Classification of the cell hierarchy structure by single cell transcriptome

• Project/Area Number: 25290071
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Medical genome science
• Research Institution: Kanazawa University
• Principal Investigator: Hashimoto Shinichi 金沢大学, 医学系, 特任教授 (00313099)
• Co-Investigator(Kenkyū-buntansha): Doi Kouichiro 東京大学, 新領域創成科学研究科, 特任講師 (10345126)
• Co-Investigator(Renkei-kenkyūsha): MATSUSHIMA Kouji 東京大学, 医学系研究科, 教授 (50222427) ; TORIGOE Toshihiko 札幌医科大学, 医学部, 教授 (20301400)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥18,330,000 (Direct Cost: ¥14,100,000、Indirect Cost: ¥4,230,000); Fiscal Year 2015: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000); Fiscal Year 2014: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000); Fiscal Year 2013: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000)
• Keywords: 遺伝子発現 / １細胞 / 癌細胞 / がん幹細胞 / 1細胞 / モニタリング / single cell / gene expression / バイオテクノロジー / ゲノム / 癌 / シングルセル

Outline of Final Research Achievements

A tissue, an organ, or even a differentiated state of cells are composed of heterogeneous cell populations. Single-cell gene-expression profiling allows you to identify and characterize various types of each cell. Here, we have developed the novel strategy (Nx1-seq) of single-cell transcriptome analysis for thousands of single cells. In our approach, single cells are deposited in a high-density microwell plate and lysed in situ. mRNA is then captured on barcoding microbeads developed by emulsion PCR and reverse transcribed. By applying this Nx1seq method for thousands of cells per experiment, we have successfully characterized 1) complex heterogeneous types of cells in the human endometrioid adenocarcinoma cancer cell line and 2) immune cells at a certain differentiated state.

Research Products

• [Journal Article] Reduced supply of monocyte-derived macrophages leads to a transition from nodular to diffuse lesions and tissue cell activation in silica-induced pulmonary fibrosis in mice. (2015)
  • Author(s): Shigeyuki Shichino, Jun Abe, Satoshi Ueha, Mikiya Otsuji, Tatsuya Tsukui, Mizuha Kosugi-Kanaya, Francis HW Shand, Shin-ichi Hashimoto, Hiroshi I. Suzuki, Teppei Morikawa, Yutaka Inagaki, and Kouji Matsushima:
  • Journal Title: Am J Pathol Volume: 185 Issue: 11 Pages: 2923-2938
  • DOI: 10.1016/j.ajpath.2015.07.013
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species. (2015)
  • Author(s): Nakatani Y, Mello CC, Hashimoto S, Shimada A, Nakamura R, Tsukahara T, Qu W, Yoshimura J, Suzuki Y, Sugano S, Takeda H, Fire A, Morishita S.
  • Journal Title: BMC Genomics Volume: 16(1) Issue: 1 Pages: 978-978
  • DOI: 10.1186/s12864-015-2198-5
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Lymph Node Stromal Cells Negatively Regulate Antigen-Specific CD4+ T Cell Responses. (2014)
  • Author(s): Abe J, Shichino S, Ueha S, Hashimoto S, Tomura M, Inagaki Y, Stein JV, Matsushima K.
  • Journal Title: J Immunol. Volume: 193 Issue: 4 Pages: 1636-1644
  • DOI: 10.4049/jimmunol.1302946
  • Peer Reviewed
• [Journal Article] Pro-inflammatory/Th1 gene expression shift in high glucose stimulated mesangial cells and tubular epithelial cells. (2014)
  • Author(s): Iwata Y, Furuichi K, Hashimoto S, Yokota K, Yasuda H, Sakai N, Kitajima S, Toyama T, Shinozaki Y, Sagara A, Matsushima K, Kaneko S, Wada T.
  • Journal Title: Biochem Biophys Res Commun Volume: 443 Issue: 3 Pages: 969-974
  • DOI: 10.1016/j.bbrc.2013.12.072
  • Peer Reviewed / Open Access
• [Journal Article] The transcription start site landscape of C. elegans (2013)
  • Author(s): Saito TL, Hashimoto S, Gu SG, Morton JJ, Stadler M, Blumenthal T, Fire A, Morishita S
  • Journal Title: Genome Research Volume: 23(8) Issue: 8 Pages: 1348-61
  • DOI: 10.1101/gr.151571.112
  • Peer Reviewed
• [Journal Article] Coordinated Changes in DNA Methylation in Antigen-Specific Memory CD4 T Cells (2013)
  • Author(s): Hashimoto S, Ogoshi K, Sasaki A, Abe J, Qu W, Nakatani Y, Ahsan B, Oshima K, Shand FH, Ametani A, Suzuki Y, Kaneko S, Wada T, Hattori M, Sugano S,Morishita S, Matsushima K
  • Journal Title: J Immunol Volume: 190 Issue: 8 Pages: 4076-4091
  • DOI: 10.4049/jimmunol.1202267
  • Peer Reviewed
• [Journal Article] Qualitative Rather than Quantitative Changes Are Hallmarks of Fibroblasts in Bleomycin-Induced Pulmonary Fibrosis (2013)
  • Author(s): Tatsuya Tsukui, Satoshi Ueha, Jun Abe, Shin-ichi Hashimoto, Shigeyuki Shichino, Takeshi Shimaoka, Francis H. W. Shand, Yasuka Arakawa, Kenshiro Oshima, Masahira Hattori, Yutaka
  • Journal Title: The American Journal of Pathology Volume: 3 Issue: 3 Pages: 758-773
  • DOI: 10.1016/j.ajpath.2013.06.005
  • Peer Reviewed
• [Journal Article] A unique dermal dendritic cell subset that skews the immune response toward Th2. (2013)
  • Author(s): 2.Murakami R, Denda-Nagai K, Hashimoto S, Nagai S, Hattori M, Irimura T.
  • Journal Title: PLoS One. Volume: 8 Issue: 9 Pages: e73270-e73270
  • DOI: 10.1371/journal.pone.0073270
  • Peer Reviewed / Open Access
• [Presentation] Comprehensive single-cell transcriptome reveals heterogeneity in cancer tissue (2015)
  • Author(s): Shinichi Hashimoto
  • Organizer: Cold Spring Harbor Laboratory, Single cell meeting
  • Place of Presentation: Cold Spring Harbor Laboratory
  • Year and Date: 2015-11-11
  • Int'l Joint Research
• [Presentation] がん組織における包括的１細胞遺伝子発現解析 (2015)
  • Author(s): 鳥越俊彦、橋本真一
  • Organizer: 第74回日本癌学会学術総会
  • Place of Presentation: 名古屋国際会議場
  • Year and Date: 2015-10-08
• [Patent(Industrial Property Rights)] 抗Ｂ型肝炎ウイルス薬 (2015)
  • Inventor(s): 橋本 真一、金子 周一、本多 政夫、白崎 尚芳、山下 太郎
  • Industrial Property Rights Holder: 橋本 真一、金子 周一、本多 政夫、白崎 尚芳、山下 太郎
  • Industrial Property Rights Type: 特許
  • Industrial Property Number: 2015-219183
  • Filing Date: 2015-11-09
• [Patent(Industrial Property Rights)] 単一細胞由来核酸の解析方法 (2014)
  • Inventor(s): 橋本真一、金子周一、松島綱治
  • Industrial Property Rights Holder: 橋本真一、金子周一、松島綱治
  • Industrial Property Rights Type: 特許
  • Industrial Property Number: 2014-095011
  • Filing Date: 2014-05-02