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Single-Cell Genomic Methods to Generate Ex Vivo Cell Sytems That Recapitulate In Vivo Biology with Improved Fidelity

Application No.


Broad Case No.


List of inventors -

Jeff Karp, Robert Langer, Benjamin Mead, Jose Ordovas-Montanes, Alexander Shalek


Disclosed here is a generally applicable framework that utilizes massively-parallel single-cell RNA-seq to compare cell types/states found in vivo to those of in vitro models. Furthermore, Applicants leverage identified discrepancies to improve model fidelity. Applicants uncover fundamental gene expression differences in lineage-defining genes between in vivo systems and in vitro systems. Using this information, molecular interventions are identified for rationally improving the physiological fidelity of the in vitro system. Applicants demonstrated functional (antimicrobial activity, niche support) improvements in Paneth cell physiology using the methods.


  • 07/04/2019

Published Patent Application

  • US2019/0204299

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