Ryuichi Okamoto Department of Gastroenterology and Hepatology Tokyo Medical and Dental University (TMDU)
1 protocol

Kohei Suzuki
  • post-doc research fellow , Internal Medicine, Division of Digestive and Liver DIseases University of Texas Southwestern Medical Center
Research focus
  • Stem cell
  • 1 Author merit

Education

Ph.D., Ph.D., 2017

Publications

1. Takenaka K, Fujii T, Suzuki K, Shimizu H, Motobayashi M, Hibiya S, Saito E, Nagahori M, Watanabe M, Ohtsuka K. Small Bowel Healing Detected by Endoscopy in Patients With Crohn's Disease After Treatment With Antibodies Against Tumor Necrosis Factor. Clin Gastroenterol Hepatol. 2020 Jun;18(7):1545-1552. doi: 10.1016/j.cgh.2019.08.024. Epub 2019 Aug 20. PubMed PMID: 31442600. 2. Takenaka K, Ohtsuka K, Fujii T, Negi M, Suzuki K, Shimizu H, Oshima S, Akiyama S, Motobayashi M, Nagahori M, Saito E, Matsuoka K, Watanabe M. Development and Validation of a Deep Neural Network for Accurate Evaluation of Endoscopic Images From Patients With Ulcerative Colitis. Gastroenterology. 2020 Jun;158(8):2150-2157. doi: 10.1053/j.gastro.2020.02.012. Epub 2020 Feb 12. PubMed PMID: 32060000. 3. Okamoto R, Shimizu H, Suzuki K, Kawamoto A, Takahashi J, Kawai M, Nagata S, Hiraguri Y, Takeoka S, Sugihara HY, Yui S, Watanabe M. Organoid-based regenerative medicine for inflammatory bowel disease. Regen Ther. 2020 Mar;13:1-6. doi: 10.1016/j.reth.2019.11.004. eCollection 2020 Mar. Review. PubMed PMID: 31970266; PubMed Central PMCID: PMC6961757. 4. Akiyama S, Matsuoka K, Fukuda K, Hamada S, Shimizu M, Nanki K, Mizuno S, Kiyohara H, Arai M, Sugimoto S, Iwao Y, Ogata H, Hisamatsu T, Naganuma M, Motobayashi M, Suzuki K, Takenaka K, Fujii T, Saito E, Nagahori M, Ohtsuka K, Mochizuki M, Watanabe M, Hashiguchi M, Kanai T. Long-term effect of NUDT15 R139C on hematologic indices in inflammatory bowel disease patients treated with thiopurine. J Gastroenterol Hepatol. 2019 Oct;34(10):1751-1757. doi: 10.1111/jgh.14693. Epub 2019 Jun 26. PubMed PMID: 31045285. 5. Shimizu H, Suzuki K, Watanabe M, Okamoto R. Stem cell-based therapy for inflammatory bowel disease. Intest Res. 2019 Jul;17(3):311-316. doi: 10.5217/ir.2019.00043. Epub 2019 Jul 25. Review. PubMed PMID: 31352774; PubMed Central PMCID: PMC6667367. 6. Kawamoto A, Nagata S, Anzai S, Takahashi J, Kawai M, Hama M, Nogawa D, Yamamoto K, Kuno R, Suzuki K, Shimizu H, Hiraguri Y, Yui S, Oshima S, Tsuchiya K, Nakamura T, Ohtsuka K, Kitagawa M, Okamoto R, Watanabe M. Ubiquitin D is Upregulated by Synergy of Notch Signalling and TNF-α in the Inflamed Intestinal Epithelia of IBD Patients. J Crohns Colitis. 2019 Mar 30;13(4):495-509. doi: 10.1093/ecco-jcc/jjy180. PubMed PMID: 30395194. 7. Suzuki K, Murano T, Shimizu H, Ito G, Nakata T, Fujii S, Ishibashi F, Kawamoto A, Anzai S, Kuno R, Kuwabara K, Takahashi J, Hama M, Nagata S, Hiraguri Y, Takenaka K, Yui S, Tsuchiya K, Nakamura T, Ohtsuka K, Watanabe M, Okamoto R. Single cell analysis of Crohn's disease patient-derived small intestinal organoids reveals disease activity-dependent modification of stem cell properties. J Gastroenterol. 2018 Sep;53(9):1035-1047. doi: 10.1007/s00535-018-1437-3. Epub 2018 Jan 27. PubMed PMID: 29374777; PubMed Central PMCID: PMC6132922. 8. Ishibashi F, Shimizu H, Nakata T, Fujii S, Suzuki K, Kawamoto A, Anzai S, Kuno R, Nagata S, Ito G, Murano T, Mizutani T, Oshima S, Tsuchiya K, Nakamura T, Watanabe M, Okamoto R. Contribution of ATOH1+ Cells to the Homeostasis, Repair, and Tumorigenesis of the Colonic Epithelium. Stem Cell Reports. 2018 Jan 9;10(1):27-42. doi: 10.1016/j.stemcr.2017.11.006. Epub 2017 Dec 7. PubMed PMID: 29233556; PubMed Central PMCID: PMC5768891. 9. Nakata T, Shimizu H, Nagata S, Ito G, Fujii S, Suzuki K, Kawamoto A, Ishibashi F, Kuno R, Anzai S, Murano T, Mizutani T, Oshima S, Tsuchiya K, Nakamura T, Hozumi K, Watanabe M, Okamoto R. Data showing proliferation and differentiation of intestinal epithelial cells under targeted depletion of Notch ligands in mouse intestine. Data Brief. 2017 Feb;10:551-556. doi: 10.1016/j.dib.2016.12.045. eCollection 2017 Feb. PubMed PMID: 28124021; PubMed Central PMCID: PMC5220229. 10. Nakata T, Shimizu H, Nagata S, Ito G, Fujii S, Suzuki K, Kawamoto A, Ishibashi F, Kuno R, Anzai S, Murano T, Mizutani T, Oshima S, Tsuchiya K, Nakamura T, Hozumi K, Watanabe M, Okamoto R. Indispensable role of Notch ligand-dependent signaling in the proliferation and stem cell niche maintenance of APC-deficient intestinal tumors. Biochem Biophys Res Commun. 2017 Jan 22;482(4):1296-1303. doi: 10.1016/j.bbrc.2016.12.031. Epub 2016 Dec 8. PubMed PMID: 27939883. 11. Fujii S, Suzuki K, Kawamoto A, Ishibashi F, Nakata T, Murano T, Ito G, Shimizu H, Mizutani T, Oshima S, Tsuchiya K, Nakamura T, Araki A, Ohtsuka K, Okamoto R, Watanabe M. PGE2 is a direct and robust mediator of anion/fluid secretion by human intestinal epithelial cells. Sci Rep. 2016 Nov 9;6:36795. doi: 10.1038/srep36795. PubMed PMID: 27827428; PubMed Central PMCID: PMC5101536. 12. Shimizu H, Okamoto R, Ito G, Fujii S, Nakata T, Suzuki K, Murano T, Mizutani T, Tsuchiya K, Nakamura T, Hozumi K, Watanabe M. Distinct expression patterns of Notch ligands, Dll1 and Dll4, in normal and inflamed mice intestine. PeerJ. 2014;2:e370. doi: 10.7717/peerj.370. eCollection 2014. PubMed PMID: 24860699; PubMed Central PMCID:
1 Protocol published
Fluidigm Based Single-cell Gene Expression Library Preparation from Patient-derived Small Intestinal Organoids
Authors:  Kohei Suzuki and Ryuichi Okamoto, date: 10/05/2020, view: 229, Q&A: 0
In this protocol, we describe our methods to isolate crypts from patients' biopsy samples and to culture human intestinal stem cells as it’s called “organoid.” Beyond that, we describe how to dissociate organoids cells into single cells for ...
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