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1. A thin superconducting solenoid magnet for particle astrophysics

Author

Yamamoto, A., Makida, Y., Yamaoka, H., Ohmiya, H., Tanaka, K., Haruyama, T., Yoshida, T., Yoshimura, K., Matsuda, S., Kikuchi, K., Ootani, Y., and Mizumaki, S.

Subjects
Superconducting magnets -- Research, Electrical equipment and supplies industry -- Research, Cosmic rays -- Research, Astrophysics -- Research, Spectrometer -- Research, Electrical engineering, Business, Electronics, Electronics and electrical industries, European Organization for Nuclear Research -- Conferences, meetings and seminars
Abstract

A thin superconducting magnet being developed for long-duration balloon flights in Antarctica is discussed. BESS-Polar is being prepared as part of the Balloon-borne Experiment with a Superconducting Solenoid Magnet Spectrometer, or BESS, which has been carried out as a US-Japan cooperative scientific effort since 1993, investigating cosmic rays.

Published
2002

2. Trans-ethnic meta-analysis of white blood cell phenotypes

Author

Keller, Margaux F, Reiner, Alexander P, Okada, Yukinori, van Rooij, Frank J. A, Johnson, Andrew D, Chen, Ming Huei, Smith, Albert V, Morris, Andrew P, Tanaka, Toshiko, Ferrucci, Luigi, Zonderman, Alan B, Lettre, Guillaume, Harris, Tamara, Garcia, Melissa, Bandinelli, Stefania, Qayyum, Rehan, Yanek, Lisa R, Becker, Diane M, Becker, Lewis C, Kooperberg, Charles, Keating, Brendan, Reis, Jared, Tang, Hua, Boerwinkle, Eric, Kamatani, Yoichiro, Matsuda, Koichi, Kamatani, Naoyuki, Nakamura, Yusuke, Kubo, Michiaki, Liu, Simin, Dehghan, Abbas, Felix, Janine F, Hofman, Albert, Uitterlinden, André G, van Duijn, Cornelia M, Franco, Oscar H, Longo, Dan L, Singleton, Andrew B, Psaty, Bruce M, Evans, Michelle K, Cupples, L. Adrienne, Rotter, Jerome I, O'Donnell, Christopher J, Takahashi, Atsushi, Wilson, James G, Ganesh, Santhi K, Nalls, Mike A, Arepalli, S, Bandinelli, S, Biffi, A, Bis, Jc, Boerwinkle, E, Chakravarti, A, Chen, Mh, Chong, S, Coresh, J, Couper, Dj, Cupples, L, Dehghan, A, Do'Ring, A, Eiriksdottir, G, Felix, Jf, Ferrucci, L, Folsom, Ar, Fox, Cs, Frayling, Tm, Ganesh, Sk, Garcia, M, Garner, Sf, Gasparini, Paolo, Gieger, C, Glazer, Nl, Gouskova, Na, Greinacher, A, Gudnason, V, Harris, Tb, Hernandez, Dg, Hofman, A, Illig, T, Kamatani, Y, Kamatani, N, Kubo, M, Kuhnel, B, Lagou, V, Lettre, G, Levi, D, Lin, J, Liu, Y, Longo, Dl, Lumley, T, Mangino, M, Matsuda, K, Meisinger, C, Melzer, D, Menzel, S, Moore, M, Nakamura, Y, Nalls, Ma, Nauck, M, O'Donnell, Cj, Okada, Y, Oostra, Ba, Ouwehand, Wh, Patel, Kv, Pirastu, Nicola, Pistis, Giorgio, Prokisch, H, Prokopenko, I, Psaty, Bm, Reiner, Ap, Rendon, A, Sambrook, J, Singleton, Ab, Smith, Av, Soranzo, N, Spector, Td, Stephens, J, Stumvoll, M, Takahashi, A, Tanaka, T, Taylor, K, Teumer, A, Thein, Sl, To'Njes, A, Toniolo, D, Tsunoda, T, Uitterlinden, Ag, van Duijn CM, van Rooij FJ, Vo'Lker, U, Vo'Lzke, H, Wichmann, H., Wiggins, Kl, Wilson, Jg, Witteman, Jc, Wood, Ar, Yamamoto, K, Yang, Q, Zakai, Na, Austin, Ma, Becker, Dm, Britton, A, Chen, Z, Couper, D, Curb, J, Dean, E, Eaton, Cb, Evans, Mk, Fornage, M, Grant, Sf, Hernandez, D, Kamatini, N, Keating, Bj, Lacroix, A, Lange, La, Liu, S, Lohman, K, Mathias, R, Meng, Y, Mohler ER 3rd, Musani, S, Palmer, Cd, Papanicolaou, Gj, Snively, Bm, Tang, H, Taylor HA Jr, Thomson, C, Yanek, Lr, Yang, L, Ziv, E, Zonderman, Ab, Higasa, K, Hirota, T, Hosono, N, Kumasaka, N, Ohmiya, H, Tamari, M, Yamaguchi Kabata, Y, Yamamoto, K., Epidemiology, Medical Informatics, Urology, Erasmus MC other, Internal Medicine, Keller, Margaux F, Reiner, Alexander P, Okada, Yukinori, van Rooij, Frank J. A, Johnson, Andrew D, Chen, Ming Huei, Smith, Albert V, Morris, Andrew P, Tanaka, Toshiko, Ferrucci, Luigi, Zonderman, Alan B, Lettre, Guillaume, Harris, Tamara, Garcia, Melissa, Bandinelli, Stefania, Qayyum, Rehan, Yanek, Lisa R, Becker, Diane M, Becker, Lewis C, Kooperberg, Charle, Keating, Brendan, Reis, Jared, Tang, Hua, Boerwinkle, Eric, Kamatani, Yoichiro, Matsuda, Koichi, Kamatani, Naoyuki, Nakamura, Yusuke, Kubo, Michiaki, Liu, Simin, Dehghan, Abba, Felix, Janine F, Hofman, Albert, Uitterlinden, André G, van Duijn, Cornelia M, Franco, Oscar H, Longo, Dan L, Singleton, Andrew B, Psaty, Bruce M, Evans, Michelle K, Cupples, L. Adrienne, Rotter, Jerome I, O'Donnell, Christopher J, Takahashi, Atsushi, Wilson, James G, Ganesh, Santhi K, Nalls, Mike A, Arepalli, S, Bandinelli, S, Biffi, A, Bis, Jc, Boerwinkle, E, Chakravarti, A, Chen, Mh, Chong, S, Coresh, J, Couper, Dj, Cupples, L, Dehghan, A, Do'Ring, A, Eiriksdottir, G, Felix, Jf, Ferrucci, L, Folsom, Ar, Fox, C, Frayling, Tm, Ganesh, Sk, Garcia, M, Garner, Sf, Gasparini, Paolo, Gieger, C, Glazer, Nl, Gouskova, Na, Greinacher, A, Gudnason, V, Harris, Tb, Hernandez, Dg, Hofman, A, Illig, T, Kamatani, Y, Kamatani, N, Kubo, M, Kuhnel, B, Lagou, V, Lettre, G, Levi, D, Lin, J, Liu, Y, Longo, Dl, Lumley, T, Mangino, M, Matsuda, K, Meisinger, C, Melzer, D, Menzel, S, Moore, M, Nakamura, Y, Nalls, Ma, Nauck, M, O'Donnell, Cj, Okada, Y, Oostra, Ba, Ouwehand, Wh, Patel, Kv, Pirastu, Nicola, Pistis, Giorgio, Prokisch, H, Prokopenko, I, Psaty, Bm, Reiner, Ap, Rendon, A, Sambrook, J, Singleton, Ab, Smith, Av, Soranzo, N, Spector, Td, Stephens, J, Stumvoll, M, Takahashi, A, Tanaka, T, Taylor, K, Teumer, A, Thein, Sl, To'Njes, A, Toniolo, D, Tsunoda, T, Uitterlinden, Ag, van Duijn, Cm, van Rooij, Fj, Vo'Lker, U, Vo'Lzke, H, Wichmann, H., Wiggins, Kl, Wilson, Jg, Witteman, Jc, Wood, Ar, Yamamoto, K, Yang, Q, Zakai, Na, Austin, Ma, Becker, Dm, Britton, A, Chen, Z, Couper, D, Curb, J, Dean, E, Eaton, Cb, Evans, Mk, Fornage, M, Grant, Sf, Hernandez, D, Kamatini, N, Keating, Bj, Lacroix, A, Lange, La, Liu, S, Lohman, K, Mathias, R, Meng, Y, Mohler ER, 3rd, Musani, S, Palmer, Cd, Papanicolaou, Gj, Snively, Bm, Tang, H, Taylor HA, Jr, Thomson, C, Yanek, Lr, Yang, L, Ziv, E, Zonderman, Ab, Higasa, K, Hirota, T, Hosono, N, Kumasaka, N, Ohmiya, H, Tamari, M, Yamaguchi Kabata, Y, and Yamamoto, K.

Subjects
Linkage disequilibrium, Genotype, Quantitative Trait Loci, White blood cell count, Single-nucleotide polymorphism, Genome-wide association study, Quantitative trait locus, Biology, Polymorphism, Single Nucleotide, Linkage Disequilibrium, White People, white blood cell phenotypes, Leukocyte Count, SDG 3 - Good Health and Well-being, Asian People, Polymorphism (computer science), Genetics, Leukocytes, Humans, Allele, Molecular Biology, Genetics (clinical), White blood cell count, Trans-ethnic meta-analysis, white blood cell phenotypes, Genome, Human, Association Studies Articles, Bayes Theorem, General Medicine, Heritability, Black or African American, Phenotype, Trans-ethnic meta-analysis, Genome-Wide Association Study
Abstract

White blood cell (WBC) count is a common clinical measure used as a predictor of certain aspects of human health, including immunity and infection status. WBC count is also a complex trait that varies among individuals and ancestry groups. Differences in linkage disequilibrium structure and heterogeneity in allelic effects are expected to play a role in the associations observed between populations. Prior genome-wide association study (GWAS) meta-analyses have identified genomic loci associated with WBC and its subtypes, but much of the heritability of these phenotypes remains unexplained. Using GWAS summary statistics for over 50 000 individuals from three diverse populations (Japanese, African-American and European ancestry), a Bayesian model methodology was employed to account for heterogeneity between ancestry groups. This approach was used to perform a trans-ethnic meta-analysis of total WBC, neutrophil and monocyte counts. Ten previously known associations were replicated and six new loci were identified, including several regions harboring genes related to inflammation and immune cell function. Ninety-five percent credible interval regions were calculated to narrow the association signals and fine-map the putatively causal variants within loci. Finally, a conditional analysis was performed on the most significant SNPs identified by the trans-ethnic meta-analysis (MA), and nine secondary signals within loci previously associated with WBC or its subtypes were identified. This work illustrates the potential of trans-ethnic analysis and ascribes a critical role to multi-ethnic cohorts and consortia in exploring complex phenotypes with respect to variants that lie outside the European-biased GWAS pool.

Published
2014

3. The statistical geometry of transcriptome divergence in cell-type evolution and cancer

Author

Liang, C, Alam, I, Albanese, D, Altschuler, G, Andersson, R, Arakawa, T, Archer, J, Arner, E, Arner, P, Babina, M, Baillie, K, Bajic, V, Baker, S, Balic, A, Balwierz, P, Beckhouse, A, Bertin, N, Blake, Ja, Blumenthal, A, Bodega, B, Bonetti, A, Briggs, J, Brombacher, F, Burroughs, M, Califano, A, Cannistraci, C, Carbajo, D, Carninci, P, Chen, Yang, Chierici, M, Ciani, Y, Clevers, H, Dalla, Emiliano, Daub, C, Davis, C, De Hoon, M, De Lima Morais, D, Dermar, M, Diehl, A, Dimont, E, Dohl, T, Drabros, F, Edge, A, Edinger, M, Ekwall, K, Endoh, M, Enomoto, H, Fagiolini, M, Fairbairn, L, Fang, H, Farach Carson, Mc, Faulkner, G, Favorov, A, Fisher, M, Forrest, A, Francescatto, M, Freeman, T, Frith, M, Fujita, R, Fukuda, S, Furlanello, C, Furuno, M, Furusawa, J, Geijtenbeek, Tb, Gibson, A, Gingeras, T, Goldowithz, D, Gough, J, Guhl, S, Guler, R, Gustincich, Stefano, Ha, T, Haberle, V, Hamaguchi, M, Hara, M, Harbers, M, Harshbarger, J, Hasegawa, A, Hasegawa, Y, Hashimoto, T, Hayashizaki, Y, Herlyn, M, Heutink, P, Hide, W, Hitchens, K, Ho Sui, S, Hofmann, O, Hoof, I, Hori, F, Hume, D, Huminiecki, L, Iida, K, Ikawa, T, Ishizu, Y, Itoh, M, Jankovic, B, Jia, H, Jorgensen, M, Joshi, A, Jurman, G, Kaczkowski, B, Kai, C, Kaida, K, Kaiho, A, Kajiyama, K, Kanamori Katayama, M, Kasianov, A, Kasukawa, T, Katayama, S, Kato Ishikawa, S, Kawaguchi, S, Kawai, J, Kawaji, H, Kawamoto, H, Kawamura, Y, Kawashima, T, Kempfle, J, Kenna, T, Kere, J, Khachigian, L, Kitamura, T, Klinken, P, Knox, A, Kojima, M, Kojima, S, Kondo, N, Koseki, H, Koyasu, S, Krampitz, S, Kubosaki, A, Kulakovskiy, I, Kwon, At, Laros, J, Lassmann, T, Lenhard, B, Lennartsson, A, Li, K, Lilji, B, Lipovich, L, Lizio, M, Mackay Sim, A, Makeev, V, Manabe, R, Mar, J, Marchand, B, Mathelier, A, Medvedeva, Y, Meehan, Tf, Mejhert, N, Meynert, A, Mizuno, Y, Morikawa, H, Morimoto, M, Moro, K, Motakis, E, Motohashi, H, Mummery, C, Mungall, Cj, Murata, M, Nagao Sato, S, Nakachi, Y, Nakahara, F, Nakamura, T, Nakamura, Y, Nakazato, K, Ninomiya Fukuda, N, Nishiyori Sueki, H, Noma, S, Nozaki, T, Ogishima, S, Ohkura, N, Ohmiya, H, Ohno, H, Ohshima, M, Okada Hatakeyama, M, Okazaki, Y, Orlando, V, Ovchinnikov, D, Pain, A, Passier, R, Persson, H, Piazza, Silvano, Plessy, C, Pradhan Bhatt, S, Prendergast, J, Rackham, O, Ramilowski, J, Rashid, M, Ravasi, T, Rehli, M, Rizzu, P, Roncador, M, Roy, S, Rye, M, Saijyo, E, Sajantila, A, Saka, A, Sakaguchi, S, Sakai, M, Sandelin, A, Sato, H, Satoh, H, Suzana, S, Alka, S, Schaefer, U, Schmeier, S, Schmidl, C, Schneider, C, Schultes, Ea, Schulze Tanzil, G, Schwegmann, A, Semple, C, Sengstag, T, Severin, J, Sheng, G, Shimoji, H, Shimoni, Y, Shin, J, Simon, C, Sugiyama, D, Sugiyama, T, Summers, K, Suzuki, H, Suzuki, M, Suzuki, N, Swoboda, R, Hoen P, T, Tagami, M, Takahashi, N, Takai, J, Tanaka, H, Tatsukawa, H, Tatum, Z, Taylor, M, Thompson, M, Toyoda, H, Toyoda, T, Valen, E, Van De Wetering, M, Van Den Berg, L, Van Nimwegen, E, Verardo, R, Vijayan, D, Vitezic, M, Vorontzov, I, Wasserman, W, Watanabe, S, Wells, C, Winteringham, L, Wolvetang, E, Wood, Ej, Yamaguchi, Y, Yamamoto, M, Yoneda, M, Yonekura, Y, Yoshida, Shin'Ichirou, Young, R, Zabierowski, Se, Zhang, P, Zhao, X, Zucchelli, Silvia, Forrest, Ar, Wagner, Gp, Hubrecht Institute for Developmental Biology and Stem Cell Research, AII - Amsterdam institute for Infection and Immunity, Infectious diseases, and Experimental Immunology

Subjects
Cell type, General Physics and Astronomy, rna-seq data, phylogenetic networks, Biology, ENCODE, General Biochemistry, Genetics and Molecular Biology, Divergence, Transcriptome, Models, Settore BIO/13 - Biologia Applicata, Neoplasms, Humans, Genetics, Models, Statistical, Multidisciplinary, Statistical model, General Chemistry, Statistical, Biological Evolution, Body plan, Tree structure, Evolutionary biology, Cancer cell
Abstract

In evolution, body plan complexity increases due to an increase in the number of individualized cell types. Yet, there is very little understanding of the mechanisms that produce this form of organismal complexity. One model for the origin of novel cell types is the sister cell-type model. According to this model, each cell type arises together with a sister cell type through specialization from an ancestral cell type. A key prediction of the sister cell-type model is that gene expression profiles of cell types exhibit tree structure. Here we present a statistical model for detecting tree structure in transcriptomic data and apply it to transcriptomes from ENCODE and FANTOM5. We show that transcriptomes of normal cells harbour substantial amounts of hierarchical structure. In contrast, cancer cell lines have less tree structure, suggesting that the emergence of cancer cells follows different principles from that of evolutionary cell-type origination.

Published
2015
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4. Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

Author

Morikawa, H, Ohkura, N, Vandenbon, A, Itoh, M, Nagao Sato, S, Kawaji, H, Lassmann, T, Carninci, P, Hayashizaki, Y, Forrest, Ar, Standley, Dm, Date, H, Sakaguchi, S, FANTOM Consortium (Forrest AR, Rehli, M, Baillie, Jk, de Hoon MJ, Haberle, V, Kulakovskiy, Iv, Lizio, M, Andersson, R, Mungall, Cj, Meehan, Tf, Schmeier, S, Bertin, N, Jørgensen, M, Dimont, E, Arner, E, Schmidl, C, Schaefer, U, Medvedeva, Ya, Plessy, C, Vitezic, M, Severin, J, Semple, Ca, Ishizu, Y, Francescatto, M, Alam, I, Albanese, D, Altschuler, Gm, Archer, Ja, Arner, P, Babina, M, Baker, S, Balwierz, Pj, Beckhouse, Ag, Pradhan Bhatt, S, Blake, Ja, Blumenthal, A, Bodega, B, Bonetti, A, Briggs, J, Brombacher, F, Burroughs, Am, Califano, A, Cannistraci, Cv, Carbajo, D, Chen, Y, Chierici, M, Ciani, Y, Clevers, Hc, Dalla, E, Davis, Ca, Deplancke, B, Detmar, M, Diehl, Ad, Dohi, T, Drabløs, F, Edge, As, Edinger, M, Ekwall, K, Endoh, M, Enomoto, H, Fagiolini, M, Fairbairn, L, Fang, H, Farach Carson MC, Faulkner, Gj, Favorov, Av, Fisher, Me, Frith, Mc, Fujita, R, Fukuda, S, Furlanello, C, Furuno, M, Furusawa, J, Geijtenbeek, Tb, Gibson, A, Gingeras, T, Goldowitz, D, Gough, J, Guhl, S, Guler, R, Gustincich, Stefano, Ha, Tj, Hamaguchi, M, Hara, M, Harbers, M, Harshbarger, J, Hasegawa, A, Hasegawa, Y, Hashimoto, T, Herlyn, M, Hitchens, Kj, Ho Sui SJ, Hofmann, Om, Hoof, I, Hori, F, Huminiecki, L, Iida, K, Ikawa, T, Jankovic, Br, Jia, H, Joshi, A, Jurman, G, Kaczkowski, B, Kai, C, Kaida, K, Kaiho, A, Kajiyama, K, Kanamori Katayama, M, Kasianov, As, Kasukawa, T, Katayama, S, Kato, S, Kawaguchi, S, Kawamoto, H, Kawamura, Yi, Kawashima, T, Kempfle, Js, Kenna, Tj, Kere, J, Khachigian, Lm, Kitamura, T, Klinken, Sp, Knox, Aj, Kojima, M, Kojima, S, Kondo, N, Koseki, H, Koyasu, S, Krampitz, S, Kubosaki, A, Kwon, At, Laros, Jf, Lee, W, Lennartsson, A, Li, K, Lilje, B, Lipovich, L, Mackay Sim, A, Manabe, R, Mar, Jc, Marchand, B, Mathelier, A, Mejhert, N, Meynert, A, Mizuno, Y, Morais, Da, Morimoto, M, Moro, K, Motakis, E, Motohashi, H, Mummery, Cl, Murata, M, Nakachi, Y, Nakahara, F, Nakamura, T, Nakamura, Y, Nakazato, K, van Nimwegen, E, Ninomiya, N, Nishiyori, H, Noma, S, Nozaki, T, Ogishima, S, Ohmiya, H, Ohno, H, Ohshima, M, Okada Hatakeyama, M, Okazaki, Y, Orlando, V, Ovchinnikov, Da, Pain, A, Passier, R, Patrikakis, M, Persson, H, Piazza, S, Prendergast, Jg, Rackham, Oj, Ramilowski, Ja, Rashid, M, Ravasi, T, Rizzu, P, Roncador, M, Roy, S, Rye, Mb, Saijyo, E, Sajantila, A, Saka, A, Sakai, M, Sato, H, Satoh, H, Savvi, S, Saxena, A, Schneider, C, Schultes, Ea, Schulze Tanzil GG, Schwegmann, A, Sengstag, T, Sheng, G, Shimoji, H, Shimoni, Y, Shin, Jw, Simon, C, Sugiyama, D, Sugiyama, T, Suzuki, M, Swoboda, Rk, 't Hoen PA, Tagami, M, Takahashi, N, Takai, J, Tanaka, H, Tatsukawa, H, Tatum, Z, Thompson, M, Toyoda, H, Toyoda, T, Valen, E, van de Wetering, M, van den Berg LM, Verardo, R, Vijayan, D, Vorontsov, Ie, Wasserman, Ww, Watanabe, S, Wells, Ca, Winteringham, Ln, Wolvetang, E, Wood, Ej, Yamaguchi, Y, Yamamoto, M, Yoneda, M, Yonekura, Y, Yoshida, S, Zabierowski, Se, Zhang, Pg, Zhao, X, Zucchelli, S, Summers, Km, Suzuki, H, Daub, Co, Kawai, J, Heutink, P, Hide, W, Freeman, Tc, Lenhard, B, Bajic, Vb, Taylor, Ms, Makeev, Vj, Sandelin, A, Hume, Da, Hayashizaki, Y., AII - Amsterdam institute for Infection and Immunity, Infectious diseases, Experimental Immunology, and Hubrecht Institute for Developmental Biology and Stem Cell Research

Subjects
Transcription, Genetic, Regulatory T cell, T-Lymphocytes, Down-Regulation, chemical and pharmacologic phenomena, Biology, Inbred C57BL, T-Lymphocytes, Regulatory, Epigenesis, Genetic, Mice, Genetic, Settore BIO/13 - Biologia Applicata, medicine, Transcriptional regulation, Animals, Epigenetics, Gene, Inbred BALB C, Genetics, Regulation of gene expression, Mice, Inbred BALB C, Multidisciplinary, Binding Sites, FOXP3, hemic and immune systems, Forkhead Transcription Factors, DNA Methylation, Biological Sciences, Regulatory, Cap analysis gene expression, Mice, Inbred C57BL, medicine.anatomical_structure, Gene Expression Regulation, DNA methylation, Transcription, Epigenesis
Abstract

Naturally occurring regulatory T (Treg) cells, which specifically express the transcription factor forkhead box P3 (Foxp3), are engaged in the maintenance of immunological self-tolerance and homeostasis. By transcriptional start site cluster analysis, we assessed here how genome-wide patterns of DNA methylation or Foxp3 binding sites were associated with Treg-specific gene expression. We found that Treg-specific DNA hypomethylated regions were closely associated with Treg up-regulated transcriptional start site clusters, whereas Foxp3 binding regions had no significant correlation with either up- or down-regulated clusters in nonactivated Treg cells. However, in activated Treg cells, Foxp3 binding regions showed a strong correlation with down-regulated clusters. In accordance with these findings, the above two features of activation-dependent gene regulation in Treg cells tend to occur at different locations in the genome. The results collectively indicate that Treg-specific DNA hypomethylation is instrumental in gene up-regulation in steady state Treg cells, whereas Foxp3 down-regulates the expression of its target genes in activated Treg cells. Thus, the two events seem to play distinct but complementary roles in Treg-specific gene expression.

Published
2014
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5. Identification of nine novel loci associated with white blood cell subtypes in a Japanese population

Author

Okada, Y. (Yukinori), Hirota, T. (Tomomitsu), Kamatani, Y. (Yoichiro), Takahashi, A. (Atsushi), Ohmiya, H. (Hiroko), Kumasaka, N. (Natsuhiko), Higasa, K. (Koichiro), Yamaguchi-Kabata, Y. (Yumi), Hosono, N. (Naoya), Nalls, M.A. (Michael), Chen, M-H. (Ming-Huei), Rooij, F.J.A. (Frank) van, Smith, A.V. (Albert Vernon), Tanaka, T. (Toshiko), Couper, D. (David), Zakai, N.A. (Neil), Ferrucci, L. (Luigi), Longo, D.L. (Dan), Hernandez, D.G. (Dena), Witteman, J.C.M. (Jacqueline), Harris, T.B. (Tamara), O'Donnell, C.J. (Christopher), Ganesh, S.K. (Santhi), Matsuda, K. (Koichi), Tsunoda, T. (Tatsuhiko), Kubo, M. (Michiaki), Nakamura, Y. (Yusuke), Tamari, M. (Mayumi), Yamamoto, K. (Kazuhiko), Okada, Y. (Yukinori), Hirota, T. (Tomomitsu), Kamatani, Y. (Yoichiro), Takahashi, A. (Atsushi), Ohmiya, H. (Hiroko), Kumasaka, N. (Natsuhiko), Higasa, K. (Koichiro), Yamaguchi-Kabata, Y. (Yumi), Hosono, N. (Naoya), Nalls, M.A. (Michael), Chen, M-H. (Ming-Huei), Rooij, F.J.A. (Frank) van, Smith, A.V. (Albert Vernon), Tanaka, T. (Toshiko), Couper, D. (David), Zakai, N.A. (Neil), Ferrucci, L. (Luigi), Longo, D.L. (Dan), Hernandez, D.G. (Dena), Witteman, J.C.M. (Jacqueline), Harris, T.B. (Tamara), O'Donnell, C.J. (Christopher), Ganesh, S.K. (Santhi), Matsuda, K. (Koichi), Tsunoda, T. (Tatsuhiko), Kubo, M. (Michiaki), Nakamura, Y. (Yusuke), Tamari, M. (Mayumi), and Yamamoto, K. (Kazuhiko)

Abstract

White blood cells (WBCs) mediate immune systems and consist of various subtypes with distinct roles. Elucidation of the mechanism that regulates the counts of the WBC subtypes would provide useful insights into both the etiology of the immune system and disease pathogenesis. In this study, we report results of genome-wide association studies (GWAS) and a replication study for the counts of the 5 main WBC subtypes (neutrophils, lymphocytes, monocytes, basophils, and eosinophils) using 14,792 Japanese subjects enrolled in the BioBank Japan Project. We identified 12 significantly associated loci that satisfied the genome-wide significance threshold of P<5.0×10-8, of which 9 loci were novel (the CDK6 locus for the neutrophil count; the ITG

Published
2011
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23. A study of simplified methods for longitudinal control decoupling

Author

Joslin, R, Ohmiya, H, and Ellis, D. R

Subjects
Aircraft Stability And Control
Abstract

Using an inflight simulator, a simple longitudinal decoupling concept was compared with conventional airplane characteristics for the approach and landing tasks. The decoupling system allowed the pilot to command flight path angle changes with the stick with little or no accompanying speed change; likewise, speed changes with only small accompanying flight path changes could be made with throttle only. The unique feature of the concept is that it is an open loop (that is, nonfeedback) control system. Results indicate that in calm air and up to moderate levels of turbulence the decoupling system provides a substantial reduction in pilot workload.

Published
1977

24. Selective inhibition by ionophore A23187 of the enzyme isomerization in the catalytic cycle of Na+, K+ -ATPase.

Author

Hara, H, Ohmiya, H, and Kanazawa, T

Abstract

The effect of an ionophore A23187 on the purified Na+,K+-ATPase from the outer medulla of pig kidney was investigated. When the enzyme was pretreated with A23187 in the presence of Na+ and K+, the ATPase activity was inhibited almost completely. When the pretreatment was performed in the presence of Na+ and absence of K+, formation of the phosphoenzyme (EP) from ATP was only slightly retarded. The steady state level of EP thus formed was not altered, but EP decomposition was strongly inhibited. Under these conditions, the accumulated EP was sensitive to ADP and insensitive to K+. On the other hand, when the pretreatment was performed in the absence of Na+ and presence of K+, EP formation following simultaneous addition of Na+ and ATP was extremely slow, but the steady state level of EP was not substantially altered. When the pretreatment was performed in the absence of Na+ and presence of K+, EP formation from Pi was unaffected, and the EP formed was in rapid equilibrium with Pi of the medium. These results demonstrate that A23187 selectively inhibits isomerization of the enzyme between the high Na+ and low K+ affinity form and the low Na+ and high K+ affinity form in the catalytic cycle, whether or not the enzyme is phosphorylated. This inhibition is quite similar to the A23187-induced inhibition of the enzyme isomerization in the catalytic cycle of the Ca2+ -ATPase from sarcoplasmic reticulum (Hara, H., and Kanazawa, T. (1986)J. Biol. Chem.261, 16584-16590). These findings suggest that some common mechanism, which is involved in the enzyme isomerization, between these two transport ATPases is strongly disturbed by A23187.

Published
1988
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29. Organic photoredox-catalyzed unimolecular PCET of benzylic alcohols.

Author

Matsuo T, Sano M, Sumida Y, and Ohmiya H

Abstract

Proton-coupled electron transfer (PCET) is a crucial chemical process involving the simultaneous or sequential transfer of protons and electrons, playing a vital role in biological processes and energy conversion technologies. This study investigates the use of an organic photoredox catalyst to facilitate a unimolecular PCET process for the generation of alkyl radicals from benzylic alcohols, with a particular focus on alcohols containing electron-rich arene units. By employing a benzophenone derivative as the catalyst, the reaction proceeds efficiently under photoirradiation, achieving significant yields without the need for a Brønsted base. The findings highlight the potential of this unimolecular PCET mechanism to streamline radical generation in organic synthesis, offering a more efficient and flexible alternative to conventional methods., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Published
2025
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30. Synthesis of tertiary alkylphosphonate oligonucleotides through light-driven radical-polar crossover reactions.

Author

Ota K, Nagao K, Hata D, Sugiyama H, Segawa Y, Tokunoh R, Seki T, Miyamoto N, Sasaki Y, and Ohmiya H

Abstract

Chemical modification of nucleotides can improve the metabolic stability and target specificity of oligonucleotide therapeutics, and alkylphosphonates have been employed as charge-neutral replacements for naturally-occurring phosphodiester backbones in these compounds. However, at present, the alkyl moieties that can be attached to phosphorus atoms in these compounds are limited to methyl groups or primary/secondary alkyls, and such alkylphosphonate moieties can degrade during oligonucleotide synthesis. The present work demonstrates the tertiary alkylation of the phosphorus atoms of phosphites bearing two 2'-deoxynuclosides. This process utilizes a carbocation generated via a light-driven radical-polar crossover mechanism. This protocol provides tertiary alkylphosphonate structures that are difficult to synthesize using existing methods. The conversion of these species to oligonucleotides having charge-neutral alkylphosphonate linkages through a phosphoramidite-based approach was also confirmed in this study., (© 2023. The Author(s).)

Published
2023
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31. Biomimetic design of an α-ketoacylphosphonium-based light-activated oxygenation auxiliary.

Author

Oya R, Ota K, Fuki M, Kobori Y, Higashi M, Nagao K, and Ohmiya H

Abstract

The biomimetic design of a transition metal complex based on the iron(iv)-oxo porphyrin π-cation radical species in cytochrome P450 enzymes has been studied extensively. Herein, we translate the functions of this iron(iv)-oxo porphyrin π-cation radical species to an α-ketoacyl phosphonium species comprised of non-metal atoms and utilize it as a light-activated oxygenation auxiliary for ortho -selective oxygenation of anilines. Visible light irradiation converts the α-ketoacyl phosphonium species to the excited state, which acts as a transiently generated oxidant. The intramolecular nature of the process ensures high regioselectivity and chemoselectivity. The auxiliary is easily removable. A one-pot protocol is also described., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Published
2023
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32. The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.

Author

Walker K, Kalra D, Lowdon R, Chen G, Molik D, Soto DC, Dabbaghie F, Khleifat AA, Mahmoud M, Paulin LF, Raza MS, Pfeifer SP, Agustinho DP, Aliyev E, Avdeyev P, Barrozo ER, Behera S, Billingsley K, Chong LC, Choubey D, De Coster W, Fu Y, Gener AR, Hefferon T, Henke DM, Höps W, Illarionova A, Jochum MD, Jose M, Kesharwani RK, Kolora SRR, Kubica J, Lakra P, Lattimer D, Liew CS, Lo BW, Lo C, Lötter A, Majidian S, Mendem SK, Mondal R, Ohmiya H, Parvin N, Peralta C, Poon CL, Prabhakaran R, Saitou M, Sammi A, Sanio P, Sapoval N, Syed N, Treangen T, Wang G, Xu T, Yang J, Zhang S, Zhou W, Sedlazeck FJ, and Busby B

Subjects
Humans, Genomics, Software, SARS-CoV-2 genetics, COVID-19
Abstract

In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics., Competing Interests: Competing interests: Ben Busby is a full-time employee of DNAnexus. Rebecca Lowdon is a full-time employee of Bayer Crop Sciences. Ramanandan Prabhakaran is a full-time employee of Hoffmann-La Roche Limited. Luis F Paulin is sponsored by Genentech, Inc. Wouter De Coster has received travel reimbursement and free consumables from ONT. FJS received research support from ONT and PacBio. Alejandro Rafael Gener is an editorial board member of AIDS, and has received poster bursaries from ONT in 2019., (Copyright: © 2022 Walker K et al.)

Published
2022
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33. Organophotoredox-catalyzed semipinacol rearrangement via radical-polar crossover.

Author

Kodo T, Nagao K, and Ohmiya H

Subjects
Catalysis, Oxidation-Reduction, Carbon, Cyclohexenes
Abstract

Over the past century, significant progress in semipinacol rearrangement involving 1,2-migration of α-hydroxy carbocations has been made in the areas of catalysis and total synthesis of natural products. To access the α-hydroxy carbocation intermediate, conventional acid-mediated or electrochemical approaches have been employed. However, the photochemical semipinacol rearrangement has been underdeveloped. Herein, we report the organophotoredox-catalyzed semipinacol rearrangement via radical-polar crossover (RPC). A phenothiazine-based organophotoredox catalyst facilitates the generation of an α-hydroxy non-benzylic alkyl radical followed by oxidation to the corresponding carbocation, which can be exploited to undergo the semipinacol rearrangement. As a result, the photochemical approach enables decarboxylative semipinacol rearrangement of β-hydroxycarboxylic acid derivatives and alkylative semipinacol type rearrangement of allyl alcohols with carbon electrophiles, producing α-quaternary or α-tertiary carbonyls bearing sp 3 -rich scaffolds., (© 2022. The Author(s).)

Published
2022
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34. Measurement of SARS-CoV-2 Antibody Titers Improves the Prediction Accuracy of COVID-19 Maximum Severity by Machine Learning in Non-Vaccinated Patients.

Author

Kurano M, Ohmiya H, Kishi Y, Okada J, Nakano Y, Yokoyama R, Qian C, Xia F, He F, Zheng L, Yu Y, Jubishi D, Okamoto K, Moriya K, Kodama T, and Yatomi Y

Subjects
Antibody Formation immunology, COVID-19 immunology, COVID-19 pathology, COVID-19 Vaccines immunology, Coronavirus Nucleocapsid Proteins immunology, Humans, Immunoglobulin A blood, Immunoglobulin G blood, Immunoglobulin M blood, Machine Learning, Protein Domains immunology, Spike Glycoprotein, Coronavirus immunology, Time Factors, Vaccination, Antibodies, Viral blood, COVID-19 blood, COVID-19 Vaccines blood, SARS-CoV-2 immunology, Severity of Illness Index, Vaccination Hesitancy
Abstract

Numerous studies have suggested that the titers of antibodies against SARS-CoV-2 are associated with the COVID-19 severity, however, the types of antibodies associated with the disease maximum severity and the timing at which the associations are best observed, especially within one week after symptom onset, remain controversial. We attempted to elucidate the antibody responses against SARS-CoV-2 that are associated with the maximum severity of COVID-19 in the early phase of the disease, and to investigate whether antibody testing might contribute to prediction of the disease maximum severity in COVID-19 patients. We classified the patients into four groups according to the disease maximum severity (severity group 1 (did not require oxygen supplementation), severity group 2a (required oxygen supplementation at low flow rates), severity group 2b (required oxygen supplementation at relatively high flow rates), and severity group 3 (required mechanical ventilatory support)), and serially measured the titers of IgM, IgG, and IgA against the nucleocapsid protein, spike protein, and receptor-binding domain of SARS-CoV-2 until day 12 after symptom onset. The titers of all the measured antibody responses were higher in severity group 2b and 3, especially severity group 2b, as early as at one week after symptom onset. Addition of data obtained from antibody testing improved the ability of analysis models constructed using a machine learning technique to distinguish severity group 2b and 3 from severity group 1 and 2a. These models constructed with non-vaccinated COVID-19 patients could not be applied to the cases of breakthrough infections. These results suggest that antibody testing might help physicians identify non-vaccinated COVID-19 patients who are likely to require admission to an intensive care unit., Competing Interests: The present study was a collaborative research project among The University of Tokyo, Shenzhen YHLO Biotech Co., Ltd, and Medical & Biological Laboratories Co., Ltd. FX, FH, LZ, and YYu are employees of Shenzhen YHLO Biotech Co., Ltd and YK, JO, and HO are employees of Medical & Biological Laboratories Co., Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Kurano, Ohmiya, Kishi, Okada, Nakano, Yokoyama, Qian, Xia, He, Zheng, Yu, Jubishi, Okamoto, Moriya, Kodama and Yatomi.)

Published
2022
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35. Association of the Serum Levels of the Nucleocapsid Antigen of SARS-CoV-2 With the Diagnosis, Disease Severity, and Antibody Titers in Patients With COVID-19: A Retrospective Cross-Sectional Study.

Author

Yokoyama R, Kurano M, Nakano Y, Morita Y, Ohmiya H, Kishi Y, Okada J, Qian C, Xia F, He F, Zheng L, Yu Y, Mizoguchi M, Higurashi Y, Harada S, Jubishi D, Okamoto K, Moriya K, Kodama T, and Yatomi Y

Abstract

Background: Several types of laboratory tests for COVID-19 have been established to date; however, the clinical significance of the serum SARS-CoV-2 nucleocapsid (N) antigen levels remains to be fully elucidated. In the present study, we attempted to elucidate the usefulness and clinical significance of the serum N antigen levels. Methods: We measured the serum N antigen levels in 391 serum samples collected from symptomatic patients with a confirmed diagnosis of COVID-19 and 96 serum samples collected from patients with non-COVID-19, using a fully automated chemiluminescence immunoassay analyzer. Results: Receiver operating characteristic analysis identified the optimal cutoff value of the serum N antigen level (cutoff index, based on Youden's index) as 0.255, which yielded a sensitivity and specificity for the diagnosis of COVID-19 of 91.0 and 81.3%, respectively. The serum N antigen levels were significantly higher in the patient groups with moderate and severe COVID-19 than with mild disease. Moreover, a significant negative correlation was observed between the serum N antigen levels and the SARS-CoV-2 IgG antibody titers, especially in patients with severe COVID-19. Conclusion: Serum N antigen testing might be useful both for the diagnosis of COVID-19 and for obtaining a better understanding of the clinical features of the disease., Competing Interests: The present study was a collaborative research project among the University of Tokyo, Shenzhen YHLO Biotech Co., Ltd., and Medical & Biological Laboratories Co., Ltd. FX, FH, LZ, and YYu are the employees of Shenzhen YHLO Biotech Co., Ltd., and YK, JO, and HO are the employees of Medical & Biological Laboratories Co., Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Yokoyama, Kurano, Nakano, Morita, Ohmiya, Kishi, Okada, Qian, Xia, He, Zheng, Yu, Mizoguchi, Higurashi, Harada, Jubishi, Okamoto, Moriya, Kodama and Yatomi.)

Published
2021
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36. Relationship between Kita-Kyushu Lung Cancer antigen-1 expression and prognosis of cases with lung squamous cell carcinoma.

Author

Ichiki Y, Fukuyama T, Ohmiya H, Ueno M, Yanagi S, Kanasaki Y, Goto H, Mikami S, Yamazaki H, Nakanishi K, and Ishida T

Abstract

Background: Previously, we identified the highly immunogenic cancer testicular antigen named Kita-Kyushu Lung Cancer antigen-1 (KK-LC-1). In this study, we analyzed the effect of KK-LC-1 expression on the prognosis of patients with resected squamous cell lung cancer., Methods: Fifty squamous cell lung cancer patients, who received complete resection, were enrolled in this study. The expressions of KK-LC-1, CD8, human leukocyte antigen (HLA) class I, and programmed cell death protein ligand-1 (PD-L1) were assessed via immunohistochemistry staining using the specimens obtained from the participants. The association between the expression of the abovementioned molecules and patient prognosis was investigated., Results: KK-LC-1 expression was observed in 21 of 50 recruited cases (42%). However, no significant correlation was found between KK-LC-1 expression and patient prognosis. The prognosis was significantly better in lung cancer cases with KK-LC-1 expression in which CD8 + T cells infiltrated the tumor. Regardless of the HLA class I expression or the PD-L1 expression, the KK-LC-1 expression in squamous cell lung cancer could not be detected as a significant prognostic factor. Furthermore, considering the polarity of the cancer tissue as epithelium, staining of KK-LC-1 tended to be strong in the area corresponding to the basal side of the tumor tissue. The Ki-67 expression was frequently observed in cancer cells on the basal side, which was consistent with the KK-LC-1 expression in representative four cases with KK-LC-1-positive squamous cell lung cancer., Conclusions: Our results indicated that lung squamous cell cancer patients with KK-LC-1 expression and the tumor infiltrating CD8 + T cells might exhibit better prognosis. KK-LC-1 might be highly expressed in cancer cells with high proliferative capacity. Larger cohort analysis is still required for further elucidation and validation of the results of this study., Competing Interests: Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://dx.doi.org/10.21037/tcr-21-1581). The authors have no conflicts of interest to declare., (2021 Translational Cancer Research. All rights reserved.)

Published
2021
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37. Aryl radical-mediated N-heterocyclic carbene catalysis.

Author

Matsuki Y, Ohnishi N, Kakeno Y, Takemoto S, Ishii T, Nagao K, and Ohmiya H

Abstract

There have been significant advancements in radical reactions using organocatalysts in modern organic synthesis. Recently, NHC-catalyzed radical reactions initiated by single electron transfer processes have been actively studied. However, the reported examples have been limited to catalysis mediated by alkyl radicals. In this article, the NHC organocatalysis mediated by aryl radicals has been achieved. The enolate form of the Breslow intermediate derived from an aldehyde and thiazolium-type NHC in the presence of a base undergoes single electron transfer to an aryl iodide, providing an aryl radical. The catalytically generated aryl radical could be exploited as an arylating reagent for radical relay-type arylacylation of styrenes and as a hydrogen atom abstraction reagent for α-amino C(sp 3 )-H acylation of secondary amides.

Published
2021
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38. Fluorescent-Oxaboroles: Synthesis and Optical Property by Sugar Recognition.

Author

Nakano M, Nakamura R, Sumida Y, Nagao K, Furuyama T, Inagaki F, and Ohmiya H

Subjects
Boron Compounds chemical synthesis, Fluorescent Dyes chemical synthesis, Molecular Structure, Optical Phenomena, Boron Compounds chemistry, Fluorescent Dyes chemistry, NAD chemistry, Sugars analysis
Abstract

The optical property of fluorescent unit-conjugated aliphatic oxaboroles has been investigated. The oxaboroles provide good fluorescence quantum yields and selective recognition toward D-ribose and D-ribose containing molecules. The molecular recognition induced significant fluorescence quenching. The property of the boroles showed the possibility of the boron-based nicotinamide adenine dinucleotide (NAD) sensor probe.

Published
2021
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39. Recent advances in N-heterocyclic carbene-based radical catalysis.

Author

Ishii T, Nagao K, and Ohmiya H

Abstract

In nature, a number of enzymes use thiamine diphosphate as a coenzyme to catalyze the pyruvate decarboxylation. The resultant enamine, a so-called "Breslow intermediate," is known to perform single electron transfer to various electron acceptors. Inspired by this enzymatic catalysis, N-heterocyclic carbene (NHC)-catalyzed radical reactions have been developed. This minireview highlights the recent progress and developments in NHC-based radical catalysis. This minireview is categorized according to the reaction types; oxidation type reaction and carbon-carbon bond formation through single electron transfer/radical-radical coupling., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Published
2020
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40. Allylic cross-coupling using aromatic aldehydes as α-alkoxyalkyl anions.

Author

Yuasa A, Nagao K, and Ohmiya H

Abstract

The allylic cross-coupling using aromatic aldehydes as α-alkoxyalkyl anions is described. The synergistic palladium/copper-catalyzed reaction of aromatic aldehydes, allylic carbonates, and a silylboronate produces the corresponding homoallylic alcohol derivatives. This process involves the catalytic formation of a nucleophilic α-silyloxybenzylcopper(I) species and the subsequent palladium-catalyzed allylic substitution., (Copyright © 2020, Yuasa et al.; licensee Beilstein-Institut.)

Published
2020
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41. Cancer/testis antigen, Kita-Kyushu lung cancer antigen-1 and ABCD stratification for diagnosing gastric cancers.

Author

Shida A, Fukuyama T, Futawatari N, Ohmiya H, Ichiki Y, Yamashita T, Nishi Y, Kobayashi N, Yamazaki H, Watanabe M, and Takahashi Y

Subjects
Adult, Aged, Aged, 80 and over, Antibodies, Bacterial immunology, Antigens, Neoplasm immunology, Biomarkers, Tumor blood, Biomarkers, Tumor immunology, Female, Helicobacter Infections complications, Helicobacter Infections immunology, Helicobacter pylori immunology, Humans, Immunoglobulin G immunology, Male, Middle Aged, Pepsinogen A blood, Pepsinogen C blood, Stomach Neoplasms immunology, Stomach Neoplasms microbiology, Antibodies, Bacterial blood, Antigens, Neoplasm blood, Helicobacter Infections blood, Stomach Neoplasms diagnosis
Abstract

Background: The ABCD stratification [(combination of serum pepsinogen (PG) levels and titers of antibody (immunoglobulin G, IgG) against Helicobacter pylori ( H. pylori )] is effective for the classification of individuals at risk of developing gastric cancer (GC). The Kita-Kyushu lung cancer antigen-1 (KK-LC-1) is a Cancer/Testis antigen frequently expressed in GC., Aim: To evaluate the effectiveness of KK-LC-1 and ABCD stratification in the diagnosis of GC., Methods: We analyzed the gene expression of KK-LC-1 in surgical specimens obtained from GC tumors. The levels of serum PG I/PG II and IgG against H. pylori were measured. According to their serological status, the patients were classified into the four groups of the ABCD stratification., Results: Of the 77 examined patients, 63 (81.8%) expressed KK-LC-1. The IgG titers of H. pylori and PG II were significantly higher in patients expressing KK-LC-1 than those measured in patients not expressing KK-LC-1 ( P = 0.0289 and P = 0.0041, respectively). The expression of KK-LC-1 in group C [PG method (+)/ H. pylori infection (+)] was as high as 93.9% high. KK-LC-1 was also detected in group A [-/-]., Conclusion: The KK-LC-1 expression in GC was associated with H. pylori infection and atrophic status, so that, KK-LC-1 may be a useful marker for the diagnosis of GC., Competing Interests: Conflict-of-interest statement: There are no conflicts of interest to declare., (©The Author(s) 2020. Published by Baishideng Publishing Group Inc. All rights reserved.)

Published
2020
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42. Expression of Kita-Kyushu Lung Cancer Antigen-1 as Detected by a Novel Monoclonal Antibody in Gastric Cancer.

Author

Takahashi Y, Fukuyama T, Futawatari N, Ichiki Y, Ohmiya H, Chuman M, Yamashita T, Hiki N, Kumamoto Y, Yamazaki H, Nonoguchi H, Nishi Y, and Kobayashi N

Subjects
Antigens, Neoplasm genetics, Gene Expression, Humans, Metaplasia immunology, Precancerous Conditions immunology, Pylorus immunology, Antibodies, Monoclonal, Antigens, Neoplasm analysis, Stomach immunology, Stomach Neoplasms immunology
Abstract

Background/aim: Kita-Kyushu lung cancer antigen-1 (KK-LC-1) is a known cancer/testis antigen. Our group has previously shown KK-LC-1 gene expression in gastric cancer. However, could not be detected the KK-LC-1 protein due to the lack of an appropriate antibody. Here, we assessed our original monoclonal antibody (Kmab34B3) and, using it, assessed the expression of KK-LC-1 in gastric cancer., Patients and Methods: We evaluated an original monoclonal antibody against KK-LC-1 (Kmab34B3), and used this antibody to compare KK-LC-1 protein expression in tumour and non-tumour stomach cells from gastric cancer patients., Results: Kmab34B3 stained testicular germ cells, and tumour cells in nine out of 11 (82%) specimens. In non-tumorous areas, Kmab34B3 stained 13 out of 29 (45%) pyloric gland specimens. Furthermore, Kmab34B3 also stained intestinal metaplasia positive and negative areas., Conclusion: Kmab34B3 was able to detect KK-LC-1 protein within tumour cells and the pyloric gland where the gene has been shown to be expressed. Therefore, it might be an attractive tool for detecting KK-LC-1 expression in precancerous and cancerous stomach cells., (Copyright© 2019, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.)

Published
2019
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43. Effects of long-term intake of a yogurt fermented with Lactobacillus delbrueckii subsp. bulgaricus 2038 and Streptococcus thermophilus 1131 on mice.

Author

Usui Y, Kimura Y, Satoh T, Takemura N, Ouchi Y, Ohmiya H, Kobayashi K, Suzuki H, Koyama S, Hagiwara S, Tanaka H, Imoto S, Eberl G, Asami Y, Fujimoto K, and Uematsu S

Subjects
Animals, Intestines immunology, Intestines microbiology, Lactobacillus delbrueckii genetics, Lactobacillus delbrueckii immunology, Male, Mice, Mice, Inbred ICR, Streptococcus thermophilus genetics, Streptococcus thermophilus immunology, Fermentation, Lactobacillus delbrueckii metabolism, Probiotics metabolism, Streptococcus thermophilus metabolism, Yogurt microbiology
Abstract

The gut is an extremely complicated ecosystem where micro-organisms, nutrients and host cells interact vigorously. Although the function of the intestine and its barrier system weakens with age, some probiotics can potentially prevent age-related intestinal dysfunction. Lactobacillus delbrueckii subsp. bulgaricus 2038 and Streptococcus thermophilus 1131, which are the constituents of LB81 yogurt, are representative probiotics. However, it is unclear whether their long-term intake has a beneficial influence on systemic function. Here, we examined the gut microbiome, fecal metabolites and gene expression profiles of various organs in mice. Although age-related alterations were apparent in them, long-term LB81 yogurt intake led to an increased Bacteroidetes to Firmicutes ratio and elevated abundance of the bacterial family S24-7 (Bacteroidetes), which is known to be associated with butyrate and propanoate production. According to our fecal metabolite analysis to detect enrichment, long-term LB81 yogurt intake altered the intestinal metabolic pathways associated with propanoate and butanoate in the mice. Gene ontology analysis also revealed that long-term LB81 yogurt intake influenced many physiological functions related to the defense response. The profiles of various genes associated with antimicrobial peptides-, tight junctions-, adherens junctions- and mucus-associated intestinal barrier functions were also drastically altered in the LB81 yogurt-fed mice. Thus, long-term intake of LB81 yogurt has the potential to maintain systemic homeostasis, such as the gut barrier function, by controlling the intestinal microbiome and its metabolites.

Published
2018
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44. Enantiocontrol by assembled attractive interactions in copper-catalyzed asymmetric direct alkynylation of α-ketoesters with terminal alkynes: OH···O/sp 3 -CH···O two-point hydrogen bonding combined with dispersive attractions.

Author

Schwarzer MC, Fujioka A, Ishii T, Ohmiya H, Mori S, and Sawamura M

Abstract

Copper-catalyzed asymmetric direct alkynylation of α-ketoesters with terminal alkynes with chiral prolinol-phosphine ligands, most preferably (α R ,2 S )-1-(2-dicyclohexylphosphinobenzyl)-α-neopentyl-2-pyrrolidinemethanol, afforded various enantioenriched chiral propargylic tertiary alcohols. Quantum-chemical calculations using the BP86 density functional including Grimme's empirical dispersion correction [DF-BP86-D3(BJ)-PCM( t BuOH)/TZVPP//DF-BP86-D3(BJ)/SVP] show the occurrence of OH···O/sp 3 -CH···O two-point hydrogen bonding between the chiral ligand and the carbonyl group of the ketoester in the stereo-determining transition states. Combined with the hydrogen-bonding interactions orienting the ketoester substrate, dispersive attractions between the chiral ligand ( P -cyclohexyl groups) and the ketoester in the favored transition states, rather than steric repulsions in the disfavored transition state explain the enantioselectivity of the asymmetric copper catalysis.

Published
2018
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45. Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis.

Author

Yoshida E, Terao Y, Hayashi N, Mogushi K, Arakawa A, Tanaka Y, Ito Y, Ohmiya H, Hayashizaki Y, Takeda S, Itoh M, and Kawaji H

Subjects
Adult, Aged, Aged, 80 and over, Carrier Proteins genetics, Carrier Proteins metabolism, Female, Gene Expression Profiling methods, Gene Expression Regulation, Neoplastic, Humans, Lymph Nodes pathology, Lymphatic Metastasis pathology, Middle Aged, Neoplasm Recurrence, Local genetics, Neoplasm Recurrence, Local pathology, Promoter Regions, Genetic, Reverse Transcriptase Polymerase Chain Reaction methods, Semaphorins genetics, Semaphorins metabolism, Tumor Suppressor Proteins genetics, Tumor Suppressor Proteins metabolism, Biomarkers, Tumor genetics, Endometrial Neoplasms genetics, Endometrial Neoplasms pathology, Lymphatic Metastasis genetics
Abstract

For endometrial cancer patients, lymphadenectomy is recommended to exclude rarely metastasized cancer cells. This procedure is performed even in patients with low risk of recurrence despite the risk of complications such as lymphedema. A method to accurately identify cases with no lymph node metastases (LN-) before lymphadenectomy is therefore highly required. We approached this clinical problem by examining primary lesions of endometrial cancers with CAGE (Cap Analysis Gene Expression), which quantifies promoter-level expression across the genome. Fourteen profiles delineated distinct transcriptional networks between LN + and LN- cases, within those classified as having the low or intermediate risk of recurrence. Subsequent quantitative reverse transcription polymerase chain reaction (qRT-PCR) analyses of 115 primary tumors showed SEMA3D mRNA and TACC2 isoforms expressed through a novel promoter as promising biomarkers with high accuracy (area under the receiver operating characteristic curve, 0.929) when used in combination. Our high-resolution transcriptome provided evidence of distinct molecular profiles underlying LN + /LN- status in endometrial cancers, raising the possibility of preoperative diagnosis to reduce unnecessary operations in patients with minimum recurrence risk.

Published
2017
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46. Novel biomarkers that assist in accurate discrimination of squamous cell carcinoma from adenocarcinoma of the lung.

Author

Takamochi K, Ohmiya H, Itoh M, Mogushi K, Saito T, Hara K, Mitani K, Kogo Y, Yamanaka Y, Kawai J, Hayashizaki Y, Oh S, Suzuki K, and Kawaji H

Abstract

Background: Targeted therapies based on the molecular and histological features of cancer types are becoming standard practice. The most effective regimen in lung cancers is different between squamous cell carcinoma (SCC) and adenocarcinoma (AD). Therefore a precise diagnosis is crucial, but this has been difficult, particularly for poorly differentiated SCC (PDSCC) and AD without a lepidic growth component (non-lepidic AD). Biomarkers enabling a precise diagnosis are therefore urgently needed., Methods: Cap Analysis of Gene Expression (CAGE) is a method used to quantify promoter activities across the whole genome by determining the 5' ends of capped RNA molecules with next-generation sequencing. We performed CAGE on 97 frozen tissues from surgically resected lung cancers (22 SCC and 75 AD), and confirmed the findings by immunohistochemical analysis (IHC) in an independent group (29 SCC and 45 AD)., Results: Using the genome-wide promoter activity profiles, we confirmed that the expression of known molecular markers used in IHC for SCC (CK5, CK6, p40 and desmoglein-3) and AD (TTF-1 and napsin A) were different between SCC and AD. We identified two novel marker candidates, SPATS2 for SCC and ST6GALNAC1 for AD, as showing comparable performance and complementary utility to the known markers in discriminating PDSCC and non-lepidic AD. We subsequently confirmed their utility at the protein level by IHC in an independent group., Conclusions: We identified two genes, SPATS2 and ST6GALNAC1, as novel complemental biomarkers discriminating SCC and AD. These findings will contribute to a more accurate diagnosis of NSCLC, which is crucial for precision medicine for lung cancer.

Published
2016
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47. Copper-catalyzed stereoselective conjugate addition of alkylboranes to alkynoates.

Author

Wakamatsu T, Nagao K, Ohmiya H, and Sawamura M

Abstract

A copper-catalyzed conjugate addition of alkylboron compounds (alkyl-9-BBN, prepared by hydroboration of alkenes with 9-BBN-H) to alkynoates to form β-disubstituted acrylates is reported. The addition occurred in a formal syn-hydroalkylation mode. The syn stereoselectivity was excellent regardless of the substrate structure. A variety of functional groups were compatible with the conjugate addition.

Published
2015
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49. Discovery of molecular markers to discriminate corneal endothelial cells in the human body.

Author

Yoshihara M, Ohmiya H, Hara S, Kawasaki S, Hayashizaki Y, Itoh M, Kawaji H, Tsujikawa M, and Nishida K

Subjects
Biomarkers metabolism, Carrier Proteins metabolism, Cornea cytology, Corneal Transplantation methods, Egg Proteins metabolism, Endothelial Cells cytology, Endothelium, Corneal cytology, Humans, Membrane Glycoproteins metabolism, Membrane Proteins metabolism, Middle Aged, Nerve Tissue Proteins metabolism, Receptor, Serotonin, 5-HT1D metabolism, Receptors, G-Protein-Coupled metabolism, Regeneration physiology, Tissue Engineering methods, Zona Pellucida Glycoproteins, Cornea metabolism, Endothelial Cells metabolism, Endothelium, Corneal metabolism
Abstract

The corneal endothelium is a monolayer of hexagonal corneal endothelial cells (CECs) on the inner surface of the cornea. CECs are critical in maintaining corneal transparency through their barrier and pump functions. CECs in vivo have a limited capacity in proliferation, and loss of a significant number of CECs results in corneal edema called bullous keratopathy which can lead to severe visual loss. Corneal transplantation is the most effective method to treat corneal endothelial dysfunction, where it suffers from donor shortage. Therefore, regeneration of CECs from other cell types attracts increasing interests, and specific markers of CECs are crucial to identify actual CECs. However, the currently used markers are far from satisfactory because of their non-specific expression in other cell types. Here, we explored molecular markers to discriminate CECs from other cell types in the human body by integrating the published RNA-seq data of CECs and the FANTOM5 atlas representing diverse range of cell types based on expression patterns. We identified five genes, CLRN1, MRGPRX3, HTR1D, GRIP1 and ZP4 as novel markers of CECs, and the specificities of these genes were successfully confirmed by independent experiments at both the RNA and protein levels. Notably none of them have been documented in the context of CEC function. These markers could be useful for the purification of actual CECs, and also available for the evaluation of the products derived from other cell types. Our results demonstrate an effective approach to identify molecular markers for CECs and open the door for the regeneration of CECs in vitro.

Published
2015
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50. RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE).

Author

Ohmiya H, Vitezic M, Frith MC, Itoh M, Carninci P, Forrest AR, Hayashizaki Y, and Lassmann T

Subjects
Cluster Analysis, Computational Biology methods, Gene Expression Profiling, HeLa Cells, Humans, Internet, Nucleotide Motifs, Position-Specific Scoring Matrices, Reproducibility of Results, Gene Expression Regulation, RNA Caps, Software, Transcription Initiation Site
Abstract

Background: Next generation sequencing based technologies are being extensively used to study transcriptomes. Among these, cap analysis of gene expression (CAGE) is specialized in detecting the most 5' ends of RNA molecules. After mapping the sequenced reads back to a reference genome CAGE data highlights the transcriptional start sites (TSSs) and their usage at a single nucleotide resolution., Results: We propose a pipeline to group the single nucleotide TSS into larger reproducible peaks and compare their usage across biological states. Importantly, our pipeline discovers broad peaks as well as the fine structure of individual transcriptional start sites embedded within them. We assess the performance of our approach on a large CAGE datasets including 156 primary cell types and two cell lines with biological replicas. We demonstrate that genes have complicated structures of transcription initiation events. In particular, we discover that narrow peaks embedded in broader regions of transcriptional activity can be differentially used even if the larger region is not., Conclusions: By examining the reproducible fine scaled organization of TSS we can detect many differentially regulated peaks undetected by previous approaches.

Published
2014
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