Takebe Lab

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

Shinozawa, T; Kimura, M; Cai, Y; Saiki, N; Yoneyama, Y; Ouchi, R; Koike, H; Maezawa, M; Zhang, RR; Dunn, A; et al. 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; et al. Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis. Nature Communications. 2020; 11.

Koido, M; Kawakami, E; Fukumura, J; Noguchi, Y; Ohori, M; Nio, Y; Nicoletti, P; Aithal, GP; Daly, AK; Watkins, PB; et al. 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; et al. 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; et al. 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; et al. 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; et al. 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; et al. Vascularized and functional human liver from an iPSC-derived organ bud transplant. Nature. 2013; 499:481-484.

Mechanical guidance of self-condensation patterns of differentiating progeny. iScience. 2022.

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.

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

Jurickova, I; Bonkowski, E; Angerman, E; Novak, E; Huron, A; Akers, G; Iwasawa, K; Braun, T; Hadar, R; Hooker, M; et al. 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. 00:1863-1872.

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

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

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

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

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.

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; et al. Mammalian enteral ventilation ameliorates respiratory failure. 2021; 2:773-783.e5.

Marsee, A; Roos, FJ M; Verstegen, MM A; Clevers, H; Vallier, L; Takebe, T; Huch, M; Peng, WC; Forbes, S; Lemaigre, F; et al. Building consensus on definition and nomenclature of hepatic, pancreatic, and biliary organoids. Cell Stem Cell. 2021; 28:816-832.

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

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

Hayashi, H; Osaka, S; Sakabe, K; Fukami, A; Kishimoto, E; Aihara, E; Sabu, Y; Mizutani, A; Kusuhara, H; Naritaka, N; et al. 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; et al. 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.

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.

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

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

Han, L; Chaturvedi, P; Kishimoto, K; Koike, H; Nasr, T; Iwasawa, K; Giesbrecht, K; Witcher, PC; Eicher, A; Haines, L; et al. Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis. Nature Communications. 2020; 11.

Sekine, K; Ogawa, S; Tsuzuki, S; Ikeda, K; Nakanishi, N; Takeuchi, K; Kanai, E; Otake, Y; Okamoto, S; Kobayashi, T; et al. Generation of human induced pluripotent stem cell-derived liver buds with chemically defined and animal origin-free media. Scientific Reports. 2020; 10.

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

Okabe, R; Chen-Yoshikawa, TF; Yoshizawa, A; Hirashima, T; Saito, M; Date, H; Takebe, T. Orthotopic foetal lung tissue direct injection into lung showed a preventive effect against paraquat-induced acute lung injury in mice. European Journal of Cardio-thoracic Surgery. 2020; 58:638-645.

Kobayashi, N; Togo, S; Matsuzaki, T; Hashiseko, K; Kawamura, R; Suganuma, M; Nakabayashi, S; Yoneyama, Y; Ouchi, R; Takebe, T; et al. Stiffness distribution analysis in indentation depth direction reveals clear mechanical features of cells and organoids by using AFM. Applied Physics Express. 2020; 13.

Iizuka, S; Nishii, S; Tanimoto, E; Nakazawa, H; Kodaka, A; Takebe, T. Waiting Time Analysis at University Hospitals Based on Visitor Psychology. Lecture Notes in Computer Science. 2020; 12184:212-221.

Thompson, WL; Takebe, T. Generation of multi-cellular human liver organoids from pluripotent stem cells. . 2020.

Sakabe, K; Takebe, T; Asai, A. Organoid Medicine in Hepatology. Clinical Liver Disease. 2020; 15:3-8.

Fang, H; Yao, S; Chen, Q; Liu, C; Cai, Y; Geng, S; Bai, Y; Tian, Z; Zacharias, AL; Takebe, T; et al. De Novo-Designed Near-Infrared Nanoaggregates for Super-Resolution Monitoring of Lysosomes in Cells, in Whole Organoids, and in Vivo. ACS Nano. 2019; 13:14426-14436.

Liu, T; Zhou, L; Yang, K; Iwasawa, K; Kadekaro, AL; Takebe, T; Andl, T; Zhang, Y. The β-catenin/YAP signaling axis is a key regulator of melanoma-associated fibroblasts. Signal Transduction and Targeted Therapy. 2019; 4.

Liu, T; Zhou, L; Yang, K; Iwasawa, K; Kadekaro, AL; Takebe, T; Andl, T; Zhang, Y. The β-catenin/YAP signaling axis is a key regulator of melanoma-associated fibroblasts. Signal Transduction and Targeted Therapy. 2019; 4.

Koike, H; Iwasawa, K; Ouchi, R; Maezawa, M; Giesbrecht, K; Saiki, N; Ferguson, A; Kimura, M; Thompson, WL; Wells, JM; et al. 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; et al. Modeling Steatohepatitis in Humans with Pluripotent Stem Cell-Derived Organoids. Cell Metabolism. 2019; 30:374-384.e6.

Iizuka, S; Takebe, T; Nishii, S; Kodaka, A. (2019) Approach for Communication Design for Motivation to Health Behavior. 11569:425-436.

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

Nio, Y; Takebe, T. Organoid Models of Development and Disease Towards Therapy. Medical Applications of iPS Cells. 2019.

Matsuzaki, T; Matsumoto, S; Kasai, T; Yoshizawa, E; Okamoto, S; Yoshikawa, HY; Taniguchi, H; Takebe, T. Defining Lineage-Specific Membrane Fluidity Signatures that Regulate Adhesion Kinetics. Stem Cell Reports. 2018; 11:852-860.

Lewis, K; Takebe, T. Tumoroid à la carte: Path for personalization. Hepatology. 2018; 68:1189-1191.

Nie, Y; Zheng, Y; Miyakawa, K; Murata, S; Zhang, R; Sekine, K; Ueno, Y; Takebe, T; Wakita, T; Ryo, A; et al. Recapitulation of hepatitis B virus-host interactions in liver organoids from human induced pluripotent stem cells. EBioMedicine. 2018; 35:114-123.

Ayabe, H; Anada, T; Kamoya, T; Sato, T; Kimura, M; Yoshizawa, E; Kikuchi, S; Ueno, Y; Sekine, K; Camp, JG; et al. Optimal Hypoxia Regulates Human iPSC-Derived Liver Bud Differentiation through Intercellular TGFB Signaling. Stem Cell Reports. 2018; 11:306-316.

Kimura, M; Azuma, M; Zhang, R; Thompson, W; Mayhew, CN; Takebe, T. Digitalized Human Organoid for Wireless Phenotyping. iScience. 2018; 4:294-301.

Rao, MS; Pei, Y; Garcia, TY; Chew, S; Kasai, T; Hisai, T; Taniguchi, H; Takebe, T; Lamba, DA; Zeng, X. Illustrating the potency of current Good Manufacturing Practice-compliant induced pluripotent stem cell lines as a source of multiple cell lineages using standardized protocols. Cytotherapy. 2018; 20:861-872.

Takebe, T; Wells, JM; Helmrath, MA; Zorn, AM. Organoid Center Strategies for Accelerating Clinical Translation. Cell Stem Cell. 2018; 22:806-809.

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.

Takahashi, Y; Takebe, T; Taniguchi, H. Methods for Generating Vascularized Islet-Like Organoids Via Self-Condensation. Current Protocols in Stem Cell Biology. 2018; 45.

Zhang, R; Koido, M; Tadokoro, T; Ouchi, R; Matsuno, T; Ueno, Y; Sekine, K; Takebe, T; Taniguchi, H. Human iPSC-Derived Posterior Gut Progenitors Are Expandable and Capable of Forming Gut and Liver Organoids. Stem Cell Reports. 2018; 10:780-793.