Takebe Lab | Gastroenterology, Hepatology and Nutrition

Selected Publications

Yoneyama, Y; Zhang, RR; Maezawa, M; Masaki, H; Kimura, M; Cai, Y; Adam, M; Parameswaran, S; Mizuno, N; Bhadury, J; Nakauchi, H; Potter, SS; Weirauch, MT; Takebe, T. Intercellular mRNA transfer alters the human pluripotent stem cell state. Proceedings of the National Academy of Sciences of USA. 2025; 122:e2413351122.

Yoneyama, Y; Wu, Y; Mori, K; Takebe, T. In toto biological framework: Modeling interconnectedness during human development. Developmental Cell. 2025; 60:8-20.

Osonoi, S; Takebe, T. Organoid-guided precision hepatology for metabolic liver disease. Journal of Hepatology. 2024; 80:805-821.

Kawakami, E; Saiki, N; Yoneyama, Y; Moriya, C; Maezawa, M; Kawamura, S; Kinebuchi, A; Kono, T; Funata, M; Sakoda, A; Itoh, Y; Takayama, K; Nio, Y; Takebe, T. Complement factor D targeting protects endotheliopathy in organoid and monkey models of COVID-19. Cell Stem Cell. 2023; 30:1315-1330.e10.

Kimura, M; Iguchi, T; Iwasawa, K; Dunn, A; Thompson, WL; Yoneyama, Y; Chaturvedi, P; Zorn, AM; Wintzinger, M; Quattrocelli, M; Myers, RP; Subramanian, GM; Hwa, V; Takebe, T. En masse organoid phenotyping informs metabolic-associated genetic susceptibility to NASH. Cell. 2022; 185:4216-4232.e16.

Okabe, R; Chen-Yoshikawa, TF; Yoneyama, Y; Yokoyama, Y; Tanaka, S; Yoshizawa, A; Thompson, WL; Kannan, G; Kobayashi, E; Date, H; Takebe, T. Mammalian enteral ventilation ameliorates respiratory failure. Med. 2021; 2:773-783.e5.

Marsee, A; Roos, FJ M; Verstegen, MM A; Clevers, H; Vallier, L; Takebe, T; Huch, M; Peng, WC; Forbes, SJ; Lemaigre, F; Hu, H; Fuchs, S; Hendriks, D; van der Laan, LJ W. Building consensus on definition and nomenclature of hepatic, pancreatic, and biliary organoids. Cell Stem Cell. 2021; 28:816-832.

Shinozawa, T; Kimura, M; Cai, Y; Saiki, N; Yoneyama, Y; Ouchi, R; Koike, H; Maezawa, M; Zhang, RR; Dunn, A; Lewis, K; Thompson, WL; Asai, A; Takebe, T. High-Fidelity Drug-Induced Liver Injury Screen Using Human Pluripotent Stem Cell-Derived Organoids. Gastroenterology. 2021; 160:831-846.e10.

Han, L; Chaturvedi, P; Kishimoto, K; Koike, H; Nasr, T; Iwasawa, K; Giesbrecht, K; Witcher, PC; Eicher, A; Haines, L; Morimoto, M; Wells, JM; Takebe, T; Zorn, AM. Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis. Nature Communications. 2020; 11:4158.

Koido, M; Kawakami, E; Fukumura, J; Noguchi, Y; Ohori, M; Nio, Y; Nicoletti, P; Aithal, GP; Daly, AK; Watkins, PB; Anayama, H; Dragan, Y; Shinozawa, T; Takebe, T. Polygenic architecture informs potential vulnerability to drug-induced liver injury. Nature Medicine. 2020; 26:1541-1548.

Koike, H; Iwasawa, K; Ouchi, R; Maezawa, M; Giesbrecht, K; Saiki, N; Ferguson, A; Kimura, M; Thompson, WL; Wells, JM; Zorn, AM; Takebe, T. Modelling human hepato-biliary-pancreatic organogenesis from the foregut-midgut boundary. Nature. 2019; 574:112-116.

Ouchi, R; Togo, S; Kimura, M; Shinozawa, T; Koido, M; Koike, H; Thompson, W; Karns, RA; Mayhew, CN; McGrath, PS; Akazawa, C; Yoshikawa, HY; Wells, JM; Takebe, T. Modeling Steatohepatitis in Humans with Pluripotent Stem Cell-Derived Organoids. Cell Metabolism. 2019; 30:374-384.e6.

Takebe, T; Wells, JM. Organoids by design. Science. 2019; 364:956-959.

Takahashi, Y; Sekine, K; Kin, T; Takebe, T; Taniguchi, H. Self-Condensation Culture Enables Vascularization of Tissue Fragments for Efficient Therapeutic Transplantation. Cell Reports. 2018; 23:1620-1629.

Camp, JG; Sekine, K; Gerber, T; Loeffler-Wirth, H; Binder, H; Gac, M; Kanton, S; Kageyama, J; Damm, G; Seehofer, D; Ayabe, H; Taniguchi, H; Takebe, T; Treutlein, B. Multilineage communication regulates human liver bud development from pluripotency. Nature. 2017; 546:533-538.

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. 2015; 16:556-565.

Takebe, T; Sekine, K; Enomura, M; Koike, H; Kimura, M; Ogaeri, T; Zhang, R; Ueno, Y; Zheng, Y; Koike, N; Aoyama, S; Adachi, Y; Taniguchi, H. Vascularized and functional human liver from an iPSC-derived organ bud transplant. Nature. 2013; 499:481-484.

2025

Fukunaga, I; Takebe, T. In vitro liver models for toxicological research. Drug Metabolism and Pharmacokinetics. 2025; 62:101478.

Ashmore-Harris, C; Ayabe, H; Yoshizawa, E; Arisawa, T; Takada, Y; Takebe, T; Fruhwirth, GO. Gene editing enables non-invasive in vivo PET imaging of human induced pluripotent stem cell-derived liver bud organoids. Molecular Therapy-Methods & Clinical Development. 2025; 33:101406.

Jurickova, I; Dreskin, BW; Angerman, E; Bonkowski, E; Nguyen, J; Villarreal, R; Tominaga, K; Iwasawa, K; Braun, T; Takebe, T; Helmrath, MA; Haberman, Y; Wells, JM; Denson, LA. Eicosatetraynoic Acid Regulates Profibrotic Pathways in an Induced Pluripotent Stem Cell-Derived Macrophage-Human Intestinal Organoid Model of Crohn's Disease. Journal of Crohn's and Colitis. 2025; 19:jjae139.

Liu, YJ; Kimura, M; Li, X; Sulc, J; Wang, Q; Rodríguez-López, S; Scantlebery, AM L; Strotjohann, K; Gallart-Ayala, H; Vijayakumar, A; Houtkooper, RH; Subramanian, GM; Takebe, T; Auwerx, J. ACMSD inhibition corrects fibrosis, inflammation, and DNA damage in MASLD/MASH. Journal of Hepatology. 2025; 82:174-188.

Yoneyama, Y; Zhang, RR; Maezawa, M; Masaki, H; Kimura, M; Cai, Y; Adam, M; Parameswaran, S; Mizuno, N; Bhadury, J; Nakauchi, H; Potter, SS; Weirauch, MT; Takebe, T. Intercellular mRNA transfer alters the human pluripotent stem cell state. Proceedings of the National Academy of Sciences of USA. 2025; 122:e2413351122.

Murata, N; Nishii, S; Usuha, R; Kodaka, A; Fujimori, M; Sugawara, H; Kiriyama, T; Uchikado, H; Okumura, Y; Takebe, T. A Gamified N-back App for Identifying Mild-cognitive Impairment in Older Adults. 2025; 8:174-182.

Yoneyama, Y; Wu, Y; Mori, K; Takebe, T. In toto biological framework: Modeling interconnectedness during human development. Developmental Cell. 2025; 60:8-20.

Wu, Y; Pan, J; Kawamura, S; Oda, M; Hayashi, Y; Takebe, T; Rueckert, D; Mori, K. A Deployable Microscopic Image Segmentation Look-Up Table Based on A Dilated CNN. Medical Optical Imaging and Virtual Microscopy Image Analysis. : Springer Nature; Springer Nature; 2025.

Wu, Y; Menten, MJ; Kreitner, L; Kawamura, S; Oda, M; Hayashi, Y; Takebe, T; Rueckert, D; Mori, K. CLSMI2T3: 3D CLSM Vasculature Volume Reconstruction from A Single 2D Slice by Off-Focal Plane Signal Using Synthetic Data. Medical Optical Imaging and Virtual Microscopy Image Analysis. : Springer Nature; Springer Nature; 2025.

Tominaga, K; Kechele, DO; Sanchez, JG; Vales, S; Jurickova, I; Roman, L; Asai, A; Enriquez, JR; McCauley, HA; Kishimoto, K; Zorn, AM; Helmrath, MA; Denson, LA; Wells, JM. Deriving Human Intestinal Organoids with Functional Tissue-Resident Macrophages All From Pluripotent Stem Cells. CMGH Cellular and Molecular Gastroenterology and Hepatology. 2025; 19:101444.

2024

Lutolf, MP; Radisic, M; Beekman, J; Huh, DD; Huch, M; Turco, MY; Birgani, ZN T; Gao, D; Yao, R; Lin, H; Takebe, T. In vitro human cell-based models: What can they do and what are their limitations?. Trends in Biotechnology. 2024; 42:1577-1582.

Poling, HM; Sundaram, N; Fisher, GW; Singh, A; Shiley, JR; Nattamai, K; Govindarajah, V; Cortez, AR; Krutko, MO; Ménoret, S; Mayhew, CN; Takebe, T; Mahe, MM; Helmrath, MA. Human pluripotent stem cell-derived organoids repair damaged bowel in vivo. Cell Stem Cell. 2024; 31:1513-1523.e7.

Sheth, M; Sharma, M; Lehn, M; Reza, HA; Takebe, T; Takiar, V; Wise-Draper, T; Esfandiari, L. Three-dimensional matrix stiffness modulates mechanosensitive and phenotypic alterations in oral squamous cell carcinoma spheroids. APL Bioengineering. 2024; 8:036106.

Kang, SY; Kimura, M; Shrestha, S; Lewis, P; Lee, S; Cai, Y; Joshi, P; Acharya, P; Liu, J; Yang, Y; Alsberg, E; Wells, JM; Takebe, T; Lee, MY. A Pillar and Perfusion Plate Platform for Robust Human Organoid Culture and Analysis. Advanced healthcare materials. 2024; 13:e2302502.

Kimura, M; Takebe, T. Cellotype-phenotype associations using 'organoid villages'. Trends in Endocrinology and Metabolism. 2024; 35:462-465.

Nishimura, T; Takebe, T. Synthetic human gonadal tissues for toxicology. Reproductive Toxicology. 2024; 126:108598.

Osonoi, S; Takebe, T. Organoid-guided precision hepatology for metabolic liver disease. Journal of Hepatology. 2024; 80:805-821.

Naraoka, Y; Mabuchi, Y; Kiuchi, M; Kumagai, K; Hisamatsu, D; Yoneyama, Y; Takebe, T; Akazawa, C. Quality Control of Stem Cell-Based Cultured Meat According to Specific Differentiation Abilities. Cells. 2024; 13:135.

2023

Reza, HA; Farooqui, Z; Reza, AA; Conroy, C; Iwasawa, K; Ogura, Y; Okita, K; Osafune, K; Takebe, T. Synthetic augmentation of bilirubin metabolism in human pluripotent stem cell-derived liver organoids. Stem Cell Reports. 2023; 18:2071-2083.

Múnera, JO; Kechele, DO; Bouffi, C; Qu, N; Jing, R; Maity, P; Enriquez, JR; Han, L; Campbell, I; Mahe, MM; Hu, YC; Takebe, T; Helmrath, MA; Wells, JM. Development of functional resident macrophages in human pluripotent stem cell-derived colonic organoids and human fetal colon. Cell Stem Cell. 2023; 30:1434-1451.e9.

Kawakami, E; Saiki, N; Yoneyama, Y; Moriya, C; Maezawa, M; Kawamura, S; Kinebuchi, A; Kono, T; Funata, M; Sakoda, A; Itoh, Y; Takayama, K; Nio, Y; Takebe, T. Complement factor D targeting protects endotheliopathy in organoid and monkey models of COVID-19. Cell Stem Cell. 2023; 30:1315-1330.e10.

Matsuzaki, T; Kawano, Y; Horikiri, M; Shimokawa, Y; Yamazaki, T; Okuma, N; Koike, H; Kimura, M; Kawamura, R; Yoneyama, Y; Nakauchi, H; Taniguchi, H; Takebe, T; Yoshikawa, HY. Preparation of mechanically patterned hydrogels for controlling the self-condensation of cells. Star Protocols. 2023; 4:102471.

Tamaoki, N; Siebert, S; Maeda, T; Ha, NH; Good, ML; Huang, Y; Vodnala, SK; Haro-Mora, JJ; Uchida, N; Tisdale, JF; Robey, PG; Kruhlak, MJ; Restifo, NP; Vizcardo, R. Self-organized yolk sac-like organoids allow for scalable generation of multipotent hematopoietic progenitor cells from induced pluripotent stem cells. Cell Reports: Methods. 2023; 3:100460.

Wu, Y; Oda, M; Hayashi, Y; Kawamura, S; Takebe, T; Mori, K. (2023) Thrombosis region extraction and quantitative analysis in confocal laser scanning microscopic image sequence in in-vivo imaging. SPIE, the international society for optics and photonics. 12468:124680f-124680f-7.

Fujii, T; Yoneyama, Y; Kinebuchi, A; Ozeki, N; Maeda, S; Saiki, N; Chen-Yoshikawa, TF; Date, H; Nishiwaki, K; Takebe, T. Enteral liquid ventilation oxygenates a hypoxic pig model. iScience. 2023; 26:106142.

2022

Mizuno, M; Matsuzaki, T; Ozeki, N; Katano, H; Koga, H; Takebe, T; Yoshikawa, HY; Sekiya, I. Cell membrane fluidity and ROS resistance define DMSO tolerance of cryopreserved synovial MSCs and HUVECs. Stem Cell Research and Therapy. 2022; 13:177.

Lansing, F; Mukhametzyanova, L; Rojo-Romanos, T; Iwasawa, K; Kimura, M; Paszkowski-Rogacz, M; Karpinski, J; Grass, T; Sonntag, J; Schneider, PM; Rodriguez-Muela, N; Knöfler, R; Takebe, T; Buchholz, F. Correction of a Factor VIII genomic inversion with designer-recombinases. Nature Communications. 2022; 13:422.

Kishimoto, K; Iwasawa, K; Sorel, A; Ferran-Heredia, C; Han, L; Morimoto, M; Wells, JM; Takebe, T; Zorn, AM. Directed differentiation of human pluripotent stem cells into diverse organ-specific mesenchyme of the digestive and respiratory systems. Nature Protocols. 2022; 17:2699-2719.

Kimura, M; Iguchi, T; Iwasawa, K; Dunn, A; Thompson, WL; Yoneyama, Y; Chaturvedi, P; Zorn, AM; Wintzinger, M; Quattrocelli, M; Myers, RP; Subramanian, GM; Hwa, V; Takebe, T. En masse organoid phenotyping informs metabolic-associated genetic susceptibility to NASH. Cell. 2022; 185:4216-4232.e16.

Matsuzaki, T; Shimokawa, Y; Koike, H; Kimura, M; Kawano, Y; Okuma, N; Kawamura, R; Yoneyama, Y; Furuichi, Y; Hakuno, F; Nakauchi, H; Taniguchi, H; Takebe, T; Yoshikawa, HY. Mechanical guidance of self-condensation patterns of differentiating progeny. iScience. 2022; 25:105109.

Lee, IS; Takebe, T. Narrative engineering of the liver. Current Opinion in Genetics and Development. 2022; 75:101925.

Jurickova, I; Bonkowski, E; Angerman, E; Novak, E; Huron, A; Akers, G; Iwasawa, K; Braun, T; Hadar, R; Hooker, M; Takebe, T; Mollen, KP; Haberman, Y; Denson, LA. Eicosatetraynoic Acid and Butyrate Regulate Human Intestinal Organoid Mitochondrial and Extracellular Matrix Pathways Implicated in Crohn's Disease Strictures. Inflammatory Bowel Diseases. 2022; 28:988-1003.

Wu, Y; Oda, M; Hayashi, Y; Takebe, T; Nagata, S; Wang, C; Mori, K. (2022) Blood Vessel Segmentation from Low-Contrast and Wide-Field Optical Microscopic Images of Cranial Window by Attention-Gate-Based Network. Institute of Electrical and Electronics Engineers (IEEE). 00:1863-1872.

2021

Dunn, AW; Cai, Y; Iwasawa, K; Kimura, M; Takebe, T. Synthesis and application of POLYseq for profiling human liver organoids. Star Protocols. 2021; 2:100976.

Iwasawa, K; Takebe, T. Organogenesis in vitro. Current Opinion in Cell Biology. 2021; 73:84-91.

Lewis, K; Yoshimoto, M; Takebe, T. Fetal liver hematopoiesis: from development to delivery. Stem Cell Research and Therapy. 2021; 12:139.

Fang, H; Geng, S; Hao, M; Chen, Q; Liu, M; Liu, C; Tian, Z; Wang, C; Takebe, T; Guan, JL; Chen, Y; Guo, Z; He, W; Diao, J. Simultaneous Zn2+ tracking in multiple organelles using super-resolution morphology-correlated organelle identification in living cells. Nature Communications. 2021; 12:109.

Reza, HA; Okabe, R; Takebe, T. Organoid transplant approaches for the liver. Transplant International. 2021; 34:2031-2045.

Naraoka, Y; Mabuchi, Y; Yoneyama, Y; Suto, EG; Hisamatsu, D; Ikeda, M; Ito, R; Nakamura, T; Takebe, T; Akazawa, C. Isolation and Characterization of Tissue Resident CD29-Positive Progenitor Cells in Livestock to Generate a Three-Dimensional Meat Bud. Cells. 2021; 10:2499.

Dunn, A; Cai, Y; Iwasawa, K; Kimura, M; Takebe, T. POLYseq: A poly(β-amino ester)-based vector for multifunctional cellular barcoding. Stem Cell Reports. 2021; 16:2149-2158.

Okabe, R; Chen-Yoshikawa, TF; Yoneyama, Y; Yokoyama, Y; Tanaka, S; Yoshizawa, A; Thompson, WL; Kannan, G; Kobayashi, E; Date, H; Takebe, T. Mammalian enteral ventilation ameliorates respiratory failure. Med. 2021; 2:773-783.e5.

Marsee, A; Roos, FJ M; Verstegen, MM A; Clevers, H; Vallier, L; Takebe, T; Huch, M; Peng, WC; Forbes, SJ; Lemaigre, F; Hu, H; Fuchs, S; Hendriks, D; van der Laan, LJ W. Building consensus on definition and nomenclature of hepatic, pancreatic, and biliary organoids. Cell Stem Cell. 2021; 28:816-832.

Dobrindt, K; Hoagland, DA; Seah, C; Kassim, B; O'Shea, CP; Murphy, A; Iskhakova, M; Fernando, MB; Powell, SK; Deans, PJ M; Huckins, LM; tenOever, BR; Akbarian, S; Brennand, KJ. Common Genetic Variation in Humans Impacts In Vitro Susceptibility to SARS-CoV-2 Infection. Stem Cell Reports. 2021; 16:505-518.

Annabi, N; Baker, M; Boettiger, A; Chakraborty, D; Chen, Y; Corbett, KS; Correia, B; Dahlman, J; de Oliveira, T; Ertuerk, A; Takebe, T; Vandenberghe, LH; Varshney, RK; Wang, J. Voices of biotech research. Nature Biotechnology. 2021; 39:281-286.

Hayashi, H; Osaka, S; Sakabe, K; Fukami, A; Kishimoto, E; Aihara, E; Sabu, Y; Mizutani, A; Kusuhara, H; Naritaka, N; Mayhew, C; Setchell, K; Takebe, T; Asai, A. Modeling Human Bile Acid Transport and Synthesis in Stem Cell-Derived Hepatocytes with a Patient-Specific Mutation. Stem Cell Reports. 2021; 16:309-323.

Shinozawa, T; Kimura, M; Cai, Y; Saiki, N; Yoneyama, Y; Ouchi, R; Koike, H; Maezawa, M; Zhang, RR; Dunn, A; Lewis, K; Thompson, WL; Asai, A; Takebe, T. High-Fidelity Drug-Induced Liver Injury Screen Using Human Pluripotent Stem Cell-Derived Organoids. Gastroenterology. 2021; 160:831-846.e10.

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. Nature Protocols. 2021; 16:919-936.

Thompson, WL; Takebe, T. Human liver model systems in a dish. Development, Growth and Differentiation. 2021; 63:47-58.

Funata, M; Nio, Y; Erion, DM; Thompson, WL; Takebe, T. The promise of human organoids in the digestive system. Cell Death and Differentiation. 2021; 28:84-94.

YONEYAMA, Y; OKABE, R; TAKEBE, T. Enteral ventilation technology to combat severe respiratory failure. 2021; 3:93-97.

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