Research Articles

                                                                                                 
  1. Faruk Azam Shaik, Satoshi Ihida, YoshihoIkeuchi, AgnèsTixier-Mita, HiroshiToshiyoshia. TFT sensor array for real-time cellular characterization, stimulation, impedance measurement and optical imaging of in-vitro neural cells. Biosensors and Bioelectronics Volume 169, 1 December 2020, 112546. Received 9 June 2020, Revised 20 August 2020, Accepted 22 August 2020, Available online 30 August 2020. https://doi.org/10.1016/j.bios.2020.112546
  2. Chanda A, Ikeuchi Y, Karve K, Sarkar A, Chandhoke AS, Deng L, Bonni A, Bonni S. PIAS1 and TIF1γ collaborate to promote SnoN SUMOylation and suppression of epithelial-mesenchymal transition. Cell Death Differ. 2020 Aug 7. doi: 10.1038/s41418-020-0599-8. Epub ahead of print. Erratum in: Cell Death Differ. 2020 Aug 18;: PMID: 32770107.
  3. Misawa R, Minami T, Okamoto A, Ikeuchi Y. A Light-Inducible Hedgehog Signaling Activator Modulates Proliferation and Differentiation of Neural Cells. ACS Chem Biol. 2020 Jun 19;15(6):1595-1603. doi: 10.1021/acschembio.0c00195. Epub 2020 May 11. PMID: 32343549.
  4. Tsuboyama K, Osaki T, Matsuura-Suzuki E, Kozuka-Hata H, Okada Y, Oyama M, Ikeuchi Y , Iwasaki S, Tomari Y. A widespread family of heat-resistant obscure (Hero) proteins protect against protein instability and aggregation. PLoS Biol . 2020 Mar 12;18(3):e3000632. doi: 10.1371/journal.pbio.3000632. PMID: 32163402; PMCID: PMC7067378.
  5. Kaneda S, Kawada J, Shinohara M, Kumemura M, Ueno R, Kawamoto T, Suzuki K, Kim B, Ikeuchi Y, Sakai Y, Collard D, Fujita H, Fujii T. Boyden chamber-based compartmentalized tumor spheroid culture system to implement localized anticancer drug treatment. Biomicrofluidics. 2019 Oct 24;13(5):054111. doi: 10.1063/1.5125650. PMID: 31893010; PMCID: PMC6932857.
  6. Akiyama T, Suzuki N, Ishikawa M, Fujimori K, Sone T, Kawada J, Funayama R, Fujishima F, Mitsuzawa S, Ikeda K, Ono H, Shijo T, Osana S, Shirota M, Nakagawa T, Kitajima Y, Nishiyama A, Izumi R, Morimoto S, Okada Y, Kamei T, Nishida M, Nogami M, Kaneda S, Ikeuchi Y, Mitsuhashi H, Nakayama K, Fujii T, Warita H, Okano H, Aoki M. Aberrant axon branching via Fos-B dysregulation in FUS-ALS motor neurons. EBioMedicine. 2019 Jul;45:362-378. doi: 10.1016/j.ebiom.2019.06.013. Epub 2019 Jun 29. PMID: 31262712; PMCID: PMC6642224.
  7. Kirihara T, Luo Z, Chow SYA, Misawa R, Kawada J, Shibata S, Khoyratee F, Vollette CA, Volz V, Levi T, Fujii T, Ikeuchi Y. A Human Induced Pluripotent Stem Cell-Derived Tissue Model of a Cerebral Tract Connecting Two Cortical Regions. iScience. 2019 Apr 26;14:301-311. doi: 10.1016/j.isci.2019.03.012. Epub 2019 Apr 18. PMID: 31006610; PMCID: PMC6489017.
  8. Chen X, Chanda A, Ikeuchi Y, Zhang X, Goodman JV, Reddy NC, Majidi SP, Wu DY, Smith SE, Godec A, Oldenborg A, Gabel HW, Zhao G, Bonni S, Bonni A. The Transcriptional Regulator SnoN Promotes the Proliferation of Cerebellar Granule Neuron Precursors in the Postnatal Mouse Brain. J Neurosci. 2019 Jan 2;39(1):44-62. doi: 10.1523/JNEUROSCI.0688-18.2018. Epub 2018 Nov 13. PMID: 30425119; PMCID: PMC6325268.
  9. Faruk Azam Shaik, Grant Alexander Cathcart, Satoshi Ihida, Yoshiho Ikeuchi, Agnes Tixier-Mita, Hiroshi Toshiyoshi. “Electrical Stimulation, Recording and Impedance-Based Real-Time Position Detection of Cultured Neurons Using Thin-Film-Transistor Array.” Journal of Microelectromechanical Systems 2018, 27, 424 - 433
  10. Cheng C, Deng PY, Ikeuchi Y, Yuede C, Li D, Rensing N, Huang J, Baldridge D, Maloney SE, Dougherty JD, Constantino J, Jahani-Asl A, Wong M, Wozniak DF, Wang T, Klyachko VA, Bonni A. Characterization of a Mouse Model of Börjeson-Forssman- Lehmann Syndrome. Cell Rep. 2018 Nov 6;25(6):1404-1414.e6. doi: 10.1016/j.celrep.2018.10.043. PMID: 30403997; PMCID: PMC6261530.
  11. Umegaki Y, Brotons AM, Nakanishi Y, Luo Z, Zhang H, Bonni A, Ikeuchi Y. Palladin Is a Neuron-Specific Translational Target of mTOR Signaling That Regulates Axon Morphogenesis. J Neurosci. 2018 May 23;38(21):4985-4995. doi: 10.1523/JNEUROSCI.2370-17.2018. Epub 2018 Apr 30. PMID: 29712777; PMCID: PMC5966794.
  12. Asano K, Suzuki T, Saito A, Wei FY, Ikeuchi Y, Numata T, Tanaka R, Yamane Y, Yamamoto T, Goto T, Kishita Y, Murayama K, Ohtake A, Okazaki Y, Tomizawa K, Sakaguchi Y, Suzuki T. Metabolic and chemical regulation of tRNA modification associated with taurine deficiency and human disease. Nucleic Acids Res. 2018 Feb 28;46(4):1565-1583. doi: 10.1093/nar/gky068. PMID: 29390138; PMCID: PMC5829720.
  13. Stephany Mai Nishikawa, Soo Hyeon Kim, Zhongyue Luo, Takaaki Kirihara, Yoshiho Ikeuchi, Teruo Fujii, Timothée Levi. "Biomimetic microfluidic neurons for bio-hybrid experiments" Artificial Life and Robotics 2018
  14. Levi T, Khoyratee F, Saïghi S, Ikeuchi Y. "Digital implementation of Hodgkin–Huxley neuron model for neurological diseases studies" Artificial Life and Robotics 2018, 23, 10-14
  15. Kawada J, Kaneda S, Kirihara T, Maroof A, Levi T, Eggan K, Fujii T, Ikeuchi Y. Generation of a Motor Nerve Organoid with Human Stem Cell-Derived Neurons. Stem Cell Reports. 2017 Nov 14;9(5):1441-1449. doi: 10.1016/j.stemcr.2017.09.021. Epub 2017 Oct 26. PMID: 29107592; PMCID: PMC5831012.
  16. Tachizawa S, Takahashi H, Kim YJ, Odawara A, Pauty J, Ikeuchi Y, Suzuki I, Kikuchi A, Matsunaga YT. Bundle Gel Fibers with a Tunable Microenvironment for in Vitro Neuron Cell Guiding. ACS Appl Mater Interfaces. 2017 Dec 13;9(49):43250-43257. doi: 10.1021/acsami.7b14585. Epub 2017 Nov 29. PMID: 29086563.
  17. Kaneda S, Kawada J, Akutsu H, Ichida J, Ikeuchi Y, Fujii T. Compartmentalized embryoid body culture for induction of spatially patterned differentiation. Biomicrofluidics. 2017 Aug 2;11(4):041101. doi: 10.1063/1.4994989. PMID: 28852428; PMCID: PMC5552387.
  18. Huang J, Ikeuchi Y, Malumbres M, Bonni A. A Cdh1-APC/FMRP Ubiquitin Signaling Link Drives mGluR-Dependent Synaptic Plasticity in the Mammalian Brain. Neuron. 2015 May 6;86(3):726-39. doi: 10.1016/j.neuron.2015.03.049. Epub 2015 Apr 23. PMID: 25913861; PMCID: PMC4492466.
  19. Ito H, Shiwaku H, Yoshida C, Homma H, Luo H, Chen X, Fujita K, Musante L, Fischer U, Frints SG, Romano C, Ikeuchi Y, Shimamura T, Imoto S, Miyano S, Muramatsu SI, Kawauchi T, Hoshino M, Sudol M, Arumughan A, Wanker EE, Rich T, Schwartz C, Matsuzaki F, Bonni A, Kalscheuer VM, Okazawa H. "In utero gene therapy rescues microcephaly caused by Pqbp1-hypofunction in neural stem progenitor cells." Mol Psychiatry vol 20, pp459-71, 2015
  20. Ikeuchi Y, de la Torre-Ubieta L, Matsuda T, Steen H, Okazawa H, Bonni A. “The XLID Protein PQBP1 and the GTPase Dynamin 2 Define a Signaling Link that Orchestrates Ciliary Morphogenesis in Postmitotic Neurons.” Cell Reports vol 4, pp879-89, 2013
  21. Ito S, Akamatsu Y, Noma A, Kimura S, Miyauchi K, Ikeuchi Y, Suzuki T, Suzuki T. A single acetylation of 18 S rRNA is essential for biogenesis of the small ribosomal subunit in Saccharomyces cerevisiae. J Biol Chem. 2014 Sep 19;289(38):26201-12. doi: 10.1074/jbc.M114.593996. Epub 2014 Aug 1. PMID: 25086048; PMCID: PMC4176211.
  22. Kimura S, Miyauchi K, Ikeuchi Y, Thiaville PC, Crécy-Lagard Vd, Suzuki T. Discovery of the β-barrel-type RNA methyltransferase responsible for N6-methylation of N6-threonylcarbamoyladenosine in tRNAs. Nucleic Acids Res. 2014 Aug;42(14):9350-65. doi: 10.1093/nar/gku618. Epub 2014 Jul 24. PMID: 25063302; PMCID: PMC4132733.
  23. Ikeuchi Y, de la Torre-Ubieta L, Matsuda T, Steen H, Okazawa H, Bonni A. The XLID protein PQBP1 and the GTPase Dynamin 2 define a signaling link that orchestrates ciliary morphogenesis in postmitotic neurons. Cell Rep. 2013 Sep 12;4(5):879-89. doi: 10.1016/j.celrep.2013.07.042. Epub 2013 Aug 29. PMID: 23994472; PMCID: PMC4013279.
  24. Mejia LA, Litterman N, Ikeuchi Y, de la Torre-Ubieta L, Bennett EJ, Zhang C, Harper JW, Bonni A. A novel Hap1-Tsc1 interaction regulates neuronal mTORC1 signaling and morphogenesis in the brain. J Neurosci. 2013 Nov 13;33(46):18015-21. doi: 10.1523/JNEUROSCI.2290-13.2013. PMID: 24227713; PMCID: PMC3828457.
  25. Zhang C, Mejia LA, Huang J, Valnegri P, Bennett EJ, Anckar J, Jahani-Asl A, Gallardo G, Ikeuchi Y, Yamada T, Rudnicki M, Harper JW, Bonni A. The X-linked intellectual disability protein PHF6 associates with the PAF1 complex and regulates neuronal migration in the mammalian brain. Neuron. 2013 Jun 19;78(6):986-93. doi: 10.1016/j.neuron.2013.04.021. PMID: 23791194; PMCID: PMC3694281.
  26. Kimura S, Ikeuchi Y, Kitahara K, Sakaguchi Y, Suzuki T, Suzuki T. Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity. Nucleic Acids Res. 2012 May;40(9):4071-85. doi: 10.1093/nar/gkr1287. Epub 2011 Dec 30. PMID: 22210896; PMCID: PMC3351187.
  27. Huynh MA, Ikeuchi Y, Netherton S, de la Torre-Ubieta L, Kanadia R, Stegmüller J, Cepko C, Bonni S, Bonni A. An isoform-specific SnoN1-FOXO1 repressor complex controls neuronal morphogenesis and positioning in the mammalian brain. Neuron. 2011 Mar 10;69(5):930-44. doi: 10.1016/j.neuron.2011.02.008. PMID: 21382553; PMCID: PMC3073069.
  28. Litterman N, Ikeuchi Y, Gallardo G, O'Connell BC, Sowa ME, Gygi SP, Harper JW, Bonni A. An OBSL1-Cul7Fbxw8 ubiquitin ligase signaling mechanism regulates Golgi morphology and dendrite patterning. PLoS Biol. 2011 May;9(5):e1001060. doi: 10.1371/journal.pbio.1001060. Epub 2011 May 10. PMID: 21572988; PMCID: PMC3091842.
  29. Puram SV, Kim AH, Ikeuchi Y, Wilson-Grady JT, Merdes A, Gygi SP, Bonni A. A CaMKIIβ signaling pathway at the centrosome regulates dendrite patterning in the brain. Nat Neurosci. 2011 Jul 3;14(8):973-83. doi: 10.1038/nn.2857. PMID: 21725312; PMCID: PMC3391735.
  30. Puram SV, Riccio A, Koirala S, Ikeuchi Y, Kim AH, Corfas G, Bonni A. A TRPC5-regulated calcium signaling pathway controls dendrite patterning in the mammalian brain. Genes Dev. 2011 Dec 15;25(24):2659-73. doi: 10.1101/gad.174060.111. Epub 2011 Dec 1. PMID: 22135323; PMCID: PMC3248686.
  31. Bilimoria PM, de la Torre-Ubieta L, Ikeuchi Y, Becker EB, Reiner O, Bonni A. A JIP3-regulated GSK3β/DCX signaling pathway restricts axon branching. J Neurosci. 2010 Dec 15;30(50):16766-76. doi: 10.1523/JNEUROSCI.1362-10.2010. PMID: 21159948; PMCID: PMC3409248.
  32. de la Torre-Ubieta L, Gaudillière B, Yang Y, Ikeuchi Y, Yamada T, DiBacco S, Stegmüller J, Schüller U, Salih DA, Rowitch D, Brunet A, Bonni A. A FOXO-Pak1 transcriptional pathway controls neuronal polarity. Genes Dev. 2010 Apr 15;24(8):799-813. doi: 10.1101/gad.1880510. PMID: 20395366; PMCID: PMC2854394.
  33. Ikeuchi Y, Stegmüller J, Netherton S, Huynh MA, Masu M, Frank D, Bonni S, Bonni A. A SnoN-Ccd1 pathway promotes axonal morphogenesis in the mammalian brain. J Neurosci. 2009 Apr 1;29(13):4312-21. doi: 10.1523/JNEUROSCI.0126-09.2009. PMID: 19339625; PMCID: PMC2853192.
  34. Kim AH, Puram SV, Bilimoria PM, Ikeuchi Y, Keough S, Wong M, Rowitch D, Bonni A. A centrosomal Cdc20-APC pathway controls dendrite morphogenesis in postmitotic neurons. Cell. 2009 Jan 23;136(2):322-36. doi: 10.1016/j.cell.2008.11.050. PMID: 19167333; PMCID: PMC2707082.
  35. Yang Y, Kim AH, Yamada T, Wu B, Bilimoria PM, Ikeuchi Y, de la Iglesia N, Shen J, Bonni A. A Cdc20-APC ubiquitin signaling pathway regulates presynaptic differentiation. Science. 2009 Oct 23;326(5952):575-8. doi: 10.1126/science.1177087. PMID: 19900895; PMCID: PMC2846784.
  36. Ikeuchi Y, Kimura S, Numata T, Nakamura D, Yokogawa T, Ogata T, Wada T, Suzuki T, Suzuki T. Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. Nat Chem Biol. 2010 Apr;6(4):277-82. doi: 10.1038/nchembio.323. Epub 2010 Feb 7. PMID: 20139989.
  37. Kimura S, Ikeuchi Y, Kitahara K, Sakaguchi Y, Suzuki T, Suzuki T. “Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity.” Nucleic Acid Research 2011
  38. Chimnaronk S, Suzuki T, Manita T, Ikeuchi Y, Yao M, Suzuki T, Tanaka I. RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon. EMBO J. 2009 May 6;28(9):1362-73. doi: 10.1038/emboj.2009.69. Epub 2009 Mar 26. PMID: 19322199; PMCID: PMC2683049.
  39. Ikeuchi Y, Kitahara K, Suzuki T. The RNA acetyltransferase driven by ATP hydrolysis synthesizes N4-acetylcytidine of tRNA anticodon. EMBO J. 2008 Aug 20;27(16):2194-203. doi: 10.1038/emboj.2008.154. Epub 2008 Jul 31. PMID: 18668122; PMCID: PMC2500205.
  40. Suzuki T, Ikeuchi Y, Noma A, Suzuki T, Sakaguchi Y. Mass spectrometric identification and characterization of RNA-modifying enzymes. Methods Enzymol. 2007;425:211-29. doi: 10.1016/S0076-6879(07)25009-8. PMID: 17673085.
  41. Numata T, Ikeuchi Y, Fukai S, Suzuki T, Nureki O. Snapshots of tRNA sulphuration via an adenylated intermediate. Nature. 2006 Jul 27;442(7101):419-24. doi: 10.1038/nature04896. PMID: 16871210.
  42. Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol Cell. 2006 Jan 6;21(1):97-108. doi: 10.1016/j.molcel.2005.11.001. PMID: 16387657.
  43. Takeda H, Toyooka T, Ikeuchi Y, Yokobori S, Okadome K, Takano F, Oshima T, Suzuki T, Endo Y, Hori H. The substrate specificity of tRNA (m1G37) methyltransferase (TrmD) from Aquifex aeolicus. Genes Cells. 2006 Dec;11(12):1353-65. doi: 10.1111/j.1365-2443.2006.01022.x. PMID: 17121543.
  44. Noma A, Kirino Y, Ikeuchi Y, Suzuki T. Biosynthesis of wybutosine, a hyper- modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 2006 May 17;25(10):2142-54. doi: 10.1038/sj.emboj.7601105. Epub 2006 Apr 27. PMID: 16642040; PMCID: PMC1462984.
  45. Numata T, Ikeuchi Y, Fukai S, Adachi H, Matsumura H, Takano K, Murakami S, Inoue T, Mori Y, Sasaki T, Suzuki T, Nureki O. Crystallization and preliminary X-ray analysis of the tRNA thiolation enzyme MnmA from Escherichia coli complexed with tRNA(Glu). Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Apr 1;62(Pt 4):368-71. doi: 10.1107/S174430910600738X. Epub 2006 Mar 10. PMID: 16582487; PMCID: PMC2222564.
  46. Takano Y, Takayanagi N, Hori H, Ikeuchi Y, Suzuki T, Kimura A, Okuno T. A gene involved in modifying transfer RNA is required for fungal pathogenicity and stress tolerance of Colletotrichum lagenarium. Mol Microbiol. 2006 Apr;60(1):81-92. doi: 10.1111/j.1365-2958.2006.05080.x. PMID: 16556222.
  47. Numata T, Fukai S, Ikeuchi Y, Suzuki T, Nureki O. Structural basis for sulfur relay to RNA mediated by heterohexameric TusBCD complex. Structure. 2006 Feb;14(2):357-66. doi: 10.1016/j.str.2005.11.009. PMID: 16472754.
  48. Ote T, Hashimoto M, Ikeuchi Y, Su'etsugu M, Suzuki T, Katayama T, Kato J. Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation. Mol Microbiol. 2006 Jan;59(1):265-75. doi: 10.1111/j.1365-2958.2005.04932.x. Erratum in: Mol Microbiol. 2006 Apr;60(1):252. PMID: 16359333.
  49. Ikeuchi Y, Soma A, Ote T, Kato J, Sekine Y, Suzuki T. molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition. Mol Cell. 2005 Jul 22;19(2):235-46. doi: 10.1016/j.molcel.20
  50. Nakanishi K, Fukai S, Ikeuchi Y, Soma A, Sekine Y, Suzuki T, Nureki O. Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain. Proc Natl Acad Sci U S A. 2005 May 24;102(21):7487-92. doi: 10.1073/pnas.0501003102. Epub 2005 May 13. PMID: 15894617; PMCID: PMC1140429.
  51. Okamoto H, Watanabe K, Ikeuchi Y, Suzuki T, Endo Y, Hori H. Substrate tRNA recognition mechanism of tRNA (m7G46) methyltransferase from Aquifex aeolicus. J Biol Chem. 2004 Nov 19;279(47):49151-9. doi: 10.1074/jbc.M408209200. Epub 2004 Sep 8. PMID: 15358762.
  52. Soma A, Ikeuchi Y, Kanemasa S, Kobayashi K, Ogasawara N, Ote T, Kato J, Watanabe K, Sekine Y, Suzuki T. An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol Cell. 2003 Sep;12(3):689-98. doi: 10.1016/s1097-2765(03)00346-0. PMID: 14527414.

Reviews

  1. Chow A, Ikeuchi Y. "New approaches to understand dynamics of protein synthesis in neurons" SEISAN KENKYU vol 69, pp 115-121, 2017
  2. Pot I, Ikeuchi Y, Bonni A, Bonni S. “SnoN: bridging neurobiology and cancer biology.” Current Molecular Medicine vol 10, pp667-73, 2010

日本語論文・総説

  1. 梅垣祐介,池内与志穂 「神経特異的な制御を受けて生産される新生タンパク質の探索」 生産研究 vol 68, pp 201-204, 2016
  2. 川田治良,藤井輝夫,池内与志穂 「神経変性疾患の理解と治療へ向けた研究の概況と新しいアプローチ」 生産研究 vol 68, pp 205-210, 2016
  3. 池内 与志穂,鈴木 勉. 「RNA修飾に関わる硫黄リレータンパク質群の同定」 細胞工学 vol 25, pp 400-1, 2006
  4. 鈴木 勉,池内 与志穂,鈴木 健夫. 「機能性RNAのマススペクトロメトリー」 実験医学増刊 vol 22, pp 2511-22, 2004
  5. 池内 与志穂,鈴木 勉. 「リボヌクレオーム解析:RNA修飾遺伝子の網羅的探索」細胞工学 vol 22, pp 945-50, 2003