Respiratory Syncytial Virus Infection Induces Chromatin Remodeling to Activate Growth Factor and Extracellular Matrix Secretion Pathways

Xiaofang Xu,Morgan Mann,Dianhua Qiao,Roberto P Garofalo,Allan R Brasier

doi:10.3390/v12080804

Abstract

Lower respiratory tract infection (LRTI) with respiratory syncytial virus (RSV) is associated with reduced lung function through unclear mechanisms. In this study, we test the hypothesis that RSV infection induces genomic reprogramming of extracellular matrix remodeling pathways. For this purpose, we sought to identify transcriptionally active open chromatin domains using assay for transposase-accessible-next generation sequencing (ATAC-Seq) in highly differentiated lower airway epithelial cells. High confidence nucleosome-free regions were those predicted independently using two peak-calling algorithms. In uninfected cells, ~12,650 high-confidence open chromatin regions were identified. These mapped to ~8700 gene bodies, whose genes functionally controlled organelle synthesis and Th2 pathways (IL6, TSLP). These latter cytokines are preferentially secreted by RSV-infected bronchiolar cells and linked to mucous production, obstruction, and atopy. By contrast, in RSV infection, we identify ~1700 high confidence open chromatin domains formed in 1120 genes, primarily in introns. These induced chromatin modifications are associated with complex gene expression profiles controlling tyrosine kinase growth factor signaling and extracellular matrix (ECM) secretory pathways. Of these, RSV induces formation of nucleosome-free regions on TGFB1/JUNB//FN1/MMP9 genes and the rate limiting enzyme in the hexosamine biosynthetic pathway (HBP), Glutamine-Fructose-6-Phosphate Transaminase 2 (GFPT2). RSV-induced open chromatin domains are highly enriched in AP1 binding motifs and overlap experimentally determined JUN peaks in GEO ChIP-Seq data sets. Our results provide a topographical map of chromatin accessibility and suggest a growth factor and AP1-dependent mechanism for upregulation of the HBP and ECM remodeling in lower epithelial cells that may be linked to long-term airway remodeling.

Highlights

Respiratory syncytial virus (RSV) is single-stranded, negative-sense member of the Orthopneumovirus genus of the Pneuomoviridae family that represents a major cause of acute pulmonary disease in children, adults with chronic airway disease and the hospitalized elderly
We examined the resting and inducible chromatin landscape in human small airway epithelial cells. hSAECs are derived from Scgb1a1+-expressing progenitor cells, representing the distal bronchiole phenotype associated with pathogenicity of RSV pneumonia in vivo [7]
Uninfected and RSV infected hSAECs (MOI = 1, 24 h) were subjected to assay for transposase-accessible chromatin (ATAC)-Seq and paired end reads were obtained on a NovaSeq 6000

Summary

Introduction

Respiratory syncytial virus (RSV) is single-stranded, negative-sense member of the Orthopneumovirus genus of the Pneuomoviridae family that represents a major cause of acute pulmonary disease in children, adults with chronic airway disease and the hospitalized elderly. Virtually all children are infected by the age of two [1]. A subgroup of those infected, estimated to number ~2.1 million children under five years of age, require medical attention in the US annually [2]. RSV represents the most common cause of pediatric hospitalization in children less than five years of age [3]. A subset will develop severe lower respiratory tract infections (LRTIs), such as bronchiolitis and pneumonia. LRTIs are linked to recurrent virus induced wheezing [4], atopy [5], and decreased lung function [6]

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Results

Conclusion