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Kimura S, Seki M, Kawai T, Goto H, Yoshida K, Isobe T, Sekiguchi M, Watanabe K, Kubota Y, Nannya Y, Ueno H, Shiozawa Y, Suzuki H, Shiraishi Y, Ohki K, Kato M, Koh K, Kobayashi R, Deguchi T, Hashii Y, Imamura T, Sato A, Kiyokawa N, Manabe A, Sanada M, Mansour MR, Ohara A, Horibe K, Kobayashi M, Oka A, Hayashi Y, Miyano S, Hata K, Ogawa S, Takita J. DNA methylation-based classification reveals difference between pediatric T-cell acute lymphoblastic leukemia and normal thymocytes. Leukemia 2019; 34:1163-1168. [PMID: 31732719 DOI: 10.1038/s41375-019-0626-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 10/17/2019] [Accepted: 11/03/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Shunsuke Kimura
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan
| | - Masafumi Seki
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hiroaki Goto
- Division of Hematology/Oncology and Regenerative Medicine, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomoya Isobe
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masahiro Sekiguchi
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kentaro Watanabe
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuo Kubota
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroo Ueno
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Pediatrics, Kyoto University, Kyoto, Japan
| | - Yusuke Shiozawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiromichi Suzuki
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Kentaro Ohki
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Ryoji Kobayashi
- Department of Pediatrics, Sapporo Hokuyu Hospital, Sapporo, Japan
| | - Takao Deguchi
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Yoshiko Hashii
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Toshihiko Imamura
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan
| | - Atsushi Sato
- Department of Hematology and Oncology, Miyagi Children's Hospital, Sendai, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Atsushi Manabe
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Masashi Sanada
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Marc R Mansour
- Department of Haematology, University College London Cancer Institute, London, UK
| | - Akira Ohara
- Department of Pediatrics, Toho University, Tokyo, Japan
| | - Keizo Horibe
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Masao Kobayashi
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuhide Hayashi
- Institute of Physiology and Medicine, Jobu University, Takasaki, Japan
| | - Satoru Miyano
- Human Genome Center Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. .,Department of Pediatrics, Kyoto University, Kyoto, Japan.
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3
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Rodríguez-Zavala JS, Calleja LF, Moreno-Sánchez R, Yoval-Sánchez B. Role of Aldehyde Dehydrogenases in Physiopathological Processes. Chem Res Toxicol 2019; 32:405-420. [PMID: 30628442 DOI: 10.1021/acs.chemrestox.8b00256] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Many different diseases are associated with oxidative stress. One of the main consequences of oxidative stress at the cellular level is lipid peroxidation, from which toxic aldehydes may be generated. Below their toxicity thresholds, some aldehydes are involved in signaling processes, while others are intermediaries in the metabolism of lipids, amino acids, neurotransmitters, and carbohydrates. Some aldehydes ubiquitously distributed in the environment, such as acrolein or formaldehyde, are extremely toxic to the cell. On the other hand, aldehyde dehydrogenases (ALDHs) are able to detoxify a wide variety of aldehydes to their corresponding carboxylic acids, thus helping to protect from oxidative stress. ALDHs are located in different subcellular compartments such as cytosol, mitochondria, nucleus, and endoplasmic reticulum. The aim of this review is to analyze, and highlight, the role of different ALDH isoforms in the detoxification of aldehydes generated in processes that involve high levels of oxidative stress. The ALDH physiological relevance becomes evident by the observation that their expression and activity are enhanced in different pathologies that involve oxidative stress such as neurodegenerative disorders, cardiopathies, atherosclerosis, and cancer as well as inflammatory processes. Furthermore, ALDH mutations bring about several disorders in the cell. Thus, understanding the mechanisms by which these enzymes participate in diverse cellular processes may lead to better contend with the damage caused by toxic aldehydes in different pathologies by designing modulators and/or protocols to modify their activity or expression.
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Affiliation(s)
| | | | - Rafael Moreno-Sánchez
- Departamento de Bioquímica , Instituto Nacional de Cardiología , México 14080 , México
| | - Belem Yoval-Sánchez
- Departamento de Bioquímica , Instituto Nacional de Cardiología , México 14080 , México
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4
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De Ford C, Penchalaiah K, Kreft A, Humar M, Heydenreuter W, Kangani M, Sieber SA, Tietze LF, Merfort I. Bifunctional Duocarmycin Analogues as Inhibitors of Protein Tyrosine Kinases. JOURNAL OF NATURAL PRODUCTS 2019; 82:16-26. [PMID: 30620194 DOI: 10.1021/acs.jnatprod.8b00233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bifunctional duocarmycin analogues are highly cytotoxic compounds that have been shown to be irreversible aldehyde dehydrogenase 1 inhibitors. Interestingly, cells with low aldehyde dehydrogenase 1 expression are also sensitive to bifunctional duocarmycin analogues, suggesting the existence of another target. Through in silico approaches, including principal component analysis, structure-similarity search, and docking calculations, protein tyrosine kinases, and especially the vascular endothelial growth factor receptor 2 (VEGFR-2), were predicted as targets of bifunctional duocarmycin analogues. Biochemical validation was performed in vitro, confirming the in silico results. Structural optimization was performed to mainly target VEGFR-2, but not aldehyde dehydrogenase 1. The optimized bifunctional duocarmycin analogue was synthesized. In vitro assays revealed this bifunctional duocarmycin analogue as a strong inhibitor of VEGFR-2, with low residual aldehyde dehydrogenase 1 activity. Altogether, studies revealed bifunctional duocarmycin analogues as a new class of naturally derived compounds that express a very high cytotoxicity to cancer cells overexpressing aldehyde dehydrogenase 1 as well as VEGFR-2.
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Affiliation(s)
- Christian De Ford
- Department of Pharmaceutical Biology and Biotechnology , Albert Ludwigs University Freiburg , Stefan-Meier-Strasse 19 , D-79104 Freiburg , Germany
- Spemann Graduate School of Biology and Medicine (SGBM) , Albert Ludwigs University Freiburg , Albertstrasse 19a , 79104 Freiburg , Germany
| | - Kamala Penchalaiah
- Institute of Organic and Biomolecular Chemistry , Georg-August University , Tammannstrasse 2 , 37077 Göttingen , Germany
| | - Alexander Kreft
- Institute of Organic and Biomolecular Chemistry , Georg-August University , Tammannstrasse 2 , 37077 Göttingen , Germany
| | - Matjaz Humar
- Department of Pharmaceutical Biology and Biotechnology , Albert Ludwigs University Freiburg , Stefan-Meier-Strasse 19 , D-79104 Freiburg , Germany
| | - Wolfgang Heydenreuter
- Institute of Organic Chemistry II , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
| | - Mehrnoush Kangani
- Institute of Organic and Biomolecular Chemistry , Georg-August University , Tammannstrasse 2 , 37077 Göttingen , Germany
| | - Stephan A Sieber
- Institute of Organic Chemistry II , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
| | - Lutz F Tietze
- Institute of Organic and Biomolecular Chemistry , Georg-August University , Tammannstrasse 2 , 37077 Göttingen , Germany
| | - Irmgard Merfort
- Department of Pharmaceutical Biology and Biotechnology , Albert Ludwigs University Freiburg , Stefan-Meier-Strasse 19 , D-79104 Freiburg , Germany
- Spemann Graduate School of Biology and Medicine (SGBM) , Albert Ludwigs University Freiburg , Albertstrasse 19a , 79104 Freiburg , Germany
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5
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Neuroevolution as a tool for microarray gene expression pattern identification in cancer research. J Biomed Inform 2018; 89:122-133. [PMID: 30521855 DOI: 10.1016/j.jbi.2018.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/12/2018] [Accepted: 11/27/2018] [Indexed: 12/16/2022]
Abstract
Microarrays are still one of the major techniques employed to study cancer biology. However, the identification of expression patterns from microarray datasets is still a significant challenge to overcome. In this work, a new approach using Neuroevolution, a machine learning field that combines neural networks and evolutionary computation, provides aid in this challenge by simultaneously classifying microarray data and selecting the subset of more relevant genes. The main algorithm, FS-NEAT, was adapted by the addition of new structural operators designed for this high dimensional data. In addition, a rigorous filtering and preprocessing protocol was employed to select quality microarray datasets for the proposed method, selecting 13 datasets from three different cancer types. The results show that Neuroevolution was able to successfully classify microarray samples when compared with other methods in the literature, while also finding subsets of genes that can be generalized for other algorithms and carry relevant biological information. This approach detected 177 genes, and 82 were validated as already being associated to their respective cancer types and 44 were associated to other types of cancer, becoming potential targets to be explored as cancer biomarkers. Five long non-coding RNAs were also detected, from which four don't have described functions yet. The expression patterns found are intrinsically related to extracellular matrix, exosomes and cell proliferation. The results obtained in this work could aid in unraveling the molecular mechanisms underlying the tumoral process and describe new potential targets to be explored in future works.
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6
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Tan TK, Zhang C, Sanda T. Oncogenic transcriptional program driven by TAL1 in T-cell acute lymphoblastic leukemia. Int J Hematol 2018; 109:5-17. [PMID: 30145780 DOI: 10.1007/s12185-018-2518-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/21/2018] [Accepted: 08/06/2018] [Indexed: 12/12/2022]
Abstract
TAL1/SCL is a prime example of an oncogenic transcription factor that is abnormally expressed in acute leukemia due to the replacement of regulator elements. This gene has also been recognized as an essential regulator of hematopoiesis. TAL1 expression is strictly regulated in a lineage- and stage-specific manner. Such precise control is crucial for the switching of the transcriptional program. The misexpression of TAL1 in immature thymocytes leads to a widespread series of orchestrated downstream events that affect several different cellular machineries, resulting in a lethal consequence, namely T-cell acute lymphoblastic leukemia (T-ALL). In this article, we will discuss the transcriptional regulatory network and downstream target genes, including protein-coding genes and non-coding RNAs, controlled by TAL1 in normal hematopoiesis and T-cell leukemogenesis.
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Affiliation(s)
- Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, #12-01, Singapore, 117599, Singapore
| | - Chujing Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, #12-01, Singapore, 117599, Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, #12-01, Singapore, 117599, Singapore. .,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
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