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.
Bibliographical noteFunding Information:
This research was supported by the HHS j National Institutes of Health (NIH) [grant number 1R01-CA180126-01 to J.V., Y.S. and S.D.S.].
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.]. 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.
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- alveolar cell
- bronchial cell
- laser capture microdissection
- RNA sequencing
- whole-genome bisulfite sequencing