Integrated Transcriptomic and Epigenomic Analysis of Primary Human Lung Epithelial Cell Differentiation

Abstract

Elucidation of the epigenetic basis for cell-type specific gene regulation is key to gaining a full understanding of how the distinct phenotypes of differentiated cells are achieved and maintained. Here we examined how epigenetic changes are integrated with transcriptional activation to determine cell phenotype during differentiation. We performed epigenomic profiling in conjunction with transcriptomic profiling using in vitro differentiation of human primary alveolar epithelial cells (AEC). This model recapitulates an in vivo process in which AEC transition from one differentiated cell type to another during regeneration following lung injury. Interrogation of histone marks over time revealed enrichment of specific transcription factor binding motifs within regions of changing chromatin structure. Cross-referencing of these motifs with pathways showing transcriptional changes revealed known regulatory pathways of distal alveolar differentiation, such as the WNT and transforming growth factor beta (TGFB) pathways, and putative novel regulators of adult AEC differentiation including hepatocyte nuclear factor 4 alpha (HNF4A), and the retinoid X receptor (RXR) signaling pathways. Inhibition of the RXR pathway confirmed its functional relevance for alveolar differentiation. Our incorporation of epigenetic data allowed specific identification of transcription factors that are potential direct upstream regulators of the differentiation process, demonstrating the power of this approach. Integration of epigenomic data with transcriptomic profiling has broad application for the identification of regulatory pathways in other models of differentiation.

Tissue-Specific Control of Tissue-Resident Memory T Cells

“…These lung T RM niches are the tissue repair-associated regions and co-localize with the production of T RM promoting factors TGF-β and IL-15. 47,72 Notably, the regeneration of damaged airway epithelium is also TGF-β-dependent, 78 providing an example of complex functions of TGF-β signaling in both local immunity and tissue homeostasis. The gradual decline of lung T RM cells is caused by the completion of injured lung regeneration and the shrinking of lung T RM niches.…”

Combinations of differentiation markers distinguish subpopulations of alveolar epithelial cells in adult lung

“…Paraffin-embedded normal human lungs were prepared from rejected lung transplant donors (13). This study was approved by the Institutional Review Board for Human Subjects Research and the Institutional Animal Care and Use Committee of the University of Southern California.…”

Knockout Mice Reveal Key Roles for Claudin 18 in Alveolar Barrier Properties and Fluid Homeostasis

“…Analysis of gene expression in human AEC transdifferentiation was recently described (16). Whole lung gene expression analysis of wild-type (WT) versus C18 KO mice was performed using the Illumina MouseRef8 v2 platform (Illumina, San Diego, CA).…”