Comprehensive epigenomic profiling of human alveolar epithelial differentiation identifies key epigenetic states and transcription factor co-regulatory networks for maintenance of distal lung identity

B Zhou,D Mullen,K D Siegmund,S K Lynch,T R Stueve,E A Mihalakakos,C N Marconett,L Miao,Z Borok,Y Wang,E Tran,A L Ryan,I A Offringa,Y Liu,J Luo

doi:10.1186/s12864-021-08152-6

Abstract

BackgroundDisruption of alveolar epithelial cell (AEC) differentiation is implicated in distal lung diseases such as chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and lung adenocarcinoma that impact morbidity and mortality worldwide. Elucidating underlying disease pathogenesis requires a mechanistic molecular understanding of AEC differentiation. Previous studies have focused on changes of individual transcription factors, and to date no study has comprehensively characterized the dynamic, global epigenomic alterations that facilitate this critical differentiation process in humans.ResultsWe comprehensively profiled the epigenomic states of human AECs during type 2 to type 1-like cell differentiation, including the methylome and chromatin functional domains, and integrated this with transcriptome-wide RNA expression data. Enhancer regions were drastically altered during AEC differentiation. Transcription factor binding analysis within enhancer regions revealed diverse interactive networks with enrichment for many transcription factors, including NKX2–1 and FOXA family members, as well as transcription factors with less well characterized roles in AEC differentiation, such as members of the MEF2, TEAD, and AP1 families. Additionally, associations among transcription factors changed during differentiation, implicating a complex network of heterotrimeric complex switching in driving differentiation. Integration of AEC enhancer states with the catalog of enhancer elements in the Roadmap Epigenomics Mapping Consortium and Encyclopedia of DNA Elements (ENCODE) revealed that AECs have similar epigenomic structures to other profiled epithelial cell types, including human mammary epithelial cells (HMECs), with NKX2–1 serving as a distinguishing feature of distal lung differentiation.ConclusionsEnhancer regions are hotspots of epigenomic alteration that regulate AEC differentiation. Furthermore, the differentiation process is regulated by dynamic networks of transcription factors acting in concert, rather than individually. These findings provide a roadmap for understanding the relationship between disruption of the epigenetic state during AEC differentiation and development of lung diseases that may be therapeutically amenable.

Highlights

Disruption of alveolar epithelial cell (AEC) differentiation is implicated in distal lung diseases such as chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and lung adenocarcinoma that impact morbidity and mortality worldwide
These findings provide a roadmap for understanding the relationship between disruption of the epigenetic state during AEC differentiation and development of lung diseases that may be therapeutically amenable
Our results suggest the association of forkhead box protein A1 (FOXA1), NK2 homeobox 1 (NKX2–1), and MEF2C may act in a cooperative heterotrimeric Transcription factor (TF) complex which binds to alveolar epithelial type 1 (AT1)-like enhancers as part of a coordinated effort to differentiate the alveolar epithelium, which is reflected in concomitant alterations to the epigenetic state to mediate cellular fate determination

Summary

Introduction

Disruption of alveolar epithelial cell (AEC) differentiation is implicated in distal lung diseases such as chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and lung adenocarcinoma that impact morbidity and mortality worldwide. Enhancers are epigenetic regulatory elements that can act at great distances from their target promoters to control activation of gene expression, and can play a key role in cell type specification and regulation of disease processes [14]. They are characterized by a nucleosome-depleted stretch of DNA that allows for transcription factor binding. The open region identified by FAIRE is commonly bound by transcription factors that function to regulate downstream target gene expression levels Often these regions are found to be depleted of CpG methylation [16]

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