Development of a novel epigenome editing technology using the expanded TREE system and its application in cancer study

• Project/Area Number: 19K16111
• Research Category: Grant-in-Aid for Early-Career Scientists
• Allocation Type: Multi-year Fund
• Review Section: Basic Section 43060:System genome science-related
• Research Institution: Hiroshima University
• Principal Investigator: Sakuma Tetsushi 広島大学, 統合生命科学研究科(理), 准教授 (90711143)
• Project Period (FY): 2019-04-01 – 2021-03-31
• Project Status: Completed (Fiscal Year 2020)
• Budget Amount: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2020: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2019: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
• Keywords: CRISPR-Cas9 / エピゲノム編集 / がん

Outline of Research at the Start

ゲノム編集の発展技術であるエピゲノム編集は、ゲノム配列を改変することなく遺伝子の機能を制御できること、また従来不可能であった部位特異的なエピジェネティック改変を可能にすることから、ゲノム編集に劣らぬ画期的技術として注目されている。本研究では、未だ部位特異的改変が実現していないエピゲノムの編集技術を、研究代表者らが有するエフェクター集積システム“TREE”を応用することで確立する。更に、関連性が示唆されつつもメカニズムがほとんど明らかにされていない難編集性エピゲノム修飾とがんとの関連性を、確立したシステムを用いて解明する。

Outline of Final Research Achievements

In this study, we established a comprehensive platform named "EARTH collection", where the optimal system can be selected depending on a cell type and a gene locus by expanding TREE, the unique transcriptional activation system reported in 2018. During the process of systems development, we found that the trends of transcriptional activation is similar in various target regions as long as their target gene is the same, although the optimal system is diverse depending on the target genes. In addition, By comparing the effect of transcriptional activation in multiple cell lines and in multiple gene loci using the EARTH collection and the conventional systems, we demonstrated that at least one of the systems in the EARTH collection showed statistically significant superiority against the conventional systems in all tested cases.

Academic Significance and Societal Importance of the Research Achievements

研究成果の概要欄に記載したように、各細胞株・各遺伝子座における転写活性化の最適システムは一様ではなく、あらゆるケースで最大限の効果を得るためには、多様なシステム群を整備しつつオーダーメイドでシステムを選択する必要があることが明らかとなった。本研究において確立したEARTHコレクションは、従来の択一的システムと異なり、オーダーメイド型プラットフォームとして世界でも類を見ないものである。更に本システムは、転写活性化のみならず、転写の抑制、エピゲノム編集、塩基編集、ライブイメージングなどさまざまな用途への応用が見込まれ、高活性かつ高汎用性技術として世界中で広く利用されることが期待される。

Research Products

• [Journal Article] Pou5f3.3 is involved in establishment and maintenance of hematopoietic cells during Xenopus development (2021)
  • Author(s): Ezawa Minami、Kouno Fumika、Kubo Hideo、Sakuma Tetsushi、Yamamoto Takashi、Kinoshita Tsutomu
  • Journal Title: Tissue and Cell Volume: 72 Pages: 101531-101531
  • DOI: 10.1016/j.tice.2021.101531
  • Peer Reviewed
• [Journal Article] Murine neonatal ketogenesis preserves mitochondrial energetics by preventing protein hyperacetylation (2021)
  • Author(s): Arima Yuichiro、Nakagawa Yoshiko、Takeo Toru、Ishida Toshifumi、Yamada Toshihiro、et al.
  • Journal Title: Nature Metabolism Volume: 3 Issue: 2 Pages: 196-210
  • DOI: 10.1038/s42255-021-00342-6
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] CRISPR-Cas9 editing of non-coding genomic loci as a means of controlling gene expression in the sea urchin. (2021)
  • Author(s): Pieplow A, Dastaw M, Sakuma T, Sakamoto N, Yamamoto T, Yajima M, Oulhen N, Wessel GM
  • Journal Title: Developmental Biology Volume: 472 Pages: 85-97
  • DOI: 10.1016/j.ydbio.2021.01.003
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Improvement of fatty acid productivity of thraustochytrid, Aurantiochytrium sp. by genome editing (2021)
  • Author(s): K. Watanabe, C.M.T. Perez, T. Kitahori, K. Hata, M. Aoi, H. Takahashi, T. Sakuma, Y. Okamura, Y. Nakashimada, T. Yamamoto, K. Matsuyama, S. Mayuzumi, T. Aki
  • Journal Title: J. Biosci. Bioeng. Volume: 131 Issue: 4 Pages: 373-380
  • DOI: 10.1016/j.jbiosc.2020.11.013
  • NAID: 40022545824
  • Peer Reviewed
• [Journal Article] Down syndrome-related transient abnormal myelopoiesis is attributed to a specific erythro-megakaryocytic subpopulation with GATA1 mutation. (2021)
  • Author(s): Nishinaka-Arai Y, Niwa A, Matsuo S, Kazuki Y, Yakura Y, Hiroma T, Toki T, Sakuma T, Yamamoto T, Ito E, Oshimura M, Nakahata T, Saito MK.
  • Journal Title: Haematologica Volume: 106(2) Issue: 2 Pages: 635-640
  • DOI: 10.3324/haematol.2019.242693
  • Peer Reviewed / Open Access
• [Journal Article] TALEN‐mediated generation of Nkx3.1 knockout rat model (2020)
  • Author(s): Lee Ji Min、Kim Ukjin、Yang Hyokyung、Ryu Bokyeong、Kim Jin、Sakuma Tetsushi、Yamamoto Takashi、Park Jae‐Hak
  • Journal Title: The Prostate Volume: 81 Issue: 3 Pages: 182-193
  • DOI: 10.1002/pros.24095
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Efficient and multiplexable genome editing using Platinum TALENs in oleaginous microalga, Nannochloropsis oceanica NIES‐2145 (2020)
  • Author(s): Kurita T, Moroi K, Iwai M, Okazaki K, Shimizu S, Nomura S, Saito F, Maeda S, Takami A, Sakamoto A, Ohta H, Sakuma T, Yamamoto T
  • Journal Title: Genes to Cells Volume: 25 Issue: 10 Pages: 695-702
  • DOI: 10.1111/gtc.12805
  • Peer Reviewed / Open Access
• [Journal Article] ARHGAP10, which encodes Rho GTPase-activating protein 10, is a novel gene for schizophrenia risk (2020)
  • Author(s): Mariko Sekiguchi, Akiko Kodama,... Emiko Shishido,... Daisuke Mori, Norio Ozaki
  • Journal Title: Translational psychiatry Volume: 10 Issue: 1 Pages: 1-15
  • DOI: 10.1038/s41398-020-00917-z
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Various strategies of effector accumulation to improve the efficiency of genome editing and derivative methodologies (2020)
  • Author(s): Kunii A, Yamamoto T, Sakuma T
  • Journal Title: In Vitro Cellular & Developmental Biology - Animal Volume: 56 Issue: 5 Pages: 359-366
  • DOI: 10.1007/s11626-020-00469-y
  • Peer Reviewed
• [Journal Article] Six1 is required for signaling center formation and labial-lingual asymmetry in developing lower incisors. (2020)
  • Author(s): Takahashi Masanori、Ikeda Keiko、Ohmuraya Masaki、Nakagawa Yoshiko、Sakuma Tetsushi、Yamamoto Takashi、Kawakami Kiyoshi
  • Journal Title: Developmental Dynamics Volume: 0 Issue: 9 Pages: 0-0
  • DOI: 10.1002/dvdy.174
  • Peer Reviewed
• [Journal Article] GABA-Induced GnRH Release Triggers Chordate Metamorphosis. (2020)
  • Author(s): Hozumi A, Matsunobu S, Mita K, Treen N, Sugihara T, Horie T, Sakuma T, Yamamoto T, Shiraishi A, Hamada M, Satoh N, Sakurai K, Satake H, Sasakura Y.
  • Journal Title: Current Biology Volume: 30 Issue: 8 Pages: 1555-1561
  • DOI: 10.1016/j.cub.2020.02.003
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Pathological characteristics of <i>Ccdc85c</i> knockout rats: a rat model of genetic hydrocephalus (2020)
  • Author(s): Konishi S, Tanaka N, Mashimo T, Yamamoto T, Sakuma T, Kaneko T, Tanaka M, Izawa T, Yamate J, Kuwamura M
  • Journal Title: Experimental Animals Volume: 69 Issue: 1 Pages: 26-33
  • DOI: 10.1538/expanim.19-0005
  • NAID: 130007791587
  • ISSN: 0007-5124, 1341-1357, 1881-7122
  • Peer Reviewed / Open Access
• [Journal Article] Hox13 is essential for formation of a sensory organ at the terminal end of the sperm duct in Ciona (2020)
  • Author(s): Tajima Y, Hozumi A, Yoshida K, Treen N, Sakuma T, Yamamoto T, Sasakura Y
  • Journal Title: Developmental Biology Volume: 458 Issue: 1 Pages: 120-131
  • DOI: 10.1016/j.ydbio.2019.10.028
  • Peer Reviewed
• [Journal Article] Reinvestigation of Disulfide-bonded Oligomeric Forms of the Unfolded Protein Response Transducer ATF6 (2020)
  • Author(s): Koba Hibiki、Jin Shengyu、Imada Nanami、Ishikawa Tokiro、Ninagawa Satoshi、Okada Tetsuya、Sakuma Tetsushi、Yamamoto Takashi、Mori Kazutoshi
  • Journal Title: Cell Structure and Function Volume: 45 Issue: 1 Pages: 9-21
  • DOI: 10.1247/csf.19030
  • NAID: 130007792116
  • ISSN: 0386-7196, 1347-3700
  • Peer Reviewed / Open Access
• [Journal Article] Development of a protein-based system for transient epigenetic repression of immune checkpoint molecule and enhancement of antitumour activity of natural killer cells (2020)
  • Author(s): Teratake Y, Takashina T, Iijima K, Sakuma T, Yamamoto T, Ishizaka Y
  • Journal Title: British Journal of Cancer Volume: 122 Issue: 6 Pages: 823-834
  • DOI: 10.1038/s41416-019-0708-y
  • Peer Reviewed
• [Journal Article] Three multi-allelic gene pairs are responsible for self-sterility in the ascidian Ciona intestinalis (2020)
  • Author(s): Sawada H, Yamamoto K, Yamaguchi A, Yamada L, Higuchi A, Nukaya H, Fukuoka M, Sakuma T, Yamamoto T, Sasakura Y, Shirae-Kurabayashi M
  • Journal Title: Scientific Reports Volume: 10 Issue: 1 Pages: 2514-2514
  • DOI: 10.1038/s41598-020-59147-4
  • Peer Reviewed / Open Access
• [Journal Article] EDEM2 stably disulfide-bonded to TXNDC11 catalyzes the first mannose trimming step in mammalian glycoprotein ERAD (2020)
  • Author(s): George Ginto、Ninagawa Satoshi、Yagi Hirokazu、Saito Taiki、Ishikawa Tokiro、Sakuma Tetsushi、Yamamoto Takashi、Imami Koshi、Ishihama Yasushi、Kato Koichi、Okada Tetsuya、Mori Kazutoshi
  • Journal Title: eLife Volume: 9
  • DOI: 10.7554/elife.53455
  • NAID: 120006817590
  • Peer Reviewed / Open Access
• [Journal Article] Regenerating islet-derived protein (Reg)3β plays a crucial role in attenuation of ileitis and colitis in mice (2020)
  • Author(s): Shindo Ryodai、Katagiri Takaharu、Komazawa-Sakon Sachiko、Ohmuraya Masaki、Takeda Wakami、Nakagawa Yoshiko、Nakagata Naomi、Sakuma Tetsushi、Yamamoto Takashi、Nishiyama Chiharu、Nishina Takashi、Yamazaki Soh、Kameda Hideto、Nakano Hiroyasu
  • Journal Title: Biochemistry and Biophysics Reports Volume: 21 Pages: 100738-100738
  • DOI: 10.1016/j.bbrep.2020.100738
  • Peer Reviewed / Open Access
• [Journal Article] DJ-1 is indispensable for the S-nitrosylation of Parkin, which maintains function of mitochondria (2020)
  • Author(s): Ozawa K, Tsumoto H, Miura Y, Yamaguchi J, Iguchi-Ariga SMM, Sakuma T, Yamamoto T, Uchiyama Y
  • Journal Title: Scientific Reports Volume: 10 Issue: 1 Pages: 4377-4377
  • DOI: 10.1038/s41598-020-61287-6
  • Peer Reviewed / Open Access
• [Journal Article] Efficient genome engineering using Platinum TALEN in potato (2019)
  • Author(s): Yasumoto S, Umemoto N, Lee HJ, Nakayasu M, Sawai S, Sakuma T, Yamamoto T, Mizutani M, Saito K, Muranaka T
  • Journal Title: Plant Biotechnology Volume: 36 Issue: 3 Pages: 167-173
  • DOI: 10.5511/plantbiotechnology.19.0805a
  • NAID: 130007724769
  • ISSN: 1342-4580, 1347-6114
  • Year and Date: 2019-09-25
  • Peer Reviewed / Open Access
• [Journal Article] Anephrogenic phenotype induced by SALL1 gene knockout in pigs. (2019)
  • Author(s): Watanabe M, Nakano K, Uchikura A, Matsunari H, Yashima S, Umeyama K, Takayanagi S, Sakuma T, Yamamoto T, Morita S, Horii T, Hatada I, Nishinakamura R, Nakauchi H, Nagashima H.
  • Journal Title: Sci Rep. Volume: 9 Issue: 1 Pages: 8016-8016
  • DOI: 10.1038/s41598-019-44387-w
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Establishment of knockout adult sea urchins by using a CRISPR‐Cas9 system (2019)
  • Author(s): Daming Liu, Akinori Awazu, Tetsushi Sakuma, Takashi Yamamoto, Naoaki Sakamoto
  • Journal Title: Development Growth and Regeneration Volume: 61 Issue: 6 Pages: 378-388
  • DOI: 10.1111/dgd.12624
  • Peer Reviewed
• [Journal Article] Activin Is Superior to BMP7 for Efficient Maintenance of Human iPSC-Derived Nephron Progenitors. (2019)
  • Author(s): Tanigawa S, Naganuma H, Kaku Y, Era T, Sakuma T, Yamamoto T, Taguchi A and Nishinakamura R.
  • Journal Title: Stem Cell Reports Volume: 13 Issue: 2 Pages: 322-337
  • DOI: 10.1016/j.stemcr.2019.07.003
  • Peer Reviewed / Open Access
• [Journal Article] TAp63 represses transcription of MYCN/NCYM gene and its high levels of expression are associated with favorable outcome in neuroblastoma (2019)
  • Author(s): Suenaga Yusuke、Yamamoto Mami、Sakuma Tetsushi、Sasada Manabu、Fukai Fumio、Ohira Miki、Yamaguchi Yohko、Yamamoto Takashi、Ando Kiyohiro、Ozaki Toshinori、Nakagawara Akira
  • Journal Title: Biochemical and Biophysical Research Communications Volume: 518 Issue: 2 Pages: 311-318
  • DOI: 10.1016/j.bbrc.2019.08.052
  • Peer Reviewed
• [Journal Article] Targeted mutagenesis of the ryanodine receptor by Platinum TALENs causes slow swimming behaviour in Pacific bluefin tuna (Thunnus orientalis) (2019)
  • Author(s): Higuchi K, Kazeto Y, Ozaki Y, Yamaguchi T, Shimada Y, Ina Y, Soma S, Sakakura Y, Goto R, Matsubara T, Nishiki I, Iwasaki Y, Yasuike M, Nakamura Y, Matsuura A, Masuma S, Sakuma T, Yamamoto T, Masaoka T, Kobayashi T, Fujiwara A, Gen K
  • Journal Title: Scientific Reports Volume: 9 Issue: 1 Pages: 13871-13871
  • DOI: 10.1038/s41598-019-50418-3
  • Peer Reviewed / Open Access
• [Presentation] ゲノム編集技術update -2021- (2021)
  • Author(s): 佐久間 哲史
  • Organizer: 日本ゲノム編集学会会員特別セミナー
  • Invited
• [Presentation] Development of transcriptional activation platforms of cancer-related genes using Class 1 and Class 2 CRISPR systems (2020)
  • Author(s): Tetsushi Sakuma
  • Organizer: 第79回日本癌学会学術総会
  • Invited
• [Presentation] ゲノム編集技術の現状と将来 (2020)
  • Author(s): 佐久間 哲史
  • Organizer: 第79回日本癌学会学術総会
  • Invited
• [Presentation] ゲノム編集および関連技術の最新開発動向 (2019)
  • Author(s): 佐久間 哲史
  • Organizer: 第60回日本生化学会 中国・四国支部例会
  • Invited
• [Presentation] ゲノム編集および関連技術の最新開発動向 (2019)
  • Author(s): 佐久間 哲史
  • Organizer: 第442回川崎医学会講演会
  • Invited
• [Presentation] 最先端バイオテクノロジー “ゲノム編集”の研究開発動向 (2019)
  • Author(s): 佐久間 哲史
  • Organizer: 令和元年度 広島バイオフォーラム
  • Invited
• [Book] 完全版 ゲノム編集実験スタンダード (2019)
  • Author(s): 山本 卓、佐久間 哲史
  • Total Pages: 386
  • Publisher: 羊土社
  • ISBN: 475812244X
• [Remarks] 広島大学 分子遺伝学研究室
  • URL: http://www.mls.sci.hiroshima-u.ac.jp/smg/index.html