Multidimensional endotyping using nasal proteomics predicts molecular phenotypes in the asthmatic airways

BACKGROUND

Unsupervised clustering of biomarkers derived from noninvasive samples such as nasal fluid is less evaluated as a tool for describing asthma endotypes.

OBJECTIVE

We sought to evaluate whether protein expression in nasal fluid would identify distinct clusters of patients with asthma with specific lower airway molecular phenotypes.

METHODS

Unsupervised clustering of 168 nasal inflammatory and immune proteins and Shapley values was used to stratify 43 patients with severe asthma (endotype of noneosinophilic asthma) using a 2 "modeling blocks" machine learning approach. This algorithm was also applied to nasal brushings transcriptomics from U-BIOPRED (Unbiased Biomarkers for the Prediction of Respiratory Diseases Outcomes). Feature reduction and functional gene analysis were used to compare proteomic and transcriptomic clusters. Gene set variation analysis provided enrichment scores of the endotype of noneosinophilic asthma protein signature within U-BIOPRED sputum and blood.

RESULTS

The nasal protein machine learning model identified 2 severe asthma endotypes, which were replicated in U-BIOPRED nasal transcriptomics. Cluster 1 patients had significant airway obstruction, small airways disease, air trapping, decreased diffusing capacity, and increased oxidative stress, although only 4 of 18 were current smokers. Shapley identified 20 cluster-defining proteins. Forty-one proteins were significantly higher in cluster 1. Pathways associated with proteomic and transcriptomic clusters were linked to T_H1, T_H2, neutrophil, Janus kinase-signal transducer and activator of transcription, TLR, and infection activation. Gene set variation analysis of the nasal protein and gene signatures were enriched in subjects with sputum neutrophilic/mixed granulocytic asthma and in subjects with a molecular phenotype found in sputum neutrophil-high subjects.

CONCLUSIONS

Protein or gene analysis may indicate molecular phenotypes within the asthmatic lower airway and provide a simple, noninvasive test for non-type 2 immune response asthma that is currently unavailable.

Mechanisms of allergen immunotherapy supporting its disease-modifying effect

Allergen immunotherapy (AIT) is considered the only disease-modifying treatment available at present for allergic disorders. Its main benefits include improvement of symptoms, decreased need for pharmacotherapy, prevention of new sensitizations and sustained effect after AIT completion. The key pillars of AIT-induced tolerance include a shift from Th2 to Th1 response, an increase of regulatory T and B cells, pro-inflammatory effector cell downregulation and IgE suppression, in addition to IgG4, IgA and IgD induction. AIT may also induce trained immunity, characterized by a durable decrease in group 2 of innate lymphoid cells (ILCs) and increased ILC1 and ILC3s. Understanding the immune mechanisms of AIT is essential for validating biomarkers for the prediction of AIT response and for achieving AIT success.

Precision medicine in the allergy clinic: the application of component resolved diagnosis

INTRODUCTION

A precise diagnosis is key for the optimal management of allergic diseases and asthma. In vivo or in vitro diagnostic methods that use allergen extracts often fail to identify the molecules eliciting the allergic reactions.

AREAS COVERED

Component-resolved diagnosis (CRD) has solved most of the limitations of extract-based diagnostic procedures and is currently valuable tool for the precision diagnosis in the allergy clinic, for venom and food allergy, asthma, allergic rhinitis, and atopic dermatitis. Its implementation in daily practice facilitates: a) the distinction between genuine multiple sensitizations and cross-reactive sensitization in polysensitized patients; b) the prediction of a severe, systemic reaction in food or insect venom allergy; c) the optimal selection of allergen immunotherapy based on the patient sensitization profile. This paper describes its main advantages and disadvantages, cost-effectiveness and future perspectives.

EXPERT OPINION

The diagnostic strategy based on CRD is part of the new concept of precision immunology, which aims to improve the management of allergic diseases.

Advances and highlights in asthma in 2021

Last year brought a significant advance in asthma management, unyielding to the pressure of the pandemics. Novel key findings in asthma pathogenesis focus on the resident cell compartment, epigenetics and the innate immune system. The precision immunology unbiased approach was supplemented with novel tools and greatly facilitated by the use of artificial intelligence. Several randomised clinical trials and good quality real-world evidence shed new light on asthma treatment and supported the revision of several asthma guidelines (GINA, Expert Panel Report 3, ERS/ATS guidelines on severe asthma) and the conception of new ones (EAACI Guidelines for the use of biologicals in severe asthma). Integrating asthma management within the broader context of Planetary Health has been put forward. In this review, recently published articles and clinical trials are summarised and discussed with the goal to provide clinicians and researchers with a concise update on asthma research from a translational perspective.

Critical Points on the Use of Biologicals in Allergic Diseases and Asthma

Improved understanding of the contribution of immune-inflammatory mechanisms in allergic diseases and asthma has encouraged development of biologicals and small molecules specifically targeting the innate and adaptive immune response. There are several critical points impacting the efficacy of this stratified approach, from the complexity of disease endotypes to the effectiveness in real-world settings. We discuss here how these barriers can be overcome to facilitate the development of implementation science for allergic diseases and asthma.