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Lewis J, Guilcher GMT, Greenway SC. Reviewing the impact of hydroxyurea on DNA methylation and its potential clinical implications in sickle cell disease. Eur J Haematol 2024; 113:264-272. [PMID: 38831675 DOI: 10.1111/ejh.14247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/05/2024]
Abstract
Hydroxyurea (HU) is the most common drug therapy for sickle cell disease (SCD). The clinical benefits of HU derive from its upregulation of fetal hemoglobin (HbF), which reduces aggregation of the mutated sickle hemoglobin protein (HbS) and reduces SCD symptoms and complications. However, some individuals do not respond to HU, or stop responding over time. Unfortunately, current understanding of the mechanism of action of HU is limited, hindering the ability of clinicians to identify those patients who will respond to HU and to optimize treatment for those receiving HU. Given that epigenetic modifications are essential to erythropoiesis and HbF expression, we hypothesize that some effects of HU may be mediated by epigenetic modifications, specifically DNA methylation. However, few studies have investigated this possibility and the effects of HU on DNA methylation remain relatively understudied. In this review, we discuss the evidence linking HU treatment to DNA methylation changes and associated gene expression changes, with an emphasis on studies that were performed in individuals with SCD. Overall, although HU can affect DNA methylation, research on these changes and their clinical effects remains limited. Further study is likely to contribute to our understanding of hematopoiesis and benefit patients suffering from SCD.
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Affiliation(s)
- Jasmine Lewis
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Cardiac Sciences and Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Pediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Gregory M T Guilcher
- Department of Pediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Steven C Greenway
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Cardiac Sciences and Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Pediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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2
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Wang J, Zhang Y, Ma Y, Zhao S, Wang J, Chen H, Zhang J, Liu J. TET1 inhibits liver fibrosis by blocking hepatic stellate cell activation. J Gastroenterol Hepatol 2024; 39:1403-1412. [PMID: 38369780 DOI: 10.1111/jgh.16443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 02/20/2024]
Abstract
Hepatic stellate cells (HSCs) are critical regulator contributing to the onset and progression of liver fibrosis. Chronic liver injury triggers HSCs to undergo vast changes and trans-differentiation into a myofibroblast HSCs, the mechanism remains to be elucidated. This study investigated that the involvement of hydroxymethylase TET1 (ten-eleven translocation 1) in HSC activation and liver fibrosis. It is revealed that TET1 levels were downregulated in the livers in mouse models of liver fibrosis and patients with cirrhosis, as well as activated HSCs in comparison to quiescent HSCs. In vitro data showed that the inhibition of TET1 promoted the activation HSC, whereas TET1 overexpression inhibited HSC activation. Moreover, TET1 could regulate KLF2 (Kruppel-like transcription factors) transcription by promoting hydroxymethylation of its promoter, which in turn suppressed the activation of HSCs. In vivo, it is confirmed that liver fibrosis was aggravated in Tet1 knockout mice after CCl4 injection, accompanied by excessive activation of primary stellate cells, in contrast to wild-type mice. In conclusion, we suggested that TET1 plays a significant role in HSC activation and liver fibrosis, which provides a promising target for anti-fibrotic therapies.
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Affiliation(s)
- Jingjie Wang
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yitong Zhang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yanyun Ma
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Fudan University, Shanghai, China
- Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
- Six-sector Industrial Research Institute, Fudan University, Shanghai, China
| | - Suhan Zhao
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Fudan University, Shanghai, China
- Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Hongtan Chen
- Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jun Zhang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jie Liu
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Fudan University, Shanghai, China
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3
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Hana T, Mukasa A, Nomura M, Nagae G, Yamamoto S, Tatsuno K, Ueda H, Fukuda S, Umeda T, Tanaka S, Nejo T, Kitagawa Y, Yamazawa E, Takahashi S, Koike T, Kushihara Y, Takami H, Takayanagi S, Aburatani H, Saito N. Region-specific DNA hydroxymethylation along the malignant progression of IDH-mutant gliomas. Cancer Sci 2024; 115:1706-1717. [PMID: 38433527 PMCID: PMC11093199 DOI: 10.1111/cas.16127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/05/2024] Open
Abstract
The majority of low-grade isocitrate dehydrogenase-mutant (IDHmt) gliomas undergo malignant progression (MP), but their underlying mechanism remains unclear. IDHmt gliomas exhibit global DNA methylation, and our previous report suggested that MP could be partly attributed to passive demethylation caused by accelerated cell cycles. However, during MP, there is also active demethylation mediated by ten-eleven translocation, such as DNA hydroxymethylation. Hydroxymethylation is reported to potentially contribute to gene expression regulation, but its role in MP remains under investigation. Therefore, we conducted a comprehensive analysis of hydroxymethylation during MP of IDHmt astrocytoma. Five primary/malignantly progressed IDHmt astrocytoma pairs were analyzed with oxidative bisulfite and the Infinium EPIC methylation array, detecting 5-hydroxymethyl cytosine at over 850,000 locations for region-specific hydroxymethylation assessment. Notably, we observed significant sharing of hydroxymethylated genomic regions during MP across the samples. Hydroxymethylated CpGs were enriched in open sea and intergenic regions (p < 0.001), and genes undergoing hydroxymethylation were significantly associated with cancer-related signaling pathways. RNA sequencing data integration identified 91 genes with significant positive/negative hydroxymethylation-expression correlations. Functional analysis suggested that positively correlated genes are involved in cell-cycle promotion, while negatively correlated ones are associated with antineoplastic functions. Analyses of The Cancer Genome Atlas clinical data on glioma were in line with these findings. Motif-enrichment analysis suggested the potential involvement of the transcription factor KLF4 in hydroxymethylation-based gene regulation. Our findings shed light on the significance of region-specific DNA hydroxymethylation in glioma MP and suggest its potential role in cancer-related gene expression and IDHmt glioma malignancy.
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Affiliation(s)
- Taijun Hana
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Akitake Mukasa
- Department of Neurosurgery, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Masashi Nomura
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Genta Nagae
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Shogo Yamamoto
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Kenji Tatsuno
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Hiroki Ueda
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
- Advanced Data Science Division, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Shiro Fukuda
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Takayoshi Umeda
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Shota Tanaka
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Takahide Nejo
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
- Department of Neurological SurgeryUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Yosuke Kitagawa
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Erika Yamazawa
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Satoshi Takahashi
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Tsukasa Koike
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Yoshihiro Kushihara
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Hirokazu Takami
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Shunsaku Takayanagi
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Hiroyuki Aburatani
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and TechnologyThe University of TokyoTokyoJapan
| | - Nobuhito Saito
- Department of Neurosurgery, Graduate School of MedicineThe University of TokyoTokyoJapan
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4
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Kriukienė E, Tomkuvienė M, Klimašauskas S. 5-Hydroxymethylcytosine: the many faces of the sixth base of mammalian DNA. Chem Soc Rev 2024; 53:2264-2283. [PMID: 38205583 DOI: 10.1039/d3cs00858d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Epigenetic phenomena play a central role in cell regulatory processes and are important factors for understanding complex human disease. One of the best understood epigenetic mechanisms is DNA methylation. In the mammalian genome, cytosines (C) in CpG dinucleotides were long known to undergo methylation at the 5-position of the pyrimidine ring (mC). Later it was found that mC can be oxidized to 5-hydroxymethylcytosine (hmC) or even further to 5-formylcytosine (fC) and to 5-carboxylcytosine (caC) by the action of 2-oxoglutarate-dependent dioxygenases of the TET family. These findings unveiled a long elusive mechanism of active DNA demethylation and bolstered a wave of studies in the area of epigenetic regulation in mammals. This review is dedicated to critical assessment of recent data on biochemical and chemical aspects of the formation and conversion of hmC in DNA, analytical techniques used for detection and mapping of this nucleobase in mammalian genomes as well as epigenetic roles of hmC in DNA replication, transcription, cell differentiation and human disease.
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Affiliation(s)
- Edita Kriukienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Miglė Tomkuvienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
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5
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Tseng YJ, Kageyama Y, Murdaugh RL, Kitano A, Kim JH, Hoegenauer KA, Tiessen J, Smith MH, Uryu H, Takahashi K, Martin JF, Samee MAH, Nakada D. Increased iron uptake by splenic hematopoietic stem cells promotes TET2-dependent erythroid regeneration. Nat Commun 2024; 15:538. [PMID: 38225226 PMCID: PMC10789814 DOI: 10.1038/s41467-024-44718-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Hematopoietic stem cells (HSCs) are capable of regenerating the blood system, but the instructive cues that direct HSCs to regenerate particular lineages lost to the injury remain elusive. Here, we show that iron is increasingly taken up by HSCs during anemia and induces erythroid gene expression and regeneration in a Tet2-dependent manner. Lineage tracing of HSCs reveals that HSCs respond to hemolytic anemia by increasing erythroid output. The number of HSCs in the spleen, but not bone marrow, increases upon anemia and these HSCs exhibit enhanced proliferation, erythroid differentiation, iron uptake, and TET2 protein expression. Increased iron in HSCs promotes DNA demethylation and expression of erythroid genes. Suppressing iron uptake or TET2 expression impairs erythroid genes expression and erythroid differentiation of HSCs; iron supplementation, however, augments these processes. These results establish that the physiological level of iron taken up by HSCs has an instructive role in promoting erythroid-biased differentiation of HSCs.
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Affiliation(s)
- Yu-Jung Tseng
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yuki Kageyama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rebecca L Murdaugh
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ayumi Kitano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jong Hwan Kim
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kevin A Hoegenauer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jonathan Tiessen
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mackenzie H Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hidetaka Uryu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - James F Martin
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Cardiomyocyte Renewal Laboratory, Texas Heart Institute, Houston, TX, 77030, USA
| | - Md Abul Hassan Samee
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Daisuke Nakada
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
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6
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Bieker JJ, Philipsen S. Erythroid Krüppel-Like Factor (KLF1): A Surprisingly Versatile Regulator of Erythroid Differentiation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:217-242. [PMID: 39017846 DOI: 10.1007/978-3-031-62731-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Erythroid Krüppel-like factor (KLF1), first discovered in 1992, is an erythroid-restricted transcription factor (TF) that is essential for terminal differentiation of erythroid progenitors. At face value, KLF1 is a rather inconspicuous member of the 26-strong SP/KLF TF family. However, 30 years of research have revealed that KLF1 is a jack of all trades in the molecular control of erythropoiesis. Initially described as a one-trick pony required for high-level transcription of the adult HBB gene, we now know that it orchestrates the entire erythroid differentiation program. It does so not only as an activator but also as a repressor. In addition, KLF1 was the first TF shown to be directly involved in enhancer/promoter loop formation. KLF1 variants underlie a wide range of erythroid phenotypes in the human population, varying from very mild conditions such as hereditary persistence of fetal hemoglobin and the In(Lu) blood type in the case of haploinsufficiency, to much more serious non-spherocytic hemolytic anemias in the case of compound heterozygosity, to dominant congenital dyserythropoietic anemia type IV invariably caused by a de novo variant in a highly conserved amino acid in the KLF1 DNA-binding domain. In this chapter, we present an overview of the past and present of KLF1 research and discuss the significance of human KLF1 variants.
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Affiliation(s)
- James J Bieker
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Sjaak Philipsen
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands.
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7
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Lu CF, Zhou YN, Zhang J, Su S, Liu Y, Peng GH, Zang W, Cao J. The role of epigenetic methylation/demethylation in the regulation of retinal photoreceptors. Front Cell Dev Biol 2023; 11:1149132. [PMID: 37305686 PMCID: PMC10251769 DOI: 10.3389/fcell.2023.1149132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Photoreceptors are integral and crucial for the retina, as they convert light into electrical signals. Epigenetics plays a vital role in determining the precise expression of genetic information in space and time during the development and maturation of photoreceptors, cell differentiation, degeneration, death, and various pathological processes. Epigenetic regulation has three main manifestations: histone modification, DNA methylation, and RNA-based mechanisms, where methylation is involved in two regulatory mechanisms-histone methylation and DNA methylation. DNA methylation is the most studied form of epigenetic modification, while histone methylation is a relatively stable regulatory mechanism. Evidence suggests that normal methylation regulation is essential for the growth and development of photoreceptors and the maintenance of their functions, while abnormal methylation can lead to many pathological forms of photoreceptors. However, the role of methylation/demethylation in regulating retinal photoreceptors remains unclear. Therefore, this study aims to review the role of methylation/demethylation in regulating photoreceptors in various physiological and pathological situations and discuss the underlying mechanisms involved. Given the critical role of epigenetic regulation in gene expression and cellular differentiation, investigating the specific molecular mechanisms underlying these processes in photoreceptors may provide valuable insights into the pathogenesis of retinal diseases. Moreover, understanding these mechanisms could lead to the development of novel therapies that target the epigenetic machinery, thereby promoting the maintenance of retinal function throughout an individual's lifespan.
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Affiliation(s)
- Chao-Fan Lu
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Ya-Nan Zhou
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Jingjing Zhang
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Songxue Su
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Yupeng Liu
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Guang-Hua Peng
- Department of Pathophysiology, Basic Medical College, Zhengzhou University, Zhengzhou, China
- Laboratory of Visual Cell Differentiation and Regulation, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Weidong Zang
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Jing Cao
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
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8
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Gnanapragasam MN, Planutis A, Glassberg JA, Bieker JJ. Identification of a genomic DNA sequence that quantitatively modulates KLF1 transcription factor expression in differentiating human hematopoietic cells. Sci Rep 2023; 13:7589. [PMID: 37165057 PMCID: PMC10172341 DOI: 10.1038/s41598-023-34805-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 05/08/2023] [Indexed: 05/12/2023] Open
Abstract
The onset of erythropoiesis is under strict developmental control, with direct and indirect inputs influencing its derivation from the hematopoietic stem cell. A major regulator of this transition is KLF1/EKLF, a zinc finger transcription factor that plays a global role in all aspects of erythropoiesis. Here, we have identified a short, conserved enhancer element in KLF1 intron 1 that is important for establishing optimal levels of KLF1 in mouse and human cells. Chromatin accessibility of this site exhibits cell-type specificity and is under developmental control during the differentiation of human CD34+ cells towards the erythroid lineage. This site binds GATA1, SMAD1, TAL1, and ETV6. In vivo editing of this region in cell lines and primary cells reduces KLF1 expression quantitatively. However, we find that, similar to observations seen in pedigrees of families with KLF1 mutations, downstream effects are variable, suggesting that the global architecture of the site is buffered towards keeping the KLF1 genetic region in an active state. We propose that modification of intron 1 in both alleles is not equivalent to complete loss of function of one allele.
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Affiliation(s)
- M N Gnanapragasam
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
| | - A Planutis
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA
| | - J A Glassberg
- Department of Emergency Medicine, Hematology and Medical Oncology, Mount Sinai School of Medicine, New York, NY, USA
| | - J J Bieker
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, USA.
- Tisch Cancer Institute, Mount Sinai School of Medicine, New York, USA.
- Mindich Child Health and Development Institute, Mount Sinai School of Medicine, New York, NY, USA.
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9
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Fontana L, Alahouzou Z, Miccio A, Antoniou P. Epigenetic Regulation of β-Globin Genes and the Potential to Treat Hemoglobinopathies through Epigenome Editing. Genes (Basel) 2023; 14:genes14030577. [PMID: 36980849 PMCID: PMC10048329 DOI: 10.3390/genes14030577] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Beta-like globin gene expression is developmentally regulated during life by transcription factors, chromatin looping and epigenome modifications of the β-globin locus. Epigenome modifications, such as histone methylation/demethylation and acetylation/deacetylation and DNA methylation, are associated with up- or down-regulation of gene expression. The understanding of these mechanisms and their outcome in gene expression has paved the way to the development of new therapeutic strategies for treating various diseases, such as β-hemoglobinopathies. Histone deacetylase and DNA methyl-transferase inhibitors are currently being tested in clinical trials for hemoglobinopathies patients. However, these approaches are often uncertain, non-specific and their global effect poses serious safety concerns. Epigenome editing is a recently developed and promising tool that consists of a DNA recognition domain (zinc finger, transcription activator-like effector or dead clustered regularly interspaced short palindromic repeats Cas9) fused to the catalytic domain of a chromatin-modifying enzyme. It offers a more specific targeting of disease-related genes (e.g., the ability to reactivate the fetal γ-globin genes and improve the hemoglobinopathy phenotype) and it facilitates the development of scarless gene therapy approaches. Here, we summarize the mechanisms of epigenome regulation of the β-globin locus, and we discuss the application of epigenome editing for the treatment of hemoglobinopathies.
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Affiliation(s)
- Letizia Fontana
- Laboratory of Chromatin and Gene Regulation during Development, INSERM UMR 1163, Imagine Institute, Université Paris Cité, F-75015 Paris, France
| | - Zoe Alahouzou
- Laboratory of Chromatin and Gene Regulation during Development, INSERM UMR 1163, Imagine Institute, Université Paris Cité, F-75015 Paris, France
| | - Annarita Miccio
- Laboratory of Chromatin and Gene Regulation during Development, INSERM UMR 1163, Imagine Institute, Université Paris Cité, F-75015 Paris, France
- Correspondence: (A.M.); (P.A.)
| | - Panagiotis Antoniou
- Laboratory of Chromatin and Gene Regulation during Development, INSERM UMR 1163, Imagine Institute, Université Paris Cité, F-75015 Paris, France
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, 431 50 Gothenburg, Sweden
- Correspondence: (A.M.); (P.A.)
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10
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Ruan B, Paulson RF. Metabolic regulation of stress erythropoiesis, outstanding questions, and possible paradigms. Front Physiol 2023; 13:1063294. [PMID: 36685181 PMCID: PMC9849390 DOI: 10.3389/fphys.2022.1063294] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/21/2022] [Indexed: 01/07/2023] Open
Abstract
Steady state erythropoiesis produces new erythrocytes at a constant rate to replace the senescent cells that are removed by macrophages in the liver and spleen. However, infection and tissue damage disrupt the production of erythrocytes by steady state erythropoiesis. During these times, stress erythropoiesis is induced to compensate for the loss of erythroid output. The strategy of stress erythropoiesis is different than steady state erythropoiesis. Stress erythropoiesis generates a wave of new erythrocytes to maintain homeostasis until steady state conditions are resumed. Stress erythropoiesis relies on the rapid proliferation of immature progenitor cells that do not differentiate until the increase in serum Erythropoietin (Epo) promotes the transition to committed progenitors that enables their synchronous differentiation. Emerging evidence has revealed a central role for cell metabolism in regulating the proliferation and differentiation of stress erythroid progenitors. During the initial expansion stage, the immature progenitors are supported by extensive metabolic changes which are designed to direct the use of glucose and glutamine to increase the biosynthesis of macromolecules necessary for cell growth and division. At the same time, these metabolic changes act to suppress the expression of genes involved in erythroid differentiation. In the subsequent transition stage, changes in niche signals alter progenitor metabolism which in turn removes the inhibition of erythroid differentiation generating a bolus of new erythrocytes to alleviate anemia. This review summarizes what is known about the metabolic regulation of stress erythropoiesis and discusses potential mechanisms for metabolic regulation of proliferation and differentiation.
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Affiliation(s)
- Baiye Ruan
- Pathobiology Graduate Program, Penn State University, University Park, PA, United States
| | - Robert F. Paulson
- Pathobiology Graduate Program, Penn State University, University Park, PA, United States
- Center for Molecular Immunology and Infectious Disease, Department of Veterinary and Biomedical Sciences, Penn State University, University Park, PA, United States
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11
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Zhang Z, Sun J. The Origin of Clonal Hematopoiesis and Its Implication in Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:65-83. [PMID: 38228959 DOI: 10.1007/978-981-99-7471-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Clonal expansion of hematopoietic cells is first observed in hematological malignancies where all the leukemic cells can be traced back to a single cell carrying oncogenic alterations. Interestingly, expansion of hematopoietic clones with defined genomic alterations, including single nucleotide variants (SNVs), small insertions and deletions (indels), and large structural chromosomal alterations (CAs), is also found in the healthy population. These genomic changes often affect leukemia driver genes. As a result, healthy individuals bearing such clonal hematopoiesis (CH) are at a higher risk of hematological malignancies. In addition to blood cancers, SNV/indel-related CH has been found associated with elevated cardiovascular and all-cause mortality, indicating adverse impacts of abnormalities in the blood on the normal functions of non-hematological tissues. In the past decade, much effort has been invested in understanding the origins of CH and its causal relationship with diseases in hematological and non-hematological tissues. Here, we review recent progress in these areas and discuss future directions that can be pursued to translate the acquired knowledge into better management of CH-related diseases.
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Affiliation(s)
- Zhen Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jianlong Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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12
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Hains AE, Uppal S, Cao JZ, Salwen HR, Applebaum MA, Cohn SL, Godley LA. MYCN and HIF-1 directly regulate TET1 expression to control 5-hmC gains and enhance neuroblastoma cell migration in hypoxia. Epigenetics 2022; 17:2056-2074. [PMID: 35942521 PMCID: PMC9665154 DOI: 10.1080/15592294.2022.2106078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 07/14/2022] [Indexed: 11/03/2022] Open
Abstract
Ten-Eleven-Translocation 5-methylcytosine dioxygenases 1-3 (TET1-3) convert 5-methylcytosine to 5-hydroxymethylcytosine (5-hmC), using oxygen as a co-substrate. Contrary to expectations, hypoxia induces 5-hmC gains in MYCN-amplified neuroblastoma (NB) cells via upregulation of TET1. Here, we show that MYCN directly controls TET1 expression in normoxia, and in hypoxia, HIF-1 augments TET1 expression and TET1 protein stability. Through gene-editing, we identify two MYCN and HIF-1 binding sites within TET1 that regulate gene expression. Bioinformatic analyses of 5-hmC distribution and RNA-sequencing data from hypoxic cells implicate hypoxia-regulated genes important for cell migration, including CXCR4. We show that hypoxic cells lacking the two MYCN/HIF-1 binding sites within TET1 migrate slower than controls. Treatment of MYCN-amplified NB cells with a CXCR4 antagonist results in slower migration under hypoxic conditions, suggesting that inclusion of a CXCR4 antagonist into NB treatment regimens could be beneficial for children with MYCN-amplified NBs.
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Affiliation(s)
- Anastasia E. Hains
- Section of Hematology/Oncology, Department of Medicine, and the University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA
| | - Sakshi Uppal
- Section of Hematology/Oncology, Department of Medicine, and the University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA
| | - John Z. Cao
- Section of Hematology/Oncology, Department of Medicine, and the University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA
| | - Helen R. Salwen
- Department of Pediatrics, The University of Chicago, Chicago, IL, USA
| | - Mark A. Applebaum
- Department of Pediatrics, The University of Chicago, Chicago, IL, USA
| | - Susan L. Cohn
- Department of Pediatrics, The University of Chicago, Chicago, IL, USA
| | - Lucy A. Godley
- Section of Hematology/Oncology, Department of Medicine, and the University of Chicago Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
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13
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Role of TET dioxygenases in the regulation of both normal and pathological hematopoiesis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:294. [PMID: 36203205 PMCID: PMC9540719 DOI: 10.1186/s13046-022-02496-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022]
Abstract
The family of ten-eleven translocation dioxygenases (TETs) consists of TET1, TET2, and TET3. Although all TETs are expressed in hematopoietic tissues, only TET2 is commonly found to be mutated in age-related clonal hematopoiesis and hematopoietic malignancies. TET2 mutation causes abnormal epigenetic landscape changes and results in multiple stages of lineage commitment/differentiation defects as well as genetic instability in hematopoietic stem/progenitor cells (HSPCs). TET2 mutations are founder mutations (first hits) in approximately 40–50% of cases of TET2-mutant (TET2MT) hematopoietic malignancies and are later hits in the remaining cases. In both situations, TET2MT collaborates with co-occurring mutations to promote malignant transformation. In TET2MT tumor cells, TET1 and TET3 partially compensate for TET2 activity and contribute to the pathogenesis of TET2MT hematopoietic malignancies. Here we summarize the most recent research on TETs in regulating of both normal and pathogenic hematopoiesis. We review the concomitant mutations and aberrant signals in TET2MT malignancies. We also discuss the molecular mechanisms by which concomitant mutations and aberrant signals determine lineage commitment in HSPCs and the identity of hematopoietic malignancies. Finally, we discuss potential strategies to treat TET2MT hematopoietic malignancies, including reverting the methylation state of TET2 target genes and targeting the concomitant mutations and aberrant signals.
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14
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Joshi K, Liu S, Breslin S J P, Zhang J. Mechanisms that regulate the activities of TET proteins. Cell Mol Life Sci 2022; 79:363. [PMID: 35705880 DOI: 10.1007/s00018-022-04396-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 02/08/2023]
Abstract
The ten-eleven translocation (TET) family of dioxygenases consists of three members, TET1, TET2, and TET3. All three TET enzymes have Fe+2 and α-ketoglutarate (α-KG)-dependent dioxygenase activities, catalyzing the 1st step of DNA demethylation by converting 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), and further oxidize 5hmC to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Gene knockout studies demonstrated that all three TET proteins are involved in the regulation of fetal organ generation during embryonic development and normal tissue generation postnatally. TET proteins play such roles by regulating the expression of key differentiation and fate-determining genes via (1) enzymatic activity-dependent DNA methylation of the promoters and enhancers of target genes; and (2) enzymatic activity-independent regulation of histone modification. Interacting partner proteins and post-translational regulatory mechanisms regulate the activities of TET proteins. Mutations and dysregulation of TET proteins are involved in the pathogenesis of human diseases, specifically cancers. Here, we summarize the research on the interaction partners and post-translational modifications of TET proteins. We also discuss the molecular mechanisms by which these partner proteins and modifications regulate TET functioning and target gene expression. Such information will help in the design of medications useful for targeted therapy of TET-mutant-related diseases.
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Affiliation(s)
- Kanak Joshi
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Shanhui Liu
- School of Life Sciences, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Peter Breslin S J
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA.,Departments of Molecular/Cellular Physiology and Biology, Loyola University Medical Center and Loyola University Chicago, Chicago, IL, 60660, USA
| | - Jiwang Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA. .,Departments of Pathology and Radiation Oncology, Loyola University Medical Center, Maywood, IL, 60153, USA.
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15
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Dissecting TET2 Regulatory Networks in Blood Differentiation and Cancer. Cancers (Basel) 2022; 14:cancers14030830. [PMID: 35159097 PMCID: PMC8834528 DOI: 10.3390/cancers14030830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Bone marrow disorders such as leukemia and myelodysplastic syndromes are characterized by abnormal healthy blood cells production and function. Uncontrolled growth and impaired differentiation of white blood cells hinder the correct development of healthy cells in the bone marrow. One of the most frequent alterations that appear to initiate this deregulation and persist in leukemia patients are mutations in epigenetic regulators such as TET2. This review summarizes the latest molecular findings regarding TET2 functions in hematopoietic cells and their potential implications in blood cancer origin and evolution. Our goal was to encompass and interlink up-to-date discoveries of the convoluted TET2 functional network to provide a more precise overview of the leukemic burden of this protein. Abstract Cytosine methylation (5mC) of CpG is the major epigenetic modification of mammalian DNA, playing essential roles during development and cancer. Although DNA methylation is generally associated with transcriptional repression, its role in gene regulation during cell fate decisions remains poorly understood. DNA demethylation can be either passive or active when initiated by TET dioxygenases. During active demethylation, transcription factors (TFs) recruit TET enzymes (TET1, 2, and 3) to specific gene regulatory regions to first catalyze the oxidation of 5mC to 5-hydroxymethylcytosine (5hmC) and subsequently to higher oxidized cytosine derivatives. Only TET2 is frequently mutated in the hematopoietic system from the three TET family members. These mutations initially lead to the hematopoietic stem cells (HSCs) compartment expansion, eventually evolving to give rise to a wide range of blood malignancies. This review focuses on recent advances in characterizing the main TET2-mediated molecular mechanisms that activate aberrant transcriptional programs in blood cancer onset and development. In addition, we discuss some of the key outstanding questions in the field.
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16
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Liu H, Wang Y, Zhou X. Labeling and sequencing nucleic acid modifications using bio-orthogonal tools. RSC Chem Biol 2022; 3:994-1007. [PMID: 35975003 PMCID: PMC9347354 DOI: 10.1039/d2cb00087c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/20/2022] [Indexed: 11/25/2022] Open
Abstract
The bio-orthogonal reaction is a type of reaction that can occur within a cell without interfering with the active components of the cell. Bio-orthogonal reaction techniques have been used to label and track the synthesis, metabolism, and interactions of distinct biomacromolecules in cells. Thus, it is a handy tool for analyzing biological macromolecules within cells. Nucleic acid modifications are widely distributed in DNA and RNA in cells and play a critical role in regulating physiological and pathological cellular activities. Utilizing bio-orthogonal tools to study modified bases is a critical and worthwhile research direction. The development of bio-orthogonal reactions focusing on nucleic acid modifications has enabled the mapping of nucleic acid modifications in DNA and RNA. This review discusses the recent advances in bio-orthogonal labeling and sequencing nucleic acid modifications in DNA and RNA. Labeling nucleic acid modifications using bio-orthogonal tools, then sequencing and imaging the labeled modifications in DNA and RNA.![]()
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Affiliation(s)
- Hui Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Yafen Wang
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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17
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HIF-1 directly induces TET3 expression to enhance 5-hmC density and induce erythroid gene expression in hypoxia. Blood Adv 2021; 4:3053-3062. [PMID: 32634239 DOI: 10.1182/bloodadvances.2020001535] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 06/02/2020] [Indexed: 12/20/2022] Open
Abstract
In mammalian cells, cytosines found within cytosine guanine dinucleotides can be methylated to 5-methylcytosine (5-mC) by DNA methyltransferases and further oxidized by the Ten-eleven translocation dioxygenase (TET) enzymes to 5-hydroxymethylcytosine (5-hmC). We have previously shown that hematopoietic stem and progenitor cells (HSPCs) with TET2 mutations have aberrant 5-hmC distribution and less erythroid differentiation potential. However, these experiments were performed under standard tissue culture conditions with 21% oxygen (O2), whereas HSPCs in human bone marrow reside in ∼1% O2. Therefore, to model human erythropoiesis more accurately, we compared 5-hmC distribution and gene expression in hypoxic vs normoxic conditions. Despite TET enzymes having limited O2 as a substrate in hypoxia, 5-hmC peaks were more numerous and pronounced than in normoxia. Among the TET genes, TET3 was upregulated specifically in hypoxia. We identified 2 HIF-1 binding sites in TET3 by chromatin immunoprecipitation of HIF-1α followed by sequencing, and TET3 upregulation was abrogated with deletion of both sites, indicating that TET3 is a direct HIF-1 target. Finally, we showed that loss of one or both of these HIF-1 binding sites in K562 cells disrupted erythroid differentiation in hypoxia and lowered cell viability. This work provides a molecular link between O2 availability, epigenetic modification of chromatin, and erythroid differentiation.
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18
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EnvIRONmental Aspects in Myelodysplastic Syndrome. Int J Mol Sci 2021; 22:ijms22105202. [PMID: 34068996 PMCID: PMC8156755 DOI: 10.3390/ijms22105202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 11/24/2022] Open
Abstract
Systemic iron overload is multifactorial in patients suffering from myelodysplastic syndrome (MDS). Disease-immanent ineffective erythropoiesis together with chronic red blood cell transfusion represent the main underlying reasons. However, like the genetic heterogeneity of MDS, iron homeostasis is also diverse in different MDS subtypes and can no longer be generalized. While a certain amount of iron and reactive oxygen species (ROS) are indispensable for proper hematological output, both are harmful if present in excess. Consequently, iron overload has been increasingly recognized as an important player in MDS, which is worth paying attention to. This review focuses on iron- and ROS-mediated effects in the bone marrow niche, their implications for hematopoiesis and their yet unclear involvement in clonal evolution. Moreover, we provide recent insights into hepcidin regulation in MDS and its interaction between erythropoiesis and inflammation. Based on Tet methylcytosine dioxygenase 2 (TET2), representing one of the most frequently mutated genes in MDS, leading to disturbances in both iron homeostasis and hematopoiesis, we highlight that different genetic alteration may have different implications and that a comprehensive workup is needed for a complete understanding and development of future therapies.
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19
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Clonal hematopoiesis: mechanisms driving dominance of stem cell clones. Blood 2021; 136:1590-1598. [PMID: 32746453 DOI: 10.1182/blood.2020006510] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/14/2020] [Indexed: 12/16/2022] Open
Abstract
The discovery of clonal hematopoiesis (CH) in older individuals has changed the way hematologists and stem cell biologists view aging. Somatic mutations accumulate in stem cells over time. While most mutations have no impact, some result in subtle functional differences that ultimately manifest in distinct stem cell behaviors. With a large pool of stem cells and many decades to compete, some of these differences confer advantages under specific contexts. Approximately 20 genes are recurrently found as mutated in CH, indicating they confer some advantage. The impact of these mutations has begun to be analyzed at a molecular level by modeling in cell lines and in mice. Mutations in epigenetic regulators such as DNMT3A and TET2 confer an advantage by enhancing self-renewal of stem and progenitor cells and inhibiting their differentiation. Mutations in other genes involved in the DNA damage response may simply enhance cell survival. Here, we review proposed mechanisms that lead to CH, specifically in the context of stem cell biology, based on our current understanding of the function of some of the CH-associated genes.
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20
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Reilly BM, Luger T, Park S, Lio CWJ, González-Avalos E, Wheeler EC, Lee M, Williamson L, Tanaka T, Diep D, Zhang K, Huang Y, Rao A, Bejar R. 5-Azacytidine Transiently Restores Dysregulated Erythroid Differentiation Gene Expression in TET2-Deficient Erythroleukemia Cells. Mol Cancer Res 2021; 19:451-464. [PMID: 33172974 PMCID: PMC7925369 DOI: 10.1158/1541-7786.mcr-20-0453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 10/05/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022]
Abstract
DNA methyltransferase inhibitors (DNMTI) like 5-Azacytidine (5-Aza) are the only disease-modifying drugs approved for the treatment of higher-risk myelodysplastic syndromes (MDS), however less than 50% of patients respond, and there are no predictors of response with clinical utility. Somatic mutations in the DNA methylation regulating gene tet-methylcytosine dioxygenase 2 (TET2) are associated with response to DNMTIs, however the mechanisms responsible for this association remain unknown. Using bisulfite padlock probes, mRNA sequencing, and hydroxymethylcytosine pull-down sequencing at several time points throughout 5-Aza treatment, we show that TET2 loss particularly influences DNA methylation (5mC) and hydroxymethylation (5hmC) patterns at erythroid gene enhancers and is associated with downregulation of erythroid gene expression in the human erythroleukemia cell line TF-1. 5-Aza disproportionately induces expression of these down-regulated genes in TET2KO cells and this effect is related to dynamic 5mC changes at erythroid gene enhancers after 5-Aza exposure. We identified differences in remethylation kinetics after 5-Aza exposure for several types of genomic regulatory elements, with distal enhancers exhibiting longer-lasting 5mC changes than other regions. This work highlights the role of 5mC and 5hmC dynamics at distal enhancers in regulating the expression of differentiation-associated gene signatures, and sheds light on how 5-Aza may be more effective in patients harboring TET2 mutations. IMPLICATIONS: TET2 loss in erythroleukemia cells induces hypermethylation and impaired expression of erythroid differentiation genes which can be specifically counteracted by 5-Azacytidine, providing a potential mechanism for the increased efficacy of 5-Aza in TET2-mutant patients with MDS. VISUAL OVERVIEW: http://mcr.aacrjournals.org/content/molcanres/19/3/451/F1.large.jpg.
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Affiliation(s)
- Brian M Reilly
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California
- Moores Cancer Center, University of California San Diego, La Jolla, California
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California
| | - Timothy Luger
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Soo Park
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Chan-Wang Jerry Lio
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, California
| | - Edahí González-Avalos
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, California
| | - Emily C Wheeler
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California
| | - Minjung Lee
- Center for Epigenetics and Disease Prevention, Texas A&M University Health Science Center, Houston, Texas
| | - Laura Williamson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Tiffany Tanaka
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Dinh Diep
- Department of Bioengineering, University of California San Diego, La Jolla, California
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, California
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Texas A&M University Health Science Center, Houston, Texas
| | - Anjana Rao
- Moores Cancer Center, University of California San Diego, La Jolla, California
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, California
| | - Rafael Bejar
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California.
- Moores Cancer Center, University of California San Diego, La Jolla, California
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21
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Sundaravel S, Steidl U, Wickrema A. Epigenetic modifiers in normal and aberrent erythropoeisis. Semin Hematol 2021; 58:15-26. [PMID: 33509439 PMCID: PMC7883935 DOI: 10.1053/j.seminhematol.2020.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/18/2020] [Accepted: 12/22/2020] [Indexed: 12/17/2022]
Abstract
Erythroid differentiation program is comprised of lineage commitment, erythroid progenitor proliferation, and termination differentiation. Each stage of the differentiation program is heavily influenced by epigenetic modifiers that alter the epigenome in a dynamic fashion influenced by cytokines/humeral factors and are amicable to target by drugs. The epigenetic modifiers can be classified as DNA modifiers (DNMT, TET), mRNA modifiers (RNA methylases and demethylases) and histone protein modifiers (methyltransferases, acetyltransferases, demethylases, and deacetylases). Here we describe mechanisms by which these epigenetic modifiers influence and guide erythroid-lineage differentiation during normal and malignant erythropoiesis and also benign diseases that arise from their altered structure or function.
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Affiliation(s)
- Sriram Sundaravel
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY; Department of Medicine, Albert Einstein College of Medicine-Montefiore Medical center, Bronx, NY
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22
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Kunimoto H, Nakajima H. TET2: A cornerstone in normal and malignant hematopoiesis. Cancer Sci 2020; 112:31-40. [PMID: 33048426 PMCID: PMC7780023 DOI: 10.1111/cas.14688] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/04/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022] Open
Abstract
Regulation of genome‐wide DNA methylation is fundamental for a variety of biological processes such as mammalian development, stem cell function, cellular proliferation/differentiation, and oncogenesis. Among the regulators of DNA methylation, ten‐eleven translocation 2 (TET2) is one of the most frequently mutated genes in clonal hematopoiesis of indeterminate potential and in various hematological malignancies, underscoring a pivotal role for TET2 in blood homeostasis and hematopoietic transformation. TET2 oxidizes methylated cytosines to further modify cytosines, which behave as intermediates in active/passive DNA demethylation processes. TET2 itself associates with histone modifiers, thereby regulating histone modifications and expression of target genes. A number of studies have reported pleiotropic effects of TET2 on hematopoietic stem cell self‐renewal, hematopoietic differentiation, genome instability and inflammatory response. Recent single‐cell genomics studies have identified gene promoters as well as transcription factor binding sites as TET2‐targeted genetic loci in which disruption of DNA methylation can fundamentally modify hematopoietic differentiation and promote leukemogenesis. TET2 mutations show convergent cooperativity with other disease alleles in signaling molecules, epigenetic modifiers, and spliceosome factors in hematopoietic transformation. Future studies focusing on the molecular basis of stem cell and immune regulation by TET2 loss will further deepen our understanding of the entire landscape of pathophysiology and molecular vulnerabilities of TET2‐mutated hematological malignancies.
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Affiliation(s)
- Hiroyoshi Kunimoto
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hideaki Nakajima
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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23
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Nemtsova MV, Mikhaylenko DS, Kuznetsova EB, Bykov II, Zamyatnin AA. Inactivation of Epigenetic Regulators due to Mutations in Solid Tumors. BIOCHEMISTRY (MOSCOW) 2020; 85:735-748. [PMID: 33040718 DOI: 10.1134/s0006297920070020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Main factors involved in carcinogenesis are associated with somatic mutations in oncogenes and tumor suppressor genes representing changes in the DNA nucleotide sequence. Epigenetic changes, such as aberrant DNA methylation, modifications of histone proteins, and chromatin remodeling, are equally important in the development of human neoplasms. From this perspective, mutations in the genes encoding key participants of epigenetic regulation are of particular interest including enzymes that methylate/demethylate DNA, enzymes that covalently attach or remove regulatory signals from histones, components of nucleosome remodeling multiprotein complexes, auxiliary proteins and cofactors of the above-mentioned molecules. This review describes both germline and somatic mutations in the key epigenetic regulators with emphasis on the latter ones in the solid human tumors, as well as considers functional consequences of these mutations on the cellular level. In addition, clinical associations of the somatic mutations in epigenetic regulators are presented, as well as DNA diagnostics of hereditary cancer syndromes due to germline mutations in the SMARC proteins and chemotherapy drugs directly affecting the altered epigenetic mechanisms for treatment of patients with solid neoplasms. The review is intended for a wide range of molecular biologists, geneticists, oncologists, and associated specialists.
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Affiliation(s)
- M V Nemtsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia.,Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - D S Mikhaylenko
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia. .,Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - E B Kuznetsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia
| | - I I Bykov
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia
| | - A A Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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24
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Zhang X, Jeong M, Huang X, Wang XQ, Wang X, Zhou W, Shamim MS, Gore H, Himadewi P, Liu Y, Bochkov ID, Reyes J, Doty M, Huang YH, Jung H, Heikamp E, Aiden AP, Li W, Su J, Aiden EL, Goodell MA. Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity. Mol Cell 2020; 78:506-521.e6. [PMID: 32386543 DOI: 10.1016/j.molcel.2020.04.018] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 01/06/2020] [Accepted: 04/15/2020] [Indexed: 12/22/2022]
Abstract
Higher-order chromatin structure and DNA methylation are implicated in multiple developmental processes, but their relationship to cell state is unknown. Here, we find that large (>7.3 kb) DNA methylation nadirs (termed "grand canyons") can form long loops connecting anchor loci that may be dozens of megabases (Mb) apart, as well as inter-chromosomal links. The interacting loci cover a total of ∼3.5 Mb of the human genome. The strongest interactions are associated with repressive marks made by the Polycomb complex and are diminished upon EZH2 inhibitor treatment. The data are suggestive of the formation of these loops by interactions between repressive elements in the loci, forming a genomic subcompartment, rather than by cohesion/CTCF-mediated extrusion. Interestingly, unlike previously characterized subcompartments, these interactions are present only in particular cell types, such as stem and progenitor cells. Our work reveals that H3K27me3-marked large DNA methylation grand canyons represent a set of very-long-range loops associated with cellular identity.
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Affiliation(s)
- Xiaotian Zhang
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
| | - Mira Jeong
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Xingfan Huang
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics & Department of Computer Science, Rice University, Houston, TX, USA
| | - Xue Qing Wang
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Xinyu Wang
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Wanding Zhou
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Muhammad S Shamim
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA; Medical Student Training Program, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics & Department of Computer Science, Rice University, Houston, TX, USA
| | - Haley Gore
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Pamela Himadewi
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Yushuai Liu
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Ivan D Bochkov
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jaime Reyes
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Madison Doty
- Molecular Genetic Technology Program, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yung-Hsin Huang
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA; Developmental Biology Program, Baylor College of Medicine, Houston, TX, USA
| | - Haiyoung Jung
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA; Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea, USA
| | - Emily Heikamp
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Aviva Presser Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA; Developmental Biology Program, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Wei Li
- Department of Bioinformatics, Biological Chemistry, University of California, Irvine CA, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jianzhong Su
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics & Department of Computer Science, Rice University, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Shanghai Institute for Advanced Immunochemical Studies, Shanghai Tech University, Shanghai, China.
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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25
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Lan Y, Pan H, Li C, Banks KM, Sam J, Ding B, Elemento O, Goll MG, Evans T. TETs Regulate Proepicardial Cell Migration through Extracellular Matrix Organization during Zebrafish Cardiogenesis. Cell Rep 2020; 26:720-732.e4. [PMID: 30650362 PMCID: PMC6366638 DOI: 10.1016/j.celrep.2018.12.076] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 10/30/2018] [Accepted: 12/18/2018] [Indexed: 12/22/2022] Open
Abstract
Ten-eleven translocation (Tet) enzymes (Tet1/2/3) mediate 5-methylcytosine (5mC) hydroxylation, which can facilitate DNA demethylation and thereby impact gene expression. Studied mostly for how mutant isoforms impact cancer, the normal roles for Tet enzymes during organogenesis are largely unknown. By analyzing compound mutant zebrafish, we discovered a requirement for Tet2/3 activity in the embryonic heart for recruitment of epicardial progenitors, associated with development of the atrial-ventricular canal (AVC). Through a combination of methylation, hydroxymethylation, and transcript profiling, the genes encoding the activin A subunit Inhbaa (in endocardium) and Sox9b (in myocardium) were implicated as demethylation targets of Tet2/3 and critical for organization of AVC-localized extracellular matrix (ECM), facilitating migration of epicardial progenitors onto the developing heart tube. This study elucidates essential DNA demethylation modifications that govern gene expression changes during cardiac development with striking temporal and lineage specificities, highlighting complex interactions in multiple cell populations during development of the vertebrate heart. Lan et al. show that zebrafish larvae mutant for tet2 and tet3 fail to demethylate genes encoding Inhbaa (in endocardium) and Sox9b (in myocardium), leading to defects in ECM needed to form valves and to recruit epicardial progenitors onto the heart tube.
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Affiliation(s)
- Yahui Lan
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Heng Pan
- Department of Physiology and Biophysics, Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Cheng Li
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Program in Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Kelly M Banks
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Jessica Sam
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Bo Ding
- Bonacept, LLC, 7699 Palmilla Drive, Apt. 3312, San Diego, CA 92122, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Mary G Goll
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA.
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26
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Kaner J, Desai P, Mencia-Trinchant N, Guzman ML, Roboz GJ, Hassane DC. Clonal Hematopoiesis and Premalignant Diseases. Cold Spring Harb Perspect Med 2020; 10:a035675. [PMID: 31615870 PMCID: PMC7117948 DOI: 10.1101/cshperspect.a035675] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Clonal hematopoiesis (CH) arises when mutations in the hematopoietic system confer a fitness advantage to specific clones, thereby favoring their disproportionate growth. The presence of CH increases with age and environmental exposures such as cytotoxic chemotherapy or radiotherapy. The most frequent mutations occur in epigenetic regulators, such as DNMT3A, TET2, and ASXL1, leading to dysregulation of tumor suppressor function, pathogen response, and inflammation. These dysregulated processes elevate risk of overall mortality, cardiovascular disease, and eventual hematologic malignancy (HM). CH is likely acting as an initiating event leading to HM when followed by cooperating mutations. However, further evidence suggests that CH exerts a bystander influence through its pro-inflammatory properties. Delineating the mechanisms that lead to the onset and expansion of CH as well as its contribution to risk of HM is crucial to defining a management and intervention strategy. In this review, we discuss the potential causes, consequences, technical considerations, and possible management strategies for CH in the context of HMs and pre-HMs.
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Affiliation(s)
- Justin Kaner
- Division of Hematology & Oncology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Pinkal Desai
- Division of Hematology & Oncology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Nuria Mencia-Trinchant
- Division of Hematology & Oncology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Monica L Guzman
- Division of Hematology & Oncology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Gail J Roboz
- Division of Hematology & Oncology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Duane C Hassane
- Division of Hematology & Oncology, Weill Cornell Medical College, New York, New York 10065, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, New York 10065, USA
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27
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Shokouhian M, Bagheri M, Poopak B, Chegeni R, Davari N, Saki N. Altering chromatin methylation patterns and the transcriptional network involved in regulation of hematopoietic stem cell fate. J Cell Physiol 2020; 235:6404-6423. [PMID: 32052445 DOI: 10.1002/jcp.29642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 01/31/2020] [Indexed: 12/15/2022]
Abstract
Hematopoietic stem cells (HSCs) are quiescent cells with self-renewal capacity and potential multilineage development. Various molecular regulatory mechanisms such as epigenetic modifications and transcription factor (TF) networks play crucial roles in establishing a balance between self-renewal and differentiation of HSCs. Histone/DNA methylations are important epigenetic modifications involved in transcriptional regulation of specific lineage HSCs via controlling chromatin structure and accessibility of DNA. Also, TFs contribute to either facilitation or inhibition of gene expression through binding to enhancer or promoter regions of DNA. As a result, epigenetic factors and TFs regulate the activation or repression of HSCs genes, playing a central role in normal hematopoiesis. Given the importance of histone/DNA methylation and TFs in gene expression regulation, their aberrations, including changes in HSCs-related methylation of histone/DNA and TFs (e.g., CCAAT-enhancer-binding protein α, phosphatase and tensin homolog deleted on the chromosome 10, Runt-related transcription factor 1, signal transducers and activators of transcription, and RAS family proteins) could disrupt HSCs fate. Herewith, we summarize how dysregulations in the expression of genes related to self-renewal, proliferation, and differentiation of HSCs caused by changes in epigenetic modifications and transcriptional networks lead to clonal expansion and leukemic transformation.
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Affiliation(s)
- Mohammad Shokouhian
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Marziye Bagheri
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Behzad Poopak
- Department of Hematology, Faculty of Paramedical Sciences, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Rouzbeh Chegeni
- Michener Institute of Education at University Health Network, Toronto, Canada
| | - Nader Davari
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Najmaldin Saki
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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28
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Bhagat TD, Von Ahrens D, Dawlaty M, Zou Y, Baddour J, Achreja A, Zhao H, Yang L, Patel B, Kwak C, Choudhary GS, Gordon-Mitchell S, Aluri S, Bhattacharyya S, Sahu S, Bhagat P, Yu Y, Bartenstein M, Giricz O, Suzuki M, Sohal D, Gupta S, Guerrero PA, Batra S, Goggins M, Steidl U, Greally J, Agarwal B, Pradhan K, Banerjee D, Nagrath D, Maitra A, Verma A. Lactate-mediated epigenetic reprogramming regulates formation of human pancreatic cancer-associated fibroblasts. eLife 2019; 8:e50663. [PMID: 31663852 PMCID: PMC6874475 DOI: 10.7554/elife.50663] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 10/27/2019] [Indexed: 01/18/2023] Open
Abstract
Even though pancreatic ductal adenocarcinoma (PDAC) is associated with fibrotic stroma, the molecular pathways regulating the formation of cancer associated fibroblasts (CAFs) are not well elucidated. An epigenomic analysis of patient-derived and de-novo generated CAFs demonstrated widespread loss of cytosine methylation that was associated with overexpression of various inflammatory transcripts including CXCR4. Co-culture of neoplastic cells with CAFs led to increased invasiveness that was abrogated by inhibition of CXCR4. Metabolite tracing revealed that lactate produced by neoplastic cells leads to increased production of alpha-ketoglutarate (aKG) within mesenchymal stem cells (MSCs). In turn, aKG mediated activation of the demethylase TET enzyme led to decreased cytosine methylation and increased hydroxymethylation during de novo differentiation of MSCs to CAF. Co-injection of neoplastic cells with TET-deficient MSCs inhibited tumor growth in vivo. Thus, in PDAC, a tumor-mediated lactate flux is associated with widespread epigenomic reprogramming that is seen during CAF formation.
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Affiliation(s)
- Tushar D Bhagat
- Albert Einstein College of Medicine, Montefiore Medical CenterNew YorkUnited States
| | - Dagny Von Ahrens
- Albert Einstein College of Medicine, Montefiore Medical CenterNew YorkUnited States
| | - Meelad Dawlaty
- Albert Einstein College of Medicine, Montefiore Medical CenterNew YorkUnited States
| | - Yiyu Zou
- Albert Einstein College of Medicine, Montefiore Medical CenterNew YorkUnited States
| | - Joelle Baddour
- Department of Biomedical EngineeringUniversity of MichiganAnn ArborUnited States
| | - Abhinav Achreja
- Department of Biomedical EngineeringUniversity of MichiganAnn ArborUnited States
| | - Hongyun Zhao
- Department of Biomedical EngineeringUniversity of MichiganAnn ArborUnited States
| | - Lifeng Yang
- Department of Biomedical EngineeringUniversity of MichiganAnn ArborUnited States
| | | | - Changsoo Kwak
- Department of Pathology, Sheikh Ahmed Pancreatic Cancer Research CenterUT MD Anderson Cancer CenterHoustonUnited States
- Department of Translational Molecular Pathology, Sheikh Ahmed Pancreatic Cancer Research CenterUT MD Anderson Cancer CenterHoustonUnited States
| | - Gaurav S Choudhary
- Albert Einstein College of Medicine, Montefiore Medical CenterNew YorkUnited States
| | | | - Srinivas Aluri
- Albert Einstein College of Medicine, Montefiore Medical CenterNew YorkUnited States
| | | | - Srabani Sahu
- Albert Einstein College of Medicine, Montefiore Medical CenterNew YorkUnited States
| | - Prafulla Bhagat
- Albert Einstein College of Medicine, Montefiore Medical CenterNew YorkUnited States
| | - Yiting Yu
- Albert Einstein College of Medicine, Montefiore Medical CenterNew YorkUnited States
| | - Matthias Bartenstein
- Albert Einstein College of Medicine, Montefiore Medical CenterNew YorkUnited States
| | - Orsi Giricz
- Albert Einstein College of Medicine, Montefiore Medical CenterNew YorkUnited States
| | - Masako Suzuki
- Albert Einstein College of Medicine, Montefiore Medical CenterNew YorkUnited States
| | - Davendra Sohal
- Department of MedicineCleveland ClinicClevelandUnited States
| | - Sonal Gupta
- Department of Pathology, Sheikh Ahmed Pancreatic Cancer Research CenterUT MD Anderson Cancer CenterHoustonUnited States
- Department of Translational Molecular Pathology, Sheikh Ahmed Pancreatic Cancer Research CenterUT MD Anderson Cancer CenterHoustonUnited States
| | - Paola A Guerrero
- Department of Pathology, Sheikh Ahmed Pancreatic Cancer Research CenterUT MD Anderson Cancer CenterHoustonUnited States
- Department of Translational Molecular Pathology, Sheikh Ahmed Pancreatic Cancer Research CenterUT MD Anderson Cancer CenterHoustonUnited States
| | | | | | - Ulrich Steidl
- Albert Einstein College of Medicine, Montefiore Medical CenterNew YorkUnited States
| | - John Greally
- Albert Einstein College of Medicine, Montefiore Medical CenterNew YorkUnited States
| | | | - Kith Pradhan
- Albert Einstein College of Medicine, Montefiore Medical CenterNew YorkUnited States
| | | | - Deepak Nagrath
- Biointerfaces InstituteUniversity of MichiganAnn ArborUnited States
| | - Anirban Maitra
- Department of Pathology, Sheikh Ahmed Pancreatic Cancer Research CenterUT MD Anderson Cancer CenterHoustonUnited States
- Department of Translational Molecular Pathology, Sheikh Ahmed Pancreatic Cancer Research CenterUT MD Anderson Cancer CenterHoustonUnited States
| | - Amit Verma
- Albert Einstein College of Medicine, Montefiore Medical CenterNew YorkUnited States
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29
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The diverse roles of DNA methylation in mammalian development and disease. Nat Rev Mol Cell Biol 2019; 20:590-607. [PMID: 31399642 DOI: 10.1038/s41580-019-0159-6] [Citation(s) in RCA: 1312] [Impact Index Per Article: 218.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 12/22/2022]
Abstract
DNA methylation is of paramount importance for mammalian embryonic development. DNA methylation has numerous functions: it is implicated in the repression of transposons and genes, but is also associated with actively transcribed gene bodies and, in some cases, with gene activation per se. In recent years, sensitive technologies have been developed that allow the interrogation of DNA methylation patterns from a small number of cells. The use of these technologies has greatly improved our knowledge of DNA methylation dynamics and heterogeneity in embryos and in specific tissues. Combined with genetic analyses, it is increasingly apparent that regulation of DNA methylation erasure and (re-)establishment varies considerably between different developmental stages. In this Review, we discuss the mechanisms and functions of DNA methylation and demethylation in both mice and humans at CpG-rich promoters, gene bodies and transposable elements. We highlight the dynamic erasure and re-establishment of DNA methylation in embryonic, germline and somatic cell development. Finally, we provide insights into DNA methylation gained from studying genetic diseases.
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30
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Sundaravel S, Kuo WL, Jeong JJ, Choudhary GS, Gordon-Mitchell S, Liu H, Bhagat TD, McGraw KL, Gurbuxani S, List AF, Verma A, Wickrema A. Loss of Function of DOCK4 in Myelodysplastic Syndromes Stem Cells is Restored by Inhibitors of DOCK4 Signaling Networks. Clin Cancer Res 2019; 25:5638-5649. [PMID: 31308061 DOI: 10.1158/1078-0432.ccr-19-0924] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/13/2019] [Accepted: 07/10/2019] [Indexed: 12/17/2022]
Abstract
PURPOSE Myelodysplastic syndromes (MDS) with deletion of chromosome 7q/7 [-7/(del)7q MDS] is associated with worse outcomes and needs novel insights into pathogenesis. Reduced expression of signaling protein dedicator of cytokinesis 4 (DOCK4) in patients with -7/(del)7q MDS leads to a block in hematopoietic stem cell (HSC) differentiation. Identification of targetable signaling networks downstream of DOCK4 will provide means to restore hematopoietic differentiation in MDS.Experimental Design: We utilized phosphoproteomics approaches to identify signaling proteins perturbed as a result of reduced expression of DOCK4 in human HSCs and tested their functional significance in primary model systems. RESULTS We demonstrate that reduced levels of DOCK4 lead to increased global tyrosine phosphorylation of proteins in primary human HSCs. LYN kinase and phosphatases INPP5D (SHIP1) and PTPN6 (SHP1) displayed greatest levels of tyrosine phosphorylation when DOCK4 expression levels were reduced using DOCK4-specific siRNA. Our data also found that increased phosphorylation of SHIP1 and SHP1 phosphatases were due to LYN kinase targeting these phosphatases as substrates. Increased migration and impediment of HSC differentiation were consequences of these signaling alterations. Pharmacologic inhibition of SHP1 reversed these functional aberrations in HSCs expressing low DOCK4 levels. In addition, differentiation block seen in DOCK4 haplo-insufficient [-7/(del)7q] MDS was rescued by inhibition of SHP1 phosphatase. CONCLUSIONS LYN kinase and phosphatases SHP1 and SHIP1 are perturbed when DOCK4 expression levels are low. Inhibition of SHP1 promotes erythroid differentiation in healthy HSCs and in -7/(del)7q MDS samples with low DOCK4 expression. Inhibitors of LYN, SHP1 and SHIP1 also abrogated increased migratory properties in HSCs expressing reduced levels of DOCK4.
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Affiliation(s)
- Sriram Sundaravel
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Wen-Liang Kuo
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Jong Jin Jeong
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Gaurav S Choudhary
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | | | - Hui Liu
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Tushar D Bhagat
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | | | - Sandeep Gurbuxani
- Department of Pathology, The University of Chicago, Chicago, Illinois
| | | | - Amit Verma
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Amittha Wickrema
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois.
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31
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Jeong JJ, Gu X, Nie J, Sundaravel S, Liu H, Kuo WL, Bhagat TD, Pradhan K, Cao J, Nischal S, McGraw KL, Bhattacharyya S, Bishop MR, Artz A, Thirman MJ, Moliterno A, Ji P, Levine RL, Godley LA, Steidl U, Bieker JJ, List AF, Saunthararajah Y, He C, Verma A, Wickrema A. Cytokine-Regulated Phosphorylation and Activation of TET2 by JAK2 in Hematopoiesis. Cancer Discov 2019; 9:778-795. [PMID: 30944118 DOI: 10.1158/2159-8290.cd-18-1138] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/12/2019] [Accepted: 03/29/2019] [Indexed: 01/10/2023]
Abstract
Even though the Ten-eleven translocation (TET) enzymes catalyze the generation of 5-hydroxymethylcytosines required for lineage commitment and subsequent differentiation of stem cells into erythroid cells, the mechanisms that link extracellular signals to TET activation and DNA hydroxymethylation are unknown. We demonstrate that hematopoietic cytokines phosphorylate TET2, leading to its activation in erythroid progenitors. Specifically, cytokine receptor-associated JAK2 phosphorylates TET2 at tyrosines 1939 and 1964. Phosphorylated TET2 interacts with the erythroid transcription factor KLF1, and this interaction with TET2 is increased upon exposure to erythropoietin. The activating JAK2V617F mutation seen in myeloproliferative disease patient samples and in mouse models is associated with increased TET activity and cytosine hydroxymethylation as well as genome-wide loss of cytosine methylation. These epigenetic and functional changes are also associated with increased expression of several oncogenic transcripts. Thus, we demonstrate that JAK2-mediated TET2 phosphorylation provides a mechanistic link between extracellular signals and epigenetic changes during hematopoiesis. SIGNIFICANCE: Identification of TET2 phosphorylation and activation by cytokine-stimulated JAK2 links extracellular signals to chromatin remodeling during hematopoietic differentiation. This provides potential avenues to regulate TET2 function in the context of myeloproliferative disorders and myelodysplastic syndromes associated with the JAK2V617F-activating mutation.This article is highlighted in the In This Issue feature, p. 681.
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Affiliation(s)
- Jong Jin Jeong
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Xiaorong Gu
- Cleveland Clinic Taussig Cancer Institute, Cleveland, Ohio
| | - Ji Nie
- Department of Chemistry, The University of Chicago, Chicago, Illinois
| | - Sriram Sundaravel
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Hui Liu
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Wen-Liang Kuo
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Tushar D Bhagat
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - Kith Pradhan
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - John Cao
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Sangeeta Nischal
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | | | | | - Michael R Bishop
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Andrew Artz
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Michael J Thirman
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Alison Moliterno
- Department of Hematology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Peng Ji
- Department of Pathology, Northwestern University, Chicago, Illinois
| | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lucy A Godley
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Ulrich Steidl
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
| | - James J Bieker
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai School of Medicine, New York, New York
| | | | | | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, Illinois
| | - Amit Verma
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York.
| | - Amittha Wickrema
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois.
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32
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Lio CWJ, Rao A. TET Enzymes and 5hmC in Adaptive and Innate Immune Systems. Front Immunol 2019; 10:210. [PMID: 30809228 PMCID: PMC6379312 DOI: 10.3389/fimmu.2019.00210] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/24/2019] [Indexed: 01/10/2023] Open
Abstract
DNA methylation is an abundant and stable epigenetic modification that allows inheritance of information from parental to daughter cells. At active genomic regions, DNA methylation can be reversed by TET (Ten-eleven translocation) enzymes, which are responsible for fine-tuning methylation patterns. TET enzymes oxidize the methyl group of 5-methylcytosine (5mC) to yield 5-hydroxymethylcytosine (5hmC) and other oxidized methylcytosines, facilitating both passive and active demethylation. Increasing evidence has demonstrated the essential functions of TET enzymes in regulating gene expression, promoting cell differentiation, and suppressing tumor formation. In this review, we will focus on recent discoveries of the functions of TET enzymes in the development and function of lymphoid and myeloid cells. How TET activity can be modulated by metabolites, including vitamin C and 2-hydroxyglutarate, and its potential application in shaping the course of immune response will be discussed.
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Affiliation(s)
- Chan-Wang J. Lio
- Division of Signaling and Gene Expression, La Jolla Institute, La Jolla, CA, United States
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute, La Jolla, CA, United States
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States
- Sanford Consortium for Regenerative Medicine, San Diego, CA, United States
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33
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Qu X, Zhang S, Wang S, Wang Y, Li W, Huang Y, Zhao H, Wu X, An C, Guo X, Hale J, Li J, Hillyer CD, Mohandas N, Liu J, Yazdanbakhsh K, Vinchi F, Chen L, Kang Q, An X. TET2 deficiency leads to stem cell factor-dependent clonal expansion of dysfunctional erythroid progenitors. Blood 2018; 132:2406-2417. [PMID: 30254129 PMCID: PMC6265651 DOI: 10.1182/blood-2018-05-853291] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/14/2018] [Indexed: 12/12/2022] Open
Abstract
Myelodysplastic syndromes (MDSs) are clonal hematopoietic stem cell disorders characterized by ineffective hematopoiesis. Anemia is the defining cytopenia of MDS patients, yet the molecular mechanisms for dyserythropoiesis in MDSs remain to be fully defined. Recent studies have revealed that heterozygous loss-of-function mutation of DNA dioxygenase TET2 is 1 of the most common mutations in MDSs and that TET2 deficiency disturbs erythroid differentiation. However, mechanistic insights into the role of TET2 on disordered erythropoiesis are not fully defined. Here, we show that TET2 deficiency leads initially to stem cell factor (SCF)-dependent hyperproliferation and impaired differentiation of human colony-forming unit-erythroid (CFU-E) cells, which were reversed by a c-Kit inhibitor. We further show that this was due to increased phosphorylation of c-Kit accompanied by decreased expression of phosphatase SHP-1, a negative regulator of c-Kit. At later stages, TET2 deficiency led to an accumulation of a progenitor population, which expressed surface markers characteristic of normal CFU-E cells but were functionally different. In contrast to normal CFU-E cells that require only erythropoietin (EPO) for proliferation, these abnormal progenitors required SCF and EPO and exhibited impaired differentiation. We termed this population of progenitors "marker CFU-E" cells. We further show that AXL expression was increased in marker CFU-E cells and that the increased AXL expression led to increased activation of AKT and ERK. Moreover, the altered proliferation and differentiation of marker CFU-E cells were partially rescued by an AXL inhibitor. Our findings document an important role for TET2 in erythropoiesis and have uncovered previously unknown mechanisms by which deficiency of TET2 contributes to ineffective erythropoiesis.
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Affiliation(s)
- Xiaoli Qu
- Erythrocyte Biology Laboratory, School of Life Sciences, Zhengzhou University, Zhengzhou, China
- Laboratory of Membrane Biology, New York Blood Center, New York, NY
| | - Shijie Zhang
- Erythrocyte Biology Laboratory, School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Shihui Wang
- Erythrocyte Biology Laboratory, School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yaomei Wang
- Erythrocyte Biology Laboratory, School of Life Sciences, Zhengzhou University, Zhengzhou, China
- Laboratory of Membrane Biology, New York Blood Center, New York, NY
| | - Wei Li
- Erythrocyte Biology Laboratory, School of Life Sciences, Zhengzhou University, Zhengzhou, China
- Laboratory of Membrane Biology, New York Blood Center, New York, NY
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Yumin Huang
- Laboratory of Membrane Biology, New York Blood Center, New York, NY
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huizhi Zhao
- Erythrocyte Biology Laboratory, School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Xiuyun Wu
- Erythrocyte Biology Laboratory, School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Chao An
- Laboratory of Membrane Biology, New York Blood Center, New York, NY
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinhua Guo
- Laboratory of Membrane Biology, New York Blood Center, New York, NY
| | - John Hale
- Red Cell Physiology, New York Blood Center, New York, NY
| | - Jie Li
- Erythrocyte Biology Laboratory, School of Life Sciences, Zhengzhou University, Zhengzhou, China
- Laboratory of Membrane Biology, New York Blood Center, New York, NY
| | | | - Narla Mohandas
- Red Cell Physiology, New York Blood Center, New York, NY
| | - Jing Liu
- The Province Key Laboratory of Medical Genetics and School of Life Sciences, Central South University, Changsha, China; and
| | | | | | - Lixiang Chen
- Erythrocyte Biology Laboratory, School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Qiaozhen Kang
- Erythrocyte Biology Laboratory, School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Xiuli An
- Erythrocyte Biology Laboratory, School of Life Sciences, Zhengzhou University, Zhengzhou, China
- Laboratory of Membrane Biology, New York Blood Center, New York, NY
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Wu X, Li G, Xie R. Decoding the role of TET family dioxygenases in lineage specification. Epigenetics Chromatin 2018; 11:58. [PMID: 30290828 PMCID: PMC6172806 DOI: 10.1186/s13072-018-0228-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/28/2018] [Indexed: 02/07/2023] Open
Abstract
Since the discovery of methylcytosine oxidase ten-eleven translocation (TET) proteins, we have witnessed an exponential increase in studies examining their roles in epigenetic regulation. TET family proteins catalyze the sequential oxidation of 5-methylcytosine (5mC) to oxidized methylcytosines including 5-hydroxymethylcytosine (5hmC), 5-formylcytosine, and 5-carboxylcytosine. TETs contribute to the regulation of lineage-specific gene expression via modulating DNA 5mC/5hmC balances at the proximal and distal regulatory elements of cell identity genes, and therefore enhance chromatin accessibility and gene transcription. Emerging evidence suggests that TET dioxygenases participate in the establishment and/or maintenance of hypomethylated bivalent domains at multiple differentiation-associated genes, and thus ensure developmental plasticity. Here, we review the current state of knowledge concerning TET family proteins, DNA hydroxymethylation, their distribution, and function in endoderm, mesoderm, and neuroectoderm specification. We will summarize the evidence pertaining to their crucial regulatory roles in lineage commitment and development.
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Affiliation(s)
- Xinwei Wu
- Centre of Reproduction, Development & Aging, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China
| | - Gang Li
- Centre of Reproduction, Development & Aging, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China
| | - Ruiyu Xie
- Centre of Reproduction, Development & Aging, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China.
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Padmanabhan N, Menelaou K, Gao J, Anderson A, Blake GET, Li T, Daw BN, Watson ED. Abnormal folate metabolism causes age-, sex- and parent-of-origin-specific haematological defects in mice. J Physiol 2018; 596:4341-4360. [PMID: 30024025 PMCID: PMC6138292 DOI: 10.1113/jp276419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/27/2018] [Indexed: 12/27/2022] Open
Abstract
KEY POINTS Folate (folic acid) deficiency and mutations in folate-related genes in humans result in megaloblastic anaemia. Folate metabolism, which requires the enzyme methionine synthase reductase (MTRR), is necessary for DNA synthesis and the transmission of one-carbon methyl groups for cellular methylation. In this study, we show that the hypomorphic Mtrrgt/gt mutation in mice results in late-onset and sex-specific blood defects, including macrocytic anaemia, extramedullary haematopoiesis and lymphopenia. Notably, when either parent carries an Mtrrgt allele, blood phenotypes result in their genetically wildtype adult daughters, the effects of which are parent specific. Our data establish a new model for studying the mechanism of folate metabolism in macrocytic anaemia aetiology and suggest that assessing parental folate status might be important when diagnosing adult patients with unexplained anaemia. ABSTRACT The importance of the vitamin folate (also known as folic acid) in erythrocyte formation, maturation and/or longevity is apparent since folate deficiency in humans causes megaloblastic anaemia. Megaloblastic anaemia is a type of macrocytic anaemia whereby erythrocytes are enlarged and fewer in number. Folate metabolism is required for thymidine synthesis and one-carbon metabolism, though its specific role in erythropoiesis is not well understood. Methionine synthase reductase (MTRR) is a key enzyme necessary for the progression of folate metabolism since knocking down the Mtrr gene in mice results in hyperhomocysteinaemia and global DNA hypomethylation. We demonstrate here that abnormal folate metabolism in mice caused by Mtrrgt/gt homozygosity leads to haematopoietic phenotypes that are sex and age dependent. Specifically, Mtrrgt/gt female mice displayed macrocytic anaemia, which might be due to defective erythroid differentiation at the exclusion of haemolysis. This was associated with increased renal Epo mRNA expression, hypercellular bone marrow, and splenic extramedullary haematopoiesis. In contrast, the male response differed since Mtrrgt/gt male mice were not anaemic but did display erythrocytic macrocytosis and lymphopenia. Regardless of sex, these phenotypes were late onset. Remarkably, we also show that when either parent carries an Mtrrgt allele, a haematological defect results in their adult wildtype daughters. However, the specific phenotype was dependent upon the sex of the parent. For instance, wildtype daughters of Mtrr+/gt females displayed normocytic anaemia. In contrast, wildtype daughters of Mtrr+/gt males exhibited erythrocytic microcytosis not associated with anaemia. Therefore, abnormal folate metabolism affects adult haematopoiesis in an age-, sex- and parent-specific manner.
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Affiliation(s)
- Nisha Padmanabhan
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUK
| | - Katerina Menelaou
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUK
| | - Jiali Gao
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Alexander Anderson
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUK
| | - Georgina E. T. Blake
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUK
| | - Tanya Li
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - B. Nuala Daw
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUK
| | - Erica D. Watson
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUK
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Mehlich D, Garbicz F, Włodarski PK. The emerging roles of the polycistronic miR-106b∼25 cluster in cancer - A comprehensive review. Biomed Pharmacother 2018; 107:1183-1195. [PMID: 30257332 DOI: 10.1016/j.biopha.2018.08.097] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are short, non-coding RNA molecules that regulate gene expression at the post-transcriptional level by inhibiting translation and decreasing the stability of the targeted transcripts. Over the last two decades, miRNAs have been recognized as important regulators of cancer cell biology, acting either as oncogenes or tumor suppressors. The polycistronic miR-106b∼25 cluster, located within an intron of MCM7 gene, consists of three highly conserved miRNAs: miR-25, miR-93 and miR-106b. A constantly growing body of evidence indicates that these miRNAs are overexpressed in numerous human malignancies and regulate multiple cellular processes associated with cancer development and progression, including: cell proliferation and survival, invasion, metastasis, angiogenesis and immune evasion. Furthermore, recent studies revealed that miR-106b∼25 cluster miRNAs modulate cancer stem cells characteristics and might promote resistance to anticancer therapies. In light of these novel discoveries, miRNAs belonging to the miR-106b∼25 cluster have emerged as key oncogenic drivers as well as potential biomarkers and plausible therapeutic targets in different tumor types. Herein, we comprehensively review novel findings on the roles of miR-106b∼25 cluster in human cancer, and provide a broad insight into the molecular mechanisms underlying its oncogenic properties.
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Affiliation(s)
- Dawid Mehlich
- Laboratory of Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 1B Banacha Str., 02-091 Warsaw, Poland; Laboratory of Experimental Medicine, Centre of New Technologies, University of Warsaw, 2C Banacha Str., 02-097, Warsaw, Poland
| | - Filip Garbicz
- Laboratory of Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 1B Banacha Str., 02-091 Warsaw, Poland; Postgraduate School of Molecular Medicine, Medical University of Warsaw, 61 Żwirki i Wigury Str., 02-091 Warsaw, Poland; Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, 14 Indiry Gandhi Str., 02-776 Warsaw, Poland
| | - Paweł K Włodarski
- Laboratory of Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 1B Banacha Str., 02-091 Warsaw, Poland.
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Stage-specific differential DNA methylation data analysis during human erythropoiesis in chromosome 16. Genet Res (Camb) 2018; 100:e5. [PMID: 30014809 DOI: 10.1017/s0016672318000022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Previous studies have generated controversial findings regarding the correlation between DNA methylation in the human genome and gene expression. Some reports have indicated that promoter methylation is negatively correlated with gene expression levels; however, in some cases, a poor or positive correlation was reported. Most previous findings were based on general trends observed with whole-genome data analysis. Here, we present a novel chromosome-specific statistical analysis design of empirical Bayes differential tests for five phases of erythroid development. To better understand the common methylation patterns of differentially methylated regions (DMRs) during specific stages, we defined differential phases for each CpG locus, based on a maximum log2 fold change. Analyzing hypermethylated and hypomethylated CpG loci separately showed variations in methylation patterns during erythropoiesis in the gene body, promoter and enhancer regions. Hypomethylated DMRs showed stronger associations with erythroid-specific enhancers at the differentiation start phase and with exons in the intermediate phase. To investigate the hypomethylated DMRs further, transcription factor binding site-enrichment analysis was conducted. This analysis highlighted novel transcription factors during each differentiation stage that were not detected by previous differential methylation data analysis. In contrast, hypermethylated DMRs showed a consistent methylation pattern over the different genomic regions. Thus, a closer examination of DNA methylation patterns in a single chromosome during each developmental stage can contribute to verify the association nature between gene expression and DNA methylation.
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Gnanapragasam MN, Crispino JD, Ali AM, Weinberg R, Hoffman R, Raza A, Bieker JJ. Survey and evaluation of mutations in the human KLF1 transcription unit. Sci Rep 2018; 8:6587. [PMID: 29700354 PMCID: PMC5920080 DOI: 10.1038/s41598-018-24962-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/12/2018] [Indexed: 01/03/2023] Open
Abstract
Erythroid Krüppel-like Factor (EKLF/KLF1) is an erythroid-enriched transcription factor that plays a global role in all aspects of erythropoiesis, including cell cycle control and differentiation. We queried whether its mutation might play a role in red cell malignancies by genomic sequencing of the KLF1 transcription unit in cell lines, erythroid neoplasms, dysplastic disorders, and leukemia. In addition, we queried published databases from a number of varied sources. In all cases we only found changes in commonly notated SNPs. Our results suggest that if there are mutations in KLF1 associated with erythroid malignancies, they are exceedingly rare.
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Affiliation(s)
- Merlin Nithya Gnanapragasam
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai School of Medicine, New York, NY, 10029, USA
| | - John D Crispino
- Department of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Abdullah M Ali
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Rona Weinberg
- Cellular Therapy Laboratory, New York Blood Center, New York, NY, 10065, USA
| | - Ronald Hoffman
- Department of Medicine, Mount Sinai School of Medicine, New York, NY, 10029, USA
| | - Azra Raza
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - James J Bieker
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai School of Medicine, New York, NY, 10029, USA.
- Tisch Cancer Institute, Mount Sinai School of Medicine, New York, NY, 10029, USA.
- Black Familly Stem Cell Institute, Mount Sinai School of Medicine, New York, NY, 10029, USA.
- Mindich Child Health and Development Institute, Mount Sinai School of Medicine, New York, NY, 10029, USA.
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Smeets E, Lynch AG, Prekovic S, Van den Broeck T, Moris L, Helsen C, Joniau S, Claessens F, Massie CE. The role of TET-mediated DNA hydroxymethylation in prostate cancer. Mol Cell Endocrinol 2018; 462:41-55. [PMID: 28870782 DOI: 10.1016/j.mce.2017.08.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 06/30/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
Abstract
Ten-eleven translocation (TET) proteins are recently characterized dioxygenases that regulate demethylation by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine and further derivatives. The recent finding that 5hmC is also a stable and independent epigenetic modification indicates that these proteins play an important role in diverse physiological and pathological processes such as neural and tumor development. Both the genomic distribution of (hydroxy)methylation and the expression and activity of TET proteins are dysregulated in a wide range of cancers including prostate cancer. Up to now it is still unknown how changes in TET and 5(h)mC profiles are related to the pathogenesis of prostate cancer. In this review, we explore recent advances in the current understanding of how TET expression and function are regulated in development and cancer. Furthermore, we look at the impact on 5hmC in prostate cancer and the potential underlying mechanisms. Finally, we tried to summarize the latest techniques for detecting and quantifying global and locus-specific 5hmC levels of genomic DNA.
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Affiliation(s)
- E Smeets
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| | - A G Lynch
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - S Prekovic
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - T Van den Broeck
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium; Department of Urology, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - L Moris
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium; Department of Urology, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - C Helsen
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - S Joniau
- Department of Urology, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - F Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - C E Massie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
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Ghosh S, Ranawat AS, Tolani P, Scaria V. Mitoepigenome KB a comprehensive resource for human mitochondrial epigenetic data. Mitochondrion 2017; 42:54-58. [PMID: 29129553 DOI: 10.1016/j.mito.2017.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 09/21/2017] [Accepted: 11/02/2017] [Indexed: 01/31/2023]
Abstract
Epigenetic modifications in the mitochondrial genome has been an emerging area of interest in the recent years in the field of mitochondrial biology. The renewed interest in the area has been largely fueled by a number of reports in the recent years suggesting the presence of epigenetic modifications in human mitochondrial genome and their associations with exposure to environmental factors and human diseases and or traits. Nevertheless there has been no systematic effort to curate, organize this information to enable cross-comparison between studies and datasets. We compiled 62 datasets from 9 studies on the epigenetic modifications in human mitochondrial genome to create a comprehensive catalog. This catalog is available as a user friendly interface - mitoepigenomeKB, where the data could be searched, browsed or visualized. The resource is available at URL: http://clingen.igib.res.in/mitoepigenome/. We hope mitoepigenomeKB would emerge as a central resource for datasets on epigenetic modifications in human mitochondria and would serve as the starting point to understanding the biology of human mitochondrial epigenome.
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Affiliation(s)
- Sourav Ghosh
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India; Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110 025, India
| | - Anop Singh Ranawat
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
| | - Priya Tolani
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India; Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110 025, India.
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Bhattacharyya S, Pradhan K, Campbell N, Mazdo J, Vasantkumar A, Maqbool S, Bhagat TD, Gupta S, Suzuki M, Yu Y, Greally JM, Steidl U, Bradner J, Dawlaty M, Godley L, Maitra A, Verma A. Altered hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways. Genome Res 2017; 27:1830-1842. [PMID: 28986391 PMCID: PMC5668941 DOI: 10.1101/gr.222794.117] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/14/2017] [Indexed: 01/22/2023]
Abstract
Transcriptional deregulation of oncogenic pathways is a hallmark of cancer and can be due to epigenetic alterations. 5-Hydroxymethylcytosine (5-hmC) is an epigenetic modification that has not been studied in pancreatic cancer. Genome-wide analysis of 5-hmC-enriched loci with hmC-seal was conducted in a cohort of low-passage pancreatic cancer cell lines, primary patient-derived xenografts, and pancreatic controls and revealed strikingly altered patterns in neoplastic tissues. Differentially hydroxymethylated regions preferentially affected known regulatory regions of the genome, specifically overlapping with known H3K4me1 enhancers. Furthermore, base pair resolution analysis of cytosine methylation and hydroxymethylation with oxidative bisulfite sequencing was conducted and correlated with chromatin accessibility by ATAC-seq and gene expression by RNA-seq in pancreatic cancer and control samples. 5-hmC was specifically enriched at open regions of chromatin, and gain of 5-hmC was correlated with up-regulation of the cognate transcripts, including many oncogenic pathways implicated in pancreatic neoplasia, such as MYC, KRAS, VEGFA, and BRD4 Specifically, BRD4 was overexpressed and acquired 5-hmC at enhancer regions in the majority of neoplastic samples. Functionally, acquisition of 5-hmC at BRD4 promoter was associated with increase in transcript expression in reporter assays and primary samples. Furthermore, blockade of BRD4 inhibited pancreatic cancer growth in vivo. In summary, redistribution of 5-hmC and preferential enrichment at oncogenic enhancers is a novel regulatory mechanism in human pancreatic cancer.
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Affiliation(s)
- Sanchari Bhattacharyya
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York 10461, USA
| | - Kith Pradhan
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York 10461, USA
| | | | - Jozef Mazdo
- Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Aparna Vasantkumar
- Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Shahina Maqbool
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York 10461, USA
| | - Tushar D Bhagat
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York 10461, USA
| | - Sonal Gupta
- Departments of Pathology and Translational Molecular Pathology, Sheikh Ahmed Pancreatic Cancer Research Center, UT MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Masako Suzuki
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York 10461, USA
| | - Yiting Yu
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York 10461, USA
| | - John M Greally
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York 10461, USA
| | - Ulrich Steidl
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York 10461, USA
| | - James Bradner
- Department of Medicine, Harvard Medical School and Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Meelad Dawlaty
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York 10461, USA
| | - Lucy Godley
- Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Anirban Maitra
- Departments of Pathology and Translational Molecular Pathology, Sheikh Ahmed Pancreatic Cancer Research Center, UT MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Amit Verma
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York 10461, USA
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Guo S, Jiang X, Wang Y, Chen L, Li H, Li X, Jia Y. The protective role of TET2 in erythroid iron homeostasis against oxidative stress and erythropoiesis. Cell Signal 2017; 38:106-115. [PMID: 28697999 DOI: 10.1016/j.cellsig.2017.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 07/04/2017] [Accepted: 07/07/2017] [Indexed: 01/01/2023]
Abstract
Although previous studies suggested that stress erythropoiesis and iron metabolism regulate each other to increase iron availability for hemoglobin synthesis, the molecular bases determining its different traits remain elusive. In addition, global DNA demethylation has been reported during mouse erythropoiesis in vivo. However, the understanding of iron-related genes through DNA demethylation under stress erythropoiesis is largely unknown. In the current study, we found disordered iron homeostasis and misregulated hepcidin-ferroportin axis under stress erythropoiesis. Interestingly, global 5hmC content and TET2 expression were significantly induced by oxidative stress, whereas antioxidant had the opposite's effect. Mechanistic investigation manifested that TET2-mediated DNA demethylation promotes the expression of ferroportin and erythroferrone against oxidative stress. Besides, the expression of NRF2 was significantly increased by TET2-mediated DNA demethylation during stress erythropoiesis. Elevated NRF2 expression could also modulate the activation of ferroportin and erythroferrone through a canonical antioxidant response element within its promoter. These direct and indirect pathways of TET2 synergistically cooperated to mediating iron metabolism during stress erythropoiesis. Our work revealed a critical role of TET2-mediated DNA demethylation against oxidative stress, and provided the molecular mechanisms underlying the epigenetic regulation of iron homeostasis in response to stress erythropoiesis.
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Affiliation(s)
- Shanqi Guo
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xingkang Jiang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yuanyuan Wang
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Liwei Chen
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Huzi Li
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Xiaojiang Li
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yingjie Jia
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.
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44
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Seritrakul P, Gross JM. Tet-mediated DNA hydroxymethylation regulates retinal neurogenesis by modulating cell-extrinsic signaling pathways. PLoS Genet 2017; 13:e1006987. [PMID: 28926578 PMCID: PMC5621703 DOI: 10.1371/journal.pgen.1006987] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 09/29/2017] [Accepted: 08/18/2017] [Indexed: 12/28/2022] Open
Abstract
DNA hydroxymethylation has recently been shown to play critical roles in regulating gene expression and terminal differentiation events in a variety of developmental contexts. However, little is known about its function during eye development. Methylcytosine dioxygenases of the Tet family convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), an epigenetic mark thought to serve as a precursor for DNA demethylation and as a stable mark in neurons. Here, we report a requirement for Tet activity during zebrafish retinal neurogenesis. In tet2-/-;tet3-/- mutants, retinal neurons are specified but most fail to terminally differentiate. While differentiation of the first born retinal neurons, the retinal ganglion cells (RGCs), is less affected in tet2-/-;tet3-/- mutants than other retinal cell types, the majority of RGCs do not undergo terminal morphogenesis and form axons. Moreover, the few photoreceptors that differentiate in tet2-/-;tet3-/- mutants fail to form outer segments, suggesting that Tet function is also required for terminal morphogenesis of differentiated retinal neurons. Mosaic analyses revealed a surprising cell non-autonomous requirement for tet2 and tet3 activity in facilitating retinal neurogenesis. Through a combination of candidate gene analysis, transcriptomics and pharmacological manipulations, we identified the Notch and Wnt pathways as cell-extrinsic pathways regulated by tet2 and tet3 activity during RGC differentiation and morphogenesis. Transcriptome analyses also revealed the ectopic expression of non-retinal genes in tet2-/-;tet3-/- mutant retinae, and this correlated with locus-specific reduction in 5hmC. These data provide the first evidence that Tet-dependent regulation of 5hmC formation is critical for retinal neurogenesis, and highlight an additional layer of complexity in the progression from retinal progenitor cell to differentiated retinal neuron during development of the vertebrate retina.
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Affiliation(s)
- Pawat Seritrakul
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States of America
- Departments of Ophthalmology, and Developmental Biology, The Louis J. Fox Center for Vision Restoration, The McGowan Institute for Regenerative Medicine, The University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Jeffrey M. Gross
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States of America
- Departments of Ophthalmology, and Developmental Biology, The Louis J. Fox Center for Vision Restoration, The McGowan Institute for Regenerative Medicine, The University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
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45
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Nguyen AT, Prado MA, Schmidt PJ, Sendamarai AK, Wilson-Grady JT, Min M, Campagna DR, Tian G, Shi Y, Dederer V, Kawan M, Kuehnle N, Paulo JA, Yao Y, Weiss MJ, Justice MJ, Gygi SP, Fleming MD, Finley D. UBE2O remodels the proteome during terminal erythroid differentiation. Science 2017; 357:eaan0218. [PMID: 28774900 PMCID: PMC5812729 DOI: 10.1126/science.aan0218] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/08/2017] [Indexed: 12/13/2022]
Abstract
During terminal differentiation, the global protein complement is remodeled, as epitomized by erythrocytes, whose cytosol is ~98% globin. The erythroid proteome undergoes a rapid transition at the reticulocyte stage; however, the mechanisms driving programmed elimination of preexisting cytosolic proteins are unclear. We found that a mutation in the murine Ube2o gene, which encodes a ubiquitin-conjugating enzyme induced during erythropoiesis, results in anemia. Proteomic analysis suggested that UBE2O is a broad-spectrum ubiquitinating enzyme that remodels the erythroid proteome. In particular, ribosome elimination, a hallmark of reticulocyte differentiation, was defective in Ube2o-/- mutants. UBE2O recognized ribosomal proteins and other substrates directly, targeting them to proteasomes for degradation. Thus, in reticulocytes, the induction of ubiquitinating factors may drive the transition from a complex to a simple proteome.
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Affiliation(s)
- Anthony T Nguyen
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Paul J Schmidt
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Anoop K Sendamarai
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | | | - Mingwei Min
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Dean R Campagna
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Geng Tian
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yuan Shi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Verena Dederer
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mona Kawan
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Nathalie Kuehnle
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yu Yao
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Monica J Justice
- Genetics and Genome Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario M5G 0A4, Canada
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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46
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Molecular cloning of chicken TET family genes and role of chicken TET1 in erythropoiesis. Biochem Biophys Res Commun 2017. [DOI: 10.1016/j.bbrc.2017.06.113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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47
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Ma EG, Bai YF, Cao W, Cao Y, Huang YG, Cheng HC, An RH. Cytosine 5-hydroxymethylation regulates VHL gene expression in renal clear cell carcinoma. Oncotarget 2017; 8:63780-63787. [PMID: 28969028 PMCID: PMC5609960 DOI: 10.18632/oncotarget.19070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/23/2017] [Indexed: 11/25/2022] Open
Abstract
Cytosine5-hyxymethylation (5hmC)which is a new epigenetic modification form plays important roles in the development and progression of tumors. In the present study, we observed that levels of 5hmC in the promoter region of Von Hippel-Lindau (VHL) were lower in 97 samples of renal clear cell carcinoma tissue than in matched adjacent benign tissues. Moreover, when the cancer tissue samples were divided based on pathological staging, VHL expression and the level of 5hmC in the VHL promoter were both lower in pathological grade III tumors than in grades I or II. Correspondingly, expression of TET1, which catalyzes the formation of 5hmC, was also lower in grade III renal clear cell carcinomas than in grade I or II disease. These findings suggest the 5hmC level on VHL is a key determinant of the gene's expression and may participate in the occurrence and development of renal clear cell carcinoma. Thus the 5hmC level may be a useful indicator for early diagnosis and appropriate treatment of renal clear cell carcinoma.
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Affiliation(s)
- En-Guang Ma
- The Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,The Department of Urology Surgery, The First Hospital of Harbin, Harbin, China
| | - Yu-Feng Bai
- The Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wei Cao
- The Department of Urinary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yan Cao
- The Department of Urology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yong-Gang Huang
- The Department of Urology Surgery, The First Hospital of Harbin, Harbin, China
| | - Huan-Chen Cheng
- Institute of Harbin Hematology & Oncology, The First Hospital of Harbin, Harbin, China
| | - Rui-Hua An
- The Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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48
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Shih AH, Meydan C, Shank K, Garrett-Bakelman FE, Ward PS, Intlekofer AM, Nazir A, Stein EM, Knapp K, Glass J, Travins J, Straley K, Gliser C, Mason CE, Yen K, Thompson CB, Melnick A, Levine RL. Combination Targeted Therapy to Disrupt Aberrant Oncogenic Signaling and Reverse Epigenetic Dysfunction in IDH2- and TET2-Mutant Acute Myeloid Leukemia. Cancer Discov 2017; 7:494-505. [PMID: 28193779 PMCID: PMC5413413 DOI: 10.1158/2159-8290.cd-16-1049] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 02/02/2017] [Accepted: 02/09/2017] [Indexed: 11/16/2022]
Abstract
Genomic studies in acute myeloid leukemias (AML) have identified mutations that drive altered DNA methylation, including TET2 and IDH2 Here, we show that models of AML resulting from TET2 or IDH2 mutations combined with FLT3ITD mutations are sensitive to 5-azacytidine or to the IDH2 inhibitor AG-221, respectively. 5-azacytidine and AG-221 treatment induced an attenuation of aberrant DNA methylation and transcriptional output and resulted in a reduction in leukemic blasts consistent with antileukemic activity. These therapeutic benefits were associated with restoration of leukemic cell differentiation, and the normalization of hematopoiesis was derived from mutant cells. By contrast, combining AG-221 or 5-azacytidine with FLT3 inhibition resulted in a reduction in mutant allele burden, progressive recovery of normal hematopoiesis from non-mutant stem-progenitor cells, and reversal of dysregulated DNA methylation and transcriptional output. Together, our studies suggest combined targeting of signaling and epigenetic pathways can increase therapeutic response in AML.Significance: AMLs with mutations in TET2 or IDH2 are sensitive to epigenetic therapy through inhibition of DNA methyltransferase activity by 5-azacytidine or inhibition of mutant IDH2 through AG-221. These inhibitors induce a differentiation response and can be used to inform mechanism-based combination therapy. Cancer Discov; 7(5); 494-505. ©2017 AACR.See related commentary by Thomas and Majeti, p. 459See related article by Yen et al., p. 478This article is highlighted in the In This Issue feature, p. 443.
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Affiliation(s)
- Alan H Shih
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cem Meydan
- Department of Medicine/Hematology-Oncology and Department of Pharmacology, Weill Cornell Medical College, New York, New York
- Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | - Kaitlyn Shank
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Francine E Garrett-Bakelman
- Department of Medicine/Hematology-Oncology and Department of Pharmacology, Weill Cornell Medical College, New York, New York
| | - Patrick S Ward
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew M Intlekofer
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Abbas Nazir
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eytan M Stein
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kristina Knapp
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jacob Glass
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine/Hematology-Oncology and Department of Pharmacology, Weill Cornell Medical College, New York, New York
| | | | - Kim Straley
- Agios Pharmaceuticals, Cambridge, Massachusetts
| | | | - Christopher E Mason
- Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | | | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ari Melnick
- Department of Medicine/Hematology-Oncology and Department of Pharmacology, Weill Cornell Medical College, New York, New York.
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
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49
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An J, Rao A, Ko M. TET family dioxygenases and DNA demethylation in stem cells and cancers. Exp Mol Med 2017; 49:e323. [PMID: 28450733 PMCID: PMC6130217 DOI: 10.1038/emm.2017.5] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 12/15/2022] Open
Abstract
The methylation of cytosine and subsequent oxidation constitutes a fundamental epigenetic modification in mammalian genomes, and its abnormalities are intimately coupled to various pathogenic processes including cancer development. Enzymes of the Ten–eleven translocation (TET) family catalyze the stepwise oxidation of 5-methylcytosine in DNA to 5-hydroxymethylcytosine and further oxidation products. These oxidized 5-methylcytosine derivatives represent intermediates in the reversal of cytosine methylation, and also serve as stable epigenetic modifications that exert distinctive regulatory roles. It is becoming increasingly obvious that TET proteins and their catalytic products are key regulators of embryonic development, stem cell functions and lineage specification. Over the past several years, the function of TET proteins as a barrier between normal and malignant states has been extensively investigated. Dysregulation of TET protein expression or function is commonly observed in a wide range of cancers. Notably, TET loss-of-function is causally related to the onset and progression of hematologic malignancy in vivo. In this review, we focus on recent advances in the mechanistic understanding of DNA methylation–demethylation dynamics, and their potential regulatory functions in cellular differentiation and oncogenic transformation.
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Affiliation(s)
- Jungeun An
- Department of Biological Sciences, Chonbuk National University, Jeonju, Korea
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA.,Department of Pharmacology and Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Myunggon Ko
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, Korea.,School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
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50
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Abstract
Chronic Myelomonocytic Leukemia is a chronic myeloid neoplasm occurring mostly in the elderly with overlapping features of myelodysplastic syndromes (MDS) and myeloproliferative neoplasms (MPN) characterized by chronic monocytosis. Recent progresses in the molecular and cellular pathogenesis of CMML have stirred a renewed interest in this clinically heterogeneous disorder. Here, we review the recent progresses in the biology of CMML and how it affects its current and future clinical management.
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