Pathway analysis for a genome-wide association study of pneumoconiosis

Association between polymorphisms in TLR3, TICAM1 and IFNA1 genes and covid-19 severity in Southern Brazil

BACKGROUND

A distinct phenotype in Coronavirus disease 2019 (Covid-19) was observed in severe patients, consisting of a highly impaired interferon (IFN) type I response, an exacerbated inflammatory response.

OBJECTIVE

The aim of the present study was to investigate a possible association of single nucleotide polymorphisms (SNPs), in five genes related to the immune response, rs3775291 in TLR3; rs2292151 in TICAM1; rs1758566 in IFNA1; rs1800629 in TNF, and rs1800795 in IL6 with the severity of Covid-19.

METHODS

A cross-sectional study was performed, with non-severe and severe/critical patients diagnosed with Covid-19, by two public hospitals in Brazil. In total, 300 patients were genotyped for the SNPs, 150 with the non-severe form of the disease and 150 with severe/critical form.

RESULTS

The T/T genotype of TLR3 in recessive model shows 58% of protection against severe/critical Covid-19; as well as the genotypes G/A+A/A of TICAM1 in dominant model with 60% of protection, and in a codominant model G/A with 57% and A/A with 71% of protection against severe/critical Covid-19. Comparing severe and critical cases, the T/C genotype of IFNA1 in the codominant model and TC+C/C in the dominant model showed twice the risk of critical Covid-19.

CONCLUSION

We can conclude that rs3775291, rs2292151 and rs1758566 can influence the COVID-19 severity.

[Association of gene polymorphisms of MyD88 and TICAM1 and their interactions with community-acquired pneumonia in children]

OBJECTIVES

To investigate the association of single nucleotide polymorphisms (SNPs) of myeloid differentiation factor 88 (MyD88) and Toll-like receptor adaptor molecule 1 (TICAM1) and their interactions with community-acquired pneumonia (CAP) in children.

METHODS

Improved multiple ligase detection reaction assay was used for detecting the polymorphisms of nine tagging SNPs of the MyD88 and TICAM1 genes in 375 children with CAP who attended the Department of Pediatrics of the Second Affiliated Hospital of Yan'an University Medical School from August 2015 to September 2017 and 306 healthy children who underwent physical examination. A logistic regression analysis was used to evaluate the association between the distribution of genotypes and their interactions with CAP in children.

RESULTS

The polymorphism of the TICAM1 gene at rs11466711T/C locus was closely associated with the susceptibility to CAP in children (P<0.05). The AA genotype of rs35747610G/A locus significantly reduced risk of sepsis in children with CAP (P<0.05). The AA genotype of rs6510826G/A locus was significantly associated with the increase in C-reactive protein level in children with CAP (P<0.05). The GG genotype of the MyD88 gene at rs7744A/G locus significantly increased the risk of respiratory failure and circulatory failure (P<0.05). The multiplicative interactions between MyD88 gene rs7744A/G and TICAM1 gene rs11466711T/C, rs2292151G/A, rs35299700C/T, and rs35747610G/A loci were significantly associated with the susceptibility to CAP, the severity of CAP, and the risk of sepsis in children (P<0.05).

CONCLUSIONS

The gene polymorphisms of MyD88 and TICAM1 and their interactions are closely associated with CAP in children, with a synergistic effect on the development and progression of CAP in children.

Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty?

Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.

Is individual genetic susceptibility a link between silica exposure and development or severity of silicosis? A systematic review

BACKGROUND

Silicosis is a lung disease of fibrotic nature resulting from the inhalation and deposition of dust containing crystalline silica. Subjects exposed to the same environmental factors may show distinct radiological manifestations, and since silicosis is known as a multifactorial disease, it is plausible that individual genetic susceptibility may play a role in the pathology. This review of the literature aims to provide an assessment of the present data on the genetic association studies in silicosis and describe the genes that potentially might influence silicosis susceptibility in silica-exposed individuals.

METHODS

We accessed the database of PubMed for articles published in English about interindividual genetic susceptibility to silicosis using terms related to the subject matter.

RESULTS

Following the evaluation process, 28 studies were included in this systematic review, including 23 original studies and 5 meta-analyses.

CONCLUSIONS

Regardless of the advances in the knowledge of the importance of gene variations in silicosis, more studies need to be performed, in particular, special polygenic and genome-wide investigations.

NAF1 rs4691896 Is Significantly Associated with Coal Workers' Pneumoconiosis in a Chinese Han Population: A Case-Control Study

Background

Previous studies have demonstrated the important role of genetic predisposition in coal workers’ pneumoconiosis (CWP) in addition to environmental factors. The pathogenesis of pulmonary fibrosis disease is related to telomere activity. We performed this study to assess the association between genetic variants of telomere-related genes and the risk of CWP.

Material/Methods

We enrolled 652 CWP Chinese Han patients and 648 dust-exposed controls in this case-control design study, genotyping 8 single-nucleotide polymorphisms (SNPs) including TERT (rs2736100), TERC (rs10936599 and rs12696304), and NAF1 (rs7675998, rs3822304, rs12331717, rs936562 and rs4691896) using the Sequenom MassARRAY system.

Results

We identified a significant allele association between NAF1 rs4691896 and CWP by comparing patients with controls (22.0% vs. 13.0%, odds ratio [OR]: 1.89, 95% confidence interval [CI]: 1.54–2.33, Pc=1.14×10⁻⁸). The genotype frequency of rs4691896 differed significantly between the patients and controls (Pc=1.49×10⁻⁸). In addition, rs4691896 was correlated with CWP in an additive genetic model (OR: 1.96, 95% CI: 1.58–2.44, Pc=8.96×10⁻⁹) and a dominant model (OR: 2.15, 95% CI: 1.70–2.73, Pc=2.39×10⁻⁹).

Conclusions

Our study for the first time demonstrates an association between a telomere-related gene (NAF1) and CWP in a Chinese Han population, and provides valuable insight to further understand the possible pathogenetic mechanism of fibrosis in CWP.

Correlation between TICAM1 gene polymorphisms and community-acquired pneumonia in children

This study aims to explore the relationship between single nucleotide polymorphisms (SNPs) of the TICAM1 gene and community-acquired pneumonia (CAP) in Chinese children. The polymorphisms of eight tag SNP (TagSNP) locus of TICAM1 were detected using the improved multiplex ligation detection reaction (iMLDR) assay in 375 children with CAP (average age, 37.8 ± 21.6 months) and 306 healthy children (average age, 38.5 ± 23.8 months). The correlation between polymorphisms of these TagSNPs and the risk, severity, sepsis, and CRP level of childhood CAP were evaluated using logistic regression analysis. The CC genotype of rs11466711T/C locus of TICAM1 is correlated with childhood CAP susceptibility, which significantly reduced the risk of childhood CAP (P < .05), The AA genotype of the rs6510826G/A locus and haplotype CCCA were associated with CRP level in childhood CAP, which significantly increased the risk of CRP increase (P < .05 and P < .01, respectively), The AA genotype of rs35747610G/A site is associated with sepsis in childhood CAP, significantly reduced risk of sepsis (P < .05). While the haplotype CCCG of this locus led to a significant reduction in the risks of childhood CAP, severe pneumonia and pneumonia sepsis (all P < .05). TICAM1 has multiple functional variants closely related to the development and progression of childhood CAP, and these variations may have a synergistic effect on the development of childhood CAP.

Risk of atrial fibrillation in patients with pneumoconiosis: A nationwide study in Taiwan

Background

To investigate the incidence of new‐onset atrial fibrillation (AF) among subjects with pneumoconiosis using the Taiwan National Health Insurance Research Database.

Hypothesis

Pneumoconiosis patients are at an increased risk of AF.

Methods

A total of 12 209 pneumoconiosis patients were in the exposure cohort. Patients without pneumoconiosis were included as the comparison cohort. Both cohorts were matched by gender, age, comorbidity, and index year in a 1:1 manner. Multivariable cox proportional hazard model was used to calculate the adjusted hazard ratios (HRs) after adjustment for age, sex, and all comorbidities.

Results

The risk of AF in pneumoconiosis patients was 1.30‐fold higher than that of controls (95% CI = 1.17‐1.44) was the key finding.

Conclusions

Pneumoconiosis is associated with increased risk of incident AF.

Association of gene polymorphisms of pattern-recognition receptor signaling pathway with the risk and severity of hand, foot, and mouth disease caused by enterovirus 71 in Chinese Han population

Hand, foot, and mouth disease (HFMD) caused by enterovirus 71 (EV71) presents with a wide variety of clinical manifestations. Host immune response is a factor that influences disease susceptibility and severity. We investigated the potential association of gene polymorphisms in the pattern recognition receptor (PRR) pathway with the risk and severity of EV71 infection. A total of 180 EV71 HFMD cases (108 severe case; 72 mild cases) were enrolled. A group of 201 sex- and age-matched children was included as a control. All subjects were genotyped for the most common single-nucleotide polymorphisms (SNPs) in the PRR and the PRR signaling pathway using the SNPscan multiple SNP typing method. Binary logistic regression analysis revealed statistically significant differences in polymorphism of RIG-1 between patients and controls (rs3739674 G vs C: OR = 1.502, 95%CI: 1.120-2.014; rs9695310 G vs C: OR = 1.782, 95%CI: 1.312-2.419). Polymorphisms of RIG-1 rs3739674 (G vs C: OR = 2.047, 95%CI: 1.307-3.205) and TLR3 rs5743305 (A vs T: OR = 0.346, 95%CI: 0.212-0.566) were found to be associated with disease severity. The results indicated that RIG-1 (rs3739674 and rs9695310) polymorphisms are associated with an increased risk of EV71-induced HFMD in Chinese children, whereas RIG-1 rs3739674 and TLR3 rs5743305 polymorphisms are associated with disease severity. These findings support an important role of innate immune mechanism in EV71 infection.

Pneumoconiosis increases the risk of congestive heart failure: A nationwide population-based cohort study

The purpose of the study was to determine the relationship between pneumoconiosis and congestive heart failure (CHF).We collected data from the National Health Insurance Research Database in Taiwan. The study sample comprised 8923 patients with pneumoconiosis and 35,692 nonpneumoconiosis controls enrolled from 2000 to 2011. Patients were followed up until the end of 2011 to evaluate the incidence of CHF. The risk of CHF was analyzed using Cox proportional hazard regression models, and the analysis accounted for factors such as sex, age, comorbidities, and air pollutants (μg/m).The overall incidence of CHF was higher in the pneumoconiosis cohort (15.7 per 1000 person-y) than in the nonpneumoconiosis cohort (11.2 per 1000 person-y), with a crude hazard ratio (HR) of 1.40 (P < 0.001). The HR for CHF was 1.38-fold greater in the pneumoconiosis cohort than in the nonpneumoconiosis cohort (P < 0.001) after the model was adjusted for age, sex, various comorbidities, and air pollutants (μg/m). The relative risk for CHF in the sex-specific pneumoconiosis cohort compared with the nonpneumoconiosis cohort was significant for men (adjusted HR = 1.40, 95% confidence interval = 1.21-1.62, P < 0.001). The incidence density rates of CHF increased with age; pneumoconiosis patients had a higher relative risk of CHF for all age group.Patients with pneumoconiosis were at higher risk for developing CHF than patients in the nonpneumoconiosis cohort, particularly in cases with coexisting coronary artery disease, hypertension, and chronic obstructive pulmonary disease.