Journal Article

Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome

Fingerlin, Tasha E., Rodriguez-Santana, Jose, Wesolowska-Andersen, Agata, Seibold, Max A., Liu, Andrew H., Everman, Jamie L., Eng, Celeste, Davidson, Rebecca, Rios, Cydney, Janssen, William J., Herrin, Rachelle, Oh, Sam S., Kumar, Rajesh, Burchard, Esteban G.

2017

Overview

Background Respiratory illness caused by viral infection is associated with the development and exacerbation of childhood asthma. Little is known about the effects of respiratory viral infections in the absence of illness. Using quantitative PCR (qPCR) for common respiratory viruses and for two genes known to be highly upregulated in viral infections ( CCL8 / CXCL11 ), we screened 92 asthmatic and 69 healthy children without illness for respiratory virus infections. Results We found 21 viral qPCR-positive and 2 suspected virus-infected subjects with high expression of CCL8/CXCL11 . We applied a dual RNA-seq workflow to these subjects, together with 25 viral qPCR-negative subjects, to compare qPCR with sequencing-based virus detection and to generate the airway transcriptome for analysis. RNA-seq virus detection achieved 86% sensitivity when compared to qPCR-based screening. We detected additional respiratory viruses in the two CCL8/CXCL11 -high subjects and in two of the qPCR-negative subjects. Viral read counts varied widely and were used to stratify subjects into Virus-High and Virus-Low groups. Examination of the host airway transcriptome found that the Virus-High group was characterized by immune cell airway infiltration, downregulation of cilia genes, and dampening of type 2 inflammation. Even the Virus-Low group was differentiated from the No-Virus group by 100 genes, some involved in eIF2 signaling. Conclusions Respiratory virus infection without illness is not innocuous but may determine the airway function of these subjects by driving immune cell airway infiltration, cellular remodeling, and alteration of asthmogenic gene expression.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Airway epithelium / Animal Genetics and Genomics / Asthma / Asthma - complications / Asthma - genetics / Asthma - immunology / Asymptomatic / Bioinformatics / Biomedical and Life Sciences / Case-Control Studies / Child / childhood / Children / Cilia / CXCL11 protein / Deoxyribonucleic acid / DNA / Evolutionary Biology / Gene expression / Gene Expression Profiling / gene expression regulation / Gene Expression Regulation, Viral / genes / Genomes / High-Throughput Nucleotide Sequencing / Host-Pathogen Interactions - genetics / Host-Pathogen Interactions - immunology / Human Genetics / Humans / Illnesses / Infection / Infections / inflammation / Life Sciences / Methods / Microbial Genetics and Genomics / Plant Genetics and Genomics / quantitative polymerase chain reaction / Respiratory diseases / Respiratory Mucosa - immunology / Respiratory Mucosa - metabolism / Respiratory Mucosa - virology / Respiratory tract / Respiratory Tract Infections - complications / Respiratory Tract Infections - genetics / Respiratory Tract Infections - immunology / Respiratory Tract Infections - virology / Ribonucleic acid / RNA / RNA Virus Infections - complications / RNA Virus Infections - genetics / RNA Virus Infections - immunology / RNA Virus Infections - virology / RNA viruses / RNA Viruses - genetics / RNA-seq / screening / sequence analysis / Sequence Analysis, RNA / Transcriptome / Viral infections / Virus / Viruses