Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation

Benjamin E Mead; Kazuki Hattori; Lauren Levy; Shinya Imada; Norihiro Goto; Marko Vukovic; Daphne Sze; Conner Kummerlowe; Juan D Matute; Jinzhi Duan; Robert Langer; Richard S Blumberg; Jose Ordovas-Montanes; Ömer H Yilmaz; Jeffrey M Karp; Alex K Shalek

doi:10.1038/s41551-022-00863-9

Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation

Nat Biomed Eng. 2022 Apr;6(4):476-494. doi: 10.1038/s41551-022-00863-9. Epub 2022 Mar 21.

Authors

Benjamin E Mead^#^{1

2

3

4

5

6

7}, Kazuki Hattori^#^{2

3

8}, Lauren Levy^{2

3

8}, Shinya Imada², Norihiro Goto², Marko Vukovic^{1

2

3

4

5

6

7

9}, Daphne Sze^{2

3

8}, Conner Kummerlowe^{2

3

4

5

7}, Juan D Matute^{10

11}, Jinzhi Duan¹⁰, Robert Langer^{1

2

5

12}, Richard S Blumberg¹⁰, Jose Ordovas-Montanes^{3

4

9}, Ömer H Yilmaz^{2

13}, Jeffrey M Karp^{14

15

16

17}, Alex K Shalek^{18

19

20

21

22

23

24}

Affiliations

¹ Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, MA, USA.
² Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.
³ Harvard Stem Cell Institute, Cambridge, MA, USA.
⁴ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁵ Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA.
⁶ Department of Chemistry, MIT, Cambridge, MA, USA.
⁷ Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
⁸ Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
⁹ Division of Gastroenterology Boston Children's Hospital, Program in Immunology, Harvard Medical School, Boston, MA, USA.
¹⁰ Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
¹¹ Division of Neonatology, Department of Pediatrics, MGH Harvard Medical School, Boston, MA, USA.
¹² Department of Chemical Engineering, MIT, Cambridge, MA, USA.
¹³ Department of Pathology, MGH, Harvard Medical School, Boston, MA, USA.
¹⁴ Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, MA, USA. jmkarp@bwh.harvard.edu.
¹⁵ Harvard Stem Cell Institute, Cambridge, MA, USA. jmkarp@bwh.harvard.edu.
¹⁶ Broad Institute of MIT and Harvard, Cambridge, MA, USA. jmkarp@bwh.harvard.edu.
¹⁷ Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. jmkarp@bwh.harvard.edu.
¹⁸ Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, MA, USA. shalek@mit.edu.
¹⁹ Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA. shalek@mit.edu.
²⁰ Harvard Stem Cell Institute, Cambridge, MA, USA. shalek@mit.edu.
²¹ Broad Institute of MIT and Harvard, Cambridge, MA, USA. shalek@mit.edu.
²² Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA. shalek@mit.edu.
²³ Department of Chemistry, MIT, Cambridge, MA, USA. shalek@mit.edu.
²⁴ Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. shalek@mit.edu.

^# Contributed equally.

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.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cell Differentiation
Intestines
Mice
Organoids*
Paneth Cells* / physiology
Stem Cells

Abstract

Publication types

MeSH terms

Grants and funding