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BMC Biol DOI:10.1186/s12915-018-0527-2

Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types.

Publication TypeJournal Article
Year of Publication2018
AuthorsMead, BE, Ordovas-Montanes, J, Braun, AP, Levy, LE, Bhargava, P, Szucs, MJ, Ammendolia, DA, MacMullan, MA, Yin, X, Hughes, TK, Wadsworth, MH, Ahmad, R, Rakoff-Nahoum, S, Carr, SA, Langer, R, Collins, JJ, Shalek, AK, Karp, JM
JournalBMC Biol
Date Published2018 Jun 05

BACKGROUND: Single-cell genomic methods now provide unprecedented resolution for characterizing the component cell types and states of tissues such as the epithelial subsets of the gastrointestinal tract. Nevertheless, functional studies of these subsets at scale require faithful in vitro models of identified in vivo biology. While intestinal organoids have been invaluable in providing mechanistic insights in vitro, the extent to which organoid-derived cell types recapitulate their in vivo counterparts remains formally untested, with no systematic approach for improving model fidelity.

RESULTS: Here, we present a generally applicable framework that utilizes massively parallel single-cell RNA-seq to compare cell types and states found in vivo to those of in vitro models such as organoids. Furthermore, we leverage identified discrepancies to improve model fidelity. Using the Paneth cell (PC), which supports the stem cell niche and produces the largest diversity of antimicrobials in the small intestine, as an exemplar, we uncover fundamental gene expression differences in lineage-defining genes between in vivo PCs and those of the current in vitro organoid model. With this information, we nominate a molecular intervention to rationally improve the physiological fidelity of our in vitro PCs. We then perform transcriptomic, cytometric, morphologic and proteomic characterization, and demonstrate functional (antimicrobial activity, niche support) improvements in PC physiology.

CONCLUSIONS: Our systematic approach provides a simple workflow for identifying the limitations of in vitro models and enhancing their physiological fidelity. Using adult stem cell-derived PCs within intestinal organoids as a model system, we successfully benchmark organoid representation, relative to that in vivo, of a specialized cell type and use this comparison to generate a functionally improved in vitro PC population. We predict that the generation of rationally improved cellular models will facilitate mechanistic exploration of specific disease-associated genes in their respective cell types.


Alternate JournalBMC Biol.
PubMed ID29871632
PubMed Central IDPMC5989470
Grant List2P01AI039671 / / National Institutes of Health /
R01 HL095791 / HL / NHLBI NIH HHS / United States
1DP2OD020839 / / National Institute of General Medical Sciences /
5U24AI118672 / / National Institute of Allergy and Infectious Diseases /
DE013023 / / National Institutes of Health /
R01 AI138546 / AI / NIAID NIH HHS / United States
1R33CA202820 / / National Institutes of Health /
OPP1116944 / / Bill and Melinda Gates Foundation /
OPP1137006 / / Bill and Melinda Gates Foundation /
P30 CA014051 / CA / NCI NIH HHS / United States
DRG-2274-16 / / Damon Runyon Cancer Research Foundation / United States
1U54CA217377 / / National Institutes of Health /
Breakthrough Award / / Kenneth Rainin Foundation /
R01 HL095722 / HL / NHLBI NIH HHS / United States
OPP1139972 / / Bill and Melinda Gates Foundation /
P01 AI039671 / AI / NIAID NIH HHS / United States
R33 CA202820 / CA / NCI NIH HHS / United States
1R01HL126554 / / National Institutes of Health /
R01 DE013023 / DE / NIDCR NIH HHS / United States
1R01DA046277 / / National Institutes of Health /
Graduate Research Fellowship Program / / National Science Foundation /
2R01HL095791 / / National Institutes of Health /
Beckman Young Investigator Award / / Arnold and Mabel Beckman Foundation /
U19 AI089992 / AI / NIAID NIH HHS / United States
2U19AI089992 / / National Institutes of Health /
U24 AI118672 / AI / NIAID NIH HHS / United States
R56 HL126554 / HL / NHLBI NIH HHS / United States
HL095722 / / National Institutes of Health /
1R01AI138546 / / National Institutes of Health /
RM1 HG006193 / HG / NHGRI NIH HHS / United States
U54 CA217377 / CA / NCI NIH HHS / United States
2RM1HG006193 / / National Human Genome Research Institute /
Shark Tank Pilot Grant / / Brigham and Women's Hospital /
R01 DA046277 / DA / NIDA NIH HHS / United States