Global, integrated analysis of methylomes and transcriptomes from laser capture microdissected bronchial and alveolar cells in human lung

ABSTRACT

Gene regulatory analysis of highly diverse human tissues in vivo is essentially constrained by the challenge of performing genome-wide, integrated epigenetic and transcriptomic analysis in small selected groups of specific cell types. Here we performed genome-wide bisulfite sequencing and RNA-seq from the same small groups of bronchial and alveolar cells isolated by laser capture microdissection from flash-frozen lung tissue of 12 donors and their peripheral blood T cells. Methylation and transcriptome patterns differed between alveolar and bronchial cells, while each of these epithelia showed more differences from mesodermally-derived T cells. Differentially methylated regions (DMRs) between alveolar and bronchial cells tended to locate at regulatory regions affecting promoters of 4,350 genes. A large number of pathways enriched for these DMRs including GTPase signal transduction, cell death, and skeletal muscle. Similar patterns of transcriptome differences were observed: 4,108 differentially expressed genes (DEGs) enriched in GTPase signal transduction, inflammation, cilium assembly, and others. Prioritizing using DMR-DEG regulatory network, we highlighted genes, e.g., ETS1, PPARG, and RXRG, at prominent alveolar vs. bronchial cell discriminant nodes. Our results show that multi-omic analysis of small, highly specific cells is feasible and yields unique physiologic loci distinguishing human lung cell types in situ.

KEYWORDS:

• alveolar cell
• bronchial cell
• laser capture microdissection
• whole-genome bisulfite sequencing
• RNA sequencing

Disclosure of potential conflicts of interest

X.D., M.L. and J.V. are co-founders of SingulOmics Corp. M.S. is the founder of Evergreen Biotech Group, Inc. Others declare no conflict of interest.

Acknowledgments

The authors thank Shahina B. Maqbool from Epigenomics Core and Jidong Shan from Molecular Cytogenetic Core of Department of Genetics, Albert Einstein College of Medicine for providing sequencing and T cell isolation services.

Authors' contributions

J.V., Y.S. and S.D.S. conceived this study and designed the experiments. M.S., M.L., R.T., S.G. and W.H. performed the experiments. X.D., S.Y., T.W., and Z.Z. analyzed the data. X.D., M.S., M.L., R.T., J.V., Y.S. and S.D.S wrote the manuscript.

Additional information

Funding

This research was supported by the HHS | National Institutes of Health (NIH) [grant number 1R01-CA180126-01 to J.V., Y.S. and S.D.S.].