Multi-ancestry genome-wide association study of asthma exacerbations

Structure-based design and disulfide stapling of interfacial cyclic peptidic inhibitors from thymic stromal lymphopoietin (TSLP) receptor to competitively target TSLP

Human thymic stromal lymphopoietin (TSLP) is a pro-inflammatory cytokine located at the top of inflammatory cascade that makes it a promising therapeutic target in allergic asthma. The cell surface receptor of TSLP is a heterodimer consisting of a TSLP receptor (TSLPR) and an interleukin-17 receptor α (IL-7Rα). The TSLPR subunit should be first added to the free TSLP to form a TSLPR/TSLP pre-complex, which further recruits the IL-7Rα subunit to obtain the final TSLPR/IL-7Rα/TSLP complex. Previous works have been focused on targeting the IL-7Rα-binding site of TSLP. Instead, we herein reported an attempt for rational design of cyclic peptidic inhibitors to competitively disrupt the TSLPR-TSLP interaction based on their complex crystal structure by integrating dynamics simulation and energetics analysis as well as experimental assays at molecular level. An interfacial peptide segment derived from the hotspots of TSLPR that cover a specific TSLP-binding site on the TSLPR interface, which is expected to natively form a U-shaped conformation recognized by TSLP and thus compete with the cognate TSLPR for TSLP. The eS4P peptide was further stapled by a disulfide bridge between different residue pairs across its two arms, thus separately resulting in its two stapled cyclic counterparts, i.e. eS4P[189-198] and eS4P[188-200] peptides. Circular dichroism characterized that the stapling can effectively constrain the peptide into a native-like U-shpared conformation in free state, thus largely minimizing the entropy penalty upon its binding to TSLP. Affinity assays revealed that the stapling can considerably improve the peptide binding potency to TSLP by 2.9-fold and 8.3-fold at molecular level. In addition, we further demonstrated that the potent eS4P[188-200] peptide has a good selectivity for its cognate TSLP over other four noncognate cytokines IL-2, IL-7, IL-13 and IL-22 that are relevant with the TSLP. In this respect, it is considered that the disulfide-stapled cyclic peptide-mediated blockade of TLSP inflammatory cascade may be a new and promising therapeutic strategy against allergic asthma.

Pharmacogenetics of childhood uncontrolled asthma

INTRODUCTION

Asthma is a heterogeneous, multifactorial disease with multiple genetic and environmental risk factors playing a role in pathogenesis and therapeutic response. Understanding of pharmacogenetics can help with matching individualized treatments to specific genotypes of asthma to improve therapeutic outcomes especially in uncontrolled or severe asthma.

AREAS COVERED

In this review, we outline novel information about biology, pathways, and mechanisms related to interindividual variability in drug response (corticosteroids, bronchodilators, leukotriene modifiers, and biologics) for childhood asthma. We discuss candidate gene, genome-wide association studies and newer omics studies including epigenomics, transcriptomics, proteomics, and metabolomics as well as integrative genomics and systems biology methods related to childhood asthma. The articles were obtained after a series of searches, last updated November 2022, using database PubMed/CINAHL DB.

EXPERT OPINION

Implementation of pharmacogenetic algorithms can improve therapeutic targeting in children with asthma, particularly with severe or uncontrolled asthma who typically have challenges in clinical management and carry considerable financial burden. Future studies focusing on potential biomarkers both clinical and pharmacogenetic can help formulate a prognostic test for asthma treatment response that would represent true bench to bedside clinical implementation.

Peripheral blood miRNAs are associated with airflow below threshold in children with asthma

BACKGROUND

MicroRNAs (miRNAs) are crucial post-transcriptional regulators involved in inflammatory diseases, such as asthma. Poor lung function and airflow issues in childhood are linked to the development of chronic obstructive pulmonary disease (COPD) in adulthood.

METHODS

We analyzed small RNA-Seq data from 365 peripheral whole blood samples from the Genetics of Asthma in Costa Rica Study (GACRS) for association with airflow levels measured by FEV1/FVC. Differentially expressed (DE) miRNAs were identified using DESeq2 in R, adjusting for covariates and applying a 10% false discovery rate (FDR). The analysis included 361 samples and 649 miRNAs. The two DE miRNAs were further tested for association with airflow obstruction in a study of adult former smokers with and without COPD.

RESULTS

We found 1 upregulated and 1 downregulated miRNA in participants with airflow below the threshold compared to those above it. In the adult study, the same miRNAs were upregulated and downregulated in individuals with FEV1/FVC < 0.7 versus those with FEV1/FVC > 0.7, showing suggestive statistical evidence. The target genes of these miRNAs were enriched for PI3K-Akt, Hippo, WNT, MAPK, and focal adhesion pathways.

CONCLUSIONS

Two differentially expressed miRNAs were associated with airflow levels in children with asthma and airflow obstruction in adults with COPD. This suggests that shared genetic regulatory systems may influence childhood airflow and contribute to adulthood airflow obstruction.

Multi-omics in exploring the pathophysiology of diabetic retinopathy

Diabetic retinopathy (DR) is a leading global cause of vision impairment, with its prevalence increasing alongside the rising rates of diabetes mellitus (DM). Despite the retina's complex structure, the underlying pathology of DR remains incompletely understood. Single-cell RNA sequencing (scRNA-seq) and recent advancements in multi-omics analyses have revolutionized molecular profiling, enabling high-throughput analysis and comprehensive characterization of complex biological systems. This review highlights the significant contributions of scRNA-seq, in conjunction with other multi-omics technologies, to DR research. Integrated scRNA-seq and transcriptomic analyses have revealed novel insights into DR pathogenesis, including alternative transcription start site events, fluctuations in cell populations, altered gene expression profiles, and critical signaling pathways within retinal cells. Furthermore, by integrating scRNA-seq with genetic association studies and multi-omics analyses, researchers have identified novel biomarkers, susceptibility genes, and potential therapeutic targets for DR, emphasizing the importance of specific retinal cell types in disease progression. The integration of scRNA-seq with metabolomics has also been instrumental in identifying specific metabolites and dysregulated pathways associated with DR. It is highly conceivable that the continued synergy between scRNA-seq and other multi-omics approaches will accelerate the discovery of underlying mechanisms and the development of novel therapeutic interventions for DR.

Haplotype-Aware Detection of SERPINA1 Variants by Nanopore Sequencing

α-1 Antitrypsin (AAT) is an acute-phase reactant with immunomodulatory properties that mainly inhibits neutrophil elastase. Low serum levels cause AAT deficiency (AATD), an underdiagnosed condition that predisposes to pulmonary and hepatic diseases. The SERPINA1 gene, which encodes AAT, contains >500 variants. PI∗Z and PI∗S alleles are the most diagnosed causes of AATD, but the role of the SERPINA1 haplotypes in AAT function remains unknown. SERPINA1 gene was PCR amplified from 94 patients with asthma, using primers with tails for indexing. Sequencing libraries were loaded into a MinION-Mk1C, and MinKNOW was used for basecalling and demultiplexing. Nanofilt and Minimap2 were used for filtering and mapping/alignment. Variant calling/phasing were performed with PEPPER-Margin-DeepVariant. SERPINA1 gene was 100% covered for all samples, with a minimum sequencing depth of 500×. A total of 75 single-nucleotide variants (SNVs) and 4 insertions/deletions were detected, with 45 and 2 of them highly polymorphic (minor allele frequency >0.1), respectively. Nine of the SNVs showed differences in allele frequencies when compared with the overall Spanish population. More than 90% of heterozygous SNVs were phased, yielding 91 and 58 different haplotypes for each SERPINA1 amplified region. Haplotype-based linkage disequilibrium analysis suggests that a recombination hotspot could generate variation in the SERPINA1 gene. The proposed workflow enables haplotype-aware genotyping of the SERPINA1 gene by nanopore sequencing, which will allow the development of novel AATD diagnostic strategies.

Genetics of chronic respiratory disease

Chronic respiratory diseases, such as chronic obstructive pulmonary disease (COPD), asthma and interstitial lung diseases are frequently occurring disorders with a polygenic basis that account for a large global burden of morbidity and mortality. Recent large-scale genetic epidemiology studies have identified associations between genetic variation and individual respiratory diseases and linked specific genetic variants to quantitative traits related to lung function. These associations have improved our understanding of the genetic basis and mechanisms underlying common lung diseases. Moreover, examining the overlap between genetic associations of different respiratory conditions, along with evidence for gene-environment interactions, has yielded additional biological insights into affected molecular pathways. This genetic information could inform the assessment of respiratory disease risk and contribute to stratified treatment approaches.

5-HTP inhibits eosinophilia via intracellular endothelial 5-HTRs; SNPs in 5-HTRs associate with asthmatic lung function

Background

Previous research showed that 5-hydroxytryptophan (5HTP), a metabolic precursor of serotonin, reduces allergic lung inflammation by inhibiting eosinophil migration across endothelial monolayers.

Objective

It is unknown if serotonin receptors are involved in mediating this 5HTP function or if serotonin receptor (HTR) single nucleotide polymorphisms (SNPs) associate with lung function in humans.

Methods

Serotonin receptor subtypes were assessed by qPCR, western blot, confocal microscopy, pharmacological inhibitors and siRNA knockdown. HTR SNPs were assessed in two cohorts.

Results

Pharmacological inhibition or siRNA knockdown of the serotonin receptors HTR1A or HTR1B in endothelial cells abrogated the inhibitory effects of 5HTP on eosinophil transendothelial migration. In contrast, eosinophil transendothelial migration was not inhibited by siRNA knockdown of HTR1A or HTR1B in eosinophils. Surprisingly, these HTRs were intracellular in endothelial cells and an extracellular supplementation with serotonin did not inhibit eosinophil transendothelial migration. This is consistent with the inability of serotonin to cross membranes, the lack of selective serotonin reuptake receptors on endothelial cells, and the studies showing minimal impact of selective serotonin reuptake inhibitors on asthma. To extend our HTR studies to humans with asthma, we examined the CHIRAH and GALA cohorts for HTR SNPs that affect HTR function or are associated with behavior disorders. A polygenic index of SNPs in HTRs was associated with lower lung function in asthmatics.

Conclusions

Serotonin receptors mediate 5HTP inhibition of transendothelial migration and HTR SNPs associate with lower lung function. These results may serve to aid in design of novel interventions for allergic inflammation.

Asthma exacerbations and eosinophilia in the UK Biobank: a genome-wide association study

Background

Asthma exacerbations reflect disease severity, affect morbidity and mortality, and may lead to declining lung function. Inflammatory endotypes (e.g. T2-high (eosinophilic)) may play a key role in asthma exacerbations. We aimed to assess whether genetic susceptibility underlies asthma exacerbation risk and additionally tested for an interaction between genetic variants and eosinophilia on exacerbation risk.

Methods

UK Biobank data were used to perform a genome-wide association study of individuals with asthma and at least one exacerbation compared to individuals with asthma and no history of exacerbations. Individuals with asthma were identified using self-reported data, hospitalisation data and general practitioner records. Exacerbations were identified as either asthma-related hospitalisation, general practitioner record of asthma exacerbation or an oral corticosteroid burst prescription. A logistic regression model adjusted for age, sex, smoking status and genetic ancestry via principal components was used to assess the association between genetic variants and asthma exacerbations. We sought replication for suggestive associations (p<5×10-6) in the GERA cohort.

Results

In the UK Biobank, we identified 11 604 cases and 37 890 controls. While no variants reached genome-wide significance (p<5×10-8) in the primary analysis, 116 signals were suggestively significant (p<5×10-6). In GERA, two single nucleotide polymorphisms (rs34643691 and rs149721630) replicated (p<0.05), representing signals near the NTRK3 and ABCA13 genes.

Conclusions

Our study has identified reproducible associations with asthma exacerbations in the UK Biobank and GERA cohorts. Confirmation of these findings in different asthma subphenotypes in diverse ancestries and functional investigation will be required to understand their mechanisms of action and potentially inform therapeutic development.

Prediction of asthma using a four-locus gene model including IL13, IL4, FCER1B, and ADRB2 in children of Kazak nationality

BACKGROUND

To study whether the four locus gene model consisting of ADRB2 rs1042713, IL4 rs2243250, FCER1B rs569108 and L13 rs20541 can predict asthma of the Kazak children in Xinjiang, China.

METHODS

Four single nucleotide polymorphisms about the 4 genes were genotyped in asthma group and control group of Han children and Kazak children respectively. The frequencies of different genotypes and alleles were compared between the asthma group and the control group in the two nationalities. Different risk genotypes for asthma were evaluated in the two nationalities.

RESULTS

The differences about frequencies of genotypes in ADRB2 rs1042713 and IL4 rs2243250 and IL13 rs20541 between asthma group and control group were statistically significant in Han children, as were the frequencies of alleles in the 3 single nucleotide polymorphisms, but there were no statistical differences in FCER1B rs569108(P > 0.05). For the Kazak children, no differences were existed among all the genotypes and alleles in asthma group and control group. For the Han children, more children were asthma high risk genotype in the asthma group than those in the control group and no difference was found in the Kazak children.

CONCLUSIONS

The four locus gene model consisting of ADRB2 rs1042713, IL4 rs2243250, FCER1B rs569108 and L13 rs20541 can predict asthma of Han children but not for the Kazak children in Xinjiang, which illustrating that the difference of asthma prevalence between different races is closely related to the genetic background.

Human genetics influences microbiome composition involved in asthma exacerbations despite inhaled corticosteroid treatment

BACKGROUND

The upper-airway microbiome is involved in asthma exacerbations despite inhaled corticosteroid (ICS) treatment. Although human genetics regulates microbiome composition, its influence on asthma-related airway bacteria remains unknown.

OBJECTIVE

We sought to identify genes and biological pathways regulating airway-microbiome traits involved in asthma exacerbations and ICS response.

METHODS

Saliva, nasal, and pharyngeal samples from 257 European patients with asthma were analyzed. The association of 6,296,951 genetic variants with exacerbation-related microbiome traits despite ICS treatment was tested through microbiome genome-wide association studies. Variants with 1 × 10-4 

RESULTS

Genes associated with exacerbation-related airway-microbiome traits were enriched in asthma comorbidities development (ie, reflux esophagitis, obesity, and smoking), and were likely regulated by trichostatin A and the nuclear factor-κB, the glucocorticosteroid receptor, and CCAAT/enhancer-binding protein transcription factors (7.8 × 10-13 ≤ false discovery rate ≤ 0.022). Enrichment in smoking, trichostatin A, nuclear factor-κB, and glucocorticosteroid receptor were replicated in the saliva samples from diverse populations (4.42 × 10-9 ≤ P ≤ .008). The ICS-response-associated single nucleotide polymorphisms rs5995653 (APOBEC3B-APOBEC3C), rs6467778 (TRIM24), and rs5752429 (TPST2) were identified as microbiome quantitative trait loci of Streptococcus, Tannerella, and Campylobacter in the upper airway (0.027 ≤ false discovery rate ≤ 0.050).

CONCLUSIONS

Genes associated with asthma exacerbation-related microbiome traits might influence asthma comorbidities. We reinforced the therapeutic interest of trichostatin A, nuclear factor-κB, the glucocorticosteroid receptor, and CCAAT/enhancer-binding protein in asthma exacerbations.

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Key Words

• Airway microbiome
• CEBP
• NF-κB
• NR3C1
• gastroesophageal reflux disease
• inhaled corticosteroids
• mGWAS
• obesity
• smoking
• trichostatin A

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MESH Headings

• Humans
• Anti-Asthmatic Agents/therapeutic use
• Genome-Wide Association Study
• NF-kappa B/genetics
• Administration, Inhalation
• Asthma/drug therapy
• Asthma/genetics
• Adrenal Cortex Hormones/therapeutic use
• Human Genetics
• Cytidine Deaminase
• Minor Histocompatibility Antigens
• Carrier Proteins/genetics

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Grants

• R01 ES015794 NIEHS NIH HHS
• UL1 TR001872 NCATS NIH HHS
• R01 HL135156 NHLBI NIH HHS
• R21 ES024844 NIEHS NIH HHS
• R01 HL117004 NHLBI NIH HHS
• P60 MD006902 NIMHD NIH HHS
• RL5 GM118984 NIGMS NIH HHS
• R01 MD010443 NIMHD NIH HHS

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Affiliation(s)

Javier Perez-Garcia Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain
Antonio Espuela-Ortiz Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain
José M Hernández-Pérez Pulmonary Medicine Service, Hospital Universitario N.S de Candelaria, La Laguna, Tenerife, Spain; Pulmonary Medicine Section, Hospital Universitario de La Palma, La Palma, Spain
Ruperto González-Pérez Severe Asthma Unit, Allergy Department, Hospital Universitario de Canarias, La Laguna, Tenerife, Spain
Paloma Poza-Guedes Severe Asthma Unit, Allergy Department, Hospital Universitario de Canarias, La Laguna, Tenerife, Spain
Elena Martin-Gonzalez Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain
Celeste Eng Department of Medicine, University of California San Francisco (UCSF), San Francisco, Calif
Olaia Sardón-Prado Division of Pediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain; Department of Pediatrics, University of the Basque Country (UPV/EHU), San Sebastián, Spain
Elena Mederos-Luis Allergy Department, Hospital Universitario de Canarias, La Laguna, Tenerife, Spain
Paula Corcuera-Elosegui Division of Pediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain
Inmaculada Sánchez-Machín Allergy Department, Hospital Universitario de Canarias, La Laguna, Tenerife, Spain
Javier Korta-Murua Division of Pediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain
Jesús Villar CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Multidisciplinary Organ Dysfunction Evaluation Research Network, Research Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran Canaria, Spain; Li Ka Shing Knowledge Institute at the St. Michael's Hospital, Toronto, Ontario, Canada
Esteban G Burchard Department of Medicine, University of California San Francisco (UCSF), San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco (UCSF), San Francisco, Calif
Fabian Lorenzo-Diaz Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain; Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain.
Maria Pino-Yanes Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Tecnologías Biomédicas, Universidad de La Laguna (ULL), La Laguna, Tenerife, Spain.

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Immunogenetics and pharmacogenetics of allergic asthma in Africa

Asthma is a common chronic condition in children and in an African setting is often highly prevalent in urban areas as compared to rural areas. Asthma is a heritable disease and the genetic risk is often exacerbated by unique localised environmental factors. The Global Initiative for Asthma (GINA) recommendation for the control of asthma includes inhaled corticosteroids (ICS) alone or together with short-acting β₂-agonists (SABA) or long-acting β₂-agonists (LABA). While these drugs can relieve asthma symptoms, there is evidence of reduced efficacy in people of African ancestry. Whether this is due to immunogenetics, genomic variability in drug metabolising genes (pharmacogenetics) or genetics of asthma-related traits is not well defined. Pharmacogenetic evidence of first-line asthma drugs in people of African ancestry is lacking and is further compounded by the lack of representative genetic association studies in the continent. In this review, we will discuss the paucity of data related to the pharmacogenetics of asthma drugs in people of African ancestry, mainly drawing from African American data. We will further discuss how this gap can be bridged to improve asthma health outcomes in Africa.

Asthma Exacerbations: The Genes Behind the Scenes

The clinical and socioeconomic burden of asthma exacerbations (AEs) constitutes a major public health problem. In the last 4 years, there has been an increase in ethnic diversity in candidate-gene and genome-wide association studies of AEs, which in the latter case led to the identification of novel genes and underlying pathobiological processes. Pharmacogenomics, admixture mapping analyses, and the combination of multiple "omics" layers have helped to prioritize genomic regions of interest and/or facilitated our understanding of the functional consequences of genetic variation. Nevertheless, the field still lags behind the genomics of asthma, where a vast compendium of genetic approaches has been used (eg, gene-environment nteractions, next-generation sequencing, and polygenic risk scores). Furthermore, the roles of the DNA methylome and histone modifications in AEs have received little attention, and microRNA findings remain to be validated in independent studies. Likewise, the most recent transcriptomic studies highlight the importance of the host-airway microbiome interaction in the modulation of risk of AEs. Leveraging -omics and deep-phenotyping data from subtypes or homogenous subgroups of patients will be crucial if we are to overcome the inherent heterogeneity of AEs, boost the identification of potential therapeutic targets, and implement precision medicine approaches to AEs in clinical practice.

Understanding and controlling asthma in Latin America: A review of recent research informed by the SCAALA programme

Asthma is an important health concern in Latin America (LA) where it is associated with variable prevalence and disease burden between countries. High prevalence and morbidity have been observed in some regions, particularly marginalized urban populations. Research over the past 10 years from LA has shown that childhood disease is primarily non-atopic. The attenuation of atopy may be explained by enhanced immune regulation induced by intense exposures to environmental factors such as childhood infections and poor environmental conditions of the urban poor. Non-atopic symptoms are associated with environmental and lifestyle factors including poor living conditions, respiratory infections, psychosocial stress, obesity, and a diet of highly processed foods. Ancestry (particularly African) and genetic factors increase asthma risk, and some of these factors may be specific to LA settings. Asthma in LA tends to be poorly controlled and depends on access to health care and medications. There is a need to improve management and access to medication through primary health care. Future research should consider the heterogeneity of asthma to identify relevant endotypes and underlying causes. The outcome of such research will need to focus on implementable strategies relevant to populations living in resource-poor settings where the disease burden is greatest.

The upper-airway microbiome as a biomarker of asthma exacerbations despite inhaled corticosteroid treatment

BACKGROUND

The response to inhaled corticosteroids (ICS) in asthma is affected by the interplay of several factors. Among these, the role of the upper-airway microbiome has been scarcely investigated. We aimed to evaluate the association between the salivary, pharyngeal, and nasal microbiome with asthma exacerbations despite receipt of ICS.

METHODS

Samples from 250 asthma patients from the Genomics and Metagenomics of Asthma Severity (GEMAS) study treated with ICS were analyzed. Control/case subjects were defined by the absence/presence of asthma exacerbations in the past 6 months despite being treated with ICS. The bacterial microbiota was profiled by sequencing the V3-V4 region of the 16S rRNA gene. Differences between groups were assessed by PERMANOVA and regression models adjusted for potential confounders. A false discovery rate (FDR) of 5% was used to correct for multiple comparisons. Classification models of asthma exacerbations despite ICS treatment were built with machine learning approaches based on clinical, genetic, and microbiome data.

RESULTS

In nasal and saliva samples, case subjects had lower bacterial diversity (Richness, Shannon, and Faith indices) than control subjects (.007 ≤ P ≤ .037). Asthma exacerbations accounted for 8% to 9% of the interindividual variation of the salivary and nasal microbiomes (.003 ≤ P ≤ .046). Three, 4, and 11 bacterial genera from the salivary, pharyngeal, and nasal microbiomes were differentially abundant between groups (4.09 × 10^-12 ≤ FDR ≤ 0.047). Integrating clinical, genetic, and microbiome data showed good discrimination for the development of asthma exacerbations despite receipt of ICS (AUC_training: 0.82 and AUC_validation: 0.77).

CONCLUSION

The diversity and composition of the upper-airway microbiome are associated with asthma exacerbations despite ICS treatment. The salivary microbiome has a potential application as a biomarker of asthma exacerbations despite receipt of ICS.