Genetic polymorphisms in lung disease: bandwagon or breakthrough?

Predisposition to Myocardial Infarction Influenced by Interleukin 13 Gene Polymorphisms: A Case-Control Study

BACKGROUND

Additional inflammatory responses and subsequent damage-arising from enhance transcriptional activity or forming the more active protein due to existence of polymorphic sites in the pro-inflammatory cytokines gene loci-give rise to myocardial infarction susceptibility.

OBJECTIVES

The aim of our study was to explore whether two interleukin-13 gene polymorphisms (-1512A/C and +2044G/A) could serve as underpins genetic susceptibility of myocardial infarction.

METHODS

The Iranian population that belong to the Parsis ethnic group was involved in the present study. A total 250 patients with definite myocardial infarction-meeting hypertension, hypercholesterolemia, hyperglycemia, and coronary artery disease requirements-were recruited from the Shiraz urban hospitals. 250 age- and sex-matched healthy individuals without a history of cardiovascular disease and heart disease related risk factors constituted the control group. PCR-restriction fragment length polymorphism technique applied to genotyping at -1512A/C and +2044G/A loci. Hardy-Weinberg equilibrium test was performed (combined cases and controls). The differences of the genotype frequencies in cases and controls were analyzed using a chi-square test. Logistic regression analysis was performed to assess the association between the genotypes and most important risk factors for myocardial infarction. All statistical analyses were performed in SPSS Version 22.0. p-values below 0.05 were hailed as statistically significant.

RESULTS

Deviation from Hardy-Weinberg equilibrium was not significant in the -1512A/C locus. Statistically significant difference between our study groups was found in genotype frequency of the -1512A/C. This variant was found in associated with myocardial infarction risk factors. The +2044G/A polymorphism was not in Hardy-Weinberg equilibrium and no significant difference observed in the distribution of +2044G/A genotype frequency among cases and controls. However, further analysis revealed that this genotype associated with an increased susceptibility to myocardial infarction risk factors.

CONCLUSIONS

The presence of interleukin-13 -1512A/C and +2044G/A gene polymorphisms underpin myocardial infarction predisposition in the ethnic Parsis of the Iranian population.

Refinement of coding SNPs in the human aryl hydrocarbon receptor gene using ISNPranker: An integrative-SNP ranking web-tool

Different bioinformatic methods apply various approaches to predict how much the effect of a SNP could be deleterious and therefore their results may differ significantly. However, variation studies often need to consider an integrated prediction result to analyze the effect of SNPs. To address this problem, we used an algorithm to map ordinal predictions to a numeral space and averaging them, and based on it we developed the ISNPranker web-tool (http://isnpranker.semilab.ir/). It takes heterogonous outputs of different predictors and generates integrated numerical predictions and ranks SNPs based on them. Afterward, we used ISNPranker to identify the most deleterious coding SNPs (cSNPs) of the human aryl hydrocarbon receptor (AHR) gene. AHR is a ligand-activated transcription factor that governs many molecular and cellular mechanisms and cSNPs may affect its structure, interactions, and function. Forty validated cSNPs of AHR were initially analyzed using 16 publicly available SNP analyzers and the results were introduced to the ISNPranker and integrated predictions were obtained. The cSNPs were ranked in 34 levels of danger and rs200257782 in the ARNT dimerization domain (ADD_121-289) of AHR was identified as the most deleterious cSNP. The rs148360742, which affect ADD_40-79 and Hsp90 binding domain (HBD_27-79) was in the second rank and the third and fourth ranks were occupied by ADD_121-289-located variations rs571123681 and rs141667112 respectively. In conclusion, we introduced ISNPranker, which is a web-tool for integrative ranking of SNPs, and we showed that AHR structure and function may be highly sensitive to the cSNPs in the ARNT dimerization domain.

The association between XRCC1 polymorphism and laryngeal cancer susceptibility in different ethnic groups in Xinjiang, China

Reduction in DNA repair capacity is associated with increased rates of birth defects, cancer, and accelerated aging. According to some earlier studies, genetic polymorphisms in DNA repair genes might influence the repair activities of the enzymes predisposing individuals to cancer risk. Owing to the presence of these genetic variants, inter-individual and ethnic differences in DNA repair capacity have been observed in various populations. Polymorphisms in DNA repair genes and differences in repair capacity between individuals have been widely reported in different cancers. We conducted a case-control study to examine the role of genetic polymorphisms in XRCC1 Gln632Gln (rs3547), Arg399Gln (rs25487), Arg280His (rs25489), Arg194Trp (rs1799782) in the risk of laryngeal cancer in different ethnic groups in Xinjiang. This study included 58 laryngeal cancer patients and 120 healthy controls age- and sex-matched without cancer. The genotypes of XRCC1Gln632Gln (rs3547), Arg399Gln (rs25487), Arg280His (rs25489) and Arg194Trp (rs1799782) were analyzed by PCR-RFLP, and the odds ratio (OR) and 95% confidence interval (CI) were calculated using an unconditional logistic regression model. C/T (hybrid) and T/T (mutant) genotypes of XRCC1 Arg280His (rs25489) revealed no statistical significance in the risk of laryngeal cancer (P>0.05), whereas the genotypes of XRCC1 Gln632Gln (rs3547), Arg399Gln (rs25487), Arg280His (rs25489), Arg194Trp (rs1799782) showed a higher risk than the controls (P<0.01) in Han, Uygur, and Kazak nations. In conclusion, the current study suggests that XRCC1 Gln632Gln (rs3547), Arg399Gln (rs25487), and Arg194Trp (rs1799782) polymorphisms may be associated with laryngeal cancer risk in the Han, Uygur, and Kazakh populations in Xinjiang. Individuals carrying genotype Arg/Gln+Gln/Gln showed a greater risk than those carrying Arg/Arg for laryngeal cancer in the Han, Uygur and Kazakh ethnic groups, and the odds ratios are 1.47, 1.32, and 0.77.

Association of Single Nucleotide Polymorphisms in XRCC1 (194) and XPD (751) with Age-related cataract

PURPOSE

Age-related cataract (ARC) is a multifactorial disease and different risk factors, including genetic and environmental, are responsible for the development of its various types. The aim of this study was to find out a correlation, if any, between ARC and the single nucleotide polymorphisms (SNPs) in DNA repair genes XRCC1 (X-ray repair cross-complementary-1) [Arg194Trp (rs1799782)] and XPD (xerodermapigmentosa complementation group D) [Lys751Gln (rs13,181].

METHOD

The genotype at these two SNPs was analyzed in 260 subjects (125 control and 135 patients) from Southern Punjab population (Pakistan) by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) method. Genotype at both analyzed codons was correlated either individually or in various combinations with the studied epidemiological factors known to be associated with ARC.

RESULTS

Our results indicated that both SNPs Arg194Trp in XRCC1 (P = 0.967) and Lys751Gln in XPD (P = 0.995) were not associated with ARC whether they were analyzed individually or in combined form (P > 0.05). Analysis of epidemiological factors revealed that age (P < 0.001), cast of subjects (P = 0.001), diabetes (P < 0.001), hypertension (P = 0.001), smoking habit (P = 0.01), drug abuse (P < 0.05), steroid use (P = 0.001) and body weight (P < 0.001) can influence the incidence of ARC in enrolled subjects. After applying Binary logistic regression it was found that the weight (P < 0.01), family history (P = 0.05), drug abuse (P = 0.05), smoking (P < 0.05) and steroid use (P < 0.05) has a significant association with the phenotype of the subjects. All epidemiological factors were also studied in association with various genotypic combinations of both SNPS, diabetes was the only factor that had a significant association (P < 0.001) association with ARC. Hypertension (P = 0.01), body weight (P < 0.05) and cast (P < 0.001) were found associated with ARC when epidemiological factors were individually correlated with ARC. Result of the two proportion test indicated that gender had no influence on the incidence of disease.

CONCLUSION

It is concluded that studied SNPs in XRCC1 and XPD have no association with the incidence of age related cataract in the analyzed group of subjects.

DNA repair gene polymorphisms at XRCC1, XRCC3, XPD, and OGG1 Loci in the hyderabad population of India

BACKGROUND

DNA repair is one of the crucial defense mechanism against mutagenic exposure. Inherited SNPs of DNA repair genes may contribute to variation in DNA repair capacity and susceptibility to cancer. Due to the presence of these variants, inter-individual and ethnic differences in DNA repair capacity have been established in various populations. India harbors enormous genetic and cultural diversity.

MATERIALS AND METHODS

In the present study we aimed to determine the genotypes and allele frequencies of XRCC1 Arg399Gln (rs25487), XRCC3 Thr241Met (rs861539), XPD Lys751Gln (rs13181), and OGG1 Ser326Cys (rs1052133) gene polymorphisms in 186 healthy individuals residing in the Hyderabad region of India and to compare them with HapMap and other populations.

RESULTS AND CONCLUSIONS

The genotype and allele frequency distribution at the four DNA repair gene loci among Hyderabad population of India revealed a characteristic pattern. Comparison of these gene polymorphisms with other populations revealed a distinctiveness of Hyderabad population from the Deccan region of India. To the best of our knowledge, this is the first report of such DNA repair gene polymorphisms in the Deccan Indian population.

Implications of XRCC1, XPD and APE1 gene polymorphism in North Indian population: a comparative approach in different ethnic groups worldwide

Identifying risk factors for human cancers should consider combinations of genetic variations and environmental exposures. Several polymorphisms in DNA repair genes have impact on repair and cancer susceptibility. We focused on X-ray repair cross-complementing group 1 (XRCC1), Xeroderma pigmentosum D (XPD) and apurinic/apyrimidinic endonuclease (APE1) as these are most extensively studied in cancer. Present study was conducted to determine distribution of XRCC1 C26304T, G27466A, G23591A, APE1 T2197G and XPD A35931C gene polymorphisms in North Indian population and compare with different populations globally. PCR-based analysis was conducted in 209 normal healthy individuals of similar ethnicity. Allelic frequencies in wild type of XRCC1 C26304T were 91.1% C(Arg); G27466A 62.9% G(Arg); G23591A 60.3% G(Arg); APE1 T2197G 75.1% T(Asp) and XPD A35931C 71.8% A(Lys). The variant allele frequency were 8.9% T(Trp) in XRCC1 C26304T; 37.1% A(His) in G27466A; 39.7% A(Gln) in G23591A; 24.9% G(Glu) in APE1 and 28.2% C(Gln) in XPD respectively. We further compared frequency distribution for these genes with various published studies in different ethnicity. Our results suggest that frequency in these DNA repair genes exhibit distinctive pattern in India that could be attributed to ethnicity variation. This could assist in high-risk screening of humans exposed to environmental carcinogens and cancer predisposition in different ethnic groups.

Future directions in sarcoidosis research: summary of an NHLBI working group

Sarcoidosis is a systemic granulomatous disease of unknown etiology that primarily affects the lungs. The etiology remains unclear; however, environmental, genetic, ethnic, and familial factors probably modify expression of the disease. As an example, African Americans are at greater risk of mortality and morbidity than are white Americans, and more often have a family history of sarcoidosis. Most patients with sarcoidosis recover spontaneously, but some develop chronic, debilitating disease. Corticosteroids and other drugs, although effective at controlling disease activity, may not influence the overall course of disease. Because of the many uncertainties about the pathogenesis, course, and management of sarcoidosis, the National Heart, Lung, and Blood Institute convened a working group to identify future research directions and opportunities for sarcoidosis. These include developing a tissue bank, using novel methods to identify genetic factors, studying the immunopathogenesis with human tissue and animal models, exploring new approaches to diagnose and manage disease, and, finally, conducting randomized controlled trials to assess new therapies.

Genetic susceptibility to acute lung injury

OBJECTIVE

To review the complex interactions of markers of genetic susceptibility for critical illness and acute lung injury. These may affect the responses of critically ill patients to acute lung injury and acute respiratory distress syndrome and may affect outcome.

DATA SOURCES AND STUDY SELECTION

Published research and review articles related to genetic factors associated with susceptibility to critical illnesses and pulmonary disease.

DATA EXTRACTION AND SYNTHESIS

Critical illness in adults often is followed by acute lung injury, a phenomenon of acute diffuse lung inflammation. Physicians have long known that each patient responds differently to drugs and has a different risk for a particular event or outcome. Now, there is some evidence that cellular and humoral immune responses are subject to polymorphic genetic control, which explains the well-known diversity of clinical manifestations and outcomes in critically ill patients with the same disease. By revealing altered expression of relatively few genes involved in the responses to lung injury and repair, some investigators have found that these responses, and susceptibility to acute lung injury, are heritable. In the last 5 yrs, we have discovered that an individual's risks and cellular responses can be related to his or her own unique DNA.

CONCLUSIONS

The search for an association between functional variants of a gene and clinical phenotype may help to identify key pathophysiological processes of disease. In the future, we will know much about which therapy is best for each individual patient in the intensive care unit.