Versatile workflow for storage, characterization and cell-type resolved transcriptional and epigenetic profiling of human lung samples.

The complexity of lung microenvironment together with changes in cellular composition during disease progression hampered deeper understanding of molecular mechanisms leading to development of lung pathologies. Although recent advances in cell type resolved sequencing and single cell -omics hold great promise for studying complex diseases, their implementation greatly relies on local access to fresh tissue, as traditional tissue storage formats do not allow viable cell isolation. To overcome these hurdles, we developed a versatile workflow that allows long term storage of lung tissue with high cell viability, permits thorough sample quality check before cell isolation, and is compatible with next generation sequencing-based profiling, including single cell approaches. We demonstrate that cryopreservation is suitable for isolation of multiple cell types from different lung locations and is applicable to both healthy and tumor tissue. Basal cells isolated from cryopreserved airways retain ability to differentiate, indicating that cellular identity is not altered by cryopreservation. Importantly, using RNAseq and EPIC Array we show that genome-wide gene expression and DNA methylation signatures are preserved upon cryopreservation, emphasizing the suitability of our workflow for -omics profiling of lung cells. In addition, we obtained high quality single-cell RNAseq from cryopreserved lung tissue, demonstrating that cryopreservation empowers single-cell approaches. Overall, thanks to its simplicity, our cryopreservation workflow is well-suited for prospective tissue collection by academic collaborators and biobanks, opening worldwide access to tissue.