Identification of gene biomarkers with expression profiles in patients with allergic rhinitis

SerpinB3/B4 Abates Epithelial Cell-Derived CXCL8/IL-8 Expression in Chronic Rhinosinusitis with Nasal Polyps

Background

Serine proteinase inhibitors, clade B, member 3 (SerpinB3) and B4 are highly similar in amino acid sequences and associated with inflammation regulation. We investigated SerpinB3 and B4 expression and their roles in chronic rhinosinusitis with nasal polyps (CRSwNP).

Methods

The expression of SerpinB3 and B4 in nasal mucosa tissues, brush cells, and secretions from CRSwNP patients was measured, and their regulation by inflammatory cytokines were investigated. Their functions were also analyzed using air-liquid interface (ALI)-cultured primary human nasal epithelial cells (HNECs) and transcriptomic analysis.

Results

Both SerpinB3 and B4 expression was higher in nasal mucosa, brush cells, and secretions from eosinophilic (E) CRSwNP and nonECRSwNP patients than in healthy controls. Immunofluorescence staining indicated that SerpinB3 and B4 were primarily expressed in epithelial cells and their expression was higher in CRSwNP patients. SerpinB3 and B4 expression was upregulated by interleukin-4 (IL-4), IL-5, IL-6, and IL-17a. Transcriptomic analysis identified differentially expressed genes (DEGs) in response to recombinant SerpinB3 and B4 stimulation. Both the DEGs of SerpinB3 and B4 were associated with disease genes of nasal polyps and inflammation in DisGeNET database. Pathway enrichment indicated that downregulated DEGs of SerpinB3 and B4 were both enriched in cytokine-cytokine receptor interactions, with CXCL8 as the hub gene in the protein-protein interaction networks. Furthermore, CXCL8/IL-8 expression was downregulated by recombinant SerpinB3 and B4 protein in ALI-cultured HNECs, and upregulated when knockdown of SerpinB3/B4.

Conclusion

SerpinB3/B4 expression is upregulated in nasal mucosa of CRSwNP patients. SerpinB3/B4 may play an anti-inflammatory role in CRSwNP by inhibiting the expression of epithelial cell-derived CXCL8/IL-8.

Genetic Association of Allergic Rhinitis with Sleep and Neuropsychological Disorders: A Mendelian Randomization Study

BACKGROUND

The genetic association of allergic rhinitis (AR) with other physiological systems throughout the human body remains unknown.

OBJECTIVE

The aim of this Mendelian randomization (MR) study was to explore the association of this respiratory disorder with multiple common sleep and neuropsychological disorders at the genetic level.

METHODS

Summary data for total AR and pollen AR were collected from the most updated FinnGen genome-wide association studies involving more than 340 000 European subjects. Summary data for 12 sleep and neuropsychological disorders (including snoring) were included from UK Biobank studies involving 63 392 to 462 933 European subjects. Three MR methods, including inverse-variance weighting (IVW), weighted median and MR-Egger, were used to determine the relationships between the exposures and outcomes. Several sensitivity analyses, including Cochran's Q, MR-Egger intercept, MR-PRESSO, "leave-one-out" test and funnel plot, were used to detect heterogeneity and horizontal pleiotropy.

RESULTS

IVW revealed that total and pollen AR were associated with an increased risk of snoring (odds ratio (OR) = 1.011, 95% confidence interval (CI) = 1.004∼1.019, P = .003; OR = 1.006, 95% CI = 1.001∼1.011, P = .014). Two other MR methods supported the results from the IVW analysis. No heterogeneity or horizontal pleiotropy was confirmed by sensitivity analyses. In addition, IVW did not reveal any association between AR and other included disorders.

CONCLUSION

AR (specifically AR caused by pollen) might be an independent risk factor for snoring at the genetic level, which should be verified in the future.

Association of serum CD14 level and functional polymorphism C-159T in the promoter region of CD14 gene with allergic rhinitis

Allergic rhinitis (AR) is an inflammatory disease of the upper respiratory tract affecting a significant number of the world's population. It occurs as an IgE-mediated immune response of the nasal mucosa to inhaled allergens. The human Cluster of Differentiation 14 (CD14) is a glycosyl-phosphatidylinositol-anchored molecule expressed on the surface of monocytes and macrophages and functions as a receptor to lipopolysaccharides and inhaled endotoxins that may stimulate interleukins production by antigen-presenting cells. Consequently, CD14 plays a substantial role in allergic diseases and may become one of their etiological causes. This study aimed to determine the association between C-159T polymorphism in the CD14 gene promoter region and serum CD14 levels and the risk of Allergic rhinitis Egyptian patients and to test the validity of serum CD14 level measurement in predicting AR. This case-control study included 45 patients with AR referred to Allergy and Immunology Unit, Zagazig University Hospital, Zagazig, Egypt, and 45 healthy subjects as controls. Serum CD14 levels were measured by ELISA. The polymerase chain reaction-restriction fragment length polymorphism technique was used to detect C-159T gene polymorphism in the CD14 promoter region. There was a significant association between CD14 serum levels and AR incidence (P < 0.001), with patients having higher serum CD14 levels than controls. In addition, a significant association (P < 0.001) was detected between serum CD14 levels and the severity of AR, as well as elevated serum CD14 levels in severe and the most severe cases. On the molecular level, there was a statistically significant relationship between patients and the control group regarding the CD14 genotype (P < 0.001), where CT and TT genotypes and T allele were primarily associated with the cases group, indicating that the risk of AR was significantly associated with the inheritance of the TT genotype. Additionally, a statistically significant association was found between the severity of AR and CD14 genotype (P < 0.001), where TT genotypes were mainly associated with severe and the most severe cases. In the studied groups, there was a statistically significant difference (P < 0.05) between the CD14 genotype and serum CD14 levels, with TT genotypes being associated with higher CD14 levels. The results obtained in this study revealed that serum CD14 level is a potential biomarker for the diagnosis of AR and, at the genetic level, a potential predictor of disease.

Environmental Risk Factors, Protective Factors, and Biomarkers for Allergic Rhinitis: A Systematic Umbrella Review of the Evidence

Many potential environmental risk factors, protective factors, and biomarkers of AR have been published, but so far, the strength and consistency of their evidence are unclear. We conducted a comprehensive review of environmental risk, protective factors, and biomarkers for AR to establish the evidence hierarchy. We systematically searched Embase, PubMed, Cochrane Library, and Web of Science electronic database from inception to December 31, 2022. We calculated summary effect estimate (odds ratio (OR), relative risk (RR), hazard ratio (HR), and standardized mean difference (SMD)), 95% confidence interval, random effects p value, I2 statistic, 95% prediction interval, small study effects, and excess significance biases, and stratification of the level of evidence. Methodological quality was assessed by AMSTAR 2 (A Measurement Tool to Assess Systematic Reviews 2). We retrieved 4478 articles, of which 43 met the inclusion criteria. The 43 eligible articles identified 31 potential environmental risk factors (10,806,206 total population, two study not reported), 11 potential environmental protective factors (823,883 total population), and 34 potential biomarkers (158,716 total population) for meta-analyses. The credibility of evidence was convincing (class I) for tic disorders (OR = 2.89, 95% CI 2.11-3.95); and highly suggestive (class II) for early-life antibiotic use (OR = 3.73, 95% CI 3.06-4.55), exposure to indoor dampness (OR = 1.49, 95% CI 1.27-1.75), acetaminophen exposure (OR = 1.54, 95% CI 1.41-1.69), childhood acid suppressant use (OR = 1.40, 95% CI 1.23-1.59), exposure to indoor mold (OR = 1.66, 95% CI 1.26-2.18), coronavirus disease 2019 (OR = 0.11, 95% CI 0.06-0.22), and prolonged breastfeeding (OR = 0.72, 95% CI 0.65-0.79). This study is registered in PROSPERO (CRD42022384320).

Identification and analysis of lipid metabolism-related genes in allergic rhinitis

BACKGROUND

Studies have shown that the lipid metabolism mediator leukotriene and prostaglandins are associated with the pathogenesis of allergic rhinitis (AR). The aim of this study was to identify key lipid metabolism-related genes (LMRGs) related to the diagnosis and treatment of AR.

MATERIALS AND METHODS

AR-related expression datasets (GSE75011, GSE46171) were downloaded through the Gene Expression Omnibus (GEO) database. First, weighted gene co-expression network analysis (WGCNA) was used to get AR-related genes (ARRGs). Next, between control and AR groups in GSE75011, differentially expressed genes (DEGs) were screened, and DEGs were intersected with LMRGs to obtain lipid metabolism-related differentially expressed genes (LMR DEGs). Protein-protein interaction (PPI) networks were constructed for these LMR DEGs. Hub genes were then identified through stress, radiality, closeness and edge percolated component (EPC) analysis and intersected with the ARRGs to obtain candidate genes. Biomarkers with diagnostic value were screened via receiver operating characteristic (ROC) curves. Differential immune cells screened between control and AR groups were then assessed for correlation with the diagnostic genes, and clinical correlation analysis and enrichment analysis were performed. Finally, real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) was made on blood samples from control and AR patients to validate these identified diagnostic genes.

RESULTS

73 LMR DEGs were obtained, which were involved in biological processes such as metabolism of lipids and lipid biosynthetic processes. 66 ARRGs and 22 hub genes were intersected to obtain four candidate genes. Three diagnostic genes (LPCAT1, SGPP1, SMARCD3) with diagnostic value were screened according to the AUC > 0.7, with markedly variant between control and AR groups. In addition, two immune cells, regulatory T cells (Treg) and T follicular helper cells (TFH), were marked variations between control and AR groups, and SMARCD3 was significantly associated with TFH. Moreover, SMARCD3 was relevant to immune-related pathways, and correlated significantly with clinical characteristics (age and sex). Finally, RT-qPCR results indicated that changes in the expression of LPCAT1 and SMARCD3 between control and AR groups were consistent with the GSE75011 and GSE46171.

CONCLUSION

LPCAT1, SGPP1 and SMARCD3 might be used as biomarkers for AR.

Mechanistic and Therapeutic Approaches to Occupational Exposure-Associated Allergic and Non-Allergic Asthmatic Disease

PURPOSE OF REVIEW

Occupational lung disease, including asthma, is a significant cause of disability worldwide. The dose, exposure frequency, and nature of the causal agent influence the inflammatory pathomechanisms that inform asthma disease phenotype and progression. While surveillance, systems engineering, and exposure mitigation strategies are essential preventative considerations, no targeted medical therapies are currently available to ameliorate lung injury post-exposure and prevent chronic airway disease development.

RECENT FINDINGS

This article reviews contemporary understanding of allergic and non-allergic occupational asthma mechanisms. In addition, we discuss the available therapeutic options, patient-specific susceptibility and prevention measures, and recent scientific advances in post-exposure treatment conception. The course of occupational lung disease that follows exposure is informed by individual predisposition, immunobiologic response, agent identity, overall environmental risk, and preventative workplace practices. When protective strategies fail, knowledge of underlying disease mechanisms is necessary to inform targeted therapy development to lessen occupational asthma disease severity and occurrence.

Gene Signatures and Associated Transcription Factors of Allergic Rhinitis: KLF4 Expression Is Associated with Immune Response

This study is aimed at investigating the potential molecular features of allergic rhinitis (AR) and identifying gene signatures and related transcription factors using transcriptome analysis and in silico datasets. Transcriptome profiles were obtained using three independent cohorts (GSE101720, GSE19190, and GSE46171) comprising healthy controls (HC) and patients with AR. The pooled dataset (n = 82) was used to identify the critical signatures of AR compared with HC. Subsequently, key transcription factors were identified by a combined analysis using transcriptome and in silico datasets. Gene ontology: bioprocess (GO: BP) analysis using differentially expressed genes (DEGs) revealed that immune response-related genes were significantly enriched in AR compared with HC. Among them, IL1RL1, CD274, and CD44 were significantly higher in AR patients. We also identified key transcription factors between HC and AR using the in silico dataset and found that AR samples frequently express KLF transcription factor 4 (KLF4), which regulates immune response-related genes including IL1RL1, CD274, and CD44 in human nasal epithelial cells. Our integrative analysis of transcriptomic regulation provides new insights into AR, which may help in developing precision management for patients with AR.

ARG1 as a promising biomarker for sepsis diagnosis and prognosis: evidence from WGCNA and PPI network

Background

Sepsis is a life-threatening multi-organ dysfunction caused by the dysregulated host response to infection. Sepsis remains a major global concern with high mortality and morbidity, while management of sepsis patients relies heavily on early recognition and rapid stratification. This study aims to identify the crucial genes and biomarkers for sepsis which could guide clinicians to make rapid diagnosis and prognostication.

Methods

Preliminary analysis of multiple global datasets, including 170 samples from patients with sepsis and 110 healthy control samples, revealed common differentially expressed genes (DEGs) in peripheral blood of patients with sepsis. After Gene Oncology (GO) and pathway analysis, the Weighted Gene Correlation Network Analysis (WGCNA) was used to screen for genes most related with clinical diagnosis. Also, the Protein-Protein Interaction Network (PPI Network) was constructed based on the DEGs and the hub genes were found. The results of WGCNA and PPI network were compared and one shared gene was discovered. Then more datasets of 728 experimental samples and 355 control samples were used to prove the diagnostic and prognostic value of this gene. Last, we used real-time PCR to confirm the bioinformatic results.

Results

Four hundred forty-four common differentially expressed genes in the blood of sepsis patients from different ethnicities were identified. Fifteen genes most related with clinical diagnosis were found by WGCNA, and 24 hub genes with most node degrees were identified by PPI network. ARG1 turned out to be the unique overlapped gene. Further analysis using more datasets showed that ARG1 was not only sharply up-regulated in sepsis than in healthy controls, but also significantly high-expressed in septic shock than in non-septic shock, significantly high-expressed in severe or lethal sepsis than in uncomplicated sepsis, and significantly high-expressed in non-responders than in responders upon early treatment. These all demonstrate the performance of ARG1 as a key biomarker. Last, the up-regulation of ARG1 in the blood was confirmed experimentally.

Conclusions

We identified crucial genes that may play significant roles in sepsis by WGCNA and PPI network. ARG1 was the only overlapped gene in both results and could be used to make an accurate diagnosis, discriminate the severity and predict the treatment response of sepsis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s41065-022-00240-1.