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High-dimensional immune phenotyping and transcriptional analyses reveal robust recovery of viable human immune and epithelial cells from frozen gastrointestinal tissue


Simultaneous analyses of peripheral and mucosal immune compartments can yield insight into the pathogenesis of mucosal-associated diseases. Although methods to preserve peripheral immune cells are well established, studies involving mucosal immune cells have been hampered by lack of simple storage techniques. We provide a cryopreservation protocol allowing for storage of gastrointestinal (GI) tissue with preservation of viability and functionality of both immune and epithelial cells. These methods will facilitate translational studies allowing for batch analysis of mucosal tissue to investigate disease pathogenesis, biomarker discovery and treatment responsiveness.

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L.K. is a recipient of a Career Development Award Grant from the Crohn’s and Colitis Foundation of America (CDA 422348). S.B.S. is supported by NIH Grants: R01 DK115217, R56 AI125766; P30DK034854, the Helmsley Charitable Trust, and the Wolpow Family Chair in IBD Treatment and Research. C.R. is supported by NIH K08 DK106562-01A1. D.T.B. is supported by R01DK084056, the Timothy Murphy Fund, the IDDRC P30HD18655 and the HDDC P30DK034854. V.M. is supported by 5 T32 DK7533

Authors contributions

L.K., G.B., A.R., J.C., S.W., V.M., and M.F. performed the CyTOF experiments. L.K., G.B., and A.R. analyzed the CyTOF data. C.R. and F.Z. performed the enteroid experiments. W.G. and S.J. performed and analyzed the RNAseq data. J.L. provided the RNAseq samples and analyzed the data. V.T.T. performed and analyzed the FACS experiments. J.D.G. provided BCH samples. M.B. provided the Penn samples. L.K., G.B., A.R., J.C., W.G., V.M., D.T.B., M.M., and S.B.S. conceived the experiments and analyzed the data. L.K. and S.B.S. wrote the manuscript.

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Competing interests

Conflicts of Interest: S.B.S. is supported by grants or in-kind contributions from Pfizer, Janssen, Merck, and Regeneron. He is on the scientific advisory boards of Pfizer, Janssen, IFM Therapeutics, Lycera, Inc., Celgene, Pandion Therapeutics, and Applied Molecular Transport. He has consulted for Amgen and Hoffman La-Roche. Except for support from Pfizer that performed the RNA seq experiments in this work and assisted in the analytics, there are no conflicts of interest that are related to this work.

Correspondence to Scott B. Snapper.

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