IL1RAP expression and the enrichment of IL-33 activation signatures in severe neutrophilic asthma

Abstract

Background: Interleukin (IL)-33 is an upstream regulator of type 2 (T2) eosinophilic inflammation and has been proposed as a key driver of some asthma phenotypes.

Objective: To derive gene signatures from in vitro studies of IL-33-stimulated cells and use these to determine IL-33-associated enrichment patterns in asthma.

Methods: Signatures downstream of IL-33 stimulation were derived from our in vitro study of human mast cells and from public datasets of in vitro stimulated human basophils, type 2 innate lymphoid cells (ILC2), regulatory T cells (Treg) and endothelial cells. Gene Set Variation Analysis (GSVA) was used to probe U-BIOPRED and ADEPT sputum transcriptomics to determine enrichment scores (ES) for each signature according to asthma severity, sputum granulocyte status and previously defined molecular phenotypes.

Results: IL-33-activated gene signatures were cell-specific with little gene overlap. Individual signatures, however, were associated with similar signalling pathways (TNF, NF-κB, IL-17 and JAK/STAT signalling) and immune cell differentiation pathways (Th17, Th1 and Th2 differentiation). ES for IL-33-activated gene signatures were significantly enriched in asthmatic sputum, particularly in patients with neutrophilic and mixed granulocytic phenotypes. IL-33 mRNA expression was not elevated in asthma whereas the expression of mRNA for IL1RL1, the IL-33 receptor, was up-regulated in the sputum of severe eosinophilic asthma. The mRNA expression for IL1RAP, the IL1RL1 co-receptor, was greatest in severe neutrophilic and mixed granulocytic asthma.

Conclusions: IL-33-activated gene signatures are elevated in neutrophilic and mixed granulocytic asthma corresponding with IL1RAP co-receptor expression. This suggests incorporating T2-low asthma in anti-IL-33 trials.

Keywords: IL-33; gene set variation analysis; severe asthma.

FIGURE 1

Venn diagram plot of the different cell type generated IL‐33 signatures for (A) up‐regulated (B) and down‐regulated signatures. No consensus overlap is seen; however, there is noted overlap between pairs of signatures

FIGURE 2

Gene Set Variation Analysis (GSVA) boxplots of U‐BIOPRED blood asthma enrichment scores by severity cohort (HC = healthy control; MMA = mild–moderate asthma; SAs/ex = severe asthma smoking/ex‐smoking; and SAns = severe asthma non‐smoking) for the mast cell, basophil, ILC2 and HUVEC cell‐derived IL‐33‐activated up‐regulated gene signatures for blood (A‐D) and sputum (E‐H)

FIGURE 3

Gene Set Variation Analysis (GSVA) boxplots of U‐BIOPRED sputum enrichment scores for the mast cell, basophil, ILC2 and HUVEC cell‐derived IL‐33‐activated up‐regulated gene signatures by granulocytic subtype (HC = healthy control, P = paucigranulocytic, E = eosinophilic, N = neutrophilic and M = mixed) (A‐D) and transcriptome associated cluster (TAC) which reflects eosinophilic and non‐eosinophilic phenotypes of asthma (TAC1 = eosinophilic asthma, TAC2 = neutrophilic asthma, TAC3 = mixed or paucigranulocytic asthma) (E‐H). These TAC subtypes are novel asthma phenotypes which were derived from clustering performed on differential gene expression analysis between eosinophilic and non‐eosinophilic U‐BIOPRED asthmatic sputum transcriptomics

FIGURE 4

Gene Set Variation Analysis (GSVA) boxplots of ADEPT sputum asthma enrichment scores for the mast cell, basophil, ILC2 and HUVEC cell‐derived IL‐33‐activated up‐regulated gene signatures by severity cohort (SA = severe asthma; ModA = moderate asthma; MldA = mild asthma; and HC = healthy control) (A‐D) and granulocytic subtype (HC = healthy control, P = paucigranulocytic, E = eosinophilic, N = neutrophilic, and M = mixed) (E‐H)

FIGURE 5

Boxplots of U‐BIOPRED blood asthma gene expression for IL‐33, IL1RL1 (ST2) and IL1RAP (co‐dimer of the IL‐33 receptor) by severity cohort (HC = healthy control; MMA = mild–moderate asthma; SAs/ex = severe asthma smoking/ex‐smoking; and SAns = severe asthma non‐smoking) (A, D, G), granulocytic subtype (HC = Healthy Control, P = Paucigranulocytic, E = Eosinophilic, N = Neutrophilic and M = Mixed) (B, E, H), and transcriptome associated cluster (C, F, I) which reflects eosinophilic and non‐eosinophilic phenotypes of asthma (TAC1 = eosinophilic asthma, TAC2 = neutrophilic asthma and TAC3 = mixed or paucigranulocytic asthma)

FIGURE 6

Boxplots of U‐BIOPRED sputum asthma gene expression for IL‐33, IL1RL1 (ST2) and IL1RAP (co‐dimer of the IL‐33 receptor) by severity cohort (HC = healthy control; MMA = mild–moderate asthma; SAs/ex = severe asthma smoking/ex‐smoking; SAns = severe asthma non‐smoking) (A, D, G), granulocytic subtype (HC = healthy control, P = paucigranulocytic, E = eosinophilic, N = neutrophilic and M = mixed) (B, E, H), and transcriptome associated cluster (C, F, I) which reflects eosinophilic and non‐eosinophilic phenotypes of asthma (TAC1 = eosinophilic asthma, TAC2 = neutrophilic asthma and TAC3 = mixed or paucigranulocytic asthma)