Details of a Researcher - Sasaki, Takashi

Papers - Sasaki, Takashi

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Subclinical hypopigmentation of the skin and hair in a Japanese patient with Hermansky-Pudlak syndrome type 3.

Saito S, Tanaka R, Sasaki T, Aoki S, Yasuhara R, Nakayama Y, Nagai T, Sonobe H, Ozawa Y, Kubo A

The Journal of dermatology 2019.10

ISSN 0385-2407

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Sex-specific effects of apolipoprotein ε4 allele on mortality in very old and centenarian Japanese men.

Sasaki T, Nishimoto Y, Abe Y, Takayama M, Hirose N, Okano H, Arai Y

The journals of gerontology. Series A, Biological sciences and medical sciences 2019.10

ISSN 1079-5006

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[Genetic Protective Factors for Dementia Isolated by Centenarian Researches].

Sasaki T, Nishimoto Y, Hirose N, Arai Y

Brain and nerve = Shinkei kenkyu no shinpo 71 ( 10 ) 1061 - 1070 2019.10

ISSN 1881-6096

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Recovery of FRI-5 carbapenemase at a Japanese hospital where FRI-4 carbapenemase was discovered

Uwamino, Y., Kubota, H., Sasaki, T., Kosaka, A., Furuhashi, M., Uno, S., Kudoh, J., Murata, M. and Hasegawa, N.

J Antimicrob Chemother 74 ( 11 ) 3390 - 3392 2019.08

ISSN 1460-2091

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Clonal Expansion of Second-Hit Cells with Somatic Recombinations or C>T Transitions Form Porokeratosis in MVD or MVK Mutant Heterozygotes.

Kubo A, Sasaki T, Suzuki H, Shiohama A, Aoki S, Sato S, Fujita H, Ono N, Umegaki-Arao N, Kawai T, Nakabayashi K, Hata K, Yamada D, Matsubara Y, Kosaki K, Amagai M

The Journal of investigative dermatology 2019.06

ISSN 0022-202X

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Induced Pluripotent Stem Cells Reprogrammed with Three Inhibitors Show Accelerated Differentiation Potentials with High Levels of 2-Cell Stage Marker Expression

Nishihara K., Shiga T., Nakamura E., Akiyama T., Sasaki T., Suzuki S., Ko M., Tada N., Okano H., Akamatsu W.

Stem Cell Reports (Stem Cell Reports) 12 ( 2 ) 305 - 318 2019.02

ISSN 22136711

© 2019 The Authors Although pluripotent stem cells can generate various types of differentiated cells, it is unclear why lineage-committed stem/progenitor cells derived from pluripotent stem cells are decelerated and why the differentiation-resistant propensity of embryonic stem cell (ESC)/induced pluripotent stem cell (iPSC)-derived cells is predominant compared with the in vivo equivalents derived from embryonic/adult tissues. In this study, we demonstrated that iPSCs reprogrammed and maintained with three chemical inhibitors of the fibroblast growth factor 4-mitogen-activated protein kinase cascade and GSK3β (3i) could be differentiated into all three germ layers more efficiently than the iPSCs reprogrammed without the 3i chemicals, even though they were maintained with 3i chemicals once they were reprogrammed. Although the iPSCs reprogrammed with 3i had increased numbers of Zscan4-positive cells, the Zscan4-positive cells among iPSCs that were reprogrammed without 3i did not have an accelerated differentiation ability. These observations suggest that 3i exposure during the reprogramming period determines the accelerated differentiation/maturation potentials of iPSCs that are stably maintained at the distinct state.

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APOE Alleles and extreme human longevity

Sebastiani P., Gurinovich A., Nygaard M., Sasaki T., Sweigart B., Bae H., Andersen S., Villa F., Atzmon G., Christensen K., Arai Y., Barzilai N., Puca A., Christiansen L., Hirose N., Perls T.

Journals of Gerontology - Series A Biological Sciences and Medical Sciences (Journals of Gerontology - Series A Biological Sciences and Medical Sciences) 74 ( 1 ) 44 - 51 2019.01

ISSN 10795006

© 2018 The Author(s). Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. We assembled a collection of 28,297 participants from seven studies of longevity and healthy aging comprising New England Centenarian, Long Life Family, Longevity Gene Population, Southern Italian Centenarian, Japanese Centenarian, the Danish Longevity, and the Health and Retirement Studies to investigate the association between the APOE alleles ϵ 2 ϵ 3 and ϵ 4 and extreme human longevity and age at death. By using three different genetic models and two definitions of extreme longevity based on either a threshold model or age at death, we show that ϵ 4 is associated with a substantially decreased odds for extreme longevity, and increased risk for death that persists even beyond ages reached by less than 1% of the population. We also show that carrying the ϵ 2 ϵ 2 or ϵ 2 ϵ 3 genotype is associated with significantly increased odds to reach extreme longevity, with decreased risk for death compared with carrying the genotype ϵ 3 ϵ 3 but with only a modest reduction in risk for death beyond an age reached by less than 1% of the population.

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The desmosome is a mesoscale lipid raft–like membrane domain

Lewis J., Caldara A., Zimmer S., Stahley S., Seybold A., Strong N., Frangakis A., Levental I., Wahl J., Mattheyses A., Sasaki T., Nakabayashi K., Hata K., Matsubara Y., Ishida-Yamamoto A., Amagai M., Kubo A., Kowalczyk A.

Molecular Biology of the Cell (Molecular Biology of the Cell) 30 ( 12 ) 1390 - 1405 2019

ISSN 10591524

© 2019 Lewis, Caldara, et al. Desmogleins (Dsgs) are cadherin family adhesion molecules essential for epidermal integrity. Previous studies have shown that desmogleins associate with lipid rafts, but the significance of this association was not clear. Here, we report that the desmoglein transmembrane domain (TMD) is the primary determinant of raft association. Further, we identify a novel mutation in the DSG1 TMD (G562R) that causes severe dermatitis, multiple allergies, and metabolic wasting syndrome. Molecular modeling predicts that this G-to-R mutation shortens the DSG1 TMD, and experiments directly demonstrate that this mutation compromises both lipid raft association and desmosome incorporation. Finally, cryo-electron tomography indicates that the lipid bilayer within the desmosome is ∼10% thicker than adjacent regions of the plasma membrane. These findings suggest that differences in bilayer thickness influence the organization of adhesion molecules within the epithelial plasma membrane, with cadherin TMDs recruited to the desmosome via the establishment of a specialized mesoscale lipid raft–like membrane domain.

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Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

Okada Yukinori, Momozawa Yukihide, Sakaue Saori, Kanai Masahiro, Ishigaki Kazuyoshi, Akiyama Masato, Kishikawa Toshihiro, Arai Yasumichi, Sasaki Takashi, Kosaki Kenjiro, Suematsu Makoto, Matsuda Koichi, Yamamoto Kazuhiko, Kubo Michiaki, Hirose Nobuyoshi, Kamatani Yoichiro

Nature Communications (Nature Communications) 9 ( 1 ) 1631 2018.12

ISSN 2041-1723

Understanding natural selection is crucial to unveiling evolution of modern humans. Here, we report natural selection signatures in the Japanese population using 2234 high-depth whole-genome sequence (WGS) data (25.9×). Using rare singletons, we identify signals of very recent selection for the past 2000-3000 years in multiple loci (ADH cluster, MHC region, BRAP-ALDH2, SERHL2). In large-scale genome-wide association study (GWAS) dataset (n = 171,176), variants with selection signatures show enrichment in heterogeneity of derived allele frequency spectra among the geographic regions of Japan, highlighted by two major regional clusters (Hondo and Ryukyu). While the selection signatures do not show enrichment in archaic hominin-derived genome sequences, they overlap with the SNPs associated with the modern human traits. The strongest overlaps are observed for the alcohol or nutrition metabolism-related traits. Our study illustrates the value of high-depth WGS to understand evolution and their relationship with disease risk.

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Intragenic copy number variation within human epiplakin 1 (EPPK1) generates variation of molecular size of epiplakin

Ishikawa Kazushi, Furuhashi Mie, Sasaki Takashi, Kudoh Jun, Tsuchisaka Atsunari, Hashimoto Takashi, Sasaki Takako, Yoshioka Hidekatsu, Eshima Nobuoki, Matsuda-Hirose Haruna, Sakai Takashi, Hatano Yutaka, Fujiwara Sakuhei

Journal of Dermatological Science 91 ( 2 ) 228 - 231 2018.08

ISSN 0923-1811

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HER2 heterogeneity is associated with poor survival in HER2-positive breast cancer

Hosonaga Mari, Arima Yoshimi, Sampetrean Oltea, Komura Daisuke, Koya Ikuko, Sasaki Takashi, Sato Eiichi, Okano Hideyuki, Kudoh Jun, Ishikawa Shumpei, Saya Hideyuki, Ishikawa Takashi

International journal of molecular sciences (International Journal of Molecular Sciences) 19 ( 8 ) 2018.08

ISSN 1661-6596

Intratumoral human epidermal growth factor receptor 2 (HER2) heterogeneity has been reported in 16–36% of HER2-positive breast cancer and its clinical impact is under discussion. We examined the biological effects of HER2-heterogeneity on mouse models and analyzed metastatic brains by RNA sequence analysis. A metastatic mouse model was developed using 231-Luc (triple negative cells) and 2 HER2-positive cell lines, namely, HER2-60 and HER2-90 which showed heterogeneous and monotonous HER2 expressions, respectively. Metastatic lesions developed in 3 weeks in all the mice injected with HER2-60 cells, and in 69% of the mice injected with HER2-90 and 87.5% of the mice injected with 231-Luc. The median survival days of mice injected with 231-Luc, HER2-60, and HER2-90 cells were 29 (n = 24), 24 (n = 22) and 30 (n = 13) days, respectively. RNA sequence analysis showed that CASP-1 and its related genes were significantly downregulated in metastatic brain tumors with HER2-60 cells. The low expression of caspase-1 could be a new prognostic biomarker for early relapse in HER2-positive breast cancer.

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A familial case of nail patella syndrome with a heterozygous in-frame indel mutation in the LIM domain of LMX1B

Mukai Miho, Fujita Harumi, Umegaki-Arao Noriko, Sasaki Takashi, Yasuda-Sekiguchi Fumiyo, Isojima Tsuyoshi, Kitanaka Sachiko, Amagai Masayuki, Kubo Akiharu

Journal of Dermatological Science 90 ( 1 ) 90 - 93 2018.04

ISSN 0923-1811

Nail patella syndrome is a autosomal dominant disorder caused by a genetic alteration in LMX1B. We identified a novel heterozygous in-frame indel mutation of LMX1B in a family of Nail patella syndrome. Impaired transcriptional activity but not dominant negative effect of mutant LMX1B were revealed using a transcriptional reporter assay, indicating that the mutation caused nail patella syndrome in this family via haploinsufficiency of the transcriptional activity of LMX1B.

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Junctional epidermolysis bullosa without pyloric atresia due to a homozygous missense mutation in ITGB4

Yoshida Kenji, Sadamoto Mariko, Sasaki Takashi, Kubo Akiharu, Ishiko Akira

Journal of Dermatology 2018.01

ISSN 0385-2407

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Demographic, phenotypic, and genetic characteristics of centenarians in Okinawa and Honshu, Japan: Part 2 Honshu, Japan

Arai, Y., Sasaki, T. and Hirose, N.

Mech Ageing Dev 165 ( Pt B ) 80 - 85 2017.07

ISSN 1872-6216

The scope and purpose of this review was to summarize the aims, methods, findings, and future of centenarian and (semi)-supercentenarian studies in Japan, particularly those from our own interdisciplinary laboratory. Medically, approximately 97% of centenarians contract chronic diseases including hypertension and gastrointestinal disease; however, they present with few cardiovascular risk factors. The low prevalence of diabetes mellitus and carotid atherosclerotic plaques is peculiarities of centenarians, which could be associated with high adiponectin levels. While conducting the Tokyo centenarian study (TCS), we found that only 20% of centenarians enjoyed physical and cognitive independence at the age of 100 years, although most remained independent in daily living until into their 90s. Those who maintained physical independence at 100 years of age were highly likely to become semi-supercentenarians (over 105 years) or even supercentenarians (beyond 110 years). We also describe parts of results of the Japan Semi-supercentenarian Study (JSS), which showed that the suppression of chronic inflammation is an important driver of successful aging at extreme old age. Telomere maintenance and an extremely low frequency of APOE-epsilon4 alleles are genetic peculiarities of (semi)-supercentenarians. The available data confirm our conviction that semi-supercentenarians are a more appropriate model for the study of human longevity.

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Novel nonsense mutation in SERPINB7 and the treatment of foot odor in a patient with Nagashima-type palmoplantar keratosis

Katsuno, M., Shiohama, A., Aoki, S., Kitamura, H., Sasaki, T., Amagai, M. and Kubo, A.

J Dermatol 44 ( 7 ) e146 - e147 2017.07

ISSN 1346-8138

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Association study of childhood food allergy with genome-wide association studies-discovered loci of atopic dermatitis and eosinophilic esophagitis

Hirota, T., Nakayama, T., Sato, S., Yanagida, N., Matsui, T., Sugiura, S., Takaoka, Y., Hizawa, N., Fujieda, S., Miyatake, A., Sasaki, T., Amagai, M., Doi, S., Ito, K., Ebisawa, M. and Tamari, M.

J Allergy Clin Immunol 2017.06

ISSN 1097-6825

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Somatic HRAS p.G12S mosaic mutation causes unilaterally distributed epidermal nevi, woolly hair and palmoplantar keratosis

Honda, A., Umegaki-Arao, N., Sasaki, T., Nakabayashi, K., Hata, K., Matsubara, Y., Tanikawa, A., Amagai, M. and Kubo, A.

J Dermatol 44 ( 6 ) e109 - e110 2017.06

ISSN 1346-8138

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Distinct phenotype of epidermolysis bullosa simplex with infantile migratory circinate erythema due to frameshift mutations in the V2 domain of KRT5

Kumagai, Y., Umegaki-Arao, N., Sasaki, T., Nakamura, Y., Takahashi, H., Ashida, A., Tsunemi, Y., Kawashima, M., Shimizu, A., Ishiko, A., Nakamura, K., Tsuchihashi, H., Amagai, M. and Kubo, A.

J Eur Acad Dermatol Venereol 31 ( 5 ) e241 - e243 2017.05

ISSN 1468-3083

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Inflammatory Linear Verrucous Epidermal Nevus with a Postzygotic GJA1 Mutation Is a Mosaic Erythrokeratodermia Variabilis et Progressiva

Umegaki-Arao Noriko, Sasaki Takashi, Fujita Harumi, Aoki Satomi, Kameyama Kaori, Amagai Masayuki, Seishima Mariko, Kubo Akiharu

Journal of Investigative Dermatology 137 ( 4 ) 967 - 970 2017.04

ISSN 0022-202X

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Inflammatory Linear Verrucous Epidermal Nevus with a Postzygotic GJA1 Mutation Is a Mosaic Erythrokeratodermia Variabilis et Progressiva

Umegaki-Arao, N., Sasaki, T., Fujita, H., Aoki, S., Kameyama, K., Amagai, M., Seishima, M. and Kubo, A.

J Invest Dermatol 137 ( 4 ) 967 - 970 2017.04

ISSN 1523-1747

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Induction of hair follicle dermal papilla cell properties in human induced pluripotent stem cell-derived multipotent LNGFR(+)THY-1(+) mesenchymal cells

Veraitch, O., Mabuchi, Y., Matsuzaki, Y., Sasaki, T., Okuno, H., Tsukashima, A., Amagai, M., Okano, H. and Ohyama, M.

Sci Rep 7 42777 2017.02

ISSN 2045-2322

The dermal papilla (DP) is a specialised mesenchymal component of the hair follicle (HF) that plays key roles in HF morphogenesis and regeneration. Current technical difficulties in preparing trichogenic human DP cells could be overcome by the use of highly proliferative and plastic human induced pluripotent stem cells (hiPSCs). In this study, hiPSCs were differentiated into induced mesenchymal cells (iMCs) with a bone marrow stromal cell phenotype. A highly proliferative and plastic LNGFR(+)THY-1(+) subset of iMCs was subsequently programmed using retinoic acid and DP cell activating culture medium to acquire DP properties. The resultant cells (induced DP-substituting cells [iDPSCs]) exhibited up-regulated DP markers, interacted with human keratinocytes to up-regulate HF related genes, and when co-grafted with human keratinocytes in vivo gave rise to fibre structures with a hair cuticle-like coat resembling the hair shaft, as confirmed by scanning electron microscope analysis. Furthermore, iDPSCs responded to the clinically used hair growth reagent, minoxidil sulfate, to up-regulate DP genes, further supporting that they were capable of, at least in part, reproducing DP properties. Thus, LNGFR(+)THY-1(+) iMCs may provide material for HF bioengineering and drug screening for hair diseases.

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Identification of factors contributing to phenotypic divergence via quantitative image analyses of autosomal recessive woolly hair/hypotrichosis with homozygous c.736T>A LIPH mutation

Kinoshita-Ise M., Kubo A., Sasaki T., Umegaki-Arao N., Amagai M., Ohyama M.

British Journal of Dermatology 176 ( 1 ) 138 - 144 2017.01

ISSN 0007-0963

Background: Autosomal recessive woolly hair/hypotrichosis (ARWH/H) is caused by mutations in LIPH. Homozygotes for the LIPH c.736T>A (p.C246S) mutation, the most prevalent genotype in Japanese patients, present varying degrees of hair loss; however, determinants of this phenotypic diversity remain elusive. Objectives: To establish methodologies for quantitative assessment of clinical severity and provide a detailed characterization to elucidate the factors contributing to phenotypic divergence. Methods: Digital image analyses were conducted to convert clinical severities into numerical values. Eight patients with ARWH/H were classified into three groups (mild, severe, very severe), based on severity scores. Dermoscopic images were collected and assessed for total hair numbers and hair thickness for intergroup comparisons. Results: The image analysis detected a difference in hair thickness but not in total hair numbers, between mild and severe cases. A marked decrease in total hair number was noted in an atypical very severe case. Histopathologically, a patient with a mild case demonstrated hair miniaturization and a high telogen/anagen ratio without a decrease in total hair count, endorsing dermoscopic observations. Two children demonstrated spontaneous improvement without an increase in total hair numbers, and two adults responded well to topical minoxidil with increased total hair numbers and hair thickness. Conclusions: The difference in the frequency of underdeveloped hairs may be a major factor contributing to the clinical diversity of hair sparseness in LIPH c.736T>A homozygotes with ARWH/H. Hence, pharmacological modification to thicken existing fine hairs may provide a therapeutic strategy.

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Identification of factors contributing to phenotypic divergence via quantitative image analyses of autosomal recessive woolly hair/hypotrichosis with homozygous c.736T>A LIPH mutation

Kinoshita-Ise, M., Kubo, A., Sasaki, T., Umegaki-Arao, N., Amagai, M. and Ohyama, M.

Br J Dermatol 176 ( 1 ) 138 - 144 2017.01

ISSN 1365-2133

BACKGROUND: Autosomal recessive woolly hair/hypotrichosis (ARWH/H) is caused by mutations in LIPH. Homozygotes for the LIPH c.736T>A (p.C246S) mutation, the most prevalent genotype in Japanese patients, present varying degrees of hair loss; however, determinants of this phenotypic diversity remain elusive. OBJECTIVES: To establish methodologies for quantitative assessment of clinical severity and provide a detailed characterization to elucidate the factors contributing to phenotypic divergence. METHODS: Digital image analyses were conducted to convert clinical severities into numerical values. Eight patients with ARWH/H were classified into three groups (mild, severe, very severe), based on severity scores. Dermoscopic images were collected and assessed for total hair numbers and hair thickness for intergroup comparisons. RESULTS: The image analysis detected a difference in hair thickness but not in total hair numbers, between mild and severe cases. A marked decrease in total hair number was noted in an atypical very severe case. Histopathologically, a patient with a mild case demonstrated hair miniaturization and a high telogen/anagen ratio without a decrease in total hair count, endorsing dermoscopic observations. Two children demonstrated spontaneous improvement without an increase in total hair numbers, and two adults responded well to topical minoxidil with increased total hair numbers and hair thickness. CONCLUSIONS: The difference in the frequency of underdeveloped hairs may be a major factor contributing to the clinical diversity of hair sparseness in LIPH c.736T>A homozygotes with ARWH/H. Hence, pharmacological modification to thicken existing fine hairs may provide a therapeutic strategy.

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Case of dominant dystrophic epidermolysis bullosa with amniotic band syndrome

Sakiyama, T., Umegaki-Arao, N., Sasaki, T., Kosaki, K., Amagai, M. and Kubo, A.

J Dermatol 44 ( 1 ) 102 - 103 2017.01

ISSN 1346-8138

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Novel KRT9 missense mutation in a Japanese case of epidermolytic palmoplantar keratoderma

Fukunaga Yoshie, Kubo Akiharu, Sasaki Takashi, Tsuruta Daisuke, Fukai Kazuyoshi

Journal of Dermatology 2017

ISSN 0385-2407

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RNA Sequencing Analysis Reveals Interactions between Breast Cancer or Melanoma Cells and the Tissue Microenvironment during Brain Metastasis

Sato Ryo, Nakano Teppei, Hosonaga Mari, Sampetrean Oltea, Harigai Ritsuko, Sasaki Takashi, Koya Ikuko, Okano Hideyuki, Kudoh Jun, Saya Hideyuki, Arima Yoshimi

BioMed Research International 2017 2017

ISSN 2314-6133

Metastasis is the main cause of treatment failure and death in cancer patients. Metastasis of tumor cells to the brain occurs frequently in individuals with breast cancer, non-small cell lung cancer, or melanoma. Despite recent advances in our understanding of the causes and in the treatment of primary tumors, the biological and molecular mechanisms underlying the metastasis of cancer cells to the brain have remained unclear. Metastasizing cancer cells interact with their microenvironment in the brain to establish metastases. We have now developed mouse models of brain metastasis based on intracardiac injection of human breast cancer or melanoma cell lines, and we have performed RNA sequencing analysis to identify genes in mouse brain tissue and the human cancer cells whose expression is associated specifically with metastasis. We found that the expressions of the mouse genes Tph2, Sspo, Ptprq, and Pole as well as those of the human genes CXCR4, PLLP, TNFSF4, VCAM1, SLC8A2, and SLC7A11 were upregulated in brain tissue harboring metastases. Further characterization of such genes that contribute to the establishment of brain metastases may provide a basis for the development of new therapeutic strategies and consequent improvement in the prognosis of cancer patients.

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Identification and Characterization of a Recessive Missense Mutation p.P277L in SERPINB7 in Nagashima-Type Palmoplantar Keratosis

Shiohama, A., Sasaki, T., Sato, S., Sakabe, J., Ito, T., Isoda, H., Zenke, Y., Nakano, T., Maeda, T., Ishiko, A., Kabashima, K., Tokura, Y., Mitsuhashi, Y., Amagai, M. and Kubo, A.

J Invest Dermatol 136 ( 1 ) 325 - 8 2016.01

ISSN 1523-1747

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Japanese recurrent mutation c.6216+5G>T in COL7A1 leads to a mild phenotype of dystrophic epidermolysis bullosa

Masunaga, T., Saito, M., Sasaki, T., Kubo, A., Amagai, M. and Ishiko, A.

J Dermatol Sci 80 ( 3 ) 220 - 3 2015.12

ISSN 1873-569X

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Pathological characterization of pachydermia in pachydermoperiostosis

Tanese, K., Niizeki, H., Seki, A., Otsuka, A., Kabashima, K., Kosaki, K., Kuwahara, M., Miyakawa, S., Miyasaka, M., Matsuoka, K., Okuyama, T., Shiohama, A., Sasaki, T., Kudoh, J., Amagai, M. and Ishiko, A.

J Dermatol 42 ( 7 ) 710 - 4 2015.07

ISSN 1346-8138

Pachydermoperiostosis is a rare hereditary disease, which presents with the cutaneous manifestations of pachydermia and cutis verticis gyrata. Histological findings in pachydermia frequently include dermal edema, mucin deposition, elastic fiber degeneration, dermal fibrosis and adnexal hyperplasia. However, the severity of these findings varies between clinical reports, and a systematic multiple-case clinicopathological correlative analysis has not been performed to date. In the present study, we reviewed the skin biopsy specimens obtained from the pachydermia of six pachydermoperiostosis patients. The severity of the characteristic histological features was semiquantitatively evaluated and correlated with the grade of pachydermia. Dermal edema, mucin deposition and elastic fiber degeneration were observed in all cases. Patients with severe pachydermia had sebaceous gland hyperplasia and fibrosis. These results suggest that the triad of mucin deposition, dermal edema and elastic fiber degeneration are found from very early stage pachydermia, and could be considered diagnostic findings. To ensure an earlier diagnosis of pachydermoperiostosis, a biopsy should be taken when a patient has grade 1 pachydermia to determine the presence of this histological triad.

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YAP is essential for tissue tension to ensure vertebrate 3D body shape

Porazinski, S., Wang, H., Asaoka, Y., Behrndt, M., Miyamoto, T., Morita, H., Hata, S., Sasaki, T., Krens, S. F. G., Osada, Y., Asaka, S., Momoi, A., Linton, S., Miesfeld, J. B., Link, B. A., Senga, T., Shimizu, N., Nagase, H., Matsuura, S., Bagby, S., Kondoh, H., Nishina, H., Heisenberg, C. P. and Furutani-Seiki, M.

Nature 521 ( 7551 ) 217 - 221 2015.05

ISSN 1476-4687

Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues.

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Long-term safety issues of iPSC-based cell therapy in a spinal cord injury model: oncogenic transformation with epithelial-mesenchymal transition

Nori, S., Okada, Y., Nishimura, S., Sasaki, T., Itakura, G., Kobayashi, Y., Renault-Mihara, F., Shimizu, A., Koya, I., Yoshida, R., Kudoh, J., Koike, M., Uchiyama, Y., Ikeda, E., Toyama, Y., Nakamura, M. and Okano, H.

Stem Cell Reports 4 ( 3 ) 360 - 73 2015.03

ISSN 2213-6711

Previously, we described the safety and therapeutic potential of neurospheres (NSs) derived from a human induced pluripotent stem cell (iPSC) clone, 201B7, in a spinal cord injury (SCI) mouse model. However, several safety issues concerning iPSC-based cell therapy remain unresolved. Here, we investigated another iPSC clone, 253G1, that we established by transducing OCT4, SOX2, and KLF4 into adult human dermal fibroblasts collected from the same donor who provided the 201B7 clone. The grafted 253G1-NSs survived, differentiated into three neural lineages, and promoted functional recovery accompanied by stimulated synapse formation 47 days after transplantation. However, long-term observation (for up to 103 days) revealed deteriorated motor function accompanied by tumor formation. The tumors consisted of Nestin(+) undifferentiated neural cells and exhibited activation of the OCT4 transgene. Transcriptome analysis revealed that a heightened mesenchymal transition may have contributed to the progression of tumors derived from grafted cells.

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Case of non-Herlitz junctional epidermolysis bullosa with COL17A1 mutation

Kasai, H., Sasaki, T., Matsuzaki, H., Yoshioka, T., Nagao, K., Amagai, M., Ishiko, A. and Kubo, A.

J Dermatol 42 ( 3 ) 323 - 5 2015.03

ISSN 1346-8138

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Global gene expression analysis following spinal cord injury in non-human primates

Nishimura, S., Sasaki, T., Shimizu, A., Yoshida, K., Iwai, H., Koya, I., Kobayashi, Y., Itakura, G., Shibata, S., Ebise, H., Horiuchi, K., Kudoh, J., Toyama, Y., Anderson, A. J., Okano, H. and Nakamura, M.

Exp Neurol 261 171 - 9 2014.11

ISSN 1090-2430

Spinal cord injury (SCI) is a devastating condition with no established treatment. To better understand the pathology and develop a treatment modality for SCI, an understanding of the physiological changes following SCI at the molecular level is essential. However, studies on SCI have primarily used rodent models, and few studies have examined SCI in non-human primates. In this study, we analyzed the temporal changes in gene expression patterns following SCI in common marmosets (Callithrix jacchus) using microarray analysis and mRNA deep sequencing. This analysis revealed that, although the sequence of events is comparable between primates and rodents, the inflammatory response following SCI is significantly prolonged and the onset of glial scar formation is temporally delayed in primates compared with rodents. These observations indicate that the optimal time window to treat SCI significantly differs among different species. This study provides the first extensive analysis of gene expression following SCI in non-human primates and will serve as a valuable resource in understanding the pathology of SCI.

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Application of moisturizer to neonates prevents development of atopic dermatitis

Horimukai, K., Morita, K., Narita, M., Kondo, M., Kitazawa, H., Nozaki, M., Shigematsu, Y., Yoshida, K., Niizeki, H., Motomura, K., Sago, H., Takimoto, T., Inoue, E., Kamemura, N., Kido, H., Hisatsune, J., Sugai, M., Murota, H., Katayama, I., Sasaki, T., Amagai, M., Morita, H., Matsuda, A., Matsumoto, K., Saito, H. and Ohya, Y.

J Allergy Clin Immunol 134 ( 4 ) 824 - 830 e6 2014.10

ISSN 1097-6825

BACKGROUND: Recent studies have suggested that epidermal barrier dysfunction contributes to the development of atopic dermatitis (AD) and other allergic diseases. OBJECTIVE: We performed a prospective, randomized controlled trial to investigate whether protecting the skin barrier with a moisturizer during the neonatal period prevents development of AD and allergic sensitization. METHODS: An emulsion-type moisturizer was applied daily during the first 32 weeks of life to 59 of 118 neonates at high risk for AD (based on having a parent or sibling with AD) who were enrolled in this study. The onset of AD (eczematous symptoms lasting >4 weeks) and eczema (lasting >2 weeks) was assessed by a dermatology specialist on the basis of the modified Hanifin and Rajka criteria. The primary outcome was the cumulative incidence of AD plus eczema (AD/eczema) at week 32 of life. A secondary outcome, allergic sensitization, was evaluated based on serum levels of allergen-specific IgE determined by using a high-sensitivity allergen microarray of diamond-like carbon-coated chips. RESULTS: Approximately 32% fewer neonates who received the moisturizer had AD/eczema by week 32 than control subjects (P = .012, log-rank test). We did not show a statistically significant effect of emollient on allergic sensitization based on the level of IgE antibody against egg white at 0.34 kUA/L CAP-FEIA equivalents. However, the sensitization rate was significantly higher in infants who had AD/eczema than in those who did not (odds ratio, 2.86; 95% CI, 1.22-6.73). CONCLUSION: Daily application of moisturizer during the first 32 weeks of life reduces the risk of AD/eczema in infants. Allergic sensitization during this time period is associated with the presence of eczematous skin but not with moisturizer use.

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Filaggrin loss-of-function mutations are not a predisposing factor for atopic dermatitis in an Ishigaki Island under subtropical climate

Sasaki, T., Furusyo, N., Shiohama, A., Takeuchi, S., Nakahara, T., Uchi, H., Hirota, T., Tamari, M., Shimizu, N., Ebihara, T., Amagai, M., Furue, M., Hayashi, J. and Kudoh, J.

J Dermatol Sci 76 ( 1 ) 10 - 5 2014.10

ISSN 1873-569X

BACKGROUND: Filaggrin (FLG) is a major protein component of the stratum corneum (SC) layer, and FLG loss-of-function mutations are a predisposing factor for atopic dermatitis (AD). Previous cohort studies of children from northern and western Europe have reported FLG loss-of-function mutation frequencies of 15.1-20.9% and 5.8-13.0% in AD and non-AD groups, respectively. OBJECTIVE: To elucidate the association between AD prevalence of FLG loss-of-function mutation carriers and climate conditions, we determined the AD prevalence and FLG loss-of-function mutation frequencies in a cohort of children from Ishigaki Island. Ishigaki Island has a subtropical climate with high humidity (monthly average, 60.8-78.7%) and high temperature (monthly average, 18.5-29.4 degrees C) throughout the year. METHODS: We diagnosed AD prevalence and analyzed eight FLG loss-of-function mutations in the Japanese population against a cohort of 721 children from the Kyushu University Ishigaki Atopic Dermatitis Study (KIDS) cohort. Parents gave consent for the mutation analysis during their medical examinations from 2001 to 2006. RESULTS: Average AD prevalence was 7.3% per year, and a total of 127 children (17.6%) were diagnosed with AD at least once between 2001 and 2006. The average total serum IgE level differed significantly between the AD and non-AD groups (199.0 and 69.0IU/ml, respectively). Although five kinds of FLG loss-of-function mutations isolated in previous Japanese FLG mutation studies were identified, the FLG loss-of-function mutation frequency in children of the KIDS cohort was not significantly different between the AD and non-AD groups (7.9% and 6.1%, respectively; P=0.174). CONCLUSION: The FLG loss-of-function mutation frequency was not significantly different between the AD and non-AD groups in a cohort of children from Ishigaki Island, which has a subtropical climate, suggesting that FLG loss-of-function mutations are not always a predisposing factor for AD prevalence.

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The complete type of pachydermoperiostosis: a novel nonsense mutation p.E141* of the SLCO2A1 gene

Niizeki, H., Shiohama, A., Sasaki, T., Seki, A., Kabashima, K., Otsuka, A., Kosaki, K., Ogo, A., Yamada, T., Miyasaka, M., Matsuoka, K., Hirakiyama, A., Okuyama, T., Matsuda, M., Nakabayashi, K., Tanese, K., Ishiko, A., Amagai, M. and Kudoh, J.

J Dermatol Sci 75 ( 3 ) 193 - 5 2014.09

ISSN 1873-569X

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The novel SLCO2A1 heterozygous missense mutation p.E427K and nonsense mutation p.R603* in a female patient with pachydermoperiostosis with an atypical phenotype

Niizeki, H., Shiohama, A., Sasaki, T., Seki, A., Kabashima, K., Otsuka, A., Takeshita, M., Hirakiyama, A., Okuyama, T., Tanese, K., Ishiko, A., Amagai, M. and Kudoh, J.

Br J Dermatol 170 ( 5 ) 1187 - 9 2014.05

ISSN 1365-2133

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[Mouse models for spontaneous dermatitis due to impaired skin barrier formation]

Sasaki, T., Shiohama, A. and Amagai, M.

Nihon Rinsho Meneki Gakkai Kaishi 37 ( 3 ) 160 - 5 2014

ISSN 1349-7413

Flaky tail mice possess two distinct autosomal recessive mutations, hair abnormality (matted: ma) and stratum corneum layer abnormality (flaky tail: ft), and develop dermatitis spontaneously with high serum IgE even under specific pathogen free condition. We demonstrated that flaky tail mice possess loss of function mutation in Filaggrin (Flg) which is one of the major component of stratum corneum, and showed skin barrier abnormality, although our genetically engineered Flg null mice did not develop dermatitis spontaneously. As a result of segregation of ft and ma mutations, we identified that ma mutation is responsible for the dermatitis phenotype in flaky tail mice, and Tmem79 nonsense mutation (Tmem79(ma)) is corresponding to the ma mutation. Tmem79 is expressed in outermost cell of stratum granulosum layer, and ma mice showed abnormal lamellar granule secretory system and abnormal formation of stratum corneum. Thus, Tmem79(ma/ma) mice provides a useful mouse model for spontaneous dermatitis caused by skin barrier gene deficiency. Further analysis for Tmem79(ma/ma) mice would elucidate important mechanisms for development of atopic dermatitis.

フィラグリン(fillagrin)

雅行, 佐々木　貴史、天谷

分子消化器病 11(2) 88 - 93 2014

皮膚バリア異常を示す自然発症皮膚炎モデルマウス

雅行, 佐々木　貴史、塩濱　愛子、天谷

日本臨床免疫学会会誌 37(3) 160 - 165 2014

A homozygous nonsense mutation in the gene for Tmem79, a component for the lamellar granule secretory system, produces spontaneous eczema in an experimental model of atopic dermatitis

Sasaki, Takashi, Shiohama, Aiko, Kubo, Akiharu, Kawasaki, Hiroshi, Ishida-Yamamoto, Akemi, Yamada, Taketo, Hachiya, Takayuki, Shimizu, Atsushi, Okano, Hideyuki, Kudoh, Jun, Amagai, Masayuki

JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY 132 ( 5 ) 1111 - + 2013.11

Research paper (scientific journal), ISSN 0091-6749

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Mutations in SERPINB7, Encoding a Member of the Serine Protease Inhibitor Superfamily, Cause Nagashima-type Palmoplantar Keratosis

Kubo, Akiharu, Shiohama, Aiko, Sasaki, Takashi, Nakabayashi, Kazuhiko, Kawasaki, Hiroshi, Atsugi, Toru, Sato, Showbu, Shimizu, Atsushi, Mikami, Shuji, Tanizaki, Hideaki, Uchiyama, Masaki, Maeda, Tatsuo, Ito, Taisuke, Sakabe, Jun-ichi, Heike, Toshio, Okuyama, Torayuki, Kosaki, Rika, Kosaki, Kenjiro, Kudoh, Jun, Hata, Kenichiro, Umezawa, Akihiro, Tokura, Yoshiki, Ishiko, Akira, Niizeki, Hironori, Kabashima, Kenji, Mitsuhashi, Yoshihiko, Amagai, Masayuki

AMERICAN JOURNAL OF HUMAN GENETICS 93 ( 5 ) 945 - 956 2013.11

Research paper (scientific journal), ISSN 0002-9297

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Human Induced Pluripotent Stem Cell-Derived Ectodermal Precursor Cells Contribute to Hair Follicle Morphogenesis In Vivo

Veraitch, Ophelia, Kobayashi, Tetsuro, Imaizumi, Yoichi, Akamatsu, Wado, Sasaki, Takashi, Yamanaka, Shinya, Amagai, Masayuki, Okano, Hideyuki, Ohyama, Manabu

JOURNAL OF INVESTIGATIVE DERMATOLOGY 133 ( 6 ) 1479 - 1488 2013.06

Research paper (scientific journal), ISSN 0022-202X

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Characterization of canine filaggrin: gene structure and protein expression in dog skin

Kanda, Satoko, Sasaki, Takashi, Shiohama, Aiko, Nishifuji, Koji, Amagai, Masayuki, Iwasaki, Toshiroh, Kudoh, Jun

VETERINARY DERMATOLOGY 24 ( 1 ) 25 - + 2013.02

Research paper (scientific journal), ISSN 0959-4493

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Dpysl4 is involved in tooth germ morphogenesis through growth regulation, polarization and differentiation of dental epithelial cells

Yasukawa, M., Ishida, K., Yuge, Y., Hanaoka, M., Minami, Y., Ogawa, M., Sasaki, T., Saito, M. and Tsuji, T.

Int J Biol Sci 9 ( 4 ) 382 - 90 2013

ISSN 1449-2288

Dihydropyrimidinase-related protein 4 (Dpysl4) is a known regulator of hippocampal neuron development. Here, we report that Dpysl4 is involved in growth regulation, polarization and differentiation of dental epithelial cells during tooth germ morphogenesis. A reduction in Dpysl4 gene expression in the tooth germ produced a loss of ameloblasts, resulting in the decrease of synthesis and secretion of enamel. The inhibition of Dpysl4 gene expression led to promotion of cell proliferation of inner enamel epithelial cells and inhibition of the differentiation of these cells into pre-ameloblasts, which was confirmed by analyzing cell polarization, columnar cell structure formation and the expression of ameloblast marker genes. By contrast, overexpression of Dpysl4 in dental epithelial cells induces inhibition of growth and increases the expression of the inner enamel epithelial cell marker gene, Msx2. These findings suggest that Dpysl4 plays essential roles in tooth germ morphogenesis through the regulation of dental epithelial cell proliferation, cell polarization and differentiation.

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アトピー生皮膚炎の皮膚バリアからみた病態

雅行, 佐々木　貴史、天谷

臨床免疫・アレルギー科 60(3) 276 - 281 2013

Genome-wide association study identifies eight new susceptibility loci for atopic dermatitis in the Japanese population

Hirota, Tomomitsu, Takahashi, Atsushi, Kubo, Michiaki, Tsunoda, Tatsuhiko, Tomita, Kaori, Sakashita, Masafumi, Yamada, Takechiyo, Fujieda, Shigeharu, Tanaka, Shota, Doi, Satoru, Miyatake, Akihiko, Enomoto, Tadao, Nishiyama, Chiharu, Nakano, Nobuhiro, Maeda, Keiko, Okumura, Ko, Ogawa, Hideoki, Ikeda, Shigaku, Noguchi, Emiko, Sakamoto, Tohru, Hizawa, Nobuyuki, Ebe, Koji, Saeki, Hidehisa, Sasaki, Takashi, Ebihara, Tamotsu, Amagai, Masayuki, Takeuchi, Satoshi, Furue, Masutaka, Nakamura, Yusuke, Tamari, Mayumi

NATURE GENETICS 44 ( 11 ) 1222 - 1226 2012.11

Research paper (scientific journal), ISSN 1061-4036

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Identification of mutations in the prostaglandin transporter gene SLCO2A1 and its phenotype-genotype correlation in Japanese patients with pachydermoperiostosis

Sasaki, Takashi, Niizeki, Hironori, Shimizu, Atsushi, Shiohama, Aiko, Hirakiyama, Asami, Okuyama, Torayuki, Seki, Atsuhito, Kabashima, Kenji, Otsuka, Atsushi, Ishiko, Akira, Tanese, Keiji, Miyakawa, Shun-ichi, Sakabe, Jun-ichi, Kuwahara, Masamitsu, Amagai, Masayuki, Okano, Hideyuki, Suematsu, Makoto, Kudoh, Jun

JOURNAL OF DERMATOLOGICAL SCIENCE 68 ( 1 ) 36 - 44 2012.10

Research paper (scientific journal), ISSN 0923-1811

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Restoration of the intrinsic properties of human dermal papilla in vitro

Ohyama, Manabu, Kobayashi, Tetsuro, Sasaki, Takashi, Shimizu, Atsushi, Amagai, Masayuki

JOURNAL OF CELL SCIENCE 125 ( 17 ) 4114 - 4125 2012.09

Research paper (scientific journal), ISSN 0021-9533

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Variants of C-C Motif Chemokine 22 (CCL22) Are Associated with Susceptibility to Atopic Dermatitis: Case-Control Studies

Hirota, Tomomitsu, Saeki, Hidehisa, Tomita, Kaori, Tanaka, Shota, Ebe, Kouji, Sakashita, Masafumi, Yamada, Takechiyo, Fujieda, Shigeharu, Miyatake, Akihiko, Doi, Satoru, Enomoto, Tadao, Hizawa, Nobuyuki, Sakamoto, Tohru, Masuko, Hironori, Sasaki, Takashi, Ebihara, Tamotsu, Amagai, Masayuki, Esaki, Hitokazu, Takeuchi, Satoshi, Furue, Masutaka, Noguchi, Emiko, Kamatani, Naoyuki, Nakamura, Yusuke, Kubo, Michiaki, Tamari, Mayumi

PLOS ONE 6 ( 11 ) 25 - + 2011.11

Research paper (scientific journal), ISSN 1932-6203

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Transgenic rescue of desmoglein 3 null mice with desmoglein 1 to develop a syngeneic mouse model for pemphigus vulgaris

Hata, Tsuyoshi, Nishifuji, Koji, Shimoda, Kouji, Sasaki, Takashi, Yamada, Taketo, Nishikawa, Takeji, Koyasu, Shigeo, Amagai, Masayuki

JOURNAL OF DERMATOLOGICAL SCIENCE 63 ( 1 ) 33 - 39 2011.07

Research paper (scientific journal), ISSN 0923-1811

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Loss-of-function mutations within the filaggrin gene and atopic dermatitis

Kawasaki, H., Kubo, A., Sasaki, T. and Amagai, M.

Curr Probl Dermatol 41 35 - 46 2011

ISSN 1662-2944

Atopic dermatitis (AD) is a chronic relapsing eczematous skin disorder that is frequently associated with elevated serum IgE levels and a personal or family history of AD, allergic rhinitis and/or asthma. Filaggrin is a major constituent of the stratum corneum (SC) and contributes to keratin filament aggregation. Its breakdown products form natural moisturizing factor, which plays a central role in hydration of the SC. Sequence analysis and epidemiological studies indicate that loss-of-function mutations in the filaggrin gene known to cause the autosomal dominant scaly skin disorder ichthyosis vulgaris are major genetic predisposing factors of AD. Mutations in filaggrin are also associated with atopic asthma. These findings established the 'filaggrin hypothesis,' which states that AD can be triggered by the chronic exposure of barrier-disrupted skin to percutaneous antigens due to abnormalities in filaggrin. In this chapter, we summarize the genome-wide screening of AD susceptibility loci, filaggrin biochemistry and recent epidemiological studies on filaggrin mutations and allergic diseases. We also summarize recent advances in the study of skin barrier mechanisms and filaggrin-associated skin barrier abnormalities in animal models. Taken together, these findings provide novel perspectives on the pathophysiology of AD and effective therapeutic methods for the treatment and/or prevention of AD through the modification of skin barrier dysfunction.

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アレルギー性皮膚疾患とバリア機能異常

雅行, 佐々木　貴史、天谷

小児科 52(6) 833 - 842 2011

イヌゲノム解析の最前線ーヒト疾患遺伝子同定への新たなアプローチ

佐々木貴史、塩濱愛子、工藤純

実験医学 28(8) 1268 - 1274 2011

次世代シーケンサーを使いこなす　目的別解析法からデータ処理まで

貴史, 清水　厚志、佐々木

細胞工学 30(8) 790 - 795 2011

マルチプレックス法によるバクテリアゲノムのde novo DNA配列解読

貴史, 佐々木

細胞工学 30(8) 796 - 800 2011

Retinoic acid signaling positively regulates liver specification by inducing wnt2bb gene expression in medaka

Negishi, T., Nagai, Y., Asaoka, Y., Ohno, M., Namae, M., Mitani, H., Sasaki, T., Shimizu, N., Terai, S., Sakaida, I., Kondoh, H., Katada, T., Furutani-Seiki, M. and Nishina, H.

Hepatology 51 ( 3 ) 1037 - 45 2010.03

ISSN 1527-3350

UNLABELLED: During vertebrate embryogenesis, the liver develops at a precise location along the endodermal primitive gut tube because of signaling delivered by adjacent mesodermal tissues. Although several signaling molecules have been associated with liver formation, the molecular mechanism that regulates liver specification is still unclear. We previously performed a screen in medaka to isolate mutants with impaired liver development. The medaka hio mutants exhibit a profound (but transient) defect in liver specification that resembles the liver formation defect found in zebrafish prometheus (prt) mutants, whose mutation occurs in the wnt2bb gene. In addition to their liver abnormality, hio mutants lack pectoral fins and die after hatching. Positional cloning indicated that the hio mutation affects the raldh2 gene encoding retinaldehyde dehydrogenase type2 (RALDH2), the enzyme principally responsible for retinoic acid (RA) biosynthesis. Mutations of raldh2 in zebrafish preclude the development of pectoral fins. Interestingly, in hio mutants, expression of wnt2bb in the lateral plate mesoderm (LPM) directly adjacent to the liver-forming endoderm was completely lost. CONCLUSION: Our data reveal the unexpected finding that RA signaling positively regulates the wnt2bb gene expression required for liver specification in medaka. These results suggest that a common molecular mechanism may underlie liver and pectoral fin specification during piscine embryogenesis.

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Ethylnitrosourea-induced thymus-defective mutants identify roles of KIAA1440, TRRAP, and SKIV2L2 in teleost organ development

Iwanami, N., Okada, M., Hoa, V. Q., Seo, Y., Mitani, H., Sasaki, T., Shimizu, N., Kondoh, H., Furutani-Seiki, M. and Takahama, Y.

Eur J Immunol 39 ( 9 ) 2606 - 16 2009.09

ISSN 1521-4141

The thymus is an organ where T lymphocytes develop. Thymus development requires interactions of cells derived from three germ layers. However, the molecular mechanisms that control thymus development are not fully understood. To identify the genes that regulate thymus development, we previously carried out a large-scale screening for ethylnitrosourea-induced mutagenesis using medaka, Oryzias latipes, and established a panel of recessive thymus-lacking mutants. Here we report the identification of three genes responsible for these mutations. We found that the mutations in KIAA1440, TRRAP, and SKIV2L2 caused the defects in distinct steps of thymus development. We also found that these genes were widely expressed in many organs and that the mutations in these genes caused defects in the development of various other organs. These results enabled us to identify previously unknown roles of widely expressed genes in medaka organ development. The possible reasons why thymus-defective teleost mutants could be used to identify widely expressed genes and future strategies to increase the likelihood of identifying genes that specifically regulate thymus development are discussed.

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The KK-Periome database for transcripts of periodontal ligament development

Saito, M., Nishida, E., Sasaki, T., Yoneda, T. and Shimizu, N.

J Exp Zool B Mol Dev Evol 312B ( 5 ) 495 - 502 2009.07

ISSN 1552-5015

The periodontal ligament (PDL) is a strong connective tissue that surrounds the tooth root, absorbs occlusal forces, and functions as a sense organ. PDL originated from dental follicle (DF), which possessed mesenchymal progenitors in the developing tooth germ. However, as specific marker genes for PDL and DF are currently unavailable, the molecular mechanisms of PDL development are yet to be clarified. To facilitate the identification of such genes, we have previously established a transcriptome database of the human PDL (the KK-Periome database) and screened for specific genes expressed during PDL development. Initial screening of the database revealed two marker genes for distinguishing DF and PDL. The KK-Periome database thus appears to offer a useful resource for investigating genes involved in PDL development.

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A homozygous frameshift mutation in the mouse Flg gene facilitates enhanced percutaneous allergen priming

Fallon, Padraic G., Sasaki, Takashi, Sandilands, Aileen, Campbell, Linda E., Saunders, Sean P., Mangan, Niamh E., Callanan, John J., Kawasaki, Hiroshi, Shiohama, Aiko, Kubo, Akiharu, Sundberg, John P., Presland, Richard B., Fleckman, Philip, Shimizu, Nobuyoshi, Kudoh, Jun, Irvine, Alan D., Amagai, Masayuki, McLean, W. H. Irwin

NATURE GENETICS 41 ( 5 ) 602 - 608 2009.05

Research paper (scientific journal), ISSN 1061-4036

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臓器置換再生医療の現実を目指してー歯の再生をモデルとした技術開発ー

孝, 佐々木　貴史、辻

化学と教育 57(10) 454 - 457 2009

WDR55 is a nucleolar modulator of ribosomal RNA synthesis, cell cycle progression, and teleost organ development

Iwanami, N., Higuchi, T., Sasano, Y., Fujiwara, T., Hoa, V. Q., Okada, M., Talukder, S. R., Kunimatsu, S., Li, J., Saito, F., Bhattacharya, C., Matin, A., Sasaki, T., Shimizu, N., Mitani, H., Himmelbauer, H., Momoi, A., Kondoh, H., Furutani-Seiki, M. and Takahama, Y.

PLoS Genet 4 ( 8 ) e1000171 2008.08

ISSN 1553-7404

The thymus is a vertebrate-specific organ where T lymphocytes are generated. Genetic programs that lead to thymus development are incompletely understood. We previously screened ethylnitrosourea-induced medaka mutants for recessive defects in thymus development. Here we report that one of those mutants is caused by a missense mutation in a gene encoding the previously uncharacterized protein WDR55 carrying the tryptophan-aspartate-repeat motif. We find that WDR55 is a novel nucleolar protein involved in the production of ribosomal RNA (rRNA). Defects in WDR55 cause aberrant accumulation of rRNA intermediates and cell cycle arrest. A mutation in WDR55 in zebrafish also leads to analogous defects in thymus development, whereas WDR55-null mice are lethal before implantation. These results indicate that WDR55 is a nuclear modulator of rRNA synthesis, cell cycle progression, and embryonic organogenesis including teleost thymus development.

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Sequence analysis of filaggrin gene by novel shotgun method in Japanese atopic dermatitis

Sasaki, Takashi, Kudoh, Jun, Ebihara, Tamotsu, Shiohama, Aiko, Asakawa, Shuichi, Shimizu, Atsushi, Takayanagi, Atsushi, Dekio, Itaru, Sadahira, Chieko, Amagai, Masayuki, Shimizu, Nobuyoshi

JOURNAL OF DERMATOLOGICAL SCIENCE 51 ( 2 ) 113 - 120 2008.08

Research paper (scientific journal), ISSN 0923-1811

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Complete nucleotide sequences of mitochondrial genomes of two solitary entoprocts, Loxocorone allax and Loxosomella aloxiata: implications for lophotrochozoan phylogeny

Yokobori, S., Iseto, T., Asakawa, S., Sasaki, T., Shimizu, N., Yamagishi, A., Oshima, T. and Hirose, E.

Mol Phylogenet Evol 47 ( 2 ) 612 - 28 2008.05

ISSN 1055-7903

The complete nucleotide sequences of the mitochondrial (mt) genomes of the entoprocts Loxocorone allax and Loxosomella aloxiata were determined. Both species carry the typical gene set of metazoan mt genomes and have similar organizations of their mt genes. However, they show differences in the positions of two tRNA(Leu) genes. Additionally, the tRNA(Val) gene, and half of the long non-coding region, is duplicated and inverted in the Loxos. aloxiata mt genome. The initiation codon of the Loxos. aloxiata cytochrome oxidase subunit I gene is expected to be ACG rather than AUG. The mt gene organizations in these two entoproct species most closely resemble those of mollusks such as Katharina tunicata and Octopus vulgaris, which have the most evolutionarily conserved mt gene organization reported to date in mollusks. Analyses of the mt gene organization in the lophotrochozoan phyla (Annelida, Brachiopoda, Echiura, Entoprocta, Mollusca, Nemertea, and Phoronida) suggested a close phylogenetic relationship between Brachiopoda, Annelida, and Echiura. However, Phoronida was excluded from this grouping. Molecular phylogenetic analyses based on the sequences of mt protein-coding genes suggested a possible close relationship between Entoprocta and Phoronida, and a close relationship among Brachiopoda, Annelida, and Echiura.

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Myocyte enhancer factor 2 regulates expression of medaka Oryzias latipes fast skeletal myosin heavy chain genes in a temperature-dependent manner

Liang, C. S., Ikeda, D., Kinoshita, S., Shimizu, A., Sasaki, T., Asakawa, S., Shimizu, N. and Watabe, S.

Gene 407 ( 1-2 ) 42 - 53 2008.01

ISSN 0378-1119

We characterized the promoter activity of fast skeletal myosin heavy chain genes (MYHs) from medaka Oryzias latipes. The 5'-flanking region of approximately 6 kb in medaka MYHs, mMYH10 and mMYH30, predominantly expressed in medaka acclimated to 10 degrees C and 30 degrees C, respectively, contained various cis-elements that are supposed to bind to transcriptional regulatory factors such as MyoD and myocyte enhancer factor 2 (MEF2) family members and nuclear factor of activated T cells. To localize functional regions responsible for the mMYH expression in a temperature-dependent manner, a series of deletion and site mutation constructs prepared from the 5'-flanking regions were fused to the luciferase gene in a commercially available plasmid and directly injected into the dorsal fast muscle of medaka acclimated to 10 degrees C and 30 degrees C. The truncation of MEF2 binding site located at -966 to -957 in the 5'-flanking region of mMYH10 resulted in distinct gene expression at 10 degrees C. The activation effect by the removal of this binding site was further confirmed by the mutation construct. One of the E box sites, to which MyoD family members are supposed to bind, was located at -613 to -607 of mMYH10, and found to be responsible for the transcriptional activity. In contrast, the MEF2 binding site located at -960 to -951 of mMYH30 was involved in the activation at 30 degrees C. Thus, these transient transfection assays demonstrated that the MEF2 binding site is crucial for a temperature-dependent expression of mMYHs.

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UTGB/medaka: genomic resource database for medaka biology

Ahsan, B., Kobayashi, D., Yamada, T., Kasahara, M., Sasaki, S., Saito, T. L., Nagayasu, Y., Doi, K., Nakatani, Y., Qu, W., Jindo, T., Shimada, A., Naruse, K., Toyoda, A., Kuroki, Y., Fujiyama, A., Sasaki, T., Shimizu, A., Asakawa, S., Shimizu, N., Hashimoto, S., Yang, J., Lee, Y., Matsushima, K., Sugano, S., Sakaizumi, M., Narita, T., Ohishi, K., Haga, S., Ohta, F., Nomoto, H., Nogata, K., Morishita, T., Endo, T., Shin, I. T., Takeda, H., Kohara, Y. and Morishita, S.

Nucleic Acids Res 36 ( Database issue ) D747 - 52 2008.01

ISSN 1362-4962

Medaka (Oryzias latipes) is a small egg-laying freshwater teleost native to East Asia that has become an excellent model system for developmental genetics and evolutionary biology. The draft medaka genome sequence (700 Mb) was reported in June 2007, and its substantial genomic resources have been opened to the public through the University of Tokyo Genome Browser Medaka (UTGB/medaka) database. This database provides basic genomic information, such as predicted genes, expressed sequence tags (ESTs), guanine/cytosine (GC) content, repeats and comparative genomics, as well as unique data resources including (i) 2473 genetic markers and experimentally confirmed PCR primers that amplify these markers, (ii) 142,414 bacterial artificial chromosome (BAC) and 217,344 fosmid end sequences that amount to 15.0- and 11.1-fold clone coverage of the entire genome, respectively, and were used for draft genome assembly, (iii) 16,519,460 single nucleotide polymorphisms (SNPs), and 2 859 905 insertions/deletions detected between two medaka inbred strain genomes and (iv) 841 235 5'-end serial analyses of gene-expression (SAGE) tags that identified 344 266 transcription start sites on the genome. UTGB/medaka is available at: http://medaka.utgenome.org/.

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Nucleolar localization of DGCR8 and identification of eleven DGCR8-associated proteins

Shiohama, A., Sasaki, T., Noda, S., Minoshima, S. and Shimizu, N.

Exp Cell Res 313 ( 20 ) 4196 - 207 2007.12

ISSN 0014-4827

We identified 11 proteins that are associated with DGCR8 by immunoprecipitation assay and mass spectrometry. These proteins included Nucleolin, ILF3 and others, most of which appeared to be involved in the RNA processing or RNA transportation. We detected at least four kinds of protein complex, such as DROSHA/DGCR8, DGCR8/Nucleolin, DGCR8/ILF3 and ILF3/XPO5, by co-immunoprecipitation. The complex formation of DGCR8 with Nucleolin was dependent on RNA. Subcellular localization analysis by the immunofluorescent microscopy and immunoelectron microscopy indicated that DGCR8 locates at the nucleolus and small foci adjacent to splicing speckles in the nucleoplasm. Furthermore, the localization of DGCR8 at the nucleolus was changed by the inhibition of RNA transcription. Thus, our studies provided additional new evidence for the involvement of various protein complexes in the molecular mechanisms of apparently complex innate RNA interference machinery.

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Transcriptome database KK-Periome for periodontal ligament development: expression profiles of the extracellular matrix genes

Nishida, E., Sasaki, T., Ishikawa, S. K., Kosaka, K., Aino, M., Noguchi, T., Teranaka, T., Shimizu, N. and Saito, M.

Gene 404 ( 1-2 ) 70 - 9 2007.12

ISSN 0378-1119

Specialized connective tissues such as tendon/ligament develop through a series of events that require temporal and spatial expression of numerous genes in mesenchymal progenitors. However, the genes required for tendon/ligament development have not been identified yet. To solve this problem, we made a cDNA library from periodontal ligament and sequenced 11,520 cDNA clones, as a model for investigating tendon/ligament development. The resulting sequence data was assembled to 617 expressed sequence tag (EST) clusters, and an EST database for human periodontal ligament (PDL) was constructed (designated as the KK-Periome database). In the KK-Periome database, the top 13 EST clusters were related to extracellular matrix (ECM) genes. The temporal and spatial expression patterns of these genes during mouse PDL development were examined by in situ hybridization. Among these genes, F-spondin was expressed specifically in dental follicle (DF) cells during tooth germ development, whereas tenascin-N was strongly expressed in the terminally differentiated PDL. This characteristic expression profile was confirmed by in vivo differentiation assay of human PDL (hPDL) cells in the mouse transplant. Thus, the KK-Periome database was proven to be a useful resource for PDL-derived ESTs (transcriptome), and in fact, initial evidence indicated that F-spondin and tenascin-N might serve as markers for DF and PDL, respectively.

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Identification of three novel proteins (SGSM1, 2, 3) which modulate small G protein (RAP and RAB)-mediated signaling pathway

Yang, H., Sasaki, T., Minoshima, S. and Shimizu, N.

Genomics 90 ( 2 ) 249 - 60 2007.08

ISSN 0888-7543

We report a novel protein family consisting of three members, each of which contains RUN and TBC motifs and appears to be associated with small G protein-mediated signal transduction pathway. We named these proteins as small G protein signaling modulators (SGSM1/2/3). Northern blot analysis revealed that human SGSM2/3 are expressed ubiquitously in various tissues, whereas SGSM1 is expressed mainly in brain, heart, and testis. Mouse possessed the same protein family genes, and the in situ hybridization and immunohistochemical staining of tissue sections revealed that mouse Sgsm1/2/3 are expressed in the neurons of central nervous system, indicating the strong association of Sgsm family with neuronal function. Furthermore, endogenous Sgsm1 protein was localized in the trans-Golgi network of mouse Neuro2a cells by immunofluorescence microscopy. Expression of various cDNA constructs followed by immunoprecipitation assay revealed that human SGSM1/2/3 proteins are coprecipitated with RAP and RAB subfamily members of the small G protein superfamily. Based on these results, we postulated that the SGSM family members function as modulators of the small G protein RAP and RAB-mediated neuronal signal transduction and vesicular transportation pathways.

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Evolutionary conservation of a unique amino acid sequence in human DICER protein essential for binding to Argonaute family proteins

Sasaki, T. and Shimizu, N.

Gene 396 ( 2 ) 312 - 20 2007.07

ISSN 0378-1119

The Argonaute family and DICER proteins are major key proteins involved in the RNA-mediated gene silencing mechanism of various species. In this mechanism, cleavage of messenger RNAs (mRNA) or suppression of mRNA translation takes place via small RNAs that are uniquely processed by DICER. Previously, we demonstrated that human Argonaute family proteins bind to DICER. In this study, we identified a unique amino acid sequence of 127 amino acids in the RIBOc-A domain of human DICER protein as a "binding site" to Argonaute proteins. Comparative genomics analysis revealed that this unique amino acid sequence is highly conserved in the vertebrates, but not found in the non-vertebrate species. Significant difference in the RIBOc-A domain of DICER protein between vertebrate and non-vertebrate species may help exploring the functional complexity in the RNA-mediated gene silencing mechanism.

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Radiation hybrid maps of Medaka chromosomes LG 12, 17, and 22

Su, F., Osada, Y., Ekker, M., Chevrette, M., Shimizu, A., Asakawa, S., Shiohama, A., Sasaki, T., Shimizu, N., Yamanaka, T., Sasado, T., Mitani, H., Geisler, R., Kondoh, H. and Furutani-Seiki, M.

DNA Res 14 ( 3 ) 135 - 40 2007.06

ISSN 1340-2838

The Medaka is an excellent genetic system for studies of vertebrate development and disease and environmental and evolutionary biology studies. To facilitate the mapping of markers or the cloning of affected genes in Medaka mutants identified by forward-genetic screens, we have established a panel of whole-genome radiation hybrids (RHs) and RH maps for three Medaka chromosomes. RH mapping is useful, since markers to be mapped need not be polymorphic and one can establish the order of markers that are difficult to resolve by genetic mapping owing to low genetic recombination rates. RHs were generated by fusing the irradiated donor, OLF-136 Medaka cell line, with the host B78 mouse melanoma cells. Of 290 initial RH clones, we selected 93 on the basis of high retention of fragments of the Medaka genome to establish a panel that allows genotyping in the 96-well format. RH maps for linkage groups 12, 17, and 22 were generated using 159 markers. The average retention for the three chromosomes was 19% and the average break point frequency was approximately 33 kb/cR. We estimate the potential resolution of the RH panel to be approximately 186 kb, which is high enough for integrating RH data with bacterial artificial chromosome clones. Thus, this first RH panel will be a useful tool for mapping mutated genes in Medaka.

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The medaka draft genome and insights into vertebrate genome evolution

Kasahara, M., Naruse, K., Sasaki, S., Nakatani, Y., Qu, W., Ahsan, B., Yamada, T., Nagayasu, Y., Doi, K., Kasai, Y., Jindo, T., Kobayashi, D., Shimada, A., Toyoda, A., Kuroki, Y., Fujiyama, A., Sasaki, T., Shimizu, A., Asakawa, S., Shimizu, N., Hashimoto, S., Yang, J., Lee, Y., Matsushima, K., Sugano, S., Sakaizumi, M., Narita, T., Ohishi, K., Haga, S., Ohta, F., Nomoto, H., Nogata, K., Morishita, T., Endo, T., Shin, I. T., Takeda, H., Morishita, S. and Kohara, Y.

Nature 447 ( 7145 ) 714 - 9 2007.06

ISSN 1476-4687

Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats. Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published, analysis of more fish genomes is desirable. Here we report a high-quality draft genome sequence of a small egg-laying freshwater teleost, medaka (Oryzias latipes). Medaka is native to East Asia and an excellent model system for a wide range of biology, including ecotoxicology, carcinogenesis, sex determination and developmental genetics. In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including approximately 2,900 new genes, using 5'-end serial analysis of gene expression tag information. We found single nucleotide polymorphisms (SNPs) at an average rate of 3.42% between the two inbred strains derived from two regional populations; this is the highest SNP rate seen in any vertebrate species. Analyses based on the dense SNP information show a strict genetic separation of 4 million years (Myr) between the two populations, and suggest that differential selective pressures acted on specific gene categories. Four-way comparisons with the human, pufferfish (Tetraodon), zebrafish and medaka genomes revealed that eight major interchromosomal rearrangements took place in a remarkably short period of approximately 50 Myr after the whole-genome duplication event in the teleost ancestor and afterwards, intriguingly, the medaka genome preserved its ancestral karyotype for more than 300 Myr.

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The hotei mutation of medaka in the anti-Mullerian hormone receptor causes the dysregulation of germ cell and sexual development

Morinaga, C., Saito, D., Nakamura, S., Sasaki, T., Asakawa, S., Shimizu, N., Mitani, H., Furutani-Seiki, M., Tanaka, M. and Kondoh, H.

Proc Natl Acad Sci U S A 104 ( 23 ) 9691 - 6 2007.06

ISSN 0027-8424

We previously performed mutant screens in the medaka for defects in gonadal development and identified a mutant of interest in this regard, which was designated as hotei (hot). This mutant manifests a number of remarkable phenotypic abnormalities including: (i) excessive proliferation of germ cells that initiates at around the hatching stage regardless of the genetic sex of the fish; (ii) initiation of premature meiosis in phenotypically male hot homozygotes; (iii) one-half of the hot-homozygous XY fish undergo sex reversal, which accompanies the expression of the female-characteristic aromatase gene in the somatic cells of the gonad; and (iv) in phenotypically female homozygotes, follicular development is arrested at an early stage. We have also performed genetic mapping, chromosome walking, and candidate gene sequencing analysis of hot and demonstrate that the underlying mutation occurs in the recently identified medaka anti-Mullerian hormone (Amh) receptor type II (amhrII) gene. Moreover, this gene was found to be responsible for each of the hot phenotypes, as an amhrII transgene rescues these abnormalities. In addition, the amhrII gene is expressed in the somatic cells of the gonads of both sexes. The phenotypes of the hot homozygotes indicate that there are multiple regulatory functions of the AMH/AMHRII signaling system in the development of the gonad, including the sex-dependent regulation of germ cell proliferation and follicular development. These presumably represent the basic roles of Amh, which precede Mullerian duct evolution during phylogeny.

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Fast skeletal muscle myosin heavy chain gene cluster of medaka Oryzias latipes enrolled in temperature adaptation

Liang, C. S., Kobiyama, A., Shimizu, A., Sasaki, T., Asakawa, S., Shimizu, N. and Watabe, S.

Physiol Genomics 29 ( 2 ) 201 - 14 2007.04

ISSN 1531-2267

To disclose mechanisms involved in temperature acclimation of fish muscle, we subjected eurythermal fish of medaka Oryzias latipes to cloning of myosin heavy chain genes (MYHs). We cloned cDNAs encoding fast skeletal muscle myosin heavy chain (MYH) isoforms from cDNA libraries of medaka acclimated to 10 and 30 degrees C and observed that different MYH cDNA clones are expressed in the two temperature-acclimated fish. Subsequently, we isolated several overlapping MYH contigs by shotgun cloning strategy from a medaka genomic library. Contig assembly of the complete medaka MYH (mMYH) locus of 219 kbp revealed a cluster of tandemly arrayed 11 mMYHs, in which eight genes are actually transcribed, with the remaining three being pseudogenes. Expression analysis of the transcribed genes revealed that two genes were each highly expressed in medaka acclimated to 10 and 30 degrees C, whereas comparatively lower expression levels of the three genes were exclusively observed in medaka acclimated to 30 degrees C. cDNAs of the remaining genes were too underrepresented in the libraries to determine the expression levels, and the transcripts could only be obtained by reverse transcription-polymerase chain reaction. Deduced amino acid sequences in the loop 1 and loop 2 regions of mMYHs were highly variable, suggesting that these isoforms were functionally different. The present findings consolidate our knowledge on teleost MYH multigene family and would provide further insight into the mechanisms by which expressions of individual MYH molecules are fine-tuned with environmental temperature fluctuations with further functional analysis of the genes concerned.

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The genome size evolution of medaka (Oryzias latipes) and fugu (Takifugu rubripes)

Imai, S., Sasaki, T., Shimizu, A., Asakawa, S., Hori, H. and Shimizu, N.

Genes Genet Syst 82 ( 2 ) 135 - 44 2007.04

ISSN 1341-7568

Evolution of the genome size in eukaryotes is often affected by changes in the noncoding sequences, for which insertions and deletions (indels) of small nucleotide sequences and amplification of repetitive elements are considered responsible. In this study, we compared the genomic DNA sequences of two kinds of fish, medaka (Oryzias latipes) and fugu (Takifugu rubripes), which show two-fold difference in the genome size (800 Mb vs. 400 Mb). We selected a contiguous DNA sequence of 790 kb from the medaka chromosome LG22 (linkage group 22), and made a precise comparison with the sequence (387 kb) of the corresponding region of Takifugu. The sequence of 178 kb in total was aligned common between two fishes, and the remaining sequences (612 kb for medaka and 209 kb for fugu) were found abundant in various repetitive elements including many types of unclassified low copy repeats, all of which accounted for more than a half (54%) of the genome size difference. Furthermore, we identified a significant difference in the length ratio of the unaligned sequences that locate between the aligned sequences (USBAS), particularly after eliminating known repetitive elements. These USBAS with no repetitive elements (USBAS-nr) located within the intron and intergenic region. These results strongly indicated that amplification of repetitive elements and compilation of indels are major driving forces to facilitate changes in the genome size.

The DNA sequence of medaka chromosome LG22

Sasaki, T., Shimizu, A., Ishikawa, S. K., Imai, S., Asakawa, S., Murayama, Y., Khorasani, M. Z., Mitani, H., Furutani-Seiki, M., Kondoh, H., Nanda, I., Schmid, M., Schartl, M., Nonaka, M., Takeda, H., Hori, H., Himmelbauer, H., Shima, A. and Shimizu, N.

Genomics 89 ( 1 ) 124 - 33 2007.01

ISSN 0888-7543

We report the genomic DNA sequence of a single chromosome (linkage group 22; LG22) of the small teleost fish medaka (Oryzias latipes) as a first whole chromosome sequence from a non-mammalian vertebrate. The order and orientation of 633 protein-coding genes were deduced from 18,803,338 bp of DNA sequence, providing the opportunity to analyze chromosome evolution of vertebrate genomes by direct comparison with the human genome. The average number of genes in the "conserved gene cluster" (CGC), a strict definition of "synteny" at the sequence basis, between medaka and human was 1.6. These and other data suggest that approximately 38.8% of pair-wise gene relationships would have been broken from their common ancestor in the human and medaka lineages and further imply that approx 20,000 (15,520-23,280) breaks would have occurred from the entire genome of the common ancestor. These breaks were generated mainly by intra-chromosomal shufflings at a specific era in the vertebrate lineage. These precise comparative genomics allowed us to identify the pieces of ancient chromosomes of the common vertebrate ancestor and estimate chromosomal evolution in the vertebrate lineage.

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Genomic organization of the sex-determining and adjacent regions of the sex chromosomes of medaka

Kondo, M., Hornung, U., Nanda, I., Imai, S., Sasaki, T., Shimizu, A., Asakawa, S., Hori, H., Schmid, M., Shimizu, N. and Schartl, M.

Genome Res 16 ( 7 ) 815 - 26 2006.07

ISSN 1088-9051

Sequencing of the human Y chromosome has uncovered the peculiarities of the genomic organization of a heterogametic sex chromosome of old evolutionary age, and has led to many insights into the evolutionary changes that occurred during its long history. We have studied the genomic organization of the medaka fish Y chromosome, which is one of the youngest heterogametic sex chromosomes on which molecular data are available. The Y specific and adjacent regions were sequenced and compared to the X. The male sex-determining gene, dmrt1bY, appears to be the only functional gene in the Y-specific region. The Y-specific region itself is derived from the duplication of a 43-kb fragment from linkage group 9. All other coduplicated genes except dmrt1bY degenerated. The Y-specific region has accumulated large stretches of repetitive sequences and duplicated pieces of DNA from elsewhere in the genome, thereby growing to 258 kb. Interestingly the non-recombining part of the Y did not spread out considerably from the original duplicated fragment, possibly because of a large sequence duplication bordering the Y-specific fragment. This may have conserved the more ancestral structure of the medaka Y and provides insights into some of the initial processes of Y chromosome evolution.

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Comparative genomics of medaka and fugu

Shimizu, N., Sasaki, T., Asakawa, S., Shimizu, A., Ishikawa, S. K., Imai, S., Murayama, Y., Himmelbauer, H., Mitani, H., Furutani-Seiki, M., Kondoh, H., Schartl, M., Nonaka, M., Takeda, H., Hori, H. and Shima, A.

Comp Biochem Physiol Part D Genomics Proteomics 1 ( 1 ) 6 - 12 2006.03

ISSN 1878-0407

A small freshwater fish medaka (Oryzias latipes) has been one of the most attractive experimental systems for research in genetics and developmental biology. We have formed an international consortium Medaka Genome Initiative (MGI) to collect and share various information and resources on medaka. The MGI has set an ambitious goal aiming at the complete sequencing of the medaka genome and as a feasibility study we have begun sequencing one particular chromosome, linkage group 22 (LG22) of approximately 22 Mb in size. Initial sequence analysis revealed unique features of the medaka genome in comparison to fugu genome.

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DNA sequence and analysis of human chromosome 8

Nusbaum, C., Mikkelsen, T. S., Zody, M. C., Asakawa, S., Taudien, S., Garber, M., Kodira, C. D., Schueler, M. G., Shimizu, A., Whittaker, C. A., Chang, J. L., Cuomo, C. A., Dewar, K., FitzGerald, M. G., Yang, X., Allen, N. R., Anderson, S., Asakawa, T., Blechschmidt, K., Bloom, T., Borowsky, M. L., Butler, J., Cook, A., Corum, B., DeArellano, K., DeCaprio, D., Dooley, K. T., Dorris, L., 3rd, Engels, R., Glockner, G., Hafez, N., Hagopian, D. S., Hall, J. L., Ishikawa, S. K., Jaffe, D. B., Kamat, A., Kudoh, J., Lehmann, R., Lokitsang, T., Macdonald, P., Major, J. E., Matthews, C. D., Mauceli, E., Menzel, U., Mihalev, A. H., Minoshima, S., Murayama, Y., Naylor, J. W., Nicol, R., Nguyen, C., O'Leary, S. B., O'Neill, K., Parker, S. C., Polley, A., Raymond, C. K., Reichwald, K., Rodriguez, J., Sasaki, T., Schilhabel, M., Siddiqui, R., Smith, C. L., Sneddon, T. P., Talamas, J. A., Tenzin, P., Topham, K., Venkataraman, V., Wen, G., Yamazaki, S., Young, S. K., Zeng, Q., Zimmer, A. R., Rosenthal, A., Birren, B. W., Platzer, M., Shimizu, N. and Lander, E. S.

Nature 439 ( 7074 ) 331 - 5 2006.01

ISSN 1476-4687

The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome. As part of this project, we have focused on chromosome 8. Although some chromosomes exhibit extreme characteristics in terms of length, gene content, repeat content and fraction segmentally duplicated, chromosome 8 is distinctly typical in character, being very close to the genome median in each of these aspects. This work describes a finished sequence and gene catalogue for the chromosome, which represents just over 5% of the euchromatic human genome. A unique feature of the chromosome is a vast region of approximately 15 megabases on distal 8p that appears to have a strikingly high mutation rate, which has accelerated in the hominids relative to other sequenced mammals. This fast-evolving region contains a number of genes related to innate immunity and the nervous system, including loci that appear to be under positive selection--these include the major defensin (DEF) gene cluster and MCPH1, a gene that may have contributed to the evolution of expanded brain size in the great apes. The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution.

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The medaka genome: why we need multiple fish models in vertebrate functional genomics

Mitani, H., Kamei, Y., Fukamachi, S., Oda, S., Sasaki, T., Asakawa, S., Todo, T. and Shimizu, N.

Genome Dyn 2 165 - 82 2006

ISSN 1660-9263

Medaka (Oryzias latipes) is widely used in research in the fields of biology, medicine, environmental science and fisheries. Zebrafish and medaka are well established as genetic model systems in which large-scale mutagenesis has been successfully performed, and for which EST data, BAC libraries, and fine linkage maps have been accumulated. Among rayfinned fish, there is a large evolutionary distance between medaka and zebrafish. In contrast, the evolutionary distance between medaka and two species of pufferfish, fugu (Takifugu rubripes), and tetraodon (Tetraodon nigroviridis), is almost comparable to that between humans and rodents, and the current genome project is showing that their genome organization is well conserved. Comparison of genome structure among teleosts and mammals helps our understanding of the orthologous gene structure and the evolution of gene families in vertebrates. In addition, gene functions have to be analyzed by both forward and reverse genetics. The Targeting Induced Local Lesions IN Genome (TILLING) system, which includes random mutagenesis, followed by screening for induced mutations in the target genes, is a powerful tool for studying the functional genomics of both medaka and zebrafish.

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MEPD: a resource for medaka gene expression patterns

Henrich, T., Ramialison, M., Wittbrodt, B., Assouline, B., Bourrat, F., Berger, A., Himmelbauer, H., Sasaki, T., Shimizu, N., Westerfield, M., Kondoh, H. and Wittbrodt, J.

Bioinformatics 21 ( 14 ) 3195 - 7 2005.07

ISSN 1367-4803

The Medaka Expression Pattern Database (MEPD) is a database for gene expression patterns determined by in situ hybridization in the small freshwater fish medaka (Oryzias latipes). Data have been collected from various research groups and MEPD is developing into a central expression pattern depository within the medaka community. Gene expression patterns are described by images and terms of a detailed medaka anatomy ontology of over 4000 terms, which we have developed for this purpose and submitted to Open Biological Ontologies. Sequences have been annotated via BLAST match results and using Gene Ontology terms. These new features will facilitate data analyses using bioinformatics approaches and allow cross-species comparisons of gene expression patterns. Presently, MEPD has 19,757 entries, for 1024 of them the expression pattern has been determined.

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Genomic sequences encoding two types of medaka hemopexin-like protein Wap65, and their gene expression profiles in embryos

Nakaniwa, M., Hirayama, M., Shimizu, A., Sasaki, T., Asakawa, S., Shimizu, N. and Watabe, S.

J Exp Biol 208 ( Pt 10 ) 1915 - 25 2005.05

ISSN 0022-0949

Medaka genomic BAC clones, which contained two types of medaka hemopexin-like protein gene (Wap65), mWap65-1 and mWap65-2, were screened and their genomic sequences were determined by the shotgun strategy. The exon-intron organizations were highly conserved between both mWap65s and human hemopexin genes. The 5'-flanking regions of mWap65-1 and mWap65-2 contained various putative transcription factor binding sites including elements for developmental regulation. The expression patterns of mWap65s during embryonic development were examined by quantitative real-time PCR, demonstrating that both mWap65 transcripts were observed in early embryonic stages, but their expression patterns were different. Interestingly, in situ hybridization revealed that mWap65-2 transcripts were restricted to liver, whereas mWap65-1 transcripts were detected along the edge of pectoral fin buds and the median fin fold of tail buds in embryos at stage 32. Furthermore, we generated transgenic medaka expressing GFP driven by mWap65-1 and mWap65-2 promoters and observed GFP expression patterns during ontogeny. Although localizations of GFP varied among individuals, embryos uniformly expressed GFP 1 day after injection of mWap65-1-hrGFP and mWap65-2-hrGFP constructs, suggesting that mWap65-1 and mWap65-2 promoters were activated in very early stages. The differences between mWap65-1 and mWap65-2 in their expression profiles indicate their distinct roles during ontogeny.

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Finishing the Euchromatic Sequence of the Human Genome

International Human Genome Sequencing Consortium

Nature 431 ( 7011 ) 931-945 2004.10

Research paper (scientific journal), Joint Work, Accepted

Identification and Characterization of a Novel Gene Family YPEL in a Wide Spectrum of Eukaryotic Species

Hosono, K., Sasaki, T., Minoshima, S. and Shimizu, N.

Gene 340 ( 1 ) 31-43 2004.10

Research paper (scientific journal), Joint Work, Accepted

The Minimal Eukaryotic Ribosomal DNA Units in the Primitive Red Alga Cyanidioschyzon merolae

Maruyama, S., Misumi, O., Ishii, Y., Asakawa, S., Shimizu, A., Sasaki, T., Matuszaki, M., Shin-i, T., Nozaki, H., Kohara, Y., Shimizu, N. and Kuroiwa, T.

DNA Research 11 ( 2 ) 83-91 2004.05

Research paper (scientific journal), Joint Work, Accepted

The minimal eukaryotic ribosomal DNA units in the primitive red alga Cyanidioschyzon merolae

Maruyama, S., Misumi, O., Ishii, Y., Asakawa, S., Shimizu, A., Sasaki, T., Matsuzaki, M., Shin-i, T., Nozaki, H., Kohara, Y., Shimizu, N. and Kuroiwa, T.

DNA Res 11 ( 2 ) 83 - 91 2004.04

ISSN 1340-2838

Cyanidioschyzon merolae is a small unicellular red alga that is considered to belong to one of the most deeply branched taxa in the plant kingdom. Its genome size is estimated to be 16.5 Mbp, one of the smallest among free-living eukaryotes. In the nucleus containing this small genome, one nucleolus is clearly observed, but the molecular basis for the intranuclear structure including ribosomal DNA organization is still unclear. We constructed a bacterial artificial chromosome library for C. merolae 10D composed of two subsets with different insert size distributions. The two subsets have average insert sizes of 97 and 48 kb, representing 10.0- and 6.9-fold genome-equivalent coverage of the haploid genome, respectively. For application to whole-genome shotgun sequencing, the termini of each clone were sequenced as sequence-tagged connectors and mapped on the contigs assigned to chromosomes. Screening for rRNA genes by conventional colony hybridization with high-density filter blots and subsequent sequencing revealed that the C. merolae genome contained the smallest number of ribosomal DNA units among all the eukaryotes examined to date. They consist of only 3 single units of rRNA genes distributed on separate chromosomal loci, representing an implication for concerted evolution. Based on these results, the origin and evolution of the nucleolus are discussed.

Comparative genomics of the keratin-associated protein (KAP) gene clusters in human, chimpanzee, and baboon

Shibuya, K., Kudoh, J., Obayashi, I., Shimizu, A., Sasaki, T., Minoshima, S. and Shimizu, N.

Mamm Genome 15 ( 3 ) 179 - 92 2004.03

ISSN 0938-8990

We have previously identified a cluster of 16 genes that encode hair-specific proteins, called keratin-associated proteins (KAPs), located on human Chromosome (Chr) 21q22.3. Here, we have identified similar KAP gene clusters in two primates, chimpanzee and baboon. DNA sequence comparison revealed the common cluster structure consisting of 16 KAP genes for these three primates, but a significant difference was found in the baboon. Baboon possesses a new KAP gene not found in human and chimpanzee, whereas one KAP gene ( KRTAP18.12) that exists in human and chimpanzee was lost in baboon, making no change in the total number of KAP genes. Interestingly, the sequence for coding regions are highly variable among species owing to insertions and deletions, resulting in variation of gene size. On the contrary, the sequences for the 5' upstream region are highly conserved among species. These findings suggest that the ancestral KAP gene cluster was composed of 17 genes before the divergence of Old World monkeys (baboon) to the anthropoid (human and chimpanzee).

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'Comparative Genomics of the Keratin-associated Protein (KAP) Gene Clusters in Human, Chimpanzee and Baboon'

'Shibuya Kazunori, Kudoh Jun, Obayashi Izumi, Shimizu Atsushi, Sasaki Takashi, Minoshima Shinsei, Shimizu Nobuyoshi'

Mammalian genome 15 ( 3 ) 179-192 2004.03

Research paper (scientific journal), Joint Work, Accepted

Current status of medaka genetics and genomics. The Medaka Genome Initiative (MGI)

Schartl, M., Nanda, I., Kondo, M., Schmid, M., Asakawa, S., Sasaki, T., Shimizu, N., Henrich, T., Wittbrodt, J., Furutani-Seiki, M., Kondoh, H., Himmelbauer, H., Hong, Y., Koga, A., Nonaka, M., Mitani, H. and Shima, A.

Methods Cell Biol 77 173 - 99 2004

ISSN 0091-679X

Role of TBX1 in Human Del22q11.2 Syndrome

'Yagi Hisato, Furutani Yoshiyuki, Hamada Hiromichi, Sasaki Takashi, Asakawa Shuichi, Minoshima Shinsei, Ichida Fukiko, Kunitaka, Kimura Misa, Imamura Shinichiro, Kamatani Naoyuki, Momma Kazuo, Takao Atsuyoshi, Nakazawa Makoto, Shimizu Nobuyoshi, Matsuoka Rumiko'

Lancet 362 1366-1373 2003.10

Research paper (scientific journal), Joint Work, Accepted

A Novel Giant Gene CSMD3 Encoding a Protein with CUB and Sushi Multiple Domains: A Candidate Gene for Benign Adult Familial Myoclonic Epilepsy on Human Chromosome 8q23.3-q24.1

'Shimizu Atsushi, Asakawa Shuichi, Sasaki Takashi, Yamazaki Satoru, Yamagata, H., Kudoh Jun, Minoshima Shinsei, Kondo Ikuko, Shimizu Nobuyoshi'

Biochemical and biophysical research communications 309 ( 1 ) 143-154 2003.09

Research paper (scientific journal), Joint Work, Accepted

Identification of Eight Members of the Argonaute Family in the Human Genome

'Sasaki Takashi, Shiohama Aiko, Minoshima Shinsei, Shimizu Nobuyoshi'

Genomics 82 ( 3 ) 323-330 2003.08

Research paper (scientific journal), Joint Work, Accepted

Frequent Translocations Occur between Low Copy Repeats on Chromosome 22q11.2 (LCR22s) and Telomeric Bands of Partner Chromosomes

'Spiteri, E., Babcock, M., Kashork, C.D., Wakui, K., Gogineni, S., Lewis, D. A., Williams, K.M., Minoshima Shinsei, Sasaki Takashi, Shimizu Nobuyoshi, Potocki, L., Pulijaal, V., Shanske, A., Shaffer, L.G., Morrow, B.E.'

Human molecular genetics 12 ( 15 ) 1823-1837 2003.08

Research paper (scientific journal), Joint Work, Accepted

Molecular Cloning and Expression Analysis of a Novel Gene DGCR8 Located in the DiGeorge Syndrome Chromosomal Region (DGCR)

'Shiohama Aiko, Sasaki Takashi, Noda Setsuko, Minoshima Shinsei, Shimizu Nobuyoshi'

Biochemical and biophysical research communications 304 ( 1 ) 184-190 2003.04

Research paper (scientific journal), Joint Work, Accepted

ヒト22番および21番染色体のゲノム解析と疾患関連遺伝子の単離

Kudou Jun，Shibuya Kazunori，Sasaki Takashi，Minoshima Shinsei，Shimizu Nobuyoshi

蛋白質核酸酵素 12月増刊；ゲノムサイエンスの新たなる挑戦 46 ( 16 ) 2262-2270 2001.12