高深度解析を可能とする単一細胞空間オミクス技術の開発

2021 Fiscal Year Annual Research Report

• Project Area: Transomic Analysis of Metabolic Adaptation
• Project/Area Number: 20H04846
• Research Institution: Kyushu University
• Principal Investigator: 大川 恭行 九州大学, 生体防御医学研究所, 教授 (80448430)
• Project Period (FY): 2020-04-01 – 2022-03-31
• Keywords: クロマチン / トランスクリプトミクス / 組織解析

Outline of Annual Research Achievements

単一細胞オミクス技術は、トランスクリプトーム解析において、様々なデバイスや手法が開発され生体内の細胞を網羅的に解析する道を拓いた。単一細胞トランスクリプトーム解析の実現により、生体内情報である、ゲノム、エピゲノムからメタボロームに至るあらゆる細胞内の情報を1 細胞レベルで高深度に解析することを目標に多くの技術開発が進められている。一方で、過去1－2 年で、爆発的な進化を遂げているのは、これら“オーム”情報に組織や器官内の空間的位置情報を付加する空間オミクス技術である。現在開発されている技術の多くは、組織切片を用いたものであるが、単一細胞レベルでの網羅性に乏しく実用性に欠けている。そこで、本研究では、組織内の細胞の位置情報を保持した状態での1 細胞解像度の空間オミクス技術の開発を行った。まず空間情報を含めた単一細胞レベルでのトランスクリトーム解析法の確立を行い、続いてプロテオーム等の他のオームの同時解析技術を樹立させることを目指している。本技術開発では、組織切片上の細胞に空間情報を識別する固有のバーコードを付加した。その後、細胞内のトランスクリプトーム、プロテオーム等の情報を人工的なRNA に転換した。そのうえで空間バーコードとRNA に置換された細胞内情報を次世代シークエンサー(NGS)の1 回のRNAseq 解析で網羅的に解析することにより、空間・位置情報に紐づけされた単一細胞レベルの、高深度オミクス解析技術の開発を進めた。一方で、これら手法は細胞内で空間バーコードを読み取る必要があり、顕微鏡の撮像スピードが技術限界となる。そこで、今年度は網羅的なデータ取得が可能となるデバイス開発に取り組み達成した。

Research Progress Status

令和3年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和3年度が最終年度であるため、記入しない。

Research Products

• [Journal Article] Uhrf1 governs the proliferation and differentiation of muscle satellite cells. (2022)
  • Author(s): Sakai H, Sawada Y, Tokunaga N, Tanaka K, Nakagawa S, Sakakibara I, Ono Y, Fukada SI, Ohkawa Y, Kikugawa T, Saika T, Imai Y.
  • Journal Title: iScience. Volume: 25 Pages: 103928
  • DOI: 10.1016/j.isci.2022.103928.
  • Peer Reviewed / Open Access
• [Journal Article] Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant. (2022)
  • Author(s): Hirai S, Tomimatsu K, Miyawaki-Kuwakado A, Takizawa Y, Komatsu T, Tachibana T, Fukushima Y, Takeda Y, Negishi L, Kujirai T, Koyama M, Ohkawa Y, Kurumizaka H.
  • Journal Title: Nucleic Acids Res. Volume: 50 Pages: 72-91
  • DOI: 10.1093/nar/gkab1137.
  • Peer Reviewed / Open Access
• [Journal Article] Uterus-specific transcriptional regulation underlies eggshell pigment production in Japanese quail. (2022)
  • Author(s): Ishishita S, Kitahara S, Takahashi M, Iwasaki S, Tatsumoto S, Hara I, Kaneko Y, Kinoshita K, Yamaguchi K, Harada A, Ohmori Y, Ohkawa Y, Go Y, Shigenobu S, Matsuda Y, Suzuki T.
  • Journal Title: PLoS One. Volume: 17 Pages: e0265008.
  • DOI: 10.1371/journal.pone.
  • Peer Reviewed / Open Access
• [Journal Article] Direct Conversion of Human Endothelial Cells Into Liver Cancer-Forming Cells Using Nonintegrative Episomal Vectors. (2022)
  • Author(s): Goya T, Horisawa K, Udono M, Ohkawa Y, Ogawa Y, Sekiya S, Suzuki A.
  • Journal Title: Hepatol Commun. Volume: - Pages: -
  • DOI: 10.1002/hep4.1911.
  • Peer Reviewed / Open Access
• [Journal Article] Live imaging of transcription sites using an elongating RNA polymerase II-specific probe. (2022)
  • Author(s): Uchino S, Ito Y, Sato Y, Handa T, Ohkawa Y, Tokunaga M, Kimura H.
  • Journal Title: J Cell Biol. Volume: 221 Pages: e202104134
  • DOI: 10.1083/jcb.202104134.
  • Peer Reviewed / Open Access
• [Journal Article] Relayed signaling between mesenchymal progenitors and muscle stem cells ensures adaptive stem cell response to increased mechanical load. (2022)
  • Author(s): Kaneshige A, Kaji T, Zhang L, Saito H, Nakamura A, Kurosawa T, Ikemoto-Uezumi M, Tsujikawa K, Seno S, Hori M, Saito Y, Matozaki T, Maehara K, Ohkawa Y, Potente M, Watanabe S, Braun T, Uezumi A, Fukada SI.
  • Journal Title: Cell Stem Cell. Volume: 29 Pages: 265-280
  • DOI: 10.1016/j.stem.2021.11.003.
  • Peer Reviewed / Open Access
• [Journal Article] Recent advances in single-cell epigenomics. (2021)
  • Author(s): Harada A, Kimura H, Ohkawa Y.
  • Journal Title: Curr Opin Struct Biol. Volume: 71 Pages: 116-122
  • DOI: 10.1016/j.sbi.
  • Peer Reviewed / Open Access
• [Journal Article] High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq). (2021)
  • Author(s): Bartlett DA, Dileep V, Handa T, Ohkawa Y, Kimura H, Henikoff S, Gilbert DM.
  • Journal Title: J Cell Biol. Volume: 220 Pages: e202103078
  • DOI: 10.1083/jcb.202103078.
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Chromatin loading of MCM hexamers is associated with di-/tri-methylation of histone H4K20 toward S phase entry. (2021)
  • Author(s): Hayashi-Takanaka Y, Hayashi Y, Hirano Y, Miyawaki-Kuwakado A, Ohkawa Y, Obuse C, Kimura H, Haraguchi T, Hiraoka Y.
  • Journal Title: Nucleic Acids Res. Volume: 49 Pages: 12152-12166
  • DOI: 10.1093/nar/gkab1068.
  • Peer Reviewed / Open Access
• [Journal Article] Discriminative feature of cells characterizes cell populations of interest by a small subset of genes. (2021)
  • Author(s): Fujii T, Maehara K, Fujita M, Ohkawa Y.
  • Journal Title: PLoS Comput Biol. Volume: 17 Pages: e1009579
  • DOI: 10.1371/journal.pcbi.1009579.
  • Peer Reviewed / Open Access
• [Journal Article] Sex differences in metabolic pathways are regulated by Pfkfb3 and Pdk4 expression in rodent muscle. (2021)
  • Author(s): Christianto A, Baba T, Takahashi F, Inui K, Inoue M, Suyama M, Ono Y, Ohkawa Y, Morohashi KI.
  • Journal Title: Commun Biol. Volume: 4 Pages: 1264
  • DOI: 10.1038/s42003-021-02790-y.
  • Peer Reviewed / Open Access
• [Journal Article] Neural stem/precursor cells dynamically change their epigenetic landscape to differentially respond to BMP signaling for fate switching during brain development. (2021)
  • Author(s): Katada S, Takouda J, Nakagawa T, Honda M, Igarashi K, Imamura T, Ohkawa Y, Sato S, Kurumizaka H, Nakashima K.
  • Journal Title: Genes Dev. Volume: 35 Pages: 1431-1444
  • DOI: 10.1101/gad.348797.
  • Peer Reviewed / Open Access
• [Journal Article] Modeling population size independent tissue epigenomes by ChIL-seq with single thin sections. (2021)
  • Author(s): Maehara K, Tomimatsu K, Harada A, Tanaka K, Sato S, Fukuoka M, Okada S, Handa T, Kurumizaka H, Saitoh N, Kimura H, Ohkawa Y.
  • Journal Title: Mol Syst Biol. Volume: 17 Pages: e10323
  • DOI: 10.15252/msb.
  • Peer Reviewed / Open Access
• [Journal Article] Genome-wide analysis of chromatin structure changes upon MyoD binding in proliferative myoblasts during the cell cycle. (2021)
  • Author(s): Wu Q, Fujii T, Harada A, Tomimatsu K, Miyawaki-Kuwakado A, Fujita M, Maehara K, Ohkawa Y.
  • Journal Title: J Biochem. Volume: 169 Pages: 653-661
  • DOI: 10.1093/jb/mvab001.
  • Peer Reviewed / Open Access
• [Journal Article] Integrated Analysis of Transcriptome and Histone Modifications in Granulosa Cells During Ovulation in Female Mice. (2021)
  • Author(s): Shirafuta Y, Tamura I, Ohkawa Y, Maekawa R, Doi-Tanaka Y, Takagi H, Mihara Y, Shinagawa M, Taketani T, Sato S, Tamura H, Sugino N.
  • Journal Title: Endocrinology. Volume: 162 Pages: bqab128
  • DOI: 10.1210/endocr/bqab128.
  • Peer Reviewed / Open Access
• [Journal Article] An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver. (2021)
  • Author(s): Matsuzaki F, Uda S, Yamauchi Y, Matsumoto M, Soga T, Maehara K, Ohkawa Y, Nakayama KI, Kuroda S, Kubota H.
  • Journal Title: Cell Rep. Volume: 36 Pages: 109569
  • DOI: 10.1016/j.celrep.2021.
  • Peer Reviewed / Open Access
• [Journal Article] Targeted inhibition of EPAS1-driven IL-31 production by a small-molecule compound. (2021)
  • Author(s): Kamikaseda Y, Uruno T, Kunimura K, Harada A, Saiki K, Oisaki K, Sakata D, Nakahara T, Kido-Nakahara M, Kanai M, Nakamura S, Ohkawa Y, Furue M, Fukui Y.
  • Journal Title: J Allergy Clin Immunol. Volume: 148 Pages: 633-638
  • DOI: 10.1016/j.jaci.2021.03.029.
  • Peer Reviewed / Open Access
• [Journal Article] High-depth spatial transcriptome analysis by photo-isolation chemistry. (2021)
  • Author(s): Honda M, Oki S, Kimura R, Harada A, Maehara K, Tanaka K, Meno C, Ohkawa Y.
  • Journal Title: Nat Commun. Volume: 12 Pages: 4416
  • DOI: 10.1038/s41467-021-24691-8.
  • Peer Reviewed / Open Access
• [Journal Article] Transcriptome analysis of gene expression changes upon enzymatic dissociation in skeletal myoblasts. (2021)
  • Author(s): Miyawaki-Kuwakado A, Wu Q, Harada A, Tomimatsu K, Fujii T, Maehara K, Ohkawa Y.
  • Journal Title: Genes Cells. Volume: 26 Pages: 530-540
  • DOI: 10.1111/gtc.12870. Epub 2021 Jun 8.
  • Peer Reviewed / Open Access
• [Journal Article] Hoxa10 mediates positional memory to govern stem cell function in adult skeletal muscle. (2021)
  • Author(s): Yoshioka K, Nagahisa H, Miura F, Araki H, Kamei Y, Kitajima Y, Seko D, Nogami J, Tsuchiya Y, Okazaki N, Yonekura A, Ohba S, Sumita Y, Chiba K, Ito K, Asahina I, Ogawa Y, Ito T, Ohkawa Y, Ono Y.
  • Journal Title: Sci Adv. Volume: 7 Pages: eabd7924
  • DOI: 10.1126/sciadv.abd7924.
  • Peer Reviewed / Open Access
• [Journal Article] Totipotency of mouse zygotes extends to single blastomeres of embryos at the four-cell stage. (2021)
  • Author(s): Maemura M, Taketsuru H, Nakajima Y, Shao R, Kakihara A, Nogami J, Ohkawa Y, Tsukada YI.
  • Journal Title: Sci Rep. Volume: 11 Pages: 11167
  • DOI: 10.1038/s41598-021-90653-1.
  • Peer Reviewed / Open Access
• [Journal Article] Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay. (2021)
  • Author(s): Tachiwana H, Dacher M, Maehara K, Harada A, Seto Y, Katayama R, Ohkawa Y, Kimura H, Kurumizaka H, Saitoh N.
  • Journal Title: Elife Volume: 10 Pages: e66290
  • DOI: 10.7554/eLife.66290.
  • Peer Reviewed / Open Access
• [Presentation] 骨格筋再性能を制御するクロマチン構造等その破綻 (2021)
  • Author(s): 大川恭行
  • Organizer: 第94回日本生化学会大会
  • Invited
• [Presentation] 空間マルチオミクスの展開～エピゲノム, トランスクリプトームからプロテオームの空間計測の試み～ (2021)
  • Author(s): 大川恭行
  • Organizer: がん研セミナー
  • Invited
• [Presentation] Identification and Analysis of Minor Histone Variants (2021)
  • Author(s): Yasuyuki Ohkawa
  • Organizer: EMBO Workshop Physiology and function of histone variants
• [Book] Journal of Japanese Biochemical Society (2021)
  • Author(s): 原田 哲仁，大川 恭行
  • Total Pages: -
  • Publisher: 日本生化学会
• [Book] 実験医学2021年9月号 (2021)
  • Author(s): 沖 真弥、大川 恭行
  • Total Pages: 131
  • Publisher: 羊土社
  • ISBN: 978-4-7581-2547-5
• [Book] 遺伝子医学MOOK36 (2021)
  • Author(s): 富松航佑, 大川 恭行
  • Total Pages: 218
  • Publisher: 株式会社メディカルドゥ
• [Remarks] 九州大学 トランスクリプトミクス分野ホームページ
  • URL: https://tx.bioreg.kyushu-u.ac.jp/