Multilocus analysis of candidate genes involved in neurogenic inflammation in pediatric asthma and related phenotypes: a case-control study

Personalized medicine using omics approaches in acute respiratory distress syndrome to identify biological phenotypes

In the last decade, research on acute respiratory distress syndrome (ARDS) has made considerable progress. However, ARDS remains a leading cause of mortality in the intensive care unit. ARDS presents distinct subphenotypes with different clinical and biological features. The pathophysiologic mechanisms of ARDS may contribute to the biological variability and partially explain why some pharmacologic therapies for ARDS have failed to improve patient outcomes. Therefore, identifying ARDS variability and heterogeneity might be a key strategy for finding effective treatments. Research involving studies on biomarkers and genomic, metabolomic, and proteomic technologies is increasing. These new approaches, which are dedicated to the identification and quantitative analysis of components from biological matrixes, may help differentiate between different types of damage and predict clinical outcome and risk. Omics technologies offer a new opportunity for the development of diagnostic tools and personalized therapy in ARDS. This narrative review assesses recent evidence regarding genomics, proteomics, and metabolomics in ARDS research.

Novel biomarkers for acute respiratory distress syndrome: genetics, epigenetics and transcriptomics

Acute respiratory distress syndrome (ARDS) can be induced by multiple clinical factors, including sepsis, acute pancreatitis, trauma, intestinal ischemia/reperfusion and burns. However, these factors alone may poorly explain the risk and outcomes of ARDS. Emerging evidence suggests that genomic-based or transcriptomic-based biomarkers may hold the promise to establish predictive or prognostic stratification methods for ARDS, and also to help in developing novel therapeutic targets for ARDS. Notably, genetic/epigenetic variations correlated with susceptibility and prognosis of ARDS and circulating microRNAs have emerged as potential biomarkers for diagnosis or prognosis of ARDS. Although limited by sample size, ethnicity and phenotypic heterogeneity, ongoing genetic/transcriptomic research contributes to the characterization of novel biomarkers and ultimately helps to develop innovative therapeutics for ARDS patients.

Nitric Oxide Synthase 2 Promoter Polymorphism Is a Risk Factor for Allergic Asthma in Children

Background and Objectives: In paediatric population, atopic asthma is associated with increased eosinophil counts in patients, that correlate with the airway inflammation measured by the concentration of nitric oxide in exhaled air (FeNO). As the FeNO level is a biomarker of atopic asthma, we assumed that polymorphisms in nitric synthases genes may represent a risk factor for asthma development. The purpose of this study was to analyse the association of NOS genetic variants with childhood asthma in the Polish population. Materials and methods: In study we included 443 children—220 patients diagnosed with atopic asthma and 223 healthy control subjects. We have genotyped 4 single nucleotide polymorphisms (SNP) from 3 genes involved in the nitric oxide synthesis (NOS1, NOS2 and NOS3). All analyses were performed using polymerase chain reaction with restriction fragments length polymorphism (PCR-RFLP). Results: We observed significant differences between cases and controls in SNP rs10459953 in NOS2 gene, considering both genotypes (p = 0.001) and alleles (p = 0.0006). The other analyzed polymorphisms did not show association with disease. Conclusions: According to our results, 5′UTR variant within NOS2 isoform may have an impact of asthma susceptibility in the population of Polish children. Further functional studies are required to understand the role of iNOS polymorphism in NOS2 translation and to consider it as a novel risk factor in childhood asthma. The next step would be to apply this knowledge to improve diagnosis and develop novel personalized asthma therapies.

Association Study of MAP3K1 SNPs and Risk Factors with Susceptibility to Esophageal Squamous Cell Carcinoma in a Chinese Population: A Case-Control Study

Purpose

The aim of this study was to screen the predisposed population and explore possible interactions between genetic polymorphisms and risk factors involved in the tumorigenesis and progression of ESCC (esophageal squamous cell carcinoma), in hope of identifying possible therapeutic targets along the way.

Patients and Methods

Cases (1043) and controls (1315) were enrolled to evaluate the possible association between MAP3K1 SNPs and ESCC risk. Subgroup analyses include MAP3K1 variants, gender, age, smoking and drinking status.

Results

Among all three single locus polymorphisms of MAP3K1, only the heterozygote genotype of rs702689 AG is shown to be associated with increased risk for developing ESCC (OR=1.272, 95% confidence interval=1.061–1.525, p=0.009). Moreover, stratified analysis results observed altered susceptibility among patients with exposure to risk factors combined with certain genetic variant to ESCC.

Conclusion

This study reveals that MAP3K1 rs702689 AG genotype might facilitate the tumorigenesis in ESCC, particularly among women, patients who were over 63y and those who never drink nor smoke.

NGF (-198C > T, Ala35Val) and p75NTR (Ser205Leu) gene mutations are associated with liver function in different histopathological profiles of the patients with chronic viral hepatitis in the Brazilian Amazon

BACKGROUNDS

Neural growth factor (NGF) is a neurotrophin that can interact with the p75NTR receptor and initiate a cascade of reactions that determines cell survival or death, and both are associated with the physiology of liver tissue. Single nucleotide polymorphisms (SNPs) in the NGF and p75NTR genes have been investigated in different pathologies; however, there are no studies that have analyzed their biological roles in the hepatic microenvironment. In the present study, we evaluated the impact of SNPs in these genes on the maintenance of liver function at different stages of inflammation and fibrosis in patients with chronic viral liver disease in the Brazilian Amazon.

METHODS

The SNPs -198C > T, Arg80Gln, Val72Met, Ala35Val, Ala18Ala and Ser205Leu were genotyped by real-time PCR in samples from patients with chronic viral hepatitis stratified by stage of inflammation and liver fibrosis. Histopathological, viral load (VL), liver enzyme and comorbidities data were obtained from updated medical records. Other aspects were highlighted by applied epidemiological questionnaires.

RESULTS

The -198C/T and Ala35Val polymorphisms in NGF were associated with changes in histopathological profiles, VL and liver enzymes. Ser205Leu polymorphism in p75NTR was associated only with changes in VL and liver enzymes. Polymorphic frequencies were variable among different ethnic populations, mainly for biologically relevant polymorphisms. A multifactorial network of interactions has been established based on genetic, virological, behavioral and biochemical aspects.

CONCLUSION

Mutations in the NGF (-198C > T, Ala35Val) and p75NTR (Ser205Leu) genes, within the list of multifactorial aspects, are associated with liver function in different histopathological profiles of patients with chronic viral liver disease in the Brazilian Amazon.

Genetic Association Between NGFR, ADAM17 Gene Polymorphism, and Parkinson's Disease in the Chinese Han Population

Parkinson's disease (PD) is a common neurodegenerative disease characterized by neuronal loss in the substantia nigra. The p75 neurotrophin receptor (p75NTR, encoded by NGFR) was found to play an important role in the selective neuronal death of dopamine neurons in the substantia nigra, as well as the pathogenesis and development of PD. To assess the association between NGFR gene polymorphism and the susceptibility of PD, this case-control study consisting of 414 PD patients and 623 age- and sex-matched controls in a Chinese Han cohort was conducted. Twelve tag-single nucleotide polymorphisms (tag-SNPs) were selected from the NGFR gene through the construction of linkage disequilibrium blocks. One tag-SNP from the ADAM17 gene was also selected owing to its function of encoding tumor necrosis factor α-converting enzyme, which is responsible for the shedding of the extracellular domain of p75NTR. A multiplex polymerase chain reaction-ligase detection reaction (PCR-LDR) method was applied for genotyping. The associations between tag-SNPs and the risk of PD with the adjustment for age and sex were analyzed by unconditional logistic regression, and five genetic models including codominant, dominant, recessive, over-dominant, and additive models were applied. The results showed that among the 13 tag-SNPs, rs741073 was associated with a reduced risk of PD in the codominant (OR = 0.71, 95% CI = 0.54-0.93, P = 0.037), dominant (OR = 0.76, 95% CI = 0.58-0.98, P = 0.033), and over-dominant models (OR = 0.71, 95% CI = 0.54-0.92, P = 0.010), and rs1804011 was also associated with a reduced risk of PD in the codominant (OR = 0.69, 95% CI = 0.50-0.95, P = 0.049), dominant (OR = 0.69, 95% CI = 0.50-0.93, P = 0.014), over-dominant (OR = 0.70, 95% CI = 0.51-0.96, P = 0.025), and additive models (OR = 0.72, 95% CI = 0.54-0.94, P = 0.016). However, these associations did not retain after Bonferroni correction. Conclusively, our study failed to reveal the association between the selected tag-SNPs within NGFR, ADAM17, and the susceptibility of PD. The role of p75NTR and its gene polymorphisms in the pathogenesis of PD needs to be further studied.

Genetic Variation in MAP3K1 Associates with Ventilator-Free Days in Acute Respiratory Distress Syndrome

Mitogen-activated protein kinase kinase kinase 1 (MAP3K1) regulates numerous intracellular signaling pathways involved in inflammation and apoptosis. We hypothesized that genetic variation in MAP3K1 might be associated with outcomes in patients with acute respiratory distress syndrome (ARDS), and that these variants would alter MAP3K1-mediated changes in inflammation and transcriptional regulation. To test this hypothesis, we genotyped single-nucleotide polymorphisms covering linkage disequilibrium bins in MAP3K1 in 306 subjects with ARDS from the ARDSNet FACTT (Fluid and Catheter Treatment Trial) study, and tested for associations between MAP3K1 single-nucleotide polymorphisms and ventilator-free days (VFDs) and mortality. We then validated these associations in a separate cohort of 241 patients with ARDS from Harborview Medical Center (Seattle, WA). We found the variant allele of rs832582 (MAP3K1_906Val) was significantly associated with decreased VFDs using multivariate linear regression (-6.1 d, false discovery rate = 0.06) in the FACTT cohort. In the Harborview Medical Center cohort, subjects homozygous for MAP3K1_906Val also had decreased VFDs (-15.1 d, false discovery rate < 0.01), and increased 28-day mortality (all subjects homozygous for the rare allele died). In whole blood stimulated with various innate immune agonists ex vivo, MAP3K1_906Val was associated with increased IL-1β, IL-6, IL-8, monocyte chemoattractant protein 1, and TNF-α production. Transcriptome analysis of whole blood stimulated with Toll-like receptor 4 agonist ex vivo demonstrated enrichment of inflammatory gene sets in subjects homozygous for MAP3K1_906Val. Our findings show a robust association between the variant allele of rs832582 (MAP3K1_906Val) and decreased VFDs in patients with ARDS and suggest that this variant may predispose individuals to a greater inflammatory response.

Neurotrophins in Asthma

PURPOSE OF REVIEW

Asthma is a chronic airway disease that affects more than 300 million people worldwide. Current treatment focuses on symptomatic relief by temporally dampening inflammation and relaxing the airway. Novel combative strategies against asthma and hopefully a cure are yet to be developed. The goal of this review is to summarize recent literature on neurotrophins (NTs) in experimental models and clinical settings of asthma research.

RECENT FINDINGS

We highlight studies of early phases of asthma that collectively reveal a profound impact of elevated NT levels following initial detrimental insults on long-term airway dysfunction. We hope this review will foster insights into the complex interaction between NTs, nerves, immune cells, and airway structural cells during a critical time window of development and disease susceptibility. Future studies are required to better understand the role of NTs in asthma pathophysiology and to evaluate whether NTs and their receptors may serve as new drug targets.

Association between Val66Met polymorphisms in brain-derived neurotrophic factor gene and asthma risk: a meta-analysis

OBJECTIVE

The Val66Met polymorphisms in brain-derived neurotrophic factor (BDNF) gene have been reported to be associated with asthma risk, while the results are inconclusive. Considering a single study may lack the power to provide reliable conclusion, we performed a meta-analysis to investigate the association between the Val66Met polymorphisms and asthma susceptibility.

METHODS

A comprehensive literature search of PubMed, Embase, China National Knowledge Infrastructure (CNKI) and Wanfang databases was conducted before February 12, 2015. The pooled odds ratio (OR) with 95 % confidence intervals (CIs) were calculated.

RESULTS

Six eligible studies with a total of 3501 subjects were finally included in this meta-analysis. Overall, a significantly increased risk was detected in the Val66Met G allele (G vs. A: OR 1.33, 95 % CI 1.19-1.49, P = 5.61E-07; GG vs. GA + AA: OR 1.48, 95 % CI 1.20-1.83, P = 3.14E-04; GG vs. GA: OR 1.48, 95 % CI 1.17-1.89, P = 0.001; GG vs. AA: OR 1.62, 95 % CI 1.20-2.19, P = 0.002). Moreover, stratification by ethnicity indicated marked association between the Val66Met G allele and asthma risk in Caucasians (G vs. A: OR 1.29, 95 % CI 1.12-1.49, P = 0.001; GG + GA vs. AA: OR 1.59, 95 % CI 1.03-2.46, P = 0.039; GG vs. GA + AA: OR 1.32, 95 % CI 1.11-1.57, P = 0.001; GG vs. GA: OR 1.28, 95 % CI 1.07-1.53, P = 0.007; GG vs. AA: OR 1.72, 95 % CI 1.11-2.68, P = 0.015).

CONCLUSION

Our present meta-analysis suggests that the Val66Met polymorphisms in BDNF gene are potentially associated with asthma risk in Caucasians. Further well-designed case-control studies with larger sample size and more ethnic groups are needed to confirm these conclusions.

Val66Met polymorphism in the BDNF gene in children with bronchial asthma

OBJECTIVES

Bronchial asthma is a chronic respiratory disease characterized by airway inflammation. There is increasing evidence that neurotrophins play an important role in the development and maintenance of neurogenic airway inflammation in chronic allergic diseases.

WORKING HYPOTHESIS

Brain-derived neurotrophic factor (BDNF) is a member of the neurotrophin family and has several important functions in the airways. There are only a few reports on the association between genetic variations in the BDNF gene and various allergic diseases, and the results are generally conflicting. Therefore, we aimed to study the functional polymorphism Val66Met (also called rs6265 or G196A) in the BDNF gene in a group of asthmatic children and healthy controls.

STUDY DESIGN, PATIENT-SELECTION, AND METHODOLOGY

We studied 248 asthmatic patients (aged 12.28 ± 0.24 years) and 249 healthy children (aged 13.14 ± 0.48 years). Analysis of the Val66Met polymorphism of the BDNF gene was performed by polymerase chain reaction (PCR) and PCR products were digested by PmlI.

RESULTS

The prevalence of the Val66Met polymorphisms (Val/Val, Val/Met, and Met/Met) was 61.7%, 33.5%, and 4.8% in asthmatics, respectively, and 47.0%, 51.8%, and 1.2% in healthy subjects, respectively. We observed a significant association of the Met/Met variant genotype with asthmatics (OR = 4.17, 95% CI = 1.16-14.96, P = 0.018). The Val/Met genotype was protective against bronchial asthma (OR = 0.69, 95% CI = 0.48-0.99, P = 0.045), especially in girls (OR = 0.34, 95% CI = 0.20-0.59, P = 0.001).

CONCLUSION

Specific BDNF gene polymorphism may contribute to bronchial asthma susceptibility. Our study suggested the positive association between selected functional BDNF polymorphism (rs6265) and asthma in children.

Impact of genetic polymorphisms on paediatric atopic dermatitis

In order to investigate whether polymorphisms of genes encoding some factors of innate and adaptive immunity play a role in the development of, or protection against atopic dermatitis (AD) and condition its severity, we genotyped 33 candidate genes and 47 single nucleotide polymorphisms (SNPs) using Custom TaqMan Array Microfluidic Cards and an ABI 7900HT analyser (Applied Biosystems, Foster City, CA, USA). The study involved 104 children with AD (29 with mild-to-moderate and 75 with severe disease; 42 girls; mean age ± SD, 5.8 ± 3.3 years) and 119 healthy controls (49 girls; mean age, 4.8 ± 3.0 years). IL10-rs1800872T, TG and MBL2-rs500737AG were all significantly more frequent among the children with AD ( P = 0.015, P = 0.004 and P = 0.030), whereas IL10-rs1800896C and TC were more frequent in those without AD ( P = 0.028 and P = 0.032). The VEGFA-rs2146326A and CTLA4-rs3087243AG SNPs were significantly more frequent in the children with mild/moderate AD than in those with severe AD ( P = 0.048 and P = 0.036). IL10-rs1800872T and TG were significantly more frequent in the children with AD and other allergic diseases than in the controls ( P = 0.014 and P = 0.007), whereas IL10-rs1800896TC and C were more frequent in the controls than in the children with AD and other allergic diseases ( P = 0.0055 and P = 0.0034). These findings show that some of the polymorphisms involved in the immune response are also involved in some aspects of the development and course of AD and, although not conclusive, support the immunological hypothesis of the origin of the inflammatory lesions.

Genetic polymorphisms and risk of recurrent wheezing in pediatric age

Background

Wheezing during early life is a very common disorder, but the reasons underlying the different wheezing phenotypes are still unclear. The aims of this study were to analyse the potential correlations between the risk of developing recurrent wheezing and the presence of specific polymorphisms of some genes regulating immune system function, and to study the relative importance of the associations of different viruses and genetic polymorphisms in causing recurrent episodes.

Methods

The study involved 119 otherwise healthy infants admitted to hospital for a first episode of wheezing (74 of whom subsequently experienced recurrent episodes) and 119 age- and sex-matched subjects without any history of respiratory problem randomly selected from those attending our outpatient clinic during the study period. All of the study subjects were followed up for two years, and 47 single nucleotide polymorphisms (SNPs) in 33 candidate genes were genotyped on whole blood using an ABI PRISM 7900 HT Fast Real-time instrument.

Results

IL8-rs4073AT, VEGFA-rs833058CT, MBL2-rs1800450CT and IKBKB-rs3747811AT were associated with a significantly increased risk of developing wheezing (p = 0.02, p = 0.03, p = 0.05 and p = 0.0018), whereas CTLA4-rs3087243AG and NFKBIB-rs3136641TT were associated with a significantly reduced risk (p = 0.05 and p = 0.04). IL8-rs4073AT, VEGFA-rs2146323AA and NFKBIA-rs2233419AG were associated with a significantly increased risk of developing recurrent wheezing (p = 0.04, p = 0.04 and p = 0.03), whereas TLR3-rs3775291TC was associated with a significantly reduced risk (p = 0.03). Interestingly, the study of gene-environment interactions showed that rhinovirus was significantly associated with recurrent wheezing in the presence of IL4Ra-rs1801275GG and G (odds ratio [OR] 6.03, 95% confidence interval [CI]: 1.21-30.10, p = 0.03) and MAP3K1-rs702689AA (OR 4.09, 95% CI: 1.14-14.61, p = 0.03).

Conclusions

This study shows a clear relationship between the risk of wheezing and polymorphisms of some genes involved in the immune response. Although further studies are needed to confirm the results, these findings may be useful for the early identification of children at the highest risk of developing recurrent episodes and possibly subsequent asthma.

Mutation analysis of mitogen activated protein kinase 1 gene in Indian cases of 46,XY disorder of sex development

BACKGROUND:

Determination of sex is the result of cascade of molecular events that cause undifferentiated bipotential gonad to develop as a testis or an ovary. A series of genes such as SRY, steroidogenic factor-1 (SF1), AR, SRD5 α, Desert hedgehog (DHH) etc., have been reported to have a significant role in development of sex in the fetus and secondary sexual characteristics at the time of puberty. Recently, mitogen activated protein kinase kinase kinase 1 (MAP3K1) gene was found to be associated with 46, XY disorders of sex development (DSD).

AIM:

The present study is focused to identify mutations in MAP3K1 gene in the cohort of 10 Indian patients with 46,XY DSD including one family with two affected sisters. These patients were already screened for SRY, SF1 and DHH gene, but no mutation was observed in any of these genes.

MATERIALS AND METHODS:

The entire coding regions of MAP3K1 were amplified and sequenced using the gene specific primers.

RESULTS AND DISCUSSIONS:

Sequence analysis of MAP3K1 gene has revealed four variants including one missense, two silent and one deletion mutation. The missense mutation p.D806N was observed in four patients with hypospadias. Two patients showed the presence of silent mutation p.Q1028Q present in exon 14. Another silent mutation p.T428T was observed in a patient with gonadal dysgenesis. We have also observed one deletion mutation p. 942insT present in two patients. The pathogenicity of the missense mutation p.D806N was carried out using in-silico approach. Sequence homology analysis has revealed that the aspartate at 806 was found to be well-conserved across species, indicated the importance of this residue. The score for polyphen analysis of this mutation was found to be 0.999 indicating to be pathogenic mutation. Since, p.D806N mutation was found to be important residue; it might contribute to sexual development. We have reported the presence of mutations/polymorphism in MAP3K1 gene. All the mutations were found to be polymorphism upon comparing to single nucleotide polymorphism database. However, in-silico analysis of the missense mutation revealed to be a pathogenic mutation.