Dissecting Cell Fate Decision by Single Cell Genomics

• Project/Area Number: 15K06921
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: System genome science
• Research Institution: Kyoto University
• Principal Investigator: Watanabe Akira 京都大学, iPS細胞研究所, 特定拠点助教 (60506765)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2017: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2016: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2015: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: シングルセル / 遺伝子発現 / iPS細胞 / RNA-seq / ATAC-seq / 心筋細胞 / シングルセル解析

Outline of Final Research Achievements

Human pluripotent stem cell-derived cardiomyocytes show promise for clinical application. To reach this potential, however, improved maturity and reduced cellular heterogeneity of in vitro differentiated cardiomyocytes is needed. Here, we addressed transcriptional heterogeneity in induced pluripotent stem cell (iPSC)-derived cardiomyocytes (iPSC-CMs) by single-cell RNA sequencing. We successfully defined differentiation states at the single-cell level and clarified heterogeneities in the gene expression patterns of iPSC-CMs, especially those cultured over long periods. We developed a novel maturation index to perform in silico sorting and score the maturation level of the cells. Additionally, we identified a new cell surface marker of mature iPSC-CMs by which we could enrich well-matured iPSC-CMs from a heterogeneous population of iPSC-CMs. Our single-cell RNA sequencing approach could help clarify variation of in vitro differentiated cells.

Research Products

• [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): 10.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
• [Journal Article] Autologous Induced Stem Cell-Derived Retinal Cells for Macular Degeneration (2017)
  • Author(s): M. Mandai, A. Watanabe, Y. Kurimoto, 他36名
  • Journal Title: New England Journal of Medicine Volume: 376 Issue: 11 Pages: 1038-1046
  • DOI: 10.1056/nejmoa1608368
  • Peer Reviewed
• [Journal Article] Identification of a High-Frequency Somatic NLRC4 Mutation as a Cause of Autoinflammation by Pluripotent Cell-Based Phenotype Dissection. (2017)
  • Author(s): Kawasaki Y, Oda H, Ito J, Niwa A, Tanaka T, Hijikata A, Seki R, Nagahashi A, Osawa M, Asaka I, Watanabe A, Nishimata S, Shirai T, Kawashima H, Ohara O, Nakahata T, Nishikomori R, Heike T, Saito MK.
  • Journal Title: Arthritis Rheumatol. Volume: 69 Issue: 2 Pages: 447-459
  • DOI: 10.1002/art.39960
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells. (2017)
  • Author(s): Sugiyama H, Takahashi K, Yamamoto T, Iwasaki M, Narita M, Nakamura M, Rand TA, Nakagawa M, Watanabe A, Yamanaka S.
  • Journal Title: Proc Natl Acad Sci U S A. Volume: 114 Issue: 2 Pages: 340-345
  • DOI: 10.1073/pnas.1617234114
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Transcriptional Analysis of Intravenous Immunoglobulin Resistance in Kawasaki Disease Using an Induced Pluripotent Stem Cell Disease Model (2017)
  • Author(s): Ikeda K, Mizoro Y, Ameku T, Nomiya Y, Mae SI, Matsui S, Kuchitsu Y, Suzuki C, Hamaoka-Okamoto A, Yahata T, Sone M, Okita K, Watanabe A, Osafune K, Hamaoka K.
  • Journal Title: Circulation Journal Volume: 81 Issue: 1 Pages: 110-118
  • DOI: 10.1253/circj.CJ-16-0541
  • NAID: 130005252647
  • ISSN: 1346-9843, 1347-4820
  • Peer Reviewed / Open Access
• [Journal Article] Redefining definitive endoderm subtypes by robust induction of human induced pluripotent stem cells. (2016)
  • Author(s): Matsuno K, Mae SI, Okada C, Nakamura M, Watanabe A, Toyoda T, Uchida E, Osafune K.
  • Journal Title: Differentiation Volume: 92 Issue: 5 Pages: 281-290
  • DOI: 10.1016/j.diff.2016.04.002
  • Peer Reviewed
• [Journal Article] Laminin-guided highly efficient endothelial commitment from human pluripotent stem cells. (2016)
  • Author(s): Ohta R., Niwa A., Taniguchi Y., Suzuki NM., Toga J., Yagi E., Saiki N., Nishinaka-Arai Y., Okada C., Watanabe A., Nakahata T., Sekiguchi K., Saito MK.
  • Journal Title: Scientific Reports Volume: - Issue: 1 Pages: 35680-35680
  • DOI: 10.1038/srep35680
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Purification of functional human ES and iPSC-derived midbrain dopaminergic progenitors using LRTM1. (2016)
  • Author(s): Samata B, Doi D, Nishimura K, Kikuchi T, Watanabe A, Sakamoto Y, Kakuta J, Ono Y, Takahashi J.
  • Journal Title: Nat Commun. Volume: 4 Issue: 1 Pages: 13907-13907
  • DOI: 10.1038/ncomms13097
  • NAID: 120005867037
  • Peer Reviewed
• [Journal Article] Epigenetic Variation between Human Induced Pluripotent Stem Cell Lines Is an Indicator of Differentiation Capacity (2016)
  • Author(s): ③M. Nishizawa, K. Chonabayashi, M. Nomura, A. Tanaka, M. Nakamura, A. Inagaki, M. Nishikawa, I. Takei, A. Oishi, K. Tanabe, M. Ohnuki, H. Yokota, M. Koyanagi-Aoi, K. Okita, A. Watanabe, A. Takaori-Kondo, S. Yamanaka, Y. Yoshida
  • Journal Title: Cell Stem Cell Volume: 19 Issue: 3 Pages: 341-354
  • DOI: 10.1016/j.stem.2016.06.019
  • Peer Reviewed
• [Journal Article] Identification of MMP1 as a novel risk factor for intracranial aneurysms in ADPKD using iPSC models. (2016)
  • Author(s): Ameku T, Watanabe A, Osafune K et al.
  • Journal Title: Sci Rep. Volume: 6 Issue: 1 Pages: 30013-30013
  • DOI: 10.1038/srep30013
  • NAID: 120005825896
  • Peer Reviewed / Open Access
• [Journal Article] Modeling the early phenotype at the euromuscular junction of spinal muscular atrophy using patient-derived iPSCs. (2015)
  • Author(s): Yoshida, M., Kitaoka, S., Egawa N., Yamane M., Ikeda R., Tsukita K., Amano N., Watanabe A., Morimoto, M., Takahashi J., Hosoi H., Nakahatan, T., Inoue, H.,Saito, Megumu K.
  • Journal Title: Stem Cell Reports Volume: 4 Issue: 4 Pages: 1-8
  • DOI: 10.1016/j.stemcr.2015.02.010
  • Peer Reviewed
• [Journal Article] Pluripotent cell models of Fanconi anemia identify the early pathological defect in human hemoangiogenic progenitors. (2015)
  • Author(s): Suzuki NM, Niwa A, Yabe M, Hira A, Okada C, Amano N, Watanabe A, Watanabe K, Heike T, Takata M, Nakahata T, Saito MK
  • Journal Title: Stem Cells Transl Med Volume: 4 Issue: 4 Pages: 333-338
  • DOI: 10.5966/sctm.2013-0172
  • NAID: 120005980869
  • Peer Reviewed / Open Access
• [Presentation] シングルセル解析によって可視化する臓器の発生過程 (2016)
  • Author(s): 渡辺 亮
  • Organizer: 第６４回日本輸血・細胞治療学会
  • Place of Presentation: 京都
  • Year and Date: 2016-04-28
  • Invited
• [Presentation] 臓器の発生過程を可視化するシングルセル遺伝子発現解析 (2015)
  • Author(s): 渡辺 亮
  • Organizer: 第３８回分子生物学会年会
  • Place of Presentation: 神戸
  • Year and Date: 2015-12-01
• [Presentation] シングルセル遺伝子解析が明らかにするヒト発生過程における細胞運命の決定 (2015)
  • Author(s): 渡辺 亮
  • Organizer: 第６７回日本生物工学会大会
  • Place of Presentation: 鹿児島
  • Year and Date: 2015-10-26
  • Invited
• [Presentation] The Single Cell Epigenetics Dissects Cell Fate Specification (2015)
  • Author(s): Akira Watanabe
  • Organizer: Top Global University Japan, 1st Joint Symposium of International Partners
  • Place of Presentation: 京都
  • Year and Date: 2015-10-02
  • Int'l Joint Research / Invited
• [Presentation] Single Cell Transcriptome Analysis Dissects Cell Fate Specification (2015)
  • Author(s): Akira Watanabe
  • Organizer: 第５３回生物物理学会年会
  • Place of Presentation: 金沢
  • Year and Date: 2015-09-13
  • Invited
• [Presentation] 臓器の発生過程を可視化するシングルセル遺伝子解析 (2015)
  • Author(s): 渡辺 亮
  • Organizer: 第２６回臨床口腔病理学会総会学術集会
  • Place of Presentation: 札幌
  • Year and Date: 2015-07-29
  • Invited