51
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Benetatos L, Vartholomatos G. On the potential role of DNMT1 in acute myeloid leukemia and myelodysplastic syndromes: not another mutated epigenetic driver. Ann Hematol 2016; 95:1571-82. [PMID: 26983918 DOI: 10.1007/s00277-016-2636-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/04/2016] [Indexed: 12/19/2022]
Abstract
DNA methylation is the most common epigenetic modification in the mammalian genome. DNA methylation is governed by the DNA methyltransferases mainly DNMT1, DNMT3A, and DNMT3B. DNMT1 methylates hemimethylated DNA ensuring accurate DNA methylation maintenance. DNMT1 is involved in the proper differentiation of hematopoietic stem cells (HSCs) through the interaction with effector molecules. DNMT1 is deregulated in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) as early as the leukemic stem cell stage. Through the interaction with fundamental transcription factors, non-coding RNAs, fusion oncogenes and by modulating core members of signaling pathways, it can affect leukemic cells biology. DNMT1 action might be also catalytic-independent highlighting a methylation-independent mode of action. In this review, we have gathered some current facts of DNMT1 role in AML and MDS and we also propose some perspectives for future studies.
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52
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de Goede OM, Lavoie PM, Robinson WP. Characterizing the hypomethylated DNA methylation profile of nucleated red blood cells from cord blood. Epigenomics 2016; 8:1481-1494. [PMID: 27687885 DOI: 10.2217/epi-2016-0069] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
AIM To provide insight into fetal nucleated red blood cell (nRBC) development using genome-wide DNA methylation (DNAm) profiling. MATERIALS & METHODS The DNAm profile (Illumina 450K array) of cord blood (n = 7) derived nRBCs was compared with B cells, CD4 and CD8 T cells, natural killer cells, granulocytes, monocytes and placenta (n = 5). RESULTS nRBCs and placenta had similarly low array-wide DNAm compared with white blood cells, but their patterns of hypomethylation differed at biologically relevant subsets of the array. High interindividual variability in nRBC DNAm was driven by a negative association between DNAm and nRBC count. CONCLUSION nRBC hypomethylation is likely an epigenetic signature of erythropoiesis rather than of early development. Variability in nRBC DNAm may stem from differences in the cell population's maturity or hematopoietic source.
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Affiliation(s)
- Olivia M de Goede
- Child & Family Research Institute, Vancouver, British Columbia, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Pascal M Lavoie
- Child & Family Research Institute, Vancouver, British Columbia, V5Z 4H4, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Wendy P Robinson
- Child & Family Research Institute, Vancouver, British Columbia, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
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53
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Abstract
Mammalian embryonic development is a tightly regulated process that, from a single zygote, produces a large number of cell types with hugely divergent functions. Distinct cellular differentiation programmes are facilitated by tight transcriptional and epigenetic regulation. However, the contribution of epigenetic regulation to tissue homeostasis after the completion of development is less well understood. In this Review, we explore the effects of epigenetic dysregulation on adult stem cell function. We conclude that, depending on the tissue type and the epigenetic regulator affected, the consequences range from negligible to stem cell malfunction and disruption of tissue homeostasis, which may predispose to diseases such as cancer.
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54
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Clinical potential of DNA methylation in organ transplantation. J Heart Lung Transplant 2016; 35:843-50. [DOI: 10.1016/j.healun.2016.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/18/2016] [Accepted: 02/26/2016] [Indexed: 01/17/2023] Open
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55
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DNA methylation in hematopoietic development and disease. Exp Hematol 2016; 44:783-790. [PMID: 27178734 DOI: 10.1016/j.exphem.2016.04.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 12/28/2022]
Abstract
DNA methylation is an important epigenetic modification that can have profound and widespread effects on gene expression and on cellular fate and function. Recent work has indicated that DNA methylation plays a critical role in hematopoietic development and hematopoietic disease. DNA methyltransferases and Ten-eleven translocation enzymes are required to add and remove methyl "marks" from DNA, respectively, and both sets of genes have been found necessary for proper formation and maintenance of hematopoietic stem cells and for differentiation of downstream hematopoietic lineages during development. DNA methylation and demethylation enzymes have also been implicated in hematopoietic disorders such as acute myeloid leukemia and myelodysplastic syndrome. Here, we review some of the recent literature regarding the role of DNA methylation in hematopoietic health and disease.
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56
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Pagano F, De Marinis E, Grignani F, Nervi C. Epigenetic role of miRNAs in normal and leukemic hematopoiesis. Epigenomics 2016; 5:539-52. [PMID: 24059800 DOI: 10.2217/epi.13.55] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Hematopoiesis is a regulated multistep process, whereby transcriptional and epigenetic events contribute to progenitor fate determination. miRNAs have emerged as key players in hematopoietic cell development, differentiation and malignant transformation. From embryonic development through to adult life, miRNAs cooperate with, or are regulated, by epigenetic factors. Moreover, recent findings suggest that they contribute to chromatin structural modification, and the functional relevance of this 'epigenetic-miRNA axis' will be discussed in this article. Finally, emerging evidence has highlighted that miRNAs have functional control in human hematopoietic cells, involving targeted recruitment of epigenetic complexes to evolutionarily conserved complementary genomic loci. We propose the existence of epigenetic-miRNA loops that are able to organize the whole gene expression profile in hematopoietic cells.
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Affiliation(s)
- Francesca Pagano
- Department of Medical-Surgical Sciences & Biotechnologies, University La Sapienza, Latina, 04100, Italy
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57
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Chitikova Z, Steiner FA. Cell type-specific epigenome profiling using affinity-purified nuclei. Genesis 2016; 54:160-9. [PMID: 26789661 DOI: 10.1002/dvg.22919] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/08/2016] [Accepted: 01/14/2016] [Indexed: 11/08/2022]
Abstract
The development of a multicellular organism from a single zygote depends on the differentiation of progenitor cells to specialized cell types. The differentiation of these cell types is associated with changes in gene expression and the underlying chromatin landscape. To understand how these processes are regulated, it is desirable to understand how the chromatin features that constitute the epigenome differ between cell types at any given time during development. INTACT, a method for the cell type-specific purification of nuclei that can be used for the isolation of both RNA and chromatin, has emerged as a powerful tool to simultaneously study gene expression and chromatin profiles specifically in cell types of interest. In this review, we focus on the application of INTACT to different model organisms and discuss its potential for profiling cell types in their developmental context.
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Affiliation(s)
- Zhanna Chitikova
- Department of Molecular Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Florian A Steiner
- Department of Molecular Biology, Sciences III, University of Geneva, Geneva, Switzerland
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58
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Abstract
Aberrant DNA methylation is a characteristic feature of cancer including blood malignancies. Mutations in the DNA methylation regulators DNMT3A, TET1/2 and IDH1/2 are recurrent in leukemia and lymphoma. Specific and distinct DNA methylation patterns characterize subtypes of AML and lymphoma. Regulatory regions such as promoter CpG islands, CpG shores and enhancers show changes in methylation during transformation. However, the reported poor correlation between changes in methylation and gene expression in many mouse models and human studies reflects the complexity in the precise molecular mechanism for why aberrant DNA methylation promotes malignancies. This review will summarize current concepts regarding the mechanisms behind aberrant DNA methylation in hematopoietic malignancy and discuss its importance in cancer prognosis, tumor heterogeneity and relapse.
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Affiliation(s)
- Maria Guillamot
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, 10016, USA
| | - Luisa Cimmino
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, 10016, USA
| | - Iannis Aifantis
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, 10016, USA
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59
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McCullough SD, Bowers EC, On DM, Morgan DS, Dailey LA, Hines RN, Devlin RB, Diaz-Sanchez D. Baseline Chromatin Modification Levels May Predict Interindividual Variability in Ozone-Induced Gene Expression. Toxicol Sci 2015; 150:216-24. [PMID: 26719369 DOI: 10.1093/toxsci/kfv324] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Traditional toxicological paradigms have relied on factors such as age, genotype, and disease status to explain variability in responsiveness to toxicant exposure; however, these are neither sufficient to faithfully identify differentially responsive individuals nor are they modifiable factors that can be leveraged to mitigate the exposure effects. Unlike these factors, the epigenome is dynamic and shaped by an individual's environment. We sought to determine whether baseline levels of specific chromatin modifications correlated with the interindividual variability in their ozone (O3)-mediated induction in an air-liquid interface model using primary human bronchial epithelial cells from a panel of 11 donors. We characterized the relationship between the baseline abundance of 6 epigenetic markers with established roles as key regulators of gene expression-histone H3 lysine 4 trimethylation (H3K4me3), H3K27 acetylation (H3K27ac), pan-acetyl H4 (H4ac), histone H3K27 di/trimethylation (H3K27me2/3), unmodified H3, and 5-hydroxymethylcytosine (5-hmC)-and the variability in the O3-induced expression of IL-8, IL-6, COX2, and HMOX1. Baseline levels of H3K4me3, H3K27me2/3, and 5-hmC, but not H3K27ac, H4ac, and total H3, correlated with the interindividual variability in O3-mediated induction of HMOX1 and COX2. In contrast, none of the chromatin modifications that we examined correlated with the induction of IL-8 and IL-6. From these findings, we propose an "epigenetic seed and soil" model in which chromatin modification states between individuals differ in the relative abundance of specific modifications (the "soil") that govern how receptive the gene is to toxicant-mediated cellular signals (the "seed") and thus regulate the magnitude of exposure-related gene induction.
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Affiliation(s)
- Shaun D McCullough
- *National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711; and
| | - Emma C Bowers
- Curriculum in Toxicology, University of North Carolina - Chapel Hill, Chapel Hill, North Carolina 27599
| | - Doan M On
- *National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711; and
| | - David S Morgan
- *National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711; and
| | - Lisa A Dailey
- *National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711; and
| | - Ronald N Hines
- *National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711; and
| | - Robert B Devlin
- *National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711; and
| | - David Diaz-Sanchez
- *National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711; and
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60
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Paul DS, Jones A, Sellar RS, Mayor NP, Feber A, Webster AP, Afonso N, Sergeant R, Szydlo RM, Apperley JF, Widschwendter M, Mackinnon S, Marsh SGE, Madrigal JA, Rakyan VK, Peggs KS, Beck S. A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation. Genome Med 2015; 7:128. [PMID: 26669438 PMCID: PMC4681168 DOI: 10.1186/s13073-015-0246-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 11/12/2015] [Indexed: 02/07/2023] Open
Abstract
Background Allogeneic hematopoietic stem cell transplantation (HSCT) is a curative treatment for many hematological conditions. Acute graft-versus-host disease (aGVHD) is a prevalent immune-mediated complication following HSCT. Current diagnostic biomarkers that correlate with aGVHD severity, progression, and therapy response in graft recipients are insufficient. Here, we investigated whether epigenetic marks measured in peripheral blood of healthy graft donors stratify aGVHD severity in human leukocyte antigen (HLA)-matched sibling recipients prior to T cell-depleted HSCT. Methods We measured DNA methylation levels genome-wide at single-nucleotide resolution in peripheral blood of 85 HSCT donors, matched to recipients with various transplant outcomes, with Illumina Infinium HumanMethylation450 BeadChips. Results Using genome-wide DNA methylation profiling, we showed that epigenetic signatures underlying aGVHD severity in recipients correspond to immune pathways relevant to aGVHD etiology. We discovered 31 DNA methylation marks in donors that associated with aGVHD severity status in recipients, and demonstrated strong predictive performance of these markers in internal cross-validation experiments (AUC = 0.98, 95 % CI = 0.96–0.99). We replicated the top-ranked CpG classifier using an alternative, clinical DNA methylation assay (P = 0.039). In an independent cohort of 32 HSCT donors, we demonstrated the utility of the epigenetic classifier in the context of a T cell-replete conditioning regimen (P = 0.050). Conclusions Our findings suggest that epigenetic typing of HSCT donors in a clinical setting may be used in conjunction with HLA genotyping to inform both donor selection and transplantation strategy, with the ultimate aim of improving patient outcome. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0246-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dirk S Paul
- UCL Cancer Institute, University College London, London, UK.
| | - Allison Jones
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK
| | - Rob S Sellar
- UCL Cancer Institute, University College London, London, UK.,Department of Haematology, University College London, University College London Hospital, London, UK
| | - Neema P Mayor
- UCL Cancer Institute, University College London, London, UK.,Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - Andrew Feber
- UCL Cancer Institute, University College London, London, UK
| | - Amy P Webster
- UCL Cancer Institute, University College London, London, UK
| | - Neuza Afonso
- Department of Haematology, University College London, Royal Free Hospital, London, UK
| | - Ruhena Sergeant
- Clinical Immunology, Imperial NHS Trust Hammersmith Hospital, London, UK
| | - Richard M Szydlo
- Centre for Haematology, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, UK.,Department of Clinical Haematology, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, UK
| | - Jane F Apperley
- Centre for Haematology, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, UK.,Department of Clinical Haematology, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, UK
| | - Martin Widschwendter
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK
| | - Stephen Mackinnon
- UCL Cancer Institute, University College London, London, UK.,Department of Haematology, University College London, Royal Free Hospital, London, UK
| | - Steven G E Marsh
- UCL Cancer Institute, University College London, London, UK.,Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - J Alejandro Madrigal
- UCL Cancer Institute, University College London, London, UK.,Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - Vardhman K Rakyan
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Karl S Peggs
- UCL Cancer Institute, University College London, London, UK. .,Department of Haematology, University College London, University College London Hospital, London, UK.
| | - Stephan Beck
- UCL Cancer Institute, University College London, London, UK.
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61
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Cell-Cycle-Dependent Reconfiguration of the DNA Methylome during Terminal Differentiation of Human B Cells into Plasma Cells. Cell Rep 2015; 13:1059-71. [DOI: 10.1016/j.celrep.2015.09.051] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 07/06/2015] [Accepted: 09/17/2015] [Indexed: 01/22/2023] Open
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62
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Lipka DB, Wang Q, Cabezas-Wallscheid N, Klimmeck D, Weichenhan D, Herrmann C, Lier A, Brocks D, von Paleske L, Renders S, Wünsche P, Zeisberger P, Gu L, Haas S, Essers MA, Brors B, Eils R, Trumpp A, Milsom MD, Plass C. Identification of DNA methylation changes at cis-regulatory elements during early steps of HSC differentiation using tagmentation-based whole genome bisulfite sequencing. Cell Cycle 2015; 13:3476-87. [PMID: 25483069 DOI: 10.4161/15384101.2014.973334] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Epigenetic alterations during cellular differentiation are a key molecular mechanism which both instructs and reinforces the process of lineage commitment. Within the haematopoietic system, progressive changes in the DNA methylome of haematopoietic stem cells (HSCs) are essential for the effective production of mature blood cells. Inhibition or loss of function of the cellular DNA methylation machinery has been shown to lead to a severe perturbation in blood production and is also an important driver of malignant transformation. HSCs constitute a very rare cell population in the bone marrow, capable of life-long self-renewal and multi-lineage differentiation. The low abundance of HSCs has been a major technological barrier to the global analysis of the CpG methylation status within both HSCs and their immediate progeny, the multipotent progenitors (MPPs). Within this Extra View article, we review the current understanding of how the DNA methylome regulates normal and malignant hematopoiesis. We also discuss the current methodologies that are available for interrogating the DNA methylation status of HSCs and MPPs and describe a new data set that was generated using tagmentation-based whole genome bisulfite sequencing (TWGBS) in order to comprehensively map methylated cytosines using the limited amount of genomic DNA that can be harvested from rare cell populations. Extended analysis of this data set clearly demonstrates the added value of genome-wide sequencing of methylated cytosines and identifies novel important cis-acting regulatory regions that are dynamically remodeled during the first steps of haematopoietic differentiation.
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Affiliation(s)
- Daniel B Lipka
- a Division of Epigenomics and Cancer Risk Factors , German Cancer Research Center (DKFZ) ; Heidelberg , Germany
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63
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Nucleated red blood cells impact DNA methylation and expression analyses of cord blood hematopoietic cells. Clin Epigenetics 2015; 7:95. [PMID: 26366232 PMCID: PMC4567832 DOI: 10.1186/s13148-015-0129-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/31/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Genome-wide DNA methylation (DNAm) studies have proven extremely useful to understand human hematopoiesis. Due to their active DNA content, nucleated red blood cells (nRBCs) contribute to epigenetic and transcriptomic studies derived from whole cord blood. Genomic studies of cord blood hematopoietic cells isolated by fluorescence-activated cell sorting (FACS) may be significantly altered by heterotopic interactions with nRBCs during conventional cell sorting. RESULTS We report that cord blood T cells, and to a lesser extent monocytes and B cells, physically engage with nRBCs during FACS. These heterotopic interactions resulted in significant cross-contamination of genome-wide epigenetic and transcriptomic data. Formal exclusion of erythroid lineage-specific markers yielded DNAm profiles (measured by the Illumina 450K array) of cord blood CD4 and CD8 T lymphocytes, B lymphocytes, natural killer (NK) cells, granulocytes, monocytes, and nRBCs that were more consistent with expected hematopoietic lineage relationships. Additionally, we identified eight highly differentially methylated CpG sites in nRBCs (false detection rate <5 %, |Δβ| >0.50) that can be used to detect nRBC contamination of purified hematopoietic cells or to assess the impact of nRBCs on whole cord blood DNAm profiles. Several of these erythroid markers are located in or near genes involved in erythropoiesis (ZFPM1, HDAC4) or immune function (MAP3K14, IFIT1B), reinforcing a possible immune regulatory role for nRBCs in early life. CONCLUSIONS Heterotopic interactions between erythroid cells and white blood cells can result in contaminated cell populations if not properly excluded during cell sorting. Cord blood nRBCs have a distinct DNAm profile that can significantly skew epigenetic studies. Our findings have major implications for the design and interpretation of genome-wide epigenetic and transcriptomic studies using human cord blood.
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64
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Abou Zahr A, Saad Aldin E, Barbarotta L, Podoltsev N, Zeidan AM. The clinical use of DNA methyltransferase inhibitors in myelodysplastic syndromes. Expert Rev Anticancer Ther 2015; 15:1019-36. [DOI: 10.1586/14737140.2015.1061936] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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65
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Making the case for chromatin profiling: a new tool to investigate the immune-regulatory landscape. Nat Rev Immunol 2015; 15:585-94. [DOI: 10.1038/nri3884] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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66
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Yang L, Lian X, Zhang W, Guo J, Wang Q, Li Y, Chen Y, Yin X, Yang P, Lan F, He QY, Zhang G, Wang T. Finding Missing Proteins from the Epigenetically Manipulated Human Cell with Stringent Quality Criteria. J Proteome Res 2015. [DOI: 10.1021/acs.jproteome.5b00480] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Lijuan Yang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xinlei Lian
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Wanling Zhang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jie Guo
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Qing Wang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yaxing Li
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yang Chen
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xingfeng Yin
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | | | | | - Qing-Yu He
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Gong Zhang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Tong Wang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
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67
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Guièze R, Wu CJ. Genomic and epigenomic heterogeneity in chronic lymphocytic leukemia. Blood 2015; 126:445-53. [PMID: 26065654 PMCID: PMC4513249 DOI: 10.1182/blood-2015-02-585042] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/01/2015] [Indexed: 12/15/2022] Open
Abstract
Defining features of chronic lymphocytic leukemia (CLL) are not only its immunophenotype of CD19(+)CD5(+)CD23(+)sIgdim expressing clonal mature B cells but also its highly variable clinical course. In recent years, advances in massively parallel sequencing technologies have led to rapid progress in our understanding of the CLL genome and epigenome. Overall, these studies have clearly demarcated not only the vast degree of genetic and epigenetic heterogeneity among individuals with CLL but also even within individual patient leukemias. We herein review the rapidly growing series of studies assessing the genetic and epigenetic features of CLL within clinically defined periods of its growth. These studies strongly suggest an evolving spectrum of lesions over time and that these features may have clinical impact.
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Affiliation(s)
- Romain Guièze
- CHU Clermont-Ferrand, Service d'Hématologie Clinique Adulte et de Thérapie Cellulaire, and Université d'Auvergne, Clermont-Ferrand, France; Division of Hematologic Neoplasia, Dana-Farber Cancer Institute, Boston, MA; Cancer Program, Broad Institute, Cambridge, MA; and Division of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Catherine J Wu
- Division of Hematologic Neoplasia, Dana-Farber Cancer Institute, Boston, MA; Cancer Program, Broad Institute, Cambridge, MA; and Division of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
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Wagatsuma K, Tani-ichi S, Liang B, Shitara S, Ishihara K, Abe M, Miyachi H, Kitano S, Hara T, Nanno M, Ishikawa H, Sakimura K, Nakao M, Kimura H, Ikuta K. STAT5 Orchestrates Local Epigenetic Changes for Chromatin Accessibility and Rearrangements by Direct Binding to the TCRγ Locus. THE JOURNAL OF IMMUNOLOGY 2015. [PMID: 26195811 DOI: 10.4049/jimmunol.1302456] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The transcription factor STAT5, which is activated by IL-7R, controls chromatin accessibility and rearrangements of the TCRγ locus. Although STAT-binding motifs are conserved in Jγ promoters and Eγ enhancers, little is known about their precise roles in rearrangements of the TCRγ locus in vivo. To address this question, we established two lines of Jγ1 promoter mutant mice: one harboring a deletion in the Jγ1 promoter, including three STAT motifs (Jγ1P(Δ/Δ)), and the other carrying point mutations in the three STAT motifs in that promoter (Jγ1P(mS/mS)). Both Jγ1P(Δ/Δ) and Jγ1P(mS/mS) mice showed impaired recruitment of STAT5 and chromatin remodeling factor BRG1 at the Jγ1 gene segment. This resulted in severe and specific reduction in germline transcription, histone H3 acetylation, and histone H4 lysine 4 methylation of the Jγ1 gene segment in adult thymus. Rearrangement and DNA cleavage of the segment were severely diminished, and Jγ1 promoter mutant mice showed profoundly decreased numbers of γδ T cells of γ1 cluster origin. Finally, compared with controls, both mutant mice showed a severe reduction in rearrangements of the Jγ1 gene segment, perturbed development of γδ T cells of γ1 cluster origin in fetal thymus, and fewer Vγ3(+) dendritic epidermal T cells. Furthermore, interaction with the Jγ1 promoter and Eγ1, a TCRγ enhancer, was dependent on STAT motifs in the Jγ1 promoter. Overall, this study strongly suggests that direct binding of STAT5 to STAT motifs in the Jγ promoter is essential for local chromatin accessibility and Jγ/Eγ chromatin interaction, triggering rearrangements of the TCRγ locus.
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Affiliation(s)
- Keisuke Wagatsuma
- Laboratory of Biological Protection, Department of Biological Responses, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan; Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Shizue Tani-ichi
- Laboratory of Biological Protection, Department of Biological Responses, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Bingfei Liang
- Laboratory of Biological Protection, Department of Biological Responses, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan; Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Soichiro Shitara
- Laboratory of Biological Protection, Department of Biological Responses, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Ko Ishihara
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto 860-0811, Japan
| | - Manabu Abe
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Hitoshi Miyachi
- Reproductive Engineering Team, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Satsuki Kitano
- Reproductive Engineering Team, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Takahiro Hara
- Laboratory of Biological Protection, Department of Biological Responses, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Masanobu Nanno
- Yakult Central Institute, Kunitachi, Tokyo 186-8650, Japan
| | | | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan; Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Hiroshi Kimura
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan; Graduate School of Frontier Bioscience, Osaka University, Suita 565-0871, Japan; and Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Koichi Ikuta
- Laboratory of Biological Protection, Department of Biological Responses, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan;
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Maccani JZ, Maccani MA. Altered placental DNA methylation patterns associated with maternal smoking: current perspectives. ADVANCES IN GENOMICS AND GENETICS 2015; 2015:205-214. [PMID: 26203295 PMCID: PMC4507353 DOI: 10.2147/agg.s61518] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The developmental origins of health and disease hypothesis states that adverse early life exposures can have lasting, detrimental effects on lifelong health. Exposure to maternal cigarette smoking during pregnancy is associated with morbidity and mortality in offspring, including increased risks for miscarriage, stillbirth, low birth weight, preterm birth, asthma, obesity, altered neurobehavior, and other conditions. Maternal cigarette smoking during pregnancy interferes with placental growth and functioning, and it has been proposed that this may occur through the disruption of normal and necessary placental epigenetic patterns. Epigenome-wide association studies have identified a number of differentially methylated placental genes that are associated with maternal smoking during pregnancy, including RUNX3, PURA, GTF2H2, GCA, GPR135, and HKR1. The placental methylation status of RUNX3 and NR3C1 has also been linked to adverse infant outcomes, including preterm birth and low birth weight, respectively. Candidate gene analyses have also found maternal smoking-associated placental methylation differences in the NR3C1, CYP1A1, HTR2A, and HSD11B2 genes, as well as in the repetitive elements LINE-1 and AluYb8. The differential methylation patterns of several genes have been confirmed to also exhibit altered gene expression patterns, including CYP1A1, CYP19A1, NR3C1, and HTR2A. Placental methylation patterns associated with maternal smoking during pregnancy may be largely gene-specific and tissue-specific and, to a lesser degree, involve global changes. It is important for future research to investigate the mechanistic roles that these differentially methylated genes may play in mediating the association between maternal smoking during pregnancy and disease in later life, as well as to elucidate the potential influence of emerging tobacco product use during pregnancy, including the use of electronic cigarettes, on placental epigenetics.
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Affiliation(s)
- Jennifer Zj Maccani
- Penn State Tobacco Center of Regulatory Science, College of Medicine, Department of Public Health Sciences, Hershey, PA, USA
| | - Matthew A Maccani
- Penn State Tobacco Center of Regulatory Science, College of Medicine, Department of Public Health Sciences, Hershey, PA, USA
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70
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Maresca A, Zaffagnini M, Caporali L, Carelli V, Zanna C. DNA methyltransferase 1 mutations and mitochondrial pathology: is mtDNA methylated? Front Genet 2015; 6:90. [PMID: 25815005 PMCID: PMC4357308 DOI: 10.3389/fgene.2015.00090] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 02/19/2015] [Indexed: 01/31/2023] Open
Abstract
Autosomal dominant cerebellar ataxia-deafness and narcolepsy (ADCA-DN) and Hereditary sensory neuropathy with dementia and hearing loss (HSN1E) are two rare, overlapping neurodegenerative syndromes that have been recently linked to allelic dominant pathogenic mutations in the DNMT1 gene, coding for DNA (cytosine-5)-methyltransferase 1 (DNMT1). DNMT1 is the enzyme responsible for maintaining the nuclear genome methylation patterns during the DNA replication and repair, thus regulating gene expression. The mutations responsible for ADCA-DN and HSN1E affect the replication foci targeting sequence domain, which regulates DNMT1 binding to chromatin. DNMT1 dysfunction is anticipated to lead to a global alteration of the DNA methylation pattern with predictable downstream consequences on gene expression. Interestingly, ADCA-DN and HSN1E phenotypes share some clinical features typical of mitochondrial diseases, such as optic atrophy, peripheral neuropathy, and deafness, and some biochemical evidence of mitochondrial dysfunction. The recent discovery of a mitochondrial isoform of DNMT1 and its proposed role in methylating mitochondrial DNA (mtDNA) suggests that DNMT1 mutations may directly affect mtDNA and mitochondrial physiology. On the basis of this latter finding the link between DNMT1 abnormal activity and mitochondrial dysfunction in ADCA-DN and HSN1E appears intuitive, however, mtDNA methylation remains highly debated. In the last years several groups demonstrated the presence of 5-methylcytosine in mtDNA by different approaches, but, on the other end, the opposite evidence that mtDNA is not methylated has also been published. Since over 1500 mitochondrial proteins are encoded by the nuclear genome, the altered methylation of these genes may well have a critical role in leading to the mitochondrial impairment observed in ADCA-DN and HSN1E. Thus, many open questions still remain unanswered, such as why mtDNA should be methylated, and how this process is regulated and executed?
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Affiliation(s)
- Alessandra Maresca
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences, University of Bologna Bologna, Italy
| | - Mirko Zaffagnini
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences, University of Bologna Bologna, Italy
| | - Leonardo Caporali
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences, University of Bologna Bologna, Italy
| | - Valerio Carelli
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences, University of Bologna Bologna, Italy
| | - Claudia Zanna
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences, University of Bologna Bologna, Italy
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71
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Abstract
DNA methylation patterns are disrupted in various malignancies, suggesting a role in the development of cancer, but genetic aberrations directly linking the DNA methylation machinery to malignancies were rarely observed, so this association remained largely correlative. Recently, however, mutations in the gene encoding DNA methyltransferase 3A (DNMT3A) were reported in patients with acute myeloid leukaemia (AML), and subsequently in patients with various other haematological malignancies, pointing to DNMT3A as a critically important new tumour suppressor. Here, we review the clinical findings related to DNMT3A, tie these data to insights from basic science studies conducted over the past 20 years and present a roadmap for future research that should advance the agenda for new therapeutic strategies.
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Affiliation(s)
- Liubin Yang
- 1] Department of Molecular and Human Genetics, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA. [2]
| | - Rachel Rau
- 1] Department of Pediatrics, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA. [2]
| | - Margaret A Goodell
- 1] Department of Molecular and Human Genetics, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA. [2] Department of Pediatrics, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
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72
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Karamitros D, Patmanidi AL, Kotantaki P, Potocnik AJ, Bähr-Ivacevic T, Benes V, Lygerou Z, Kioussis D, Taraviras S. Geminin deletion increases the number of fetal hematopoietic stem cells by affecting the expression of key transcription factors. Development 2015; 142:70-81. [PMID: 25516969 DOI: 10.1242/dev.109454] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Balancing stem cell self-renewal and initiation of lineage specification programs is essential for the development and homeostasis of the hematopoietic system. We have specifically ablated geminin in the developing murine hematopoietic system and observed profound defects in the generation of mature blood cells, leading to embryonic lethality. Hematopoietic stem cells (HSCs) accumulated in the fetal liver following geminin ablation, while committed progenitors were reduced. Genome-wide transcriptome analysis identified key HSC transcription factors as being upregulated upon geminin deletion, revealing a gene network linked with geminin that controls fetal hematopoiesis. In order to obtain mechanistic insight into the ability of geminin to regulate transcription, we examined Hoxa9 as an example of a key gene in definitive hematopoiesis. We demonstrate that in human K562 cells geminin is associated with HOXA9 regulatory elements and its absence increases HOXA9 transcription similarly to that observed in vivo. Moreover, silencing geminin reduced recruitment of the PRC2 component SUZ12 to the HOXA9 locus and resulted in an increase in RNA polymerase II recruitment and H3K4 trimethylation (H3K4me3), whereas the repressive marks H3K9me3 and H3K27me3 were reduced. The chromatin landscape was also modified at the regulatory regions of HOXA10 and GATA1. K562 cells showed a reduced ability to differentiate to erythrocytes and megakaryocytes upon geminin silencing. Our data suggest that geminin is indispensable for fetal hematopoiesis and regulates the generation of a physiological pool of stem and progenitor cells in the fetal hematopoietic system.
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Affiliation(s)
- Dimitris Karamitros
- Department of Physiology, Medical School, University of Patras, Rio, Patras 26504, Greece
| | - Alexandra L Patmanidi
- Department of Physiology, Medical School, University of Patras, Rio, Patras 26504, Greece
| | - Panoraia Kotantaki
- Department of Physiology, Medical School, University of Patras, Rio, Patras 26504, Greece
| | - Alexandre J Potocnik
- Division of Molecular Immunology, MRC/National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - Tomi Bähr-Ivacevic
- European Molecular Biology Laboratory (EMBL), Core Facilities and Services, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Vladimir Benes
- European Molecular Biology Laboratory (EMBL), Core Facilities and Services, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Zoi Lygerou
- Department of Biology, Medical School, University of Patras, Rio, Patras 26504, Greece
| | - Dimitris Kioussis
- Division of Molecular Immunology, MRC/National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - Stavros Taraviras
- Department of Physiology, Medical School, University of Patras, Rio, Patras 26504, Greece
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73
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Abstract
Follicular lymphoma (FL) is the most common indolent lymphoma. The vast majority of cases are associated with the chromosome translocation t(14;18), a somatic rearrangement that leads to constitutive expression of the anti-apoptotic BCL2 protein. Although t(14;18) clearly represents an important early event in FL pathogenesis, abundant evidence indicates that it is not sufficient. In particular, the recent application of next-generation DNA sequencing technology has uncovered numerous recurrent somatic genomic alterations associated with FL, most of which affect tumor suppressor genes (TSGs). In this article we review the existing literature on TSGs involved in the development and progression of FL. We consider the genes that are most frequently targeted by deleterious mutation, deletion or epigenetic silencing, along with strategies for developing new treatments that exploit the susceptibilities that may be conferred on lymphoma cells by the loss of particular TSGs.
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74
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Abstract
The mammalian gastrointestinal tract is home to trillions of commensal microorganisms that collectively make up the intestinal microbiota. These microbes are important environmental factors that regulate homeostasis, and alterations in the composition of the microbiota have been associated with several diseases, including inflammatory bowel disease, diabetes, and cancer. New research is beginning to uncover epigenomic pathways that may regulate this relationship with the microbiota. Epigenomic modifications alter the structure of the chromatin and therefore regulate the transcriptional program of a cell. These modifications are maintained by the dynamic activity of various modifying and demodifying enzymes, the activities of which can be influenced by metabolites and other environmental cues. Histone deacetylases (HDACs) are a class of epigenomic-modifying enzymes that are regulated by both endogenous and exogenous factors, and recent studies have suggested that host HDAC expression is important for regulating communication between the intestinal microbiota and mammalian host cells.
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Affiliation(s)
- Theresa Alenghat
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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75
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Histone acetylation mediated by Brd1 is crucial for Cd8 gene activation during early thymocyte development. Nat Commun 2014; 5:5872. [PMID: 25519988 DOI: 10.1038/ncomms6872] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 11/14/2014] [Indexed: 11/08/2022] Open
Abstract
During T-cell development, Cd8 expression is controlled via dynamic regulation of its cis-regulatory enhancer elements. Insufficiency of enhancer activity causes variegated Cd8 expression in CD4(+)CD8(+) double-positive (DP) thymocytes. Brd1 is a subunit of the Hbo1 histone acetyltransferase (HAT) complex responsible for acetylation of histone H3 at lysine 14 (H3K14). Here we show that deletion of Brd1 in haematopoietic progenitors causes variegated expression of Cd8, resulting in the appearance of CD4(+)CD8(-)TCRβ(-/low) thymocytes indistinguishable from DP thymocytes in their properties. Biochemical analysis confirms that Brd1 forms a HAT complex with Hbo1 in thymocytes. ChIP analysis demonstrates that Brd1 localizes at the known enhancers in the Cd8 genes and is responsible for acetylation at H3K14. These findings indicate that the Brd1-mediated HAT activity is crucial for efficient activation of Cd8 expression via acetylation at H3K14, which serves as an epigenetic mark that promotes the recruitment of transcription machinery to the Cd8 enhancers.
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76
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Woods BA, Levine RL. The role of mutations in epigenetic regulators in myeloid malignancies. Immunol Rev 2014; 263:22-35. [DOI: 10.1111/imr.12246] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Brittany A. Woods
- Louis V. Gerstner Sloan Kettering Graduate School of Biomedical Sciences; Memorial Sloan Kettering Cancer Center; New York NY USA
- Human Oncology and Pathogenesis Program; Memorial Sloan Kettering Cancer Center; New York NY USA
| | - Ross L. Levine
- Louis V. Gerstner Sloan Kettering Graduate School of Biomedical Sciences; Memorial Sloan Kettering Cancer Center; New York NY USA
- Human Oncology and Pathogenesis Program; Memorial Sloan Kettering Cancer Center; New York NY USA
- Leukemia Service; Department of Medicine; Memorial Sloan Kettering Cancer Center; New York NY USA
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77
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Abstract
Analysis of the mechanisms underlying cell fates requires the molecular quantification of cellular features. Classical techniques use population average readouts at single time points. However, these approaches mask cellular heterogeneity and dynamics and are limited for studying rare and heterogeneous cell populations like stem cells. Techniques for single-cell analyses, ideally allowing non-invasive quantification of molecular dynamics and cellular behaviour over time, are required for studying stem cells. Here, we review the development and application of these techniques to stem cell research.
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78
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Tang H, An S, Zhen H, Chen F. Characterization of combinatorial histone modifications on lineage-affiliated genes during hematopoietic stem cell myeloid commitment. Acta Biochim Biophys Sin (Shanghai) 2014; 46:894-901. [PMID: 25205219 DOI: 10.1093/abbs/gmu078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are multipotent stem cells capable of self-renewal and multilineage differentiation. Mechanisms regulating the maintenance of HSCs' multipotency and differentiation are still unclear. In this study, we observed the role of combinatorial histone modification pattern in the maintenance of HSCs' pluripotency and differentiation. HSCs (CD34(+)CD38(low)) were collected from human umbilical cord blood and induced to differentiate to committed cells in vitro. The histone modifications on lineage-specific transcription factors/genes in multipotent HSCs and differentiated progenies, including megakaryocytes, granulocytes, and erythrocytes, were analyzed by chromatin immunoprecipitation-quantitative polymerase chain reaction. Our results showed that a certain level of acH4 and acH3 together with high level of H3K4me2, low level of H3K4me3, and a certain level of H3K9me3 and H3K27me3 were present in lineage-specific genes in CD34(+)CD38(low) HSCs. As CD34(+)CD38(low) cells differentiated into granulocytes, erythroid cells, and megakaryocytes, the modification levels of acH3, acH4, and H3K4me2 on lineage-specific genes remained the same or elevated, while H3K4me3 level was increased greatly. At the same time, H3K9me3 and H3K27me3 modification levels became lower. In non-lineage-specific genes, the acH3 and acH4 levels were decreased, and H3K4me3 level remained at low level, while H3K9me3 and H3K27me3 levels were increased drastically. Our data suggest that combinatorial histone modification patterns have implicated function in maintaining the multipotency of HSCs and keeping the accuracy of gene expression program during HSC differentiation.
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Affiliation(s)
- Huarong Tang
- Department of Radiation Therapy, Zhejiang Key Laboratory of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China Department of Hematology, Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Shimin An
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Huanying Zhen
- Department of Physiology, Central South University, Xiangya School of Medicine, Changsha 410013, China
| | - Fangping Chen
- Department of Hematology, Third Xiangya Hospital, Central South University, Changsha 410013, China
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79
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Benton CB, Thomas DA, Yang H, Ravandi F, Rytting M, O'Brien S, Franklin AR, Borthakur G, Dara S, Kwari M, Pierce SR, Jabbour E, Kantarjian H, Garcia-Manero G. Safety and clinical activity of 5-aza-2'-deoxycytidine (decitabine) with or without Hyper-CVAD in relapsed/refractory acute lymphocytic leukaemia. Br J Haematol 2014; 167:356-65. [PMID: 25066676 DOI: 10.1111/bjh.13050] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 06/23/2014] [Indexed: 12/31/2022]
Abstract
To test the safety and activity of 5-aza-2'-deoxycytidine (decitabine) in patients with relapsed/refractory acute lymphocytic leukaemia (ALL), we conducted a phase 1 study with two parts: administering decitabine alone or in combination with Hyper-CVAD (fractionated cyclophosphamide, vincristine, doxorubicin and dexamethasone alternating with high-dose methotrexate and cytarabine). Patients participated in either part of the study or in both parts sequentially. In the initial part, decitabine was administered intravenously at doses of 10-120 mg/m(2) per d for 5 d every other week in cycles of 28 d. In the combination part, patients were treated on the first 5 d of Hyper-CVAD with intravenous decitabine at 5-60 mg/m(2) per d. A total of 39 patients received treatment in the study: 14 in the first part only, 16 sequentially in both parts and 9 in the second part only. Decitabine was tolerated at all doses administered, and grade 3 or 4 toxic effects included non-life-threatening hepatotoxicity and hyperglycaemia. Induction of DNA hypomethylation was observed at doses of decitabine up to 80 mg/m(2) . Some patients who had previously progressed on Hyper-CVAD alone achieved a complete response when decitabine was added. Decitabine alone or given with Hyper-CVAD is safe and has clinical activity in patients with advanced ALL.
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Affiliation(s)
- Christopher B Benton
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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80
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Lucas JS, Zhang Y, Dudko OK, Murre C. 3D trajectories adopted by coding and regulatory DNA elements: first-passage times for genomic interactions. Cell 2014; 158:339-352. [PMID: 24998931 DOI: 10.1016/j.cell.2014.05.036] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/19/2014] [Accepted: 05/01/2014] [Indexed: 12/01/2022]
Abstract
During B lymphocyte development, immunoglobulin heavy-chain variable (VH), diversity (DH), and joining (JH) segments assemble to generate a diverse antigen receptor repertoire. Here, we have marked the distal VH and DH-JH-Eμ regions with Tet-operator binding sites and traced their 3D trajectories in pro-B cells transduced with a retrovirus encoding Tet-repressor-EGFP. We found that these elements displayed fractional Langevin motion (fLm) due to the viscoelastic hindrance from the surrounding network of proteins and chromatin fibers. Using fractional Langevin dynamics modeling, we found that, with high probability, DHJH elements reach a VH element within minutes. Spatial confinement emerged as the dominant parameter that determined the frequency of such encounters. We propose that the viscoelastic nature of the nuclear environment causes coding elements and regulatory elements to bounce back and forth in a spring-like fashion until specific genomic interactions are established and that spatial confinement of topological domains largely controls first-passage times for genomic interactions.
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Affiliation(s)
- Joseph S Lucas
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yaojun Zhang
- Department of Physics and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Olga K Dudko
- Department of Physics and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Cornelis Murre
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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81
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Aravind L, Burroughs AM, Zhang D, Iyer LM. Protein and DNA modifications: evolutionary imprints of bacterial biochemical diversification and geochemistry on the provenance of eukaryotic epigenetics. Cold Spring Harb Perspect Biol 2014; 6:a016063. [PMID: 24984775 DOI: 10.1101/cshperspect.a016063] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Epigenetic information, which plays a major role in eukaryotic biology, is transmitted by covalent modifications of nuclear proteins (e.g., histones) and DNA, along with poorly understood processes involving cytoplasmic/secreted proteins and RNAs. The origin of eukaryotes was accompanied by emergence of a highly developed biochemical apparatus for encoding, resetting, and reading covalent epigenetic marks in proteins such as histones and tubulins. The provenance of this apparatus remained unclear until recently. Developments in comparative genomics show that key components of eukaryotic epigenetics emerged as part of the extensive biochemical innovation of secondary metabolism and intergenomic/interorganismal conflict systems in prokaryotes, particularly bacteria. These supplied not only enzymatic components for encoding and removing epigenetic modifications, but also readers of some of these marks. Diversification of these prokaryotic systems and subsequently eukaryotic epigenetics appear to have been considerably influenced by the great oxygenation event in the Earth's history.
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Affiliation(s)
- L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
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82
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Chauvistré H, Küstermann C, Rehage N, Klisch T, Mitzka S, Felker P, Rose-John S, Zenke M, Seré KM. Dendritic cell development requires histone deacetylase activity. Eur J Immunol 2014; 44:2478-88. [PMID: 24810486 PMCID: PMC4209797 DOI: 10.1002/eji.201344150] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 04/08/2014] [Accepted: 04/30/2014] [Indexed: 01/24/2023]
Abstract
DCs develop from multipotent progenitors (MPPs), which commit into DC-restricted common dendritic cell progenitors (CDPs). CDPs further differentiate into classical DCs (cDCs) and plasmacytoid DCs (pDCs). Here, we studied the impact of histone acetylation on DC development in C57BL/6 mice by interfering with histone acetylation and deacetylation, employing histone deacetylase (HDAC) inhibitors. We observed that commitment of MPPs into CDPs was attenuated by HDAC inhibition and that pDC development was specifically blocked. Gene expression profiling revealed that HDAC inhibition prevents establishment of a DC-specific gene expression repertoire. Importantly, protein levels of the core DC transcription factor PU.1 were reduced in HDAC inhibitor-treated cells and consequently PU.1 recruitment at PU.1 target genes Fms-like tyrosine kinase 3 (Flt3), interferon regulatory factor 8 (IRF8), and PU.1 itself was impaired. Thus, our results demonstrate that attenuation of PU.1 expression by HDAC inhibition causes reduced expression of key DC regulators, which results in attenuation of DC development. We propose that chromatin modifiers, such as HDACs, are required for establishing a DC gene network, where Flt3/STAT3 signaling drives PU.1 and IRF8 expression and DC development. Taken together, our study identifies HDACs as critical regulators of DC lineage commitment and development.
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Affiliation(s)
- Heike Chauvistré
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, Aachen, Germany; Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
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83
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Dorritie KA, Redner RL, Johnson DE. STAT transcription factors in normal and cancer stem cells. Adv Biol Regul 2014; 56:30-44. [PMID: 24931719 DOI: 10.1016/j.jbior.2014.05.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 01/02/2023]
Abstract
Signal transducer and activator of transcription proteins (STATs) play vital roles in the regulation of cellular proliferation and survival in normal hematopoietic cells, including hematopoietic stem cells. However, aberrant activation of STATs is commonly observed in a number of hematologic malignancies, and recent studies indicate that targeting of STATs may have therapeutic benefit in these diseases. Additional studies have provided greater understanding of the cells responsible for leukemia initiation, referred to as leukemia stem cells. Emerging evidence indicates that STATs are important in maintaining leukemia stem cells and represent a promising target for eradication of this dangerous cell population. Here we summarize what is known about normal hematopoietic stem cells and the origin of leukemic stem cells. We further describe the roles of STAT proteins in these cell populations, as well as current progress toward the development of novel agents and strategies for targeting the STAT proteins.
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Affiliation(s)
- Kathleen A Dorritie
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, The University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA.
| | - Robert L Redner
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, The University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Daniel E Johnson
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, The University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA; Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
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84
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Steegenga WT, Boekschoten MV, Lute C, Hooiveld GJ, de Groot PJ, Morris TJ, Teschendorff AE, Butcher LM, Beck S, Müller M. Genome-wide age-related changes in DNA methylation and gene expression in human PBMCs. AGE (DORDRECHT, NETHERLANDS) 2014; 36:9648. [PMID: 24789080 PMCID: PMC4082572 DOI: 10.1007/s11357-014-9648-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 03/18/2014] [Indexed: 05/13/2023]
Abstract
Aging is a progressive process that results in the accumulation of intra- and extracellular alterations that in turn contribute to a reduction in health. Age-related changes in DNA methylation have been reported before and may be responsible for aging-induced changes in gene expression, although a causal relationship has yet to be shown. Using genome-wide assays, we analyzed age-induced changes in DNA methylation and their effect on gene expression with and without transient induction with the synthetic transcription modulating agent WY14,643. To demonstrate feasibility of the approach, we isolated peripheral blood mononucleated cells (PBMCs) from five young and five old healthy male volunteers and cultured them with or without WY14,643. Infinium 450K BeadChip and Affymetrix Human Gene 1.1 ST expression array analysis revealed significant differential methylation of at least 5 % (ΔYO > 5 %) at 10,625 CpG sites between young and old subjects, but only a subset of the associated genes were also differentially expressed. Age-related differential methylation of previously reported epigenetic biomarkers of aging including ELOVL2, FHL2, PENK, and KLF14 was confirmed in our study, but these genes did not display an age-related change in gene expression in PBMCs. Bioinformatic analysis revealed that differentially methylated genes that lack an age-related expression change predominantly represent genes involved in carcinogenesis and developmental processes, and expression of most of these genes were silenced in PBMCs. No changes in DNA methylation were found in genes displaying transiently induced changes in gene expression. In conclusion, aging-induced differential methylation often targets developmental genes and occurs mostly without change in gene expression.
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Affiliation(s)
- Wilma T Steegenga
- Division of Human Nutrition, Wageningen University, Bomenweg 2, Wageningen, 6703 HD, The Netherlands,
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85
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Mowen KA, David M. Unconventional post-translational modifications in immunological signaling. Nat Immunol 2014; 15:512-20. [DOI: 10.1038/ni.2873] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 03/21/2014] [Indexed: 02/07/2023]
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86
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Chaurasia P, Gajzer DC, Schaniel C, D'Souza S, Hoffman R. Epigenetic reprogramming induces the expansion of cord blood stem cells. J Clin Invest 2014; 124:2378-95. [PMID: 24762436 DOI: 10.1172/jci70313] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cord blood (CB) cells that express CD34 have extensive hematopoietic capacity and rapidly divide ex vivo in the presence of cytokine combinations; however, many of these CB CD34+ cells lose their marrow-repopulating potential. To overcome this decline in function, we treated dividing CB CD34+ cells ex vivo with several histone deacetylase inhibitors (HDACIs). Treatment of CB CD34+ cells with the most active HDACI, valproic acid (VPA), following an initial 16-hour cytokine priming, increased the number of multipotent cells (CD34+CD90+) generated; however, the degree of expansion was substantially greater in the presence of both VPA and cytokines for a full 7 days. Treated CD34+ cells were characterized based on the upregulation of pluripotency genes, increased aldehyde dehydrogenase activity, and enhanced expression of CD90, c-Kit (CD117), integrin α6 (CD49f), and CXCR4 (CD184). Furthermore, siRNA-mediated inhibition of pluripotency gene expression reduced the generation of CD34+CD90+ cells by 89%. Compared with CB CD34+ cells, VPA-treated CD34+ cells produced a greater number of SCID-repopulating cells and established multilineage hematopoiesis in primary and secondary immune-deficient recipient mice. These data indicate that dividing CB CD34+ cells can be epigenetically reprogrammed by treatment with VPA so as to generate greater numbers of functional CB stem cells for use as transplantation grafts.
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87
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Heideman MR, Lancini C, Proost N, Yanover E, Jacobs H, Dannenberg JH. Sin3a-associated Hdac1 and Hdac2 are essential for hematopoietic stem cell homeostasis and contribute differentially to hematopoiesis. Haematologica 2014; 99:1292-303. [PMID: 24763403 DOI: 10.3324/haematol.2013.092643] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Class I histone deacetylases are critical regulators of gene transcription by erasing lysine acetylation. Targeting histone deacetylases using relative non-specific small molecule inhibitors is of major interest in the treatment of cancer, neurological disorders and acquired immune deficiency syndrome. Harnessing the therapeutic potential of histone deacetylase inhibitors requires full knowledge of individual histone deacetylases in vivo. As hematologic malignancies show increased sensitivity towards histone deacetylase inhibitors we targeted deletion of class I Hdac1 and Hdac2 to hematopoietic cell lineages. Here, we show that Hdac1 and Hdac2 together control hematopoietic stem cell homeostasis, in a cell-autonomous fashion. Simultaneous loss of Hdac1 and Hdac2 resulted in loss of hematopoietic stem cells and consequently bone marrow failure. Bone-marrow-specific deletion of Sin3a, a major Hdac1/2 co-repressor, phenocopied loss of Hdac1 and Hdac2 indicating that Sin3a-associated HDAC1/2-activity is essential for hematopoietic stem cell homeostasis. Although Hdac1 and Hdac2 show compensatory and overlapping functions in hematopoiesis, mice expressing mono-allelic Hdac1 or Hdac2 revealed that Hdac1 and Hdac2 contribute differently to the development of specific hematopoietic lineages.
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Affiliation(s)
- Marinus R Heideman
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Cesare Lancini
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Natalie Proost
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Eva Yanover
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Heinz Jacobs
- Division of Biological Stress Response, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jan-Hermen Dannenberg
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
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88
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Hawkins ED, Turner ML, Wellard CJ, Zhou JHS, Dowling MR, Hodgkin PD. Quantal and graded stimulation of B lymphocytes as alternative strategies for regulating adaptive immune responses. Nat Commun 2014; 4:2406. [PMID: 24009041 PMCID: PMC3778729 DOI: 10.1038/ncomms3406] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 08/06/2013] [Indexed: 12/15/2022] Open
Abstract
Lymphocytes undergo a typical response pattern following stimulation in vivo: they proliferate, differentiate to effector cells, cease dividing and predominantly die, leaving a small proportion of long-lived memory and effector cells. This pattern results from cell-intrinsic processes following activation and the influence of external regulation. Here we apply quantitative methods to study B-cell responses in vitro. Our results reveal that B cells stimulated through two Toll-like receptors (TLRs) require minimal external direction to undergo the basic pattern typical of immunity. Altering the stimulus strength regulates the outcome in a quantal manner by varying the number of cells that participate in the response. In contrast, the T-cell-dependent CD40 activation signal induces a response where division times and differentiation rates vary in relation to stimulus strength. These studies offer insight into how the adaptive antibody response may have evolved from simple autonomous response patterns to the highly regulable state that is now observed in mammals.
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Affiliation(s)
- E D Hawkins
- 1] Immunology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia [2] Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia [3]
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89
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Przybilla J, Rohlf T, Loeffler M, Galle J. Understanding epigenetic changes in aging stem cells--a computational model approach. Aging Cell 2014; 13:320-8. [PMID: 24428552 PMCID: PMC4331773 DOI: 10.1111/acel.12177] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2013] [Indexed: 12/29/2022] Open
Abstract
During aging, a decline in stem cell function is observed in many tissues. This decline is accompanied by complex changes of the chromatin structure among them changes in histone modifications and DNA methylation which both affect transcription of a tissue-specific subset of genes. A mechanistic understanding of these age-associated processes, their interrelations and environmental dependence is currently lacking. Here, we discuss related questions on the molecular, cellular, and population level. We combine an individual cell-based model of stem cell populations with a model of epigenetic regulation of transcription. The novel model enables to simulate age-related changes of trimethylation of lysine 4 at histone H3 and of DNA methylation. These changes entail expression changes of genes that induce age-related phenotypes (ARPs) of cells. We compare age-related changes of regulatory states in quiescent stem cells occupying a niche with those observed in proliferating cells. Moreover, we analyze the impact of the activity of the involved epigenetic modifiers on these changes. We find that epigenetic aging strongly affects stem cell heterogeneity and that homing at stem cell niches retards epigenetic aging. Our model provides a mechanistic explanation how increased stem cell proliferation can lead to progeroid phenotypes. Adapting our model to properties observed for aged hematopoietic stem cell (HSC) clones, we predict that the hematopoietic ARP activates young HSCs and thereby retards aging of the entire HSC population. In addition, our model suggests that the experimentally observed high interindividual variance in HSC numbers originates in a variance of histone methyltransferase activity.
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Affiliation(s)
- Jens Przybilla
- Interdisciplinary Center for Bioinformatics University Leipzig Haertelstr. 16‐1804107Leipzig Germany
| | - Thimo Rohlf
- Interdisciplinary Center for Bioinformatics University Leipzig Haertelstr. 16‐1804107Leipzig Germany
- Max‐Planck‐Institute for Mathematics in the Sciences Inselstr. 2204103 Leipzig Germany
| | - Markus Loeffler
- Interdisciplinary Center for Bioinformatics University Leipzig Haertelstr. 16‐1804107Leipzig Germany
- Institute for Medical Informatics, Statistics and Epidemiology University Leipzig Haertelstr. 16‐1804107Leipzig Germany
| | - Joerg Galle
- Interdisciplinary Center for Bioinformatics University Leipzig Haertelstr. 16‐1804107Leipzig Germany
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90
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Langevin SM, Houseman EA, Accomando WP, Koestler DC, Christensen BC, Nelson HH, Karagas MR, Marsit CJ, Wiencke JK, Kelsey KT. Leukocyte-adjusted epigenome-wide association studies of blood from solid tumor patients. Epigenetics 2014; 9:884-95. [PMID: 24671036 DOI: 10.4161/epi.28575] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Epigenome-wide studies of DNA methylation using blood-derived DNA from cancer patients are complicated by the heterogeneity of cell types within blood and the associated cell lineage specification of DNA methylation signatures. Here, we applied a novel set of analytic approaches to assess the association between cancer case-status and DNA methylation adjusted for leukocyte variation using blood specimens from three case-control cancer studies (bladder: 223 cases, 205 controls; head and neck: 92 cases, 92 controls; and ovarian: 131 cases, 274 controls). Using previously published data on leukocyte-specific CpG loci and a recently described approach to deconvolute subject-specific blood composition, we performed an epigenome-wide analysis to examine the association between blood-based DNA methylation patterns and each of the three aforementioned solid tumor types adjusted for cellular heterogeneity in blood. After adjusting for leukocyte profile in our epigenome-wide analysis, the omnibus association between case-status and methylation was significant for all three studies (bladder cancer: P = 0.047; HNSCC: P = 0.013; ovarian cancer: P = 0.0002). Subsequent analyses revealed that CpG sites associated with cancer were enriched for transcription factor binding motifs involved with cancer-associated pathways. These results support the existence of cancer-associated DNA methylation profiles in the blood of solid tumor patients that are independent of alterations in normal leukocyte distributions. Adoption of the methods developed here will make it feasible to rigorously assess the influence of variability of normal leukocyte profiles when investigating cancer related changes in blood-based epigenome-wide association studies.
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Affiliation(s)
- Scott M Langevin
- Department of Environmental Health; University of Cincinnati College of Medicine; Cincinnati, OH USA; Department of Epidemiology; Brown University; Providence, RI USA
| | - E Andres Houseman
- Department of Biostatistics; Oregon State University College of Public Health and Human Sciences; Corvallis, OR USA
| | - William P Accomando
- Department of Pathology & Laboratory Medicine; Brown University; Providence, RI USA
| | - Devin C Koestler
- Department of Community and Family Medicine; Section of Biostatistics and Epidemiology; Dartmouth Medical School; Lebanon, NH USA
| | - Brock C Christensen
- Department of Community and Family Medicine; Section of Biostatistics and Epidemiology; Dartmouth Medical School; Lebanon, NH USA; Department of Pharmacology and Toxicology; Dartmouth Medical School; Lebanon, NH USA
| | - Heather H Nelson
- Division of Epidemiology and Community Health; University of Minnesota Masonic Cancer Center; Minneapolis, MN USA
| | - Margaret R Karagas
- Department of Community and Family Medicine; Section of Biostatistics and Epidemiology; Dartmouth Medical School; Lebanon, NH USA
| | - Carmen J Marsit
- Department of Community and Family Medicine; Section of Biostatistics and Epidemiology; Dartmouth Medical School; Lebanon, NH USA; Department of Pharmacology and Toxicology; Dartmouth Medical School; Lebanon, NH USA
| | - John K Wiencke
- Department of Neurological Surgery; University of California San Francisco; San Francisco, CA USA
| | - Karl T Kelsey
- Department of Epidemiology; Brown University; Providence, RI USA; Department of Pathology & Laboratory Medicine; Brown University; Providence, RI USA
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91
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Kar S, Parbin S, Deb M, Shilpi A, Sengupta D, Rath SK, Rakshit M, Patra A, Patra SK. Epigenetic choreography of stem cells: the DNA demethylation episode of development. Cell Mol Life Sci 2014; 71:1017-32. [PMID: 24114325 PMCID: PMC11113617 DOI: 10.1007/s00018-013-1482-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/12/2013] [Accepted: 09/16/2013] [Indexed: 12/17/2022]
Abstract
Reversible DNA methylation is a fundamental epigenetic manipulator of the genomic information in eukaryotes. DNA demethylation plays a very significant role during embryonic development and stands out for its contribution in molecular reconfiguration during cellular differentiation for determining stem cell fate. DNA demethylation arbitrated extensive make-over of the genome via reprogramming in the early embryo results in stem cell plasticity followed by commitment to the principal cell lineages. This article attempts to highlight the sequential phases and hierarchical mode of DNA demethylation events during enactment of the molecular strategy for developmental transition. A comprehensive knowledge regarding the pattern of DNA demethylation during embryogenesis and organogenesis and study of the related lacunae will offer exciting avenues for future biomedical research and stem cell-based regenerative therapy.
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Affiliation(s)
- Swayamsiddha Kar
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Sabnam Parbin
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Moonmoon Deb
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Arunima Shilpi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Dipta Sengupta
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Sandip Kumar Rath
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Madhumita Rakshit
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Aditi Patra
- Additional Block Animal Health Centre, Veterinary Office, Oodlabari, Malbazar, Jalpaiguri, West Bengal India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
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92
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Rare event of histone demethylation can initiate singular gene expression of olfactory receptors. Proc Natl Acad Sci U S A 2014; 110:21148-52. [PMID: 24344257 DOI: 10.1073/pnas.1321511111] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Mammals sense odors through the gene family of olfactory receptors (ORs). Despite the enormous number of OR genes (∼1,400 in mouse), each olfactory sensory neuron expresses one, and only one, of them. In neurobiology, it remains a long-standing mystery how this singularity can be achieved despite intrinsic stochasticity of gene expression. Recent experiments showed an epigenetic mechanism for maintaining singular OR expression: Once any ORs are activated, their expression inhibits further OR activation by down-regulating a histone demethylase Lsd1 (also known as Aof2 or Kdm1a), an enzyme required for the removal of the repressive histone marker H3K9me3 on OR genes. However, it remains unclear at a quantitative level how singularity can be initiated in the first place. In particular, does a simple activation/feedback scheme suffice to generate singularity? Here we show theoretically that rare events of histone demethylation can indeed produce robust singularity by separating two timescales: slow OR activation by stepwise H3K9me3 demethylation, and fast feedback to turn off Lsd1. Given a typical 1-h response of transcriptional feedback, to achieve the observed extent of singularity (only 2% of neurons express more than one ORs), we predict that OR activation must be as slow as 5–10 d-a timescale compatible with experiments. Our model further suggests H3K9me3-to-H3K9me2 demethylation as an additional rate-limiting step responsible for OR singularity. Our conclusions may be generally applicable to other systems where monoallelic expression is desired, and provide guidelines for the design of a synthetic system of singular expression.
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93
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Pham K, Sacirbegovic F, Russell SM. Polarized cells, polarized views: asymmetric cell division in hematopoietic cells. Front Immunol 2014; 5:26. [PMID: 24550912 PMCID: PMC3909886 DOI: 10.3389/fimmu.2014.00026] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 01/16/2014] [Indexed: 11/17/2022] Open
Abstract
It has long been recognized that alterations in cell shape and polarity play important roles in coordinating lymphocyte functions. In the last decade, a new aspect of lymphocyte polarity has attracted much attention, termed asymmetric cell division (ACD). ACD has previously been shown to dictate or influence many aspects of development in model organisms such as the worm and the fly, and to be disrupted in disease. Recent observations that ACD also occurs in lymphocytes led to exciting speculations that ACD might influence lymphocyte differentiation and function, and leukemia. Dissecting the role that ACD might play in these activities has not been straightforward, and the evidence to date for a functional role in lymphocyte fate determination has been controversial. In this review, we discuss the evidence to date for ACD in lymphocytes, and how it might influence lymphocyte fate. We also discuss current gaps in our knowledge, and suggest approaches to definitively test the physiological role of ACD in lymphocytes.
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Affiliation(s)
- Kim Pham
- Immune Signalling Laboratory, Peter MacCallum Cancer Centre , East Melbourne, VIC , Australia ; Centre for Micro-Photonics, Faculty of Engineering and Industrial Sciences, Swinburne University of Technology , Hawthorn, VIC , Australia
| | - Faruk Sacirbegovic
- Department of Pathology, University of Melbourne , Melbourne, VIC , Australia
| | - Sarah M Russell
- Immune Signalling Laboratory, Peter MacCallum Cancer Centre , East Melbourne, VIC , Australia ; Centre for Micro-Photonics, Faculty of Engineering and Industrial Sciences, Swinburne University of Technology , Hawthorn, VIC , Australia ; Department of Pathology, University of Melbourne , Melbourne, VIC , Australia ; Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne, VIC , Australia
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94
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Vigano MA, Ivanek R, Balwierz P, Berninger P, van Nimwegen E, Karjalainen K, Rolink A. An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants. Eur J Immunol 2014; 44:1181-93. [PMID: 24374622 DOI: 10.1002/eji.201344022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 12/04/2013] [Accepted: 12/20/2013] [Indexed: 01/01/2023]
Abstract
Cellular differentiation of the T-cell branch of the immune system begins with the HSC, which undergoes a series of stages characterized by progressive restriction in multipotency and acquisition of specific lineage identity At the molecular level, the restriction of cell potential, commitment, and differentiation to a specific lineage is achieved through the coordinated control of gene expression and epigenetic mechanisms. Here, we analyzed and compared the gene expression profiles and the genome-wide histone modification marks H3K4me3 (H3 lysine 4 trimethylation) and H3K27me3 (H3 lysine 27 trimethylation) in (i) in vitro propagated HSCs, (ii) in vitro generated and propagated pro-T cells derived from these stem cells, and (iii) double-positive thymocytes derived from these pro-T cells after injection into Rag-deficient mice. The combined analyses of the different datasets in this unique experimental system highlighted the importance of both transcriptional and epigenetic repression in shaping the early phases of T-cell development.
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Affiliation(s)
- Maria Alessandra Vigano
- Developmental and Molecular Immunology Group, Department of Biomedicine, University of Basel, Basel, Switzerland
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95
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Tian T, Smith-Miles K. Mathematical modeling of GATA-switching for regulating the differentiation of hematopoietic stem cell. BMC SYSTEMS BIOLOGY 2014; 8 Suppl 1:S8. [PMID: 24565335 PMCID: PMC4080254 DOI: 10.1186/1752-0509-8-s1-s8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Background Hematopoiesis is a highly orchestrated developmental process that comprises various developmental stages of the hematopoietic stem cells (HSCs). During development, the decision to leave the self-renewing state and selection of a differentiation pathway is regulated by a number of transcription factors. Among them, genes GATA-1 and PU.1 form a core negative feedback module to regulate the genetic switching between the cell fate choices of HSCs. Although extensive experimental studies have revealed the mechanisms to regulate the expression of these two genes, it is still unclear how this simple module regulates the genetic switching. Methods In this work we proposed a mathematical model to study the mechanisms of the GATA-PU.1 gene network in the determination of HSC differentiation pathways. We incorporated the mechanisms of GATA switch into the module, and developed a mathematical model that comprises three genes GATA-1, GATA-2 and PU.1. In addition, a novel multiple-objective optimization method was designed to infer unknown parameters in the proposed model by realizing different experimental observations. A stochastic model was also designed to describe the critical function of noise, due to the small copy numbers of molecular species, in determining the differentiation pathways. Results The proposed deterministic model has successfully realized three stable steady states representing the priming and different progenitor cells as well as genetic switching between the genetic states under various experimental conditions. Using different values of GATA-1 synthesis rate for the GATA-1 protein availability in the chromatin sites during the time period of GATA switch, stochastic simulations for the first time have realized different proportions of cells leading to different developmental pathways under various experimental conditions. Conclusions Mathematical models provide testable predictions regarding the mechanisms and conditions for realizing different differentiation pathways of hematopoietic stem cells. This work represents the first attempt at using a discrete stochastic model to realize the decision of HSC differentiation pathways showing a multimodal distribution.
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96
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Domingo-Gonzalez R, Moore BB. Innate Immunity Post-Hematopoietic Stem Cell Transplantation: Focus on Epigenetics. ACTA ACUST UNITED AC 2014; 5:189-197. [PMID: 26709355 DOI: 10.3233/nib-140079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Epigenetic regulation of gene expression is important for normal biological processes like immune cell development, immune responses, and differentiation from hematopoietic stem cells. Furthermore, it is well understood that epigenetic mechanisms can include methylation, histone modification, and more recently, microRNAs. Interestingly, aberrant epigenetic modification can also promote pathology in many diseases like cancer. The effects of methylation on gene expression and its resulting phenotype have been extensively studied. In this review, we discuss the inhibition of innate immunity that occurs in humans and animal models post-stem cell transplant. In addition, we highlight the changes methylation and microRNA profiles have on regulating pulmonary innate immune responses in the context of hematopoietic stem cell transplantation in experimental animal models.
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Affiliation(s)
| | - Bethany B Moore
- Pulmonary and Critical Care Medicine Division, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA ; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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97
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Hu G, Zhao K. Correlating histone modification patterns with gene expression data during hematopoiesis. Methods Mol Biol 2014; 1150:175-87. [PMID: 24743998 DOI: 10.1007/978-1-4939-0512-6_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Hematopoietic stem cells (HSC) in mammals are an ideal system to study differentiation. While transcription factors (TFs) control the differentiation of HSCs to distinctive terminal blood cells, accumulating evidence suggests that chromatin structure and modifications constitute another critical layer of gene regulation. Recent genome-wide studies based on next-generation sequencing reveal that histone modifications are linked to gene expression and contribute to hematopoiesis. Here, we briefly review the bioinformatics aspects for ChIP-Seq and RNA-Seq data analysis with applications to the epigenetic studies of hematopoiesis and provide a practical guide to several basic data analysis methods.
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Affiliation(s)
- Gangqing Hu
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA,
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98
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Liu B, Yee KM, Tahk S, Mackie R, Hsu C, Shuai K. PIAS1 SUMO ligase regulates the self-renewal and differentiation of hematopoietic stem cells. EMBO J 2013; 33:101-13. [PMID: 24357619 DOI: 10.1002/embj.201283326] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The selective and temporal DNA methylation plays an important role in the self-renewal and differentiation of hematopoietic stem cells (HSCs), but the molecular mechanism that controls the dynamics of DNA methylation is not understood. Here, we report that the PIAS1 epigenetic pathway plays an important role in regulating HSC self-renewal and differentiation. PIAS1 is required for maintaining the quiescence of dormant HSCs and the long-term repopulating capacity of HSC. Pias1 disruption caused the abnormal expression of lineage-associated genes. Bisulfite sequencing analysis revealed the premature promoter demethylation of Gata1, a key myeloerythroid transcription factor and a PIAS1-target gene, in Pias1(-/-) HSCs. As a result, Pias1 disruption caused the inappropriate induction of Gata1 in HSCs and common lymphoid progenitors (CLPs). The expression of other myeloerythroid genes was also enhanced in CLPs and lineage-negative progenitors, with a concurrent repression of B cell-specific genes. Consistently, Pias1 disruption caused enhanced myeloerythroid, but reduced B lymphoid lineage differentiation. These results identify a novel role of PIAS1 in maintaining the quiescence of dormant HSCs and in the epigenetic repression of the myeloerythroid program.
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Affiliation(s)
- Bin Liu
- Division of Hematology-Oncology Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
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Kitajima K, Kawaguchi M, Iacovino M, Kyba M, Hara T. Molecular Functions of the LIM-Homeobox Transcription FactorLhx2in Hematopoietic Progenitor Cells Derived from Mouse Embryonic Stem Cells. Stem Cells 2013; 31:2680-9. [DOI: 10.1002/stem.1500] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 06/14/2013] [Accepted: 07/05/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Kenji Kitajima
- Stem Cell Project Group; Tokyo Metropolitan Institute of Medical Science; Tokyo Japan
| | - Manami Kawaguchi
- Stem Cell Project Group; Tokyo Metropolitan Institute of Medical Science; Tokyo Japan
| | - Michelina Iacovino
- Lillehei Heart Institute, Department of Pediatrics; University of Minnesota; Minneapolis Minnesota USA
| | - Michael Kyba
- Lillehei Heart Institute, Department of Pediatrics; University of Minnesota; Minneapolis Minnesota USA
| | - Takahiko Hara
- Stem Cell Project Group; Tokyo Metropolitan Institute of Medical Science; Tokyo Japan
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Genome-wide methylation analyses of primary human leukocyte subsets identifies functionally important cell-type-specific hypomethylated regions. Blood 2013; 122:e52-60. [PMID: 24159175 DOI: 10.1182/blood-2013-05-503201] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
DNA methylation is an important mechanism by which gene transcription and hence cellular function are regulated. Here, we provide detailed functional genome-wide methylome maps of 5 primary peripheral blood leukocyte subsets including T cells, B cells, monocytes/macrophages, and neutrophils obtained from healthy individuals. A comparison of these methylomes revealed highly specific cell-lineage and cell-subset methylation profiles. DNA hypomethylation is known to be permissive for gene expression and we identified cell-subset-specific hypomethylated regions (HMRs) that strongly correlate with gene transcription levels suggesting these HMRs may regulate corresponding cell functions. Single-nucleotide polymorphisms associated with immune-mediated disease in genome-wide association studies preferentially localized to these cell-specific regulatory HMRs, offering insight into pathogenesis by highlighting cell subsets in which specific epigenetic changes may drive disease. Our data provide a valuable reference tool for researchers aiming to investigate the role of DNA methylation in regulating primary leukocyte function in health and immune-mediated disease.
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