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Versatile workflow for cell-type resolved transcriptional and epigenetic profiles from cryopreserved human lung

Prada, Maria Llamazares, Espinet, Elisa, Mijosek, Vedrana, Schwartz, Uwe, Lutsik, Pavlo, Tamas, Raluca, Richter, Mandy, Behrendt, Annika, Pohl, Stephanie T., Benz, Naja P., Muley, Thomas, Warth, Arne, Heusel, Claus Peter, Winter, Hauke, Landry, Jonathan J.M., Herth, Felix J.F., Mertens, Tinne C.J., Karmouty-Quintana, Harry, Koch, Ina, Benes, Vladimir, Korbel, Jan O., Waszak, Sebastian M., Trumpp, Andreas, Wyatt, David M., Stahl, Heiko F., Plass, Christoph and Jurkowska, Renata Z. 2021. Versatile workflow for cell-type resolved transcriptional and epigenetic profiles from cryopreserved human lung. JCI Insight 6 (5) , e140443. 10.1172/jci.insight.140443

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Abstract

Complexity of lung microenvironment and changes in cellular composition during disease make it exceptionally hard to understand molecular mechanisms driving development of chronic lung diseases. Although recent advances in cell type–resolved approaches hold great promise for studying complex diseases, their implementation relies on local access to fresh tissue, as traditional tissue storage methods do not allow viable cell isolation. To overcome these hurdles, we developed a versatile workflow that allows storage of lung tissue with high viability, permits thorough sample quality check before cell isolation, and befits sequencing-based profiling. We demonstrate that cryopreservation enables isolation of multiple cell types from both healthy and diseased lungs. Basal cells from cryopreserved airways retain their differentiation ability, indicating that cellular identity is not altered by cryopreservation. Importantly, using RNA sequencing and EPIC Array, we show that gene expression and DNA methylation signatures are preserved upon cryopreservation, emphasizing the suitability of our workflow for omics profiling of lung cells. Moreover, we obtained high-quality single-cell RNA-sequencing data of cells from cryopreserved human lungs, demonstrating that cryopreservation empowers single-cell approaches. Overall, thanks to its simplicity, our workflow is well suited for prospective tissue collection by academic collaborators and biobanks, opening worldwide access to viable human tissue.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Biosciences
Publisher: American Society for Clinical Investigation
ISSN: 2379-3708
Date of First Compliant Deposit: 16 February 2021
Date of Acceptance: 10 February 2021
Last Modified: 22 Mar 2021 17:14
URI: https://orca.cardiff.ac.uk/id/eprint/138584

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