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Functional, structural and pathological analysis of SAMD9/SAMD9L, liquid-liquid phase separation-related molecules

Research Project

Project/Area Number 19H03627
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 52050:Embryonic medicine and pediatrics-related
Research InstitutionNational Center for Child Health and Development

Principal Investigator

Satoshi Narumi  国立研究開発法人国立成育医療研究センター, 分子内分泌研究部, 室長 (40365317)

Co-Investigator(Kenkyū-buntansha) 金蔵 孝介  東京医科大学, 医学部, 准教授 (10508568)
伊原 健太郎  国立研究開発法人理化学研究所, 生命機能科学研究センター, 研究員 (90647207)
Project Period (FY) 2019-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥17,030,000 (Direct Cost: ¥13,100,000、Indirect Cost: ¥3,930,000)
Fiscal Year 2022: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000)
Fiscal Year 2021: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2020: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2019: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Keywords液液相分離 / SAMD9 / MIRAGE症候群 / 先天性疾患 / 単一遺伝子疾患 / 液相分離 / 遺伝性疾患 / 相分離 / 構造解析 / 機能解析
Outline of Research at the Start

細胞の内部は「均一なスープ」ではなく、局所ごとに異なる分子が集まり、様々な反応を効率良く行うと考えられてきた。オルガネラと呼ばれる脂質二重膜で区分された空間がこれまで主な研究対象であったが、近年、細胞内の不均一性を説明するメカニズムとして大きな着目を集めるようになったのが「液-液相分離」である。本研究は、液-液相分離に関わると想定される新タイプの分子に対し集中的な構造・機能解析を行う。本研究を通じて液-液相分離の制御機構を分子レベルで明らかにするとともに、液-液相分離とヒト疾患との関わりを明らかにしたい。

Outline of Final Research Achievements

Using live cell imaging and protein purification techniques, we examined the relationship between SAMD9 and liquid-liquid phase separation and the effects of mutations. Stable production and purification of full-length SAMD9 molecules were successfully achieved, showing that the protein solution exhibits droplet formation in a salt-dependent manner. Arsenite-induced stress granule formation was reduced in 293 cells expressing the mutant, but purified samples of the E974K mutant retained droplet formation. It is possible that the mutation affects functions other than droplet formation of SAMD9, such as nucleic acid binding ability. We tried cryo-EM analysis using purified protein samples, but could not fully observe the single SAMD9 molecules due to aggregation.

Academic Significance and Societal Importance of the Research Achievements

SAMD9/SAMD9Lは先天性疾患MIRAGE症候群および小脳失調汎血球減少症候群の責任遺伝子であるが、これら分子の機能は不明であった。本研究を通じ、SAMD9/SAMD9Lが液液相分離に関与する分子であることを示し、その分子病態の背景には細胞内での適切な分子集合の障害がある可能性を示唆した。今後のMIRAGE症候群および小脳失調汎血球減少症候群の分子病態解明に向け重要な知見を得ることができた。研究期間中に臨床症例に対する遺伝子解析を積極的に進めた。研究プロジェクト全体としては、4年間の研究期間中に9編の査読つき英文論文を発表し、今後の研究基盤を形成する知見を提供した。

Report

(5 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • Research Products

    (29 results)

All 2023 2022 2021 2020 2019 Other

All Int'l Joint Research (3 results) Journal Article (14 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 14 results,  Open Access: 11 results) Presentation (12 results) (of which Int'l Joint Research: 3 results,  Invited: 9 results)

  • [Int'l Joint Research] セントジュード小児研究病院(米国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] セントジュード小児研究病院(米国)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] セントジュード小児研究病院(米国)

    • Related Report
      2020 Annual Research Report
  • [Journal Article] A Small-for-Gestational-Age Infant with MIRAGE Syndrome Who Developed Heat Stroke and Rhabdomyolysis due to Severe Temperature Instability2023

    • Author(s)
      Saito K, Nakagawa R, Narumi S, Ohashi H, Ishiguro A, Kabe K.
    • Journal Title

      Neonatology.

      Volume: in press Issue: 3 Pages: 390-394

    • DOI

      10.1159/000529762

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cord Blood Transplantation in 2 Infants Presenting Monosomy 7 Clonal Hematopoiesis: SAMD9 / SAMD9L Germline Mutation.2022

    • Author(s)
      Hirai M, Yagasaki H, Kanezawa K, Ueno M, Shimozawa K, Imai K, Morio T, Kato M, Gocho Y, Narumi S, Ebihara Y, Morioka I.
    • Journal Title

      J Pediatr Hematol Oncol.

      Volume: 45 Issue: 2 Pages: e290-e293

    • DOI

      10.1097/mph.0000000000002578

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Discovery of MIRAGE syndrome.2022

    • Author(s)
      Narumi S.
    • Journal Title

      Pediatr Int.

      Volume: 64 Issue: 1

    • DOI

      10.1111/ped.15283

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Acquired uniparental disomy of chromosome 7 in a patient with MIRAGE syndrome that veiled a pathogenic <i>SAMD9</i> variant2021

    • Author(s)
      Tanase-Nakao K, Kawai M, Wada K, Kagami M, Narumi S.
    • Journal Title

      Clinical Pediatric Endocrinology

      Volume: 30 Issue: 4 Pages: 163-169

    • DOI

      10.1297/cpe.30.163

    • NAID

      130008095741

    • ISSN
      0918-5739, 1347-7358
    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The case of a patient with MIRAGE syndrome with familial dysautonomia-like symptoms.2021

    • Author(s)
      Kawashima-Sonoyama Y, Okuno K, Dohmoto T, Tanase-Nakao K, Narumi S, Namba N.
    • Journal Title

      Hum Genome Var.

      Volume: 8 Issue: 1 Pages: 27-27

    • DOI

      10.1038/s41439-021-00158-6

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Role of liquid-liquid separation in endocrine and living cells.2021

    • Author(s)
      Akiba K, Katoh-Fukui Y, Yoshida K, Narumi S, Miyado M, Hasegawa Y and Fukami M.
    • Journal Title

      Journal of the Endocrine Society

      Volume: 5 Issue: 10

    • DOI

      10.1210/jendso/bvab126

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Phase separation and toxicity of C9orf72 poly(PR) depends on alternate distribution of arginine.2021

    • Author(s)
      Chen C, Yamanaka Y, Ueda K, Li P, Miyagi T, Harada Y, Tezuka S, Narumi S, Sugimoto M, Kuroda M, Hayamizu Y, Kanekura K.
    • Journal Title

      J Cell Biol.

      Volume: 220 Issue: 11

    • DOI

      10.1083/jcb.202103160

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] An improved macromolecular crowding sensor CRONOS for detection of crowding changes in membrane-less organelles under stressed conditions.2021

    • Author(s)
      Miyagi T, Yamanaka Y, Harada Y, Narumi S, Hayamizu Y, Kuroda M, Kanekura K.
    • Journal Title

      Biochem Biophys Res Commun.

      Volume: 583 Pages: 29-34

    • DOI

      10.1016/j.bbrc.2021.10.055

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Clinical and Immunological Analyses of Ten Patients with MIRAGE Syndrome.2021

    • Author(s)
      Mitsui-Sekinaka K, Narumi S, Sekinaka Y, Uematsu K, Yoshida Y, Amano N, Shima H, Hasegawa T, Nonoyama S.
    • Journal Title

      J Clin Immunol.

      Volume: 41 Issue: 3 Pages: 709-711

    • DOI

      10.1007/s10875-020-00964-7

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Prevalence of germline GATA2 and SAMD9/9L variants in paediatric haematological disorders with monosomy 72020

    • Author(s)
      Yoshida, M. Tanase-Nakao, K. Shima, H. Shirai, R. Yoshida, K. Osumi, T. Deguchi, T. Mori, M. Arakawa, Y. Takagi, M. Miyamura, T. Sakaguchi, K. Toyoda, H. Ishida, H. Sakata, N. Imamura, T. Kawahara, Y. Morimoto, A. Koike, T. Yagasaki, H. Ito, S. Tomizawa, D. Kiyokawa, N. Narumi, S. Kato, M.
    • Journal Title

      British Journal of Haematology

      Volume: 191 Issue: 5 Pages: 835-843

    • DOI

      10.1111/bjh.17006

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] A girl with MIRAGE syndrome who developed steroid-resistant nephrotic syndrome: a case report.2020

    • Author(s)
      Ishiwa S, Kamei K, Tanase-Nakao K, Shibata S, Matsunami K, Takeuchi I, Sato M, Ishikura K, Narumi S.
    • Journal Title

      BMC Nephrol.

      Volume: 12 Issue: 1 Pages: 340-340

    • DOI

      10.1186/s12882-020-02011-4

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] SOX9 is colocalized with paraspeckle protein NONO in cultured murine sertoli cells and features structural characteristics of intrinsically disordered proteins2020

    • Author(s)
      Akiba Kazuhisa、Narumi Satoshi、Nishimura Riko、Kato‐Fukui Yuko、Takada Shuji、Hasegawa Yukihiro、Fukami Maki
    • Journal Title

      Molecular Reproduction and Development

      Volume: 87 Issue: 11 Pages: 1124-1125

    • DOI

      10.1002/mrd.23425

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] MIRAGE syndrome with recurrent pneumonia probably associated with gastroesophageal reflux and achalasia: A case report2019

    • Author(s)
      Yoshizaki K, Hachiya R, Tomobe Y, Kaku U, Akiba K, Shima H, Narumi S, Hasegawa Y.
    • Journal Title

      Clinical Pediatric Endocrinology

      Volume: 28 Issue: 4 Pages: 147-153

    • DOI

      10.1297/cpe.28.147

    • NAID

      130007731284

    • ISSN
      0918-5739, 1347-7358
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] MIRAGE syndrome caused by a novel missense variant (p.Ala1479Ser) in the SAMD9 gene.2019

    • Author(s)
      Onuma S, Wada T, Araki R, Wada K, Tanase-Nakao K, Narumi S, Fukui M, Shoji Y, Etani Y, Ida S, Kawai M.
    • Journal Title

      Hum Genome Var.

      Volume: 7 Issue: 1 Pages: 4-4

    • DOI

      10.1038/s41439-020-0091-5

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Development of a drug screening method for molecular targeted therapy of MIRAGE syndrome.2023

    • Author(s)
      Narumi S.
    • Organizer
      11th International Meeting of Pediatric Endocrinology.
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 成長障害をきたす全身性疾患MIRAGE症候群の発見と見えてきた課題.2022

    • Author(s)
      鳴海覚志
    • Organizer
      広島小児内分泌講演会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] MIRAGE症候群とSAMD9変異2022

    • Author(s)
      鳴海覚志
    • Organizer
      埼玉県立小児医療センター研究会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 成長障害をきたす全身性疾患MIRAGE症候群の“発見”と“その後の学び”2022

    • Author(s)
      鳴海覚志
    • Organizer
      東海小児内分泌講演会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 新世代技術によるタンパク質相互作用解析2021

    • Author(s)
      鳴海覚志
    • Organizer
      日本内分泌学会学術集会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 成長障害をきたす全身性疾患MIRAGE症候群が教えてくれたこと2021

    • Author(s)
      鳴海覚志
    • Organizer
      日本小児遺伝学会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] たぶん医学系学会で最も詳しいAlphaFoldの解説2021

    • Author(s)
      鳴海覚志
    • Organizer
      日本小児内分泌学会学術集会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 文献レビューに基づくMIRAGE症候群の臨床的特徴2021

    • Author(s)
      中尾佳奈子, 長谷川奉延, 鳴海覚志
    • Organizer
      日本小児内分泌学会学術集会
    • Related Report
      2021 Annual Research Report
  • [Presentation] SAMD9分子標的療法に向けた構造解析と治療薬スクリーニング系の開発2019

    • Author(s)
      中尾佳奈子、伊原健太郎、三嶋千恵美、 新野睦子、白水美香子、 鳴海覚志
    • Organizer
      第53回日本小児内分泌学会
    • Related Report
      2019 Annual Research Report
  • [Presentation] The Basic Research on the SAMD9 Protein: What, Where and With Whom?2019

    • Author(s)
      Narumi S
    • Organizer
      Bone Marrow Failure Expert Meeting 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] MIRAGE2019

    • Author(s)
      Narumi S
    • Organizer
      Bone Marrow Failure Expert Meeting 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 先天性副腎低形成症における遺伝子変異2019

    • Author(s)
      鳴海覚志
    • Organizer
      日本内分泌病理学会
    • Related Report
      2019 Annual Research Report
    • Invited

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Published: 2019-04-18   Modified: 2024-01-30  

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