名古屋大学 大学院 理学研究科 理学専攻 生命理学講座 分子発現制御学グループ

Group of Gene Expression and Regulation, Nagoya University

2024

• Patient-derived organoids of pancreatic ductal adenocarcinoma for subtype determination and clinical outcome prediction.
  J. Gastroenterol., Online ahead of print, 2024.

  膵管腺癌（PDAC）には、“Classical “と “Basal-like “という分子サブタイプが提唱されているが、PDACの患者由来オルガノイド（PDO）を樹立することにより形態学的にサブタイプを分類できるようになり、臨床転帰の予測が容易になった。

• The complex etiology of autism spectrum disorder due to missense mutations of CHD8.
  Mol. Phychiatry, Online ahead of print, 2024.

  CHD8は自閉スペクトラム症（ASD）で頻繁に変異する遺伝子である。ASD患者におけるCHD8ミスセンス変異を予測スコアに従って特徴付け、そのような変異がCHD8の生化学的活性、胚性幹細胞の神経分化、マウスの行動に及ぼす影響を解析した。

2023

• Mechanistic dissection of premature translation termination induced by acidic residues-enriched nascent peptide.
  Cell Rep. 42(12): 113569, 2023.

  大腸菌における内在性リボソーム不安定化（IRD）の詳細な分子機構を明らかにした。酸性リッチアミノ酸配列の翻訳によって、70Sリボソームのコンフォメーションが異常な状態に変化して非正規の翻訳終結が起こる。

• RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function.
  Nat. Commun. 14(1): 2131, 2023.

  心臓や骨格筋などの横紋筋特異的に、RPL3のパラログであるRPL3Lが発現しており、横紋筋にはRPL3Lを含むMyo-ribosomeが存在していた。
  Myo-ribosomeは心臓の収縮に関わる遺伝子の効率的な翻訳に重要であり、Myo-ribosomeを欠損したマウスは心臓の収縮能が低下していた。

• The ASC-1 complex promotes translation initiation by scanning ribosomes.
  EMBO J. 42(12): e112869, 2023.

  ASC-1複合体は衝突した80Sリボソーム（ダイソーム）の解離に寄与することが知られていたが、Sel-TCP-MSという新技術を開発することにより、ASC-1複合体は走査リボソームにも結合していることを見出した。ASC-1複合体の欠損により走査リボソームの動態が乱れた。

2022

• Kastor and Polluks polypeptides encoded by a single gene locus cooperatively regulate VDAC and spermatogenesis.
  Nat. Commun. 13(1): 1071, 2022.

  単一のノンコーディングRNAの遺伝子座から、アミノ酸配列が異なる２つの新規ポリペプチドが翻訳されていることを発見し、これらを双子座の星に
  由来するKastorとPolluksと名付けた。KastorとPolluksはどちらもVDACに結合し、これらを欠損する雄マウスは不妊になる。

2021

• A ubiquitin-like protein encoded by the “noncoding” RNA TINCR promotes keratinocyte proliferation and wound healing.
  PLOS Genet. 17(8): e1009686, 2021.

  TINCRは皮膚科学において有名なノンコーディングRNAの一つであったが、TINCRがユビキチン様ドメインを持つ新規タンパク質を翻訳することを
  明らかにした。このタンパク質は皮膚の再生を促進する役割を担っていた。

• Combinatorial analysis of translation dynamics reveals eIF2 dependence of translation initiation at near-cognate codons.
  Nucleic Acids Res. 49(13): 7298-7317, 2021.

  Sel-TCP-seq, Ribo-seq, TI-seqを組み合わせて解析するTISCAを開発し、翻訳開始点を精密に同定できるようになった。TISCAにより多くのタンパク質がNon-AUG開始コドンからも翻訳されることを見出し、Non-AUG開始コドンの大部分はeIF2AやeIF2DでなくeIF2依存的に翻訳されることを明らかにした。

2017

• mTORC1 and muscle regeneration are regulated by the LINC00961 encoded SPAR polypeptide.
  Nature 12;541(7636): 228-232, 2017.

  ノンコーディングRNAと思われていたLINC00961がポリペプチドを翻訳すること、さらにそのポリペプチドはアミノ酸依存的なmTORC1シグナルを
  制御することを明らかにした。

2024

• Patient-derived organoids of pancreatic ductal adenocarcinoma for subtype determination and clinical outcome prediction.
  Matsumoto K., Fujimori N., Ichihara K., Takeno A., Murakami M., Ohno A., Kakehashi S., Teramatsu K., Ueda K., Nakata K., Sugahara O., Yamamoto T., Matsumoto A., Nakayama KI., Oda Y., Nakamura M., Ogawa Y.
  J. Gastroenterol., Online ahead of print, 2024.
• The complex etiology of autism spectrum disorder due to missense mutations of CHD8.
  Shiraishi T., Katayama Y., Nishiyama M., Shoji H., Miyakawa T., Mizoo T., Matsumoto A., Hijikata A., Shirai T., Mayanagi K., Nakayama KI.
  Mol. Phychiatry, Online ahead of print, 2024.
• Large-scale animal model study uncovers altered brain pH and lactate levels as a transdiagnostic endophenotype of neuropsychiatric disorders involving cognitive impairment.
  Hagihara H., International Brain pH Project Consortium, and Miyakawa T.
  eLife, 12: RP89376, 2024.

2023

• Mechanistic dissection of premature translation termination induced by acidic residues-enriched nascent peptide.
  Chadani Y., Kanamori T., Niwa T., Ichihara K., Nakayama KI., Matsumoto A., Taguchi H.
  Cell Rep. 42(12): 113569, 2023.
• RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function.
  Shiraishi C.^†, Matsumoto A.^†*, Ichihara K., Yamamoto T., Yokoyama T., Mizoo T., Hatano A., Matsumoto M., Tanaka Y., Matsuura-Suzuki E., Iwasaki S., Matsushima S., Tsutsui H., Nakayama KI.*
  (†co-first author, *corresponding authors)
  Nat. Commun. 14(1): 2131, 2023.
• The ASC-1 complex promotes translation initiation by scanning ribosomes.
  Kito Y.^†, Matsumoto A.^†*, Ichihara K.^†, Shiraishi C., Tang R., Hatano A., Matsumoto M., Han P., Iwasaki S., Nakayama KI.*
  (†co-first author, *corresponding authors)
  EMBO J. 42(12): e112869, 2023.
• Identification of unannotated coding sequences and their physiological functions.
  Ichihara K., Nakayama KI.*, Matsumoto A.*
  (*corresponding authors)
  J. Biochem. 173(4): 237-242, 2023.

2022

• Spatiotemporal reprogramming of differentiated cells underlies regeneration and neoplasia in the intestinal epithelium.
  Higa T., Okita Y., Matsumoto A., Nakayama S., Oka T., Sugahara O., Koga D., Takeishi S., Nakatsumi H., Hosen N., Robine S., Taketo MM., Sato T., Nakayama KI.
  Nat. Commun. 13(1): 1500, 2022.
• Kastor and Polluks polypeptides encoded by a single gene locus cooperatively regulate VDAC and spermatogenesis.
  Mise S.^†, Matsumoto A.^†*, Shimada K., Hosaka T., Takahashi M., Ichihara K., Shimizu H., Shiraishi C., Saito D., Suyama M., Yasuda T., Ide T., Izumi Y., Bamba T., Kimura-Someya T., Shirouzu M., Miyata H., Ikawa M., Nakayama KI.*
  (†co-first author, *corresponding authors)
  Nat. Commun. 13(1): 1071, 2022.

2021

• A ubiquitin-like protein encoded by the “noncoding” RNA TINCR promotes keratinocyte proliferation and wound healing.
  Nita A., Matsumoto A.*, Tang R., Shiraishi C., Ichihara K., Saito D., Suyama M., Yasuda T., Tsuji G., Furue M., Katayama B., Ozawa T., Murata T., Dainichi T., Kabashima K., Hatano A., Matsumoto M., Nakayama KI.*
  (*corresponding authors)
  PLOS Genet. 17(8): e1009686, 2021.
• Combinatorial analysis of translation dynamics reveals eIF2 dependence of translation initiation at near-cognate codons.
  Ichihara K.^†, Matsumoto A.^†*, Nishida H., Kito Y., Shimizu H., Shichino Y., Iwasaki S., Imami K., Ishihama Y., Nakayama KI.*
  (†co-first author, *corresponding authors)
  Nucleic Acids Res. 49(13): 7298-7317, 2021.
• The autism-related protein CHD8 contributes to the stemness and differentiation of mouse hematopoietic stem cells.
  Nita A., Muto Y., Katayama Y., Matsumoto A., Nishiyama M., Nakayama KI.
  Cell Rep. 34(5): 108688, 2021.

2020

• A lipid bilayer formed on a hydrogel bead for single ion channel recordings.
  Hirano M., Yamamoto D., Asakura M., Hayakawa T., Mise S., Matsumoto A., Ide T.
  Micromachines 11(12): 1070, 2020.
• Cell cycle-dependent localization of the proteasome to chromatin.
  Kito Y., Matsumoto M., Hatano A., Takami T., Oshikawa K., Matsumoto A., Nakayama KI.
  Sci. Rep. 10(1): 5801 – 5801, 2020.

2019

• Intragenic antagonistic roles of protein and circRNA in tumorigenesis.
  Guarnerio J., Zhang Y., Cheloni G., Panella R., Mae Katon J., Simpson M., Matsumoto A., Papa A., Loretelli C., Petri A., Kauppinen S., Garbutt C., Nielsen GP., Deshpande V., Castillo-Martin M., Cordon-Cardo C., Dimitrios S., Clohessy JG., Batish M., Pandolfi PP.
  Cell Res. 29(8): 628-640, 2019.

2018

• Hidden peptides encoded by putative noncoding RNAs.
  Matsumoto A.*, Nakayama KI.
  (*corresponding author)
  Cell. Struct. Funct. 43(1): 75-83, 2018.

2006~2017

• SPAR, a lncRNA encoded mTORC1 inhibitor.
  Matsumoto A., Clohessy JG, Pandolfi PP.
  Cell Cycle 16: 815-816, 2017.
• mTORC1 and muscle regeneration are regulated by the LINC00961 encoded SPAR polypeptide.
  Matsumoto A., Pasut A., Matsumoto M., Yamashita R., Fung J., Monteleone E. Saghatelian A., Nakayama KI., Clohessy JG, Pandolfi PP.
  Nature 12;541(7636): 228-232, 2017.
• The pleiotropic role of non-coding genes in development and cancer.
  Pasut A, Matsumoto A., Clohessy JG, Pandolfi PP.
  Curr. Opin. Cell Biol. 16;43: 104-113, 2016.
• Fbw7 targets GATA3 through CDK2-dependent proteolysis and contributes to regulation of T-cell development.
  Kitagawa K., Shibata K., Matsumoto A., Matsumoto M., Ohhata T., Nakayama KI., Niida H., Kitagawa M.
  Mol. Cell. Biol. 34: 2732-2744, 2014.
• p57 regulates T cell development and prevents lymphomagenesis by balancing p53 activity and pre-TCR signaling.
  Matsumoto A.^†, Takeishi S.^†, Nakayama KI.
  (†co-first author)
  Blood 29;123(22): 3429-3439, 2014.
• Zoledronic acid enhances lipopolysaccharide-stimulated proinflammatory reactions through controlled expression of SOCS1 in macrophages.
  Muratsu D., Yoshiga D., Taketomi T., Onimura T., Seki Y., Matsumoto A., Nakamura S.
  PLOS One 9: 8(7), 2013.
• p57 controls adult neural stem cell quiescence and modulates the pace of lifelong neurogenesis.
  Furutachi S., Matsumoto A., Nakayama KI., Gotoh Y.
  EMBO J. 32: 970-981, 2013.
• Ablation of Fbxw7 eliminates leukemia-initiating cells by preventing quiescence.
  Takeishi S., Matsumoto A., Onoyama I., Naka K., Hirao A., Nakayama KI.
  Cancer Cell 23: 347-361, 2013.
• Role of key regulators of the cell cycle in maintenance of hematopoietic stem cells.
  Matsumoto A., Nakayama KI.
  Biochem. Biophys. Acta 1830: 2335-2344, 2013.
• Development of mice without Cip/Kip CDK inhibitors.
  Tateishi Y., Matsumoto A., Kanie T., Hara E., Nakayama K., Nakayama KI.
  Biochem. Biophys. Res. Commun. 427: 285-292, 2012.
• Increased efficiency in the generation of induced pluripotent stem cells by Fbxw7 ablation.
  Okita Y.^†, Matsumoto A.^†, Yumimoto K., Isoshita R., Nakayama KI.
  (†co-first author)
  Genes Cells 17: 768-777, 2012.
• SCF^Fbw7 modulates the NFκB signaling pathway by targeting NFκB2 for ubiquitination and destruction.
  Fukushima H.^†, Matsumoto A.^†, Inuzuka H.^†, Zhai B., Lau A., Wan A., Gao D., Shaik S., Yuan M., Gygi S., Jimi E., Asara J., Nakayama K., Nakayama KI., Wei W.
  (†co-first author)
  Cell Rep. 1: 434-443, 2012.
• Genetic reevaluation of the role of F-box proteins in cyclin D1 degradation.
  Kanie T., Onoyama I., Matsumoto A., Yamada M., Nakatsumi H., Tateishi Y., Yamamura S., Tsunematsu R., Matsumoto M., Nakayama KI.
  Mol. Cell. Biol. 32: 590-605, 2012.
• p57 is required for quiescence and maintenance of adult hematopoietic stem cells.
  Matsumoto A., Takeishi S., Kanie T., Susaki E., Onoyama I., Tateishi Y., Nakayama K., Nakayama KI.
  Cell Stem Cell 9: 262-271, 2011.
• Deregulation of the p57-E2F1-p53 axis results in nonobstructive hydrocephalus and cerebellar malformation in mice.
  Matsumoto A., Susaki E., Onoyama I., Nakayama K., Mikio H., Nakayama KI.
  Mol. Cell. Biol. 31: 4176-4192, 2011.
• Fbxw7-dependent degradation of Notch is required for control of "stemness" and neuronal-glial differentiation in neural stem cells.
  Matsumoto A., Onoyama I., Sunabori T., Kageyama R., Okano H., Nakayama KI.
  J. Biol. Chem. 286: 13754-13764, 2011.
• Fbxw7β resides in the endoplasmic reticulum membrane and protects cells from oxidative stress.
  Matsumoto A., Tateishi Y., Onoyama I., Okita Y., Nakayama K., Nakayama KI.
  Cancer Sci. 102: 749-755, 2011.
• Fbxw7 regulates lipid metabolism and cell fate decisions in the mouse liver.
  Onoyama I., Suzuki A., Matsumoto A., Tomita K., Katagiri H., Oike Y., Nakayama K., Nakayama KI.
  J. Clin. Invest. 121: 342-354, 2011.
• Conditional inactivation of Fbxw7 impairs cell-cycle exit during T cell differentiation and results in lymphomatogenesis.
  Onoyama I., Tsunematsu R., Matsumoto A., Kimura T., de Alboran I. M., Nakayama K., Nakayama KI.
  J. Exp. Med. 204: 2875-2888, 2007.
• Expression of mouse Fbxw7 isoforms is regulated in a cell cycle- or p53-dependent manner.
  Matsumoto A., Onoyama I., Nakayama KI.
  Biochem. Biophys. Res. Commun. 350: 114-119, 2006.
• Fbxw7 contributes to tumor suppression by targeting multiple proteins for ubiquitin-dependent degradation.
  Fujii Y., Yada M., Nishiyama M., Kamura T., Takahashi H., Tsunematsu R., Susaki E., Nakagawa T., Matsumoto A., Nakayama KI.
  Cancer Sci. 97: 729-736, 2006.