Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types
Year: 2018
Type: article
Abstract: 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.
Source: BMC Biology
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
Institutions: Broad Institute, Brigham and Women's Hospital, Harvard University, Harvard–MIT Division of Health Sciences and Technology, Harvard Stem Cell Institute, Koch Institute for Integrative Cancer Research At MIT, Massachusetts Institute of Technology, Boston Children's Hospital, Wyss Institute for Biologically Inspired Engineering, Ragon Institute of MGH, MIT and Harvard
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,690
Funders: National Science Foundation, Howard Hughes Medical Institute, Bill and Melinda Gates Foundation, Arnold and Mabel Beckman Foundation, Damon Runyon Cancer Research Foundation, Brigham and Women's Hospital, Massachusetts Institute of Technology, Kenneth Rainin Foundation, Searle Scholars Program, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Hokkaido University, National Institutes of Health, National Heart, Lung, and Blood Institute, National Institute on Drug Abuse, National Human Genome Research Institute, National Cancer Institute, National Institute of General Medical Sciences, National Institute of Allergy and Infectious Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Dental and Craniofacial Research
Awards: G1083602967, G1095256556, G1129124601, A systems biology approach to fingerprint HIV immune defense in Elite Controllers, Center for Cell Circuits, G2360436881, Engineered Induction of a Stem Cell Homing Response, G2488319905, G2838808439, G3085841307, G3812106259, G3992607959, G4186406324, G4553958427, G4774430914, G4796228306, G5108852245, G5735053113, G582655688, Africa Health Research Institute NPC - to investigate the hypothesis that there exists a tipping point for tuberculosis (TB) infection, where cell death of some of the TB infected immune..., G6407940759, G6418439082, G6795728463, G7640925840, G7888124300, G7981823491, G8116125018, G8248692706, G8435249515, Novel Polymers for Tissue Engineering, G8863986071, G8996809783, G9000008053, G9000016445, G9000033974, G9000074672, G9000146431, G9000155476, G9000165427, G9000173916, G9000187672, G9000203899, G9000347873, Costimulatory Mechanisms of Autoimmunity, Integrated Epithelial and Muscosal Biology, Cancer Center Support (Core) Grant, G941982536
OpenAlex ID: W2805176058