HIF1A gene rs10873142 polymorphism is associated with risk of chronic obstructive pulmonary disease in a Chinese Han population: a case-control study

Genetic polymorphisms in MIR1208 and MIR5708 are associated with susceptibility to COPD in the Chinese population

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by limited airflow and is influenced by genetic and environmental factors. The purpose of this study was to investigate the effects of gene polymorphisms in MIR5708 and MIR1208 on COPD risk.

METHODS

Four single nucleotide polymorphisms (SNPs) in MIR5708 (rs6473227 and rs16907751) and MIR1208 (rs2608029 and rs13280095) were selected and genotyped among 315 COPD patients and 314 healthy controls using the Agena MassARRAY platform. SPSS 18.0 was used for statistical analysis and data processing. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the association between genetic variants of MIR1208 and MIR5708 and COPD risk.

RESULTS

The results suggested that rs16907751 variants in MIR5708 contributed to an increased susceptibility to COPD in the allelic (P = 0.001), co-dominant (homozygous) (P = 0.001), dominant (P = 0.017), recessive (P = 0.002), and additive (P = 0.002) models. The effects of MIR5708 and MIR1208 gene polymorphisms on the risk of COPD were age-, sex-, smoking status-, and BMI-related. Furthermore, the C-A and G-A haplotypes of rs2608029 and rs13280095 in MIR1208 were identified as risk factors for COPD in the population over 70 years (P = 0.029) and in women (P = 0.049), respectively. Finally, significant associations between rs16907751genotypes with pulse rate and forced expiratory volume in 1 s were found among COPD patients.

CONCLUSION

Genetic polymorphisms in MIR5708 and MIR1208 are associated with increased risk of COPD in China.

The impact of COVID-19 on populations living at high altitude: Role of hypoxia-inducible factors (HIFs) signaling pathway in SARS-CoV-2 infection and replication

Cases of coronavirus disease 2019 (COVID-19) have been reported worldwide. However, one epidemiological report has claimed a lower incidence of the disease in people living at high altitude (>2,500 m), proposing the hypothesis that adaptation to hypoxia may prove to be advantageous with respect to SARS-CoV-2 infection. This publication was initially greeted with skepticism, because social, genetic, or environmental parametric variables could underlie a difference in susceptibility to the virus for people living in chronic hypobaric hypoxia atmospheres. Moreover, in some patients positive for SARS-CoV-2, early post-infection ‘happy hypoxia” requires immediate ventilation, since it is associated with poor clinical outcome. If, however, we accept to consider the hypothesis according to which the adaptation to hypoxia may prove to be advantageous with respect to SARS-CoV-2 infection, identification of the molecular rational behind it is needed. Among several possibilities, HIF-1 regulation appears to be a molecular hub from which different signaling pathways linking hypoxia and COVID-19 are controlled. Interestingly, HIF-1α was reported to inhibit the infection of lung cells by SARS-CoV-2 by reducing ACE2 viral receptor expression. Moreover, an association of the rs11549465 variant of HIF-1α with COVID-19 susceptibility was recently discovered. Here, we review the evidence for a link between HIF-1α, ACE2 and AT1R expression, and the incidence/severity of COVID-19. We highlight the central role played by the HIF-1α signaling pathway in the pathophysiology of COVID-19.

Interaction between the HIF-1α gene rs1957757 polymorphism and CpG island methylation in the promoter region is associated with the risk of anti-tuberculosis drug-induced liver injury in humans: A case-control study

WHAT IS KNOWN AND OBJECTIVE

HIF-1α gene polymorphisms, including rs11549465, rs11549467, rs1957757 and rs10873142, cause liver cell damage or pulmonary disease. The aim of this study was to analyse the association between the polymorphisms of the loci of the HIF-1α gene and its CpG island methylation in the promoter region with the risk of anti-tuberculosis drug-induced liver injury (ADLI).

METHODS

286 patients with tuberculosis (TB) and ADLI (case group) and 286 patients with TB but without liver injury (control group) were matched one-to-one, among the 1728 TB patients recruited from July 2019 to July 2020. Genotyping of the four loci of the HIF-1α gene was confirmed using PCR-RFLP technology. Methylation of the HIF-1α gene was measured using the MSP method. The comparison of risk factors, HIF-1α genotype and methylation status between the case group and the control group was all achieved through univariate and multivariate conditional logistic regression.

RESULTS AND DISCUSSION

Univariate analysis showed that the frequency of rs1957757 mutation genotype and CpG island methylation was significantly higher in the case group than in the control group (P<0.001, all). In contrast, there was no statistical difference in the frequency of mutated genotypes at the other three loci between the two groups (p = 0.21, p = 0.12 and p = 0.55, respectively). Further, multivariate analysis showed that CpG islands were methylated, the mutation genotype of the rs1957757 locus was independently associated with the high risk of ADLI, and the adjusted OR (95%CI) reached 1.92 (1.32-2.63) and 2.01 (1.32-2.83), respectively. Furthermore, taking the rs1957757 locus wild genotype and CpG islands without methylation as the reference group, the mutation genotype and CpG island methylation increased the risk of ADLI, and the probability of ADLI could reach 4.73 times that of the reference group.

WHAT IS NEW AND CONCLUSION

This is the first demonstration of the association of HIF-1α gene polymorphism and CpG island methylation with ADLI risk stratification. The interaction between CpG islands methylated in the promoter region of the HIF-1α gene and its rs1957757 locus mutant genotype was associated with a higher risk of ADLI.

Identification and Validation of Autophagy-Related Genes in Chronic Obstructive Pulmonary Disease

Purpose

Autophagy plays essential roles in the development of COPD. We aim to identify and validate the potential autophagy-related genes of COPD through bioinformatics analysis and experiment validation.

Methods

The mRNA expression profile dataset GSE38974 was obtained from GEO database. The potential differentially expressed autophagy-related genes of COPD were screened by R software. Then, protein–protein interactions (PPI), correlation analysis, gene-ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were applied for the differentially expressed autophagy-related genes. Finally, RNA expression of top five differentially expressed autophagy-related genes was validated in blood samples from COPD patients and healthy controls by qRT-PCR.

Results

A total of 40 differentially expressed autophagy-related genes (14 up-regulated genes and 26 down-regulated genes) were identified between 23 COPD patients and 9 healthy controls. The PPI results demonstrated that these autophagy-related genes interacted with each other. The GO and KEGG enrichment analysis of differentially expressed autophagy-related genes indicated several enriched terms related to autophagy and mitophagy. The results of qRT-PCR showed that the expression levels of HIF1A, CDKN1A, BAG3, ERBB2 and ATG16L1 in COPD patients and healthy controls were consistent with the bioinformatics analysis results from mRNA microarray.

Conclusion

We identified 40 potential autophagy-related genes of COPD through bioinformatics analysis. HIF1A, CDKN1A, BAG3, ERBB2 and ATG16L1 may affect the development of COPD by regulating autophagy. These results may expand our understanding of COPD and might be useful in the treatment of COPD.

Endothelial HIF-2α as a Key Endogenous Mediator Preventing Emphysema

Rationale: Endothelial injury may provoke emphysema, but molecular pathways of disease development require further discernment. Emphysematous lungs exhibit decreased expression of HIF-2α (hypoxia-inducible factor-2α)-regulated genes, and tobacco smoke decreases pulmonary HIF-2α concentrations. These findings suggest that decreased HIF-2α expression is important in the development of emphysema.Objectives: The objective of this study was to evaluate the roles of endothelial-cell (EC) HIF-2α in the pathogenesis of emphysema in mice.Methods: Mouse lungs were examined for emphysema after either the loss or the overexpression of EC Hif-2α. In addition, SU5416, a VEGFR2 inhibitor, was used to induce emphysema. Lungs were evaluated for HGF (hepatocyte growth factor), a protein involved in alveolar development and homeostasis. Lungs from patients with emphysema were measured for endothelial HIF-2α expression.Measurements and Main Results: EC Hif-2α deletion resulted in emphysema in association with fewer ECs and pericytes. After SU5416 exposure, EC Hif-2α-knockout mice developed more severe emphysema, whereas EC Hif-2α-overexpressing mice were protected. EC Hif-2α-knockout mice demonstrated lower levels of HGF. Human emphysema lung samples exhibited reduced EC HIF-2α expression.Conclusions: Here, we demonstrate a unique protective role for pulmonary endothelial HIF-2α and how decreased expression of this endogenous factor causes emphysema; its pivotal protective function is suggested by its ability to overcome VEGF antagonism. HIF-2α may maintain alveolar architecture by promoting vascular survival and associated HGF production. In summary, HIF-2α may be a key endogenous factor that prevents the development of emphysema, and its upregulation has the potential to foster lung health in at-risk patients.

Prediction of potential deleterious nonsynonymous single nucleotide polymorphisms of HIF1A gene: A computational approach

Hypoxia-inducible factor-1α (HIF-1α) is the oxygen sensitive subunit of HIF1 transcription factor. Its variations is associated with several diseases including different type of cancer, cardiovascular diseases, and liver and kidney failure. Despite all the investigations carried out on the single nucleotide polymorphisms (SNPs) of HIF1A gene and diseases, there are many uncharacterized nonsynonymous SNPs of this gene, which might have damaging effect on the protein function. Therefore, it is worthwhile to analyze these potential damaging nsSNPs, using different bioinformatics tools before launching large population studies. The objective of the present study was to predict the possible deleterious nsSNPs of HIF1A gene and their effects on the function and structure of HIF-1alpha protein, using different bioinformatics tools. Various prediction servers were used including SIFT, PROVEAN, PolyPhen-2, PANTHER, phD-SNP, SNP-GO, I-Mutant 2.0, Fathmm, SNPeffect 4.0, Mutation taster, CADD and RAMPAGE in a stepwise approach. After analyzing all 454 missense variants of the HIF1A gene using the abovementioned tools, we reported 11 variants with a significant impact on the function or structure of HIF-1α protein. Furthermore, among these variants only S274 P was predicted as stability enhancing variant with effect on protein function by increasing its stability. Although there are many advantages for computational analysis, the results has to be confirmed by experimental investigations.