Faculty Profiles - OGI Tomoo

Papers - OGI Tomoo

Division display 101 - 120 of about 179 ／ All the affair displays >>

A heterozygous SERPINB7 mutation is a possible modifying factor for epidermolytic palmoplantar keratoderma. International journal

Takenori Yoshikawa, Takuya Takeichi, Tomoo Ogi, Yasushi Suga, Yoshinao Muro, Masashi Akiyama

Journal of dermatological science Vol. 100 ( 2 ) page： 148 - 151 2020.11

Comprehensive pathogen detection in sera of Kawasaki disease patients by high-throughput sequencing: a retrospective exploratory study Open Access

Torii Yuka, Horiba Kazuhiro, Hayano Satoshi, Kato Taichi, Suzuki Takako, Kawada Jun-ichi, Takahashi Yoshiyuki, Kojima Seiji, Okuno Yusuke, Ogi Tomoo, Ito Yoshinori

BMC PEDIATRICS Vol. 20 ( 1 ) page： 482 2020.10

Gene Expression Profile at the Motor Endplate of the Neuromuscular Junction of Fast-Twitch Muscle. International journal Open Access

Kun Huang, Jin Li, Mikako Ito, Jun-Ichi Takeda, Bisei Ohkawara, Tomoo Ogi, Akio Masuda, Kinji Ohno

Frontiers in molecular neuroscience Vol. 13 page： 154 - 154 2020.9

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

The neuromuscular junction (NMJ) is a prototypic chemical synapse between the spinal motor neuron and the motor endplate. Gene expression profiles of the motor endplate are not fully elucidated. Collagen Q (ColQ) is a collagenic tail subunit of asymmetric forms of acetylcholinesterase and is driven by two distinct promoters. pColQ1 is active throughout the slow-twitch muscle, whereas pColQ1a is active at the motor endplate of fast-twitch muscle. We made a transgenic mouse line that expresses nuclear localization signal (NLS)-attached Cre recombinase under the control of pColQ1a (pColQ1a-Cre mouse). RiboTag mouse expresses an HA-tagged ribosomal subunit, RPL22, in cells expressing Cre recombinase. We generated pColQ1a-Cre:RiboTag mouse, and confirmed that HA-tagged RPL22 was enriched at the NMJ of tibialis anterior (TA) muscle. Next, we confirmed that Chrne and Musk that are specifically expressed at the NMJ were indeed enriched in HA-immunoprecipitated (IP) RNA, whereas Sox10 and S100b, markers for Schwann cells, and Icam1, a marker for vascular endothelial cells, and Pax3, a marker for muscle satellite cells, were scarcely detected. Gene set enrichment analysis (GSEA) of RNA-seq data showed that "phosphatidylinositol signaling system" and "extracellular matrix receptor interaction" were enriched at the motor endplate. Subsequent analysis revealed that genes encoding diacylglycerol kinases, phosphatidylinositol kinases, phospholipases, integrins, and laminins were enriched at the motor endplate. We first characterized the gene expression profile under translation at the motor endplate of TA muscle using the RiboTag technique. We expect that our gene expression profiling will help elucidate molecular mechanisms of the development, maintenance, and pathology of the NMJ.

DOI： 10.3389/fnmol.2020.00154

NUS1 mutation in a family with epilepsy, cerebellar ataxia, and tremor. Reviewed International journal

Kunihiko Araki, Ryoichi Nakamura, Daisuke Ito, Kohji Kato, Yohei Iguchi, Kentaro Sahashi, Miho Toyama, Kensuke Hamada, Nobuhiko Okamoto, Yoshinao Wada, Tomohiko Nakamura, Tomoo Ogi, Masahisa Katsuno

Epilepsy research Vol. 164 page： 106371 - 106371 2020.8

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

We report on familial 5 epilepsy patients with autosomal dominant inheritance of a novel heterozygous NUS1 frameshift mutation. All patients had cerebellar ataxia and tremor. Three patients were diagnosed with childhood absence epilepsy, 1 patient with generalized epilepsy, and 1 patient with parkinsonism without epilepsy. Our cases and previously reported cases with deletions of chromosome 6q22 that include NUS1 share these common symptoms. In a cellular experiment, NUS1 mutation led to a substantial reduction of the protein level of NUS1. NUS1 mutation could contribute to epilepsy pathogenesis and also constitute a distinct syndromic entity with cerebellar ataxia and tremor.

DOI： 10.1016/j.eplepsyres.2020.106371

Web of Science

Scopus

PubMed

Topoisomerase I-driven repair of UV-induced damage in NER-deficient cells. Reviewed International journal Open Access

Liton Kumar Saha, Mitsuo Wakasugi, Salma Akter, Rajendra Prasad, Samuel H Wilson, Naoto Shimizu, Hiroyuki Sasanuma, Shar-Yin Naomi Huang, Keli Agama, Yves Pommier, Tsukasa Matsunaga, Kouji Hirota, Shigenori Iwai, Yuka Nakazawa, Tomoo Ogi, Shunichi Takeda

Proceedings of the National Academy of Sciences of the United States of America Vol. 117 ( 25 ) page： 14412 - 14420 2020.6

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

Nucleotide excision repair (NER) removes helix-destabilizing adducts including ultraviolet (UV) lesions, cyclobutane pyrimidine dimers (CPDs), and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs). In comparison with CPDs, 6-4PPs have greater cytotoxicity and more strongly destabilizing properties of the DNA helix. It is generally believed that NER is the only DNA repair pathway that removes the UV lesions as evidenced by the previous data since no repair of UV lesions was detected in NER-deficient skin fibroblasts. Topoisomerase I (TOP1) constantly creates transient single-strand breaks (SSBs) releasing the torsional stress in genomic duplex DNA. Stalled TOP1-SSB complexes can form near DNA lesions including abasic sites and ribonucleotides embedded in chromosomal DNA. Here we show that base excision repair (BER) increases cellular tolerance to UV independently of NER in cancer cells. UV lesions irreversibly trap stable TOP1-SSB complexes near the UV damage in NER-deficient cells, and the resulting SSBs activate BER. Biochemical experiments show that 6-4PPs efficiently induce stable TOP1-SSB complexes, and the long-patch repair synthesis of BER removes 6-4PPs downstream of the SSB. Furthermore, NER-deficient cancer cell lines remove 6-4PPs within 24 h, but not CPDs, and the removal correlates with TOP1 expression. NER-deficient skin fibroblasts weakly express TOP1 and show no detectable repair of 6-4PPs. Remarkably, the ectopic expression of TOP1 in these fibroblasts led them to completely repair 6-4PPs within 24 h. In conclusion, we reveal a DNA repair pathway initiated by TOP1, which significantly contributes to cellular tolerance to UV-induced lesions particularly in malignant cancer cells overexpressing TOP1.

DOI： 10.1073/pnas.1920165117

Web of Science

Scopus

PubMed

InMeRF: prediction of pathogenicity of missense variants by individual modeling for each amino acid substitution Open Access

Jun-ichi Takeda, Kentaro Nanatsue, Ryosuke Yamagishi, Mikako Ito, Nobuhiko Haga, Hiromi Hirata, Tomoo Ogi, Kinji Ohno

NAR Genomics and Bioinformatics Vol. 2 ( 2 ) page： lqaa038 2020.6

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP)

<title>Abstract</title>
In predicting the pathogenicity of a nonsynonymous single-nucleotide variant (nsSNV), a radical change in amino acid properties is prone to be classified as being pathogenic. However, not all such nsSNVs are associated with human diseases. We generated random forest (RF) models individually for each amino acid substitution to differentiate pathogenic nsSNVs in the Human Gene Mutation Database and common nsSNVs in dbSNP. We named a set of our models ‘Individual Meta RF’ (InMeRF). Ten-fold cross-validation of InMeRF showed that the areas under the curves (AUCs) of receiver operating characteristic (ROC) and precision–recall curves were on average 0.941 and 0.957, respectively. To compare InMeRF with seven other tools, the eight tools were generated using the same training dataset, and were compared using the same three testing datasets. ROC-AUCs of InMeRF were ranked first in the eight tools. We applied InMeRF to 155 pathogenic and 125 common nsSNVs in seven major genes causing congenital myasthenic syndromes, as well as in VANGL1 causing spina bifida, and found that the sensitivity and specificity of InMeRF were 0.942 and 0.848, respectively. We made the InMeRF web service, and also made genome-wide InMeRF scores available online (https://www.med.nagoya-u.ac.jp/neurogenetics/InMeRF/).

DOI： 10.1093/nargab/lqaa038

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

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

Authorship：Corresponding author 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

Severe achondroplasia due to two de novo variants in the transmembrane domain of FGFR3 on the same allele: A case report. Reviewed International journal Open Access

Tadashi Nagata, Masaki Matsushita, Kenichi Mishima, Yasunari Kamiya, Kohji Kato, Miho Toyama, Tomoo Ogi, Naoki Ishiguro, Hiroshi Kitoh

Molecular genetics & genomic medicine Vol. 8 ( 3 ) page： e1148 2020.3

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

BACKGROUND: Achondroplasia (ACH), the most common form of short-limbed skeletal dysplasia, is caused by gain-of-function mutations in the fibroblast growth factor receptor 3 (FGFR3) gene. More than 97% of patients result from a heterozygous p.G380R mutation in the FGFR3 gene. We present here a child who had two de novo variants in the FGFR3 on the same allele, a common p.G380R mutation and a novel p.S378N variant. METHODS: A 3-year-old Japanese girl born from non-consanguineous healthy parents showed more severe clinical and radiological phenotypes than classic ACH, including severe short-limbed short stature with marked ossification defects in the metaphysis and epiphysis, hydrocephalus and cervicomedullary compression due to foramen magnum stenosis, prolonged pulmonary hypoplasia, and significant delay in the gross motor development. Genomic DNA was extracted from the proband and whole-exome sequencing was performed. The variants were subsequently confirmed by Sanger sequencing. RESULTS: Mutation analysis demonstrated that the proband had p.S378N (c.1133G>A) and p.G380R (c.1138G>A) variants in the FGFR3 gene. Both variants were not detected in her parents and therefore considered de novo. An allele-specific PCR was developed in order to determine whether these mutations were on the same allele (cis) or on different alleles (trans). The c.1138G>A mutation was found in the PCR product generated with the primer for the mutant 1133A, but it was not detected in the product with the wild-type 1133G, confirming that p.S378N and p.G380R variants were located on the same allele (cis). CONCLUSION: This is the second case who had two FGFR3 variants in the transmembrane domain on the same allele. The p.S378N variant may provide an additive effect on the activating receptor with the p.G380R mutation and alter the protein function, which could be responsible for the severe phenotype of the present case.

DOI： 10.1002/mgg3.1148

Reduced stratum corneum acylceramides in autosomal recessive congenital ichthyosis with a NIPAL4 mutation. Reviewed International journal Open Access

Yuya Murase, Takuya Takeichi, Akane Kawamoto, Kana Tanahashi, Yusuke Okuno, Hiroyuki Takama, Eri Shimizu, Junko Ishikawa, Tomoo Ogi, Masashi Akiyama

Journal of dermatological science Vol. 97 ( 1 ) page： 50 - 56 2020.1

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

BACKGROUND: NIPAL4, encoding the NIPA-like domain containing 4 protein (NIPAL4), is one of the causative genes of autosomal recessive congenital ichthyosis (ARCI). The physiological role of NIPAL4 and the pathogenetic mechanisms of ARCI caused by NIPAL4 mutations remain unclear. OBJECTIVE: To clarify the changes of ceramide components in the lesional stratum corneum (SC) and the gene expression profile in the lesional skin of an ARCI patient with a novel frameshift mutation in NIPAL4. METHODS: We performed ultrastructural and immunohistochemical analyses of the skin. We used RNA sequencing to determine the mRNA expression in the skin of the patient and healthy individuals. We investigated ceramide components using tape stripped SC samples from the patient. RESULTS: mRNA expression profiling in the patient's skin showed significant upregulation of IL-17/TNFα-related genes (IL17C, IL36A, IL36G, S100A7A, S100A9) and psoriasis hallmark genes (VNN3, LCE3D, PLA2G4D), and significant downregulation of lipid-associated genes (GAL, HAO2, FABP7). Ceramide analysis in the patient's SC revealed amounts of CER[NS] with carbon chain-length (C) 32-52 were increased, while amounts of most acylceramide with C66:2 - C72:2 were reduced relatively to those in healthy individuals. After the retinoid treatment, CER[NS] with carbon chains C46-54, CER[EOH] and CER[EOP] increased. CONCLUSION: IL-17C and IL-36 family cytokines might be involved in the pathogenetic process of ARCI with NIPAL4 mutations. Reduced amounts of the acylceramides in the SC are associated with the skin phenotype due to NIPAL4 mutations. Efficacy of the oral retinoid treatment might be due to restored amounts of CER[EOH] and CER[EOP] in the SC.

DOI： 10.1016/j.jdermsci.2019.12.001

Whole Exome Sequencing Contributes to Genetic Diagnosis of IBMFS Patients

Muramatsu Hideki, Hamada Motoharu, Okuno Yusuke, Wakamatsu Manabu, Taniguchi Rieko, Narita Koutarou, Kawashima Nozomu, Kitazawa Hironobu, Ichikawa Daisuke, Nishikawa Eri, Kawashima Nazomu, Narita Atsushi, Nishio Nobuhiro, Kojima Seiji, Ogi Tomoo, Takahashi Yoshiyuki

PEDIATRIC BLOOD & CANCER Vol. 66 page： S63 - S64 2019.12

Whole Exome Sequencing Contributes to Genetic Diagnosis of IBMFS Patients

PEDIATRIC BLOOD & CANCER Vol. 66 page： S63-S64 2019.12

Comprehensive Mutational Analysis of Juvenile Myelomonocytic Leukemia Using Whole-Genome Sequencing Open Access

Okuno Yusuke, Muramatsu Hideki, Murakami Norihiro, Kawashima Nozomu, Wakamatsu Manabu, Kitazawa Hironobu, Ogi Tomoo, Takahashi Yoshiyuki

BLOOD Vol. 134 2019.11

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

Kato K, Oka Y, Muramatsu H, Vasilev FF, Otomo T, Oishi H, Kawano Y, Kidokoro H, Nakazawa Y, Ogi T, Takahashi Y, Saitoh S

Journal of medical genetics 2019.11

A novel NCSTN missense mutation in the signal peptide domain causes hidradenitis suppurativa, which has features characteristic of an autoinflammatory keratinization disease Open Access

Takeichi T., Matsumoto T., Nomura T., Takeda M., Niwa H., Kono M., Shimizu H., Ogi T., Akiyama M.

BRITISH JOURNAL OF DERMATOLOGY 2019.10

Hailey-Hailey disease with oesophageal involvement due to a previously unreported ATP2C1 mutation. Reviewed International journal

Michihiro Kono, Masanari Kodera, Yu Inasaka, Izumi Hasegawa, Yoshinao Muro, Yuka Nakazawa, Tomoo Ogi, Masashi Akiyama

European journal of dermatology : EJD Vol. in press 2019.8

Bi-allelic TARS Mutations Are Associated with Brittle Hair Phenotype Open Access

Thei Arjan F., Botta Elena, Raams Anja, Smith Desiree E. C., Mendes Marisa I, Caligiuri Giuseppina, Giachetti Sarah, Bione Silvia, Carriero Roberta, Liberi Giordano, Zardoni Luca, Swagemakers Sigrid M. A., Salomons Gajja S., Sarasin Alain, Lehmann Alan, van der Spek Peter J., Ogi Tomoo, Hoeijmakers Jan H. J., Vermeulen Wim, orioli Donata

AMERICAN JOURNAL OF HUMAN GENETICS Vol. 105 ( 2 ) page： 434-440 2019.8

Unravelling the pivotal role of DDA1 in transcription-coupled nucleotide excision repair

Pines A., Guo C., Akita M., Theil A., Quist B., Wienholz F., Marteijn J., Demmers J., van Attikum H., Vertegaal A., Vermeulen M., Ogi T., Vermeulen W.

BRITISH JOURNAL OF DERMATOLOGY Vol. 180 ( 6 ) page： E230 - E230 2019.6

Unravelling the pivotal role of DDA1 in transcription-coupled nucleotide excision repair

Pines A, Guo C, Akita M, Theil A, Quist B, Wienholz F, Marteijn J, Demmers J, van Attikum H, Vertegaal A, Vermeulen M, Ogi T, Vermeulen W

BRITISH JOURNAL OF DERMATOLOGY Vol. 180 ( 6 ) page： E230-E230 2019.6

JAK/STAT3 and NF-κB Signaling Pathways Regulate Cancer Stem-Cell Properties in Anaplastic Thyroid Cancer Cells Reviewed Open Access

Ken Shiraiwa, Michiko Matsuse, Yuka Nakazawa, Tomoo Ogi, Keiji Suzuki, Vladimir Saenko, Shuhang Xu, Kazuo Umezawa, Shunichi Yamashita, Kazuhiro Tsukamoto, Norisato Mitsutake

Thyroid Vol. 29 ( 5 ) page： 674 - 682 2019.5

A Japanese Case of Galli-Galli Disease due to a Previously Unreported POGLUT1 Mutation Open Access

Kono Michihiro, Sawada Masaki, Nakazawa Yuka, Ogi Tomoo, Muro Yoshinao, Akiyama Masashi

ACTA DERMATO-VENEREOLOGICA Vol. 99 ( 4 ) page： 458-459 2019.4

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Papers - OGI Tomoo