Publications

(*corresponding author)

Original paper

2024

Cui, M., Yamano, K., Yamamoto, K., Yamamoto-Imoto, H., Minami, S., Yamamoto, T., Matsui, S., Kaminishi, T., Shima, T., Ogura, M., Tsuchiya, M., Nishino, K., Layden, B., Kato, H., Ogawa, H., Oki, S., Okada, Y., Isaka, Y., Kosako, H., Matsuda, N., *Yoshimori, T., *Nakamura, S. HKDC1, a target of TFEB, is essential to maintain both mitochondrial and lysosomal homeostasis, preventing cellular senescence. PNAS 121(2), (2024)
Kakuda, K., *Ikenaka, K., Kuma, A., Doi, J., Aguirre, C., Wang, N., Ajiki, T., Choong, C., Kimura, Y., Mohamed, S., Badawy, M., Shima, T., Nakamura, S, Baba, K., Nagano, S., Nagai, Y., Yoshimori, T., *Mochizuki, H. Lysophagy protects against propagation of α-synuclein aggregation through ruptured lysosomal vesicles. PNAS 121(1), (2024)

2023

Ogura, M., Kaminishi, T., Shima, T., Torigata, M., Bekku, N., Tabata, K., Minami, S., Nishino, K., Nezu, A., Hamasaki, M., Kosako, H., *Yoshimori, T., *Nakamura, S. Microautophagy regulated by STK38 and GABARAPs is essential to repair lysosomes and prevent aging. EMBO Rep., e57300, (2023).
Shima, T., Ogura, M., Matsuda, R., Nakamura, S., Jin, N., *Yoshimori, T., *Kuma, A. The TMEM192-mKeima probe specifically assays lysophagy and reveals its initial steps. J. Cell Biol., 222 (12): e202204048, (2023).
*Tsai, CY., Sakakibara, S., Kuan, YD., Omori, H., El Hussien, MA., Okuzaki, D., Lu, SL., Noda, T., Tabata, K., Nakamura, S., Yoshimori, T., Kikutani, H. Opposing roles of RUBCN isoforms in autophagy and memory B cell generation. Sci Signal., 16(803):eade3599, (2023).
Shioda, T., Ikenaka, K., Fujita, N., Kanki, T., Oka, T., Mochizuki, H., Antebi, A., *Yoshimori, T., *Nakamura, S. Neuronal MML-1/MXL-2 regulates systemic aging via glutamate transporter and cell non-autonomous autophagic and peroxidase activity. PNAS., 120, e2221553120, (2023).
Debès, C., Papadakis, A., Grönke, S., Karalay, Ö., Tain, LS., Mizi, A., Nakamura, S., Hahn, O., Weigelt, C., Josipovic, N., Zirkel, A., Brusius, I., Sofiadis, K., Lamprousi, M., Lu, YX., Huang, W., Esmaillie, R., Kubacki, T., Späth, MR., Schermer, B., Benzing, T., Müller, RU., *Antebi, A., *Partridge, L., *Papantonis, A., *Beyer, A. Ageing-associated changes in transcriptional elongation influence longevity. Nature 616, 814–821 (2023).
Nakamura, J., Yamamoto, T., Takabatake, Y., Namba-Hamano, T., Minami, S., Takahashi, A., Matsuda, J., Sakai, S., Yonishi, H., Maeda, S., Matsui, S., Matsui, I., Hamano, T., Takahashi, M., Goto, M., Izumi, Y., Bamba, T., Sasai, M., Yamamoto, M., Matsusaka, T., Niimura, F., Yanagita, M., Nakamura, S., Yoshimori, T., Ballabio, A., Isaka, Y. TFEB-mediated lysosomal exocytosis alleviates high-fat diet-induced lipotoxicity in the kidney. JCI Insight 22;8(4):e162498. (2023)
Tsujimoto, K., Jo, T., Nagira, D., Konaka, H., Park, JH., Yoshimura SI., Ninomiya, A., Sugihara, F., Hirayama, T., Itotagawa, E., Matsuzaki, Y., Takaichi, Y., Aoki, W., Saita, S., Nakamura, S., Ballabio, A., Nada, S., Okada, M., Takamatsu, H., Kumanogoh, A. The lysosomal Ragulator complex activates NLRP3 inflammasome in vivo via HDAC6. EMBO J., 4;42(1):e111389. (2023)

2022

Oe, Y., Kakuda, K., Yoshimura, S., Hara, N., Hasegawa, J., Terawaki, S., Kimura, Y., Ikenaka, K., Suetsugu, S., Mochizuki, H., *Yoshimori, T., *Nakamura, S. PACSIN1 is indispensable for amphisome-lysosome fusion during basal autophagy and subsets of selective autophagy. PLoS Genet., 18(6), e1010264, (2022)
Yamamoto-Imoto, H., Minami, S., Shioda, T., Yamashita, Y., Sakai, S., Maeda, S., Yamamoto, T., Oki, S., Takashima, M., Yamamuro, T., Yanagawa, K., Edahiro, R., Iwatani, M., So, M., Tokumura, A., Abe, T., Imamura, R., Nonomura, N., Okada, Y., Ayer, E D., Ogawa, H., Hara, E., Takabatake, Y., Isaka, Y., *Nakamura, S., *Yoshimori, T. Age-associated decline of MondoA drives cellular senescence through impaired autophagy and mitochondrial homeostasis. Cell Rep., 38(9): 110444, (2022)
Yamamuro, T., *Nakamura, S., Yanagawa, K., Tokumura, A., Kawabata, T., Fukuhara, A., Teranishi, H., Hamasaki, M., Shimomura, I., *Yoshimori, T. Loss of Rubicon in adipocytes mediates the upregulation of autophagy to promote the fasting response. Autophagy,14: 1-11, (2022)
Jia, X., Knyazeva, A., Zhang, Y., Castro-Gonzalez, S., Nakamura, S., Carlson, L.A., Yoshimori, T., Corkery, D.P., Wu, YW. V. cholerae MakA is a cholesterol-binding pore-forming toxin that induces non-canonical autophagy. J Cell Biol., 221, e202206040, (2022)
Yoshida, G., Kawabata, T., Takamatsu, H., Saita, S., Nakamura, S., Nishikawa, K., Fujiwara, M., Enokidani, Y., Yamamuro, T., Tabata, K., Hamasaki, M., Ishii, M., Kumanogoh, A., *Yoshimori, T. Degradation of the NOTCH intracellular domain by elevated autophagy in osteoblasts promotes osteoblast differentiation and alleviates osteoporosis. Autophagy, 13: 1-10 (2022)

2021

Yamamuro, T., *Nakamura, S., Yamano, Y., Endo, T., Yanagawa, K., Tokumura, A., Matsumura, T., Kobayashi, K., Mori, H., Enokidani, Y., Yoshida, G., Imoto, H., Kawabata, T., Hamasaki, M., Kuma, A., Kuribayashi, S., Takezawa, K., Okada, Y., Ozawa, M., Fukuhara, S., Shinohara, T., Ikawa, M., *Yoshimori, T. Rubicon prevents autophagic degradation of GATA4 to promote Sertoli cell function. PLoS Genet., 17(8), e1009688, (2021)
Fujita, T., Kubo, S., Shioda, T., Tokumura, A., Minami, S., Tsuchiya, M., Isaka, Y., Ogawa, H., Hamasaki, M., Yu, L., *Yoshimori, T., *Nakamura, S. THOC4 regulates energy homeostasis by stabilizing TFEB mRNA during prolonged starvation. J. Cell Sci.,134(6): jcs248203, (2021)
Suzuki, N., Johmura, Y., Wang, T.W., Migita, T., Wu, W., Noguchi, R, Yamaguchi, K., Furukawa, Y., Nakamura, S., Miyoshi, I., Yoshimori, T., Ohta, T., Nakanishi, M. TP53/p53-FBXO22-TFEB controls basal autophagy to govern hormesis. Autophagy, 11, 1-18. (2021)

2020

*Nakamura, S., Shigeyama, S., Minami, S., Shima, T., Akayama, S., Matsuda, T., Esposito, A., Napolitano, G., Kuma, A., Namba-Hamano, T., Nakamura, J., Yamamoto, K., Sasai, M., Tokumura, A., Miyamoto, M., Oe, Y., Fujita, T., Terawaki, S., Takahashi, A., Hamasaki, M., Yamamoto, M., Okada, Y., Komatsu, M., Nagai, T., Takabatake, Y., Xu, H., Isaka, Y., Ballabio, A., *Yoshimori, T. LC3 lipidation is essential for TFEB activation during the lysosomal damage response to kidney injury. Nat. Cell Biol., 22(10): 1252-1263, (2020)
Choong, C.J., Okuno, T., Ikenaka, K., Baba, K., Hayakawa, H., Koike, M., Yokota, M., Doi, J., Kakuda, K., Takeuchi, T., Kuma, A., Nakamura, S., Nagai, Y., Nagano, S., Yoshimori, T., Mochizuki, H. Alternative mitochondrial quality control mediated by extracellular release. Autophagy, 10, 1-13, (2020)
Yamamuro, T., Kawabata, T., Fukuhara, A., Saita, S., Nakamura, S., Takeshita, H., Fujiwara, M., Enokidani, Y., Yoshida, G., Tabata, K., Hamasaki, M., Kuma, A., Yamamoto, K., *Shimomura, I. and *Yoshimori, T. Age-dependent loss of adipose Rubicon promotes metabolic disorders via excess autophagy. Nat. Commun., 11, 4150, (2020)
*Murase, D., Kusaka-Kikushima, A., Hachiya, A., Fullenkamp, Stepp, A., Imai, A., Ueno, M., Kawabata, K., Takahashi, Y., Hase, T., Ohuchi, A., Nakamura, S. and Yoshimori, T. Autophagy Declines with Premature Skin Aging resulting in Dynamic Alterations in Skin Pigmentation and Epidermal Differentiation. Int. J. Mol. Sci., 21, E5708, (2020)
Sakae, Y., Oikawa, A., Sugiura, Y. Mita, M. Nakamura, S., Nishimura, T., Suematsu, M. and *Tanaka, M. Starvation causes female to male sex reversal through lipid metabolism in the teleost fish, medaka (Olyzias latipes). Biol. Open, 9, bio050054, (2020)

2019

Nakamura, S., Oba, M, Suzuki M, Takahashi T, Yamamuro T, Fujiwara M, Ikenaka K, Minami M, Tabata N, Yamamoto, K., Kubo, S., Tokumura A., Akamatsu, K., Miyazaki, Y., Kawabata, T., Hamasaki, M., Fukui, K., Sango, K., Watanabe, Y., Takabatake, Y., Kitajima, S T., Okada, Y., Mochizuki, H., Isaka, Y., Antebi, A., *Yoshimori, T. Suppression of autophagic activity by Rubicon is a signature of aging. Nat Commun.,10(1): 847, (2019)
Chang, C., Young, LN., Morris, KL., von Bülow, S., Schöneberg, J., Yamamoto-Imoto, H., Oe, Y., Yamamoto, K., Nakamura, S., Stjepanovic G., Hummer G., Yoshimori T., *Hurley JH. Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics. Mol. Cell, 73, 339-353, (2019)

~2017

Tiku, V., Jain, C, Raz, Y., Nakamura, S., Heestand, B., Liu, W., Späth, M., Suchiman, H., Müller, R., Slagboom, E., Partridge, L. and *Antebi, A. Small nucleoli are a cellular hallmark of longevity. Nat. Commun., 8, 16308, (2017)
Sasai, M., Sakaguchi, N., Ma JS., Nakamura, S., Kawabata, T., Bando, H., Lee, Y., Saito, T., Akira, S., Iwasaki, A., Standley, M., Yoshimori, T. and *Yamamoto, M. Essential Role of GABARAPs in Interferon-Inducible GTPase-Mediated LC3-Independent Host Defense. Nat. Immunol., 18, 899-910, (2017)
Wang, D., Hou, L., Nakamura, S., Su, M., Li, F., Chen, W., Yan, Y., Green, CD., Chen, D., Zhang, H., Antebi, A. and *Han JJ. LIN-28 balances longevity and germline stem cell number in Caenorhabditis elegans through let-7/AKT/DAF-16 axis. Aging Cell, 16, 113-124, (2017)
Nakamura, S., Karalay, O., Jaeger, P, Horikawa, M., Nakamura, K., Latza, C., Klein, C., Templer, S., Dieterich, C., *Antebi, A. Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals. Nat Commun.,7: 10944, (2016)
Nishimura, T., Herpin, A., Kimura, T., Hara, I., Kawasaki, T., Nakamura, S., Yamamoto, Y., Saito, T, Yoshimura, J., Morishita, S., Tsukahara, T., Kobayashi, S., Naruse, K., Shigenobu, S., Sakai, N., Schartl, M., *Tanaka, M. Analysis of a novel gene, Sdgc, reveals sex chromosome-dependent differences of medaka germ cells prior to gonad formation. Development, 147(17): 3363-3369, (2014)
Horn, M., Geisen, C., Cermak, L., Becker, B., Nakamura, S., Klein, C., Pagano, M. and *Antebi, A. DRE-1/FBXO11-dependent degradation of BLMP-1/BLIMP-1 governs C. elegans developmental timing and maturation. Dev. Cell, 28, 697-710, (2014)
Nakamura, S., Watakabe, I., Nishimura, T., Picard, JY., Toyoda, A., Taniguchi, T., di Clemente, N. and *Tanaka, M. Hyperproliferation of mitotically active germ cells due to defective anti-Müllerian hormone signaling mediates sex reversal in medaka. Development, 139, 2283-2287, (2012)
Nakamura, S., Watakabe, I., Nishimura, T., Toyoda, A., Taniguchi, Y. and *Tanaka, M. Analysis of medaka sox9 orthologue reveals a conserved role in germ cell maintenance. PLoS One, 7, e29982, (2012)
Nakamura, S., Kobayashi, K., Nishimura, T., Higashijima, S. and *Tanaka, M. Identification of germline stem cells in the ovary of the teleost medaka. Science, 328, 1561-1563, (2010)
Herpin, A., Braasch, I., Kraeussling, M., Schmidt, C., Thoma, EC., Nakamura, S., Tanaka, M. and *Schartl, M. Transcriptional rewiring of the sex determining dmrt1 gene duplicate by transposable elements. PLoS Genet.,6, e1000844, (2010)
Nakamura, S., Kurokawa, H., Asakawa, S., Shimizu, N. and *Tanaka, M. Two distinct types of theca cells in the medaka gonad: germ cell-dependent maintenance of cyp19a1 expressing theca cells. Dev. Dyn., 238, 2652-2657, (2009)
Aoki, Y., Nakamura, S., Ishikawa, Y. and *Tanaka, M. Expression and syntenic analysis of four nanos genes in medaka. Zool. Sci., 26, 112-118, (2009)
Herpin, A., Nakamura, S., Wagner, T., Tanaka, M. and *Schartl, M. A highly conserved cis-regulatory motif directs differential gonadal synexpression of Dmrt1 transcripts during gonad development. Nucleic Acids Res., 37, 1510-1520, (2009)
Nakamura, S., Aoki, Y., Saito, D., Kuroki, Y., Fujiyama, A., Naruse, K. and *Tanaka, M. Sox9b/sox9a2-EGFP transgenic medaka reveals the morphological reorganization of the gonads and a common precursor of both the female and male supporting cells. Mol. Reprod. Dev., 75, 472-476, (2008)
Kurokawa, H., Saito, D., Nakamura, S., Katoh-Fukui, Y., Ohta, K., Baba,T., Morohashi K., and *Tanaka, M. Germ cells are essential for sexual dimorphism in the medaka gonad. Proc. Natl. Acad. Sci. USA, 104, 16958-16963, (2007)
Saito, D., Morinaga, C., Aoki, Y., Nakamura, S., Mitani, H., Furutani-Seiki, M., Kondoh, H. and *Tanaka, M. Proliferation of germ cells during gonadal sex differentiation in medaka: insights from germ cell depleted mutant zenzai. Dev. Biol., 310, 280-290, (2007)
Morinaga, C., Saito, D., Nakamura, S., Sasaki, T., Asakawa, S., Shimizu, N., Mitani, H., Furutani-Seiki, M., *Tanaka, M. and *Kondoh, H. The hotei mutation of medaka in the anti-Müllerian hormone receptor causes the dysregulation of germ cell and sexual development. Proc. Natl. Acad. Sci. USA, 104, 9691-9696, (2007)
Nakamura, S., Kobayashi, D., Aoki, Y., Yokoi, H., Ebe, Y., Wittbrodt, J and *Tanaka, M. Identification and lineage tracing of two population of somatic gonadal precursors in medaka embryos. Dev. Biol., 295, 678-688, (2006)
Kurokawa, H., Aoki, Y., Nakamura, S., Ebe, Y., Kobayashi, D and *Tanaka, M. Time-lapse analysis reveals different modes of primordial germ cell migration in the medaka Oryzias latipes. Develop. Growth Differ., 48, 209-221, (2006)

Review

Cuervo, AM., Elazar, Z., Evans, C., Ge, L., Hansen, M., Jäättelä, M., Liang, JRA., Loos, B., Mizushima, N., Simon, AK., Tooze, S., Yoshimori, T.,Nakamura, S.Next questions in autophagy, Nature Cell Biology (2024)
Makino, M.,*Nakamura, S. A novel probe to monitor lysosome-mitochondria contact sites opens up a new path to study neurodegenerative diseases, Cell Calcium., (2024)
*Nakamura, S., Shioda, T., *Yoshimori, T. Autophagy in aging and longevity (Chapter11), Aging Mechanism II: Longevity, Metabolism and Brain Aging (Springer) (2022)
Oe, Y., *Yoshimori, T., *Nakamura, S. Novel insights into the molecular mechanism of amphisome-lysosome fusion. Autophagy Reports, 1, 542-545, (2022)
Yamamoto-Imoto, H., Hara, E., *Nakamura, S., *Yoshimori, T. Measurement of autophagy via LC3 western blotting following DNA-damage-induced senescence. STAR Protoc., 3, 101539, (2022)
Cui, M., *Yoshimori, T., *Nakamura, S.Autophagy system as a potential therapeutic target for neurodegenerative diseases. Neurochem Int., 155, 105308, (2022)
*Nakamura, S., Akayama, S., *Yoshimori, T. Non-canonical roles of ATG8 for TFEB activation. Biochem Soc Trans., 50, 47-54, (2022)
Ogura, M., Shima, T., Yoshimori, T., *Nakamura, S. Protocols to monitor TFEB activation following lysosomal damage in cultured cells using microscopy and immunoblotting. STAR Protoc., 3, 101018, (2022)
Minami, S., *Nakamura, S., *Yoshimori, T. Rubicon in Metabolic Disease and Aging. Front. Cell Dev. Biol., 9, 816829, (2022)
Minami, S., *Nakamura, S. Therapeutic potential of Beclin1 for transition from AKI to CKD: autophagy-dependent and autophagy-independent functions. Kidney Int., 10, 13-15, (2022)
*Nakamura, S., Akayama, S., *Yoshimori, T. Autophagy-independent function of lipidated LC3 essential for TFEB activation during the lysosomal damage responses. Autophagy, 17, 581-583, (2021)
Nakamura, S. and *Yoshimori, T. Autophagy and Longevity. Mol. Cells., 41, 65-72, (2018)
Nakamura, S. and *Yoshimori, T. New insights into autophagosome-lysosome fusion. J. Cell Sci., 130, 1209-1216, (2017)
Martens, S., Nakamura, S. and *Yoshimori, T. Phospholipids in Autophagosome Formation and Fusion. J. Mol. Biol., 428, 4819-4827, (2016)
Nakamura, S., Hasegawa, J. and *Yoshimori, T. Regulation of lysosomal phosphoinositide balance by INPP5E is essential for autophagosome–lysosome fusion. Autophagy, 12, 2500-2501, (2016)
Nishimura, T., Nakamura, S. and *Tanaka, M. A Structurally and Functionally Common Unit in Testes and Ovaries of Medaka (Oryzias latipes), a Teleost Fish. Sex. Dev., 10, 159-165, (2016)
Nakamura, S., Kobayashi, K., Nishimura, T. and *Tanaka, M. Ovarian Germline Stem Cells in the Teleost Fish, Medaka (Oryzias latipes). Int. J. Biol. Sci., 7, 403-409, (2011)
Nakamura, S., Saito, D. and *Tanaka, M. Generation of transgenic medaka using modified bacterial artificial chromosome. Develop. Growth Differ., 50, 415-418, (2008)