Distribution of genetic variants of oxidative stress metabolism genes: Paraoxonase 1 (PON1) and Glutathione S-transferase (GSTM1/GSTT1) in a population from Southeastern Mexico

High-coverage whole-genome sequencing of a Jakun individual from the "Orang Asli" Proto-Malay subtribe from Peninsular Malaysia

Jakun, a Proto-Malay subtribe from Peninsular Malaysia, is believed to have inhabited the Malay Archipelago during the period of agricultural expansion approximately 4 thousand years ago (kya). However, their genetic structure and population history remain inconclusive. In this study, we report the genome structure of a Jakun female, based on whole-genome sequencing, which yielded an average coverage of 35.97-fold. We identified approximately 3.6 million single-nucleotide variations (SNVs) and 517,784 small insertions/deletions (indels). Of these, 39,916 SNVs were novel (referencing dbSNP151), and 10,167 were nonsynonymous (nsSNVs), spanning 5674 genes. Principal Component Analysis (PCA) revealed that the Jakun genome sequence closely clustered with the genomes of the Cambodians (CAM) and the Metropolitan Malays from Singapore (SG_MAS). The ADMIXTURE analysis further revealed potential admixture from the EA and North Borneo populations, as corroborated by the results from the F3, F4, and TreeMix analyses. Mitochondrial DNA analysis revealed that the Jakun genome carried the N21a haplogroup (estimated to have occurred ~19 kya), which is commonly found among Malays from Malaysia and Indonesia. From the whole-genome sequence data, we identified 825 damaging and deleterious nonsynonymous single-nucleotide polymorphisms (nsSNVs) affecting 720 genes. Some of these variants are associated with age-related macular degeneration, atrial fibrillation, and HDL cholesterol level. Additionally, we located a total of 3310 variants on 32 core adsorption, distribution, metabolism, and elimination (ADME) genes. Of these, 193 variants are listed in PharmGKB, and 21 are nsSNVs. In summary, the genetic structure identified in the Jakun individual could enhance the mapping of genetic variants for disease-based population studies and further our understanding of the human migration history in Southeast Asia.

Genetic variants of PON1, GSTM1, GSTT1, and locus 9p21.3, and the risk for premature coronary artery disease in Yucatan, Mexico

OBJECTIVE

Genetic variants of PON1, rs70587, rs662, rs854560, GSTM1, and GSTT1 and two single nucleotide polymorphisms (SNP) at 9p21.3 locus, rs1333049, and rs2383207; were evaluated in association with the risk for premature coronary artery disease (CAD) in a population of Yucatan, Mexico. These genes are involved in the inactivation of pro-oxidants and pro-inflammatory mediators, lipid and xenobiotic metabolism, detoxification of reactive oxygen species, and regulation of cellular proliferation playing key roles in the pathogenesis of atherosclerosis.

METHODS

We conducted a matched case-control study with 98 CAD cases and 101 healthy controls. Genotyping of PON1 and 9p21.2 SNP was performed by real time-PCR and for GSTM1 and GSTT1 with multiplex-PCR. Odds ratios (OR) were calculated to estimate association and generalized multifactor dimensionality reduction (GMDR) algorithm to identify gene-gene and gene-environment interactions.

RESULTS

The distribution of all allele/genotype frequencies in controls was within Hardy-Weinberg expectations (p > .05) except for GSTM1. The allele/genotype frequencies of the GSTT1 null were significantly higher in CAD cases than in controls, suggesting association with higher risk for developing CAD. The other SNPs did not show any significant independent association with premature CAD. GMDR revealed a significant interaction between GSTT1 and LL55 genotype. Likewise, the body mass index (BMI) and smoking also showed an interaction with GSTT1.

CONCLUSION

The GSTT1 null allele/genotype is associated with an increased risk of developing premature CAD, the effect of which is not modified by cardiovascular risk factors in the population of Yucatan.

The Role of Nutritional Habits and Moderate Red Wine Consumption in PON1 Status in Healthy Population

Paraoxonase 1 (PON1) plays a role as antioxidant on HDL. Including in diet additionally ingest of polyphenolic compounds can stimulate PON1 transcription and increase its activity. The aim of this study was to evaluate the effect of dietary intake, red wine consumption, and PON1 genotypes (Q192R, L55M and C-108T) on the specific activity of PON1 in a healthy population. A descriptive and analytical pilot study was conducted in Mexican volunteers clinically healthy (n = 45) aged from 21–59 years. Over 6 weeks, the study participants ingested 120 mL of red wine per day. PON1 concentration, PON1 activities, genetic polymorphisms and dietary intake were evaluated. The preliminary fingerprinting of the wine was determined to corroborate the presence of phenolic compounds such as tannins and gallotannins. Neither dietary intake nor PON1 genotypes showed an effect on the specific activity of PON1. However, a significant increase in specific AREase activity after red wine consumption period was observed in the study participants. Our data suggest that the moderate consumption of red wine has a beneficial effect on PON1 specific AREase activity in this healthy Mexican population.

Influence of Human Paraoxonase-1 Polymorphism (Q192R) on Serum Levels of Clinical Biomarkers Indicatives of Cardiovascular Diseases Risk in Mexican Women

Human paraoxonase-1 (PON1) is a hydrolytic enzyme related in the onset, establishment, and progression of inflammatory illnesses, including cardiovascular diseases (CVD). Therefore, the primary goal of this investigation was to determinate the influence of the PON1 gene polymorphism (Q192R) on prognostic biomarkers of CVD in women (n = 350) from San Luis Potosi, Mexico. For everyone enrolled, anthropometric, clinical, and biochemical measurements were acquired. Q192R polymorphism of the PON1 gene was assessed by real-time PCR using TaqMan probes. Also, quantification and/or calculation of suggested predictive CVD biomarkers were completed. The association between PON1(Q192R) polymorphism with clinical predictive CVD biomarkers was assessed using univariate and multivariate logistic regression models. Genotype PON1 (Q192R) frequencies were: 18%, 47% and 35% for QQ, QR, and RR, respectively. Besides, the frequency of the variant R allele was 0.58. Furthermore, robust significant associations were found between PON1 (Q192R) polymorphism with serum ADMA [OR (95% CI); 3.50 (1.20-5.00), p < 0.01]; FABP4 [2.50 (2.15-3.95), p < 0.01]; and miR-126 [1.50 (1.15-2.00), p < 0.01] levels after adjusting for probable confounders. Data found in this research strongly support the notion that proposes a crucial role of PON1 enzyme (Q192R polymorphism) as a genetic determinant in the CVD risk in Mexican women.

Genotypes of Common Polymorphisms in the PON1 Gene Associated with Paraoxonase Activity as Cardiovascular Risk Factor

BACKGROUND

Paraoxonase-1(PON1) exhibits hydrolytic activity and prevents the oxidation of high and low-density lipoproteins. Polymorphisms in the PON1 gene have been associated with variations in paraoxonase activity and with the risk of coronary artery disease (CAD).

AIM OF THE STUDY

This study analyzed the association between the frequencies of genotypes of the L55 M and Q192 R SNPs in the PON1 gene with the PON1 activity and with CAD risk factors.

METHODS

Women, determined by body composition, biochemical markers, and arylesterase (AREase) and paraoxonase (CMPase) activities were studied. Genotyping of L55 M and Q192 R polymorphisms was performed by TaqMan. Seventeen studies were used in the meta-analysis.

RESULTS

A significant decrease in PON1 activity in carrying the LM/MM and QQ genotypes is identified, correlations are found between the AREase activity with glucose, cholesterol and atherogenic risk index. Carriers of the LM or MM genotype were related with obesity (OR = 1.6; p = 0.039), and the MQ haplotype has an effect on the decrease in AREase (β = ‒22.4; p <0.001) and CMPase (β = ‒3.8; p <0.001). In addition, a lower proportion of Native American admixture was observed in women with LM or MM genotype, while it was higher for the European proportion compared with the LL genotype (p <0.001).

CONCLUSIONS

The LL-L55 M and QR-Q192 R genotypes are identified as the most frequently in the different states or cities of the country, and genotypic proportions are different, probably depending on the genetic structure of the populations. The association that is reported more frequently in the different studies is with enzymatic activity.

Glutathione S-transferase M1 and T1 null allele frequencies among Indonesian ethnics toward improved disease risk assessment

Genetic variations in the glutathione S-transferase genes GSTT1 and GSTM1 have been widely studied, and homozygous deletions or null genotypes have been reported in different populations. Previous studies suggest that individuals who are homozygous-null at the GSTM1 or GSTT1 locus may have an increased risk of environmentally related cancers and drug-induced hepatotoxicity. The aim of the present study was to determine the GSTM1 and GSTT1 polymorphisms in 154 healthy, unrelated individuals from the Javanese-Sundanese and Malay ethnic populations of Indonesia to provide a resource for improving the prognosis of possible susceptibilities in specific populations. The subjects were genotyped for the presence of GSTM1 and GSTT1 using the multiplex polymerase chain reaction technique. The GSTM1-null genotype was more frequent among Javanese-Sundanese ethnics (99%) than among the Indonesian Malay (67.2%). Similarly, Javanese-Sundanese ethnics showed a higher frequency of the GSTT1-null genotype (66.7%) than the Indonesian Malay (36.2%). Analysis of the combined distribution of the GSTM1 and GSTT1 genes revealed that 66.7% of the individuals from the Javanese-Sundanese population lack both the genes, whereas only 21.1% of the Indonesian Malay is GSTM1-null and GSTT1-null. This study contributes significant information on the variability of GSTT1 and GSTM1 gene polymorphisms worldwide, which can provide new knowledge about the relationship between ethnicity and the prevalence of certain diseases.

GSTT1 and GSTM1 null variants in Mestizo and Amerindian populations from northwestern Mexico and a literature review

The GSTT1 and GSTM1 genes are key molecules in cellular detoxification. Null variants in these genes are associated with increase susceptibility to developing different types of cancers. The aim of this study was to determine the prevalence of GSTT1 and GSTM1 null genotypes in Mestizo and Amerindian individuals from the Northwestern region of Mexico, and to compare them with those reported worldwide. GSTT1 and GSTM1 null variants were genotyped by multiplex PCR in 211 Mestizos and 211 Amerindian individuals. Studies reporting on frequency of GSTT1 and GSTM1 null variants worldwide were identified by a PubMed search and their geographic distribution were analyzed. We found no significant differences in the frequency of the null genotype for GSTT1 and GSM1 genes between Mestizo and Amerindian individuals. Worldwide frequencies of the GSTT1 and GSTM1 null genotypes ranges from 0.10 to 0.51, and from 0.11 to 0.67, respectively. Interestingly, in most countries the frequency of the GSTT1 null genotype is common or frequent (76%), whereas the frequency of the GSMT1 null genotype is very frequent or extremely frequent (86%). Thus, ethnic-dependent differences in the prevalence of GSTT1 and GSTM1 null variants may influence the effect of environmental carcinogens in cancer risk.