Analyses on developmental transition process of mammalian pluripotent cells and its epigenomic regulations using single cell technologies

• Project/Area Number: 18H02424
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Review Section: Basic Section 43050:Genome biology-related
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: ABE KUNIYA 国立研究開発法人理化学研究所, バイオリソース研究センター, チームリーダー (40240915)
• Project Period (FY): 2018-04-01 – 2021-03-31
• Project Status: Completed (Fiscal Year 2021)
• Budget Amount: ¥17,550,000 (Direct Cost: ¥13,500,000、Indirect Cost: ¥4,050,000); Fiscal Year 2020: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2019: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2018: ¥7,410,000 (Direct Cost: ¥5,700,000、Indirect Cost: ¥1,710,000)
• Keywords: 細胞分化 / 分化遷移 / 多能性幹細胞 / Ｘ染色体不活性化 / シングルセル解析 / エピゲノム / DNAメチル化 / シングルセル / エピジェネティクス / 多能性細胞 / ナイーブープライム変換

Outline of Final Research Achievements

Single-cell RNA-Seq analysis of naive-primed transition process was performed and 3 clusters that exhibit characteristics other than ES cells and EpiSC were identified. We estimated the time of appearance of each cluster after induction of differentiation by pseudotime analysis, and extracted a group of genes with high expression specificity to each cluster. One of the newly identified clusters had a morphology similar to that of EpiSCs but with a different expression profile, suggesting that it was a novel pluripotent stem cell. Interestingly, another cluster showed a genome-wide downregulation of gene expression, and it appears that X chromosome inactivation initiates in this cluster.

Academic Significance and Societal Importance of the Research Achievements

細胞分化の進行を考える時、1）時間の経過と伴に徐々に、しかし確実に細胞形質が漸進的に変化する場合と、(2)ある定常状態から異なる定常状態へ遷移する場合などが想定されるが、本研究では、遷移現象を解析するための再現性の高い実験系が確立したことに意義があると考える。さらにこの系を用いて、新規の多能性幹細胞やグローバルな遺伝子発現低下を起こす細胞集団の発見、そしてＸ染色体不活性化に代表されるエピゲノム変動との関連を追及するための材料を提案したことについても、今後の広範な展開に繋がる学術的な意義があると考える。

Research Products

• [Journal Article] Human iPS cell-derived cartilaginous tissue spatially and functionally replaces nucleus pulposus (2022)
  • Author(s): Kamatani Takashi、Hagizawa Hiroki、Yarimitsu Seido、Morioka Miho、Koyamatsu Saeko、Sugimoto Michihiko、Kodama Joe、Yamane Junko、Ishiguro Hiroyuki、Shichino Shigeyuki、Abe Kuniya、Fujibuchi Wataru、Fujie Hiromichi、Kaito Takashi、Tsumaki Noriyuki
  • Journal Title: Biomaterials Volume: 284 Pages: 121491-121491
  • DOI: 10.1016/j.biomaterials.2022.121491
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Visualization and quantitative analyses for mouse embryonic stem cell tracking by manipulating hierarchical data structures using time-lapse confocal microscopy images (2021)
  • Author(s): Yokota Hideo、Abe Kuniya、Chang Yuan-Hsiang、Cho Dooseon、Tsai Ming- Dar、Huang Pin-Han
  • Journal Title: Annu Int Conf IEEE Eng Med Biol Soc. 2021 Volume: - Pages: 2944-2947
  • DOI: 10.1109/embc46164.2021.9629490
  • Peer Reviewed
• [Journal Article] High Resolution U-Net for Quantitatively Analyzing Early Spatial Patterning of Human Induced Pluripotent Stem Cells on Micropatterns (2021)
  • Author(s): Chu Slo-Li、Abe Kuniya、Yokota Hideo、Cho Dooseon、Chen Yuan-Hao、Tsai Ming-Dar
  • Journal Title: Annu Int Conf IEEE Eng Med Biol Soc. 2021 Volume: - Pages: 3713-3716
  • DOI: 10.1109/embc46164.2021.9630956
  • Peer Reviewed
• [Journal Article] Human induced pluripotent stem cell region detection in bright-field microscopy images using convolutional neural networks (2019)
  • Author(s): Chang Y-H, Abe K, Yokota H, Sudo K, Nakamura Y, Tsai M-D
  • Journal Title: Biomedical Engineering: applications, basis and communications Volume: 31 Issue: 02 Pages: 1950009-1950009
  • DOI: 10.4015/s1016237219500091
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] WNT inhibition and increased FGF signaling promotes derivation of less heterogeneous primed human embryonic stem cells, compatible with differentiation (2019)
  • Author(s): Taelman J, Popovic M, Bialecka M, Tilleman L, Warrier S, Van Der Jeught M, Menten B, Deforce D, Sutter P DE, Nieuwerburgh V, Abe K, Heindryckx B, Chuva de Sausa Lopes SM
  • Journal Title: Stem Cells and Development Volume: in press Issue: 9 Pages: 579-592
  • DOI: 10.1089/scd.2018.0199
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Xist/Tsix expression dynamics during mouse peri-implantation development revealed by whole-mount 3D RNA-FISH (2019)
  • Author(s): Shiura H, Abe K.
  • Journal Title: Sci Rep. Volume: 9 Issue: 1 Pages: 3637-3637
  • DOI: 10.1038/s41598-019-38807-0
  • Peer Reviewed / Open Access
• [Presentation] Single cell transcriptome analyses reveal novel intermediate pluripotent states during transition from naive to primed pluripotent stem cells (2019)
  • Author(s): Tada Y, Bottcher M, Kondo M, Ura H, Carninci P, Carninci P, Abe K
  • Organizer: EMBO Workshop Single Cell Biology
  • Int'l Joint Research
• [Presentation] マウス初期発生過程におけるGARP complexの役割 (2019)
  • Author(s): 杉本道彦、阿部訓也
  • Organizer: 2019年度モロシヌス研究会
• [Presentation] 着床前後のマウス胚におけるトランスクリプトーム動態解析とDNAメチル化の役割 Transcriptome dynamics and DNA methylation in mouse peri-implantation embryos (2019)
  • Author(s): 田夛祐喜、志浦寛相、阿部訓也
  • Organizer: 第42回日本分子生物学会年会
• [Presentation] Single cell transcriptome analyses reveal novel intermediate pluripotent states during transition from naive to primed pluripotent stem cells (2019)
  • Author(s): Tada Y, Bottcher M, Kondo M, Ura H, Carninci P, Carninci P, Abe K
  • Organizer: EMBO Workshop Single Cell Biology（国際学会）
  • Int'l Joint Research
• [Presentation] マウス初期発生過程におけるGARP complexの役割 (2019)
  • Author(s): 杉本道彦、阿部訓也
  • Organizer: モロシヌス研究会
• [Patent(Industrial Property Rights)] 細胞の標識方法 (2022)
  • Inventor(s): 杉本道彦、阿部訓也
  • Industrial Property Rights Holder: 理化学研究所
  • Industrial Property Rights Type: 特許
  • Industrial Property Number: 2022-016576
  • Filing Date: 2022