NISHINO Koichiro

写真a

Affiliation

Faculty of Agriculture Department of Veterinary Science

Title

Professor

External Link

Degree 【 display / non-display

  • Ph.D ( 2000.3   The University of Tokyo )

Research Areas 【 display / non-display

  • Life Science / Molecular biology

  • Life Science / Cell biology

  • Life Science / Developmental biology

  • Life Science / Genetics

  • Others / Others  / Epigenetics

 

Papers 【 display / non-display

  • Comprehensive analysis of chondroitin sulfate and aggrecan in the head cartilage of bony fishes: Identification of proteoglycans in the head cartilage of sturgeon. Reviewed

    Shionoya K, Suzuki T, Takada M, Sato K, Onishi S, Dohmae N, Nishino K, Wada T, Linhardt RJ, Toida T, Higashi K

    International journal of biological macromolecules   208   333 - 342   2022.3

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.ijbiomac.2022.03.125

    PubMed

  • Identification of an epigenetic signature in human induced pluripotent stem cells using a linear machine learning model Reviewed

    Nishino K, Takasawa K, Okamura K, Arai Y, Sekiya A, Akutsu H, Umezawa A.

    Human Cell   34 ( 1 )   99 - 110   2021.1

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Human Cell  

    The use of human induced pluripotent stem cells (iPSCs), used as an alternative to human embryonic stem cells (ESCs), is a potential solution to challenges, such as immune rejection, and does not involve the ethical issues concerning the use of ESCs in regenerative medicine, thereby enabling developments in biological research. However, comparative analyses from previous studies have not indicated any specific feature that distinguishes iPSCs from ESCs. Therefore, in this study, we established a linear classification-based learning model to distinguish among ESCs, iPSCs, embryonal carcinoma cells (ECCs), and somatic cells on the basis of their DNA methylation profiles. The highest accuracy achieved by the learned models in identifying the cell type was 94.23%. In addition, the epigenetic signature of iPSCs, which is distinct from that of ESCs, was identified by component analysis of the learned models. The iPSC-specific regions with methylation fluctuations were abundant on chromosomes 7, 8, 12, and 22. The method developed in this study can be utilized with comprehensive data and widely applied to many aspects of molecular biology research.

    DOI: 10.1007/s13577-020-00446-3

    Scopus

    PubMed

  • Dog Steroidogenic Factor-1: Molecular cloning and analysis of epigenetic regulation Reviewed

    SEKIYA Asato, TAKASAWA Ken, ARAI Yoshikazu, TORISU Shidow, NISHINO Koichiro

    Journal of Veterinary Medical Science   82 ( 6 )   681 - 689   2020.4

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:JAPANESE SOCIETY OF VETERINARY SCIENCE  

    <p>Steroidogenic factor 1 (SF-1) is a nuclear receptor that is important in steroid hormone production, and adrenal and gonad development. The <i>SF-1</i> gene is highly conserved among most vertebrates. However, dog <i>SF-1</i> registered in public databases, such as CanFam3.1, lacks the 5’ end compared to other mammals including mouse, human, bovine, and cat. Whether this defect is due to species differences or database error is unclear. Here, we determined the full-length dog <i>SF-1</i> cDNA sequence and identified the missing 5’ end sequence in the databases. The coding region of the dog <i>SF-1</i> gene has 1,386 base pairs, and the protein has 461 amino acid residues. Sequence alignment analysis among vertebrates revealed that the 5’ end sequence of dog <i>SF-1</i> cDNA is highly conserved compared to other vertebrates. The genomic position of the first exon was determined, and its promoter region sequence was analyzed. The DNA methylation state at the basal promoter and the expression of dog <i>SF-1</i> in steroidogenic tissues and non-steroidogenic cells were examined. CpG sites at the basal promoter displayed methylation kinetics inversely correlated with gene expression. The promoter was hypomethylated and hypermethylated in <i>SF-1</i> expressing and non-<i>SF-1</i> expressing tissues, respectively. In conclusion, we identified the true full sequence of dog <i>SF-1</i> cDNA and determined the genome sequence around the first exon. The gene is under the control of epigenetic regulation, such as DNA methylation, at the promoter.</p>

    DOI: 10.1292/jvms.20-0050

    Scopus

    PubMed

    CiNii Research

  • DNA methylation ambiguity in the Fibrillin-1 (FBN1) CpG island shore possibly involved in Marfan syndrome Reviewed

    Nishino K, Arai Y, Takasawa k, Toyoda M, Yamazaki-Inoue M, Sugawara T, Akutsu H, Nishimura K, Ohtaka M, Nakanishi M, Umezawa A.

    Scientific Reports   10 ( 1 )   5287   2020.3

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Scientific Reports  

    Fibrillin-1 (FBN1) is responsible for haploinsufficient and autosomal dominant Marfan syndrome. Even in the same Marfan pedigree, penetrance and expressivity in heterozygous individuals can differ and result in variable disease onset and severity. Thus, other factors in addition to mutations in FBN1 are likely to contribute to the disease. In this study, we examined the regulation of FBN1 in porcine Marfan syndrome model, focusing on DNA methylation patterns distinguishable as wild-type (WT) and FBN1 null (KO) alleles in heterozygous cells. Most importantly, the ratio of the transcriptionally active hypomethylated WT allele was altered during cellular passage and highly correlated with FBN1 mRNA level compared with that in the KO allele. Transcribed FBN1 RNA from the KO allele was abolished after splicing coupled with translational initiation, suggesting that the functional FBN1 mRNA levels were affected by DNA methylation of the WT allele.

    DOI: 10.1038/s41598-020-62127-3

    Scopus

    PubMed

  • Epigenetic-scale comparison of human iPSCs generated by retrovirus, Sendai virus or episomal vectors Reviewed

    Nishino K, Arai Y, Takasawa k, Toyoda M, Yamazaki-Inoue M, Sugawara T, Akutsu H, Nishimura K, Ohtaka M, Nakanishi M, Umezawa A.

    Regenerative Therapy   9   71 - 78   2018.12

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

    Human induced pluripotent stem cells (iPSCs) are established by introducing several reprogramming factors, such as OCT3/4, SOX2, KLF4, c-MYC. Because of their pluripotency and immortality, iPSCs are considered to be a powerful tool for regenerative medicine. To date, iPSCs have been established all over the world by various gene delivery methods. All methods induced high-quality iPSCs, but epigenetic analysis of abnormalities derived from differences in the gene delivery methods has not yet been performed. Here, we generated genetically matched human iPSCs from menstrual blood cells by using three kinds of vectors, i.e., retrovirus, Sendai virus, and episomal vectors, and compared genome-wide DNA methylation profiles among them. Although comparison of aberrant methylation revealed that iPSCs generated by Sendai virus vector have lowest number of aberrant methylation sites among the three vectors, the iPSCs generated by non-integrating methods did not show vector-specific aberrant methylation. However, the differences between the iPSC lines were determined to be the number of random aberrant hypermethylated regions compared with embryonic stem cells. These random aberrant hypermethylations might be a cause of the differences in the properties of each of the iPSC lines.

    DOI: 10.1016/j.reth.2018.08.002

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Books 【 display / non-display

  • 獣医発生学

    木曽康郎、西野光一郎 他( Role: Joint translator)

    学窓社  2019.2 

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    Responsible for pages:68-78   Language:Japanese Book type:Textbook, survey, introduction

  • カラーアトラス動物発生学

    山本雅子、谷口和美、西野光一郎 他( Role: Joint translator)

    緑書房  2014.4 

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    Responsible for pages:199-211   Language:Japanese Book type:Textbook, survey, introduction

  • DNAメチル化研究法

    塩田邦郎, 田中智, 服部中, 大鐘潤, 今村拓也, 西野光一郎, 鈴木雅子, 小田真由美, 服部奈緒子, 冨川順子, ユリアクレメンスカ, 岩谷美沙( Role: Joint author)

    学会出版センター  2006.10 

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    Language:Japanese Book type:Scholarly book

MISC 【 display / non-display

  • コンパニオンアニマル再生医療における間葉系幹細胞 -自験例を中心に Invited

    関谷麻杜, 鳥巣至道, 西野光一郎

    医学のあゆみ   272 ( 10 )   1075 - 1080   2020.3

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)   Publisher:医歯薬出版株式会社  

  • 機械学習とiPS細胞研究から得られるバイオビッグデータの融合 Invited

    高澤建, 新井良和, 西野光一郎

    再生医療の開発戦略と最新研究事例集   298 - 305   2019.2

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)   Publisher:(株)技術情報協会  

  • 幹細胞・iPS細胞研究におけるエピジェネティクスと医療応用

    西野光一郎, 梅澤明弘

    エピジェネティクスの産業応用   362 - 369   2014.4

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)   Publisher:シーエムシー出版  

  • 再生医療

    梅澤明弘, 西野光一郎

    エピジェネティクスキーワード事典   235 - 241   2013.11

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)   Publisher:羊土社  

  • エピジェネティクスと病気「再生医療とエピジェネティクス」

    梅澤明弘, 西野光一郎

    遺伝子医学MOOK   25   2013.8

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (bulletin of university, research institution)   Publisher:株式会社メディカルドゥ  

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Presentations 【 display / non-display

  • DNAメチル化によるBCOR遺伝子発現制御機構の解明

    吉田 里美、関谷 麻杜、高橋 真央、新井 良和、西野 光一郎

    第114回 日本繁殖生物学会大会  (筑波市)  日本獣医学会

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    Event date: 2021.9.21 - 2021.9.24

    Language:Japanese   Presentation type:Poster presentation  

    Venue:筑波市  

  • ヒト多能性幹細胞における未分化状態維持機構の解明

    高橋 真央、関谷 麻杜、新井 良和、西野 光一郎

    第114回 日本繁殖生物学会大会  (筑波市)  日本獣医学会

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    Event date: 2021.9.21 - 2021.9.24

    Language:Japanese   Presentation type:Poster presentation  

    Venue:筑波市  

  • ヒト雄性iPS細胞における活性X染色体のDNAメチル化動態の解析

    富田 清良、関谷 麻杜、新井 良和、西野 光一郎

    第113回 日本繁殖生物学会大会  (筑波市)  日本獣医学会

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    Event date: 2020.9.23 - 2020.9.25

    Language:Japanese   Presentation type:Poster presentation  

    Venue:筑波市  

  • 免疫不全疑い犬における遺伝子診断:CD40 Ligandの点変異の同定

    森 正太郎、新井 良和、金子 泰之、鳥巣 至道、西野 光一郎

    第162回 日本獣医学会学術集会  (筑波市)  日本獣医学会

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    Event date: 2019.9.10 - 2019.9.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:筑波市  

  • 多能性を有するイヌiPS細胞の樹立と特性解析

    西本光佑、新井 良和、西野 光一郎

    第162回 日本獣医学会学術集会  (筑波市)  日本獣医学会

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    Event date: 2019.9.10 - 2019.9.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:筑波市  

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Grant-in-Aid for Scientific Research 【 display / non-display

  • DNAメチル化を基盤としたヒト心筋細胞発生分化機構の制御に関する研究

    Grant number:21H02381  2021.04 - 2024.03

    科学研究費補助金  基盤研究(B)

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    Authorship:Principal investigator  Grant type:Competitive

  • 自然発症腎形成不全マウスを用いた腎尿路発生の遺伝学的機序の解明

    Grant number:19K09732  2019.04 - 2023.03

    科学研究費補助金  基盤研究(C)

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    Authorship:Coinvestigator(s)  Grant type:Competitive

  • エピジェネティック制御によるヒトTERT遺伝子制御機構と細胞不死化獲得機構の解明

    Grant number:16K15055  2016.04 - 2018.03

    科学研究費補助金  挑戦的萌芽研究

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    Authorship:Principal investigator 

    体細胞から人工多能性幹細胞(iPS細胞)への形質転換時における細胞不死化はテロメア伸長に関わるTERT遺伝子の発現獲得と大きく関係している。申請者はこれまでヒトTERTプロモーターの遠位領域にヒト多能性幹細胞特異的DNAメチル化可変領域(TERT-DMR)を同定したが、iPS細胞樹立時におけるTERT-DMRと発現獲得機構関連については明らかとなっていない。本研究では、TERT-DMRにおけるヒストン修飾とクロマチン構造の決定、およびTERT-DMRに結合する転写因子の探索と、その機能解析を通してTERT-DMRのDNAメチル化を介したヒトTERT遺伝子のエピジェネティック発現制御機構の解明を行う。

  • 哺乳動物の中枢・末梢クロストークによる摂食と走行運動調節機構の分子生物学的研究

    Grant number:26292165  2014.04 - 2018.03

    科学研究費補助金  基盤研究(B)

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    Authorship:Coinvestigator(s)  Grant type:Competitive

  • 疾患特異的犬猫iPS細胞を用いた疾患発症機序の解明と臨床応用基盤技術の開発

    Grant number:25292187  2013.04 - 2016.03

    科学研究費補助金  基盤研究(B)

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    Authorship:Principal investigator  Grant type:Competitive

    イヌやネコは偏った交配によって疾患原因遺伝子の濃縮を伴ってきた。このためヒトにおいて希少疾患と言われるものがこれらの動物では高頻度に自然発症するケースが多い。それ故、疾患動物由来人工多能性幹細胞(iPS細胞)を用いた難病原因の解明、診断、治療法の技術基盤の確立は獣医療への応用ばかりでなくヒト疾患モデルとしてヒト医療応用への貢献度も非常に高い。しかし、これら疾患伴侶動物からiPS細胞を樹立したとする報告はまだない。本研究では変性性脊髄症(DM)イヌおよびグルタル酸尿症II型(GAII)ネコからiPS細胞を樹立し、疾患発症機序の解明と予防および治療法への応用を試みる。また、より安全なゲノムを傷つけないiPS細胞と各種動物由来フィーダー細胞の作成系を確立し、真に獣医再生医療臨床応用ができるイヌ、ネコiPS細胞の樹立を行う。