The association between polymorphisms in the MRPL4 and TNF-α genes and susceptibility to allergic rhinitis

Correlation of serum HMGB1 and HMGB2 levels with clinical symptoms in allergic rhinitis children

This research aimed to explore the serum high-mobility group box 1 (HMGB1) and high-mobility group box 2 (HMGB2) levels in allergic rhinitis (AR) children and its correlation with clinical results. This present prospective observational study enrolled 179 AR children and 100 healthy children who came to our hospital during October 2020 to August 2022. The serum HMGB1, HMGB2, interleukin (IL)-6, IL-1β, interferon-γ, and C-reactive protein (CRP) levels were measured by enzyme-linked immunosorbent assay. Demographic and clinical statistics including age, body mass index (BMI), sex, diastolic blood pressure, SBP, family history of allergy, Visual Analogue Score (VAS) and Rhinoconjunctivitis Quality of Life Questionnaire were collected. All data used SPSS 18.0 to statistical analyses. The proportion of family history of allergy was obviously higher in the AR group than that in the healthy group. The serum levels of HMGB1, HMGB2 and cytokines were remarkably enhanced in the AR patients. Spearman analysis supported that positive correlation existed among the HMGB1, HMGB2, CRP, IL-6 and IL-1β levels. Serum IL-6, CRP, HMGB2, IL-1β, VAS score and Rhinoconjunctivitis Quality of Life Questionnaire score levels were significantly higher and serum interferon-γ levels were significantly lower in the HMGB1 high expression group. Similar results were found in in the HMGB2 high group compared to the HMGB2 low group. In addition, HMGB1 and HMGB2 could be potential diagnostic biomarkers of AR patients. Finally, we found that HMGB1, HMGB2, IL-6, IL-1β, and family history of allergy were the risk factors for AR. This study showed that the serum HMGB1 and HMGB2 levels was remarkably enhanced in AR patients and closely associated with cytokines. This study may provide new targets and a comprehensive approach for the treatment of AR patients.

Pathogenesis of allergic diseases and implications for therapeutic interventions

Allergic diseases such as allergic rhinitis (AR), allergic asthma (AAS), atopic dermatitis (AD), food allergy (FA), and eczema are systemic diseases caused by an impaired immune system. Accompanied by high recurrence rates, the steadily rising incidence rates of these diseases are attracting increasing attention. The pathogenesis of allergic diseases is complex and involves many factors, including maternal-fetal environment, living environment, genetics, epigenetics, and the body's immune status. The pathogenesis of allergic diseases exhibits a marked heterogeneity, with phenotype and endotype defining visible features and associated molecular mechanisms, respectively. With the rapid development of immunology, molecular biology, and biotechnology, many new biological drugs have been designed for the treatment of allergic diseases, including anti-immunoglobulin E (IgE), anti-interleukin (IL)-5, and anti-thymic stromal lymphopoietin (TSLP)/IL-4, to control symptoms. For doctors and scientists, it is becoming more and more important to understand the influencing factors, pathogenesis, and treatment progress of allergic diseases. This review aimed to assess the epidemiology, pathogenesis, and therapeutic interventions of allergic diseases, including AR, AAS, AD, and FA. We hope to help doctors and scientists understand allergic diseases systematically.

Identification and Validation of Prognostic Markers for Lung Squamous Cell Carcinoma Associated with Chronic Obstructive Pulmonary Disease

Background

Globally, the incidence and associated mortality of chronic obstructive pulmonary disease (COPD) and lung carcinoma are showing a worsening trend. There is increasing evidence that COPD is an independent risk factor for the occurrence and progression of lung carcinoma. This study aimed to identify and validate the gene signatures associated with COPD, which may serve as potential new biomarkers for the prediction of prognosis in patients with lung carcinoma.

Methods

A total of 111 COPD patient samples and 40 control samples were obtained from the GSE76925 cohort, and a total of 4933 genes were included in the study. The weighted gene coexpression network analysis (WGCNA) was performed to identify the modular genes that were significantly associated with COPD. The KEGG pathway and GO functional enrichment analyses were also performed. The RNAseq and clinicopathological data of 490 lung squamous cell carcinoma patients were obtained from the TCGA database. Further, univariate Cox regression and Lasso analyses were performed to screen for marker genes and construct a survival analysis model. Finally, the Human Protein Atlas (HPA) database was used to assess the gene expression in normal and tumor tissues of the lungs.

Results

A 6-gene signature (DVL1, MRPL4, NRTN, NSUN3, RPH3A, and SNX32) was identified based on the Cox proportional risk analysis to construct the prognostic RiskScore survival model associated with COPD. Kaplan–Meier survival analysis indicated that the model could significantly differentiate between the prognoses of patients with lung carcinoma, wherein higher RiskScore samples were associated with a worse prognosis. Additionally, the model had a good predictive performance and reliability, as indicated by a high AUC, and these were validated in both internal and external sets. The 6-gene signature had a good predictive ability across clinical signs and could be considered an independent factor of prognostic risk. Finally, the protein expressions of the six genes were analyzed based on the HPA database. The expressions of DVL1, MRPL4, and NSUN3 were relatively higher, while that of RPH3A was relatively lower in the tumor tissues. The expression of SNX32 was high in both the tumor and paracarcinoma tissues. Results of the analyses using TCGA and GSE31446 databases were consistent with the expressions reported in the HPA database.

Conclusion

Novel COPD-associated gene markers for lung carcinoma were identified and validated in this study. The genes may be considered potential biomarkers to evaluate the prognostic risk of patients with lung carcinoma. Furthermore, some of these genes may have implications as new therapeutic targets and can be used to guide clinical applications.

Effects of Psychotropic Drugs on Ribosomal Genes and Protein Synthesis

Altered protein synthesis has been implicated in the pathophysiology of several neuropsychiatric disorders, particularly schizophrenia. Ribosomes are the machinery responsible for protein synthesis. However, there remains little information on whether current psychotropic drugs affect ribosomes and contribute to their therapeutic effects. We treated human neuronal-like (NT2-N) cells with amisulpride (10 µM), aripiprazole (0.1 µM), clozapine (10 µM), lamotrigine (50 µM), lithium (2.5 mM), quetiapine (50 µM), risperidone (0.1 µM), valproate (0.5 mM) or vehicle control for 24 h. Transcriptomic and gene set enrichment analysis (GSEA) identified that the ribosomal pathway was altered by these drugs. We found that three of the eight drugs tested significantly decreased ribosomal gene expression, whilst one increased it. Most changes were observed in the components of cytosolic ribosomes and not mitochondrial ribosomes. Protein synthesis assays revealed that aripiprazole, clozapine and lithium all decreased protein synthesis. Several currently prescribed psychotropic drugs seem to impact ribosomal gene expression and protein synthesis. This suggests the possibility of using protein synthesis inhibitors as novel therapeutic agents for neuropsychiatric disorders.

Genetics and Epigenetics in Allergic Rhinitis

The pathogenesis of allergic rhinitis is associated with genetic, environmental, and epigenetic factors. Genotyping of single nucleotide polymorphisms (SNPs) is an advanced technique in the field of molecular genetics that is closely correlated with genome-wide association studies (GWASs) in large population groups with allergic diseases. Many recent studies have paid attention to the role of epigenetics, including alteration of DNA methylation, histone acetylation, and miRNA levels in the pathogenesis of allergic rhinitis. In this review article, genetics and epigenetics of allergic rhinitis, including information regarding functions and significance of previously known and newly-discovered genes, are summarized. Directions for future genetic and epigenetic studies of allergic rhinitis are also proposed.

D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions

We combine advances in neural language modeling and structurally motivated design to develop D-SCRIPT, an interpretable and generalizable deep-learning model, which predicts interaction between two proteins using only their sequence and maintains high accuracy with limited training data and across species. We show that a D-SCRIPT model trained on 38,345 human PPIs enables significantly improved functional characterization of fly proteins compared with the state-of-the-art approach. Evaluating the same D-SCRIPT model on protein complexes with known 3D structure, we find that the inter-protein contact map output by D-SCRIPT has significant overlap with the ground truth. We apply D-SCRIPT to screen for PPIs in cow (Bos taurus) at a genome-wide scale and focusing on rumen physiology, identify functional gene modules related to metabolism and immune response. The predicted interactions can then be leveraged for function prediction at scale, addressing the genome-to-phenome challenge, especially in species where little data are available.

Replication study of susceptibility variants associated with allergic rhinitis and allergy in Han Chinese

Background

Allergic rhinitis (AR) is believed to be a complex genetic disease. The last decade has been marked by the publication of more than 20 genome-wide association studies (GWASs) of AR and associated allergic phenotypes and allergic diseases, which have shown allergic diseases and traits to share a large number of genetic susceptibility loci. The aim of present study was therefore to investigate the highly replicated allergy related genes and variants as candidates for AR in Han Chinese subjects.

Methods

A total of 762 AR patients and 760 control subjects were recruited, and a total of 58 susceptible variants previously reported to be associated with allergic traits were choose for replication.

Results

Logistic regression analyses revealed that in the co-dominant-effect model as assessed by the AIC, compared with wild-type carriers, significant AR risk were associated with rs9865818 in LPP (P = 0.029, OR = 1.469 for GG vs. AA); rs6554809 in DNAH5 (P = 0.000, OR = 1.597 for TC vs. CC); rs1438673 in WDR36-CAMK4 loci (P = 0.037, OR = 1.396 for CC vs.TT), rs7775228 in HLA region (P = 0.000, OR = 1.589 for TC vs.TT), rs7203459 in CLEC16A (P = 0.025, OR = 0.731 for TC vs. TT).

Conclusion

We replicated Han Chinese AR-specific susceptibility loci in LPP, DNAH5, HLA, CLEC16A and WDR36-CAMK4. Further understanding the molecular mechanisms underlying these associations may provide new insights into the etiology of allergic disease.

A predictive algorithm to identify genes that discriminate individuals with fibromyalgia syndrome diagnosis from healthy controls

Objectives

Fibromyalgia syndrome (FMS) is a chronic and often debilitating condition that is characterized by persistent fatigue, pain, bowel abnormalities, and sleep disturbances. Currently, there are no definitive prognostic or diagnostic biomarkers for FMS. This study attempted to utilize a novel predictive algorithm to identify a group of genes whose differential expression discriminated individuals with FMS diagnosis from healthy controls.

Methods

Secondary analysis of gene expression data from 28 women with FMS and 19 age-and race-matched healthy women. Expression of discriminatory genes were identified using fold-change differential and Fisher’s ratio (FR). Discriminatory accuracy of the differential expression of these genes was determined using leave-one-out-cross-validation. Functional networks of the discriminating genes were described from the Ingenuity’s Knowledge Base.

Results

The small-scale signature contained 57 genes whose expressions were highly discriminatory of the FMS diagnosis. The combination of these high discriminatory genes with FR higher than 1.45 provided a leave-one-out-cross-validation accuracy for the FMS diagnosis of 85.11%. The discriminatory genes were associated with 3 canonical pathways: hepatic stellate cell activation, oxidative phosphorylation, and airway pathology related to COPD.

Conclusion

The discriminating genes, especially the 2 with the highest accuracy, are associated with mitochondrial function or oxidative phosphorylation and glutamate signaling. Further validation of the clinical utility of this finding is warranted.

Chinese Society of Allergy Guidelines for Diagnosis and Treatment of Allergic Rhinitis

Allergic rhinitis (AR) is a global health problem that causes major illnesses and disabilities worldwide. Epidemiologic studies have demonstrated that the prevalence of AR has increased progressively over the last few decades in more developed countries and currently affects up to 40% of the population worldwide. Likewise, a rising trend of AR has also been observed over the last 2-3 decades in developing countries including China, with the prevalence of AR varying widely in these countries. A survey of self-reported AR over a 6-year period in the general Chinese adult population reported that the standardized prevalence of adult AR increased from 11.1% in 2005 to 17.6% in 2011. An increasing number of Journal Articles and imporclinical trials on the epidemiology, pathophysiologic mechanisms, diagnosis, management and comorbidities of AR in Chinese subjects have been published in international peer-reviewed journals over the past 2 decades, and substantially added to our understanding of this disease as a global problem. Although guidelines for the diagnosis and treatment of AR in Chinese subjects have also been published, they have not been translated into English and therefore not generally accessible for reference to non-Chinese speaking international medical communities. Moreover, methods for the diagnosis and treatment of AR in China have not been standardized entirely and some patients are still treated according to regional preferences. Thus, the present guidelines have been developed by the Chinese Society of Allergy to be accessible to both national and international medical communities involved in the management of AR patients. These guidelines have been prepared in line with existing international guidelines to provide evidence-based recommendations for the diagnosis and management of AR in China.

Association of TNF-α-3959T/C Gene Polymorphisms in the Chinese Population with Intracranial Aneurysms

Recent studies have demonstrated that cytokines play an important role in the pathogenesis of intracranial aneurysm (IA). Tumor necrosis factor-α (TNF-α) is an important proinflammatory cytokine, which was shown to influence the development of IA, but there is no research data from China. Hence, the purpose of this study was to explore the relationship between TNF-α polymorphisms and IA in China. The association of genetic variants of TNF-α gene expression was investigated in a Chinese population with IA. The TNF-α-3959T>C(rs1799964), 4127C>A(rs1800630), 4133C>T(rs1799724), 4184C>T(rs4248158), and 4752G>A(rs361525) gene polymorphisms in 192 IA cases and 112 controls were analyzed using polymerase chain reaction (PCR). Differences in genotype and allele frequencies between patients and controls were tested. There were no significant differences in 4127C>A (p = 0.072), 4133C>T (p = 0.373), 4184C>T (p = 0.749), and 4752G>A (p = 0.184) genotype frequencies between the IA group and the control group. But this case-control association study revealed that TNF-α-3959T>C (p < 0.001) was significantly associated with increased risk of IA. These results suggested that a novel TNF-α locus was found to be closely correlated with the occurrence of IA in Chinese.

Pediatric rhinitis risk factors

Rhinitis is a common global disorder that impacts on the quality of life of the sufferer and caregivers. Treatment for pediatric rhinitis is empirical and does not include a detailed history of the allergy triggers or allergy testing. Thus, allergen avoidance advice is not tailored to the child's sensitivities, which may result in adenoid hypertrophy. However, infant onset rhinitis, especially its relationship with respiratory viruses, remains to be further clarified. Rhinitis basically involves inflammation of the upper nasal lining, presenting typically with symptoms of runny nose (rhinorrhea), nasal blockage, and/or sneezing. While not typically fatal, it does impose significant health, psychological, and monetary burden to its sufferers, and is thus considered a global health problem. Previous findings showed that immunotherapy had significant clinical efficacy in children with allergic rhinitis. The present review article aims to highlight recent perspectives pertaining to the rhinitis risk factors especially in pediatric patients.

Expression profile of ADAM10 and ADAM17 in allergic rhinitis

BACKGROUND

A disintegrin and metalloprotease (ADAM) is a multifunctional gene family that contributes to the homeostasis of the extracellular matrix, transduction of specific intracellular signals, organogenesis, inflammation, tissue remodeling, adhesion, and cell migration. ADAM17 is the best characterized sheddase, with widespread putative substrates, including various inflammatory modulators. ADAM10 is the most similar ADAM to ADAM17 in terms of both protein sequence and the structural properties of their catalytic domains. The objective of this work was to assess the expression of ADAM10 and ADAM17 in allergic rhinitis to gain insight into their respective roles.

METHODS

The expression of ADAM10 and ADAM17 was investigated in the nasal mucosa under allergic and nonallergic conditions. Tissue samples were evaluated by reverse-transcription polymerase chain reaction (RT-PCR) and Western blotting, and data were analyzed semiquantitatively with densitometry.

RESULTS

The ADAM17 messenger RNA (mRNA) level was significantly (p < 0.001) lower in the allergic nasal mucosa than in the nonallergic nasal mucosa, whereas the ADAM10 mRNA level was significantly (p < 0.001) lower in the nonallergic nasal mucosa. The ADAM17 protein levels were also significantly (p < 0.001) lower in the allergic nasal mucosa, whereas the ADAM10 protein levels were lower in the nonallergic nasal mucosa (p = 0.002).

CONCLUSION

Decreased expression of ADAM17 and increased expression of ADAM10 may contribute to the development of allergic rhinitis through unknown pathways. We suggest that understanding the expression profile of ADAM17 and ADAM10 might help to elucidate the mechanism of allergic rhinitis.

Association of VDR and CYP2R1 Polymorphisms with Mite-Sensitized Persistent Allergic Rhinitis in a Chinese Population

As recent studies have described an association between vitamin D and allergic rhinitis, we hypothesized that vitamin D pathway-related genes may be candidate genes for susceptibility to allergic rhinitis. Thus, we sought to evaluate whether polymorphisms in the vitamin D receptor (VDR) and CYP2R1 genes are associated with mite-sensitized persistent allergic rhinitis (PER) in a Han Chinese population. A hospital-based case-control study consisting of 519 patients with mite-sensitized PER and 447 healthy controls was conducted. Five single nucleotide polymorphisms (SNPs) in VDR and CYP2R1 were selected for genotyping. The genotype and allele frequencies of rs9729, rs2228570, rs1544410, and rs731236 in VDR as well as rs2060793 in CYP2R1 were not significantly associated with susceptibility to mite-sensitized PER. After stratification analyses, however, both the CT and CT/TT genotypes of rs2228570 in VDR exhibited a significantly decreased risk (CT: adjusted odds ratio (OR)=0.58, 95% confidence intervals (CI)=0.37-0.91; CT/TT: adjusted OR=0.61, 95% CI=0.40-0.93) of mite-sensitized PER, while the AA genotype of rs2060793 in CYP2R1 exhibited a significantly increased risk (adjusted OR=1.85, 95% CI=1.03-3.34) of PER in the age subgroup of <16 years old. Both the AG and AG/GG genotypes of rs731236 in VDR exhibited a significantly decreased risk (AG: adjusted OR=0.43, 95% CI=0.21-0.89; AG/GG: adjusted OR=0.46, 95% CI=0.23-0.94) of PER in the female subgroup. Analysis of the locus-locus interactions of VDR and CYP2R1 revealed two models that involved combined SNPs of VDR and CYP2R1 were statistically significant (P<0.05). Our data suggest that age and gender may have an impact on the association of three SNPs (rs2228570, rs731236, and rs2060793) in genes of the vitamin D pathway with the risk of mite-sensitized PER in this Chinese population. The VDR and CYP2R1 variants may be involved in genetic interactions in the pathogenesis of PER.

Discovering susceptibility genes for allergic rhinitis and allergy using a genome-wide association study strategy

PURPOSE OF REVIEW

Allergic rhinitis and allergy are complex conditions, in which both genetic and environmental factors contribute to the pathogenesis. Genome-wide association studies (GWASs) employing common single-nucleotide polymorphisms have accelerated the search for novel and interesting genes, and also confirmed the role of some previously described genes which may be involved in the cause of allergic rhinitis and allergy. The aim of this review is to provide an overview of the genetic basis of allergic rhinitis and the associated allergic phenotypes, with particular focus on GWASs.

RECENT FINDINGS

The last decade has been marked by the publication of more than 20 GWASs of allergic rhinitis and the associated allergic phenotypes. Allergic diseases and traits have been shown to share a large number of genetic susceptibility loci, of which IL33/IL1RL1, IL-13-RAD50 and C11orf30/LRRC32 appear to be important for more than two allergic phenotypes. GWASs have further reflected the genetic heterogeneity underlying allergic phenotypes.

SUMMARY

Large-scale genome-wide association strategies are underway to discover new susceptibility variants for allergic rhinitis and allergic phenotypes. Characterization of the underlying genetics provides us with an insight into the potential targets for future studies and the corresponding interventions.