broad PON1 variability in humans, partly due to differences in genetics and age, can confer differential susceptibility because this enzyme can detoxify organophosphate pesticides and has antioxidant properties. Epigenetics plays a significant role in the mediation of the effects of environmental exposure on human health and is hypothesized to be a major contributing factor to the early-life origins of adult disease. Studies highlighted in this review demonstrate the relationship of PON1 polymorphisms with microRNA binding in addition to a link between DNA methylation in the transcriptional regulatory region with changes in PON1 enzyme levels. Other important methodologies such as ancestry informative markers and lactonase activity can enhance studies involving PON1. SUMMARY This PON1 model demonstrates that integrating genetic and epigenetic factors, as well as other novel methodologies, can improve our understanding of important susceptibility factors linked to pediatric disease.
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Affiliation(s)
- Nina Holland
- Environmental Health Sciences Division and the Center for Environmental Research and Children's Health, School of Public Health, University of California, Berkeley, California, USA
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Lenz M, Goetzke R, Schenk A, Schubert C, Veeck J, Hemeda H, Koschmieder S, Zenke M, Schuppert A, Wagner W. Epigenetic biomarker to support classification into pluripotent and non-pluripotent cells. Sci Rep 2015; 5:8973. [PMID: 25754700 PMCID: PMC4354028 DOI: 10.1038/srep08973] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/11/2015] [Indexed: 12/12/2022] Open
Abstract
Quality control of human induced pluripotent stem cells (iPSCs) can be performed by several methods. These methods are usually relatively labor-intensive, difficult to standardize, or they do not facilitate reliable quantification. Here, we describe a biomarker to distinguish between pluripotent and non-pluripotent cells based on DNA methylation (DNAm) levels at only three specific CpG sites. Two of these CpG sites were selected by their discriminatory power in 258 DNAm profiles – they were either methylated in pluripotent or non-pluripotent cells. The difference between these two β-values provides an Epi-Pluri-Score that was validated on independent DNAm-datasets (264 pluripotent and 1,951 non-pluripotent samples) with 99.9% specificity and 98.9% sensitivity. This score was complemented by a third CpG within the gene POU5F1 (OCT4), which better demarcates early differentiation events. We established pyrosequencing assays for the three relevant CpG sites and thereby correctly classified DNA of 12 pluripotent cell lines and 31 non-pluripotent cell lines. Furthermore, DNAm changes at these three CpGs were tracked in the course of differentiation of iPSCs towards mesenchymal stromal cells. The Epi-Pluri-Score does not give information on lineage-specific differentiation potential, but it provides a simple, reliable, and robust biomarker to support high-throughput classification into either pluripotent or non-pluripotent cells.
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Affiliation(s)
- Michael Lenz
- 1] Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany [2] Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany [3] Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Roman Goetzke
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Arne Schenk
- 1] Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany [2] Bayer Technology Services GmbH, Leverkusen, Germany
| | - Claudia Schubert
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | - Jürgen Veeck
- Institute of Pathology, RWTH Aachen University Medical School, Aachen, Germany
| | - Hatim Hemeda
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical School, Aachen, Germany
| | - Martin Zenke
- 1] Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany [2] Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Andreas Schuppert
- 1] Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany [2] Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany [3] Bayer Technology Services GmbH, Leverkusen, Germany
| | - Wolfgang Wagner
- 1] Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany [2] Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
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Vincent A, Kazmierczak C, Duchêne B, Jonckheere N, Leteurtre E, Van Seuningen I. Cryosectioning the intestinal crypt-villus axis: an ex vivo method to study the dynamics of epigenetic modifications from stem cells to differentiated cells. Stem Cell Res 2014; 14:105-13. [PMID: 25590428 DOI: 10.1016/j.scr.2014.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/26/2014] [Accepted: 12/12/2014] [Indexed: 11/16/2022] Open
Abstract
The intestinal epithelium is a particularly attractive biological adult model to study epigenetic mechanisms driving adult stem cell renewal and cell differentiation. Since epigenetic modifications are dynamic, we have developed an original ex vivo approach to study the expression and epigenetic profiles of key genes associated with either intestinal cell pluripotency or differentiation by isolating cryosections of the intestinal crypt-villus axis. Gene expression, DNA methylation and histone modifications were studied by qRT-PCR, methylation-specific PCR and micro-chromatin immunoprecipitation, respectively. Using this approach, it was possible to identify segment-specific methylation and chromatin profiles. We show that (i) expression of intestinal stem cell markers (Lgr5, Ascl2) exclusively in the crypt is associated with active histone marks, (ii) promoters of all pluripotency genes studied and transcription factors involved in intestinal cell fate (Cdx2) harbour a bivalent chromatin pattern in the crypts and (iii) expression of differentiation markers (Muc2, Sox9) along the crypt-villus axis is associated with DNA methylation. Hence, using an original model of cryosectioning along the crypt-villus axis that allows in situ detection of dynamic epigenetic modifications, we demonstrate that regulation of pluripotency and differentiation markers in healthy intestinal mucosa involves different and specific epigenetic mechanisms.
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Affiliation(s)
- Audrey Vincent
- Inserm, UMR837, Jean Pierre Aubert Research Center (JPARC), Team 5 "Mucins, Epithelial Differentiation and Carcinogenesis," rue Polonovski, Lille, France; Université Lille 2 Droit et Santé, Lille, France; Centre Hospitalier Régional et Universitaire de Lille, Lille, France.
| | - Catherine Kazmierczak
- Inserm, UMR837, Jean Pierre Aubert Research Center (JPARC), Team 5 "Mucins, Epithelial Differentiation and Carcinogenesis," rue Polonovski, Lille, France; Université Lille 2 Droit et Santé, Lille, France; Centre Hospitalier Régional et Universitaire de Lille, Lille, France; Centre de Biologie Pathologie, CHRU Lille, Lille, France
| | - Belinda Duchêne
- Inserm, UMR837, Jean Pierre Aubert Research Center (JPARC), Team 5 "Mucins, Epithelial Differentiation and Carcinogenesis," rue Polonovski, Lille, France; Université Lille 2 Droit et Santé, Lille, France; Centre Hospitalier Régional et Universitaire de Lille, Lille, France
| | - Nicolas Jonckheere
- Inserm, UMR837, Jean Pierre Aubert Research Center (JPARC), Team 5 "Mucins, Epithelial Differentiation and Carcinogenesis," rue Polonovski, Lille, France; Université Lille 2 Droit et Santé, Lille, France; Centre Hospitalier Régional et Universitaire de Lille, Lille, France
| | - Emmanuelle Leteurtre
- Inserm, UMR837, Jean Pierre Aubert Research Center (JPARC), Team 5 "Mucins, Epithelial Differentiation and Carcinogenesis," rue Polonovski, Lille, France; Université Lille 2 Droit et Santé, Lille, France; Centre Hospitalier Régional et Universitaire de Lille, Lille, France; Centre de Biologie Pathologie, CHRU Lille, Lille, France
| | - Isabelle Van Seuningen
- Inserm, UMR837, Jean Pierre Aubert Research Center (JPARC), Team 5 "Mucins, Epithelial Differentiation and Carcinogenesis," rue Polonovski, Lille, France; Université Lille 2 Droit et Santé, Lille, France; Centre Hospitalier Régional et Universitaire de Lille, Lille, France
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Ambrosone CB, Young AC, Sucheston LE, Wang D, Yan L, Liu S, Tang L, Hu Q, Freudenheim JL, Shields PG, Morrison CD, Demissie K, Higgins MJ. Genome-wide methylation patterns provide insight into differences in breast tumor biology between American women of African and European ancestry. Oncotarget 2014; 5:237-48. [PMID: 24368439 PMCID: PMC3960204 DOI: 10.18632/oncotarget.1599] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
American women of African ancestry (AA) are more likely than European-Americans (EA) to be diagnosed with aggressive, estrogen receptor (ER) negative breast tumors; mechanisms underlying these disparities are poorly understood. We conducted a genome wide (450K loci) methylation analysis to determine if there were differences in DNA methylation patterns between tumors from AA and EA women and if these differences were similar for both ER positive and ER negative breast cancer. Methylation levels at CpG loci within CpG islands (CGI)s and CGI-shores were significantly higher in tumors (n=138) than in reduction mammoplasty samples (n=124). In hierarchical cluster analysis, there was separation between tumor and normal samples, and in tumors, there was delineation by ER status, but not by ancestry. However, differential methylation analysis identified 157 CpG loci with a mean β value difference of at least 0.17 between races, with almost twice as many differences in ER-negative tumors compared to ER-positive cancers. This first genome-wide methylation study to address disparities indicates that there are likely differing etiologic pathways for the development of ER negative breast cancer between AA and EA women. Further investigation of the genes most differentially methylated by race in ER negative tumors can guide new approaches for cancer prevention and targeted therapies, and elucidate the biologic basis of breast cancer disparities.
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Affiliation(s)
- Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY
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AFSM sequencing approach: a simple and rapid method for genome-wide SNP and methylation site discovery and genetic mapping. Sci Rep 2014; 4:7300. [PMID: 25466435 PMCID: PMC4252907 DOI: 10.1038/srep07300] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 11/17/2014] [Indexed: 11/09/2022] Open
Abstract
We describe methods for the assessment of amplified-fragment single nucleotide polymorphism and methylation (AFSM) sites using a quick and simple molecular marker-assisted breeding strategy based on the use of two restriction enzyme pairs (EcoRI-MspI and EcoRI-HpaII) and a next-generation sequencing platform. Two sets of 85 adapter pairs were developed to concurrently identify SNPs, indels and methylation sites for 85 lines of cassava population in this study. In addition to SNPs and indels, the simplicity of the AFSM protocol makes it particularly suitable for high-throughput full methylation and hemi-methylation analyses. To further demonstrate the ease of this approach, a cassava genetic linkage map was constructed. This approach should be widely applicable for genetic mapping in a variety of organisms and will improve the application of crop genomics in assisted breeding.
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Petruzzelli R, Christensen DR, Parry KL, Sanchez-Elsner T, Houghton FD. HIF-2α regulates NANOG expression in human embryonic stem cells following hypoxia and reoxygenation through the interaction with an Oct-Sox cis regulatory element. PLoS One 2014; 9:e108309. [PMID: 25271810 PMCID: PMC4182711 DOI: 10.1371/journal.pone.0108309] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/28/2014] [Indexed: 01/06/2023] Open
Abstract
Low O2 tension is beneficial for human embryonic stem cell (hESC) maintenance but the mechanism of regulation is unknown. HIF-2α was found to bind directly to predicted hypoxic response elements (HREs) in the proximal promoter of OCT4, NANOG and SOX2 only in hESCs cultured under hypoxia (5% O2). This binding induced an array of histone modifications associated with gene transcription while a heterochromatic state existed at atmospheric O2. Interestingly, an enhanced euchromatic state was found when hESCs were exposed to hypoxia followed by 72 hours reoxygenation. This was sustained by HIF-2α which enhanced stemness by binding to an oct-sox cis-regulatory element in the NANOG promoter. Thus, these data have uncovered a novel role of HIF-2α as a direct regulator of key transcription factors controlling self-renewal in hESCs but also in the induction of epigenetic modifications ensuring a euchromatic conformation which enhances the regenerative potential of these cells.
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Affiliation(s)
- Raffaella Petruzzelli
- Centre for Human Development, Stem Cells and Regeneration, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - David R. Christensen
- Centre for Human Development, Stem Cells and Regeneration, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Kate L. Parry
- Centre for Human Development, Stem Cells and Regeneration, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Tilman Sanchez-Elsner
- Centre for Human Development, Stem Cells and Regeneration, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Franchesca D. Houghton
- Centre for Human Development, Stem Cells and Regeneration, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- * E-mail:
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He W, Kang X, Du H, Song B, Lu Z, Huang Y, Wang D, Sun X, Yu Y, Fan Y. Defining differentially methylated regions specific for the acquisition of pluripotency and maintenance in human pluripotent stem cells via microarray. PLoS One 2014; 9:e108350. [PMID: 25250679 PMCID: PMC4177110 DOI: 10.1371/journal.pone.0108350] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 08/18/2014] [Indexed: 02/08/2023] Open
Abstract
Background Epigenetic regulation is critical for the maintenance of human pluripotent stem cells. It has been shown that pluripotent stem cells, such as embryonic stem cells and induced pluripotent stem cells, appear to have a hypermethylated status compared with differentiated cells. However, the epigenetic differences in genes that maintain stemness and regulate reprogramming between embryonic stem cells and induced pluripotent stem cells remain unclear. Additionally, differential methylation patterns of induced pluripotent stem cells generated using diverse methods require further study. Methodology Here, we determined the DNA methylation profiles of 10 human cell lines, including 2 ESC lines, 4 virally derived iPSC lines, 2 episomally derived iPSC lines, and the 2 parental cell lines from which the iPSCs were derived using Illumina's Infinium HumanMethylation450 BeadChip. The iPSCs exhibited a hypermethylation status similar to that of ESCs but with distinct differences from the parental cells. Genes with a common methylation pattern between iPSCs and ESCs were classified as critical factors for stemness, whereas differences between iPSCs and ESCs suggested that iPSCs partly retained the parental characteristics and gained de novo methylation aberrances during cellular reprogramming. No significant differences were identified between virally and episomally derived iPSCs. This study determined in detail the de novo differential methylation signatures of particular stem cell lines. Conclusions This study describes the DNA methylation profiles of human iPSCs generated using both viral and episomal methods, the corresponding somatic cells, and hESCs. Series of ss-DMRs and ES-iPS-DMRs were defined with high resolution. Knowledge of this type of epigenetic information could be used as a signature for stemness and self-renewal and provides a potential method for selecting optimal pluripotent stem cells for human regenerative medicine.
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Affiliation(s)
- WenYin He
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - XiangJin Kang
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - HongZi Du
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bing Song
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - ZhenYu Lu
- Union Stem Cell & Gene Engineering Co., Ltd., Tianjin, China
| | - Yuling Huang
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ding Wang
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaofang Sun
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- * E-mail: (YY); (YF); (XFS)
| | - Yang Yu
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- * E-mail: (YY); (YF); (XFS)
| | - Yong Fan
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- * E-mail: (YY); (YF); (XFS)
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Abstract
The precise, temporal order of gene expression during development is critical to ensure proper lineage commitment, cell fate determination, and ultimately, organogenesis. Epigenetic regulation of chromatin structure is fundamental to the activation or repression of genes during embryonic development. In recent years, there has been an explosion of research relating to various modes of epigenetic regulation, such as DNA methylation, post-translational histone tail modifications, noncoding RNA control of chromatin structure, and nucleosome remodeling. Technological advances in genome-wide epigenetic profiling and pluripotent stem cell differentiation have been primary drivers for elucidating the epigenetic control of cellular identity during development and nuclear reprogramming. Not only do epigenetic mechanisms regulate transcriptional states in a cell-type-specific manner but also they establish higher order genomic topology and nuclear architecture. Here, we review the epigenetic control of pluripotency and changes associated with pluripotent stem cell differentiation. We focus on DNA methylation, DNA demethylation, and common histone tail modifications. Finally, we briefly discuss epigenetic heterogeneity among pluripotent stem cell lines and the influence of epigenetic patterns on genome topology.
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Affiliation(s)
- Michael J Boland
- From the Department of Chemical Physiology, Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Kristopher L Nazor
- From the Department of Chemical Physiology, Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Jeanne F Loring
- From the Department of Chemical Physiology, Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, CA 92037.
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Sutiwisesak R, Kitiyanant N, Kotchabhakdi N, Felsenfeld G, Andrews PW, Wongtrakoongate P. Induced pluripotency enables differentiation of human nullipotent embryonal carcinoma cells N2102Ep. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:2611-9. [PMID: 25086345 DOI: 10.1016/j.bbamcr.2014.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/18/2014] [Accepted: 07/22/2014] [Indexed: 12/21/2022]
Abstract
Embryonal carcinoma (EC) cells, which are considered to be malignant counterparts of embryonic stem cells, comprise the pluripotent stem cell component of teratocarcinomas, a form of testicular germ cell tumors (GCTs). Nevertheless, many established human EC cell lines are nullipotent with limited or no capacity to differentiate under normal circumstances. In this study, we tested whether an over-expression of Yamanaka's reprogramming factors OCT4, SOX2, c-MYC and KLF4 might enable differentiation of the human nullipotent EC cells N2102Ep. Using OCT4 knockdown differentiated N2102Ep cells, we are able to derive reprogrammed N2102Ep cell lines. The induced pluripotency of N2102Ep allows the cells to differentiate toward neural lineage by retinoic acid; the expression of SSEA3 and SSEA4 is down-regulated, whereas that of neural surface markers is up-regulated. Consistent with the up-regulation of neural surface markers, the expression of the master neuroectodermal transcription factor PAX6 is also induced in reprogrammed N2102Ep. We next investigated whether PAX6 might induce spontaneous differentiation of nullipotent stem cells N2102Ep. However, while an ectopic expression of PAX6 promotes differentiation of NTERA2, it induces cell death in N2102Ep. We nevertheless find that upon induction of retinoic acid, the reprogrammed N2102Ep cells form mature neuronal morphology similar to differentiated pluripotent stem cells NTERA2 as determined by TUJ1 expression, which is absent in N2102Ep parental cells. Altogether, we conclude that the nullipotent state of human EC cells can be reprogrammed to acquire a more relaxed state of differentiation potential by Yamanaka's factors.
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Affiliation(s)
- Rujapope Sutiwisesak
- Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhonpathom 73170, Thailand; Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Narisorn Kitiyanant
- Stem Cell Research Group, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhonpathom, 73170, Thailand
| | - Naiphinich Kotchabhakdi
- Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhonpathom 73170, Thailand
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter W Andrews
- Centre for Stem Cell Biology, University of Sheffield, S10 2TN, UK
| | - Patompon Wongtrakoongate
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Centre for Stem Cell Biology, University of Sheffield, S10 2TN, UK.
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Park HR, Jung WW, Kim HS, Park YK. Microarray-based DNA methylation study of Ewing's sarcoma of the bone. Oncol Lett 2014; 8:1613-1617. [PMID: 25202378 PMCID: PMC4156184 DOI: 10.3892/ol.2014.2322] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 05/13/2014] [Indexed: 12/24/2022] Open
Abstract
Alterations in DNA methylation patterns are a hallmark of malignancy. However, the majority of epigenetic studies of Ewing’s sarcoma have focused on the analysis of only a few candidate genes. Comprehensive studies are thus lacking and are required. The aim of the present study was to identify novel methylation markers in Ewing’s sarcoma using microarray analysis. The current study reports the microarray-based DNA methylation study of 1,505 CpG sites of 807 cancer-related genes from 69 Ewing’s sarcoma samples. The Illumina GoldenGate Methylation Cancer Panel I microarray was used, and with the appropriate controls (n=14), a total of 92 hypermethylated genes were identified in the Ewing’s sarcoma samples. The majority of the hypermethylated genes were associated with cell adhesion, cell regulation, development and signal transduction. The overall methylation mean values were compared between patients who survived and those that did not. The overall methylation mean was significantly higher in the patients who did not survive (0.25±0.03) than in those who did (0.22±0.05) (P=0.0322). However, the overall methylation mean was not found to significantly correlate with age, gender or tumor location. GDF10, OSM, APC and HOXA11 were the most significant differentially-methylated genes, however, their methylation levels were not found to significantly correlate with the survival rate. The DNA methylation profile of Ewing’s sarcoma was characterized and 92 genes that were significantly hypermethylated were detected. A trend towards a more aggressive behavior was identified in the methylated group. The results of this study indicated that methylation may be significant in the development of Ewing’s sarcoma.
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Affiliation(s)
- Hye-Rim Park
- Department of Pathology, College of Medicine, Hallym University, Anyang, Gyeonggi 431-070, Republic of Korea
| | - Woon-Won Jung
- Department of Biomedical Laboratory Science, College of Health Science, Cheongju University, Cheongju, Chungbuk 360-764, Republic of Korea
| | - Hyun-Sook Kim
- Department of Biomedical Laboratory Science, College of Health Science, Korea University, Seoul 136-703, Republic of Korea
| | - Yong-Koo Park
- Department of Pathology, College of Medicine, Kyung Hee University, Seoul 130-702, Republic of Korea
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Bariar B, Vestal CG, Richardson C. Long-term effects of chromatin remodeling and DNA damage in stem cells induced by environmental and dietary agents. J Environ Pathol Toxicol Oncol 2014; 32:307-27. [PMID: 24579784 DOI: 10.1615/jenvironpatholtoxicoloncol.2013007980] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The presence of histones acts as a barrier to protein access; thus chromatin remodeling must occur for essential processes such as transcription and replication. In conjunction with histone modifications, DNA methylation plays critical roles in gene silencing through chromatin remodeling. Chromatin remodeling is also interconnected with the DNA damage response, maintenance of stem cell properties, and cell differentiation programs. Chromatin modifications have increasingly been shown to produce long-lasting alterations in chromatin structure and transcription. Recent studies have shown environmental exposures in utero have the potential to alter normal developmental signaling networks, physiologic responses, and disease susceptibility later in life during a process known as developmental reprogramming. In this review we discuss the long-term impact of exposure to environmental compounds, the chromatin modifications that they induce, and the differentiation and developmental programs of multiple stem and progenitor cell types altered by exposure. The main focus is to highlight agents present in the human lifestyle that have the potential to promote epigenetic changes that impact developmental programs of specific cell types, may promote tumorigenesis through altering epigenetic marks, and may be transgenerational, for example, those able to be transmitted through multiple cell divisions.
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Affiliation(s)
- Bhawana Bariar
- Department of Biology, University of North Carolina at Charlotte, Charlotte, NC
| | - C Greer Vestal
- Department of Biology, University of North Carolina at Charlotte, Charlotte, NC
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