1. Oishi Y, Koike H, Kumagami N, Nakagawa Y, Araki M, Taketomi Y, Miki Y, Matsuda S, Kim H, Matsuzaka T, Ozawa H, Shimano H, Murakami M, Manabe I. (2024) Macrophage SREBP1 regulates skeletal muscle regeneration. Front Immunol 14:1251784, 2024. DOI: 10.3389/fimmu.2023.1251784

2. Sugita Y, Kuwabara Y, Katayama A, Matsuda S, Ichiro Manabe I, Suzuki S, Oishi Y. (2023)
Characteristic impairment of progesterone response in cultured cervical fibroblasts obtained from patients with refractory cervical insufficiency. Sci Rep 13:11709, 2023. DOI: 10.1038/s41598-023-37732-7

3. Watanabe A, Koike H, Kumagami N, Shimba S, Manabe I and Oishi Y. (2023)
Arntl deficiency in myeloid cells reduces neutrophil recruitment and delays skeletal muscle repair. Sci Rep 23:6747, 2023. https://doi.org/10.1038/s41598-023-33830-8

4. Cheng Y, Manabe I, Hayakawa S, Endo Y, and Oishi Y. (2023) Caspase-4 contributes to Site-1 protease cleavage and SREBP1 activation in the inflammatory response of macrophages. Front Immunol 14:1009973. doi: 10.3389/fimmu.2023.1009973

5. Nawaz A, Bilal M, Fujisaka S, Kado T, Aslam M, Ahmed S, Okabe K, Igarashi Y, Watanabe Y, Kuwano T, Tsuneyama K, Nishimura A, Nishida Y, Yamamoto S, Sasahara M, Imura J, Mori H, Matzuk M, Kudo F, Manabe I, Uezumi A, Nakagawa T, Oishi Y and Tobe K. (2022) Depletion of CD206+ M2-like macrophages induces fibro-adipogenic progenitors activation and muscle regeneration Nature Communications 13(1) https://doi.org/10.1038/s41467-022-34191-y 

6. Hayakawa S, Tamura A, Nikiforov N, Koike H, Kudo F, Cheng Y, Miyazaki T, Kubekina M, Kirichenko T, Orekhov A, Yui N, Manabe I, Oishi Y. (2022) Activated cholesterol metabolism is integral for innate macrophage responses by amplifying Myd88 signaling. JCI Insight 7, e138539. https://doi.org/10.1172/jci.insight.138539

7. Yuzawa R, Koike H, Manabe I,and Oishi Y. (2022) VDR regulates simulated microgravity-induced atrophy in C2C12 myotubes. Scientific Reports 2022.12: 1377

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

9. Kitazawa M, Hayashi S, Imamura M, Oishi Y, Takeda S, Kaneko-Ishino T, and Ishino F. (2020) Lack and overexpression of Rtl1 in the mouse cause distinct muscle abnormalities related to the Temple and Kagami-Ogata syndromes, respectively. Development 147, dev185918. doi:10.1242/dev.185918

10. Nakayama Y, Fujiu K, Yuki R, Oishi Y, Morioka M, Isagawa T, Matsuda J, Oshima T, Matsubara T, Sugita J, Kudo F, Kaneda A, Endo Y, Nakayama T, Nagai R, Komuro I, Manabe I. (2020) A long noncoding RNA regulates inflammation resolution by mouse macrophages through fatty acid oxidation activation. Proc Natl Acad Sci USA 117:14365-14375, 2020　 https://doi.org/10.1073/pnas.2005924117

11. Oishi Y, Spann, NJ, Link VM, Muse ED, Strid T, Edillor C, Kolar MJ, Matsuzaka T, Hayakawa S, Tao J, Kaikkonen M, Lam MT, Manabe I, Shimano H, Saghatelian A and Glass CK. (2017) SREBP1 contributes to resolution of pro-inflammatory TLR4 signaling by reprogramming fatty acid metabolism.  Cell Metab. 25: 412-427. 

12. Oishi Y, Hayashi S, Isagawa T, Oshima M, Iwama A, Shimba S, Okamura H and Manabe I. (2017) Bmal1 regulates inflammatory responses in macrophages by modulating enhancer RNA transcription. Sci Rep. 7:7086. 

13. Hayashi S, Manabe I, Suzuki Y, and Oishi Y. (2016) Klf5 regulates muscle differentiation by directly targeting muscle specific genes in cooperation with MyoD in mice. eLife. DOI: http://dx.doi.org/10.7554/eLife.17462.

14. Lam M, Cho H, Lesch H, Gosselin D, Heinz S, Oishi-Tanaka Y, Benner C, Kaikkonen M, Salim A, Rosenfeld M, Evans R, and Glass CK. (2013) Rev-Erbs negatively regulate macrophage gene expression by repressing enhancer-directed transcription. Nature. 498, 511-515. 

15. Eguchi K, Manabe I, Oishi-Tanaka Y, Osugi M, Kono N, Ogata F, Yagi N, Ohto U, Kimoto M, Miyake K, Tobe K, Arai H, Kadowaki T, and Nagai R. (2012)  Saturated fatty acid and TLR signaling link ß cell dysfunction and islet inflammation.  Cell Metab. 15: 518-533. 

16. Oishi Y, Manabe I, Tobe K, Osugi, M, Kubota T, Fujiu K, Maemura K, Kubota N, Kadowaki T, Nagai R. (2008) SUMOylation of KLF5 is a molecular switch regulating PPAR-δ-containing transcriptional programs of lipid metabolism.  Nat Med. 14: 656-666.

17. Oishi Y, Manabe I, Tobe K, Tsushima K, Shindo T, Fujiu K, Nishimura G, Maemura K, Yamauchi T, Kubota N, Suzuki R, Kitamura T, Akira S, Kadowaki T, Nagai R. (2005) Krüppel-like transcription factor KLF5 is a key regulator of adipocyte differentiation.  Cell Metab. 1:27-39.

1. Yoshimoto Y, Oishi Y. Mechanisms of Skeletal Muscle-Tendon Development and Regeneration/Healing as Potential Therapeutic Targets. Pharmacology & Therapeutics, 2023. 108357. https://doi.org/10.1016/j.pharmthera.2023.108357

2. Koike H, Manabe I, Oishi Y. Mechanisms of Cooperative Cell-Cell Interactions in Skeletal Muscle Regeneration. Inflammation and Regeneration 42: 48, 2022. https://doi.org/10.1186/s41232-022-00234-6

3. Oishi Y. and Manabe I. “Organ system crosstalk in cardiometabolic disease in the age of multimoribidity. Front Cardiovasc Med 7:64, 2020 

4. Oishi Y. and Manabe I. (2018) Macrophages in inflammation, repair and regeneration. International Immunology. 30:511-528. 

5. Oishi Y. and Manabe I. (2018) Kruppel –like factors in metabolic homeostasis and cardiometabolic diseases. Frontiers in cardiovascular medicine. doi: 10:3389/fcvm.2018.00069
 

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

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

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

4. Koike, H., Iwasawa, K., Ouchi, R., Maezawa, M., Giesbrecht, K., Saiki, N., Ferguson, A., Kimura, M., Thompson, W.L., Wells, J.M., Zorn, A.M., Takebe, T. Modelling human hepato-biliary-pancreatic organogenesis from the foregut–midgut boundary. Nature 574, 112-116 (2019). https://doi.org/10.1038/s41586-019-1598-0

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

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

7. Koike, H., Ueno, Y., Naito, T., Shiina, T., Nakata, S., Ouchi, R., Obana, Y., Sekine, K., Zheng, Y., Takebe, T., Isono, K., Koseki, H., Taniguchi, H. Ring1B promotes hepatic stem/progenitor cell expansion through simultaneous suppression of Cdkn1a and Cdkn2a in mice. Hepatology 60, 323-333 (2014). https://doi.org/10.1002/hep.27046

8. 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 499, 481-484 (2013). https://doi.org/10.1038/nature12271

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