title: The Healthy Infant Nasal Transcriptome: A Benchmark Study.
abstract: Responses by resident cells are likely to play a key role in determining the severity of respiratory disease. However, sampling of the airways poses a significant challenge, particularly in infants and children. Here, we report a reliable method for obtaining nasal epithelial cell RNA from infants for genome-wide transcriptomic analysis, and describe baseline expression characteristics in an asymptomatic cohort. Nasal epithelial cells were collected by brushing of the inferior turbinates, and gene expression was interrogated by RNA-seq analysis. Reliable recovery of RNA occurred in the absence of adverse events. We observed high expression of epithelial cell markers and similarity to the transcriptome for intrapulmonary airway epithelial cells. We identified genes displaying low and high expression variability, both inherently, and in response to environmental exposures. The greatest gene expression differences in this asymptomatic cohort were associated with the presence of known pathogenic viruses and/or bacteria. Robust bacteria-associated gene expression patterns were significantly associated with the presence of Moraxella. In summary, we have developed a reliable method for interrogating the infant airway transcriptome by sampling the nasal epithelium. Our data demonstrates both the fidelity and feasibility of our methodology, and describes normal gene expression and variation within a healthy infant cohort.
authors.affiliation: Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, University of Rochester Medical Center, Rochester NY, USA.
authors.forename: Chin-Yi
authors.initials: CY
authors.lastname: Chu
authors.affiliation: Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester NY, USA.
authors.forename: Xing
authors.initials: X
authors.lastname: Qiu
authors.affiliation: Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester NY, USA.
authors.forename: Lu
authors.initials: L
authors.lastname: Wang
authors.affiliation: Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, University of Rochester Medical Center, Rochester NY, USA.
authors.forename: Soumyaroop
authors.initials: S
authors.lastname: Bhattacharya
authors.affiliation: Department of Medicine, University of Rochester Medical Center, Rochester NY, USA.
authors.forename: Gerry
authors.initials: G
authors.lastname: Lofthus
authors.affiliation: Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester NY, USA.
authors.forename: Anthony
authors.initials: A
authors.lastname: Corbett
authors.affiliation: Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester NY, USA.
authors.forename: Jeanne
authors.initials: J
authors.lastname: Holden-Wiltse
authors.affiliation: Department of Microbiology and Immunology and University of Rochester Medical Center, Rochester NY, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Grier
authors.affiliation: Division of Pediatric Infectious Diseases, University of Rochester Medical Center, Rochester NY, USA.
authors.forename: Brenda
authors.initials: B
authors.lastname: Tesini
authors.affiliation: Department of Microbiology and Immunology and University of Rochester Medical Center, Rochester NY, USA.
authors.forename: Steven R
authors.initials: SR
authors.lastname: Gill
authors.affiliation: Department of Medicine, Rochester General Hospital University of Rochester Medical Center, Rochester NY, USA.
authors.forename: Ann R
authors.initials: AR
authors.lastname: Falsey
authors.affiliation: Division of Pediatric Infectious Diseases, University of Rochester Medical Center, Rochester NY, USA.
authors.forename: Mary T
authors.initials: MT
authors.lastname: Caserta
authors.affiliation: Department of Medicine, Rochester General Hospital University of Rochester Medical Center, Rochester NY, USA.
authors.forename: Edward E
authors.initials: EE
authors.lastname: Walsh
authors.affiliation: Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, University of Rochester Medical Center, Rochester NY, USA.|Department of Medicine, University of Rochester Medical Center, Rochester NY, USA.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Mariani