The genetic polymorphisms at the promoter region of HLA-DQB1 gene, creating responsive elements for NF1/CTF and converting the TFII-D binding site to GR-alpha.

Human leukocyte antigen-DQB1 (HLA-DQB1, OMIM: 604305) is the human major histocompatibility complex (MHC) system. HLA genes are classified into three classes (I, II, and III). The HLA-DQB1 belongs to class II, is mainly involved in the actions of the human immune system and plays a fundamental role in donor-recipient matching in transplantation and can be associated with most autoimmune diseases. In this study, the potential influence(s) of the G-71C (rs71542466) and T-80C (rs9274529) genetic polymorphisms were investigated. These polymorphisms, located in the HLA-DQB1 promoter region, have a significant frequency in the world population. The online software ALGGEN-PROMO.v8.3 was used in this work. The results indicate that the C allele at the -71 position actually creates a new potential binding site for NF1/CTF and the C allele at the -80 position changes the TFII-D binding site into a GR-alpha response element. The NF1/CTF plays the role of activator and the GR-alpha is the inhibitor; thus, according to the roles of these transcription factors, it is suggested that the above-mentioned polymorphisms alter the expression levels of HLA-DQB1. Therefore, this genetic variation is associated with autoimmune diseases; however, this cannot be generalized because this is the first report and more studies are needed in the future.

Susceptibility to the novel coronavirus disease (COVID-19) is associated with ABO and Rh blood groups: a case-control study from Afghanistan.

Background: There are preliminary studies about the association between COVID-19 and ABO phenotypes and the results are controversial. There are only two studies which investigated the association of Rh blood groups in addition to ABO with COVID-19; however, in the statistical analysis ABO and Rh blood groups have been considered separately. Therefore, the present case-control study was performed to determine the association of COVID-19 with ABO blood groups considering the Rh blood groups simultaneously. The study was conducted in Kunduz COVID-19 treatment specific center, Spin-Zar Hospital (Kunduz Province, North East Afghanistan). A total of 301 confirmed COVID-19 cases and 1039 healthy blood donors as control group were included in the study. Results: The Rh- phenotype strongly increased the risk of COVID-19 (OR = 2.97, 95% CI 1.86-3.89, P < 0.001). Although blood group A increased the risk of developing COVID-19, the association did not reach statistical significance. In analysis of the combination phenotypes, the A- blood group remarkably increased the risk of COVID-19 (OR = 7.24, 95% CI 3.62-14.4, P < 0.001). Multivariate analysis revealed that the interaction of Rh and ABO is significant (P < 0.013). Conclusion: These findings indicate that susceptibility to COVID-19 is strongly associated with A- blood group.

Influence of a 50bp Ins/Del polymorphism at promoter of the superoxide dismutase-1 on gene expression and risk of heroin dependency.

OBJECTIVE: Superoxide dismutase-1 (SOD1, OMIM: 147450) is one of the major antioxidant enzymes, which plays a vital role in clearance of reactive oxygen species. A genetic polymorphism of 50 bp insertion/deletion (Ins/Del) in the promoter region of the SOD1 was reported. The aims of the present study are to evaluate the influence of this polymorphism on the SOD1 mRNA levels in human peripheral blood cells and its association with risk of heroin dependency. METHODS: The present study consisted of 47 healthy students of Shiraz University (south-west Iran) for investigating the association between the Ins/Del polymorphism on expression level of SOD1, also a total of 442 heroin dependent and 799 healthy controls were included in a case-control study investigating the association between the study polymorphism and risk of dependency to heroin. The quantitative SOD1 mRNA expression levels were investigated using quantitative real-time PCR. RESULTS: Statistical analysis revealed a significant difference between the study genotypes (t = 5.17; df = 45; P < 0.001). The Del allele of the study polymorphism decreased approximately 33% of the SOD1 mRNA levels of the gene in the heterozygote individuals. Statistical analysis indicating that in both genders, neither the Ins/Del nor the Del/Del genotypes was associated with the risk of heroin addiction. CONCLUSIONS: The present study indicating that although the Ins/Del polymorphism of SOD1 is associated with the SOD1 expression levels, this polymorphism is not associated with the risk of dependency to heroin.

No association between GSTM1 and GSTT1 genetic polymorphisms and susceptibility to opium sap dependence.

Glutathione S-transferases (GSTs; EC: 2.5.1.18) are a ubiquitous family of eukaryotic and prokaryotic phase II metabolic isozymes. Genes encoding GSTM1 (OMIM: 138350), and GSTT1 (OMIM: 600436) are members of class mu and theta, respectively. The most common polymorphism in the GSTM1 is a deletion of the whole GSTM1 gene with a lack of enzyme activity. A homozygous deletion in the GSTT1 has also been reported (null genotypes of GSTT1). The aim of the present study was to investigate the association between GSTM1 and GSTT1 polymorphisms and risk of dependency to opium sap. The present study was performed in Shiraz (southern Iran). In total, 71 males dependent to opium sap and 590 healthy males (as a control group) were included in this study. The genotypes of GSTM1 and GSTT1 polymorphisms were determined by PCR. Our data indicate that neither GSTM1 (OR=0.78, 95% CI: 0.47-1.27, P=0.325) nor GSTT1 (OR=1.25, 95% CI: 0.70-2.21, P=0.442) null genotypes significantly associated with the risk of opium sap dependence. There is no additive effect of the null genotypes of GSTT1 and GSTM1 in relation to the risk of dependency to opium sap. The present study indicated that the null genotypes of GSTT1 and GSTM1 are not risk factor for opium sap dependence.

Influence of A-21T and C-262T genetic polymorphisms at the promoter region of the catalase (CAT) on gene expression.

OBJECTIVE: Catalase (CAT, OMIM: 115500) is one of the major antioxidant enzymes, which plays an important role in the clearance of reactive oxygen species. Three genetic polymorphisms of A-21T (rs7943316), C-262T (rs1001179), and C-844T (rs769214) in the promoter region of the CAT have been reported. It has been suggested that these polymorphisms may alter the recognition sites of transcriptional factors, therefore it might be concluded that these polymorphisms may alter the expression levels of the gene. The aim of the present study is to evaluate the associations between these genetic variations and the CAT mRNA levels in human peripheral blood cells. METHODS: The present study consisted of 47 healthy students of Shiraz University (south-west Iran). Genotypes of the CAT polymorphisms were determined by PCR based method. The quantitative CAT mRNA expression levels were investigated using quantitative real-time PCR. RESULTS: Analysis of variance revealed significant differences between the study genotypes (For A-21T polymorphism: F = 7.45; df = 2, 44; P = 0.002; For C-262T polymorphism: F = 15.17; df = 2, 44; P < 0.001). The studied polymorphisms showed linkage disequilibrium (D' = 1.0, r 2 = 0.1813, χ 2 = 17.03, P < 0.0001). The mRNA levels of CAT in the AC/TT, TC/TC, TC/TT, and TC/TC diplotypes significantly were higher than the mRNA levels in AC/AC diplotype. There was a significant difference between the study genotypes (F = 9.24; df = 5, 41; P < 0.001). The TC/TC and TT/TT diplotypes showed about 2 and 4 folds CAT mRNA levels compared with the AC/AC diplotype. CONCLUSIONS: The present findings indicated that these polymorphisms were significantly associated with the gene expression.

Expression levels of OPRM1 and PDYN in human SH-SY5Y cells treated with morphine and methadone.

AIMS: The opioid receptor mu-1 (OPRM1, site of action for methadone and morphine, OMIM: 600018) and prodynorphin (PDYN, OMIM: 131340) genes are belonging to the endogenous opioid family. There is no data on alterations of mRNA levels of PDYN and OPRM1 in cells exposed to methadone. Therefore, the present study was carried out. MAIN METHODS: Here we have investigated the alterations of the expression levels of OPRM1 and PDYN genes in response to methadone (final concentrations 1, 2.5, 5, 7.5, 10 µM) and morphine (final concentrations 1, 5, 10 µM) in human SH-SY5Y cells (at 1h, 24h, 72 h, 18 days of exposure times). KEY FINDINGS: The most important findings are summaries as follow: 1) In the cells treated with morphine, the mRNA level of OPRM1 significantly decreased from 1h to 72 h in a dose dependent manner, but it is increased when the cells treated for 18 days by high concentrations of morphine; 2) Although the PDYN mRNA level is increased at 1 and 24h (for 5 and 10 µM morphine), it is decreased at 72 h and 18 days; 3) The mRNA level of OPRM1 negatively is associated with a methadone dose dependent and exposure time dependent manner; 4) In overall, the PDYN mRNA level is increased in the treated cells without any obvious trend by dose of methadone or exposure time. SIGNIFICANCE: Decreasing the PDYN mRNA levels in cells exposed to morphine for long period times, and increasing the level of PDYN mRNA in methadone treated cells, can interpret why heroine-dependent persons, easily accept methadone therapy.

Genetic polymorphisms in the promoter region of catalase gene, creates new potential PAX-6 and STAT4 response elements.

Catalase (CAT, OMIM: 115500) is an endogenous antioxidant enzyme and genetic variations in the regulatory regions of the CAT gene may alter the CAT enzyme activity and subsequently may alter the risk of oxidative stress related disease. In this study, potential influence(s) of the A-21T (rs7943316) and C-262T (rs1001179) genetic polymorphisms in the CAT promoter region, using the ALGGEN-PROMO.v8.3 online software were analyzed. Our findings show that the A allele at the -21 position creates a new potential binding site for PAX-6 and the T allele at the -262 position changes the TFII-I binding site into STAT4 response element. The PAX-6 and STAT4 are the multifunctional and enhancing transcription factors.

Down-regulation of antioxidant genes in human SH-SY5Y cells after treatment with morphine.

AIMS: Morphine strongly induces reactive oxygen species (ROS). The deleterious actions of morphine can be countered by antioxidant system. In the present study, we investigated the expression levels of nine antioxidant genes in human SH-SY5Y cells treated with morphine. MAIN METHODS: The cells were treated with three final concentrations of morphine (1, 5, and 10 µmol) for four exposure times (1 h, 24 h, 72 h and 18 days). The mRNA levels were determined using quantitative real-time RCR. KEY FINDINGS: Based on the alterations of mRNA levels, the genes might be categorized into three different groups: In the first group, the mRNA levels of the CAT, SOD1 and GSTM3 genes were significantly down-regulated in all examined experimental conditions. In the second group, the mRNA levels of SOD2, NQO1, GSTM2 and GSTO1 were initially increased and then decreased. In the third group, the mRNA levels of NQO2 and GSTP1, were initially increased and then reached to the control levels. The number of down-regulated genes were significantly increased as a function of exposure time (χ(2)=7.52, P=0.006). We investigated the effect of morphine (10 µmol) in the absence and presence of N-acetyl-cysteine (NAC, 1 mmol). The mRNA levels revealed significant differences between cells exposed to morphine and cells co-treated with morphine plus NAC. In cases that morphine increased the level of mRNAs, morphine plus NAC, result in decreased mRNA levels and vice versa. SIGNIFICANCE: These findings suggested that there are different pathways for regulation of antioxidant genes after SH-SY5Y cells exposed to morphine and morphine might act through inducing ROS.

Expression patterns of antioxidant genes in human SH-SY5Y cells after treatment with methadone.

The expression levels of nine antioxidant genes in SH-SY5Y cells exposed to methadone (final concentrations 1-20µM) were investigated. Based on this study the genes could be categorized on three different groups. The number of down-regulated genes were increased as a function of exposure time (P=0.004). The methadone associated mRNA alterations were modulated by N-acetyl-cysteine. These findings suggested that different pathways for regulation of antioxidant genes could be active after exposing of SH-SY5Y cells to methadone; and also suggested that methadone might act by inducing the reactive oxygen species.

Association between VNTR Polymorphism in Promoter Region of Prodynorphin (PDYN) Gene and Methamphetamine Dependence.

AIM: Prodynorphin (PDYN; OMIM: 131340) is the precursor of the dynorphin related peptides which plays an important role in drug abuse. Previous studies have been shown that the expression of PDYN is regulated by a genetic polymorphism of VNTR in the promoter region of the gene. MATERIALS AND METHODS: The present case-control study was performed on 52 (41 males, 11 females) methamphetamine dependence patients and 635 (525 males, 110 females) healthy blood donors frequency matched with the patients according to age and gender, as a control group was participated in the study. RESULTS: The genotypes of VNTR PDYN polymorphism were determined using PCR method. The HL (OR = 1.22, 95%CI: 0.67-2.20, P = 0.500) and LL (OR = 0.86, 95%CI: 0.28-2.57, P = 0.792) genotypes does not alter the risk of methamphetamine dependence, in comparison with the HH genotypes. CONCLUSION: The present study revealed no association between the VNTR polymorphism in the promoter region of the PDYN gene and methamphetamine dependence risk.

Association between GSTM1 and GSTT1 polymorphisms and susceptibility to methamphetamine dependence.

Glutathione S-transferases (GSTs; EC: 2.5.1.18) are ubiquitous multifunctional enzymes, which play a key role in cellular detoxification. Functional genetic polymorphisms in genes encoding GSTM1 (a member of GST class mu; OMIM: 138350), and GSTT1 (a member of GST class theta; OMIM: 600436) have been well defined. The functional null alleles of GSTM1 and GSTT1 represent deletions of GSTM1 and GSTT1 genes, respectively. The aim of the present study is to investigate the association between GSTM1 and GSTT1 polymorphisms and methamphetamine dependence. The present population-based case-control study was performed in Shiraz (southern Iran). In total, 52 methamphetamine dependence (11 females, 41 males) and 635 healthy controls (110 females, 525 males) were included in this study. The genotypes of GSTM1 and GSTT1 polymorphisms were determined by PCR. Neither GSTM1 (OR=0.92, 95% CI: 0.52-1.61, P=0.771) nor GSTT1 (OR=0.71, 95% CI: 0.33-1.54, P=0.381) null genotypes were significantly associated with risk of methamphetamine dependence. It should be noted that although there was no association between the GSTM1 null genotype and risk of methamphetamine dependence, in both genders, there was significant interaction between gender and GSTM1 polymorphism (P=0.029). The combination genotypes of the GSTM1 and GSTT1 polymorphisms revealed that the genotypes of these two polymorphisms had no additive effect in relation to the susceptibility to methamphetamine dependence. The present study revealed that genetic polymorphisms of GSTT1 and GSTM1 are not risk factors for methamphetamine dependence.

Association between VNTR polymorphism in promoter region of prodynorphin (PDYN) gene and heroin dependence.

Within the core promoter region of prodynorphin (PDYN), a 68-bp sequence was found to occur as a polymorphism element, either singular or as tandemly repeated two, three or four times. We report the sequence of a novel allele (5-repeats). Our study revealed the existence of an ancestral nucleotide (A) at 29th position of the VNTR in human. In total, 442 heroin addicts and 799 controls were included in this study. The present findings revealed a male-limited association between VNTR polymorphism and heroin dependence risk.

First survey of the two polymorphisms (Arg194Trp and Arg399Gln) in XRCC1 gene in four Afghanistan populations and comparison with worldwide data.

Genetic polymorphisms in gene encoding X-ray repair cross-complementation group 1 (MIM: 194360; XRCC1) have been defined. Previous studies have revealed that there was significant difference between populations for allelic frequency of Arg194Trp (rs. 1799782) and Arg399Gln (rs. 25487) polymorphisms of XRCC1. In order to get more insight into the genetic structure of Afghanistan populations the present study was carried out. Present study was done on 656 (257 Pashtuns, 217 Tajiks, 120 Hazaras, and 62 Uzbeks) unrelated healthy Afghanis refuges living in Fars province (southern Iran). Genotypes for Arg194Trp and Arg399Gln polymorphisms of the XRCC1 were detected by RFLP-PCR method. The prevalence of the 194Trp allele in Pashtuns, Tajiks, Hazaras, and Uzbeks was 0.072, 0.085, 0.108, and 0.145, respectively. The frequency of the 399Gln in Pashtuns, Tajiks, Hazaras, and Uzbeks was 0.362, 0.378, 0.296, and 0.234, respectively. There was significant difference between these ethnic groups for the genotypic distributions of the Arg194Trp (χ(2) = 16.70, df = 6, P = 0.010) and Arg399Gln (χ(2) = 12.67, df = 6, P = 0.049) polymorphisms. Based on the complete dataset, these polymorphisms showed significant linkage disequilibrium. There was significant difference between the ethnic groups for prevalence of the haplotypes (χ(2) = 16.67, df = 6, P = 0.011). Uzbeks showed significant difference with the other ethnic groups (χ(2) = 10.09, df = 2, P = 0.006). The allelic frequencies of 194Trp and 399Gln in Pashtuns and Tajiks seem to be more similar to the Caucasians than the Asian populations. However, Uzbeks seems to be intermediate between Afghanis' Caucasian (Pashtuns and Tajiks) and Asians.

Genetic polymorphisms of glutathione S-transferase T1 (GSTT1) and M1 (GSTM1) in selected populations of Afghanistan.

Genetic polymorphisms in genes encoding glutathione S-transferase T1 (GSTT1, a member of class theta) and M1 (GSTM1, a member of class mu) have been defined. Previous studies have revealed that there was significant difference between populations for allelic frequency of several members of GSTs. In order to find the prevalence of null genotypes of GSTM1 and GSTT1 in Afghanis populations the present study was carried out. The total study subjects consisted of 656 unrelated healthy Afghanis refugees living in Fars province (southern Iran). From these 257, 217, 120, and 62 individuals were Pashtuns, Tajiks, Hazaras, and Uzbeks, respectively. Genetic polymorphisms for GSTT1 and GSTM1 were detected by multiplex PCR. The prevalence of null genotype of GSTM1 in Pashtuns, Tajiks, Hazaras, and Uzbeks was 42.4, 48.4, 52.5, and 40.3 %, respectively. There was no significant difference between these populations for the genotypic distribution of the GSTM1 polymorphism (χ(2) = 4.67, df = 3, P = 0.197). The frequency of GSTT1 null genotype in Pashtuns, Tajiks, Hazaras, and Uzbeks was 7.4, 25.3, 25.0, and 29.0 %, respectively. The observed difference between populations for prevalence of GSTT1 null genotype was statistically significant (χ(2) = 35.54, df = 3, P < 0.001). In comparison with European and Asian populations, Afghanistan populations like Iranian populations showed intermediate frequency for GSTT1 and GSTM1 null genotypes.

Consanguineous marriages in Afghanistan.

The present cross-sectional study was done in order to illustrate the prevalence and types of consanguineous marriages among Afghanistan populations. Data on types of marriages were collected using a simple questionnaire. The total number of couples in the study was 7140 from the following provinces: Badakhshan, Baghlan, Balkh, Bamyan, Kabul, Kunduz, Samangan and Takhar. Consanguineous marriages were classified by the degree of relationship between couples: double first cousins, first cousins, first cousins once removed, second cousins and beyond second cousins. The coefficient of inbreeding (F) was calculated for each couple and the mean coefficient of inbreeding (α) estimated for each population. The proportion of consanguineous marriages in the country was 46.2%, ranging from 38.2% in Kabul province to 51.2% in Bamyan province. The equivalent mean inbreeding coefficient (α) was 0.0277, and ranged from 0.0221 to 0.0293 in these two regions. There were significant differences between provinces for frequencies of different types of marriages (p<0.001). First cousin marriages (27.8%) were the most common type of consanguineous marriages, followed by double first cousin (6.9%), second cousin (5.8%), beyond second cousin (3.9%) and first cousin once removed (1.8%). There were significant differences between ethnic groups for the types of marriages (χ2=177.6, df=25, p<0.001). Tajiks (Soni) and Turkmens (also Pashtuns) showed the lowest (α=0.0250) and highest (α=0.0297) mean inbreeding coefficients, respectively, among the ethnic groups in Afghanistan. The study shows that Afghanistan's populations, like other Islamic populations, have a high level of consanguinity.