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

• Main Authors: Szucs, Matthew J (Author), Ammendolia, Dustin A (Author), MacMullan, Melanie A (Author), Rakoff-Nahoum, Seth (Author), Mead, Benjamin Elliott (Contributor), Ordovas-Montanes, Jose Manuel (Contributor), Braun, Alexandra Provost (Contributor), Levy, Lauren (Contributor), Saluja, Prerna Bhargava (Contributor), Yin, Xiaolei (Contributor), Hughes, Travis K. (Contributor), Wadsworth, Marc Havens (Contributor), Ahmad, Rushdy (Contributor), Carr, Steven A (Contributor), Langer, Robert S (Contributor), Collins, James J. (Contributor), Shalek, Alexander K (Contributor), Karp, Jeffrey Michael (Author)
• Other Authors: Massachusetts Institute of Technology. Institute for Medical Engineering & Science (Contributor), Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics (Contributor), Massachusetts Institute of Technology. Department of Biological Engineering (Contributor), Massachusetts Institute of Technology. Department of Chemical Engineering (Contributor), Massachusetts Institute of Technology. Department of Chemistry (Contributor), Massachusetts Institute of Technology. Synthetic Biology Center (Contributor), Koch Institute for Integrative Cancer Research at MIT (Contributor), Karp, Jeffrey (Contributor)
• Format: Article
• Language: English
• Published: Biomed Central Ltd, 2018-06-12T19:08:18Z.
• Subjects: Article
• Online Access: Get fulltext

 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. Keywords: Single-cell RNA-seq; Chemical biology; Stem cell-derived models; Paneth cell; Intestinal organoid; Intestinal stem cell; Differentiation; Systems biology