Updated on 2023/09/29

写真a

 
OKA Yasuyoshi
 
Organization
Research Institute of Environmental Medicine Division of Stress Adaptation and Protection Lecturer
Graduate School
Graduate School of Medicine
Title
Lecturer

Degree 1

  1. 博士 (学術) ( 2011.9   長崎大学 ) 

Research Interests 6

  1. ゲノムの安定化維持機構

  2. DNA損傷応答

  3. DNA修復

  4. 環境変異原

  5. 疾患モデル動物

  6. 遺伝性疾患

Research Areas 6

  1. Life Science / Genome biology

  2. Life Science / Molecular biology

  3. Environmental Science/Agriculture Science / Chemical substance influence on environment

  4. Environmental Science/Agriculture Science / Radiation influence

  5. Life Science / Pathological biochemistry

  6. Life Science / Genetics

▼display all

Professional Memberships 3

  1. 日本プロテオーム学会

  2. 日本分子生物学会

  3. 日本環境変異原学会

 

Papers 23

  1. Lysosomal cholesterol overload in macrophages promotes liver fibrosis in a mouse model of NASH. Reviewed International journal

    Michiko Itoh, Atsushi Tamura, Sayaka Kanai, Miyako Tanaka, Yohei Kanamori, Ibuki Shirakawa, Ayaka Ito, Yasuyoshi Oka, Isao Hidaka, Taro Takami, Yasushi Honda, Mitsuyo Maeda, Yasuyuki Saito, Yoji Murata, Takashi Matozaki, Atsushi Nakajima, Yosky Kataoka, Tomoo Ogi, Yoshihiro Ogawa, Takayoshi Suganami

    The Journal of experimental medicine   Vol. 220 ( 11 )   2023.11

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

    Accumulation of lipotoxic lipids, such as free cholesterol, induces hepatocyte death and subsequent inflammation and fibrosis in the pathogenesis of nonalcoholic steatohepatitis (NASH). However, the underlying mechanisms remain unclear. We have previously reported that hepatocyte death locally induces phenotypic changes in the macrophages surrounding the corpse and remnant lipids, thereby promoting liver fibrosis in a murine model of NASH. Here, we demonstrated that lysosomal cholesterol overload triggers lysosomal dysfunction and profibrotic activation of macrophages during the development of NASH. β-cyclodextrin polyrotaxane (βCD-PRX), a unique supramolecule, is designed to elicit free cholesterol from lysosomes. Treatment with βCD-PRX ameliorated cholesterol accumulation and profibrotic activation of macrophages surrounding dead hepatocytes with cholesterol crystals, thereby suppressing liver fibrosis in a NASH model, without affecting the hepatic cholesterol levels. In vitro experiments revealed that cholesterol-induced lysosomal stress triggered profibrotic activation in macrophages predisposed to the steatotic microenvironment. This study provides evidence that dysregulated cholesterol metabolism in macrophages would be a novel mechanism of NASH.

    DOI: 10.1084/jem.20220681

    PubMed

  2. A case of non-immune hydrops fetalis with maternal mirror syndrome diagnosed by trio-based exome sequencing: An autopsy case report and literature review Reviewed

    Tano Sho, Kotani Tomomi, Yoshihara Masato, Nakamura Noriyuki, Matsuo Seiko, Ushida Takafumi, Imai Kenji, Ito Miharu, Oka Yasuyoshi, Sato Emi, Hayashi Shin, Ogi Tomoo, Kajiyama Hiroaki

    MOLECULAR GENETICS AND METABOLISM REPORTS   Vol. 33   page: 100925   2022.12

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

    DOI: 10.1016/j.ymgmr.2022.100925

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  3. A novel missense variant in CUL3 shows altered binding ability to BTB-adaptor proteins leading to diverse phenotypes of CUL3-related disorders. Reviewed International journal

    Kohji Kato, Fuyuki Miya, Yasuyoshi Oka, Seiji Mizuno, Shinji Saitoh

    Journal of human genetics   Vol. 66 ( 5 ) page: 491 - 498   2021.5

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

    CUL3 forms Cullin-Ring ubiquitin ligases (CRL) with Ring-box protein and BTB-adaptor proteins. A variety of BTB-adaptor proteins have been reported to interact with the N-terminus of CUL3, which makes it possible to recognize various substrates for degradation. Regarding the association of CUL3 with neurodevelopmental disorders, a recent study reported three patients with global developmental delay, who carried de novo variants in CUL3. Here, we describe a novel de novo CUL3 variant (c.158G > A, p.Ser53Asn) identified in a patient with global developmental delay, who presented some novel dysmorphic features, including macrocephaly, characteristic facial features, and cutis marmorata. Immunoprecipitation and immunoblot analyses identified significantly weaker binding ability to some BTB proteins in CUL3-S53N compared to wild-type. Interestingly, label-free quantification proteomics analysis of samples immunoprecipitated by CUL3-S53N showed a significantly decreased interaction with some BTB proteins, while almost equal interaction or significantly increased interaction was observed with other BTB proteins. The binding between CUL3 and BTB proteins is essential for CRL substrate recognition, and alteration of their interaction is thought to result in the quantitative alteration in substrate proteins. It is possible that the difference of dysmorphic features between the present case and previously reported cases is caused by the distinctive effect of each CUL3 variant on substrate proteins. The clinical information of the present case will expand the picture of CUL3-related global developmental disorders, and subsequent cell biological analysis of the novel mutation will provide insight into the underlying molecular mechanism of how CUL3 pathogenic variants cause neurological disorders.

    DOI: 10.1038/s10038-020-00868-9

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  4. Digenic mutations in ALDH2 and ADH5 impair formaldehyde clearance and cause a multisystem disorder, AMeD syndrome. Reviewed International journal

    Yasuyoshi Oka, Motoharu Hamada, Yuka Nakazawa, Hideki Muramatsu, Yusuke Okuno, Koichiro Higasa, Mayuko Shimada, Honoka Takeshima, Katsuhiro Hanada, Taichi Hirano, Toshiro Kawakita, Hirotoshi Sakaguchi, Takuya Ichimura, Shuichi Ozono, Kotaro Yuge, Yoriko Watanabe, Yuko Kotani, Mutsumi Yamane, Yumiko Kasugai, Miyako Tanaka, Takayoshi Suganami, Shinichiro Nakada, Norisato Mitsutake, Yuichiro Hara, Kohji Kato, Seiji Mizuno, Noriko Miyake, Yosuke Kawai, Katsushi Tokunaga, Masao Nagasaki, Seiji Kito, Keiichi Isoyama, Masafumi Onodera, Hideo Kaneko, Naomichi Matsumoto, Fumihiko Matsuda, Keitaro Matsuo, Yoshiyuki Takahashi, Tomoji Mashimo, Seiji Kojima, Tomoo Ogi

    Science advances   Vol. 6 ( 51 )   2020.12

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

    Rs671 in the aldehyde dehydrogenase 2 gene (ALDH2) is the cause of Asian alcohol flushing response after drinking. ALDH2 detoxifies endogenous aldehydes, which are the major source of DNA damage repaired by the Fanconi anemia pathway. Here, we show that the rs671 defective allele in combination with mutations in the alcohol dehydrogenase 5 gene, which encodes formaldehyde dehydrogenase (ADH5FDH ), causes a previously unidentified disorder, AMeD (aplastic anemia, mental retardation, and dwarfism) syndrome. Cellular studies revealed that a decrease in the formaldehyde tolerance underlies a loss of differentiation and proliferation capacity of hematopoietic stem cells. Moreover, Adh5-/-Aldh2E506K/E506K double-deficient mice recapitulated key clinical features of AMeDS, showing short life span, dwarfism, and hematopoietic failure. Collectively, our results suggest that the combined deficiency of formaldehyde clearance mechanisms leads to the complex clinical features due to overload of formaldehyde-induced DNA damage, thereby saturation of DNA repair processes.

    DOI: 10.1126/sciadv.abd7197

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  5. Biallelic VPS35L pathogenic variants cause 3C/Ritscher-Schinzel-like syndrome through dysfunction of retriever complex. Reviewed International journal

    Kohji Kato, Yasuyoshi Oka, Hideki Muramatsu, Filipp F Vasilev, Takanobu Otomo, Hisashi Oishi, Yoshihiko Kawano, Hiroyuki Kidokoro, Yuka Nakazawa, Tomoo Ogi, Yoshiyuki Takahashi, Shinji Saitoh

    Journal of medical genetics   Vol. 57 ( 4 ) page: 245 - 253   2020.4

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

    BACKGROUND: 3C/Ritscher-Schinzel syndrome is characterised by congenital cranio-cerebello-cardiac dysplasia, where CCDC22 and WASHC5 are accepted as the causative genes. In combination with the retromer or retriever complex, these genes play a role in endosomal membrane protein recycling. We aimed to identify the gene abnormality responsible for the pathogenicity in siblings with a 3C/Ritscher-Schinzel-like syndrome, displaying cranio-cerebello-cardiac dysplasia, coloboma, microphthalmia, chondrodysplasia punctata and complicated skeletal malformation. METHODS: Exome sequencing was performed to identify pathogenic variants. Cellular biological analyses and generation of knockout mice were carried out to elucidate the gene function and pathophysiological significance of the identified variants. RESULTS: We identified compound heterozygous pathogenic variants (c.1097dup; p.Cys366Trpfs*28 and c.2755G>A; p.Ala919Thr) in the VPS35L gene, which encodes a core protein of the retriever complex. The identified missense variant lacked the ability to form the retriever complex, and the frameshift variant induced non-sense-mediated mRNA decay, thereby confirming biallelic loss of function of VPS35L. In addition, VPS35L knockout cells showed decreased autophagic function in nutrient-rich and starvation conditions, as well as following treatment with Torin 1. We also generated Vps35l-/- mice and demonstrated that they were embryonic lethal at an early stage, between E7.5 and E10.5. CONCLUSIONS: Our results suggest that biallelic loss-of-function variants in VPS35L underlies 3C/Ritscher-Schinzel-like syndrome. Furthermore, VPS35L is necessary for autophagic function and essential for early embryonic development. The data presented here provide a new insight into the critical role of the retriever complex in fetal development.

    DOI: 10.1136/jmedgenet-2019-106213

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  6. Ubiquitination of DNA Damage-Stalled RNAPII Promotes Transcription-Coupled Repair. Reviewed International journal

    Yuka Nakazawa, Yuichiro Hara, Yasuyoshi Oka, Okiru Komine, Diana van den Heuvel, Chaowan Guo, Yasukazu Daigaku, Mayu Isono, Yuxi He, Mayuko Shimada, Kana Kato, Nan Jia, Satoru Hashimoto, Yuko Kotani, Yuka Miyoshi, Miyako Tanaka, Akira Sobue, Norisato Mitsutake, Takayoshi Suganami, Akio Masuda, Kinji Ohno, Shinichiro Nakada, Tomoji Mashimo, Koji Yamanaka, Martijn S Luijsterburg, Tomoo Ogi

    Cell   Vol. 180 ( 6 ) page: 1228 - +   2020.3

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

    Transcription-coupled nucleotide excision repair (TC-NER) is initiated by the stalling of elongating RNA polymerase II (RNAPIIo) at DNA lesions. The ubiquitination of RNAPIIo in response to DNA damage is an evolutionarily conserved event, but its function in mammals is unknown. Here, we identified a single DNA damage-induced ubiquitination site in RNAPII at RPB1-K1268, which regulates transcription recovery and DNA damage resistance. Mechanistically, RPB1-K1268 ubiquitination stimulates the association of the core-TFIIH complex with stalled RNAPIIo through a transfer mechanism that also involves UVSSA-K414 ubiquitination. We developed a strand-specific ChIP-seq method, which revealed RPB1-K1268 ubiquitination is important for repair and the resolution of transcriptional bottlenecks at DNA lesions. Finally, RPB1-K1268R knockin mice displayed a short life-span, premature aging, and neurodegeneration. Our results reveal RNAPII ubiquitination provides a two-tier protection mechanism by activating TC-NER and, in parallel, the processing of DNA damage-stalled RNAPIIo, which together prevent prolonged transcription arrest and protect against neurodegeneration.

    DOI: 10.1016/j.cell.2020.02.010

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  7. TRAIP is a PCNA-binding ubiquitin ligase that protects genome stability after replication stress. Reviewed International journal

    Saskia Hoffmann, Stine Smedegaard, Kyosuke Nakamura, Gulnahar B Mortuza, Markus Räschle, Alain Ibañez de Opakua, Yasuyoshi Oka, Yunpeng Feng, Francisco J Blanco, Matthias Mann, Guillermo Montoya, Anja Groth, Simon Bekker-Jensen, Niels Mailand

    The Journal of cell biology   Vol. 212 ( 1 ) page: 63 - 75   2016.1

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:ROCKEFELLER UNIV PRESS  

    Cellular genomes are highly vulnerable to perturbations to chromosomal DNA replication. Proliferating cell nuclear antigen (PCNA), the processivity factor for DNA replication, plays a central role as a platform for recruitment of genome surveillance and DNA repair factors to replication forks, allowing cells to mitigate the threats to genome stability posed by replication stress. We identify the E3 ubiquitin ligase TRAIP as a new factor at active and stressed replication forks that directly interacts with PCNA via a conserved PCNA-interacting peptide (PIP) box motif. We show that TRAIP promotes ATR-dependent checkpoint signaling in human cells by facilitating the generation of RPA-bound single-stranded DNA regions upon replication stress in a manner that critically requires its E3 ligase activity and is potentiated by the PIP box. Consequently, loss of TRAIP function leads to enhanced chromosomal instability and decreased cell survival after replication stress. These findings establish TRAIP as a PCNA-binding ubiquitin ligase with an important role in protecting genome integrity after obstacles to DNA replication.

    DOI: 10.1083/jcb.201506071

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  8. Ubiquitin-like protein UBL5 promotes the functional integrity of the Fanconi anemia pathway. Reviewed International journal

    Yasuyoshi Oka, Simon Bekker-Jensen, Niels Mailand

    The EMBO journal   Vol. 34 ( 10 ) page: 1385 - 1398   2015.5

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:WILEY-BLACKWELL  

    Ubiquitin and ubiquitin-like proteins (UBLs) function in a wide array of cellular processes. UBL5 is an atypical UBL that does not form covalent conjugates with cellular proteins and which has a known role in modulating pre-mRNA splicing. Here, we report an unexpected involvement of human UBL5 in promoting the function of the Fanconi anemia (FA) pathway for repair of DNA interstrand crosslinks (ICLs), mediated by a specific interaction with the central FA pathway component FANCI. UBL5-deficient cells display spliceosome-independent reduction of FANCI protein stability, defective FANCI function in response to DNA damage and hypersensitivity to ICLs. By mapping the sequence determinants underlying UBL5-FANCI binding, we generated separation-of-function mutants to demonstrate that key aspects of FA pathway function, including FANCI-FANCD2 heterodimerization, FANCD2 and FANCI monoubiquitylation and maintenance of chromosome stability after ICLs, are compromised when the UBL5-FANCI interaction is selectively inhibited by mutations in either protein. Together, our findings establish UBL5 as a factor that promotes the functionality of the FA DNA repair pathway.

    DOI: 10.15252/embj.201490376

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  9. DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links. Reviewed International journal

    Markus Räschle, Godelieve Smeenk, Rebecca K Hansen, Tikira Temu, Yasuyoshi Oka, Marco Y Hein, Nagarjuna Nagaraj, David T Long, Johannes C Walter, Kay Hofmann, Zuzana Storchova, Jürgen Cox, Simon Bekker-Jensen, Niels Mailand, Matthias Mann

    Science (New York, N.Y.)   Vol. 348 ( 6234 ) page: 1253671 - 1253671   2015.5

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:AMER ASSOC ADVANCEMENT SCIENCE  

    DNA interstrand cross-links (ICLs) block replication fork progression by inhibiting DNA strand separation. Repair of ICLs requires sequential incisions, translesion DNA synthesis, and homologous recombination, but the full set of factors involved in these transactions remains unknown. We devised a technique called chromatin mass spectrometry (CHROMASS) to study protein recruitment dynamics during perturbed DNA replication in Xenopus egg extracts. Using CHROMASS, we systematically monitored protein assembly and disassembly on ICL-containing chromatin. Among numerous prospective DNA repair factors, we identified SLF1 and SLF2, which form a complex with RAD18 and together define a pathway that suppresses genome instability by recruiting the SMC5/6 cohesion complex to DNA lesions. Our study provides a global analysis of an entire DNA repair pathway and reveals the mechanism of SMC5/6 relocalization to damaged DNA in vertebrate cells.

    DOI: 10.1126/science.1253671

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  10. Ubiquitin-SUMO circuitry controls activated fanconi anemia ID complex dosage in response to DNA damage. Reviewed International journal

    Ian Gibbs-Seymour, Yasuyoshi Oka, Eeson Rajendra, Brian T Weinert, Lori A Passmore, Ketan J Patel, Jesper V Olsen, Chunaram Choudhary, Simon Bekker-Jensen, Niels Mailand

    Molecular cell   Vol. 57 ( 1 ) page: 150 - 164   2015.1

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:CELL PRESS  

    We show that central components of the Fanconi anemia (FA) DNA repair pathway, the tumor suppressor proteins FANCI and FANCD2 (the ID complex), are SUMOylated in response to replication fork stalling. The ID complex is SUMOylated in a manner that depends on the ATR kinase, the FA ubiquitin ligase core complex, and the SUMO E3 ligases PIAS1/PIAS4 and is antagonized by the SUMO protease SENP6. SUMOylation of the ID complex drives substrate selectivity by triggering its polyubiquitylation by the SUMO-targeted ubiquitin ligase RNF4 to promote its removal from sites of DNA damage via the DVC1-p97 ubiquitin segregase complex. Deregulation of ID complex SUMOylation compromises cell survival following replication stress. Our results uncover a regulatory role for SUMOylation in the FA pathway, and we propose that ubiquitin-SUMO signaling circuitry is a mechanism that contributes to the balance of activated ID complex dosage at sites of DNA damage.

    DOI: 10.1016/j.molcel.2014.12.001

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  11. TRIP12 and UBR5 Suppress Spreading of Chromatin Ubiquitylation at Damaged Chromosomes Reviewed

    Gudjonsson Thorkell, Altmeyer Matthias, Savic Velibor, Toledo Luis, Dinant Christoffel, Grofte Merete, Bartkova Jirina, Poulsen Maria, Oka Yasuyoshi, Bekker-Jensen Simon, Mailand Niels, Neumann Beate, Heriche Jean-Karim, Shearer Robert, Saunders Darren, Bartek Jiri, Lukas Jiri, Lukas Claudia

    CELL   Vol. 159 ( 6 ) page: 1476 - 1477   2014.12

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    DOI: 10.1016/j.cell.2014.11.027

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  12. UBL5 is essential for pre-mRNA splicing and sister chromatid cohesion in human cells. Reviewed International journal

    Yasuyoshi Oka, Hanne Varmark, Kristoffer Vitting-Seerup, Petra Beli, Johannes Waage, Anna Hakobyan, Martin Mistrik, Chunaram Choudhary, Mikkel Rohde, Simon Bekker-Jensen, Niels Mailand

    EMBO reports   Vol. 15 ( 9 ) page: 956 - 964   2014.9

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:WILEY-BLACKWELL  

    UBL5 is an atypical ubiquitin-like protein, whose function in metazoans remains largely unexplored. We show that UBL5 is required for sister chromatid cohesion maintenance in human cells. UBL5 primarily associates with spliceosomal proteins, and UBL5 depletion decreases pre-mRNA splicing efficiency, leading to globally enhanced intron retention. Defective sister chromatid cohesion is a general consequence of dysfunctional pre-mRNA splicing, resulting from the selective downregulation of the cohesion protection factor Sororin. As the UBL5 yeast orthologue, Hub1, also promotes spliceosome functions, our results show that UBL5 plays an evolutionary conserved role in pre-mRNA splicing, the integrity of which is essential for the fidelity of chromosome segregation.

    DOI: 10.15252/embr.201438679

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  13. Live-cell imaging visualizes frequent mitotic skipping during senescence-like growth arrest in mammary carcinoma cells exposed to ionizing radiation. Reviewed International journal

    Masatoshi Suzuki, Motohiro Yamauchi, Yasuyoshi Oka, Keiji Suzuki, Shunichi Yamashita

    International journal of radiation oncology, biology, physics   Vol. 83 ( 2 ) page: E241 - E250   2012.6

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:ELSEVIER SCIENCE INC  

    PURPOSE: Senescence-like growth arrest in human solid carcinomas is now recognized as the major outcome of radiotherapy. This study was designed to analyze cell cycle during the process of senescence-like growth arrest in mammary carcinoma cells exposed to X-rays. METHODS AND MATERIALS: Fluorescent ubiquitination-based cell cycle indicators were introduced into the human mammary carcinoma cell line MCF-7. Cell cycle was sequentially monitored by live-cell imaging for up to 5 days after exposure to 10 Gy of X-rays. RESULTS: Live-cell imaging revealed that cell cycle transition from G2 to G1 phase without mitosis, so-called mitotic skipping, was observed in 17.1% and 69.8% of G1- and G2-irradiated cells, respectively. Entry to G1 phase was confirmed by the nuclear accumulation of mKO(2)-hCdt1 as well as cyclin E, which was inversely correlated to the accumulation of G2-specific markers such as mAG-hGeminin and CENP-F. More than 90% of cells skipping mitosis were persistently arrested in G1 phase and showed positive staining for the senescent biochemical marker, which is senescence-associated ß-galactosidase, indicating induction of senescence-like growth arrest accompanied by mitotic skipping. While G2 irradiation with higher doses of X-rays induced mitotic skipping in approximately 80% of cells, transduction of short hairpin RNA (shRNA) for p53 significantly suppressed mitotic skipping, suggesting that ionizing radiation-induced mitotic skipping is associated with p53 function. CONCLUSIONS: The present study found the pathway of senescence-like growth arrest in G1 phase without mitotic entry following G2-irradiation.

    DOI: 10.1016/j.ijrobp.2011.12.003

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  14. Mode of ATM-dependent suppression of chromosome translocation. Reviewed International journal

    Motohiro Yamauchi, Keiji Suzuki, Yasuyoshi Oka, Masatoshi Suzuki, Hisayoshi Kondo, Shunichi Yamashita

    Biochemical and biophysical research communications   Vol. 416 ( 1-2 ) page: 111 - 118   2011.12

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:ACADEMIC PRESS INC ELSEVIER SCIENCE  

    It is well documented that deficiency in ataxia telangiectasia mutated (ATM) protein leads to elevated frequency of chromosome translocation, however, it remains poorly understood how ATM suppresses translocation frequency. In the present study, we addressed the mechanism of ATM-dependent suppression of translocation frequency. To know frequency of translocation events in a whole genome at once, we performed centromere/telomere FISH and scored dicentric chromosomes, because dicentric and translocation occur with equal frequency and by identical mechanism. By centromere/telomere FISH analysis, we confirmed that chemical inhibition or RNAi-mediated knockdown of ATM causes 2 to 2.5-fold increase in dicentric frequency at first mitosis after 2 Gy of gamma-irradiation in G0/G1. The FISH analysis revealed that ATM/p53-dependent G1 checkpoint suppresses dicentric frequency, since RNAi-mediated knockdown of p53 elevated dicentric frequency by 1.5-fold. We found ATM also suppresses dicentric occurrence independently of its checkpoint role, as ATM inhibitor showed additional effect on dicentric frequency in the context of p53 depletion and Chk1/2 inactivation. Epistasis analysis using chemical inhibitors revealed that ATM kinase functions in the same pathway that requires kinase activity of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to suppress dicentric frequency. From the results in the present study, we conclude that ATM minimizes translocation frequency through its commitment to G1 checkpoint and DNA double-strand break repair pathway that requires kinase activity of DNA-PKcs.

    DOI: 10.1016/j.bbrc.2011.11.006

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  15. Persistence and dynamics of DNA damage signal amplification determined by microcolony formation and live-cell imaging. Reviewed International journal

    Yasuyoshi Oka, Motohiro Yamauchi, Masatoshi Suzuki, Shunichi Yamashita, Keiji Suzuki

    Journal of radiation research   Vol. 52 ( 6 ) page: 766 - 774   2011.11

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:JAPAN RADIATION RESEARCH SOC  

    Cell cycle checkpoints are essential cellular process protecting the integrity of the genome from DNA damaging agents. In the present study, we developed a microcolony assay, in which normal human diploid fibroblast-like cells exposed to ionizing radiation, were plated onto coverslips at very low density (3 cells/cm(2)). Cells were grown for up to 3 days, and phosphorylated ATM at Ser1981 and 53BP1 foci were analyzed as the markers for an amplified DNA damage signal. We observed a dose-dependent increase in the fraction of non-dividing cells, whose increase was compromised by knocking down p53 expression. While large persistent foci were predominantly formed in non-dividing cells, we observed some growing colonies that contained cells with large foci. As each microcolony was derived from a single cell, it appeared that some cells could proliferate with large foci. A live-imaging analysis using hTERT-immortalized normal human diploid cells transfected with the EGFP-tagged 53BP1 gene revealed that the formation of persistent large foci was highly dynamic. Delayed appearance and disappearance of large foci were frequently observed in exposed cells visualized 12-72 hours after X-irradiation. Thus, our results indicate that amplified DNA damage signal could be ignored, which may be explained in part by the dynamic nature of the amplification process.

    DOI: 10.1269/jrr.10164

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  16. Recruitment of the cohesin loading factor NIPBL to DNA double-strand breaks depends on MDC1, RNF168 and HP1γ in human cells. Reviewed International journal

    Yasuyoshi Oka, Keiji Suzuki, Motohiro Yamauchi, Norisato Mitsutake, Shunichi Yamashita

    Biochemical and biophysical research communications   Vol. 411 ( 4 ) page: 762 - 767   2011.8

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:ACADEMIC PRESS INC ELSEVIER SCIENCE  

    The cohesin loading factor NIPBL is required for cohesin to associate with chromosomes and plays a role in DNA double-strand break (DSB) repair. Although the NIPBL homolog Scc2 is recruited to an enzymatically generated DSB and promotes cohesin-dependent DSB repair in yeast, the mechanism of the recruitment remains poorly understood. Here we show that the human NIPBL is recruited to the sites of DNA damage generated by micro-irradiation as well as to the sites of DSBs induced by homing endonuclease, I-PpoI. The recruitment of NIPBL was impaired by RNAi-mediated knockdown of MDC1 or RNF168, both of which also accumulate at DSBs. We also show that the recruitment of NIPBL to the sites of DNA damage is mediated by its C-terminal region containing HEAT repeats and Heterochromatin protein 1 (HP1) interacting motif. Furthermore, NIPBL accumulation at damaged sites was also compromised by HP1γ depletion. Taken together, our study reveals that human NIPBL is a novel protein recruited to DSB sites, and the recruitment is controlled by MDC1, RNF168 and HP1γ.

    DOI: 10.1016/j.bbrc.2011.07.021

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  17. Creating localized DNA double-strand breaks with microirradiation. Reviewed International journal

    Keiji Suzuki, Motohiro Yamauchi, Yasuyoshi Oka, Masatoshi Suzuki, Shunichi Yamashita

    Nature protocols   Vol. 6 ( 2 ) page: 134 - 139   2011.2

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:NATURE PUBLISHING GROUP  

    We describe a protocol for creating localized DNA double-strand breaks (DSBs) with minimal requirements that can be applied in cell biology and molecular biology. This protocol is based on the combination of 5-bromo-2'-deoxyuridine (BrdU) labeling and ultraviolet C (UVC) irradiation through porous membranes. Cells are labeled with 10 μM BrdU for 48-72 h, washed with Ca(2+)- and Mg(2+)-free PBS(-), covered by polycarbonate membranes with micropores and exposed to UVC light. With this protocol, localized DSBs are created within subnuclear areas, irrespective of the cell cycle phase. Recruitment of proteins involved in DNA repair, DNA damage response, chromatin remodeling and histone modifications can be visualized without any specialized equipment. The quality is the same as that obtained by laser microirradiation or by any other focal irradiation. DSBs become visible within 30 min of UVC irradiation.

    DOI: 10.1038/nprot.2010.183

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  18. A novel and simple micro-irradiation technique for creating localized DNA double-strand breaks. Reviewed International journal

    Keiji Suzuki, Motohiro Yamauchi, Yasuyoshi Oka, Masatoshi Suzuki, Shunichi Yamashita

    Nucleic acids research   Vol. 38 ( 12 ) page: e129   2010.7

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:OXFORD UNIV PRESS  

    An ataxia-telangiectasia mutated (ATM)-dependent DNA damage signal is amplified through the interaction of various factors, which are recruited to the chromatin regions with DNA double-strand breaks. Spatial and temporal regulation of such factors is analysed by fluorescence microscopy in combination with laser micro-irradiation. Here we describe a novel and simple technique for micro-irradiation that does not require a laser source. Cells were labelled with BrdU for 48-72 h, covered with porous polycarbonate membranes, and exposed to UVC. All BrdU-labelled cells showed localized foci of phosphorylated ATM, phosphorylated histone H2AX, MDC1 and 53BP1 upon irradiation, showing that these foci were induced irrespective of the cell-cycle phase. They were also detectable in nucleotide excision repair-defective XPA cells labelled with BrdU, indicating that the foci did not reflect an excision repair-related process. Furthermore, an ATM-specific inhibitor significantly attenuated the foci formation, and disappearance of the foci was significantly abrogated in non-homologous end-joining-defective cells. Thus, it can be concluded that micro-irradiation generated DNA double-strand breaks in BrdU-sensitized cells. The present technique should accelerate research in the fields of DNA damage response, DNA repair and DNA recombination, as it provides more chances to perform micro-irradiation experiments without any specific equipment.

    DOI: 10.1093/nar/gkq226

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  19. Requirement of ATM-dependent pathway for the repair of a subset of DNA double strand breaks created by restriction endonucleases. Reviewed International journal

    Keiji Suzuki, Maiko Takahashi, Yasuyoshi Oka, Motohiro Yamauchi, Masatoshi Suzuki, Shunichi Yamashita

    Genome integrity   Vol. 1 ( 1 ) page: 4 - 4   2010.5

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

    BACKGROUND: DNA double strand breaks induced by DNA damaging agents, such ionizing radiation, are repaired by multiple DNA repair pathways including non-homologous end-joining (NHEJ) repair and homologous recombination (HR) repair. ATM-dependent DNA damage checkpoint regulates a part of DNA repair pathways, however, the exact role of ATM activity remains to be elucidated. In order to define the molecular structure of DNA double strand breaks requiring ATM activity we examined repair of DNA double strand breaks induced by different restriction endonucleases in normal human diploid cells treated with or without ATM-specific inhibitor. RESULTS: Synchronized G1 cells were treated with various restriction endonucleases. DNA double strand breaks were detected by the foci of phosphorylated ATM at serine 1981 and 53BP1. DNA damage was detectable 2 hours after the treatment, and the number of foci decreased thereafter. Repair of the 3'-protruding ends created by Pst I and Sph I was efficient irrespective of ATM function, whereas the repair of a part of the blunt ends caused by Pvu II and Rsa I, and 5'-protruding ends created by Eco RI and Bam HI, respectively, were compromised by ATM inhibition. CONCLUSIONS: Our results indicate that ATM-dependent pathway plays a pivotal role in the repair of a subset of DNA double strand breaks with specific end structures.

    DOI: 10.1186/2041-9414-1-4

    Scopus

    PubMed

  20. Higher-Order Chromatin Structure and Nontargeted Effects Reviewed

    Suzuki Keiji, Yamauchi Motohiro, Oka Yasuyoshi, Yamashita Shunichi

    RADIATION HEALTH RISK SCIENCES     page: 123 - 126   2009

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    Publishing type:Research paper (scientific journal)  

    Web of Science

  21. Paracrine Interactions Between Normal, but Not Cancer, Epithelial and Normal Mesenchymal Cells Attenuate Radiation-Induced DNA Damage Reviewed

    Saenko Vladimir A., Nakazawa Yuka, Rogounovitch Tatiana I., Suzuki Keiji, Mitsutake Norisato, Matsuse Michiko, Oka Yasuyoshi, Yamashita Shunichi

    RADIATION HEALTH RISK SCIENCES     page: 294 - +   2009

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    Publishing type:Research paper (scientific journal)  

    Web of Science

  22. Growth of persistent foci of DNA damage checkpoint factors is essential for amplification of G1 checkpoint signaling. Reviewed International journal

    Motohiro Yamauchi, Yasuyoshi Oka, Masashi Yamamoto, Koichi Niimura, Motoyuki Uchida, Seiji Kodama, Masami Watanabe, Ichiro Sekine, Shunichi Yamashita, Keiji Suzuki

    DNA repair   Vol. 7 ( 3 ) page: 405 - 417   2008.3

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:ELSEVIER SCIENCE BV  

    Several DNA damage checkpoint factors form nuclear foci in response to ionizing radiation (IR). Although the number of the initial foci decreases concomitantly with DNA double-strand break repair, some fraction of foci persists. To date, the physiological role of the persistent foci has been poorly understood. Here we examined foci of Ser1981-phosphorylated ATM in normal human diploid cells exposed to 1Gy of X-rays. While the initial foci size was approximately 0.6microm, the one or two of persistent focus (foci) grew, whose diameter reached 1.6microm or more in diameter at 24h after IR. All of the grown persistent foci of phosphorylated ATM colocalized with the persistent foci of Ser139-phosphorylated histone H2AX, MDC1, 53BP1, and NBS1, which also grew similarly. When G0-synchronized normal human cells were released immediately after 1Gy of X-rays and incubated for 24h, the grown large phosphorylated ATM foci (> or =1.6microm) were rarely (av. 0.9%) observed in S phase cells, while smaller foci (<1.6microm) were frequently (av. 45.9%) found. We observed significant phosphorylation of p53 at Ser15 in cells with a single grown phosphorylated ATM focus. Furthermore, persistent inhibition of foci growth of phosphorylated ATM by an ATM inhibitor, KU55933, completely abrogated p53 phosphorylation. Defective growth of the persistent IR-induced foci was observed in primary fibroblasts derived from ataxia-telangiectasia (AT) and Nijmegen breakage syndrome (NBS) patients, which were abnormal in IR-induced G1 checkpoint. These results indicate that the growth of the persistent foci of the DNA damage checkpoint factors plays a pivotal role in G1 arrest, which amplifies G1 checkpoint signals sufficiently for phosphorylating p53 in cells with a limited number of remaining foci.

    DOI: 10.1016/j.dnarep.2007.11.011

    Web of Science

    PubMed

  23. Qualitative and quantitative analysis of phosphorylated ATM foci induced by low-dose ionizing radiation. Reviewed International journal

    Keiji Suzuki, Hiroshi Okada, Motohiro Yamauchi, Yasuyoshi Oka, Seiji Kodama, Masami Watanabe

    Radiation research   Vol. 165 ( 5 ) page: 499 - 504   2006.5

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:RADIATION RESEARCH SOC  

    We examined the formation of phosphorylated ataxia telangiectasia mutated (ATM) foci in exponentially growing normal human diploid cells exposed to low doses of X rays. Phosphorylated ATM foci were detected immediately after irradiation, and the number of foci decreased as the time after irradiation increased. The kinetics of phosphorylated ATM foci was comparable to that of phosphorylated histone H2AX. We found that there were fewer spontaneous phosphorylated ATM foci than that phosphorylated histone H2AX foci. Notably, significant numbers of phosphorylated histone H2AX foci, but not phosphorylated ATM foci, were detected in the S-phase cells. The induction of foci showed a linear dose-response relationship with doses ranging for 10 mGy to 1 Gy, and the average number of phosphorylated ATM foci per gray was approximately 50. The average size of the foci was comparable for the cells irradiated with 20 mGy and 1 Gy, and there was no significant difference in the kinetics of disappearance of foci, indicating that DNA double-strand breaks are similarly recognized by DNA damage checkpoints and are repaired irrespective of the dose.

    DOI: 10.1667/RR3542.1

    Web of Science

    PubMed

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KAKENHI (Grants-in-Aid for Scientific Research) 5

  1. Development of new technology to evaluate the transcription-coupling repair factors.

    Grant number:19H04266  2019.4 - 2022.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    Hashimoto Satoru

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    Authorship:Coinvestigator(s) 

    Exposure to various environmental factors give rise DNA damage, which is repaired by multiple mechanisms. The encounter of DNA damage by RNA polymerase in the transcription region initiate DNA repair, but the detailed mechanism remains unclear because of the lack of experimental system for evaluating the site-specific phenomenon on the genome where RNA polymerases encounter against DNA damage. In this research project, we aim to develop a new experimental system for evaluating RNA polymerase that encounter against DNA damage in order to elucidate the damage recognition mechanism by RNA polymerase.

  2. Interactome analysis after induction of DNA damage in human cells

    Grant number:18K11639  2018.4 - 2021.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

    Kurotani Kenichi

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    Authorship:Coinvestigator(s) 

    DNA damage response (DDR) is a crucial response for genome stability. A detailed understanding of their protein-protein interaction networks enables us to know the cellular function of DDR proteins. In this project, we performed the interactome analysis of DDR proteins in human cells using a high resolution mass spectrometry. In the results of our study, we identified several factors that interact with POLR2A/RPB1, the largest subunit of RNA polymerase II, after induction of DNA damage in human cells.

  3. Elucidation of the molecular pathogenesis of genetic disorders caused by defects in DNA damage response using deep proteomic analysis

    Grant number:18H03372  2018.4 - 2021.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    Oka Yasuyoshi

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    Authorship:Principal investigator 

    Grant amount:\17550000 ( Direct Cost: \13500000 、 Indirect Cost:\4050000 )

    DNA damage response is prerequisite for the maintenance of genomic stability. Mutations in genes encoding many components of DNA damage response can result in a number of genetic disorders. Recent extensive studies using NGS analysis identify pathogenic mutations in patients with genomic instability. Because the average healthy person has dozens of genetic variants predicted to severely disrupt protein-coding genes, known as loss-of-function variants, and WES is not able to detect chromosomal translocations, large chromosomal deletions and non-canonical splicing mutations, it is difficult to narrow down and identify pathogenic mutations from patients with extremely rare genetic diseases using only NGS technologies. Using deep proteome analysis, we found the novel disease-causing mutation in the RNASEH2B gene from the patient with microcephaly, cerebral atrophy, and basal ganglia calcification, who was undiagnosed using a WES analysis.

  4. DNA double strand break repair factors mutated in a new syndrome with microcephaly

    Grant number:17H01877  2017.4 - 2020.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    NAKAZAWA Yuka

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    Authorship:Coinvestigator(s) 

    In this study, we have focused on microcephaly as a commonly observed clinical feature of DNA repair deficiency disorders. We have identified several new pathogenic variants in DNA repair genes from microcephaly cases and tried to elucidate their molecular pathogenesis. We have generated mice with mutations in those newly determined genes; however, we often experienced lack of expected phenotypes. This is partly due to greater tolerance to DNA damages in mice; we decided to cross the animals with other mice with deficiency in different DNA repair processes so that overload DNA damage to elicit a phenotype. From this approach, we found that microcephaly and some types of neurodegeneration diseases can be explained by prolonged arrest of RNA polymerases at DNA damage sites during transcription. DNA damage stalled RNA polymerases are ubiquitinated to facilitate DNA repair; when this process is compromised, various neurodegenerative phenotypes, as shown in Cockayne syndrome, come up.

  5. Identification of novel pathogenic variants caused by defects of interstrand DNA crosslink repair

    Grant number:16K21084  2016.4 - 2019.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Young Scientists (B)

    OKA Yasuyoshi

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    Authorship:Principal investigator 

    Grant amount:\3900000 ( Direct Cost: \3000000 、 Indirect Cost:\900000 )

    The goal in this study is to identify novel pathogenic variants caused by the loss of genome stability from patients with microcephaly. Whole exome sequencing identified possible pathogenic variants in two different aldehyde metabolism-related genes from Japanese patients with short stature, microcephaly and hematological abnormality. To understand the molecular mechanisms by which the digenic variants cause microcephaly and hematological abnormality, we performed cellular experiments using cells derived from patients, knockout cell lines using CRISPR/Cas9-mediated genome editing technology, and umbilical cord blood CD34+ cells. These experiments showed two different aldehyde metabolism-related genes contribute to genome maintenance and hematopoietic homeostasis synergistically because simultaneous loss of function of two aldehyde metabolism-related genes leads to hypersensitivity to genotoxic stress or low differentiation ability of hematopoietic stem and progenitor cells in vitro.

Industrial property rights 1

  1. 造血不全、発育遅滞、高発がん性、精神機能障害のモデル動物

    荻朋男/岡泰由

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    Application no:特願2020-166756号  Date applied:2020.10

    Country of applicant:Domestic  

 

Teaching Experience (On-campus) 4

  1. 自然環境と人間

    2021

  2. 基盤医科学実習ベーシックトレーニング

    2021

  3. 自然環境と人間

    2020

  4. 基盤医科学実習ベーシックトレーニング

    2020

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    ヒト細胞を用いたDNA修復蛋白質の局在化の検討