Digitalization of transcription by single allele analysis

• Project/Area Number: 17KT0108
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 特設分野
• Research Field: Constructive Systems Biology
• Research Institution: Kyoto University
• Principal Investigator: Watanabe Akira 京都大学, 医学研究科, 研究員 (60506765)
• Project Period (FY): 2017-07-18 – 2020-03-31
• Project Status: Completed (Fiscal Year 2019)
• Budget Amount: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2019: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2018: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2017: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
• Keywords: シングルセル / 遺伝子発現解析 / アリル特異的発現 / iPS細胞 / シングルセル遺伝子発現解析 / RNA-seq / 遺伝子 / 発現制御 / 発生・分化 / ゲノム

Outline of Final Research Achievements

We conducted single cell RNA-sequencing in combination with SNP genotyping to describe allelic regulation of the genes. Our analysis of human ES cells displayed allelic expression of genes on X chromosome, of which epigenetic status is closely linked to pluripotency of ES and iPS cells, and found several genes in prime-type ES cells were escaped from inactivation of the chromosome. In addition, we found differential regulation of allelic expression at single cell level for Amyotrophic lateral sclerosis (ALS) cells.

Academic Significance and Societal Importance of the Research Achievements

本研究では、転写の最小の構成単位であるアリルレベルでの解析方法を提供した。従来の細胞集団を対象とした遺伝子発現解析ではできなかったX染色体のアリル転写制御を解析したことで、多能性幹細胞における分化能を判定することが可能となった。また、疾患モデル細胞における変異アリルから転写される遺伝子の解析では、疾患細胞の不均質性が示された。これらの結果は、シングルアリルレベルでの転写解析が細胞運命の理解や疾患の発症の基本原理の理解へとつながる可能性を示している。

Research Products

• [Journal Article] A Modular Differentiation System Maps Multiple Human Kidney Lineages from Pluripotent Stem Cells. (2020)
  • Author(s): Tsujimoto H, Kasahara T, Sueta SI, Araoka T, Sakamoto S, Okada C, Mae SI, Nakajima T, Okamoto N, Taura D, Nasu M, Shimizu T, Ryosaka M, Li Z, Sone M, Ikeya M, Watanabe A, Osafune K.
  • Journal Title: Cell Rep. Volume: 31 Issue: 1 Pages: 107476-107476
  • DOI: 10.1016/j.celrep.2020.03.040
  • NAID: 120006823939
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 日常化するシングルセル遺伝子発現解析が展開する医学研究 (2019)
  • Author(s): 坂本智子, 渡辺 亮
  • Journal Title: 遺伝子医学 Volume: 9 Pages: 116-121
  • NAID: 40022087132
• [Journal Article] 医学・生物学研究に実装されるシングルセルゲノミクス (2019)
  • Author(s): 渡辺 亮
  • Journal Title: 実験医学別冊「シングルセルゲノミクス」 Volume: 37 Pages: 20-22
• [Journal Article] 単細胞レベルでの膵内分泌細胞の不均一性と機能解明 (2019)
  • Author(s): 龍岡久登，坂本智子，渡辺 亮，稲垣暢也
  • Journal Title: 実験医学別冊「シングルセルゲノミクス」 Volume: 37 Pages: 68-73
• [Journal Article] 今村恵子，渡辺 亮，井上治久 (2019)
  • Author(s): iPS細胞のシングルセル遺伝子発現解析
  • Journal Title: 実験医学別冊「シングルセルゲノミクス」 Volume: 37 Pages: 145-148
• [Journal Article] Induced Pluripotent Stem Cells and Their Use in Human Models of Disease and Development. (2019)
  • Author(s): Karagiannis P, Takahashi K, Saito M, Yoshida Y, Okita K, Watanabe A, Inoue H, Yamashita JK, Todani M, Nakagawa M, Osawa M, Yashiro Y, Yamanaka S, Osafune K.
  • Journal Title: Physiol Rev Volume: 99 Issue: 1 Pages: 78-114
  • DOI: 10.1152/physrev.00039.2017
  • Peer Reviewed
• [Journal Article] シングルセルゲノミクスによる細胞個性の解析が展開する免疫学研究. (2019)
  • Author(s): 坂本智子、渡辺亮
  • Journal Title: 臨床免疫・アレルギー科, Volume: 71 Pages: 448-454
  • NAID: 40021866266
• [Journal Article] Enhancing T cell Receptor Stability in Rejuvenated iPSC-derived T cells improves their use in cancer immunotherapy (2018)
  • Author(s): Minagawa A, Yoshikawa T, Yasukawa M, Hotta A, Kunitomo M, Iriguchi S, Takiguchi M, Kassai Y, Imai E, Yasui Y, Kawai Y, Zhang R, Uemura Y, Miyoshi H, Nakanishi M, Watanabe A, Hayashi A, Kawana K, Fujii T, Nakatsura T, Kaneko S
  • Journal Title: Cell Stem Cell Volume: 23 Issue: 6 Pages: 850-858
  • DOI: 10.1016/j.stem.2018.10.005
  • Peer Reviewed / Open Access
• [Journal Article] Integration Capacity of Human Induced Pluripotent Stem Cell-Derived Cartilage. (2018)
  • Author(s): Chen X, Yamashita A, Morioka M, Senba T, Kamatani T, Watanabe A, Kosai A, Tsumaki N.
  • Journal Title: Tissue Eng Part A, Volume: 25 Issue: 5-6 Pages: 437-445
  • DOI: 10.1089/ten.tea.2018.0133
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Generation of HIV-Resistant Macrophages from IPSCs by Using Transcriptional Gene Silencing and Promoter-Targeted RNA. (2018)
  • Author(s): Higaki K, Hirao M, Kawana-Tachikawa A, Iriguchi S, Kumagai A, Ueda N, Bo W, Kamibayashi S, Watanabe A, Nakauchi H, Suzuki K, Kaneko S.
  • Journal Title: Mol Ther Nucleic Acids Volume: 12 Pages: 723-804
  • DOI: 10.1016/j.omtn.2018.07.017
  • NAID: 120006649570
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Generation of TCR-Expressing Innate Lymphoid-like Helper Cells that Induce Cytotoxic T Cell-Mediated Anti-leukemic Cell Response. (2018)
  • Author(s): Ueda N, Uemura Y, Zhang R, Kitayama S, Iriguchi S, Kawai Y, Yasui Y, Tatsumi M, Ueda T, Liu TY, Mizoro Y, Okada C, Watanabe A, Nakanishi M, Senju S, Nishimura Y, Kuzushima K, Kiyoi H, Naoe T, Kaneko S
  • Journal Title: Stem Cell Reports Volume: 10 Issue: 6 Pages: 1935-1946
  • DOI: 10.1016/j.stemcr.2018.04.025
  • NAID: 120006473765
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] MYC Releases Early Reprogrammed Human Cells from Proliferation Pause via Retinoblastoma Protein Inhibition. (2018)
  • Author(s): Rand TA, Sutou K, Tanabe K, Jeong D, Nomura M, Kitaoka F, Tomoda E, Narita M, Nakamura M, Nakamura M, Watanabe A, Rulifson E, Yamanaka S, Takahashi K.
  • Journal Title: Cell Rep. Volume: 23 Issue: 2 Pages: 361-375
  • DOI: 10.1016/j.celrep.2018.03.057
  • NAID: 120006463741
  • Peer Reviewed
• [Journal Article] 細胞運命決定機構を明らかにするシングルセル遺伝子発現解析. (2018)
  • Author(s): 坂本智子、前伸一、長船健二、岡田千尋、樺井良太朗、渡辺亮.
  • Journal Title: 日本薬理学雑誌 Volume: 153 Pages: 61-66
  • NAID: 130007595895
• [Journal Article] Human AK2 links intracellular bioenergetic redistribution to the fate of hematopoietic progenitors (2018)
  • Author(s): Oshima Koichi、Watanabe Akira、Nakahata Tatsutoshi、Saito Megumu K. et al.
  • Journal Title: Biochemical and Biophysical Research Communications Volume: 497 Issue: 2 Pages: 719-725
  • DOI: 10.1016/j.bbrc.2018.02.139
  • NAID: 120006466601
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] シングルセル解析の最前線 (2018)
  • Author(s): 渡辺亮、坂本智子
  • Journal Title: 整形・災害外科 Volume: 61 Pages: 427-431
• [Journal Article] Adrenergic receptor agonists induce the differentiation of pluripotent stem cell-derived hepatoblasts into hepatocyte-like cells (2017)
  • Author(s): Kotaka Maki、Toyoda Taro、Yasuda Katsutaro、Kitano Yuko、Okada Chihiro、Ohta Akira、Watanabe Akira、Uesugi Motonari、Osafune Kenji
  • Journal Title: Scientific Reports Volume: 7 Issue: 1 Pages: 16734-16734
  • DOI: 10.1038/s41598-017-16858-5
  • NAID: 120006817602
  • Peer Reviewed / Open Access
• [Journal Article] Insulin-producing cells derived from ‘induced pluripotent stem cells’ of patients with fulminant type 1 diabetes: Vulnerability to cytokine insults and increased expression of apoptosis-related genes (2017)
  • Author(s): Hosokawa Yoshiya、Toyoda Taro、Fukui Kenji、Baden Megu Yamaguchi、Funato Michinori、Kondo Yasushi、Sudo Tomomi、Iwahashi Hiromi、Kishida Marina、Okada Chihiro、Watanabe Akira、Asaka Isao、Osafune Kenji、Imagawa Akihisa、Shimomura Iichiro
  • Journal Title: Journal of Diabetes Investigation Volume: - Issue: 3 Pages: 481-493
  • DOI: 10.1111/jdi.12727
  • NAID: 120006498249
  • Peer Reviewed / Open Access
• [Journal Article] Rho-Associated Kinases and Non-muscle Myosin IIs Inhibit the Differentiation of Human iPSCs to Pancreatic Endoderm (2017)
  • Author(s): Toyoda Taro、Kimura Azuma、Tanaka Hiromi、Ameku Tomonaga、Mima Atsushi、Hirose Yurie、Nakamura Masahiro、Watanabe Akira、Osafune Kenji
  • Journal Title: Stem Cell Reports Volume: 9 Issue: 2 Pages: 419-428
  • DOI: 10.1016/j.stemcr.2017.07.005
  • Peer Reviewed / Open Access
• [Journal Article] iPSC-based drug repositioning identifies Src/c-Abl as a therapeutic target for ALS motor neurons (2017)
  • Author(s): Imamura K, Izumi Y, 他24名, Hosokawa M, Akiyama H, Ayaki T, Ito H, Takahashi R, Yamanaka S, Inoue H
  • Journal Title: Science Translational Medicine Volume: 9 Issue: 391 Pages: 391-391
  • DOI: 10.1126/scitranslmed.aaf3962
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Identification of a small molecule that facilitates the differentiation of human iPSCs/ESCs and mouse embryonic pancreatic explants into pancreatic endocrine cells (2017)
  • Author(s): Kondo Yasushi、Toyoda Taro、Ito Ryo、Funato Michinori、Hosokawa Yoshiya、Matsui Satoshi、Sudo Tomomi、Nakamura Masahiro、Okada Chihiro、Zhuang Xiaotong、Watanabe Akira、Ohta Akira、Inagaki Nobuya、Osafune Kenji
  • Journal Title: Diabetologia Volume: 60 Issue: 8 Pages: 1454-1466
  • DOI: 10.1007/s00125-017-4302-7
  • Peer Reviewed
• [Journal Article] Hypoxic adaptation of leukemic cells infiltrating the CNS affords a therapeutic strategy targeting VEGFA (2017)
  • Author(s): Kato Itaru、Nishinaka Yoko、Nakamura Masahiro、et al.
  • Journal Title: Blood Volume: 129 Issue: 23 Pages: 3126-3129
  • DOI: 10.1182/blood-2016-06-721712
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 幹細胞・発生研究とシングルセル解析 (2017)
  • Author(s): 渡辺亮
  • Journal Title: 実験医学別冊「シングルセル解析プロトコール」． Volume: - Pages: 26-32
• [Journal Article] エピゲノムデータベースの現状と活用 (2017)
  • Author(s): 渡辺亮、中村正裕、岡田千尋
  • Journal Title: 実験医学別冊「エピジェネティクス実験スタンダード」 Volume: - Pages: 1917-211
• [Presentation] システムズシングルセルオミックスで迫る細胞運命と医療への展開 (2019)
  • Author(s): 渡辺 亮
  • Organizer: 第83回 生化学会中部支部 例会・シンポジウム
  • Invited
• [Presentation] シングルセルゲノミクスで実践する医学研究 (2019)
  • Author(s): 渡辺 亮
  • Organizer: 第78回 日本癌学会 学術総会
• [Presentation] エピジェネティクスが解き明かすがんと発生 (2019)
  • Author(s): 第13回エピジェネティクス研究会年会
  • Organizer: 第13回エピジェネティクス研究会年会
• [Presentation] Epigenetic Landscape in Multi-step Leukemogenesis in Down Syndrome. (2018)
  • Author(s): Akira Watanabe
  • Organizer: International Symposium on Epigenome 2019
  • Int'l Joint Research
• [Presentation] シングルセル遺伝子発現解析が変える生命科学. (2018)
  • Author(s): 渡辺亮
  • Organizer: 第41回 分子生物学会 年会
• [Presentation] Epigenetic Dysregulation is a Key Signature in Multi-step Leukemogenesis in Down Syndrome. (2018)
  • Author(s): Akira Watanabe
  • Organizer: 第80回 日本血液学会 学術総会.
• [Presentation] 腫瘍学及び再生医療に応用されるシングルセルマルチオミックス (2018)
  • Author(s): 渡辺亮
  • Organizer: 第77回 日本癌学会 学術総会.
  • Invited
• [Presentation] シングルセル遺伝子発現解析で迫る細胞運命決定機構 (2018)
  • Author(s): 渡辺亮
  • Organizer: 生命医薬情報学連合大会2018.
  • Invited
• [Presentation] 膵臓の再生を明らかにするシングルセル遺伝子発現及びマルチオミックス解析. (2018)
  • Author(s): 渡辺亮
  • Organizer: 第61回日本糖尿病学会 年次学術集会.
  • Invited
• [Presentation] Challenge to Regeneration of Hair Cells in the Cochlea Sensory Epithelia by Single Cell Transcriptomics. (2018)
  • Author(s): 喜多 知子、坂本 智子、松永 麻美、長谷川 晶子、岡田 千尋、中川 隆之、渡辺 亮.
  • Organizer: Challenge to Regeneration of Hair Cells in the Cochlea Sensory Epithelia by Single Cell Transcriptomics.第41回 分子生物学会 年会.
• [Presentation] 膵臓の再生を明らかにするシングルセル遺伝子発現解析. (2018)
  • Author(s): 坂本 智子、龍岡 久登、矢部 大介、稲垣 暢也、渡辺 亮.
  • Organizer: 第41回 分子生物学会 年会
• [Book] 実験医学増刊「シングルセルゲノミクス」 (2019)
  • Author(s): 渡辺 亮、鈴木 穣（編）
  • Total Pages: 219
  • Publisher: 羊土社
  • ISBN: 9784758103831