Dupilumab Treatment Is Associated With Clinical Improvement and a Shift Toward a Health-Associated Nasal Passage Microbiota in Diffuse Type 2 Chronic Rhinosinusitis

Abstract

Background: Nasal microbiota composition of patients with diffuse type 2 chronic rhinosinusitis with nasal polyps (CRSwNP) is altered compared to healthy individuals. Dupilumab, an anti-IL-4Rα-mAb, modulates type 2 inflammation, but the effect on microbiota composition in CRSwNP is unknown. The aim of this study was to investigate longitudinal effects of dupilumab on the nasal passage and gastrointestinal microbiota in patients with diffuse type 2 CRSwNP.

Methods: Twenty-seven patients with diffuse type 2 CRSwNP treated with dupilumab 300 mg subcutaneously every 2 weeks, 10 untreated patients with CRSwNP, and 11 healthy controls were included. Nasal and stool samples were collected at Days 0, 28, 90, and 180 posttreatment of the treated CRSwNP group and at Days 0 and 28 of untreated CRSwNP and healthy controls. The samples were analyzed using 16S rRNA gene amplicon sequencing (V3/V4).

Results: In CRSwNP patients, the most abundant genera in nasal passage microbiota were Corynebacterium and Staphylococcus. Cutibacterium and Lawsonella were less abundant in CRSwNP at baseline compared to healthy controls. Dupilumab treatment was associated with increased relative abundances in the nasal passage of genera such as Lawsonella, Corynebacterium, and Dolosigranulum. Microbial diversity of the gastrointestinal microbiota in CRSwNP at baseline was significantly higher than in healthy controls. There were no changes in gastrointestinal microbiota during dupilumab treatment.

Conclusion: Dupilumab treatment was associated with a shift in the nasal passage bacterial microbiota toward that of healthy controls, whereas the composition of gastrointestinal microbiota did not change. These findings suggest that nasal passage microbiota composition is influenced by the underlying inflammatory endotype.

Keywords: CRSwNP; biologicals; dupilumab; microbiome; microbiota; type 2 inflammation.

FIGURE 1

Alpha diversity of nasal passage and gut microbiota in patients with CRSwNP treated with dupilumab. (A–H) Alpha‐diversity indices (Shannon and Chao1) of nasal passage (A, B, E, F) and gut microbiota (C, D, G, H) of CRSwNP patients treated with dupilumab compared longitudinally (A–D) and compared to healthy controls (E–H) using paired Wilcoxon signed‐rank test for longitudinal analysis (A–D) and unpaired Wilcoxon signed‐rank test for comparison to healthy controls (E–H) with adjustment for multiple testing with Benjamini–Hochberg. In A–D, only paired samples with complete data for all timepoints are included. In E–H, all samples are plotted including incomplete datasets. p values are reported above the brackets: *< 0.05, **< 0.01, ***< 0.001.

FIGURE 2

Beta diversity of nasal passage and gut microbiota in patients with CRSwNP treated with dupilumab. (A, B) Beta diversity calculated using Bray–Curtis distance of gastrointestinal (A) and nasal passage (B) microbiota of the dupilumab cohort and control samples using PERMANOVA test. The circles indicate the similarity of the microbiota diversity in each subgroup. The closer two points, the more similar in composition are the corresponding samples.

FIGURE 3

Compositional data (relative abundance) and differential abundance analysis at genus level of nasal passage and gastrointestinal microbiota. (A, B) Most prevalent (> 10%) and abundant (> 5%) genera in nasal passage microbiota (A) and gastrointestinal microbiota (B); (C–F) Differential abundance analysis of most abundant genera using relative abundance of nasal passage microbiota compared to healthy and untreated CRSwNP controls (C) and longitudinally under dupilumab therapy (E) and of gastrointestinal microbiota compared to healthy and untreated CRSwNP controls (D) and longitudinally under dupilumab treatment (F). Paired Wilcoxon signed‐rank test on centered log‐ratio‐transformed data was used in E and F, and unpaired Wilcoxon signed‐rank test in C and D. (G, H) Heatmaps of differential abundance analysis at genus level using ANCOM‐BC2 analysis of nasal passage (G) and gastrointestinal (H) microbiota of patients under dupilumab treatment compared to healthy controls at timepoint 0, 28, 90, 180. Only significant genera are plotted. Log₂ fold change of the abundance for each genus is reported. The font coloring indicates sensitivity analysis for pseudocount addition; white coloring indicates passed sensitivity analysis and black colored field indicated not passed sensitivity analysis. p values are plotted above brackets: *< 0.05, **< 0.01, ***< 0.001.