1
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Nagase H, Watanabe T, Koshikawa N, Yamamoto S, Takenaga K, Lin J. Mitochondria: Endosymbiont bacteria DNA sequence as a target against cancer. Cancer Sci 2021; 112:4834-4843. [PMID: 34533888 PMCID: PMC8645765 DOI: 10.1111/cas.15143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 12/21/2022] Open
Abstract
As the energy factory for the cell, the mitochondrion, through its role of adenosine triphosphate production by oxidative phosphorylation, can be regarded as the guardian of well regulated cellular metabolism; the integrity of mitochondrial functions, however, is particularly vulnerable in cancer due to the lack of superstructures such as histone and lamina folds to protect the mitochondrial genome from unintended exposure, which consequently elevates risks of mutation. In cancer, mechanisms responsible for enforcing quality control surveillance for identifying and eliminating defective mitochondria are often poorly regulated, and certain uneliminated mitochondrial DNA (mtDNA) mutations and polymorphisms can be advantageous for the proliferation, progression, and metastasis of tumor cells. Such pathogenic mtDNA aberrations are likely to increase and occasionally be homoplasmic in cancer cells and, intriguingly, in normal cells in the proximity of tumor microenvironments as well. Distinct characteristics of these abnormalities in mtDNA may provide a new path for cancer therapy. Here we discuss a promising novel therapeutic strategy, using the sequence‐specific properties of pyrrole‐imidazole polyamide‐triphenylphosphonium conjugates, against cancer for clearing abnormal mtDNA by reactivating mitochondrial quality control surveillance.
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Affiliation(s)
- Hiroki Nagase
- Division of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Takayoshi Watanabe
- Division of Innovative Cancer Therapeutics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Nobuko Koshikawa
- Division of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Seigi Yamamoto
- Division of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Keizo Takenaga
- Division of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Jason Lin
- Division of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba, Japan
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2
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Malinee M, Pandian GN, Sugiyama H. Targeted epigenetic induction of mitochondrial biogenesis enhances antitumor immunity in mouse model. Cell Chem Biol 2021; 29:463-475.e6. [PMID: 34520746 DOI: 10.1016/j.chembiol.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 06/04/2021] [Accepted: 08/01/2021] [Indexed: 11/25/2022]
Abstract
Considering the potential of combinatorial therapies in overcoming existing limitations of cancer immunotherapy, there is an increasing need to identify small-molecule modulators of immune cells capable of augmenting the effect of programmed cell death protein 1 (PD-1) blockade, leading to better cancer treatment. Although epigenetic drugs showed potential in combination therapy, the lack of sequence specificity is a major concern. Here, we identify and develop a DNA-based epigenetic activator with tri-arginine vector called EnPGC-1 that can trigger the targeted induction of the peroxisome proliferator-activated receptor-gamma coactivator 1 alpha/beta (PGC-1α/β), a regulator of mitochondrial biogenesis. EnPGC-1 enhances mitochondrial activation, energy metabolism, proliferation of CD8+ T cells in vitro, and, in particular, enhances oxidative phosphorylation, a feature of long-lived memory T cells. Genome-wide gene analysis suggests that EnPGC-1 and not the control compounds can regulate T cell activation as a major biological process. EnPGC-1 also synergizes with PD-1 blockade to enhance antitumor immunity and improved host survival.
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Affiliation(s)
- Madhu Malinee
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ganesh Namasivayam Pandian
- Institute of Integrated Cell Material Sciences (iCeMS), Kyoto University of Advanced Study, Kyoto, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan.
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3
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Li X, Goobie GC, Gregory AD, Kass DJ, Zhang Y. Toll-Interacting Protein in Pulmonary Diseases. Abiding by the Goldilocks Principle. Am J Respir Cell Mol Biol 2021; 64:536-546. [PMID: 33233920 PMCID: PMC8086045 DOI: 10.1165/rcmb.2020-0470tr] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
TOLLIP (Toll-interacting protein) is an intracellular adaptor protein with diverse actions throughout the body. In a context- and cell type–specific manner, TOLLIP can function as an inhibitor of inflammation and endoplasmic-reticulum stress, an activator of autophagy, or a critical regulator of intracellular vacuole trafficking. The distinct functions of this protein have been linked to innate immune responses and lung epithelial-cell apoptosis. TOLLIP genetic variants have been associated with a variety of chronic lung diseases, including idiopathic pulmonary fibrosis, asthma, and primary graft dysfunction after lung transplantation, and with infections, such as tuberculosis, Legionella pneumonia, and respiratory viruses. TOLLIP exists in a delicate homeostatic balance, with both positive and negative effects on the trajectory of pulmonary diseases. This translational review summarizes the genetic and molecular associations that link TOLLIP to the development and progression of noninfectious and infectious pulmonary diseases. We highlight current limitations of in vitro and in vivo models in assessing the role of TOLLIP in these conditions, and we describe future approaches that will enable a more nuanced exploration of the role of TOLLIP in pulmonary conditions. There has been a surge in recent research evaluating the role of this protein in human diseases, but critical mechanistic pathways require further exploration. By understanding its biologic functions in disease-specific contexts, we will be able to determine whether TOLLIP can be therapeutically modulated to treat pulmonary diseases.
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Affiliation(s)
- Xiaoyun Li
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Gillian C Goobie
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania; and.,Clinician Investigator Program, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alyssa D Gregory
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Daniel J Kass
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Yingze Zhang
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania; and
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4
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Hidaka T, Sugiyama H. Chemical Approaches to the Development of Artificial Transcription Factors Based on Pyrrole-Imidazole Polyamides. CHEM REC 2020; 21:1374-1384. [PMID: 33332727 DOI: 10.1002/tcr.202000158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/19/2022]
Abstract
To maintain the functions of living organisms, cells have developed complex gene regulatory networks. Transcription factors have a central role in spatiotemporal control of gene expression and this has motivated us to develop artificial transcription factors that mimic their function. We found that three functions could be mimicked by applying our chemical approaches: i) efficient delivery into organelles that contain target DNA, ii) specific DNA binding to the target genomic region, and iii) regulation of gene expression by interaction with other transcription coregulators. We chose pyrrole-imidazole polyamides (PIPs), sequence-selective DNA binding molecules, as DNA binding domains, and have achieved each of the required functions by introducing other functional moieties. The developed artificial transcription factors have potential as chemical tools that can be used to artificially modulate gene expression to enable cell fate control and to correct abnormal gene regulation for therapeutic purposes.
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Affiliation(s)
- Takuya Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-ku, Kyoto, 606-8501, Japan
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5
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Lee JA, An J, Taniguchi J, Kashiwazaki G, Pandian GN, Parveen N, Kang TM, Sugiyama H, De D, Kim KK. Targeted epigenetic modulation using a DNA-based histone deacetylase inhibitor enhances cardiomyogenesis in mouse embryonic stem cells. J Cell Physiol 2020; 236:3946-3962. [PMID: 33164232 DOI: 10.1002/jcp.30140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/25/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022]
Abstract
The epigenome has an essential role in orchestrating transcriptional activation and modulating key developmental processes. Previously, we developed a library of pyrrole-imidazole polyamides (PIPs) conjugated with suberoylanilide hydroxamic acid (SAHA), a histone deacetylase (HDAC) inhibitor, for the purpose of sequence-specific modification of epigenetics. Based on the gene expression profile of SAHA-PIPs and screening studies using the α-myosin heavy chain promoter-driven reporter and SAHA-PIP library, we identified that SAHA-PIP G activates cardiac-related genes. Studies in mouse ES cells showed that SAHA-PIP G could enhance the generation of spontaneous beating cells, which is consistent with upregulation of several cardiac-related genes. Moreover, ChIP-seq results confirmed that the upregulation of cardiac-related genes is highly correlated with epigenetic activation, relevant to the sequence-specific binding of SAHA-PIP G. This proof-of-concept study demonstrating the applicability of SAHA-PIP not only improves our understanding of epigenetic alterations involved in cardiomyogenesis but also provides a novel chemical-based strategy for stem cell differentiation.
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Affiliation(s)
- Jin-A Lee
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Jieun An
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Junichi Taniguchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, Japan
| | - Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, Japan
| | - Ganesh N Pandian
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, Japan
| | - Nazia Parveen
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Tong Mook Kang
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto, Japan
| | - Debojyoti De
- Department of Biotechnology, National Institute of Technology, Durgapur, Burdwan, West Bengal, India
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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6
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Bando T, Sugiyama H. Epigenetic Drug Discovery by Artificial Genetic Switches. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science Kyoto University
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7
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Bando T, Sugiyama H. Sequence-Specific PI Polyamides Make It Possible to Regulate DNA Structure and Function. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20190311] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-ku, Kyoto 606-8501, Japan
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8
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Heinrich B, Vázquez O. 4-Methyltrityl-Protected Pyrrole and Imidazole Building Blocks for Solid Phase Synthesis of DNA-Binding Polyamides. Org Lett 2020; 22:533-536. [PMID: 31904984 DOI: 10.1021/acs.orglett.9b04288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-binding polyamides are synthetic oligomers of pyrrole/imidazole units with high specificity and affinity for double-stranded DNA. To increase their synthetic diversity, we report a mild methodology based on 4-methyltrityl (Mtt) solid phase peptide synthesis (SPPS), whose building blocks are more accessible than the standard Fmoc and Boc SPPS ones. We demonstrate the robustness of the approach by preparing and studying a hairpin with all precursors. Importantly, our strategy is orthogonal and compatible with sensitive molecules and could be readily automated.
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Affiliation(s)
- Benedikt Heinrich
- Fachbereich Chemie , Philipps-Universität Marburg , Hans-Meerwein-Straße 4 , 35043 Marburg , Germany
| | - Olalla Vázquez
- Fachbereich Chemie , Philipps-Universität Marburg , Hans-Meerwein-Straße 4 , 35043 Marburg , Germany
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9
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Vaijayanthi T, Pandian GN, Sugiyama H. Chemical Control System of Epigenetics. CHEM REC 2018; 18:1833-1853. [DOI: 10.1002/tcr.201800067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/07/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Thangavel Vaijayanthi
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho, Sakyo-ku Kyoto 606-8502, Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)Kyoto University Yoshida-Ushinomaecho, Sakyo-ku Kyoto 606-8501 Japan
| | - Hiroshi Sugiyama
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho, Sakyo-ku Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)Kyoto University Yoshida-Ushinomaecho, Sakyo-ku Kyoto 606-8501 Japan
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10
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Saha HR, Kaneda-Nakashima K, Shimosaki S, Suekane A, Sarkar B, Saito Y, Ogoh H, Nakahata S, Inoue K, Watanabe T, Nagase H, Morishita K. Suppression of GPR56 expression by pyrrole-imidazole polyamide represents a novel therapeutic drug for AML with high EVI1 expression. Sci Rep 2018; 8:13741. [PMID: 30214063 PMCID: PMC6137133 DOI: 10.1038/s41598-018-32205-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 09/04/2018] [Indexed: 12/14/2022] Open
Abstract
G protein-coupled receptor 56 (GPR56) is highly expressed in acute myeloid leukemia (AML) cells with high EVI1 expression (EVI1high AML). Because GPR56 is a transcriptional target of EVI1 and silencing of GPR56 expression induces apoptosis, we developed a novel drug to suppress GPR56 expression in EVI1high AML cells. For this purpose, we generated pyrrole-imidazole (PI) polyamides specific to GPR56 (PIP/56-1 or PIP/56-2) as nuclease-resistant novel compounds that interfere with the binding of EVI1 to the GPR56 promoter in a sequence-specific manner. Treatment of EVI1high AML cell lines (UCSD/AML1 and Kasumi-3) with PIP/56-1 or PIP/56-2 effectively suppressed GPR56 expression by inhibiting binding of EVI1 to its promoter, leading to suppression of cell growth with increased rates of apoptosis. Moreover, intravenous administration of PIP/56-1 into immunodeficient Balb/c-RJ mice subcutaneously transplanted with UCSD/AML1 cells significantly inhibited tumor growth and extended survival. Furthermore, organ infiltration by leukemia cells in immunodeficient Balb/c-RJ mice, which were intravenously transplanted using UCSD/AML1 cells, was successfully inhibited by PIP/56-1 treatment with no apparent effects on murine hematopoietic cells. In addition, PIP treatment did not inhibit colony formation of human CD34+ progenitor cells. Thus, PI polyamide targeting of GPR56 using our compound is promising, useful, and safe for the treatment of EVI1high AML.
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Affiliation(s)
- Hasi Rani Saha
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Kazuko Kaneda-Nakashima
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Shunsuke Shimosaki
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Akira Suekane
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Bidhan Sarkar
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yusuke Saito
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Honami Ogoh
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Shingo Nakahata
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Kentaro Inoue
- Department of Computer Science and Systems Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki, Japan
| | - Takayoshi Watanabe
- Division of Innovative Cancer Therapeutics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Hiroki Nagase
- Division of Innovative Cancer Therapeutics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Kazuhiro Morishita
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
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11
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Wu C, Wang W, Fang L, Su W. Programmable pyrrole-imidazole polyamides: A potent tool for DNA targeting. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.05.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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12
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Alagarswamy K, Shinohara KI, Takayanagi S, Fukuyo M, Okabe A, Rahmutulla B, Yoda N, Qin R, Shiga N, Sugiura M, Sato H, Kita K, Suzuki T, Nemoto T, Kaneda A. Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide. Oncotarget 2018; 9:29316-29335. [PMID: 30034620 PMCID: PMC6047668 DOI: 10.18632/oncotarget.25451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 05/07/2018] [Indexed: 12/26/2022] Open
Abstract
Epigenome regulates gene expression to determine cell fate, and accumulation of epigenomic aberrations leads to diseases, including cancer. NCD38 inhibits lysine-specific demethylase-1 (LSD1), a histone demethylase targeting H3K4me1 and H3K4me2, but not H3K4me3. In this study, we conjugated NCD38 with a potent small molecule called pyrrole (Py) imidazole (Im) polyamide, to analyze whether targets of the inhibitor could be regulated in a sequence-specific manner. We synthesized two conjugates using β-Ala (β) as a linker, i.e., NCD38-β-β-Py-Py-Py-Py (NCD38-β2P4) recognizing WWWWWW sequence, and NCD38-β-β-Py-Im-Py-Py (NCD38-β2PIPP) recognizing WWCGWW sequence. When RKO cells were treated with NCD38, H3K4me2 levels increased in 103 regions with significant activation of nearby genes (P = 0.03), whereas H3K4me3 levels were not obviously increased. H3K27ac levels were also increased in 458 regions with significant activation of nearby genes (P = 3 × 10-10), and these activated regions frequently included GC-rich sequences, but less frequently included AT-rich sequences (P < 1 × 10-15) or WWCGWW sequences (P = 2 × 10-13). When treated with NCD38-β2P4, 234 regions showed increased H3K27ac levels with significant activation of nearby genes (P = 2 × 10-11), including significantly fewer GC-rich sequences (P < 1 × 10-15) and significantly more AT-rich sequences (P < 1 × 10-15) compared with NCD38 treatment. When treated with NCD38-β2PIPP, 82 regions showed increased H3K27ac levels, including significantly fewer GC-rich sequences (P = 1 × 10-11) and fewer AT-rich sequences (P = 0.005), but significantly more WWCGWW sequences (P = 0.0001) compared with NCD38 treatment. These indicated that target regions of epigenomic inhibitors could be modified in a sequence-specific manner and that conjugation of Py-Im polyamides may be useful for this purpose.
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Affiliation(s)
| | - Ken-Ichi Shinohara
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Shihori Takayanagi
- Department of Pharmaceutical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Okabe
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Natsumi Yoda
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Rui Qin
- Department of Pharmaceutical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Naoki Shiga
- Department of Pharmaceutical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Masahiro Sugiura
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Hiroaki Sato
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Kazuko Kita
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Takayoshi Suzuki
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tetsuhiro Nemoto
- Department of Pharmaceutical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
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13
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Geel TM, Ruiters MHJ, Cool RH, Halby L, Voshart DC, Andrade Ruiz L, Niezen-Koning KE, Arimondo PB, Rots MG. The past and presence of gene targeting: from chemicals and DNA via proteins to RNA. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170077. [PMID: 29685979 PMCID: PMC5915719 DOI: 10.1098/rstb.2017.0077] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2017] [Indexed: 12/19/2022] Open
Abstract
The ability to target DNA specifically at any given position within the genome allows many intriguing possibilities and has inspired scientists for decades. Early gene-targeting efforts exploited chemicals or DNA oligonucleotides to interfere with the DNA at a given location in order to inactivate a gene or to correct mutations. We here describe an example towards correcting a genetic mutation underlying Pompe's disease using a nucleotide-fused nuclease (TFO-MunI). In addition to the promise of gene correction, scientists soon realized that genes could be inactivated or even re-activated without inducing potentially harmful DNA damage by targeting transcriptional modulators to a particular gene. However, it proved difficult to fuse protein effector domains to the first generation of programmable DNA-binding agents. The engineering of gene-targeting proteins (zinc finger proteins (ZFPs), transcription activator-like effectors (TALEs)) circumvented this problem. The disadvantage of protein-based gene targeting is that a fusion protein needs to be engineered for every locus. The recent introduction of CRISPR/Cas offers a flexible approach to target a (fusion) protein to the locus of interest using cheap designer RNA molecules. Many research groups now exploit this platform and the first human clinical trials have been initiated: CRISPR/Cas has kicked off a new era of gene targeting and is revolutionizing biomedical sciences.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- T M Geel
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - M H J Ruiters
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - R H Cool
- Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - L Halby
- CNRS FRE3600 ETaC, bât IBCG, 31062 Toulouse, France
| | - D C Voshart
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - L Andrade Ruiz
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - K E Niezen-Koning
- Laboratory of Metabolic Diseases, Dept Laboratory Medicine, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - P B Arimondo
- CNRS FRE3600 ETaC, bât IBCG, 31062 Toulouse, France
| | - M G Rots
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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14
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Taniguchi J, Feng Y, Pandian GN, Hashiya F, Hidaka T, Hashiya K, Park S, Bando T, Ito S, Sugiyama H. Biomimetic Artificial Epigenetic Code for Targeted Acetylation of Histones. J Am Chem Soc 2018; 140:7108-7115. [DOI: 10.1021/jacs.8b01518] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Junichi Taniguchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yihong Feng
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences, Institute for Advanced Study, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Fumitaka Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Takuya Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Shinji Ito
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences, Institute for Advanced Study, Kyoto University, Sakyo, Kyoto 606-8501, Japan
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15
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Asamitsu S, Obata S, Phan AT, Hashiya K, Bando T, Sugiyama H. Simultaneous Binding of Hybrid Molecules Constructed with Dual DNA-Binding Components to a G-Quadruplex and Its Proximal Duplex. Chemistry 2018; 24:4428-4435. [DOI: 10.1002/chem.201705945] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Sefan Asamitsu
- Department of Chemistry; Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo; Kyoto 606-8502 Japan
| | - Shunsuke Obata
- Department of Chemistry; Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo; Kyoto 606-8502 Japan
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
| | - Kaori Hashiya
- Department of Chemistry; Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo; Kyoto 606-8502 Japan
| | - Toshikazu Bando
- Department of Chemistry; Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo; Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry; Graduate School of Science Kyoto University, Kitashirakawa-Oiwakecho, Sakyo; Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Science (WPI-iCeMS); Kyoto University, Sakyo; Kyoto 606-8501 Japan
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16
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Kawamoto Y, Bando T, Sugiyama H. Sequence-specific DNA binding Pyrrole-imidazole polyamides and their applications. Bioorg Med Chem 2018; 26:1393-1411. [PMID: 29439914 DOI: 10.1016/j.bmc.2018.01.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/25/2018] [Accepted: 01/28/2018] [Indexed: 12/25/2022]
Abstract
Pyrrole-imidazole polyamides (Py-Im polyamides) are cell-permeable compounds that bind to the minor groove of double-stranded DNA in a sequence-specific manner without causing denaturation of the DNA. These compounds can be used to control gene expression and to stain specific sequences in cells. Here, we review the history, structural variations, and functional investigations of Py-Im polyamides.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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17
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Taniguchi J, Pandian GN, Hidaka T, Hashiya K, Bando T, Kim KK, Sugiyama H. A synthetic DNA-binding inhibitor of SOX2 guides human induced pluripotent stem cells to differentiate into mesoderm. Nucleic Acids Res 2017; 45:9219-9228. [PMID: 28934500 PMCID: PMC5766170 DOI: 10.1093/nar/gkx693] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 12/20/2022] Open
Abstract
Targeted differentiation of human induced pluripotent stem cells (hiPSCs) using only chemicals would have value-added clinical potential in the regeneration of complex cell types including cardiomyocytes. Despite the availability of several chemical inhibitors targeting proteins involved in signaling pathways, no bioactive synthetic DNA-binding inhibitors, targeting key cell fate-controlling genes such as SOX2, are yet available. Here, we demonstrate a novel DNA-based chemical approach to guide the differentiation of hiPSCs using pyrrole-imidazole polyamides (PIPs), which are sequence-selective DNA-binding synthetic molecules. Harnessing knowledge about key transcriptional changes during the induction of cardiomyocyte, we developed a DNA-binding inhibitor termed PIP-S2, targeting the 5'-CTTTGTT-3' and demonstrated that inhibition of SOX2-DNA interaction by PIP-S2 triggers the mesoderm induction in hiPSCs. Genome-wide gene expression analyses revealed that PIP-S2 induced mesoderm by targeted alterations in SOX2-associated gene regulatory networks. Also, employment of PIP-S2 along with a Wnt/β-catenin inhibitor successfully generated spontaneously contracting cardiomyocytes, validating our concept that DNA-binding inhibitors could drive the directed differentiation of hiPSCs. Because PIPs can be fine-tuned to target specific DNA sequences, our DNA-based approach could be expanded to target and regulate key transcription factors specifically associated with desired cell types.
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Affiliation(s)
- Junichi Taniguchi
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Materials Science (WPI-iCeMS) Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Takuya Hidaka
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Materials Science (WPI-iCeMS) Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
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18
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Yu Z, Taniguchi J, Wei Y, Pandian GN, Hashiya K, Bando T, Sugiyama H. Antiproliferative and apoptotic activities of sequence-specific histone acetyltransferase inhibitors. Eur J Med Chem 2017; 138:320-327. [DOI: 10.1016/j.ejmech.2017.06.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/30/2017] [Accepted: 06/22/2017] [Indexed: 11/29/2022]
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19
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Hidaka T, Pandian GN, Taniguchi J, Nobeyama T, Hashiya K, Bando T, Sugiyama H. Creation of a Synthetic Ligand for Mitochondrial DNA Sequence Recognition and Promoter-Specific Transcription Suppression. J Am Chem Soc 2017; 139:8444-8447. [DOI: 10.1021/jacs.7b05230] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Takuya Hidaka
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Ganesh N. Pandian
- Institute
for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Junichi Taniguchi
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Tomohiro Nobeyama
- Department
of Biotechnology, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
| | - Kaori Hashiya
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute
for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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20
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Morita K, Suzuki K, Maeda S, Matsuo A, Mitsuda Y, Tokushige C, Kashiwazaki G, Taniguchi J, Maeda R, Noura M, Hirata M, Kataoka T, Yano A, Yamada Y, Kiyose H, Tokumasu M, Matsuo H, Tanaka S, Okuno Y, Muto M, Naka K, Ito K, Kitamura T, Kaneda Y, Liu PP, Bando T, Adachi S, Sugiyama H, Kamikubo Y. Genetic regulation of the RUNX transcription factor family has antitumor effects. J Clin Invest 2017; 127:2815-2828. [PMID: 28530640 DOI: 10.1172/jci91788] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 04/06/2017] [Indexed: 12/23/2022] Open
Abstract
Runt-related transcription factor 1 (RUNX1) is generally considered to function as a tumor suppressor in the development of leukemia, but a growing body of evidence suggests that it has pro-oncogenic properties in acute myeloid leukemia (AML). Here we have demonstrated that the antileukemic effect mediated by RUNX1 depletion is highly dependent on a functional p53-mediated cell death pathway. Increased expression of other RUNX family members, including RUNX2 and RUNX3, compensated for the antitumor effect elicited by RUNX1 silencing, and simultaneous attenuation of all RUNX family members as a cluster led to a much stronger antitumor effect relative to suppression of individual RUNX members. Switching off the RUNX cluster using alkylating agent-conjugated pyrrole-imidazole (PI) polyamides, which were designed to specifically bind to consensus RUNX-binding sequences, was highly effective against AML cells and against several poor-prognosis solid tumors in a xenograft mouse model of AML without notable adverse events. Taken together, these results identify a crucial role for the RUNX cluster in the maintenance and progression of cancer cells and suggest that modulation of the RUNX cluster using the PI polyamide gene-switch technology is a potential strategy to control malignancies.
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Affiliation(s)
- Ken Morita
- Department of Human Health Sciences, Graduate School of Medicine.,Department of Pediatrics, Graduate School of Medicine, and
| | - Kensho Suzuki
- Department of Human Health Sciences, Graduate School of Medicine
| | - Shintaro Maeda
- Department of Human Health Sciences, Graduate School of Medicine
| | - Akihiko Matsuo
- Department of Human Health Sciences, Graduate School of Medicine
| | | | - Chieko Tokushige
- Department of Human Health Sciences, Graduate School of Medicine
| | - Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Junichi Taniguchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Rina Maeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Mina Noura
- Department of Human Health Sciences, Graduate School of Medicine
| | - Masahiro Hirata
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Tatsuki Kataoka
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Ayaka Yano
- Department of Human Health Sciences, Graduate School of Medicine
| | - Yoshimi Yamada
- Department of Human Health Sciences, Graduate School of Medicine
| | - Hiroki Kiyose
- Department of Human Health Sciences, Graduate School of Medicine
| | - Mayu Tokumasu
- Department of Human Health Sciences, Graduate School of Medicine
| | - Hidemasa Matsuo
- Department of Human Health Sciences, Graduate School of Medicine
| | - Sunao Tanaka
- Department of Human Health Sciences, Graduate School of Medicine
| | - Yasushi Okuno
- Department of Human Health Sciences, Graduate School of Medicine
| | - Manabu Muto
- Department of Therapeutic Oncology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kazuhito Naka
- Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Kosei Ito
- Department of Molecular Bone Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Toshio Kitamura
- Division of Cellular Therapy and Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasufumi Kaneda
- Division of Gene Therapy Science, Department of Genome Biology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Paul P Liu
- Oncogenesis and Development Section, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Souichi Adachi
- Department of Human Health Sciences, Graduate School of Medicine.,Department of Pediatrics, Graduate School of Medicine, and
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
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21
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Prachayasittikul V, Prathipati P, Pratiwi R, Phanus-Umporn C, Malik AA, Schaduangrat N, Seenprachawong K, Wongchitrat P, Supokawej A, Prachayasittikul V, Wikberg JES, Nantasenamat C. Exploring the epigenetic drug discovery landscape. Expert Opin Drug Discov 2017; 12:345-362. [PMID: 28276705 DOI: 10.1080/17460441.2017.1295954] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Epigenetic modification has been implicated in a wide range of diseases and the ability to modulate such systems is a lucrative therapeutic strategy in drug discovery. Areas covered: This article focuses on the concepts and drug discovery aspects of epigenomics. This is achieved by providing a survey of the following concepts: (i) factors influencing epigenetics, (ii) diseases arising from epigenetics, (iii) epigenetic enzymes as druggable targets along with coverage of existing FDA-approved drugs and pharmacological agents, and (iv) drug repurposing/repositioning as a means for rapid discovery of pharmacological agents targeting epigenetics. Expert opinion: Despite significant interests in targeting epigenetic modifiers as a therapeutic route, certain classes of target proteins are heavily studied while some are less characterized. Thus, such orphan target proteins are not yet druggable with limited report of active modulators. Current research points towards a great future with novel drugs directed to the many complex multifactorial diseases of humans, which are still often poorly understood and difficult to treat.
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Affiliation(s)
- Veda Prachayasittikul
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Philip Prathipati
- b National Institutes of Biomedical Innovation, Health and Nutrition , Osaka , Japan
| | - Reny Pratiwi
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Chuleeporn Phanus-Umporn
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Aijaz Ahmad Malik
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Nalini Schaduangrat
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Kanokwan Seenprachawong
- c Department of Clinical Microscopy, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Prapimpun Wongchitrat
- d Center for Research and Innovation, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Aungkura Supokawej
- c Department of Clinical Microscopy, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Virapong Prachayasittikul
- e Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Jarl E S Wikberg
- f Department of Pharmaceutical Biosciences , Uppsala University , Uppsala , Sweden
| | - Chanin Nantasenamat
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
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22
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Wei Y, Pandian GN, Zou T, Taniguchi J, Sato S, Kashiwazaki G, Vaijayanthi T, Hidaka T, Bando T, Sugiyama H. A Multi-target Small Molecule for Targeted Transcriptional Activation of Therapeutically Significant Nervous System Genes. ChemistryOpen 2016; 5:517-521. [PMID: 28032018 PMCID: PMC5167308 DOI: 10.1002/open.201600125] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Indexed: 12/17/2022] Open
Abstract
An integrated multi‐target small molecule capable of altering dynamic epigenetic and transcription programs associated with the brain and nervous system has versatile applications in the regulation of therapeutic and cell‐fate genes. Recently, we have been constructing targeted epigenetic ON switches by integrating sequence‐specific DNA binding pyrrole‐imidazole polyamides with a potent histone deacetylase inhibitor SAHA. Here, we identified a DNA‐based epigenetic ON switch termed SAHA‐L as the first‐ever multi‐target small molecule capable of inducing transcription programs associated with the human neural system and brain synapses networks in BJ human foreskin fibroblasts and 201B7‐iPS cells. Ingenuity pathway analysis showed that SAHA‐L activates the signaling of synaptic receptors like glutamate and γ‐aminobutyric acid, which are key components of autism spectrum disorders. The long‐term incubation of SAHA‐L in 201B7‐iPS cells induced morphology changes and promoted a neural progenitor state. Our finding suggests that the tunable SAHA‐L could be advanced as a cell‐type‐independent multi‐target small molecule for therapeutic and/or cell‐fate gene modulation.
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Affiliation(s)
- Yulei Wei
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Ganesh N Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Tingting Zou
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Junichi Taniguchi
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Gengo Kashiwazaki
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Thangavel Vaijayanthi
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Takuya Hidaka
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Toshikazu Bando
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto606-8502 Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
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23
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Kawamoto Y, Sasaki A, Chandran A, Hashiya K, Ide S, Bando T, Maeshima K, Sugiyama H. Targeting 24 bp within Telomere Repeat Sequences with Tandem Tetramer Pyrrole–Imidazole Polyamide Probes. J Am Chem Soc 2016; 138:14100-14107. [DOI: 10.1021/jacs.6b09023] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yusuke Kawamoto
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Asuka Sasaki
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Anandhakumar Chandran
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Satoru Ide
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Toshikazu Bando
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kazuhiro Maeshima
- Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material
Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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24
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Chandran A, Syed J, Li Y, Sato S, Bando T, Sugiyama H. Genome-Wide Assessment of the Binding Effects of Artificial Transcriptional Activators by High-Throughput Sequencing. Chembiochem 2016; 17:1905-1910. [DOI: 10.1002/cbic.201600274] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Anandhakumar Chandran
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
| | - Junetha Syed
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
| | - Yue Li
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
| | - Toshikazu Bando
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
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25
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Pandian GN, Sugiyama H. Nature-Inspired Design of Smart Biomaterials Using the Chemical Biology of Nucleic Acids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20160062] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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26
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Banerjee A, Sanyal S, Dutta S, Chakraborty P, Das PP, Jana K, Vasudevan M, Das C, Dasgupta D. The plant alkaloid chelerythrine binds to chromatin, alters H3K9Ac and modulates global gene expression. J Biomol Struct Dyn 2016; 35:1491-1499. [PMID: 27494525 DOI: 10.1080/07391102.2016.1188154] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Chelerythrine (CHL), a plant alkaloid, possesses antimicrobial, anti-inflammatory, and antitumor properties. Although CHL influences several key signal transduction pathways, its ability to interact directly with nucleoprotein complex chromatin, in eukaryotic cells has so far not been looked into. Here we have demonstrated its association with hierarchically assembled chromatin components, viz. long chromatin, chromatosome, nucleosome, chromosomal DNA, and histone H3 and the consequent effect on chromatin structure. CHL was found to repress acetylation at H3K9. It is more target-specific in terms of gene expression alteration and less cytotoxic compared to its structural analog sanguinarine.
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Affiliation(s)
- Amrita Banerjee
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
| | - Sulagna Sanyal
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
| | - Shreyasi Dutta
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
| | - Payal Chakraborty
- b Genome Informatics Research Group , Bionivid Technology Pvt Ltd. , Bangalore 560043 , India
| | - Prajna Paramita Das
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
| | - Kuladip Jana
- c Division of Molecular Medicine, Centre for Translational Animal Research , Bose Institute , P 1/12, C. I. T. Road, Scheme - VIIM, Kolkata 700054 , India
| | - Madavan Vasudevan
- b Genome Informatics Research Group , Bionivid Technology Pvt Ltd. , Bangalore 560043 , India
| | - Chandrima Das
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
| | - Dipak Dasgupta
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
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27
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Huang C, Liu Y, Rokita SE. Targeting duplex DNA with the reversible reactivity of quinone methides. Signal Transduct Target Ther 2016; 1. [PMID: 28458944 PMCID: PMC5407369 DOI: 10.1038/sigtrans.2016.9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
DNA alkylation and crosslinking remains a common and effective strategy for anticancer chemotherapy despite its infamous lack of specificity. Coupling a reactive group to a sequence-directing component has the potential to enhance target selectivity but may suffer from premature degradation or the need for an external signal for activation. Alternatively, quinone methide conjugates may be employed if they form covalent but reversible adducts with their sequence directing component. The resulting self-adducts transfer their quinone methide to a chosen target without an external signal and avoid off-target reactions by alternative intramolecular self-trapping. Efficient transfer is shown to depend on the nature of the quinone methide and the sequence-directing ligand in applications involving alkylation of duplex DNA through a triplex recognition motif. Success required an electron-rich derivative that enhanced the stability of the transient quinone methide intermediate and a polypyrimidine strand of DNA to associate with its cognate polypurine/polypyrimidine target. Related quinone methide conjugates with peptide nucleic acids were capable of quinone methide transfer from their initial precursor but not from their corresponding self-adduct. The active peptide nucleic acid derivatives were highly selective for their complementary target.
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Affiliation(s)
- Chengyun Huang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Yang Liu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Steven E Rokita
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
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28
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Roostaee A, Benoit YD, Boudjadi S, Beaulieu JF. Epigenetics in Intestinal Epithelial Cell Renewal. J Cell Physiol 2016; 231:2361-7. [PMID: 27061836 PMCID: PMC5074234 DOI: 10.1002/jcp.25401] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 04/05/2016] [Indexed: 12/15/2022]
Abstract
A controlled balance between cell proliferation and differentiation is essential to maintain normal intestinal tissue renewal and physiology. Such regulation is powered by several intracellular pathways that are translated into the establishment of specific transcription programs, which influence intestinal cell fate along the crypt-villus axis. One important check-point in this process occurs in the transit amplifying zone of the intestinal crypts where different signaling pathways and transcription factors cooperate to manage cellular proliferation and differentiation, before secretory or absorptive cell lineage terminal differentiation. However, the importance of epigenetic modifications such as histone methylation and acetylation in the regulation of these processes is still incompletely understood. There have been recent advances in identifying the impact of histone modifications and chromatin remodelers on the proliferation and differentiation of normal intestinal crypt cells. In this review we discuss recent discoveries on the role of the cellular epigenome in intestinal cell fate, development, and tissue renewal. J. Cell. Physiol. 231: 2361-2367, 2016. © 2016 The Authors. Journal of Cellular Physiology Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Alireza Roostaee
- Faculty of Medicine and Health Sciences, Laboratory of Intestinal Physiopathology, Department of Anatomy and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Yannick D Benoit
- Faculty of Health Sciences, McMaster Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Salah Boudjadi
- Faculty of Medicine and Health Sciences, Laboratory of Intestinal Physiopathology, Department of Anatomy and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-François Beaulieu
- Faculty of Medicine and Health Sciences, Laboratory of Intestinal Physiopathology, Department of Anatomy and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
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29
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Chandran A, Syed J, Taylor RD, Kashiwazaki G, Sato S, Hashiya K, Bando T, Sugiyama H. Deciphering the genomic targets of alkylating polyamide conjugates using high-throughput sequencing. Nucleic Acids Res 2016; 44:4014-24. [PMID: 27098039 PMCID: PMC4872120 DOI: 10.1093/nar/gkw283] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 04/05/2016] [Indexed: 12/17/2022] Open
Abstract
Chemically engineered small molecules targeting specific genomic sequences play an important role in drug development research. Pyrrole-imidazole polyamides (PIPs) are a group of molecules that can bind to the DNA minor-groove and can be engineered to target specific sequences. Their biological effects rely primarily on their selective DNA binding. However, the binding mechanism of PIPs at the chromatinized genome level is poorly understood. Herein, we report a method using high-throughput sequencing to identify the DNA-alkylating sites of PIP-indole-seco-CBI conjugates. High-throughput sequencing analysis of conjugate 2: showed highly similar DNA-alkylating sites on synthetic oligos (histone-free DNA) and on human genomes (chromatinized DNA context). To our knowledge, this is the first report identifying alkylation sites across genomic DNA by alkylating PIP conjugates using high-throughput sequencing.
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Affiliation(s)
- Anandhakumar Chandran
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Junetha Syed
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Rhys D Taylor
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Materials Science (iCeMS) Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo, Kyoto 606-8502, Japan Institute for Integrated Cell-Materials Science (iCeMS) Kyoto University, Sakyo, Kyoto 606-8502, Japan CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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30
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Han YW, Sugiyama H, Harada Y. The application of fluorescence-conjugated pyrrole/imidazole polyamides in the characterization of protein–DNA complex formation. Biomater Sci 2016; 4:391-9. [DOI: 10.1039/c5bm00214a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fluorescent conjugates of Py–Im polyamides are used as sequence-specific fluorescent probes and applied to the characterisation of protein–DNA complex dynamics.
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Affiliation(s)
- Yong-Woon Han
- Institute for Integrated Cell-Materials Science (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Materials Science (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501
- Japan
- Department of Chemistry
| | - Yoshie Harada
- Institute for Integrated Cell-Materials Science (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501
- Japan
- Graduate School of Biostudies
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31
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Abstract
Transcription factors (TFs) are multidomain proteins that play a critical role in orchestrating stem cell differentiation, but several limitations hinder the full potential of TF-based gene regulation. Here we report a unique strategy to emulate TFs and differentiate stem cells in a nonviral approach using an artificial, nanoparticle-based transcription factor called NanoScript. The NanoScript platform consists of a gold nanoparticle functionalized with small molecules that mimic the various domains of TFs. As a result, NanoScript mimics the function and structure of TF proteins. Specifically, NanoScript was designed to regulate muscle cell differentiation by targeting myogenic regulatory factors (MRFs), which play an important role in inducing myogenesis. This NanoScript-MRF is stable in physiological environments, localizes within the nucleus, induces differentiation of adipose-derived mesenchymal stem cells into mature muscle cells in 7 days, and is naturally excreted from induced muscle cells. As such, NanoScript represents a safe and powerful tool for applications requiring gene manipulation.
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Affiliation(s)
- Sahishnu Patel
- Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Perry T. Yin
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8501, Japan
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
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32
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Han L, Pandian GN, Chandran A, Sato S, Taniguchi J, Kashiwazaki G, Sawatani Y, Hashiya K, Bando T, Xu Y, Qian X, Sugiyama H. A Synthetic DNA-Binding Domain Guides Distinct Chromatin-Modifying Small Molecules to Activate an Identical Gene Network. Angew Chem Int Ed Engl 2015; 54:8700-3. [PMID: 26094767 DOI: 10.1002/anie.201503607] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/20/2022]
Abstract
Synthetic dual-function ligands targeting specific DNA sequences and histone-modifying enzymes were applied to achieve regulatory control over multi-gene networks in living cells. Unlike the broad array of targeting small molecules for histone deacetylases (HDACs), few modulators are known for histone acetyltransferases (HATs), which play a central role in transcriptional control. As a novel chemical approach to induce selective HAT-regulated genes, we conjugated a DNA-binding domain (DBD) "I" to N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-benzamide (CTB), an artificial HAT activator. In vitro enzyme activity assays and microarray studies were used to demonstrate that distinct functional small molecules could be transformed to have identical bioactivity when conjugated with a targeting DBD. This proof-of-concept synthetic strategy validates the switchable functions of HDACs and HATs in gene regulation and provides a molecular basis for developing versatile bioactive ligands.
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Affiliation(s)
- Le Han
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan).,Shanghai Key Laboratory of Chemical Biology, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237 (China)
| | - Ganesh N Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan)
| | - Anandhakumar Chandran
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan)
| | - Junichi Taniguchi
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Yoshito Sawatani
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Yufang Xu
- Shanghai Key Laboratory of Chemical Biology, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237 (China)
| | - Xuhong Qian
- Shanghai Key Laboratory of Chemical Biology, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237 (China)
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan). .,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan).
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33
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Han L, Pandian GN, Chandran A, Sato S, Taniguchi J, Kashiwazaki G, Sawatani Y, Hashiya K, Bando T, Xu Y, Qian X, Sugiyama H. A Synthetic DNA-Binding Domain Guides Distinct Chromatin-Modifying Small Molecules to Activate an Identical Gene Network. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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34
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Syed J, Chandran A, Pandian GN, Taniguchi J, Sato S, Hashiya K, Kashiwazaki G, Bando T, Sugiyama H. A Synthetic Transcriptional Activator of Genes Associated with the Retina in Human Dermal Fibroblasts. Chembiochem 2015; 16:1497-501. [DOI: 10.1002/cbic.201500140] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 01/30/2023]
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35
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Kawamoto Y, Sasaki A, Hashiya K, Ide S, Bando T, Maeshima K, Sugiyama H. Tandem trimer pyrrole-imidazole polyamide probes targeting 18 base pairs in human telomere sequences. Chem Sci 2015; 6:2307-2312. [PMID: 29308145 PMCID: PMC5645774 DOI: 10.1039/c4sc03755c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/20/2015] [Indexed: 01/06/2023] Open
Abstract
The novel tandem trimer pyrrole-imidazole polyamide probe targeting 18 bp in telomeric repeats visualized telomeres in human cells selectively.
The binding of molecules to specific DNA sequences is important for imaging genome DNA and for studying gene expression. Increasing the number of base pairs targeted by these molecules would provide greater specificity. N-Methylpyrrole–N-methylimidazole (Py–Im) polyamides are one type of such molecules and can bind to the minor groove of DNA in a sequence-specific manner without causing denaturation of DNA. Our recent work has demonstrated that tandem hairpin Py–Im polyamides conjugated with a fluorescent dye can be synthesized easily and can serve as new probes for studying human telomeres under mild conditions. Herein, to improve their selectivities to telomeres by targeting longer sequences, we designed and synthesized a fluorescent tandem trimer Py–Im polyamide probe, comprising three hairpins and two connecting regions (hinges). The new motif bound to 18 bp dsDNA in human telomeric repeats (TTAGGG)n, the longest sequence for specific binding reported for Py–Im polyamides. We compared the binding affinities and the abilities to discriminate mismatch, the UV-visible absorption and fluorescence spectra, and telomere staining in human cells between the tandem trimer and a previously developed tandem hairpin. We found that the tandem trimer Py–Im polyamide probe has higher ability to recognize telomeric repeats and stains telomeres in chemically fixed cells with lower background signal.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Chemistry , Graduate School of Science , Kyoto University , Kyoto 606-8502 , Sakyo , Japan . ;
| | - Asuka Sasaki
- Biological Macromolecules Laboratory , Structural Biology Center , National Institute of Genetics, and Department of Genetics , School of Life Science , Graduate University for Advanced Studies (Sokendai) , Mishima , Shizuoka 411-8540 , Japan .
| | - Kaori Hashiya
- Department of Chemistry , Graduate School of Science , Kyoto University , Kyoto 606-8502 , Sakyo , Japan . ;
| | - Satoru Ide
- Biological Macromolecules Laboratory , Structural Biology Center , National Institute of Genetics, and Department of Genetics , School of Life Science , Graduate University for Advanced Studies (Sokendai) , Mishima , Shizuoka 411-8540 , Japan .
| | - Toshikazu Bando
- Department of Chemistry , Graduate School of Science , Kyoto University , Kyoto 606-8502 , Sakyo , Japan . ;
| | - Kazuhiro Maeshima
- Biological Macromolecules Laboratory , Structural Biology Center , National Institute of Genetics, and Department of Genetics , School of Life Science , Graduate University for Advanced Studies (Sokendai) , Mishima , Shizuoka 411-8540 , Japan .
| | - Hiroshi Sugiyama
- Department of Chemistry , Graduate School of Science , Kyoto University , Kyoto 606-8502 , Sakyo , Japan . ; .,Institute for Integrated Cell-Material Science (WPI-iCeMS) , Kyoto University , Kyoto 606-8501 , Sakyo , Japan
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36
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Pandian GN, Sato S, Anandhakumar C, Taniguchi J, Takashima K, Syed J, Han L, Saha A, Bando T, Nagase H, Sugiyama H. Identification of a small molecule that turns ON the pluripotency gene circuitry in human fibroblasts. ACS Chem Biol 2014; 9:2729-36. [PMID: 25366962 DOI: 10.1021/cb500724t] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A nontransgenic approach to reprogram mouse somatic cells into induced pluripotent stem cells using only small molecules got achieved to propose a potential clinical-friendly cellular reprogramming strategy. Consequently, the screening and identification of small molecules capable of inducing pluripotency genes in human cells are increasingly a focus of research. Because cellular reprogramming is multifactorial in nature, there is a need for versatile small molecules capable of modulating the complicated gene networks associated with pluripotency. We have developed a targeting small molecule called SAHA-PIP comprising the histone deacetylase inhibitor SAHA and the sequence-specific DNA binding pyrrole-imidazole polyamides for modulating distinct gene networks. Here, we report the identification of a SAHA-PIP termed Ì that could trigger genome-wide epigenetic reprogramming and turn ON the typically conserved core pluripotency gene network. Through independent lines of evidence, we report for the first time a synthetic small molecule inducer that target and activate the OCT-3/4 regulated pluripotency genes in human dermal fibroblasts.
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Affiliation(s)
- Ganesh N. Pandian
- Institute
for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Shinsuke Sato
- Institute
for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Chandran Anandhakumar
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Junichi Taniguchi
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Kazuhiro Takashima
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Junetha Syed
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Le Han
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
- Shanghai
Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor
Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | | | | | - Hiroki Nagase
- Division
of Cancer Genetics, Department of Advanced Medical Science, Nihon University School of Medicine, Tokyo 173-8610, Japan
- Division
of Cancer Genetics, Chiba Cancer Center, Research Institute, 666-2
Nitona-cho, Chuo-ku, Chiba-shi, Chiba 260-8717, Japan
| | - Hiroshi Sugiyama
- Institute
for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
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37
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Hiroshi Sugiyama. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/anie.201403997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Patel S, Jung D, Yin PT, Carlton P, Yamamoto M, Bando T, Sugiyama H, Lee KB. NanoScript: a nanoparticle-based artificial transcription factor for effective gene regulation. ACS NANO 2014; 8:8959-67. [PMID: 25133310 PMCID: PMC4174092 DOI: 10.1021/nn501589f] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 08/18/2014] [Indexed: 05/22/2023]
Abstract
Transcription factor (TF) proteins are master regulators of transcriptional activity and gene expression. TF-based gene regulation is a promising approach for many biological applications; however, several limitations hinder the full potential of TFs. Herein, we developed an artificial, nanoparticle-based transcription factor, termed NanoScript, which is designed to mimic the structure and function of TFs. NanoScript was constructed by tethering functional peptides and small molecules called synthetic transcription factors, which mimic the individual TF domains, onto gold nanoparticles. We demonstrate that NanoScript localizes within the nucleus and initiates transcription of a reporter plasmid by over 15-fold. Moreover, NanoScript can effectively transcribe targeted genes on endogenous DNA in a nonviral manner. Because NanoScript is a functional replica of TF proteins and a tunable gene-regulating platform, it has great potential for various stem cell applications.
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Affiliation(s)
- Sahishnu Patel
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Dongju Jung
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
| | - Perry T. Yin
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Peter Carlton
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
| | - Makoto Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Address correspondence to
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39
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Hirata A, Nokihara K, Kawamoto Y, Bando T, Sasaki A, Ide S, Maeshima K, Kasama T, Sugiyama H. Structural Evaluation of Tandem Hairpin Pyrrole–Imidazole Polyamides Recognizing Human Telomeres. J Am Chem Soc 2014; 136:11546-54. [DOI: 10.1021/ja506058e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Akiyoshi Hirata
- HiPep Laboratories, Nakatsukasa-cho 486-46, Kamigyo-ku Kyoto, 602-8158, Japan
| | - Kiyoshi Nokihara
- HiPep Laboratories, Nakatsukasa-cho 486-46, Kamigyo-ku Kyoto, 602-8158, Japan
| | - Yusuke Kawamoto
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Asuka Sasaki
- Biological
Macromolecules Laboratory, Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Satoru Ide
- Biological
Macromolecules Laboratory, Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- Biological
Macromolecules Laboratory, Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Takeshi Kasama
- Research
Center for Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute
for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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40
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Saha A, Pandian GN, Sato S, Taniguchi J, Kawamoto Y, Hashiya K, Bando T, Sugiyama H. Chemical Modification of a Synthetic Small Molecule Boosts Its Biological Efficacy against Pluripotency Genes in Mouse Fibroblasts. ChemMedChem 2014; 9:2374-80. [DOI: 10.1002/cmdc.201402117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Indexed: 12/25/2022]
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41
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Hiroshi Sugiyama. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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42
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Taylor RD, Kawamoto Y, Hashiya K, Bando T, Sugiyama H. Sequence-Specific DNA Alkylation by Tandem Py-Im Polyamide Conjugates. Chem Asian J 2014; 9:2527-33. [DOI: 10.1002/asia.201402331] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Indexed: 12/13/2022]
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43
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Pandian GN, Taniguchi J, Sugiyama H. Cellular reprogramming for pancreatic β-cell regeneration: clinical potential of small molecule control. Clin Transl Med 2014; 3:6. [PMID: 24679123 PMCID: PMC3984496 DOI: 10.1186/2001-1326-3-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 03/17/2014] [Indexed: 12/14/2022] Open
Abstract
Recent scientific breakthroughs in stem cell biology suggest that a sustainable treatment approach to cure diabetes mellitus (DM) can be achieved in the near future. However, the transplantation complexities and the difficulty in obtaining the stem cells from adult cells of pancreas, liver, bone morrow and other cells is a major concern. The epoch-making strategy of transcription-factor based cellular reprogramming suggest that these barriers could be overcome, and it is possible to reprogram any cells into functional β cells. Contemporary biological and analytical techniques help us to predict the key transcription factors needed for β-cell regeneration. These β cell-specific transcription factors could be modulated with diverse reprogramming protocols. Among cellular reprogramming strategies, small molecule approach gets proclaimed to have better clinical prospects because it does not involve genetic manipulation. Several small molecules targeting certain epigenetic enzymes and/or signaling pathways have been successful in helping to induce pancreatic β-cell specification. Recently, a synthetic DNA-based small molecule triggered targeted transcriptional activation of pancreas-related genes to suggest the possibility of achieving desired cellular phenotype in a precise mode. Here, we give a brief overview of treating DM by regenerating pancreatic β-cells from various cell sources. Through a comprehensive overview of the available transcription factors, small molecules and reprogramming strategies available for pancreatic β-cell regeneration, this review compiles the current progress made towards the generation of clinically relevant insulin-producing β-cells.
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Affiliation(s)
| | | | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo, Kyoto 606-8502, Japan.
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44
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Pandian GN, Taylor RD, Junetha S, Saha A, Anandhakumar C, Vaijayanthi T, Sugiyama H. Alteration of epigenetic program to recover memory and alleviate neurodegeneration: prospects of multi-target molecules. Biomater Sci 2014; 2:1043-1056. [DOI: 10.1039/c4bm00068d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Next-generation sequence-specific small molecules modulating the epigenetic enzymes (DNMT/HDAC) and signalling factors can precisely turn ‘ON’ the multi-gene network in a neural cell.
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Affiliation(s)
- Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences (iCeMS)
- Kyoto University
- Kyoto 606-8502, Japan
| | - Rhys D. Taylor
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501, Japan
| | - Syed Junetha
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501, Japan
| | - Abhijit Saha
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501, Japan
| | - Chandran Anandhakumar
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501, Japan
| | - Thangavel Vaijayanthi
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (iCeMS)
- Kyoto University
- Kyoto 606-8502, Japan
- Department of Chemistry
- Graduate School of Science
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