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Mead BE, Hattori K, Levy L, Imada S, Goto N, Vukovic M, Sze D, Kummerlowe C, Matute JD, Duan J, Langer R, Blumberg RS, Ordovas-Montanes J, Yilmaz ÖH, Karp JM, Shalek AK. Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation. Nat Biomed Eng 2022; 6:476-494. [PMID: 35314801 PMCID: PMC9046079 DOI: 10.1038/s41551-022-00863-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 02/03/2022] [Indexed: 12/12/2022]
Abstract
The cellular composition of barrier epithelia is essential to organismal homoeostasis. In particular, within the small intestine, adult stem cells establish tissue cellularity, and may provide a means to control the abundance and quality of specialized epithelial cells. Yet, methods for the identification of biological targets regulating epithelial composition and function, and of small molecules modulating them, are lacking. Here we show that druggable biological targets and small-molecule regulators of intestinal stem cell differentiation can be identified via multiplexed phenotypic screening using thousands of miniaturized organoid models of intestinal stem cell differentiation into Paneth cells, and validated via longitudinal single-cell RNA-sequencing. We found that inhibitors of the nuclear exporter Exportin 1 modulate the fate of intestinal stem cells, independently of known differentiation cues, significantly increasing the abundance of Paneth cells in the organoids and in wild-type mice. Physiological organoid models of the differentiation of intestinal stem cells could find broader utility for the screening of biological targets and small molecules that can modulate the composition and function of other barrier epithelia.
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Grants
- R01 DK088199 NIDDK NIH HHS
- Howard Hughes Medical Institute
- P30 CA014051 NCI NIH HHS
- DP2 GM119419 NIGMS NIH HHS
- R01 DE013023 NIDCR NIH HHS
- P30 DK034854 NIDDK NIH HHS
- R01 HL095722 NHLBI NIH HHS
- T32 GM087237 NIGMS NIH HHS
- R01 CA034992 NCI NIH HHS
- R01 CA211184 NCI NIH HHS
- U54 CA217377 NCI NIH HHS
- INV-006897 Bill & Melinda Gates Foundation
- The National Science Foundation graduate research fellowship program and the Massachusetts Institute of Technology – GlaxoSmithKline (MIT-GSK) Gertrude B. Elion Postdoctoral fellowship.
- Fellowships from The Japanese Biochemical Society (The Osamu Hayaishi Memorial Scholarship for Study Abroad), Mochida Memorial Foundation for Medical and Pharmaceutical Research, and The Uehara Memorial Foundation.
- NIH (DE013023)
- NIH (DK088199)
- New York Stem Cell Foundation – Robertson Investigator, the Richard and Susan Smith Family Foundation, the HHMI Damon Runyon Cancer Research Foundation Fellowship (DRG-2274-16), the AGA Research Foundation’s AGA-Takeda Pharmaceuticals Research Scholar Award in IBD – AGA2020-13-01, the HDDC Pilot and Feasibility P30 DK034854, the Food Allergy Science Initiative, and The New York Stem Cell Foundation.
- NIH (R01CA211184, R01CA034992); Pew-Stewart Trust scholar award; the Kathy and Curt Marble Cancer Research Award; a Bridge grant; and the MIT Stem Cell Initiative through Fondation MIT.
- the Kenneth Rainin Foundation Innovator and Breakthrough awards, the Crohn’s and Colitis Foundation (#624458),the NIH (HL095722), and the Harvard Digestive Disease Center and NIH grant P30DK034854.
- the Beckman Young Investigator Program, the Pew-Stewart Scholars Program for Cancer Research, a Sloan Fellowship in Chemistry, the NIH (1DP2GM119419, 1U54CA217377), the Koch Institute Support (core) Grant P30-CA14051 from the National Cancer Institute, and the MIT Stem Cell Initiative through Fondation MIT.
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Affiliation(s)
- Benjamin E Mead
- Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Department of Chemistry, MIT, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Kazuki Hattori
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren Levy
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shinya Imada
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Norihiro Goto
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Marko Vukovic
- Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Department of Chemistry, MIT, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Division of Gastroenterology Boston Children's Hospital, Program in Immunology, Harvard Medical School, Boston, MA, USA
| | - Daphne Sze
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Conner Kummerlowe
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Juan D Matute
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Neonatology, Department of Pediatrics, MGH Harvard Medical School, Boston, MA, USA
| | - Jinzhi Duan
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert Langer
- Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
| | - Richard S Blumberg
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jose Ordovas-Montanes
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Gastroenterology Boston Children's Hospital, Program in Immunology, Harvard Medical School, Boston, MA, USA
| | - Ömer H Yilmaz
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Pathology, MGH, Harvard Medical School, Boston, MA, USA
| | - Jeffrey M Karp
- Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Alex K Shalek
- Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA.
- Department of Chemistry, MIT, Cambridge, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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