Translating transcription: proteomics in chronic rhinosinusitis with nasal polyps reveals significant discordance with messenger RNA expression

Abstract

Background: Much of the literature examining chronic rhinosinusitis with nasal polyps (CRSwNP) immunopathology has been predicated on messenger RNA (mRNA) analysis with the assumption that transcriptional changes would reflect end-effector protein expression. The purpose of this study was to test this hypothesis using matched transcriptomic and proteomic data sets. Methods:Matched tissue proteomic and transcriptomic arrays were quantified in CRSwNP polyp tissue and control inferior turbinate tissue (n = 10/group). Mucus samples were additionally collected in 6 subjects from each group. Proteins were grouped into functional categories by bioinformatics and differential expression analyses. Log-log regression and Pearson correlations were performed to determine the level of agreement between data sets. Results:Of the 1310 proteins examined, 393 were significantly differentially expressed in CRSwNP. On regression analysis, differences in protein expression were poorly predicted by differences in mRNA expression (R 2 = 0.020, p < 0.05). Several genes canonically thought to be overexpressed in CRSwNP, including IL-5, IL-13, TSLP, CCL13, and CCL26, showed substantial increases in mRNA transcription, but had minimally or unchanged protein expres-sion. Others, including IgE, periostin, CCL18, and CST1/2, were increased at both the transcriptomic and proteomic levels. Among differentially regulated proteins, tissue and mucus protein levels showed weak correlation (r = 0.26, p < 0.0001).Conclusion: Proteomic analysis in CRSwNP has revealed novel disease-associated proteins and pathways, yet correlates poorly with transcriptomic data. The increasing availability of proteomic arrays opens the door to new potential explanatory mechanisms in CRSwNP and suggests that mRNA based studies should be validated with protein analysis. C 2019 ARS-AAOA, LLC.

Unexpected effects of systemic steroids on the CRSwNP proteome: is protein upregulation more important than inhibition?

“…Exosome samples were obtained from 12 CRSwNP patients; demographic data are shown in Table . Previous comprehensive proteomic work utilizing the SOMAscan platform identified 71 proteins with FD of at least 2 in CRSwNP subjects compared with control subjects (ie, 50% lower protein concentration or 100% higher protein concentration in CRSwNP). These proteins were significantly differentially expressed, and thus identified as altered in CRSwNP.…”

“…Although care was taken in our study to exclude patients with oral steroid and antibiotic exposure, the possible use of nasal steroid sprays as well as antihistamines in a subset of our patients could confound the data. Despite these limitations, proteomic analysis is likely the highest fidelity way to measure end‐effector alterations in disease, as genetic sequencing and transcriptomics do not appear to reflect differences in protein with a high degree of accuracy …”

“…CRSwNP symptomatology is severe, often requiring frequent medical and surgical interventions to lower morbidity . Recent advances in our understanding of perturbations observed in the CRSwNP proteome have brought forth new potential diagnostic and therapeutic targets . These advances have come about through large‐scale efforts to analyze the transcriptome and proteome in health and disease, through direct tissue sampling and “liquid biopsy” of exosomes.…”

“…Research efforts from several groups over the past 5 years demonstrated altered protein expression levels for a wide variety of targets in CRSwNP, [13][14][15][16] including our recent work revealing 71 proteins with a fold difference (FD) of at least 2 in CRSwNP subjects. 5 Enrichment analysis revealed that a wide variety of upregulated and downregulated biologic and molecular processes were represented by these proteins, highlighting the complex and multifactorial nature of the disease. However, it is unclear which of these proteins are static or variant to medical and surgical treatments.…”

Sample collection for laboratory‐based study of the nasal airway and sinuses: a research compendium

“…They further noted that the samples collected via polyurethane foam were stable for at least 1 month at 4°C or colder. Like other focal surface fluid collection techniques, foam sponges can be directed at different anatomic regions of interest, such as the internal nasal valve or ethmoid bulla, among others.…”