Identification of Susceptibility Genes to Allergic Rhinitis by Gene Expression Data Sets

Decoding the genetic landscape of allergic rhinitis: a comprehensive network analysis revealing key genes and potential therapeutic targets

BACKGROUND

Allergic Rhinitis (AR), an inflammatory affliction impacting the upper respiratory tract, has been registering a substantial surge in incidence across the globe.

METHODS

We embarked on examination of differentially expressed genes (DEGs) and the Weighted Gene Co-Expression Network Analysis (WGCNA). With this armory of genes identified, we engaged the tools of Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Our study continued with the establishment of a protein-protein interaction (PPI) network and the application of LASSO regression. Finally, we leveraged a docking model to elucidate potential drug-gene interactions involving these key genes.

RESULTS

Through WGCNA and different express genes screening, PPI network was performed, identifying top 20 key genes, including CD44, CD69, CD274. LASSO regression identified three independent factors, STARD5, CST1, and CHAC1, that were significantly associated with AR. A predictive model was developed with an AUC value over 0.75. Also, 105 potential therapeutic agents were discovered, including Fluorouracil, Cyclophosphamide, Doxorubicin, and Hydrocortisone, offering promising therapeutic strategies for AR.

CONCLUSION

By fuzing DEGs with key genes derived from WGCNA, this study has illuminated a comprehensive network of gene interactions involved in the pathogenesis of AR, paving the way for future biomarker and therapeutic target discovery in AR.

Differential modulation of allergic rhinitis nasal transcriptome by dupilumab and allergy immunotherapy

BACKGROUND

Nasal epithelial cells are important regulators of barrier function and immune signaling; however, in allergic rhinitis (AR) these functions can be disrupted by inflammatory mediators. We aimed to better discern AR disease mechanisms using transcriptome data from nasal brushing samples from individuals with and without AR.

METHODS

Data were drawn from a feasibility study of individuals with and without AR to Timothy grass and from a clinical trial evaluating 16 weeks of treatment with the following: dupilumab, a monoclonal antibody that binds interleukin (IL)-4Rα and inhibits type 2 inflammation by blocking signaling of both IL-4/IL-13; subcutaneous immunotherapy with Timothy grass (SCIT), which inhibits allergic responses through pleiotropic effects; SCIT + dupilumab; or placebo. Using nasal brushing samples from these studies, we defined distinct gene signatures in nasal tissue of AR disease and after nasal allergen challenge (NAC) and assessed how these signatures were modulated by study drug(s).

RESULTS

Treatment with dupilumab (normalized enrichment score [NES] = -1.73, p = .002) or SCIT + dupilumab (NES = -2.55, p < .001), but not SCIT alone (NES = +1.16, p = .107), significantly repressed the AR disease signature. Dupilumab (NES = -2.55, p < .001), SCIT (NES = -2.99, p < .001), and SCIT + dupilumab (NES = -3.15, p < .001) all repressed the NAC gene signature.

CONCLUSION

These results demonstrate type 2 inflammation is an important contributor to the pathophysiology of AR disease and that inhibition of the type 2 pathway with dupilumab may normalize nasal tissue gene expression.

Identification of hub genes related to immune cell infiltration in periodontitis using integrated bioinformatic analysis

BACKGROUND AND OBJECTIVE

Periodontitis is an inflammatory disease of the periodontium. However, the hub genes in periodontitis and their correlation with immune cells are not clear. This study aimed to identify hub genes and immune infiltration properties in periodontitis and to explore the correlation between hub genes and immune cells.

MATERIAL AND METHODS

Differentially expressed genes (DEGs) analysis and weighted gene co-expression network analysis (WGCNA) were performed both on GSE10334 and GSE173078 datasets. Hub genes were identified via WGCNA and DEGs. The proportions of infiltrating immune cells were calculated by CIBERSORT algorithm, and single-cell RNA-sequencing dataset GSE164241 was used to explore cell-type-specific expression profiles of hub genes.

RESULTS

Eight hub genes (DERL3, FKBP11, LAX1, CD27, SPAG4, ST6GAL1, MZB1, and SEL1L3) were selected via WGCNA and DEGs by combining GSE10334 and GSE173078 datasets. CIBERSORT analysis showed a significant difference in the proportion of B cells, dendritic cells resting, and neutrophils in the gingival tissues between healthy and periodontitis patients, and expressions of these genes were highly correlated with the infiltration of B cells in periodontitis. Furthermore, real-time quantitative PCR results further confirmed the overexpression of hub genes. Analysis of GSE164241dataset further identified that most of hub genes were mainly expressed in B cells.

CONCLUSIONS

By integrating WGCNA, DEGs, and CIBERSORT analysis, eight genes were identified to be the hub genes of periodontitis and most of them were mainly expressed in B cells encouraging further researches on B cells in periodontitis pathogenesis.

Nasal upregulation of CST1 in dog-sensitised children with severe allergic airway disease

Background

The clinical presentation of children sensitised to dog dander varies from asymptomatic to severe allergic airway disease, but the genetic mechanisms underlying these differences are not clear. The objective of the present study was to investigate nasal transcriptomic profiles associated with dog dander sensitisation in school children and to reveal clinical symptoms related with these profiles.

Methods

RNA was extracted from nasal epithelial cell brushings of children sensitised to dog dander and healthy controls. Blood sample analyses included IgE against dog dander, dog allergen molecules, other airborne and food allergens, basophil activation and white blood cell counts. Clinical history of asthma and rhinitis was recorded, and lung function was assessed (spirometry, methacholine provocation and exhaled nitric oxide fraction).

Results

The most overexpressed gene in children sensitised to dog dander compared to healthy controls was CST1, coding for Cystatin 1. A cluster of these children with enhanced CST1 expression showed lower forced expiratory volume in 1 s, increased bronchial hyperreactivity, pronounced eosinophilia and higher basophil allergen threshold sensitivity compared with other children sensitised to dog dander. In addition, multi-sensitisation to lipocalins was more common in this group.

Conclusions

Overexpression of CST1 is associated with more severe allergic airway disease in children sensitised to dog dander. CST1 is thus a possible biomarker of the severity of allergic airway disease and a possible therapeutic target for the future treatment of airborne allergy.