Single cell RNA sequencing of human eosinophils from nasal polyps reveals eosinophil heterogeneity in chronic rhinosinusitis tissue.

Background: Chronic rhinosinusitis with nasal polyps (CRSwNP) is characterized by type 2 inflammation in the United States, but the actual roles that eosinophils play in CRSwNP remain largely unclear.
Objective: To reveal the roles and heterogeneity of eosinophils in nasal polyp (NP) tissue, we performed single cell RNA sequencing (scRNA-Seq) analysis of NP tissue.
Methods: Sinonasal tissues (NP and control sinus tissue) and patient matched peripheral blood (PB) samples were obtained from 5 control patients and 5 patients with CRSwNP. Eosinophils were enriched before processing for scRNA-Seq. The gene expression profiles in eosinophils were determined by microwell-based scRNA-Seq technology (BD Rhapsody platform). We predicted the overall function of NP eosinophils by Gene Ontology (geneontology.org) enrichment and pathway analyses and confirmed expression of selected genes by flow cytometry.
Results: After filtering out contaminating cells, we detected 5,542 eosinophils from control PB, 3,883 eosinophils from CRSwNP PB, 101 eosinophils from control sinus tissues (not included in further analyses), and 9,727 eosinophils from NPs by scRNA-Seq. We found that 204 genes were downregulated and 354 genes upregulated in NP eosinophils compared to all PB eosinophils (>1.5-fold, P _adj  < .05). Upregulated genes in NP eosinophils were associated with activation, cytokine-mediated signaling, growth factor activity, NF-κB signaling, and antiapoptotic molecules. NP eosinophils displayed 4 clusters revealing potential heterogeneity of eosinophils in NP tissue.
Conclusions: Elevated eosinophils in NP tissue appear to exist in several subtypes that may play important pathogenic roles in CRSwNP, in part by controlling inflammation and hyperproliferation of other cells.
Competing Interests: Disclosure statement Supported in part by Regeneron Pharmaceuticals, the National Institutes of Health (grants P01AI145818, R01AI137174, and U19AI136443), and a grant from the Ernest S. Bazley Foundation. Disclosure of potential conflict of interest: W. W. Stevens has served on advisory boards for GlaxoSmithKline, Regeneron, and Melinta Therapeutics. A. T. Petershas served on advisory boards for Sanofi-Genzyme/Regeneron, Optinose, AstraZeneca, Novartis, and GSK; and has received research support from Optinose and Sanofi/Regeneron. L. C. Grammer reports personal fees from Astellas Pharmaceuticals. K. C. Welch reports consultant fees from Baxter, OptiNose, and Acclarent. D. B. Conley reports consulting fees from Medtronic and Sanofi/Regeneron. R. P. Schleimer reports personal fees from Intersect ENT, Merck, GlaxoSmithKline, Sanofi, AstraZeneca/Medimmune, Genentech, Actobio Therapeutics, Lyra Therapeutics, Astellas Pharma, and Otsuka; and has royalty rights to Siglec-8 and Siglec-8 ligand–related patents licensed by Johns Hopkins to Allakos. R. C. Kern reports consulting fees from Lyra Therapeutics, Medtronic, GSK, Genentech and Sanofi/Regeneron. B. S. Bochner has received remuneration for serving on scientific advisory board of Allakos and owns stock in Allakos; has served as consultant for GSK, Third Harmonic Bio, Lupagen, Acelyrin, and Sanofi/Regeneron; receives publication-related royalty payments from Elsevier and UpToDate; is coinventor of existing Siglec-8–related patents and thus may be entitled to a share of royalties received by Johns Hopkins University during development and potential sales of such products; and is a cofounder of Allakos, which makes him subject to certain restrictions under university policy (terms of this arrangement are being managed by Johns Hopkins University and Northwestern University in accordance with their conflict-of-interest policies). B. K. Tan reports personal fees from Sanofi/Regeneron/Genzyme and GSK. A. Kato has served on advisory board for AstraZeneca; reports gift for his research from Lyra Therapeutics; and has received research grants from Regeneron and AstraZeneca. The rest of the authors declare that they have no relevant conflicts of interest.
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