Research Center for Transomics Medicine

Research Output

Article

Histone H4 lysine 20 acetylation is associated with gene repression in human cells

Kaimori, J. Y., Maehara, K., Hayashi-Takanaka, Y., Harada, A., Fukuda, M., Yamamoto, S., Ichimaru, N., Umehara, T., Yokoyama, S., Matsuda, R., Ikura, T., Nagao, K., Obuse, C., Nozaki, N., Takahara, S., Takao, T., Ohkawa, Y., Kimura, H. & Isaka, Y., Apr 11 2016, In : Scientific reports. 6, 24318.

Research output: Contribution to journalArticle

15 Citations (Scopus)

Histone methyltransferase G9a is a key regulator of the starvation-induced behaviors in Drosophila melanogaster

Shimaji, K., Tanaka, R., Maeda, T., Ozaki, M., Yoshida, H., Ohkawa, Y., Sato, T., Suyama, M. & Yamaguchi, M., Dec 1 2017, In : Scientific reports. 7, 1, 14763.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Hsc70 contributes to cancer cell survival by preventing Rab1A degradation under stress conditions

Tanaka, M., Mun, S., Harada, A., Ohkawa, Y., Inagaki, A., Sano, S., Takahashi, K., Izumi, Y., Osada-Oka, M., Wanibuchi, H., Yamagata, M., Yukimura, T., Miura, K., Shiota, M. & Iwao, H., May 6 2014, In : PloS one. 9, 5, e96785.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Human proteins that specifically bind to 8-oxoguanine-containing RNA and their responses to oxidative stress

Hayakawa, H., Fujikane, A., Ito, R., Matsumoto, M., Nakayama, K. & Sekiguchi, M., Dec 10 2010, In : Biochemical and Biophysical Research Communications. 403, 2, p. 220-224 5 p.

Research output: Contribution to journalArticle

20 Citations (Scopus)

Human TREX component Thoc5 affects alternative polyadenylation site choice by recruiting mammalian cleavage factor I

Katahira, J., Okuzaki, D., Inoue, H., Yoneda, Y., Maehara, K. & Ohkawa, Y., Aug 1 2013, In : Nucleic acids research. 41, 14, p. 7060-7072 13 p.

Research output: Contribution to journalArticle

35 Citations (Scopus)

Hypoxanthine Secretion from Human Adipose Tissue and its Increase in Hypoxia

Nagao, H., Nishizawa, H., Tanaka, Y., Fukata, T., Mizushima, T., Furuno, M., Bamba, T., Tsushima, Y., Fujishima, Y., Kita, S., Funahashi, T., Maeda, N., Mori, M., Fukusaki, E. & Shimomura, I., Jul 2018, In : Obesity. 26, 7, p. 1168-1178 11 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Identification of Acrylamide Adducts Generated during Storage of Canned Milk Coffee

Yoshioka, T., Izumi, Y., Takahashi, M., Suzuki, K., Miyamoto, Y., Nagatomi, Y. & Bamba, T., Mar 25 2020, In : Journal of Agricultural and Food Chemistry. 68, 12, p. 3859-3867 9 p.

Research output: Contribution to journalArticle

Identification of immunoglobulin gene sequences from a small read number of mRNA-seq using hybridomas

Kuniyoshi, Y., Maehara, K., Iwasaki, T., Hayashi, M., Semba, Y., Fujita, M., Sato, Y., Kimura, H., Harada, A. & Ohkawa, Y., Oct 2016, In : PloS one. 11, 10, e0165473.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Identification of KIAA1210 as a novel X-chromosome-linked protein that localizes to the acrosome and associates with the ectoplasmic specialization in testes

Iwamori, T., Iwamori, N., Matsumoto, M., Ono, E. & Matzuk, M. M., Feb 1 2017, In : Biology of Reproduction. 96, 2, p. 469-477 9 p., bio145458.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Identification of low-abundance proteins in serum via the isolation of HSP72 complexes

Tanaka, M., Shiota, M., Nakao, T., Uemura, R., Nishi, S., Ohkawa, Y., Matsumoto, M., Yamaguchi, M., Osada-Oka, M., Inagaki, A., Takahashi, K., Nakayama, K. I., Gi, M., Izumi, Y., Miura, K. & Iwao, H., Mar 16 2016, In : Journal of Proteomics. 136, p. 214-221 8 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Identification of metabolites associated with onset of CAD in diabetic patients using ce-ms analysis: A pilot study

Omori, K., Katakami, N., Yamamoto, Y., Ninomiya, H., Takahara, M., Matsuoka, T. A., Bamba, T., Fukusaki, E. & Shimomura, I., Jan 1 2019, In : Journal of atherosclerosis and thrombosis. 26, 3, p. 233-245 13 p.

Research output: Contribution to journalArticle

Open Access
3 Citations (Scopus)

Identification of miR-305, a microRNA that promotes aging, and its target mRNAs in Drosophila

Ueda, M., Sato, T., Ohkawa, Y. & Inoue, Y. H., Feb 1 2018, In : Genes to Cells. 23, 2, p. 80-93 14 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Identification of myelin transcription factor 1 (MyT1) as a subunit of the neural cell type-specific lysine-specific demethylase 1 (LSD1) complex

Yokoyama, A., Igarashi, K., Sato, T., Takagi, K., Otsuka, M. I., Shishido, Y., Baba, T., Ito, R., Kanno, J., Ohkawa, Y., Morohashi, K. I. & Sugawara, A., Jun 27 2014, In : Journal of Biological Chemistry. 289, 26, p. 18152-18162 11 p.

Research output: Contribution to journalArticle

21 Citations (Scopus)

Identification of novel serum markers for the progression of coronary atherosclerosis in WHHLMI rabbits, an animal model of familial hypercholesterolemia

Shiomi, M., Takeda, H., Irino, Y., Kimura, N., Yamada, S., Kuniyoshi, N., Kikumori, A., Koike, Y., Koike, T., Yoshida, M., Izumi, Y., Shinohara, M., Bamba, T. & Ishida, T., May 1 2019, In : Atherosclerosis. 284, p. 18-23 6 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Identification of single-nucleotide polymorphisms in the human N-methyl-D-aspartate receptor subunit NR2D gene, GRIN2D, and association study with schizophrenia

Makino, C., Shibata, H., Ninomiya, H., Tashiro, N. & Fukumaki, Y., Sep 1 2005, In : Psychiatric Genetics. 15, 3, p. 215-221 7 p.

Research output: Contribution to journalArticle

21 Citations (Scopus)

Identification of the physiological substrates of PDIp, a pancreas-specific protein-disulfide isomerase family member

Fujimoto, T., Nakamura, O., Saito, M., Tsuru, A., Matsumoto, M., Kohno, K., Inaba, K. & Kadokura, H., Nov 30 2018, In : Journal of Biological Chemistry. 293, 48, p. 18421-18433 13 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Identifying metabolic elements that contribute to productivity of 1-propanol bioproduction using metabolomic analysis

Putri, S. P., Nakayama, Y., Shen, C., Noguchi, S., Nitta, K., Bamba, T., Pontrelli, S., Liao, J. & Fukusaki, E., Jul 1 2018, In : Metabolomics. 14, 7, 96.

Research output: Contribution to journalArticle

29 Citations (Scopus)

Improved quantitation of lipid classes using supercritical fluid chromatography with a charged aerosol detector

Takeda, H., Takahashi, M., Hara, T., Izumi, Y. & Bamba, T., Jan 1 2019, In : Journal of Lipid Research. 60, 8, p. 1465-1474 10 p.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)

Incorporation of histone H3.1 suppresses the lineage potential of skeletal muscle

Harada, A., Maehara, K., Sato, Y., Konno, D., Tachibana, T., Kimura, H. & Ohkawa, Y., Jan 30 2015, In : Nucleic acids research. 43, 2, p. 775-786 12 p.

Research output: Contribution to journalArticle

23 Citations (Scopus)

Increased dynamics of tricarboxylic acid cycle and glutamate synthesis in obese adipose tissue: In vivo metabolic turnover analysis

Nagao, H., Nishizawa, H., Bamba, T., Nakayama, Y., Isozumi, N., Nagamori, S., Kanai, Y., Tanaka, Y., Kita, S., Fukuda, S., Funahashi, T., Maeda, N., Fukusaki, E. & Shimomura, I., Mar 17 2017, In : Journal of Biological Chemistry. 292, 11, p. 4469-4483 15 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)

Increase in hepatic and decrease in peripheral insulin clearance characterize abnormal temporal patterns of serum insulin in diabetic subjects

Ohashi, K., Fujii, M., Uda, S., Kubota, H., Komada, H., Sakaguchi, K., Ogawa, W. & Kuroda, S., 2018, In : npj Systems Biology and Applications. 4, 14.

Research output: Contribution to journalArticle

Open Access

Increase in hepatic and decrease in peripheral insulin clearance characterize abnormal temporal patterns of serum insulin in diabetic subjects

Ohashi, K., Fujii, M., Uda, S., Kubota, H., Komada, H., Sakaguchi, K., Ogawa, W. & Kuroda, S., Dec 1 2018, In : npj Systems Biology and Applications. 4, 1, 14.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA

Osakabe, A., Adachi, F., Arimura, Y., Maehara, K., Ohkawa, Y. & Kurumizaka, H., Oct 7 2015, In : Open Biology. 5, 10, 150128.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Influence of yeast and lactic acid bacterium on the constituent profile of soy sauce during fermentation

Harada, R., Yuzuki, M., Ito, K., Shiga, K., Bamba, T. & Fukusaki, E., Feb 1 2017, In : Journal of Bioscience and Bioengineering. 123, 2, p. 203-208 6 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)

Inhibition of the Arabidopsis bHLH transcription factor by monomerization through abscisic acid-induced phosphorylation

Takahashi, Y., Kinoshita, T., Matsumoto, M. & Shimazaki, K. I., Sep 1 2016, In : The Plant journal : for cell and molecular biology. 87, 6, p. 559-567 9 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

Initial genome-wide scan for linkage with schizophrenia in the Japanese Schizophrenia Sib-pair Linkage Group (JSSLG) families

Arinami, T., Ishiguro, H., Minowa, Y., Ohtsuki, T., Tsujita, T., Imamura, A., Yoshikawa, T., Toyota, T., Yamada, K., Shimizu, H., Yoshitsugu, K., Shibata, H., Fujii, Y., Fukumaki, Y., Tashiro, N., Inada, T., Iijima, Y., Kitao, Y., Furuno, T., Someya, T. & 37 others, Muratake, T., Kaneko, N., Tsuji, S., Mineta, M., Takeichi, M., Ujike, H., Takehisa, Y., Tanaka, Y., Nakata, K., Kitajima, T., Nishiyama, T., Yamanouchi, Y., Iwata, N., Ozaki, N., Ohara, K., Shibuya, H., Suzuki, Y., Ohmori, O., Shinkai, T., Hori, H., Nakamura, J., Kojima, T., Takahashi, S., Tanabe, E., Yara, K., Nanko, S., Yoneda, H., Koh, J., Sakai, J., Inada, Y., Kusumi, I., Kameda, K., Koyama, T., Fukuzako, H., Hashiguchi, T., Tanabe, K. & Okazaki, Y., Jul 1 2003, In : American Journal of Medical Genetics - Neuropsychiatric Genetics. 120 B, 1, p. 22-28 7 p.

Research output: Contribution to journalArticle

18 Citations (Scopus)

In-Line Sample Processing System with an Immobilized Trypsin-Packed Fused-Silica Capillary Tube for the Proteomic Analysis of a Small Number of Mammalian Cells

Hata, K., Izumi, Y., Hara, T., Matsumoto, M. & Bamba, T., Feb 18 2020, In : Analytical chemistry. 92, 4, p. 2997-3005 9 p.

Research output: Contribution to journalArticle

Insights into the formation mechanism of chloropropanol fatty acid esters under laboratory-scale deodorization conditions

Hori, K., Hori-Koriyama, N., Tsumura, K., Fukusaki, E. & Bamba, T., Aug 1 2016, In : Journal of Bioscience and Bioengineering. 122, 2, p. 246-251 6 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Insulin-like growth factor 1 receptor stabilizes the ETV6-NTRK3 chimeric oncoprotein by blocking its KPC1/Rnf123-mediated proteasomal degradation

Tognon, C. E., Rafn, B., Cetinbas, N. M., Kamura, T., Trigo, G., Rotblat, B., Okumura, F., Matsumoto, M., Chow, C., Davare, M., Pollak, M., Mayor, T. & Sorensen, P. H., Aug 10 2018, In : Journal of Biological Chemistry. 293, 32, p. 12502-12515 14 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)
101 Citations (Scopus)

Interaction of U-box-type ubiquitin-protein ligases (E3s) with molecular chaperones

Hatakeyama, S., Matsumoto, M., Yada, M. & Nakayama, K., Jun 1 2004, In : Genes to Cells. 9, 6, p. 533-548 16 p.

Research output: Contribution to journalArticle

70 Citations (Scopus)

Inter-laboratory comparison of metabolite measurements for metabolomics data integration

Izumi, Y., Matsuda, F., Hirayama, A., Ikeda, K., Kita, Y., Horie, K., Saigusa, D., Saito, K., Sawada, Y., Nakanishi, H., Okahashi, N., Takahashi, M., Nakao, M., Hata, K., Hoshi, Y., Morihara, M., Tanabe, K., Bamba, T. & Oda, Y., Nov 2019, In : Metabolites. 9, 11, 257.

Research output: Contribution to journalArticle

Open Access

Interleukin-10-producing plasmablasts exert regulatory function in autoimmune inflammation

Matsumoto, M., Baba, A., Yokota, T., Nishikawa, H., Ohkawa, Y., Kayama, H., Kallies, A., Nutt, S. L., Sakaguchi, S., Takeda, K., Kurosaki, T. & Baba, Y., Dec 18 2014, In : Immunity. 41, 6, p. 1040-1051 12 p.

Research output: Contribution to journalArticle

216 Citations (Scopus)

Intracellular metabolite β-glucosylceramide is an endogenous Mincle ligand possessing immunostimulatory activity

Nagata, M., Izumi, Y., Ishikawa, E., Kiyotake, R., Doi, R., Iwai, S., Omahdi, Z., Yamaji, T., Miyamoto, T., Bamba, T. & Yamasaki, S., Apr 18 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 16, p. E3285-E3294

Research output: Contribution to journalArticle

39 Citations (Scopus)

Intronic variant in IQGAP3 associated with hereditary neuropathy with proximal lower dominancy, urinary disturbance, and paroxysmal dry cough

Miura, S., Kosaka, K., Shimojo, T., Matsuura, E., Noda, K., Fujioka, R., Mori, S. I., Umehara, F., Iwaki, T., Yamamoto, K., Saitsu, H. & Shibata, H., Jan 1 2020, (Accepted/In press) In : Journal of Human Genetics.

Research output: Contribution to journalArticle

In vitro steroid profiling system for the evaluation of endocrine disruptors

Nakano, Y., Yamashita, T., Okuno, M., Fukusaki, E. & Bamba, T., Sep 1 2016, In : Journal of Bioscience and Bioengineering. 122, 3, p. 370-377 8 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

In Vivo Decoding Mechanisms of the Temporal Patterns of Blood Insulin by the Insulin-AKT Pathway in the Liver

Kubota, H., Uda, S., Matsuzaki, F., Yamauchi, Y. & Kuroda, S., Jul 25 2018, In : Cell Systems. 7, 1, p. 118-128.e3

Research output: Contribution to journalArticle

5 Citations (Scopus)

Isolation and characterization of Fetal Leydig progenitor cells of male mice

Inoue, M., Shima, Y., Miyabayashi, K., Tokunaga, K., Sato, T., Baba, T., Ohkawa, Y., Akiyama, H., Suyama, M. & Morohashi, K. I., Mar 2016, In : Endocrinology. 157, 3, p. 1222-1233 12 p.

Research output: Contribution to journalArticle

22 Citations (Scopus)

JPOSTrepo: An international standard data repository for proteomes

Okuda, S., Watanabe, Y., Moriya, Y., Kawano, S., Yamamoto, T., Matsumoto, M., Takami, T., Kobayashi, D., Araki, N., Yoshizawa, A. C., Tabata, T., Sugiyama, N., Goto, S. & Ishihama, Y., Jan 1 2017, In : Nucleic acids research. 45, D1, p. D1107-D1111

Research output: Contribution to journalArticle

90 Citations (Scopus)

Kupffer cells induce Notch-mediated hepatocyte conversion in a common mouse model of intrahepatic cholangiocarcinoma

Terada, M., Horisawa, K., Miura, S., Takashima, Y., Ohkawa, Y., Sekiya, S., Matsuda-Ito, K. & Suzuki, A., Oct 4 2016, In : Scientific reports. 6, 34691.

Research output: Contribution to journalArticle

9 Citations (Scopus)

Laguerre filter analysis with partial least square regression reveals a priming effect of ERK and CREB on c-FOS induction

Kudo, T., Uda, S., Tsuchiya, T., Wada, T., Karasawa, Y., Fujii, M., Saito, T. H. & Kuroda, S., Aug 2016, In : PloS one. 11, 8, e0160548.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Large-scale analysis of the human ubiquitin-related proteome

Matsumoto, M., Hatakeyama, S., Oyamada, K., Oda, Y., Nishimura, T. & Nakayama, K. I., Nov 1 2005, In : Proteomics. 5, 16, p. 4145-4151 7 p.

Research output: Contribution to journalArticle

146 Citations (Scopus)

Large-scale proteomic analysis of tyrosine-phosphorylation induced by T-cell receptor or B-cell receptor activation reveals new signaling pathways

Matsumoto, M., Oyamada, K., Takahashi, H., Sato, T., Hatakeyama, S. & Nakayama, K., Jul 1 2009, In : Proteomics. 9, 13, p. 3549-3563 15 p.

Research output: Contribution to journalArticle

43 Citations (Scopus)

Latent process genes for cell differentiation are common decoders of neurite extension length

Watanabe, K., Akimoto, Y., Yugi, K., Uda, S., Chung, J., Nakamuta, S., Kaibuchi, K. & Kuroda, S., May 1 2012, In : Journal of cell science. 125, 9, p. 2198-2211 14 p.

Research output: Contribution to journalArticle

18 Citations (Scopus)

LATS2 positively regulates polycomb repressive complex 2

Torigata, K., Daisuke, O., Mukai, S., Hatanaka, A., Ohka, F., Motooka, D., Nakamura, S., Ohkawa, Y., Yabuta, N., Kondo, Y. & Nojima, H., Jul 1 2016, In : PloS one. 11, 7, e0158562.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Lipidomic analysis of cells and extracellular vesicles from high-and low-metastatic triple-negative breast cancer

Nishida-Aoki, N., Izumi, Y., Takeda, H., Takahashi, M., Ochiya, T. & Bamba, T., Feb 2020, In : Metabolites. 10, 2, 67.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

Lipidomic analysis of plasma lipoprotein fractions in myocardial infarction-prone rabbits

Takeda, H., Koike, T., Izumi, Y., Yamada, T., Yoshida, M., Shiomi, M., Fukusaki, E. & Bamba, T., Oct 1 2015, In : Journal of Bioscience and Bioengineering. 120, 4, p. 476-482 7 p.

Research output: Contribution to journalArticle

20 Citations (Scopus)

Lipid Profiling of Serum and Lipoprotein Fractions in Response to Pitavastatin Using an Animal Model of Familial Hypercholesterolemia

Takeda, H., Izumi, Y., Tamura, S., Koike, T., Koike, Y., Shiomi, M. & Bamba, T., Mar 6 2020, In : Journal of Proteome Research. 19, 3, p. 1100-1108 9 p.

Research output: Contribution to journalArticle

Lipophagy maintains energy homeostasis in the kidney proximal tubule during prolonged starvation

Minami, S., Yamamoto, T., Takabatake, Y., Takahashi, A., Namba, T., Matsuda, J., Kimura, T., Kaimori, J. Y., Matsui, I., Hamano, T., Takeda, H., Takahashi, M., Izumi, Y., Bamba, T., Matsusaka, T., Niimura, F. & Isaka, Y., Oct 3 2017, In : Autophagy. 13, 10, p. 1629-1647 19 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)