Updated on 2024/09/17

写真a

 
ICHIHARA Kazuya
 
Organization
Graduate School of Science Assistant Professor
Graduate School
Graduate School of Science
Undergraduate School
School of Science Department of Biological Science
Title
Assistant Professor

Research Interests 2

  1. 翻訳

  2. バイオインフォマティクス

Research Areas 2

  1. Life Science / Molecular biology

  2. Life Science / Genome biology

Research History 4

  1. 名古屋大学大学院 理学研究科 理学専攻   助教

    2023.6

  2. 九州大学 生体防御医学研究所   分子医科学分野   学術研究員

    2023.4 - 2023.5

  3. 日本学術振興会 特別研究員 (PD)

    2022.4 - 2023.3

  4. Japan Society for Promotion of Science

    2020.4 - 2022.3

Education 2

  1. Kyushu University

    2019.4 - 2022.3

  2. Kyushu University

    2017.4 - 2019.3

Professional Memberships 2

  1. 日本分子生物学会

  2. 日本RNA学会

Awards 1

  1. 第24回リトリート 最優秀ポスター賞

    2022.7   九州大学 生体防御医学研究所  

 

Papers 10

  1. Patient-derived organoids of pancreatic ductal adenocarcinoma for subtype determination and clinical outcome prediction Reviewed

    Kazuhide Matsumoto, Nao Fujimori, Kazuya Ichihara, Ayumu Takeno, Masatoshi Murakami, Akihisa Ohno, Shotaro Kakehashi, Katsuhito Teramatsu, Keijiro Ueda, Kohei Nakata, Osamu Sugahara, Takeo Yamamoto, Akinobu Matsumoto, Keiichi I. Nakayama, Yoshinao Oda, Masafumi Nakamura, Yoshihiro Ogawa

    Journal of Gastroenterology     2024.4

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    Abstract

    Background

    Recently, two molecular subtypes of pancreatic ductal adenocarcinoma (PDAC) have been proposed: the “Classical” and “Basal-like” subtypes, with the former showing better clinical outcomes than the latter. However, the “molecular” classification has not been applied in real-world clinical practice. This study aimed to establish patient-derived organoids (PDOs) for PDAC and evaluate their application in subtype classification and clinical outcome prediction.

    Methods

    We utilized tumor samples acquired through endoscopic ultrasound-guided fine-needle biopsy and established a PDO library for subsequent use in morphological assessments, RNA-seq analyses, and in vitro drug response assays. We also conducted a prospective clinical study to evaluate whether analysis using PDOs can predict treatment response and prognosis.

    Results

    PDOs of PDAC were established at a high efficiency (> 70%) with at least 100,000 live cells. Morphologically, PDOs were classified as gland-like structures (GL type) and densely proliferating inside (DP type) less than 2 weeks after tissue sampling. RNA-seq analysis revealed that the “morphological” subtype (GL vs. DP) corresponded to the “molecular” subtype (“Classical” vs. “Basal-like”). The “morphological” classification predicted the clinical treatment response and prognosis; the median overall survival of patients with GL type was significantly longer than that with DP type (P < 0.005). The GL type showed a better response to gemcitabine than the DP type in vitro, whereas the drug response of the DP type was improved by the combination of ERK inhibitor and chloroquine.

    Conclusions

    PDAC PDOs help in subtype determination and clinical outcome prediction, thereby facilitating the bench-to-bedside precision medicine for PDAC.

    DOI: 10.1007/s00535-024-02103-0

    Other Link: https://link.springer.com/article/10.1007/s00535-024-02103-0/fulltext.html

  2. Mechanistic dissection of premature translation termination induced by acidic residues-enriched nascent peptide Reviewed

    Yuhei Chadani, Takashi Kanamori, Tatsuya Niwa, Kazuya Ichihara, Keiichi I. Nakayama, Akinobu Matsumoto, Hideki Taguchi

    Cell Reports   Vol. 42 ( 12 ) page: 113569   2023.12

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.celrep.2023.113569

  3. The ASC‐1 complex promotes translation initiation by scanning ribosomes Reviewed

    Yuki Kito, Akinobu Matsumoto, Kazuya Ichihara, Chisa Shiraishi, Ronghao Tang, Atsushi Hatano, Masaki Matsumoto, Peixun Han, Shintaro Iwasaki, Keiichi I Nakayama

    The EMBO Journal     page: e112869   2023.4

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

    DOI: 10.15252/embj.2022112869

  4. RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function. Reviewed International journal

    Chisa Shiraishi, Akinobu Matsumoto, Kazuya Ichihara, Taishi Yamamoto, Takeshi Yokoyama, Taisuke Mizoo, Atsushi Hatano, Masaki Matsumoto, Yoshikazu Tanaka, Eriko Matsuura-Suzuki, Shintaro Iwasaki, Shouji Matsushima, Hiroyuki Tsutsui, Keiichi I Nakayama

    Nature communications   Vol. 14 ( 1 ) page: 2131   2023.4

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

    Although several ribosomal protein paralogs are expressed in a tissue-specific manner, how these proteins affect translation and why they are required only in certain tissues have remained unclear. Here we show that RPL3L, a paralog of RPL3 specifically expressed in heart and skeletal muscle, influences translation elongation dynamics. Deficiency of RPL3L-containing ribosomes in RPL3L knockout male mice resulted in impaired cardiac contractility. Ribosome occupancy at mRNA codons was found to be altered in the RPL3L-deficient heart, and the changes were negatively correlated with those observed in myoblasts overexpressing RPL3L. RPL3L-containing ribosomes were less prone to collisions compared with RPL3-containing canonical ribosomes. Although the loss of RPL3L-containing ribosomes altered translation elongation dynamics for the entire transcriptome, its effects were most pronounced for transcripts related to cardiac muscle contraction and dilated cardiomyopathy, with the abundance of the encoded proteins being correspondingly decreased. Our results provide further insight into the mechanisms and physiological relevance of tissue-specific translational regulation.

    DOI: 10.1038/s41467-023-37838-6

    PubMed

  5. Identification of unannotated coding sequences and their physiological functions Reviewed

    Kazuya Ichihara, Keiichi I Nakayama, Akinobu Matsumoto

    The Journal of Biochemistry     2022.8

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    Summary

    Most protein-coding sequences (CDSs) are predicted sequences based on criteria such as a size sufficient to encode a product of at least 100 amino acids and with translation starting at an AUG initiation codon. However, recent studies based on ribosome profiling and mass spectrometry have shown that several RNAs annotated as long noncoding RNAs (lncRNAs) are actually translated to generate polypeptides of fewer than 100 amino acids, and that many proteins are translated from near-cognate initiation codons such as CUG and GUG. Furthermore, studies of genetically engineered mouse models have revealed that such polypeptides and proteins contribute to diverse physiological processes. In this review, we describe the latest methods for the identification of unannotated CDSs and provide examples of their physiological functions.

    DOI: 10.1093/jb/mvac064

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Books 1

  1. 未注釈ORFの同定とその生理機能

    市原知哉, 岩崎信太郎, 松本有樹修( Role: Joint author ,  40: 2003-2010)

    実験医学増刊  2022.7 

MISC 3

  1. eIF2D counteracts intrinsic ribosome destabilization (IRD) during translation elongation

    市原知哉, 松本有樹修, 幡野敦, 松本雅記, 茶谷悠平, 田口英樹, 中山敬一

    日本分子生物学会年会プログラム・要旨集(Web)   Vol. 45th   2022

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  2. Molecular mechanism and biological significance of non-AUG translation initiation revealed by precise identification of translation initiation sites

    市原知哉, 松本有樹修, 西田紘士, 今見考志, 石濱泰, 中山敬一

    日本分子生物学会年会プログラム・要旨集(Web)   Vol. 44th   2021

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  3. Combinatorial analysis of translatome and proteome unveils the importance of hidden ORFs

    松本有樹修, 市原知哉, 西田紘士, 今見考志, 石濱泰, 中山敬一

    日本分子生物学会年会プログラム・要旨集(Web)   Vol. 44th   2021

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Presentations 4

  1. Combinatorial analysis of translation dynamics reveals eIF2 dependence of translation initiation at near-cognate codons

    Kazuya Ichihara, Akinobu Matsumoto, Hiroshi Nishida, Yuki Kito, Hideyuki Shimizu, Yuichi Shichino, Shintaro Iwasaki, Koshi Imami, Yasushi Ishihama, Keiichi I Nakayama

    2021.9.28 

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    Language:Japanese   Presentation type:Oral presentation (general)  

  2. 精密な翻訳開始点の同定により明らかとなったNon-AUG翻訳開始の分子機構と生物学的意義

    市原 知哉, 松本 有樹修, 西田 紘士, 今見 考志, 石濱 泰, 中山 敬一

    第44回日本分子生物学会年会  2021.12.3 

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    Language:Japanese   Presentation type:Oral presentation (general)  

  3. eIF2D recycles 40S ribosomal subunit during intrinsic ribosome destabilization (IRD)

    Kazuya Ichihara, Yuhei Chadani, Atsushi Hatano, Masaki Matsumoto, Hideki Taguchi, Keiichi I Nakayama, Akinobu Matsumoto

    2023.7.6 

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    Language:Japanese   Presentation type:Oral presentation (general)  

  4. 5'キャップを持たず安定的に存在するmRNAの機能解析

    市原 知哉, 平田 実奈, 野島 孝之, 中山 敬一, 松本 有樹修

    第46回日本分子生物学会年会  2023.12.8 

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    Language:Japanese   Presentation type:Oral presentation (general)  

KAKENHI (Grants-in-Aid for Scientific Research) 2

  1. 内発的リボソーム不安定化 (IRD)におけるeIF2Dの機能解明

    Grant number:24K18054  2024.4 - 2026.3

    日本学術振興会  科学研究費助成事業  若手研究

    市原 知哉

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    Authorship:Principal investigator 

    Grant amount:\4680000 ( Direct Cost: \3600000 、 Indirect Cost:\1080000 )

  2. ユビキチン修飾による鉄代謝制御系の最上流因子の探索

    Grant number:20J20906  2020.4 - 2023.3

    日本学術振興会  科学研究費助成事業 特別研究員奨励費  特別研究員奨励費

    市原 知哉

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    Authorship:Principal investigator 

    Grant amount:\2500000 ( Direct Cost: \2500000 )

 

Teaching Experience (Off-campus) 1

  1. バイオインフォマティクス

    九州大学 生体防御医学研究所)