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

Overview of attention for article published in BMC Biology, June 2018
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Title
Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types
Published in
BMC Biology, June 2018
DOI 10.1186/s12915-018-0527-2
Pubmed ID
Authors

Benjamin E. Mead, Jose Ordovas-Montanes, Alexandra P. Braun, Lauren E. Levy, Prerna Bhargava, Matthew J. Szucs, Dustin A. Ammendolia, Melanie A. MacMullan, Xiaolei Yin, Travis K. Hughes, Marc H. Wadsworth, Rushdy Ahmad, Seth Rakoff-Nahoum, Steven A. Carr, Robert Langer, James J. Collins, Alex K. Shalek, Jeffrey M. Karp

Abstract

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. 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. 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.

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Mendeley readers

The data shown below were compiled from readership statistics for 164 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 164 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 37 23%
Researcher 35 21%
Student > Master 9 5%
Student > Bachelor 9 5%
Student > Postgraduate 8 5%
Other 22 13%
Unknown 44 27%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 36 22%
Agricultural and Biological Sciences 36 22%
Medicine and Dentistry 16 10%
Immunology and Microbiology 5 3%
Chemical Engineering 5 3%
Other 18 11%
Unknown 48 29%