1
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Barral A, Zaret KS. Pioneer factors: roles and their regulation in development. Trends Genet 2024; 40:134-148. [PMID: 37940484 PMCID: PMC10873006 DOI: 10.1016/j.tig.2023.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
Pioneer factors are a subclass of transcription factors that can bind and initiate opening of silent chromatin regions. Pioneer factors subsequently regulate lineage-specific genes and enhancers and, thus, activate the zygotic genome after fertilization, guide cell fate transitions during development, and promote various forms of human cancers. As such, pioneer factors are useful in directed cell reprogramming. In this review, we define the structural and functional characteristics of pioneer factors, how they bind and initiate opening of closed chromatin regions, and the consequences for chromatin dynamics and gene expression during cell differentiation. We also discuss emerging mechanisms that modulate pioneer factors during development.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA.
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2
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Farley SJ, Grishok A, Zeldich E. Shaking up the silence: consequences of HMGN1 antagonizing PRC2 in the Down syndrome brain. Epigenetics Chromatin 2022; 15:39. [PMID: 36463299 PMCID: PMC9719135 DOI: 10.1186/s13072-022-00471-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/11/2022] [Indexed: 12/04/2022] Open
Abstract
Intellectual disability is a well-known hallmark of Down Syndrome (DS) that results from the triplication of the critical region of human chromosome 21 (HSA21). Major studies were conducted in recent years to gain an understanding about the contribution of individual triplicated genes to DS-related brain pathology. Global transcriptomic alterations and widespread changes in the establishment of neural lineages, as well as their differentiation and functional maturity, suggest genome-wide chromatin organization alterations in trisomy. High Mobility Group Nucleosome Binding Domain 1 (HMGN1), expressed from HSA21, is a chromatin remodeling protein that facilitates chromatin decompaction and is associated with acetylated lysine 27 on histone H3 (H3K27ac), a mark correlated with active transcription. Recent studies causatively linked overexpression of HMGN1 in trisomy and the development of DS-associated B cell acute lymphoblastic leukemia (B-ALL). HMGN1 has been shown to antagonize the activity of the Polycomb Repressive Complex 2 (PRC2) and prevent the deposition of histone H3 lysine 27 trimethylation mark (H3K27me3), which is associated with transcriptional repression and gene silencing. However, the possible ramifications of the increased levels of HMGN1 through the derepression of PRC2 target genes on brain cell pathology have not gained attention. In this review, we discuss the functional significance of HMGN1 in brain development and summarize accumulating reports about the essential role of PRC2 in the development of the neural system. Mechanistic understanding of how overexpression of HMGN1 may contribute to aberrant brain cell phenotypes in DS, such as altered proliferation of neural progenitors, abnormal cortical architecture, diminished myelination, neurodegeneration, and Alzheimer's disease-related pathology in trisomy 21, will facilitate the development of DS therapeutic approaches targeting chromatin.
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Affiliation(s)
- Sean J. Farley
- grid.189504.10000 0004 1936 7558Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
| | - Alla Grishok
- grid.189504.10000 0004 1936 7558Department of Biochemistry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA ,grid.189504.10000 0004 1936 7558Boston University Genome Science Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
| | - Ella Zeldich
- Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
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3
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Steinauer N, Zhang K, Guo C, Zhang J. Computational Modeling of Gene-Specific Transcriptional Repression, Activation and Chromatin Interactions in Leukemogenesis by LASSO-Regularized Logistic Regression. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2109-2122. [PMID: 33961561 PMCID: PMC8572318 DOI: 10.1109/tcbb.2021.3078128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Many physiological and pathological pathways are dependent on gene-specific on/off regulation of transcription. Some genes are repressed, while others are activated. Although many previous studies have analyzed the mechanisms of gene-specific repression and activation, these studies are mainly based on the use of candidate genes, which are either repressed or activated, without simultaneously comparing and contrasting both groups of genes. There is also insufficient consideration of gene locations. Here we describe an integrated machine learning approach, using LASSO-regularized logistic regression, to model gene-specific repression and activation and the underlying contribution of chromatin interactions. LASSO-regularized logistic regression accurately predicted gene-specific transcriptional events and robustly detected the rate-limiting factors that underlie the differences of gene activation and repression. An example was provided by the leukemogenic transcription factor AML1-ETO, which is responsible for 10-15 percent of all acute myeloid leukemia cases. The analysis of AML1-ETO has also revealed novel networks of chromatin interactions and uncovered an unexpected role for E-proteins in AML1-ETO-p300 interactions and a role for the pre-existing gene state in governing the transcriptional response. Our results show that logistic regression-based probabilistic modeling is a promising tool to decipher mechanisms that integrate gene regulation and chromatin interactions in regulated transcription.
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4
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The Multiple Interactions of RUNX with the Hippo-YAP Pathway. Cells 2021; 10:cells10112925. [PMID: 34831147 PMCID: PMC8616315 DOI: 10.3390/cells10112925] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 01/04/2023] Open
Abstract
The Hippo–YAP signaling pathway serves roles in cell proliferation, stem cell renewal/maintenance, differentiation and apoptosis. Many of its functions are central to early development, adult tissue repair/regeneration and not surprisingly, tumorigenesis and metastasis. The Hippo pathway represses the activity of YAP and paralog TAZ by modulating cell proliferation and promoting differentiation to maintain tissue homeostasis and proper organ size. Similarly, master regulators of development RUNX transcription factors have been shown to play critical roles in proliferation, differentiation, apoptosis and cell fate determination. In this review, we discuss the multiple interactions of RUNX with the Hippo–YAP pathway, their shared collaborators in Wnt, TGFβ, MYC and RB pathways, and their overlapping functions in development and tumorigenesis.
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5
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Korinfskaya S, Parameswaran S, Weirauch MT, Barski A. Runx Transcription Factors in T Cells-What Is Beyond Thymic Development? Front Immunol 2021; 12:701924. [PMID: 34421907 PMCID: PMC8377396 DOI: 10.3389/fimmu.2021.701924] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Runx proteins (also known as Runt-domain transcription factors) have been studied for a long time as key regulators of cellular differentiation. RUNX2 has been described as essential for osteogenesis, whereas RUNX1 and RUNX3 are known to control blood cell development during different stages of cell lineage specification. However, recent studies show evidence of complex relationships between RUNX proteins, chromatin-modifying machinery, the cytoskeleton and different transcription factors in various non-embryonic contexts, including mature T cell homeostasis, inflammation and cancer. In this review, we discuss the diversity of Runx functions in mature T helper cells, such as production of cytokines and chemokines by different CD4 T cell populations; apoptosis; and immunologic memory acquisition. We then briefly cover recent findings about the contribution of RUNX1, RUNX2 and RUNX3 to various immunologic diseases. Finally, we discuss areas that require further study to better understand the role that Runx proteins play in inflammation and immunity.
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Affiliation(s)
- Svetlana Korinfskaya
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Artem Barski
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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6
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Lin A, Elbezanti WO, Schirling A, Ahmed A, Van Duyne R, Cocklin S, Klase Z. Alprazolam Prompts HIV-1 Transcriptional Reactivation and Enhances CTL Response Through RUNX1 Inhibition and STAT5 Activation. Front Neurol 2021; 12:663793. [PMID: 34367046 PMCID: PMC8339301 DOI: 10.3389/fneur.2021.663793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/17/2021] [Indexed: 12/02/2022] Open
Abstract
The HIV-1 pandemic is a significant challenge to the field of medicine. Despite advancements in antiretroviral (ART) development, 38 million people worldwide still live with this disease without a cure. A significant barrier to the eradication of HIV-1 lies in the persistently latent pool that establishes early in the infection. The “shock and kill” strategy relies on the discovery of a latency-reversing agent (LRA) that can robustly reactivate the latent pool and not limit immune clearance. We have found that a benzodiazepine (BDZ), that is commonly prescribed for panic and anxiety disorder, to be an ideal candidate for latency reversal. The BDZ Alprazolam functions as an inhibitor of the transcription factor RUNX1, which negatively regulates HIV-1 transcription. In addition to the displacement of RUNX1 from the HIV-1 5′LTR, Alprazolam potentiates the activation of STAT5 and its recruitment to the viral promoter. The activation of STAT5 in cytotoxic T cells may enable immune activation which is independent of the IL-2 receptor. These findings have significance for the potential use of Alprazolam in a curative strategy and to addressing the neuroinflammation associated with neuroHIV-1.
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Affiliation(s)
- Angel Lin
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA, United States.,Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Weam Othman Elbezanti
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA, United States.,Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA, United States
| | - Alexis Schirling
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA, United States.,HIV-1 Dynamics and Replication Program, National Cancer Institute, Frederick, MD, United States
| | - Adel Ahmed
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Rachel Van Duyne
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Simon Cocklin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Zachary Klase
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, United States.,Center for Neuroimmunology and CNS Therapeutics, Institute of Molecular Medicine and Infectious Diseases, Drexel University College of Medicine, Philadelphia, PA, United States
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7
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Liu P, Liu JP, Sun SJ, Gao Y, Ai Y, Chen X, Sun Y, Zhou M, Liu Y, Xiong Y, Yuan HX. CBFB-MYH11 Fusion Sequesters RUNX1 in Cytoplasm to Prevent DNMT3A Recruitment to Target Genes in AML. Front Cell Dev Biol 2021; 9:675424. [PMID: 34336831 PMCID: PMC8321512 DOI: 10.3389/fcell.2021.675424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/16/2021] [Indexed: 12/11/2022] Open
Abstract
A growing number of human diseases have been found to be associated with aberrant DNA methylation, including cancer. Mutations targeting genes encoding DNA methyltransferase (DNMT), TET family of DNA demethylases, and isocitrate dehydrogenase (IDH1, IDH2) that produce TET inhibitory metabolite, 2-hyoxyglutarate (2-HG), are found in more than half of acute myeloid leukemia (AML). To gain new insights into the regulation of DNA de/methylation and consequence of its alteration in cancer development, we searched for genes which are mutated in a manner that is linked with gene mutations involved in DNA de/methylation in multiple cancer types. We found that recurrent CBFB-MYH11 fusions, which result in the expression of fusion protein comprising core-binding factor β (CBFB) and myosin heavy chain 11 (MYH11) and are found in 6∼8% of AML patients, occur mutually exclusively with DNMT3A mutations. Tumors bearing CBFB-MYH11 fusion show DNA hypomethylation patterns similar to those with loss-of-function mutation of DNMT3A. Expression of CBFB-MYH11 fusion or inhibition of DNMT3A similarly impairs the methylation and expression of target genes of Runt related transcription factor 1 (RUNX1), a functional partner of CBFB. We demonstrate that RUNX1 directly interacts with DNMT3A and that CBFB-MYH11 fusion protein sequesters RUNX1 in the cytoplasm, thereby preventing RUNX1 from interacting with and recruiting DNMT3A to its target genes. Our results identify a novel regulation of DNA methylation and provide a molecular basis how CBFB-MYH11 fusion contributes to leukemogenesis.
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Affiliation(s)
- Peng Liu
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jin-Pin Liu
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Si-Jia Sun
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yun Gao
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yingjie Ai
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Xiufei Chen
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yiping Sun
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Mengyu Zhou
- Ministry of Education (MOE) Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yun Liu
- Ministry of Education (MOE) Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yue Xiong
- Cullgen Inc., San Diego, CA, United States
| | - Hai-Xin Yuan
- The Fifth People's Hospital of Shanghai and the Molecular and Cell Biology Research Lab of the Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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8
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Onishi-Seebacher M, Erikson G, Sawitzki Z, Ryan D, Greve G, Lübbert M, Jenuwein T. Repeat to gene expression ratios in leukemic blast cells can stratify risk prediction in acute myeloid leukemia. BMC Med Genomics 2021; 14:166. [PMID: 34174884 PMCID: PMC8234671 DOI: 10.1186/s12920-021-01003-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 06/07/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Repeat elements constitute a large proportion of the human genome and recent evidence indicates that repeat element expression has functional roles in both physiological and pathological states. Specifically for cancer, transcription of endogenous retrotransposons is often suppressed to attenuate an anti-tumor immune response, whereas aberrant expression of heterochromatin-derived satellite RNA has been identified as a tumor driver. These insights demonstrate separate functions for the dysregulation of distinct repeat subclasses in either the attenuation or progression of human solid tumors. For hematopoietic malignancies, such as Acute Myeloid Leukemia (AML), only very few studies on the expression/dysregulation of repeat elements were done. METHODS To study the expression of repeat elements in AML, we performed total-RNA sequencing of healthy CD34 + cells and of leukemic blast cells from primary AML patient material. We also developed an integrative bioinformatic approach that can quantify the expression of repeat transcripts from all repeat subclasses (SINE/ALU, LINE, ERV and satellites) in relation to the expression of gene and other non-repeat transcripts (i.e. R/G ratio). This novel approach can be used as an instructive signature for repeat element expression and has been extended to the analysis of poly(A)-RNA sequencing datasets from Blueprint and TCGA consortia that together comprise 120 AML patient samples. RESULTS We identified that repeat element expression is generally down-regulated during hematopoietic differentiation and that relative changes in repeat to gene expression can stratify risk prediction of AML patients and correlate with overall survival probabilities. A high R/G ratio identifies AML patient subgroups with a favorable prognosis, whereas a low R/G ratio is prevalent in AML patient subgroups with a poor prognosis. CONCLUSIONS We developed an integrative bioinformatic approach that defines a general model for the analysis of repeat element dysregulation in physiological and pathological development. We find that changes in repeat to gene expression (i.e. R/G ratios) correlate with hematopoietic differentiation and can sub-stratify AML patients into low-risk and high-risk subgroups. Thus, the definition of a R/G ratio can serve as a valuable biomarker for AML and could also provide insights into differential patient response to epigenetic drug treatment.
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Affiliation(s)
- M Onishi-Seebacher
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Novartis Institute for Biomedical Research (NIBR), Basel, Switzerland
| | - G Erikson
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Z Sawitzki
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB) and University of Freiburg, Freiburg, Germany
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - D Ryan
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - G Greve
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - M Lübbert
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Freiburg, Germany
| | - T Jenuwein
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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9
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RUNX1 contributes to the mesenchymal subtype of glioblastoma in a TGFβ pathway-dependent manner. Cell Death Dis 2019; 10:877. [PMID: 31754093 PMCID: PMC6872557 DOI: 10.1038/s41419-019-2108-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 11/08/2022]
Abstract
Runt-Related Transcription Factor 1 (RUNX1) is highly expressed in the Mesenchymal (Mes) subtype of glioblastoma (GBM). However, the specific molecular mechanism of RUNX1 in Mes GBM remains largely elusive. In this study, cell and tumor tissue typing were performed by RNA-sequencing. Co-immunoprecipitation (co-IP) and immunofluorescence (IF) were employed to identify members of the RUNX1 transcriptional protein complex. Bioinformatics analysis, chromatin immunoprecipitation (ChIP), and luciferase reporter experiments were utilized to verify target genes. Analyses of The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) verified the expression levels and prognoses associated with RUNX1/p-SMAD3/SUV39H1 target genes. In vivo patient-derived xenograft (PDX) studies and in vitro functional studies verified the impact of RUNX1 on the occurrence and development of GBM. The results showed that RUNX1 was upregulated in Mes GBM cell lines, tissues and patients and promoted proliferation and invasion in GBM in a TGFβ pathway-dependent manner in vivo and in vitro. We found and verified that BCL3 and MGP are transcriptionally activated by p-SMAD3 /RUNX1, while MXI1 is transcriptionally suppressed by the RUNX1/SUV39H1-H3K9me3 axis. This finding offers a theoretical rationale for using molecular markers and choosing therapeutic targets for the Mes type of GBM.
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10
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De Smedt E, Lui H, Maes K, De Veirman K, Menu E, Vanderkerken K, De Bruyne E. The Epigenome in Multiple Myeloma: Impact on Tumor Cell Plasticity and Drug Response. Front Oncol 2018; 8:566. [PMID: 30619733 PMCID: PMC6297718 DOI: 10.3389/fonc.2018.00566] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/13/2018] [Indexed: 01/19/2023] Open
Abstract
Multiple myeloma (MM) is a clonal plasma cell malignancy that develops primarily in the bone marrow (BM), where reciprocal interactions with the BM niche foster MM cell survival, growth, and drug resistance. MM cells furthermore reshape the BM to their own needs by affecting the different BM stromal cell types resulting in angiogenesis, bone destruction, and immune suppression. Despite recent advances in treatment modalities, MM remains most often incurable due to the development of drug resistance to all standard of care agents. This underscores the unmet need for these heavily treated relapsed/refractory patients. Disruptions in epigenetic regulation are a well-known hallmark of cancer cells, contributing to both cancer onset and progression. In MM, sequencing and gene expression profiling studies have also identified numerous epigenetic defects, including locus-specific DNA hypermethylation of cancer-related and B cell specific genes, genome-wide DNA hypomethylation and genetic defects, copy number variations and/or abnormal expression patterns of various chromatin modifying enzymes. Importantly, these so-called epimutations contribute to genomic instability, disease progression, and a worse outcome. Moreover, the frequency of mutations observed in genes encoding for histone methyltransferases and DNA methylation modifiers increases following treatment, indicating a role in the emergence of drug resistance. In support of this, accumulating evidence also suggest a role for the epigenetic machinery in MM cell plasticity, driving the differentiation of the malignant cells to a less mature and drug resistant state. This review discusses the current state of knowledge on the role of epigenetics in MM, with a focus on deregulated histone methylation modifiers and the impact on MM cell plasticity and drug resistance. We also provide insight into the potential of epigenetic modulating agents to enhance clinical drug responses and avoid disease relapse.
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Affiliation(s)
- Eva De Smedt
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Hui Lui
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Ken Maes
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kim De Veirman
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Eline Menu
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Karin Vanderkerken
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Elke De Bruyne
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
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11
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Combination treatment of acute myeloid leukemia cells with DNMT and HDAC inhibitors: predominant synergistic gene downregulation associated with gene body demethylation. Leukemia 2018; 33:945-956. [PMID: 30470836 DOI: 10.1038/s41375-018-0293-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 06/21/2018] [Accepted: 09/06/2018] [Indexed: 12/20/2022]
Abstract
DNA methyltransferase inhibitors (DNMTi) approved for older AML patients are clinically tested in combination with histone deacetylase inhibitors (HDACi). The mechanism of action of these drugs is still under debate. In colon cancer cells, 5-aza-2'-deoxycytidine (DAC) can downregulate oncogenes and metabolic genes by reversing gene body DNA methylation, thus implicating gene body methylation as a novel drug target. We asked whether DAC-induced gene body demethylation in AML cells is also associated with gene repression, and whether the latter is enhanced by HDACi.Transcriptome analyses revealed that a combined treatment with DAC and the HDACi panobinostat or valproic acid affected significantly more transcripts than the sum of the genes regulated by either treatment alone, demonstrating a quantitative synergistic effect on genome-wide expression in U937 cells. This effect was particularly striking for downregulated genes. Integrative methylome and transcriptome analyses showed that a massive downregulation of genes, including oncogenes (e.g., MYC) and epigenetic modifiers (e.g., KDM2B, SUV39H1) often overexpressed in cancer, was associated predominantly with gene body DNA demethylation and changes in acH3K9/27. These findings have implications for the mechanism of action of combined epigenetic treatments, and for a better understanding of responses in trials where this approach is clinically tested.
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12
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Pulikkan JA, Hegde M, Ahmad HM, Belaghzal H, Illendula A, Yu J, O'Hagan K, Ou J, Muller-Tidow C, Wolfe SA, Zhu LJ, Dekker J, Bushweller JH, Castilla LH. CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. Cell 2018; 174:172-186.e21. [PMID: 29958106 PMCID: PMC6211564 DOI: 10.1016/j.cell.2018.05.048] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 02/12/2018] [Accepted: 05/23/2018] [Indexed: 12/25/2022]
Abstract
The fusion oncoprotein CBFβ-SMMHC, expressed in leukemia cases with chromosome 16 inversion, drives leukemia development and maintenance by altering the activity of the transcription factor RUNX1. Here, we demonstrate that CBFβ-SMMHC maintains cell viability by neutralizing RUNX1-mediated repression of MYC expression. Upon pharmacologic inhibition of the CBFβ-SMMHC/RUNX1 interaction, RUNX1 shows increased binding at three MYC distal enhancers, where it represses MYC expression by mediating the replacement of the SWI/SNF complex component BRG1 with the polycomb-repressive complex component RING1B, leading to apoptosis. Combining the CBFβ-SMMHC inhibitor with the BET inhibitor JQ1 eliminates inv(16) leukemia in human cells and a mouse model. Enhancer-interaction analysis indicated that the three enhancers are physically connected with the MYC promoter, and genome-editing analysis demonstrated that they are functionally implicated in deregulation of MYC expression. This study reveals a mechanism whereby CBFβ-SMMHC drives leukemia maintenance and suggests that inhibitors targeting chromatin activity may prove effective in inv(16) leukemia therapy.
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MESH Headings
- Animals
- Apoptosis/drug effects
- Azepines/pharmacology
- Azepines/therapeutic use
- Benzimidazoles/pharmacology
- Benzimidazoles/therapeutic use
- Cell Line, Tumor
- Chromatin/metabolism
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosome Inversion/drug effects
- Core Binding Factor Alpha 2 Subunit/chemistry
- Core Binding Factor Alpha 2 Subunit/metabolism
- DNA/chemistry
- DNA/metabolism
- DNA Helicases/metabolism
- Disease Models, Animal
- Humans
- Kaplan-Meier Estimate
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred C57BL
- Nuclear Proteins/metabolism
- Oncogene Proteins, Fusion/antagonists & inhibitors
- Oncogene Proteins, Fusion/metabolism
- Polycomb Repressive Complex 1/metabolism
- Promoter Regions, Genetic
- Protein Binding
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- Transcription Factors/chemistry
- Transcription Factors/metabolism
- Triazoles/pharmacology
- Triazoles/therapeutic use
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Affiliation(s)
- John Anto Pulikkan
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mahesh Hegde
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hafiz Mohd Ahmad
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Houda Belaghzal
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anuradha Illendula
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Jun Yu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Kelsey O'Hagan
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jianhong Ou
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Carsten Muller-Tidow
- Department of Medicine, Hematology, Oncology, and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Job Dekker
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - John Hackett Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Lucio Hernán Castilla
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.
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13
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Larmonie NSD, Arentsen-Peters TCJM, Obulkasim A, Valerio D, Sonneveld E, Danen-van Oorschot AA, de Haas V, Reinhardt D, Zimmermann M, Trka J, Baruchel A, Pieters R, van den Heuvel-Eibrink MM, Zwaan CM, Fornerod M. MN1 overexpression is driven by loss of DNMT3B methylation activity in inv(16) pediatric AML. Oncogene 2018; 37:107-115. [PMID: 28892045 DOI: 10.1038/onc.2017.293] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 06/09/2017] [Accepted: 07/17/2017] [Indexed: 12/15/2022]
Abstract
In acute myeloid leukemia (AML), specific genomic aberrations induce aberrant methylation, thus directly influencing the transcriptional programing of leukemic cells. Therefore, therapies targeting epigenetic processes are advocated as a promising therapeutic tool for AML treatment. However, to develop new therapies, a comprehensive understanding of the mechanism(s) driving the epigenetic changes as a result of acquired genetic abnormalities is necessary. This understanding is still lacking. In this study, we performed genome-wide CpG-island methylation profiling on pediatric AML samples. Six differentially methylated genomic regions within two genes, discriminating inv(16)(p13;q22) from non-inv(16) pediatric AML samples, were identified. All six regions had a hypomethylated phenotype in inv(16) AML samples, and this was most prominent at the regions encompassing the meningioma (disrupted in balanced translocation) 1 (MN1) oncogene. MN1 expression primarily correlated with the methylation level of the 3' end of the MN1 exon-1 locus. Decitabine treatment of different cell lines showed that induced loss of methylation at the MN1 locus can result in an increase of MN1 expression, indicating that MN1 expression is coregulated by DNA methylation. To investigate this methylation-associated mechanism, we determined the expression of DNA methyltransferases in inv(16) AML. We found that DNMT3B expression was significantly lower in inv(16) samples. Furthermore, DNMT3B expression correlated negatively with MN1 expression in pediatric AML samples. Importantly, depletion of DNMT3B impaired remethylation efficiency of the MN1 exon-1 locus in AML cells after decitabine exposure. These findings identify DNMT3B as an important coregulator of MN1 methylation. Taken together, this study shows that the methylation level of the MN1 exon-1 locus regulates MN1 expression levels in inv(16) pediatric AML. This methylation level is dependent on DNMT3B, thus suggesting a role for DNMT3B in leukemogenesis in inv(16) AML, through MN1 methylation regulation.
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MESH Headings
- Adolescent
- Azacitidine/analogs & derivatives
- Azacitidine/pharmacology
- Carcinogenesis/genetics
- Cell Line, Tumor
- Child
- Child, Preschool
- CpG Islands/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation/drug effects
- DNA Methylation/genetics
- Decitabine
- Epigenesis, Genetic/genetics
- Exons/genetics
- Female
- Gene Expression Regulation, Leukemic
- Humans
- Infant
- Infant, Newborn
- Leukemia, Myeloid, Acute/blood
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Male
- Nucleic Acid Hybridization/methods
- Oligonucleotide Array Sequence Analysis/methods
- Oncogene Proteins, Fusion/genetics
- Promoter Regions, Genetic/genetics
- Trans-Activators
- Tumor Suppressor Proteins/genetics
- DNA Methyltransferase 3B
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Affiliation(s)
- N S D Larmonie
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - T C J M Arentsen-Peters
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - A Obulkasim
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - D Valerio
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - E Sonneveld
- Dutch Childhood Oncology Group (DCOG), The Hague, The Netherlands
| | - A A Danen-van Oorschot
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - V de Haas
- Dutch Childhood Oncology Group (DCOG), The Hague, The Netherlands
| | - D Reinhardt
- Department of Pediatric Oncology/Hematology, Medical High School, Hannover, Germany
| | - M Zimmermann
- Department of Pediatric Oncology/Hematology, Medical High School, Hannover, Germany
| | - J Trka
- Pediatric Hematology/Oncology, 2nd Medical School, Charles University, Prague, Czech Republic
| | - A Baruchel
- CHU de Paris-Hôpital Robert Debré, Paris, France
| | - R Pieters
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - C M Zwaan
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - M Fornerod
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
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14
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Tang X, Sun L, Wang G, Chen B, Luo F. RUNX1: A Regulator of NF-kB Signaling in Pulmonary Diseases. Curr Protein Pept Sci 2018; 19:172-178. [PMID: 28990531 PMCID: PMC5876917 DOI: 10.2174/1389203718666171009111835] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/27/2017] [Accepted: 09/27/2017] [Indexed: 02/05/2023]
Abstract
Runt-related transcription factor 1 (RUNX1), a member of the RUNX family, is one of the key regulatory proteins in vertebrates. RUNX1 is involved in embryonic development, hematopoiesis, angiogenesis, tumorigenesis and immune response. In the past few decades, studies mainly focused on the effect of RUNX1 on acute leukemia and cancer. Only few studies about the function of RUNX1 in the pathological process of pulmonary diseases have been reported. Recent studies have demonstrated that RUNX1 is highly expressed in both mesenchymal and epithelial compartments of the developing and postnatal lung and that it plays a critical role in the lipopolysaccharide induced lung inflammation by regulating the NF-kB pathway. RUNX1 participates in the regulation of the NF-kB signaling pathway through interaction with IkB kinase complex in the cytoplasm or interaction with the NF-kB subunit P50. NF-kB is well-known signaling pathway necessary for inflammatory response in the lung. This review is to highlight the RUNX1 structure, isoforms and to present the mechanism that RUNX1 regulates NF-kB. This will illustrate the great potential role of RUNX1 in the inflammation signaling pathway in pulmonary diseases.
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Affiliation(s)
- Xiaoju Tang
- Department of Pulmonary and Critical Care Medicine
| | - Ling Sun
- Laboratory of Cardiovascular Diseases, Research Center of Regeneration Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Gang Wang
- Department of Pulmonary and Critical Care Medicine
| | - Bojiang Chen
- Department of Pulmonary and Critical Care Medicine
| | - Fengming Luo
- Department of Pulmonary and Critical Care Medicine
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15
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Distinct mechanisms of regulation of the ITGA6 and ITGB4 genes by RUNX1 in myeloid cells. J Cell Physiol 2017; 233:3439-3453. [DOI: 10.1002/jcp.26197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/14/2017] [Indexed: 01/04/2023]
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16
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RUNX1 regulates site specificity of DNA demethylation by recruitment of DNA demethylation machineries in hematopoietic cells. Blood Adv 2017; 1:1699-1711. [PMID: 29296817 DOI: 10.1182/bloodadvances.2017005710] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 07/20/2017] [Indexed: 11/20/2022] Open
Abstract
RUNX1 is an essential master transcription factor in hematopoietic development and plays important roles in immune functions. Although the gene regulatory mechanism of RUNX1 has been characterized extensively, the epigenetic role of RUNX1 remains unclear. Here, we demonstrate that RUNX1 contributes DNA demethylation in a binding site-directed manner in human hematopoietic cells. Overexpression analysis of RUNX1 showed the RUNX1-binding site-directed DNA demethylation. The RUNX1-mediated DNA demethylation was also observed in DNA replication-arrested cells, suggesting an involvement of active demethylation mechanism. Coimmunoprecipitation in hematopoietic cells showed physical interactions between RUNX1 and DNA demethylation machinery enzymes TET2, TET3, TDG, and GADD45. Further chromatin immunoprecipitation sequencing revealed colocalization of RUNX1 and TET2 in the same genomic regions, indicating recruitment of DNA demethylation machinery by RUNX1. Finally, methylome analysis revealed significant overrepresentation of RUNX1-binding sites at demethylated regions during hematopoietic development. Collectively, the present data provide evidence that RUNX1 contributes site specificity of DNA demethylation by recruitment of TET and other demethylation-related enzymes to its binding sites in hematopoietic cells.
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17
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Issuree PDA, Ng CP, Littman DR. Heritable Gene Regulation in the CD4:CD8 T Cell Lineage Choice. Front Immunol 2017; 8:291. [PMID: 28382035 PMCID: PMC5360760 DOI: 10.3389/fimmu.2017.00291] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/28/2017] [Indexed: 12/04/2022] Open
Abstract
The adaptive immune system is dependent on functionally distinct lineages of T cell antigen receptor αβ-expressing T cells that differentiate from a common progenitor in the thymus. CD4+CD8+ progenitor thymocytes undergo selection following interaction with MHC class I and class II molecules bearing peptide self-antigens, giving rise to CD8+ cytotoxic and CD4+ helper or regulatory T cell lineages, respectively. The strict correspondence of CD4 and CD8 expression with distinct cellular phenotypes has made their genes useful surrogates for investigating molecular mechanisms of lineage commitment. Studies of Cd4 and Cd8 transcriptional regulation have uncovered cis-regulatory elements that are critical for mediating epigenetic modifications at distinct stages of development to establish heritable transcriptional programs. In this review, we examine the epigenetic mechanisms involved in Cd4 and Cd8 gene regulation during T cell lineage specification and highlight the features that make this an attractive system for uncovering molecular mechanisms of heritability.
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Affiliation(s)
- Priya D A Issuree
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine , New York, NY , USA
| | - Charles P Ng
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine , New York, NY , USA
| | - Dan R Littman
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
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18
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Covalent Modifications of RUNX Proteins: Structure Affects Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 962:33-44. [DOI: 10.1007/978-981-10-3233-2_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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19
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Bonifer C, Levantini E, Kouskoff V, Lacaud G. Runx1 Structure and Function in Blood Cell Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 962:65-81. [PMID: 28299651 DOI: 10.1007/978-981-10-3233-2_5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RUNX transcription factors belong to a highly conserved class of transcriptional regulators which play various roles in the development of the majority of metazoans. In this review we focus on the founding member of the family, RUNX1, and its role in the transcriptional control of blood cell development in mammals. We summarize data showing that RUNX1 functions both as activator and repressor within a chromatin environment, a feature that requires its interaction with multiple other transcription factors and co-factors. Furthermore, we outline how RUNX1 works together with other factors to reshape the epigenetic landscape and the three-dimensional structure of gene loci within the nucleus. Finally, we review how aberrant forms of RUNX1 deregulate blood cell development and cause hematopoietic malignancies.
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Affiliation(s)
- Constanze Bonifer
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
| | - Elena Levantini
- Beth Israel Diaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Richerche, Pisa, Italy
| | - Valerie Kouskoff
- Division of Developmental Biology & Medicine, The University of Manchester, Manchester, UK
| | - Georges Lacaud
- Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
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20
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Kohrs N, Kolodziej S, Kuvardina ON, Herglotz J, Yillah J, Herkt S, Piechatzek A, Salinas Riester G, Lingner T, Wichmann C, Bonig H, Seifried E, Platzbecker U, Medyouf H, Grez M, Lausen J. MiR144/451 Expression Is Repressed by RUNX1 During Megakaryopoiesis and Disturbed by RUNX1/ETO. PLoS Genet 2016; 12:e1005946. [PMID: 26990877 PMCID: PMC4798443 DOI: 10.1371/journal.pgen.1005946] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/01/2016] [Indexed: 01/22/2023] Open
Abstract
A network of lineage-specific transcription factors and microRNAs tightly regulates differentiation of hematopoietic stem cells along the distinct lineages. Deregulation of this regulatory network contributes to impaired lineage fidelity and leukemogenesis. We found that the hematopoietic master regulator RUNX1 controls the expression of certain microRNAs, of importance during erythroid/megakaryocytic differentiation. In particular, we show that the erythorid miR144/451 cluster is epigenetically repressed by RUNX1 during megakaryopoiesis. Furthermore, the leukemogenic RUNX1/ETO fusion protein transcriptionally represses the miR144/451 pre-microRNA. Thus RUNX1/ETO contributes to increased expression of miR451 target genes and interferes with normal gene expression during differentiation. Furthermore, we observed that inhibition of RUNX1/ETO in Kasumi1 cells and in RUNX1/ETO positive primary acute myeloid leukemia patient samples leads to up-regulation of miR144/451. RUNX1 thus emerges as a key regulator of a microRNA network, driving differentiation at the megakaryocytic/erythroid branching point. The network is disturbed by the leukemogenic RUNX1/ETO fusion product.
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Affiliation(s)
- Nicole Kohrs
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
| | - Stephan Kolodziej
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
| | - Olga N. Kuvardina
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
| | - Julia Herglotz
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Jasmin Yillah
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
| | - Stefanie Herkt
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
| | - Alexander Piechatzek
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
| | | | - Thomas Lingner
- Medical-University Goettingen, Transcriptome Analysis Laboratory, Goettingen, Germany
| | - Christian Wichmann
- Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, Ludwig-Maximilian University Hospital, Munich, Germany
| | - Halvard Bonig
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Erhard Seifried
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Uwe Platzbecker
- Department of Hematology, Medical Clinic and Polyclinic I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Hind Medyouf
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
| | - Manuel Grez
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
| | - Jörn Lausen
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
- * E-mail:
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21
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Leong WY, Guo H, Ma O, Huang H, Cantor AB, Friedman AD. Runx1 Phosphorylation by Src Increases Trans-activation via Augmented Stability, Reduced Histone Deacetylase (HDAC) Binding, and Increased DNA Affinity, and Activated Runx1 Favors Granulopoiesis. J Biol Chem 2015; 291:826-36. [PMID: 26598521 DOI: 10.1074/jbc.m115.674234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Indexed: 12/19/2022] Open
Abstract
Src phosphorylates Runx1 on one central and four C-terminal tyrosines. We find that activated Src synergizes with Runx1 to activate a Runx1 luciferase reporter. Mutation of the four Runx1 C-terminal tyrosines to aspartate or glutamate to mimic phosphorylation increases trans-activation of the reporter in 293T cells and allows induction of Cebpa or Pu.1 mRNAs in 32Dcl3 myeloid cells, whereas mutation of these residues to phenylalanine to prevent phosphorylation obviates these effects. Three mechanisms contribute to increased Runx1 activity upon tyrosine modification as follows: increased stability, reduced histone deacetylase (HDAC) interaction, and increased DNA binding. Mutation of the five modified Runx1 tyrosines to aspartate markedly reduced co-immunoprecipitation with HDAC1 and HDAC3, markedly increased stability in cycloheximide or in the presence of co-expressed Cdh1, an E3 ubiquitin ligase coactivator, with reduced ubiquitination, and allowed DNA-binding in gel shift assay similar to wild-type Runx1. In contrast, mutation of these residues to phenylalanine modestly increased HDAC interaction, modestly reduced stability, and markedly reduced DNA binding in gel shift assays and as assessed by chromatin immunoprecipitation with the -14-kb Pu.1 or +37-kb Cebpa enhancers after stable expression in 32Dcl3 cells. Affinity for CBFβ, the Runx1 DNA-binding partner, was not affected by these tyrosine modifications, and in vitro translated CBFβ markedly increased DNA affinity of both the translated phenylalanine and aspartate Runx1 variants. Finally, further supporting a positive role for Runx1 tyrosine phosphorylation during granulopoiesis, mutation of the five Src-modified residues to aspartate but not phenylalanine allows Runx1 to increase Cebpa and granulocyte colony formation by Runx1-deleted murine marrow.
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Affiliation(s)
- Wan Yee Leong
- From the Division of Pediatric Oncology, The Johns Hopkins University, Baltimore, Maryland 21231 and
| | - Hong Guo
- From the Division of Pediatric Oncology, The Johns Hopkins University, Baltimore, Maryland 21231 and
| | - Ou Ma
- From the Division of Pediatric Oncology, The Johns Hopkins University, Baltimore, Maryland 21231 and
| | - Hui Huang
- the Department of Pediatric Hematology-Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Alan B Cantor
- the Department of Pediatric Hematology-Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Alan D Friedman
- From the Division of Pediatric Oncology, The Johns Hopkins University, Baltimore, Maryland 21231 and
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22
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Sound of silence: the properties and functions of repressive Lys methyltransferases. Nat Rev Mol Cell Biol 2015. [PMID: 26204160 DOI: 10.1038/nrm4029] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The methylation of histone Lys residues by Lys methyltransferases (KMTs) regulates chromatin organization and either activates or represses gene expression, depending on the residue that is targeted. KMTs are emerging as key components in several cellular processes, and their deregulation is often associated with pathogenesis. Here, we review the current knowledge on the main KMTs that are associated with gene silencing: namely, those responsible for methylating histone H3 Lys 9 (H3K9), H3K27 and H4K20. We discuss their biochemical properties and the various mechanisms by which they are targeted to the chromatin and regulate gene expression, as well as new data on the interplay between them and other chromatin modifiers.
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23
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Brettingham-Moore KH, Taberlay PC, Holloway AF. Interplay between Transcription Factors and the Epigenome: Insight from the Role of RUNX1 in Leukemia. Front Immunol 2015; 6:499. [PMID: 26483790 PMCID: PMC4586508 DOI: 10.3389/fimmu.2015.00499] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/14/2015] [Indexed: 01/13/2023] Open
Abstract
The genome has the ability to respond in a precise and co-ordinated manner to cellular signals. It achieves this through the concerted actions of transcription factors and the chromatin platform, which are targets of the signaling pathways. Our understanding of the molecular mechanisms through which transcription factors and the chromatin landscape each control gene activity has expanded dramatically over recent years, and attention has now turned to understanding the complex, multifaceted interplay between these regulatory layers in normal and disease states. It has become apparent that transcription factors as well as the components and modifiers of the epigenetic machinery are frequent targets of genomic alterations in cancer cells. Through the study of these factors, we can gain unique insight into the dynamic interplay between transcription factors and the epigenome, and how their dysregulation leads to aberrant gene expression programs in cancer. Here, we will highlight how these factors normally co-operate to establish and maintain the transcriptional and epigenetic landscape of cells, and how this is reprogramed in cancer, focusing on the RUNX1 transcription factor and oncogenic derivative RUNX1–ETO in leukemia as paradigms of transcriptional and epigenetic reprograming.
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Affiliation(s)
| | - Phillippa C Taberlay
- Genomics and Epigenetics Program, The Garvan Institute of Medical Research , Sydney, NSW , Australia
| | - Adele F Holloway
- School of Medicine, University of Tasmania , Hobart, TAS , Australia
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24
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Regha K, Assi SA, Tsoulaki O, Gilmour J, Lacaud G, Bonifer C. Developmental-stage-dependent transcriptional response to leukaemic oncogene expression. Nat Commun 2015; 6:7203. [PMID: 26018585 PMCID: PMC4458875 DOI: 10.1038/ncomms8203] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 04/17/2015] [Indexed: 12/31/2022] Open
Abstract
Acute myeloid leukaemia (AML) is characterized by a block in myeloid differentiation the stage of which is dependent on the nature of the transforming oncogene and the developmental stage of the oncogenic hit. This is also true for the t(8;21) translocation that gives rise to the RUNX1-ETO fusion protein and initiates the most common form of human AML. Here we study the differentiation of mouse embryonic stem cells expressing an inducible RUNX1-ETO gene into blood cells as a model, combined with genome-wide analyses of transcription factor binding and gene expression. RUNX1-ETO interferes with both the activating and repressive function of its normal counterpart, RUNX1, at early and late stages of blood cell development. However, the response of the transcriptional network to RUNX1-ETO expression is developmental stage specific, highlighting the molecular mechanisms determining specific target cell expansion after an oncogenic hit.
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Affiliation(s)
- Kakkad Regha
- School of Cancer Sciences, Institute for Biomedical Research, University of Birmingham at Edgbaston, Birmingham B15 2TT, UK
| | - Salam A. Assi
- School of Cancer Sciences, Institute for Biomedical Research, University of Birmingham at Edgbaston, Birmingham B15 2TT, UK
| | - Olga Tsoulaki
- CRUK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Jane Gilmour
- School of Cancer Sciences, Institute for Biomedical Research, University of Birmingham at Edgbaston, Birmingham B15 2TT, UK
| | - Georges Lacaud
- CRUK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Constanze Bonifer
- School of Cancer Sciences, Institute for Biomedical Research, University of Birmingham at Edgbaston, Birmingham B15 2TT, UK
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25
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Lai YS, Chen JY, Tsai HJ, Chen TY, Hung WC. The SUV39H1 inhibitor chaetocin induces differentiation and shows synergistic cytotoxicity with other epigenetic drugs in acute myeloid leukemia cells. Blood Cancer J 2015; 5:e313. [PMID: 25978433 PMCID: PMC4476016 DOI: 10.1038/bcj.2015.37] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 04/14/2015] [Indexed: 12/26/2022] Open
Abstract
Epigenetic modifying enzymes have a crucial role in the pathogenesis of acute myeloid leukemia (AML). Methylation of lysine 9 on histone H3 by the methyltransferase G9a and SUV39H1 is associated with inhibition of tumor suppressor genes. We studied the effect of G9a and SUV39H1 inhibitors on viability and differentiation of AML cells and tested the cytotoxicity induced by combination of G9a and SUV39H1 inhibitors and various epigenetic drugs. The SUV39H1 inhibitor (chaetocin) and the G9a inhibitor (UNC0638) caused cell death in AML cells at high concentrations. However, only chaetocin-induced CD11b expression and differentiation of AML cells at non-cytotoxic concentration. HL-60 and KG-1a cells were more sensitive to chaetocin than U937 cells. Long-term incubation of chaetocin led to downregulation of SUV39H1 and reduction of H3K9 tri-methylation in HL-60 and KG-1a cells. Combination of chaetocin with suberoylanilide hydroxamic acid (SAHA, a histone deacetylase inhibitor) or JQ (a BET (bromodomain extra terminal) bromodomain inhibitor) showed synergistic cytotoxicity. Conversely, no synergism was found by combining chaetocin and UNC0638. More importantly, chaetocin-induced differentiation and combined cytotoxicity were also found in the primary cells of AML patients. Collectively, the SUV39H1 inhibitor chaetocin alone or in combination with other epigenetic drugs may be effective for the treatment of AML.
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Affiliation(s)
- Y-S Lai
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - J-Y Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - H-J Tsai
- 1] National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan [2] Division of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - T-Y Chen
- Division of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - W-C Hung
- 1] National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan [2] Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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Posttranslational modifications of RUNX1 as potential anticancer targets. Oncogene 2014; 34:3483-92. [PMID: 25263451 DOI: 10.1038/onc.2014.305] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 08/13/2014] [Accepted: 08/14/2014] [Indexed: 12/31/2022]
Abstract
The transcription factor RUNX1 is a master regulator of hematopoiesis. Disruption of RUNX1 activity has been implicated in the development of hematopoietic neoplasms. Recent studies also highlight the importance of RUNX1 in solid tumors both as a tumor promoter and a suppressor. Given its central role in cancer development, RUNX1 is an excellent candidate for targeted therapy. A potential strategy to target RUNX1 is through modulation of its posttranslational modifications (PTMs). Numerous studies have shown that RUNX1 activity is regulated by PTMs, including phosphorylation, acetylation, methylation and ubiquitination. These PTMs regulate RUNX1 activity either positively or negatively by altering RUNX1-mediated transcription, promoting protein degradation and affecting protein interactions. In this review, we first summarize the available data on the context- and dosage-dependent roles of RUNX1 in various types of neoplasms. We then provide a comprehensive overview of RUNX1 PTMs from biochemical and biologic perspectives. Finally, we discuss how aberrant PTMs of RUNX1 might contribute to tumorigenesis and also strategies to develop anticancer therapies targeting RUNX1 PTMs.
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Plant homeodomain finger protein 2 promotes bone formation by demethylating and activating Runx2 for osteoblast differentiation. Cell Res 2014; 24:1231-49. [PMID: 25257467 DOI: 10.1038/cr.2014.127] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 07/09/2014] [Accepted: 08/05/2014] [Indexed: 12/21/2022] Open
Abstract
Plant homeodomain finger protein 2 (PHF2), which contains a plant homeodomain and a Jumonji-C domain, is an epigenetic regulator that demethylates lysine 9 in histone 3 (H3K9me2). On the other hand, runt-related transcription factor 2 (Runx2) plays essential roles in bone development and regeneration. Given previous reports that the PHF2 mutation can cause dwarfism in mice and that PHF2 expression is correlated with that of Runx2 in differentiating thymocytes, we investigated whether PHF2 regulates Runx2-mediated bone formation. Overexpression of PHF2 facilitated bone development in newborn mice, and viral shRNA-mediated knockdown of PHF2 delayed calvarial bone regeneration in adult rats. In primary osteoblasts and C2C12 precursor cells, PHF2 enhances osteoblast differentiation by demethylating Runx2, while suppressor of variegation 3-9 homolog 1 (SUV39H1) inhibits bone formation by methylating it. The PHF2-Runx2 interaction is mediated by the Jumonji-C and Runt domains of the two proteins, respectively. The interaction between Runx2 and osteocalcin promoter is regulated by the methylation status of Runx2, i.e., the interaction is augmented when Runx2 is demethylated. Our results suggest that SUV39H1 and PHF2 reciprocally regulate osteoblast differentiation by modulating Runx2-driven transcription at the post-translational level. This study may provide a theoretical basis for the development of new therapeutic modalities for patients with impaired bone development or delayed fracture healing.
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Ptasinska A, Assi SA, Martinez-Soria N, Imperato MR, Piper J, Cauchy P, Pickin A, James SR, Hoogenkamp M, Williamson D, Wu M, Tenen DG, Ott S, Westhead DR, Cockerill PN, Heidenreich O, Bonifer C. Identification of a dynamic core transcriptional network in t(8;21) AML that regulates differentiation block and self-renewal. Cell Rep 2014; 8:1974-1988. [PMID: 25242324 PMCID: PMC4487811 DOI: 10.1016/j.celrep.2014.08.024] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 06/19/2014] [Accepted: 08/12/2014] [Indexed: 11/29/2022] Open
Abstract
Oncogenic transcription factors such as RUNX1/ETO, which is generated by the chromosomal translocation t(8;21), subvert normal blood cell development by impairing differentiation and driving malignant self-renewal. Here, we use digital footprinting and chromatin immunoprecipitation sequencing (ChIP-seq) to identify the core RUNX1/ETO-responsive transcriptional network of t(8;21) cells. We show that the transcriptional program underlying leukemic propagation is regulated by a dynamic equilibrium between RUNX1/ETO and RUNX1 complexes, which bind to identical DNA sites in a mutually exclusive fashion. Perturbation of this equilibrium in t(8;21) cells by RUNX1/ETO depletion leads to a global redistribution of transcription factor complexes within preexisting open chromatin, resulting in the formation of a transcriptional network that drives myeloid differentiation. Our work demonstrates on a genome-wide level that the extent of impaired myeloid differentiation in t(8;21) is controlled by the dynamic balance between RUNX1/ETO and RUNX1 activities through the repression of transcription factors that drive differentiation. RUNX1/ETO drives a t(8;21)-specific transcriptional network RUNX1/ETO and RUNX1 dynamically compete for the same genomic sites RUNX1/ETO targets transcription factor complexes that control differentiation RUNX1/ETO depletion activates a transcriptional network dominated by C/EBPα
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Affiliation(s)
- Anetta Ptasinska
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Salam A Assi
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Natalia Martinez-Soria
- Northern Institute for Cancer Research, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Maria Rosaria Imperato
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Jason Piper
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Pierre Cauchy
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Anna Pickin
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Sally R James
- Section of Experimental Haematology, Leeds Institute for Molecular Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Maarten Hoogenkamp
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Dan Williamson
- Northern Institute for Cancer Research, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Mengchu Wu
- Cancer Science Institute, National University of Singapore, Republic of Singapore, Singapore 117456, Singapore
| | - Daniel G Tenen
- Cancer Science Institute, National University of Singapore, Republic of Singapore, Singapore 117456, Singapore
| | - Sascha Ott
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - David R Westhead
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Peter N Cockerill
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Olaf Heidenreich
- Northern Institute for Cancer Research, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK.
| | - Constanze Bonifer
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK.
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29
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Cleveland SM, Goodings C, Tripathi RM, Elliott N, Thompson MA, Guo Y, Shyr Y, Davé UP. LMO2 induces T-cell leukemia with epigenetic deregulation of CD4. Exp Hematol 2014; 42:581-93.e5. [PMID: 24792354 PMCID: PMC4241760 DOI: 10.1016/j.exphem.2014.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 04/18/2014] [Accepted: 04/23/2014] [Indexed: 02/05/2023]
Abstract
In this study, we present a remarkable clonal cell line, 32080, derived from a CD2-Lmo2- transgenic T-cell leukemia with differentiation arrest at the transition from the intermediate single positive to double positive stages of T-cell development. We observed that 32080 cells had a striking variegated pattern in CD4 expression. There was cell-to-cell variability, with some cells expressing no CD4 and others expressing high CD4. The two populations were isogenic and yet differed in their rates of apoptosis and sensitivity to glucocorticoid. We sorted the 32080 line for CD4-positive or CD4-negative cells and observed them in culture. After 1 week, both sorted populations showed variegated CD4 expression, like the parental line, showing that the two populations could interconvert. We determined that cell replication was necessary to transit from CD4(+) to CD4(-) and CD4(-) to CD4(+). Lmo2 knockdown decreased CD4 expression, while inhibition of intracellular NOTCH1 or histone deacetylase activity induced CD4 expression. Enforced expression of RUNX1 repressed CD4 expression. We analyzed the CD4 locus by Histone 3 chromatin immunoprecipitation and found silencing marks in the CD4(-) cells and activating marks in the CD4(+) population. The 32080 cell line is a striking model of intermediate single positive to double positive T-cell plasticity and invokes a novel mechanism for LMO2's oncogenic functions.
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Affiliation(s)
- Susan M Cleveland
- Tennessee Valley Healthcare System and the Vanderbilt University Medical Center, Departments of Medicine and Cancer Biology, Nashville, Tennessee, USA
| | - Charnise Goodings
- Tennessee Valley Healthcare System and the Vanderbilt University Medical Center, Departments of Medicine and Cancer Biology, Nashville, Tennessee, USA
| | - Rati M Tripathi
- Tennessee Valley Healthcare System and the Vanderbilt University Medical Center, Departments of Medicine and Cancer Biology, Nashville, Tennessee, USA
| | - Natalina Elliott
- Tennessee Valley Healthcare System and the Vanderbilt University Medical Center, Departments of Medicine and Cancer Biology, Nashville, Tennessee, USA
| | - Mary Ann Thompson
- Vanderbilt University Medical Center, Department of Pathology, Microbiology, and Immunology, Nashville, Tennessee, USA
| | - Yan Guo
- Center for Quantitative Sciences, Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yu Shyr
- Center for Quantitative Sciences, Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Utpal P Davé
- Tennessee Valley Healthcare System and the Vanderbilt University Medical Center, Departments of Medicine and Cancer Biology, Nashville, Tennessee, USA.
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30
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Newton TP, Cummings CT, Graham DK, Bernt KM. Epigenetics and chemoresistance in childhood acute lymphoblastic leukemia. Int J Hematol Oncol 2014. [DOI: 10.2217/ijh.13.68] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
SUMMARY For children with acute lymphoblastic leukemia (ALL) who relapse, prognosis is poor and novel therapeutic strategies are needed. In the last decade, it has become apparent that ALL exhibits unique epigenetic patterns in addition to the well known cytogenetic findings. Furthermore, whole genome sequencing efforts are revealing recurrent mutations in epigenetic modifiers in ALL. Aberrant epigenetic modulation may be involved in leukemic transformation and resistance to chemotherapy. Consequently, compounds that specifically modulate the maintenance of such epigenetic programs may offer new approaches to therapy, including the modulation or prevention of chemoresistance in ALL. In this article, we review some of the most recent findings with regard to epigenetic aberrations in ALL, and discuss therapeutic strategies that are currently in development.
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Affiliation(s)
- Timothy P Newton
- Center for Cancer & Blood Disorders, Children’s Hospital Colorado & Department of Pediatrics, Section of Hematology, Oncology & Bone Marrow Transplantation, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, RC1N, Mail Stop 8302, Aurora, CO 80045, USA
| | - Christopher T Cummings
- Center for Cancer & Blood Disorders, Children’s Hospital Colorado & Department of Pediatrics, Section of Hematology, Oncology & Bone Marrow Transplantation, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, RC1N, Mail Stop 8302, Aurora, CO 80045, USA
| | - Douglas K Graham
- Center for Cancer & Blood Disorders, Children’s Hospital Colorado & Department of Pediatrics, Section of Hematology, Oncology & Bone Marrow Transplantation, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, RC1N, Mail Stop 8302, Aurora, CO 80045, USA
| | - Kathrin M Bernt
- Center for Cancer & Blood Disorders, Children’s Hospital Colorado & Department of Pediatrics, Section of Hematology, Oncology & Bone Marrow Transplantation, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, RC1N, Mail Stop 8302, Aurora, CO 80045, USA.
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31
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Tle4 regulates epigenetic silencing of gamma interferon expression during effector T helper cell tolerance. Mol Cell Biol 2013; 34:233-45. [PMID: 24190972 DOI: 10.1128/mcb.00902-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In response to suboptimal activation, T cells become hyporesponsive, with a severely reduced capacity to proliferate and produce cytokines upon reencounter with antigen. Chromatin analysis of T cells made tolerant by use of different in vitro and in vivo approaches reveals that the expression of gamma interferon (IFN-γ) is epigenetically silenced in anergic effector TH1 cells. In those T cells, calcium signaling triggers the expression of Tle4, a member of the Groucho family of corepressors, which is then recruited to a distal regulatory element in the Ifng locus and causes the establishment of repressive epigenetic marks at the Ifng gene regulatory elements. Consequently, impaired Tle4 activity results in a markedly reduced capacity to inhibit IFN-γ production in tolerized T cells. We propose that Blimp1-dependent recruitment of Tle4 to the Ifng locus causes epigenetic silencing of the expression of the Ifng gene in anergic TH1 cells. These results define a novel function of Groucho family corepressors in peripheral T cells and demonstrate that specific mechanisms are activated in tolerant T helper cells to directly repress expression of effector cytokines, supporting the hypothesis that stable epigenetic imprinting contributes to the maintenance of the tolerance-associated hyporesponsive phenotype in T cells.
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32
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Al-Sady B, Madhani HD, Narlikar GJ. Division of labor between the chromodomains of HP1 and Suv39 methylase enables coordination of heterochromatin spread. Mol Cell 2013; 51:80-91. [PMID: 23849629 DOI: 10.1016/j.molcel.2013.06.013] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 05/15/2013] [Accepted: 06/20/2013] [Indexed: 01/22/2023]
Abstract
In Schizosaccharomyces pombe, heterochromatin spread, which is marked by histone 3 lysine 9 methylation (H3K9me), requires the chromodomains (CDs) of the H3K9 methylase Suv39/Clr4 and the HP1/Swi6 protein. It is unclear how the actions of these two H3K9me-recognizing CDs are coordinated. We find that the intrinsic preference of Suv39/Clr4 is to generate dimethylated H3K9 product. The recognition of pre-existing H3K9me marks by the CD of Suv39/Clr4 stimulates overall catalysis, enabling the accumulation of small amounts of trimethylated product in vivo. Coincidentally, the Suv39/Clr4 CD, unlike the HP1/Swi6 CD, has been shown to prefer the trimethyl state over the dimethyl state. We show that this preference enables efficient heterochromatin spread in vivo by reducing competition with HP1 proteins for the more prevalent dimethyl state. Our results reveal a strategy by which "writers" and "readers" of a chromatin mark exploit different methylation states on the same residue in order to facilitate collaboration and avoid competition.
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Affiliation(s)
- Bassem Al-Sady
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
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33
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Naito T, Taniuchi I. Roles of repressive epigenetic machinery in lineage decision of T cells. Immunology 2013; 139:151-7. [PMID: 23278842 DOI: 10.1111/imm.12058] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 12/11/2012] [Accepted: 12/12/2012] [Indexed: 01/01/2023] Open
Abstract
DNA methylation and histone modifications are central to epigenetic gene regulation, which has been shown to play a crucial role in development. Epigenetics has often been discussed in the context of the maintenance of cell identity because of the heritable nature of gene expression status. Indeed, crucial roles of the epigenetic machinery in establishment and maintenance of particular lineages during early development have been well documented. However, unexpected observation of a developmental plasticity retained in mature T lymphocytes, in particular in CD4(+) T-cell subsets, by recent studies is accelerating studies that focus on roles of each epigenetic pathway in cell fate decisions of T lymphocytes. Here, we focus on the repressive epigenetic machinery, i.e. DNA methylation, histone deacetylation, H3K9 methylation and Polycomb repressive complexes, and briefly review the studies examining the role of these mechanisms during T-lymphocyte differentiation. We also discuss the current challenges faced when analysing the function of the epigenetic machinery and potential directions to overcome the problems.
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Affiliation(s)
- Taku Naito
- Laboratory for Transcriptional Regulation, Research Centre for Allergy and Immunology, RIKEN, Yokohama, Japan.
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34
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A germline point mutation in Runx1 uncouples its role in definitive hematopoiesis from differentiation. Exp Hematol 2013; 41:980-991.e1. [PMID: 23823022 DOI: 10.1016/j.exphem.2013.06.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 06/04/2013] [Accepted: 06/06/2013] [Indexed: 12/14/2022]
Abstract
Definitive hematopoiesis requires the master hematopoietic transcription factor Runx1, which is a frequent target of leukemia-related chromosomal translocations. Several of the translocation-generated fusion proteins retain the DNA binding activity of Runx1, but lose subnuclear targeting and associated transactivation potential. Complete loss of these functions in vivo resembles Runx1 ablation, which causes embryonic lethality. We developed a knock-in mouse that expresses full-length Runx1 with a mutation in the subnuclear targeting cofactor interaction domain, Runx1(HTY350-352AAA). Mutant mice survive to adulthood, and hematopoietic stem cell emergence appears to be unaltered. However, defects are observed in multiple differentiated hematopoietic lineages at stages where Runx1 is known to play key roles. Thus, a germline mutation in Runx1 reveals uncoupling of its functions during developmental hematopoiesis from subsequent differentiation across multiple hematopoietic lineages in the adult. These findings indicate that subnuclear targeting and cofactor interactions with Runx1 are important in many compartments throughout hematopoietic differentiation.
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35
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Chuang LSH, Ito K, Ito Y. RUNX family: Regulation and diversification of roles through interacting proteins. Int J Cancer 2012. [PMID: 23180629 DOI: 10.1002/ijc.27964] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Runt-related transcription factors (RUNX) belong to an ancient family of metazoan genes involved in developmental processes. Through multiple protein-interacting partners, RUNX proteins have been implicated in diverse signaling pathways and cellular processes. The frequent inactivation of RUNX genes in cancer indicates crucial roles for RUNX in tumor suppression. This review discusses the abilities of RUNX proteins, in particular RUNX3, to integrate oncogenic signals or environmental cues and to initiate appropriate tumor suppressive responses.
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36
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Tijchon E, Havinga J, van Leeuwen FN, Scheijen B. B-lineage transcription factors and cooperating gene lesions required for leukemia development. Leukemia 2012; 27:541-52. [PMID: 23047478 DOI: 10.1038/leu.2012.293] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Differentiation of hematopoietic stem cells into B lymphocytes requires the concerted action of specific transcription factors, such as RUNX1, IKZF1, E2A, EBF1 and PAX5. As key determinants of normal B-cell development, B-lineage transcription factors are frequently deregulated in hematological malignancies, such as B-cell precursor acute lymphoblastic leukemia (BCP-ALL), and affected by either chromosomal translocations, gene deletions or point mutations. However, genetic aberrations in this developmental pathway are generally insufficient to induce BCP-ALL, and often complemented by genetic defects in cytokine receptors and tyrosine kinases (IL-7Rα, CRLF2, JAK2 and c-ABL1), transcriptional cofactors (TBL1XR1, CBP and BTG1), as well as the regulatory pathways that mediate cell-cycle control (pRB and INK4A/B). Here we provide a detailed overview of the genetic pathways that interact with these B-lineage specification factors, and describe how mutations affecting these master regulators together with cooperating lesions drive leukemia development.
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Affiliation(s)
- E Tijchon
- Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
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37
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Bandyopadhyay S, Montagna C, Macian F. Silencing of the Il2 gene transcription is regulated by epigenetic changes in anergic T cells. Eur J Immunol 2012; 42:2471-83. [PMID: 22684523 DOI: 10.1002/eji.201142307] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 04/24/2012] [Accepted: 05/30/2012] [Indexed: 11/11/2022]
Abstract
Anergy is induced in T cells as a consequence of a partial or suboptimal stimulation. Anergic T cells become unresponsive and fail to proliferate and produce cytokines. We had previously shown that in anergic CD4(+) T cells, Ikaros participates in the transcriptional repression of the Il2 gene by recruiting histone deacetylases that cause core histone deacetylation at the Il2 promoter. Here we show that deacetylation at the Il2 promoter is the initial step in a process that leads to the stable silencing of the Il2 gene transcription in anergic T cells. We have found that anergy-induced deacetylation of the Il2 promoter permits binding of the histone methyl-transferase Suv39H1, which trimethylates lysine-9 of histone H3 (Me3H3-K9). Furthermore, the establishment of the Me3H3-K9 mark allows the recruitment of the heterochromatin protein HP1, allowing the silenced Il2 loci to reposition close to heterochromatin-rich regions. Our results indicate that silencing of Il2 transcription in anergic T cells is attained through a series of epigenetic changes that involve the establishment of repressive marks and the subsequent nuclear repositioning of the Il2 loci, which become juxtaposed to transcriptionally silent regions. This mechanism may account for the stable nature of the inhibition of IL-2 production in anergic cells.
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Affiliation(s)
- Sanmay Bandyopadhyay
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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38
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Maiques-Diaz A, Chou FS, Wunderlich M, Gómez-López G, Jacinto FV, Rodriguez-Perales S, Larrayoz MJ, Calasanz MJ, Mulloy JC, Cigudosa JC, Alvarez S. Chromatin modifications induced by the AML1-ETO fusion protein reversibly silence its genomic targets through AML1 and Sp1 binding motifs. Leukemia 2012; 26:1329-37. [DOI: 10.1038/leu.2011.376] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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39
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The ability of MLL to bind RUNX1 and methylate H3K4 at PU.1 regulatory regions is impaired by MDS/AML-associated RUNX1/AML1 mutations. Blood 2011; 118:6544-52. [PMID: 22012064 DOI: 10.1182/blood-2010-11-317909] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The mixed-lineage leukemia (MLL) H3K4 methyltransferase protein, and the heterodimeric RUNX1/CBFβ transcription factor complex, are critical for definitive and adult hematopoiesis, and both are frequently targeted in human acute leukemia. We identified a physical and functional interaction between RUNX1 (AML1) and MLL and show that both are required to maintain the histone lysine 4 trimethyl mark (H3K4me3) at 2 critical regulatory regions of the AML1 target gene PU.1. Similar to CBFβ, we show that MLL binds to AML1 abrogating its proteasome-dependent degradation. Furthermore, a subset of previously uncharacterized frame-shift and missense mutations at the N terminus of AML1, found in MDS and AML patients, impairs its interaction with MLL, resulting in loss of the H3K4me3 mark within PU.1 regulatory regions, and decreased PU.1 expression. The interaction between MLL and AML1 provides a mechanism for the sequence-specific binding of MLL to DNA, and identifies RUNX1 target genes as potential effectors of MLL function.
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40
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Wang L, Xiong Y, Bosselut R. Maintaining CD4-CD8 lineage integrity in T cells: where plasticity serves versatility. Semin Immunol 2011; 23:360-7. [PMID: 21963088 PMCID: PMC3740965 DOI: 10.1016/j.smim.2011.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 08/19/2011] [Indexed: 01/10/2023]
Abstract
The divergence of the two αβ T cell subsets defined by the mutually exclusive expression of CD4 and CD8 glycoproteins is an important event during the intrathymic differentiation of T lymphocytes. This reviews briefly summarizes the mechanisms that promote commitment to the CD4 or CD8 lineage in the thymus, and discusses the transcription factor circuits and epigenetic mechanisms that concur to maintain lineage integrity in post-thymic cells and yet allow effector cell differentiation.
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Affiliation(s)
- Lie Wang
- Laboratory of Immune Cell Biology, Center for Cancer Research (CCR), NCI, NIH, Bethesda, MD 20892-4259, USA
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41
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Yoshimi A, Kurokawa M. Key roles of histone methyltransferase and demethylase in leukemogenesis. J Cell Biochem 2011; 112:415-24. [DOI: 10.1002/jcb.22972] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Lemaire M, Deleu S, De Bruyne E, Van Valckenborgh E, Menu E, Vanderkerken K. The microenvironment and molecular biology of the multiple myeloma tumor. Adv Cancer Res 2011; 110:19-42. [PMID: 21704227 DOI: 10.1016/b978-0-12-386469-7.00002-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Multiple myeloma (MM) is a deadly plasma cell cancer that resides in the bone marrow (BM). Numerous studies have demonstrated the involvement of the BM microenvironment supporting tumor growth, angiogenesis, bone disease and drug resistance. Reciprocal interactions between the different components of the BM microenvironment and the MM cells are necessary to regulate migration, differentiation, proliferation and survival of the malignant plasma cells. In this review we focus on the interactions and molecular mechanisms by which the BM microenvironment exert these effects. Better understanding of these interactions and the study of the epigenetic changes that tumor cells undergo are necessary in order to improve current treatments and for the discovery of new therapies that may eventually lead to a potential cure.
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43
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The epigenetic landscape of lineage choice: lessons from the heritability of CD4 and CD8 expression. Curr Top Microbiol Immunol 2011; 356:165-88. [PMID: 21989924 PMCID: PMC4417357 DOI: 10.1007/82_2011_175] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Developing αβ T cells choose between the helper and cytotoxic lineages, depending upon the specificity of their T cell receptors for MHC molecules. The expression of the CD4 co-receptor on helper cells and the CD8 co-receptor on cytotoxic cells is intimately linked to this decision, and their regulation at the transcriptional level has been the subject of intense study to better understand lineage choice. Indeed, as the fate of developing T cells is decided, the expression status of these genes is accordingly locked. Genetic models have revealed important transcriptional elements and the ability to manipulate these elements in the framework of development has added a new perspective on the temporal nature of their function and the epigenetic maintenance of gene expression. We examine here novel insights into epigenetic mechanisms that have arisen through the study of these genes.
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Guo H, Friedman AD. Phosphorylation of RUNX1 by cyclin-dependent kinase reduces direct interaction with HDAC1 and HDAC3. J Biol Chem 2010; 286:208-15. [PMID: 21059642 DOI: 10.1074/jbc.m110.149013] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
RUNX1 regulates formation of the definitive hematopoietic stem cell and its subsequent lineage maturation, and mutations of RUNX1 contribute to leukemic transformation. Phosphorylation of Ser-48, Ser-303, and Ser-424 by cyclin-dependent kinases (cdks) increases RUNX1 trans-activation activity without perturbing p300 interaction. We now find that endogenous RUNX1 interacts with endogenous HDAC1 or HDAC3. Mutation of the three RUNX1 serines to aspartic acid reduces co-immunoprecipitation with HDAC1 or HDAC3 when expressed in 293T cells; mutation of these three serines to alanine increases HDAC interaction, and mutation of each serine individually to aspartic acid also reduces these interactions. GST-RUNX1 isolated from bacterial extracts bound in vitro translated HDAC1 or HDAC3, and these interactions were weakened by mutation of Ser-48, Ser-303, and Ser-424 to aspartic acid. The ability of RUNX1 phosphorylation and not only serine to aspartic acid conversion to reduce HDAC1 binding was demonstrated using wild-type GST-RUNX1 phosphorylated in vitro using cdk1/cyclinB and by exposure of 293T cells transduced with RUNX1 and HDAC1 to roscovitine, a cdk inhibitor. Finally, RUNX1 or RUNX1(tripleD), in which Ser-48, Ser-303, and Ser-424 are mutated to aspartic acid, stimulated proliferation of transduced, lineage-negative murine marrow progenitors more potently than did RUNX1(tripleA), in which these serines are mutated to alanine, suggesting that stimulation of RUNX1 trans-activation by cdk-mediated reduction in HDAC interaction increases marrow progenitor cell proliferation.
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Affiliation(s)
- Hong Guo
- Division of Pediatric Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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Philipot O, Joliot V, Ait-Mohamed O, Pellentz C, Robin P, Fritsch L, Ait-Si-Ali S. The core binding factor CBF negatively regulates skeletal muscle terminal differentiation. PLoS One 2010; 5:e9425. [PMID: 20195544 PMCID: PMC2828485 DOI: 10.1371/journal.pone.0009425] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 02/03/2010] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Core Binding Factor or CBF is a transcription factor composed of two subunits, Runx1/AML-1 and CBF beta or CBFbeta. CBF was originally described as a regulator of hematopoiesis. METHODOLOGY/PRINCIPAL FINDINGS Here we show that CBF is involved in the control of skeletal muscle terminal differentiation. Indeed, downregulation of either Runx1 or CBFbeta protein level accelerates cell cycle exit and muscle terminal differentiation. Conversely, overexpression of CBFbeta in myoblasts slows terminal differentiation. CBF interacts directly with the master myogenic transcription factor MyoD, preferentially in proliferating myoblasts, via Runx1 subunit. In addition, we show a preferential recruitment of Runx1 protein to MyoD target genes in proliferating myoblasts. The MyoD/CBF complex contains several chromatin modifying enzymes that inhibits MyoD activity, such as HDACs, Suv39h1 and HP1beta. When overexpressed, CBFbeta induced an inhibition of activating histone modification marks concomitant with an increase in repressive modifications at MyoD target promoters. CONCLUSIONS/SIGNIFICANCE Taken together, our data show a new role for Runx1/CBFbeta in the control of the proliferation/differentiation in skeletal myoblasts.
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Affiliation(s)
- Ophélie Philipot
- Institut André Lwoff, FRE2944, CNRS and Université Paris-Sud, Villejuif, France
| | - Véronique Joliot
- Institut André Lwoff, FRE2944, CNRS and Université Paris-Sud, Villejuif, France
| | - Ouardia Ait-Mohamed
- Institut André Lwoff, FRE2944, CNRS and Université Paris-Sud, Villejuif, France
| | - Céline Pellentz
- Institut André Lwoff, FRE2944, CNRS and Université Paris-Sud, Villejuif, France
| | - Philippe Robin
- Institut André Lwoff, FRE2944, CNRS and Université Paris-Sud, Villejuif, France
| | - Lauriane Fritsch
- Institut André Lwoff, FRE2944, CNRS and Université Paris-Sud, Villejuif, France
| | - Slimane Ait-Si-Ali
- Institut André Lwoff, FRE2944, CNRS and Université Paris-Sud, Villejuif, France
- * E-mail:
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Myeloid translocation gene 16 (MTG16) interacts with Notch transcription complex components to integrate Notch signaling in hematopoietic cell fate specification. Mol Cell Biol 2010; 30:1852-63. [PMID: 20123979 DOI: 10.1128/mcb.01342-09] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The Notch signaling pathway regulates gene expression programs to influence the specification of cell fate in diverse tissues. In response to ligand binding, the intracellular domain of the Notch receptor is cleaved by the gamma-secretase complex and then translocates to the nucleus. There, it binds the transcriptional repressor CSL, triggering its conversion to an activator of Notch target gene expression. The events that control this conversion are poorly understood. We show that the transcriptional corepressor, MTG16, interacts with both CSL and the intracellular domains of Notch receptors, suggesting a pivotal role in regulation of the Notch transcription complex. The Notch1 intracellular domain disrupts the MTG16-CSL interaction. Ex vivo fate specification in response to Notch signal activation is impaired in Mtg16-/- hematopoietic progenitors, and restored by MTG16 expression. An MTG16 derivative lacking the binding site for the intracellular domain of Notch1 fails to restore Notch-dependent cell fate. These data suggest that MTG16 interfaces with critical components of the Notch transcription complex to affect Notch-dependent lineage allocation in hematopoiesis.
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Fathi AT, Grant S, Karp JE. Exploiting cellular pathways to develop new treatment strategies for AML. Cancer Treat Rev 2010; 36:142-50. [PMID: 20056334 DOI: 10.1016/j.ctrv.2009.12.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Revised: 12/01/2009] [Accepted: 12/05/2009] [Indexed: 12/14/2022]
Abstract
The standard approaches to the treatment of acute myeloid leukemia (AML) have been predominantly based on cytarabine and anthracyclines. Yet, the outcomes associated with AML continue to be poor, especially for those patients who are older or carry higher-risk disease. In recent years, extensive research has led to the development and study of novel agents which target AML by diverse and varied mechanisms. Among these are targeted therapeutics such as kinase inhibitors and oligonucleotide constructs. These aim to suppress the production or activity of proteins, such as FLT3 and BCL2, among others, and thus disrupt related signaling cascades essential for leukemogenesis and proliferation. In addition, other agents like flavopiridol appear to target the myeloid blast by various mechanisms including suppression of cyclin-dependent kinases and interference with nucleotide synthesis. Another class of novel therapies includes inhibitors of histone deacetylase, which cause growth arrest and apoptosis through histone acetylation and resultant conformational changes. Clinical trials are now studying these and other agents alone and in combination with traditional cytotoxic therapies, with some encouraging results. In this review, we aim to provide a summary of the preclinical and clinical investigations of selected promising agents currently under study.
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Affiliation(s)
- Amir T Fathi
- Division of Hematologic Malignancies, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, 1650 Orleans Street, Baltimore, MD 21231, USA.
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48
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Dowdy CR, Xie R, Frederick D, Hussain S, Zaidi SK, Vradii D, Javed A, Li X, Jones SN, Lian JB, van Wijnen AJ, Stein JL, Stein GS. Definitive hematopoiesis requires Runx1 C-terminal-mediated subnuclear targeting and transactivation. Hum Mol Genet 2009; 19:1048-57. [PMID: 20035012 DOI: 10.1093/hmg/ddp568] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Runx1 is a key hematopoietic transcription factor required for definitive hematopoiesis and is a frequent target of leukemia-related chromosomal translocations. The resulting fusion proteins, while retaining DNA binding activity, display loss of subnuclear targeting and associated transactivation functions encoded by the C-terminus of the protein. To define the precise contribution of the Runx1 C-terminus in development and leukemia, we created a knock-in mouse with a C-terminal truncation by introducing a single nucleic acid substitution in the native Runx1 locus. This mutation (Runx1(Q307X)) models genetic lesions observed in patients with leukemia and myeloproliferative disorders. The Runx1(Q307X) homozygous mouse exhibits embryonic lethality at E12.5 due to central nervous system hemorrhages and a complete lack of hematopoietic stem cell function. While able to bind DNA, Runx1(Q307X) is unable to activate target genes, resulting in deregulation of various hematopoietic markers. Thus, we demonstrate that the subnuclear targeting and transcriptional regulatory activities of the Runx1 C-terminus are critical for hematopoietic development. We propose that compromising the C-terminal functions of Runx1 is a common mechanism for the pathological consequences of a variety of somatic mutations and Runx1-related leukemic fusion proteins observed in human patients.
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Affiliation(s)
- Christopher R Dowdy
- Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, Worcester, MA 01655, USA
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Loss of the putative catalytic domain of HDAC4 leads to reduced thermal nociception and seizures while allowing normal bone development. PLoS One 2009; 4:e6612. [PMID: 19672313 PMCID: PMC2720538 DOI: 10.1371/journal.pone.0006612] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 07/06/2009] [Indexed: 12/02/2022] Open
Abstract
Histone deacetylase 4 (HDAC4) has been associated with muscle & bone development [1]–[6]. N-terminal MEF2 and RUNX2 binding domains of HDAC4 have been shown to mediate these effects in vitro. A complete gene knockout has been reported to result in premature ossification and associated defects resulting in postnatal lethality [6]. We report a viral insertion mutation that deletes the putative deacetylase domain, while preserving the N-terminal portion of the protein. Western blot and immuno-precipitation analysis confirm expression of truncated HDAC4 containing N-terminal amino acids 1-747. These mutant mice are viable, living to at least one year of age with no gross defects in muscle or bone. At 2–4 months of age no behavioral or physiological abnormalities were detected except for an increased latency to respond to a thermal nociceptive stimulus. As the mutant mice aged past 5 months, convulsions appeared, often elicited by handling. Our findings confirm the sufficiency of the N-terminal domain for muscle and bone development, while revealing other roles of HDAC4.
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Abstract
The Runt domain (Runx) is a 128 amino acid sequence motif that defines a metazoan family of sequence-specific DNA binding proteins, which appears to have originated in concert with the intercellular signaling systems that coordinate multicellular development in animals. In the model organisms where they have been studied (fruit fly, mouse, sea urchin, and nematode) Runx genes are essential for normal development, and in humans they are causally associated with a variety of cancers, manifesting both oncogenic and tumor suppressive attributes. During development Runx proteins support both cell proliferation and differentiation, and function in both transcriptional activation and repression. Runx function is thus context-dependent, with the context provided genetically by cis-regulatory sequence architecture and epigenetically by development. This context dependency makes it difficult to formulate reductionistic generalizations concerning Runx function in normal and carcinogenic development. However, a growing body of literature links Runx function to each of the major intercellular signaling systems in animals, suggesting that the general function of Runx transcription factors may be to potentiate and govern genomic responsiveness to developmental signaling.
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Affiliation(s)
- James A Coffman
- Mount Desert Island Biological Laboratory, Salisbury Cove, Maine 04672, USA.
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