Transcriptomic Differentiation of Phenotypes in Chronic Rhinosinusitis and Its Implications for Understanding the Underlying Mechanisms

Abstract

Chronic rhinosinusitis (CRS) is a multifaceted disease with variable clinical courses and outcomes. We aimed to determine CRS-associated nasal-tissue transcriptome in clinically well-characterized and phenotyped individuals, to gain a novel insight into the biological pathways of the disease. RNA-sequencing of tissue samples of patients with CRS with polyps (CRSwNP), without polyps (CRSsNP), and controls were performed. Characterization of differently expressed genes (DEGs) and functional and pathway analysis was undertaken. We identified 782 common CRS-associated nasal-tissue DEGs, while 375 and 328 DEGs were CRSwNP- and CRSsNP-specific, respectively. Common key DEGs were found to be involved in dendritic cell maturation, the neuroinflammation pathway, and the inhibition of the matrix metalloproteinases. Distinct CRSwNP-specific DEGs were involved in NF-kβ canonical pathways, Toll-like receptor signaling, HIF1α regulation, and the Th2 pathway. CRSsNP involved the NFAT pathway and changes in the calcium pathway. Our findings offer new insights into the common and distinct molecular mechanisms underlying CRSwNP and CRSsNP, providing further understanding of the complex pathophysiology of the CRS, with future research directions for novel treatment strategies.

Keywords: RNA; phenotype; sequence analysis; sinusitis; transcriptome.

Figure 1

Venn diagram (A) and differential gene expression (B) in CRSwNP, CRSsNP, and controls. The proposed unique phenotype-associated DEGs with the highest differential expression in one of the phenotypes are presented in red (●) for CRSwNP and blue (●) for CRSsNP.

Figure 2

Comparison of enriched canonical pathways in CRSwNP and CRSsNP. The plot is based on the Z-score calculations obtained for a given set of genes using QIAGEN’s Ingenuity® Pathway Analysis (IPA®, QIAGEN, www.qiagen.com/ingenuity (accessed on 20 November 2021)). A positive Z-score represents strongly activated (Z-score > 2) pathways, and a negative Z-score represents significantly inhibited (Z-score < −2) pathways. Proposed unique phenotype-associated pathways are presented in red (●) for CRSwNP and in blue (●) for CRSsNP. Details in Supplementary Table S2 (Canonical pathways).

Figure 3

Comparison of enriched upstream regulators in CRSwNP and CRSsNP. The plot is based on the Z-score calculations obtained for a given set of genes, using the IPA analysis. A positive Z-score represents strongly activated (Z-score > 2) pathways, and a negative Z-score represents significantly inhibited (Z-score < −2) pathways. Proposed unique phenotype-associated pathways are presented in red (●) for CRSwNP and in blue (●) for CRSsNP. Details in Supplementary Table S3 (Canonical pathways).

Figure 4

Comparison of enriched diseases and functions in CRSwNP and CRSsNP. The plot is based on the Z-score calculations obtained for a given set of genes, using the IPA analysis. A positive Z-score represents strongly activated (Z-score > 2) pathways, and a negative Z-score represents significantly inhibited (Z-score < −2) pathways. Proposed unique phenotype-associated pathways are presented in red (●) for CRSwNP and blue (●) for CRSsNP. Details in Supplementary Table S4 (Diseases and functions).

Figure 5

The inclusion flowchart.

Figure 6

Graphical-study flowchart depicting several steps from initial tissue biopsy to RNA extraction, assessment of RNA quality, sample library preparation, and sequencing, with final stages of DEG and functional analysis using QIAGEN’s Ingenuity^® Pathway Analysis (IPA^®, QIAGEN, www.qiagen.com/ingenuity (accessed on 20 November 2021)).