Tissue Eosinophilia is Superior to an Analysis by Polyp Status for the Chronic Rhinosinusitis Transcriptome: An RNA Study

Abstract

ObjectiveRNA sequencing (transcriptomics) is used to study biological pathways. However, the yield of data depends on comparing well‐characterized cohorts. We compared tissue eosinophilia versus nasal polyp (NP) status as the metric to characterize transcriptomic mechanisms at play in eosinophilic and non‐eosinophilic chronic rhinosinusitis (CRS) versus controls.MethodsRNA sequencing was conducted on sinonasal tissue samples of CRS and controls. Analyses were conducted based on polyp status [with nasal polyps (CRSwNP) and without nasal polyps (CRSsNP)] as well as tissue eosinophil levels per high power field (eos/hpf)[non‐eosinophilic (<10 eos/hpf, neCRS) or eosinophilic (≥10 eos/hpf, eCRS)]. The yield of differentially expressed genes (DEGs) and biological pathways through Ingenuity Pathway Analysis (IPA) were compared.ResultsCRS tissue differed from controls by 736 statistically significant DEGs. Both NP status and tissue eosinophilia were effective in differentiating CRS from controls and into two distinct subgroups. Statistically significant DEGs identified when comparing CRS by NP status were 60, whereas 110 DEGs were identified using eosinophil cutoff ≥10 and <10 eos/hpf. Additionally, heatmaps showed greater homogeneity within each CRS subgroup when analyzed by tissue eosinophilia versus NP status. On IPA, the IL‐17 signaling pathway was significantly different only by tissue eosinophilia status, not NP status, being higher in CRS <10 eos/hpf.ConclusionTissue eosinophilia is superior to an analysis by NP status for the study of CRS transcriptome by RNA sequencing in identifying DEGs. Classification of CRS samples by eosinophil counts agnostic of NP status may offer advantageous insights into CRS pathogenetic mechanisms.Level of Evidence3 Laryngoscope, 133:2480–2489, 2023

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

“…We have also confirmed a series of downregulated antimicrobial genes such as lacritin LACRT, the proline-rich protein Haell subfamily 2 PRH2 [ 57 , 58 ], or immune-response-inducing lipocalin 1 LCN1 [ 59 ]. The latter was also confirmed in eosinophilic CRS by Brar et al [ 18 ]. CRSwNP patients have a downregulated secretagogin SCGN gene, proven to be involved in early-onset inflammatory bowel disease; the alteration of their gene expression might reveal modified innate immunity, thus also showing a possible genetic basis for the inflammatory reaction [ 60 ].…”

“…Common pathways of T2 inflammation in asthma or atopic dermatitis may help identify cardinal processes [ 16 , 17 ]. Rigorous study design in a clear-cut phenotype is a prerequisite to successfully interpreting big data in any genetic study [ 2 , 18 ]. This study aimed to shed new light on the biological pathways and markers of different phenotypes in CRS (CRSsNP and CRSwNP) compared to healthy individuals, with a transcriptomic analysis of genes, and to share the publicly available dataset to fulfill the gaps in understanding of the pathophysiology of CRS.…”

Genome-wide Epigenetic Study of Chronic Rhinosinusitis Tissues Reveals Dysregulated Inflammatory, Immunologic and Remodeling Pathways

“…In other studies, we continue to find biomarkers to create tighter cohorts for genetic studies. 82 We also do not currently understand the role of some of the pathways identified, particularly for CRSsNP. However, results from the differential analysis are likely plausible, given the identification of several previously identified candidates such as TGFB1 and TNF, similar to Asian studies.…”

Genomewide epigenetic study shows significant DNA hypermethylation in chronic rhinosinusitis versus control ethmoidal tissue

“…Additionally, we identified Th1 and Th2 activation pathway and Th2 pathway in CRS/CRSwNP versus controls, evidence that polyp status alone may not be an accurate marker to subclassify CRS. 10 TGFβ1 and SMAD3 emerged as one of the top URs in comparing CRS/CRSwNP with controls. TGFβ1 has been widely implicated in other genetic/epigenetic studies in CRS.…”

“…In our previous study, comparing inferior turbinate mucosa (ITM) of controls with ethmoidal tissue (ET) of CRS subjects, we found methylation differences in inflammatory, immunologic, and remodeling pathways. 2 Other DNA methylation studies come from outside the United States, and also used ITM or uncinate process or "nasal mucosa tissue" as control tissue. 3,4 This study investigates differential DNA methylation in ET from both CRS and controls, constituting the first of its kind genome-wide DNA methylation study in CRS.…”