Publications

*:corresponding author, #:equal contribution

Original Articles

1. Koike H*, Sugimura M, Ouchi R, Yoshimoto Y, Manabe I, Oishi Y*. Macrophage subpopulation promotes skeletal muscle regeneration through HGF/MET signaling-mediated skeletal muscle stem cell proliferation. Aging Cell. 24 (6): e70042. 2025. https://doi.org/10.1111/acel.70042

2. Honda A, Koike H, Dohi T, Toyohara E, Hayakawa S, Tobe K, Manabe I, Ogawa R, Oishi Y*. CD206+ macrophages facilitate wound healing through interactions with Gpnmbhi fibroblasts. EMBO Rep. 26 (14): pp.3679-3704. 2025. https://doi.org/10.1038/s44319-025-00496-4

3. Oishi Y*,#, Koike H# (#:co-first authors), Kumagami N#, Nakagawa Y, Araki M, Taketomi Y, Miki Y, Matsuda S, Kim H, Matsuzaka T, Ozawa H, Shimano H, Murakami M, Manabe I. Macrophage SREBP1 regulates skeletal muscle regeneration. Front. Immunol. 14: 1251784. 2024. https://doi.org/10.3389/fimmu.2023.1251784

4. Otomo K, Omura T, Nozawa Y, Edwards SJ, Sato Y, Saito Y, Yagishita S, Uchida H, Watakabe Y, Naitou K, Yanai R, Sahara N, Takagi S, Katayama R, Iwata Y, Shiokawa T, Hayakawa Y, Otsuka K, Watanabe-Takano H, Haneda Y, Fukuhara S, Fujiwara M, Nii T, Meno C, Takeshita N, Yashiro K, Rosales Rocabado JM, Kaku M, Yamada T, Oishi Y, Koike H, Cheng Y, Sekine K, Koga JI, Sugiyama K, Kimura K, Karube F, Kim H, Manabe I, Nemoto T, Tainaka K, Hamada A, Brismar H, Susaki EA*. descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques. Nat. Commun. 15 (1): 4941. 2024. https://doi.org/10.1038/s41467-024-49131-1

5. Watanabe A, Koike H*, Kumagami N, Shimba S, Manabe I, Oishi Y*. Arntl deficiency in myeloid cells reduces neutrophil recruitment and delays skeletal muscle repair. Sci. Rep. 13 (1): 6747. 2023. https://doi.org/10.1038/s41598-023-33830-8

6. Matsuzaki T*, Kawano Y, Horikiri M, Shimokawa Y, Yamazaki T, Okuma N, Koike H, Kimura M, Kawamura R, Yoneyama Y, Furuichi Y, Hakuno F, Takahashi S, Nakabayashi S, Okamoto S, Nakauchi H, Taniguchi H, Takebe T*, Yoshikawa HY*. Preparation of mechanically patterned hydrogels for controlling the self-condensation of cells. STAR Protoc. 4 (3): 102471. 2023. https://doi.org/10.1016/j.xpro.2023.102471

7. Yuzawa R, Koike H, Manabe I, Oishi Y*. VDR regulates simulated microgravity-induced atrophy in C2C12 myotubes. Sci. Rep. 12 (1): 1377. 2022. https://doi.org/10.1038/s41598-022-05354-0

8. Matsuzaki T*, Shimokawa Y, Koike H, Kimura M, Kawano Y, Okuma N, Kawamura R, Yoneyama Y, Furuichi Y, Hakuno F, Takahashi S, Nakabayashi S, Okamoto S, Nakauchi H, Taniguchi H, Takebe T*, Yoshikawa HY*. Mechanical guidance of self-condensation patterns of differentiating progeny. iScience. 25 (10): 105109, 2022. https://doi.org/10.1016/j.isci.2022.105109

9. Hayakawa S, Tamura A, Nikiforov N, Koike H, Kudo F, Cheng Y, Miyazaki T, Kubekina M, Kirichenko TV, Orekhov AN, Yui N, Manabe I*, Oishi Y*. JCI Insight. 7 (22): e138539. 2022. https://doi.org/10.1172/jci.insight.138539

10. Koike H, Iwasawa K, Ouchi R, Maezawa M, Kimura M, Kodaka A, Nishii S, Thompson WL, Takebe T*, Engineering human hepato-biliary-pancreatic organoids from pluripotent stem cells. Nat. Protoc. 16 (2): pp.919-936, 2021. https://doi.org/10.1038/s41596-020-00441-w

11. Liu L, Koike H, Ono T, Hayashi S, Kudo F, Kaneda A, Kagechika H, Manabe I, Nakashima T, Oishi Y*. Identification of a novel KLF5-dependent program and drug development for skeletal muscle atrophy. Proc. Natl. Acad. Sci. U.S.A. 118 (35): e2102895118, 2021. https://doi.org/10.1073/pnas.2102895118

12. Shinozawa T, Kimura M, Cai Y, Saiki N, Yoneyama Y, Ouchi R, Koike H, Maezawa M, Zhang RR, Dunn A, Ferguson A, Togo S, Lewis K, Thompson W, Asai A, Takebe T*, High-Fidelity Drug Induced Liver Injury Screen Using Human PSC-derived Organoids. Gastroenterology. 160 (3): pp.831-846, 2021. https://doi.org/10.1053/j.gastro.2020.10.002

13. Han L#, Chaturvedi P#, Kishimoto K#, Koike H# (#:co-first authors), Nasr T, Iwasawa K, Giesbrecht K, Witcher PC, Eicher A, Haines L, Lee Y, Shannon JM, Morimoto M, Wells JM, Takebe T, Zorn AM*, Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis. Nat. Commun. 11 (1): 4158, 2020. https://doi.org/10.1038/s41467-020-17968-x

14. Koike H, Iwasawa K, Ouchi R, Maezawa M, Giesbrecht K, Saiki N, Ferguson A, Kimura M, Thompson WL, Wells JM, Zorn AM, Takebe T*, Modeling human hepato-biliary-pancreatic organogenesis from the foregut-midgut boundary, Nature, 574 (7776): pp.112-116, 2019. https://doi.org/10.1038/s41586-019-1598-0

15. Ouchi R, Togo S, Kimura M, Shinozawa T, Koido M, Koike H, Thompson W, Karns RA, Mayhew CN, McGrath PS, McCauley HA, Zhang RR, Lewis K, Hakozaki S, Ferguson A, Saiki N, Yoneyama Y, Takeuchi I, Mabuchi Y, Akazawa C, Yoshikawa HY, Wells JM, Takebe T*. Modeling Steatohepatitis in Humans with Pluripotent Stem Cell-Derived Organoids. Cell Metab. 30 (2): pp.374-384, 2019. https://doi.org/10.1016/j.cmet.2019.05.007

16. Ong J, Serra MP, Segal J, Cujba AM, Ng SS, Butler R, Millar V, Hatch S, Zimri S, Koike H, Chan K, Bonham A, Walk M, Voss T, Heaton N, Mitry R, Dhawan A, Ebner D, Danovi D, Nakauchi H, Rashid ST*. Imaging-Based Screen Identifies Laminin 411 as a Physiologically Relevant Niche Factor with Importance for i-Hep Applications. Stem Cell Rep. 10 (3): pp.693-702, 2018. https://doi.org/10.1016/j.stemcr.2018.01.025

17. Koike H, Zhang RR, Ueno Y, Sekine K, Zheng YW, Takebe T*, Taniguchi H*. Nutritional modulation of mouse and human liver bud growth through a branched-amino acid metabolism. Development. 144 (6): pp.1018-1024, 2017. https://doi.org/10.1242/dev.143032

18. Takebe T*, Enomura M, Yoshizawa E, Kimura M, Koike H, Ueno Y, Matsuzaki T, Yamazaki T, Toyohara T, Osafune K, Nakauchi H, Yoshikawa HY*, Taniguchi H. Vascularized and complex organ buds from diverse tissues via mesenchymal cell-driven condensation. Cell Stem Cell. 16 (5): pp.556-565, 2015. https://doi.org/10.1016/j.stem.2015.03.004

19. Koike H, Ueno Y, Naito T, Shiina T, Nakata S, Ouchi R, Obana Y, Sekine K, Zheng YW, Takebe T, Isono K, Koseki H, Taniguchi H*, Ring1B Promotes Hepatic Stem/Progenitor Cell Expansion by Simultaneous Repression of Cdkn1a and Cdkn2a, Hepatology. 60 (1): pp.323-333, 2014. https://doi.org/10.1002/hep.27046

20. Koike H, Ouchi R, Ueno Y, Nakata S, Obana Y, Sekine K, Zheng YW, Takebe T, Isono K, Koseki H, Taniguchi H*. Polycomb group protein Ezh2 regulates hepatic progenitor cell proliferation and differentiation in murine embryonic liver. PLoS One. 9 (8): e104776. 2014. https://doi.org/10.1371/journal.pone.0104776

21. Takebe T*, Zhang R#, Koike H# (#:co-second authors), Kimura M, Yoshizawa E, Enomura M, Sekine K, Taniguchi H*, Generation of a vascularized and functional human liver from an iPSC-derived organ bud transplant. Nat. Protoc. 9 (2): pp.396-409. 2014. https://doi.org/10.1038/nprot.2014.020

22. Zhang R, Takebe T*, Sekine K, Koike H, Zheng YW, Taniguchi H*. Identification of proliferating human hepatic cells from human induced pluripotent stem cells. Transplant. proc. 46 (4): pp.1201-1204. 2014. https://doi.org/10.1016/j.transproceed.2013.12.021

23. Zhang R, Takebe T*, Miyazaki L, Takayama M, Koike H, Kimura M, Enomura M, Zheng YW, Sekine K, Taniguchi H, Efficient Hepatic Differentiation of Human Induced Pluripotent Stem Cells in a Three-Dimensional Microscale Culture, Methods Mol. Biol. 1210: pp.131-141, 2014. https://doi.org/10.1007/978-1-4939-1435-7_10

24. Takebe T*, Sekine K, Enomura M, Koike H, Kimura M, Ogaeri T, Zhang RR, Ueno Y, Zheng YW, Koike N, Aoyama S, Adachi Y, Taniguchi H*. Vascularized and functional human liver from an iPSC-derived organ bud transplant. Nature. 499 (7459): pp.481-484, 2013. https://doi.org/10.1038/nature12271

25. Koike H, Kubota K, Sekine K, Takebe T, Ouchi R, Zheng YW, Ueno Y, Tanigawa N, Taniguchi H*, Establishment of automated culture system for murine induced pluripotent stem cells. BMC biotechnol. 12: 81, 2012. https://doi.org/10.1186/1472-6750-12-81

Review Articles

1. Ouchi R*, Koike H*. Modeling human liver organ development and diseases with pluripotent stem cell-derived organoids. Front. Cell Dev. Biol. 11: 1133534 , 2023. https://doi.org/10.3389/fcell.2023.1133534

2. Koike H, Manabe I, Oishi Y*. Mechanisms of cooperative cell-cell interactions in skeletal muscle regeneration. Inflamm. Regen. 42 (1): 48, 2022. https://doi.org/10.1186/s41232-022-00234-6

3. Koike H, Takebe T*, Generating Mini-Organs in Culture, Curr. Pathobiol. Rep. 4 (2): pp.59-68, 2016 https://doi.org/10.1007/s40139-016-0101-y

Review Articles in Japanese

1. 小池 博之, 大石 由美子. 骨格筋萎縮に対するビタミンA誘導体の機能評価. 実験医学. 40 (7): pp.1027-1031, 2022

2. 小池 博之, 大石 由美子. 骨格筋組織再生を対象としたシングルセルRNA-seq解析. 医学のあゆみ. 276 (5): pp.443-447, 2021

3. 小池 博之, 武部 貴則. 多能性幹細胞を用いたヒト肝・胆・膵システムの一括創出. 実験医学. 38 (4): pp.590-593, 2020

4. 小池 博之, 武部 貴則. 臓器の芽を創出する革新的な培養手法を確立. 自動車技術, 69 (11): pp.108-109, 2015

5. 大崎 達哉, 福田 淳二, 小池 博之, 武部 貴則. ヒトiPS細胞を用いた複雑臓器の成形加工と移植医療への応用. 実験医学. 33 (8): pp.1259-1265, 2015

6. 谷口 英樹, 小池 博之. 膵がんにおけるがん幹細胞の特性解析. 実験医学. 29 (20): pp.3254-3261, 2011

7. 小池 博之, 中田 晋, 谷口 英樹. 膵癌. 臨床検査. 55 (5): pp.495-499, 2011. https://doi.org/10.11477/mf.1542102623