Analysis of cancer attractors on gene expression potentials by gene-environment (GxE) interactions

• Project/Area Number: 25330333
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Life / Health / Medical informatics
• Research Institution: Tohoku University
• Principal Investigator: OGISHIMA Soichi 東北大学, 東北メディカル・メガバンク機構, 准教授 (40447496)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2015: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2014: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2013: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: 生命情報 / 癌アトラクター / 疾患アトラクター / 遺伝子-環境相互作用 / GxE

Outline of Final Research Achievements

Toward systems-level understanding of transition of cancer attractors, we clarified cancer attractors and their transitions on gene expression potential during epithelial-mesenchymal transition in cancer metastasis by analyzing time-course gene expression data. We conducted PCA on gene expression data to reduce their dimension, and inferred gene regulatory network regulating cancer attractors. As for cancer metastasis, we evaluated effects on gene expression potential by gene-environment (GxE) interactions, and clarified stability of cancer cells on gene expression potentials and trajectory of their attractors under certain condition of gene and environment.

Research Products

• [Journal Article] AlzPathway, an Updated Map of Curated Signaling Pathways: Towards Deciphering Alzheimer's Disease Pathogenesis. (2016)
  • Author(s): Ogishima S, Mizuno S, Kikuchi M, Miyashita A, Kuwano R, Tanaka H, Nakaya J.
  • Journal Title: Methods Mol Biol. Volume: 1303 Pages: 423-32
  • DOI: 10.1007/978-1-4939-2627-5_25
  • ISBN: 9781493926268, 9781493926275
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Network-Based Analysis for Uncovering Mechanisms Underlying Alzheimer's Disease. (2016)
  • Author(s): Kikuchi M, Ogishima S, Mizuno S, Miyashita A, Kuwano R, Nakaya J, Tanaka H.
  • Journal Title: Methods Mol Biol. Volume: 1303 Pages: 479-91
  • DOI: 10.1007/978-1-4939-2627-5_29
  • ISBN: 9781493926268, 9781493926275
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Network Analysis of a Comprehensive Knowledge Repository Reveals a Dual Role for Ceramide in Alzheimer's Disease. (2016)
  • Author(s): Mizuno S, Ogishima S, Kitatani K, Kikuchi M, Tanaka H, Yaegashi N, Nakaya J.
  • Journal Title: PLoS One. Volume: 11 Issue: 2 Pages: e0148431-e0148431
  • DOI: 10.1371/journal.pone.0148431
  • Peer Reviewed / Open Access
• [Journal Article] Network biology approach to epithelial-mesenchymal transition in cancer metastasis: three stage theory. (2015)
  • Author(s): Tanaka H, Ogishima S.
  • Journal Title: J Mol Cell Biol Volume: 7 Issue: 3 Pages: 253-66
  • DOI: 10.1093/jmcb/mjv035
  • Peer Reviewed
• [Journal Article] Implementation of linked data in the life sciences at BioHackathon 2011 (2015)
  • Author(s): Aoki-Kinoshita KF et al.
  • Journal Title: Journal of Biomedical Semantics Volume: 6 Issue: 1 Pages: 3-3
  • DOI: 10.1186/2041-1480-6-3
  • Peer Reviewed / Open Access
• [Journal Article] Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. (2015)
  • Author(s): Carbajo D, Magi S, Itoh M, Kawaji H, Lassmann T, Arner E, Forrest AR, Carninci P, Hayashizaki Y, Daub CO; FANTOM consortium, Okada-Hatakeyama M, Mar JC.
  • Journal Title: PLoS One. Volume: 10(12) Issue: 12 Pages: e0144176-e0144176
  • DOI: 10.1371/journal.pone.0144176
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome. (2015)
  • Author(s): Hurst LD, Ghanbarian AT, Forrest AR; FANTOM consortium, Huminiecki L.
  • Journal Title: PLoS Biol. Volume: 13(12) Issue: 12 Pages: e1002315-e1002315
  • DOI: 10.1371/journal.pbio.1002315
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] A method to associate all possible combinations of genetic and environmental factors using GxE landscape plot (2015)
  • Author(s): Nagaie S, Ogishima S, Nakaya J, Tanaka H
  • Journal Title: Bioinformation Volume: 11 Pages: 161-4
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Gene regulation. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells (2015)
  • Author(s): Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, et al.
  • Journal Title: Science Volume: 347 Issue: 6225 Pages: 1010-1014
  • DOI: 10.1126/science.1259418
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] The statistical geometry of transcriptome divergence in cell-type evolution and cancer (2015)
  • Author(s): Liang C; FANTOM Consortium, Forrest AR, Wagner GP
  • Journal Title: Nat Commun. Volume: 6 Issue: 1 Pages: 6066-6066
  • DOI: 10.1038/ncomms7066
  • Peer Reviewed / Open Access
• [Journal Article] Future Direction of IMIA Standardization. Report from the IMIA Standardization Working Group (2014)
  • Author(s): Nakaya J, Kimura M, Ogishima S, Shabo A, Kim IK, Parisot C, de Faria Leao B
  • Journal Title: Yearb Med Inform. Volume: 9 Issue: 01 Pages: 105-9
  • DOI: 10.15265/iy-2014-0010
  • Peer Reviewed / Open Access
• [Journal Article] CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes (2014)
  • Author(s): Hasegawa Y, Tang D, Takahashi N, Hayashizaki Y, Forrest AR; FANTOM Consortium, Suzuki H
  • Journal Title: Sci Rep. Volume: 4 Issue: 1 Pages: 5228-5228
  • DOI: 10.1038/srep05228
  • Peer Reviewed / Open Access
• [Journal Article] Differential roles of epigenetic changes and Foxp3 expression in regulatory Tcell-specific transcriptional regulation. (2014)
  • Author(s): Morikawa H, Ohkura N, Vandenbon A, Itoh M Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Standley DM, Date H, Sakaguchi S; FANTOM Consortium. Collaborators(259) Enomoto H, etc.
  • Journal Title: Proc Natl Acad Sci U S A. Volume: 111 Issue: 14 Pages: 5289-5294
  • DOI: 10.1073/pnas.1312717110
  • Peer Reviewed / Open Access
• [Journal Article] A promoter-level mammalian expression atlas. (2014)
  • Author(s): Forrest, A.R.R., Kawaji, H., Rehli, M., Baillie, J.K, de Hoon, M.J.L., Haberle, V., Lassmann, T., Kulakovskiy, I.V., Lizio, M., Itoh, M., Andersson, R., Mungall, C. J.,et al.
  • Journal Title: Nature Volume: 507 Issue: 7493 Pages: 462-470
  • DOI: 10.1038/nature13182
  • Peer Reviewed / Open Access
• [Journal Article] An atlas of active enhancers across human cell types and tissues. (2014)
  • Author(s): Anderson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Collaborators(261) Enomoto H, etc.
  • Journal Title: Nature Volume: 507 Issue: 7493 Pages: 455-461
  • DOI: 10.1038/nature12787
  • Peer Reviewed / Open Access
• [Journal Article] BioHackathon series in 2011 and 2012 : penetration of ontology and linked data in life science domains (2014)
  • Author(s): Katayama T, Komiyama Y, et al.
  • Journal Title: Journal of Biomedical Semantics Volume: 5 Issue: 1 Pages: 5-5
  • DOI: 10.1186/2041-1480-5-5
  • Peer Reviewed / Open Access
• [Journal Article] 15. Identification of unstable network modules reveals disease modules associated with the progression of Alzheimer's disease (2013)
  • Author(s): Kikuchi M, Ogishima S, Miyamoto T, Miyashita A, Kuwano R, Nakaya J, Tanaka H
  • Journal Title: PLoS One Volume: 8 Issue: 11 Pages: e76162-e76162
  • DOI: 10.1371/journal.pone.0076162
  • Peer Reviewed
• [Journal Article] Analysis of L-glutamic acid fermentation by using a dynamic metabolic simulation model of Escherichia coli. (2013)
  • Author(s): Nishio Y, Ogishima S, Ichikawa M, Yamada Y, Usuda Y, Masuda T, Tanaka H.
  • Journal Title: BMC Syst Biol Volume: 7 Issue: 1 Pages: 92-92
  • DOI: 10.1186/1752-0509-7-92
  • Peer Reviewed
• [Journal Article] A map of Alzheimer'sdisease-signaling pathways: a hope for drug target discovery (2013)
  • Author(s): Ogishima S, Mizuno S, Kikuchi M, Miyashita A, Kuwano R, Tanaka H, Nakaya J.
  • Journal Title: Clin Pharmacol Ther Volume: 93(5) Issue: 5 Pages: 399-401
  • DOI: 10.1038/clpt.2013.37
  • Peer Reviewed
• [Presentation] 東北メディカル・メガバンク事業におけるゲノム・オミックス情報と医療情報等の統合 (2013)
  • Author(s): 荻島創一
  • Organizer: 生命医薬情報学連合大会2013年大会
  • Place of Presentation: タワーホール船堀
  • Invited
• [Presentation] 細胞の分化・誘導に関わる発現ポテンシャル解析 (2013)
  • Author(s): 荻島創一
  • Organizer: 次世代シーケンス現場の会第3回大会
  • Place of Presentation: 神戸国際会議場
  • Invited