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

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.

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.

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.

Gastroenterology, Hepatology and Nutrition
Takebe Lab

Takebe Research Lab

Modeling Complex Human Development Towards Therapy

Publications

Science Blog

Takebe Receives Vilcek Foundation Award for Creative Promise

Engineered Organoids Might Serve as Bridge to Liver Transplantation in Severe Jaundice

Human Vascular Organoids Reveal Clues for a Potential COVID Treatment

JSPS PRIZE Recipient

Contact Us