Use of a multiplex transcript method for analysis of Pseudomonas aeruginosa gene expression profiles in the cystic fibrosis lung

Alex H. Gifford, Sven D. Willger, Emily L. Dolben, Lisa A. Moulton, Dana B. Dorman, Heather Bean, Jane E. Hill, Thomas H. Hampton, Alix Ashare, Deborah A. Hogan

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

The discovery of therapies that modulate Pseudomonas aeruginosa virulence or that can eradicate chronic P. aeruginosa lung infections associated with cystic fibrosis (CF) will be advanced by an improved understanding of P. aeruginosa behavior in vivo. We demonstrate the use of multiplexed Nanostring technology to monitor relative abundances of P. aeruginosa transcripts across clinical isolates, in serial samples, and for the purposes of comparing microbial physiology in vitro and in vivo. The expression of 75 transcripts encoded by genes implicated in CF lung disease was measured in a variety of P. aeruginosa strains as well as RNA serial sputum samples from four P. aeruginosa-colonized subjects with CF collected over 6 months. We present data on reproducibility, the results from different methods of normalization, and demonstrate high concordance between transcript relative abundance data obtained by Nanostring or transcriptome sequencing (RNA-Seq) analysis. Furthermore, we address considerations regarding sequence variation between strains during probe design. Analysis of P. aeruginosa grown in vitro identified transcripts that correlated with the different phenotypes commonly observed in CF clinical isolates. P. aeruginosa transcript profiles in RNA from CF sputum indicated alginate production in vivo, and transcripts involved in quorum-sensing regulation were less abundant in sputum than strains grown in the laboratory. P. aeruginosa gene expression patterns from sputum clustered closely together relative to patterns for laboratory-grown cultures; in contrast, laboratory-grown P. aeruginosa showed much greater transcriptional variation with only loose clustering of strains with different phenotypes. The clustering within and between subjects was surprising in light of differences in inhaled antibiotic and respiratory symptoms, suggesting that the pathways represented by these 75 transcripts are stable in chronic CF P. aeruginosa lung infections.

Original languageEnglish (US)
Pages (from-to)2995-3006
Number of pages12
JournalInfection and Immunity
Volume84
Issue number10
DOIs
StatePublished - 2016

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Transcriptome
Cystic Fibrosis
Pseudomonas aeruginosa
Lung
Sputum
Cluster Analysis
RNA
RNA Sequence Analysis
Phenotype
Quorum Sensing
Infection
Reproducibility of Results
Lung Diseases
Virulence
Anti-Bacterial Agents
Technology
Gene Expression

ASJC Scopus subject areas

  • Parasitology
  • Microbiology
  • Immunology
  • Infectious Diseases

Cite this

Use of a multiplex transcript method for analysis of Pseudomonas aeruginosa gene expression profiles in the cystic fibrosis lung. / Gifford, Alex H.; Willger, Sven D.; Dolben, Emily L.; Moulton, Lisa A.; Dorman, Dana B.; Bean, Heather; Hill, Jane E.; Hampton, Thomas H.; Ashare, Alix; Hogan, Deborah A.

In: Infection and Immunity, Vol. 84, No. 10, 2016, p. 2995-3006.

Research output: Contribution to journalArticle

Gifford, AH, Willger, SD, Dolben, EL, Moulton, LA, Dorman, DB, Bean, H, Hill, JE, Hampton, TH, Ashare, A & Hogan, DA 2016, 'Use of a multiplex transcript method for analysis of Pseudomonas aeruginosa gene expression profiles in the cystic fibrosis lung', Infection and Immunity, vol. 84, no. 10, pp. 2995-3006. https://doi.org/10.1128/IAI.00437-16
Gifford, Alex H. ; Willger, Sven D. ; Dolben, Emily L. ; Moulton, Lisa A. ; Dorman, Dana B. ; Bean, Heather ; Hill, Jane E. ; Hampton, Thomas H. ; Ashare, Alix ; Hogan, Deborah A. / Use of a multiplex transcript method for analysis of Pseudomonas aeruginosa gene expression profiles in the cystic fibrosis lung. In: Infection and Immunity. 2016 ; Vol. 84, No. 10. pp. 2995-3006.
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