Frequency Of TT Genotype Research Articles

The important roles of ERAP1, ERAP2 genes polymorphisms and their DNA methylation levels in pulmonary tuberculosis

BackgroundGenetic variations in endoplasmic reticulum aminopeptidase (ERAP1, ERAP2) genes are associated with the pathogenesis of multiple diseases, including infectious diseases. The objective of our study was to assess whether ERAP1, ERAP2 genes polymorphisms and methylation levels affect the risk of pulmonary tuberculosis (PTB).MethodsWe genotyped ten single nucleotide polymorphisms (SNPs) in ERAP1, ERAP2 genes among 497 PTB patients and 502 controls by SNPscan technique. Additionally, we detected the ERAP1, ERAP2 genes methylation levels in 98 PTB patients and 97 controls through Illumina Hiseq platform.ResultsOur results showed that the GG genotype, G allele frequencies of ERAP2 gene rs2549782 were significantly increased in PTB patients compared to controls, and rs2549782 polymorphism was related to the increased risk of PTB under recessive model. In addition, no significant relationship was found between ERAP1 gene rs13167972, rs17086651, rs469783, rs26618, rs3734016, ERAP2 gene rs17524572, rs1230358, rs2549794, rs117041256 and PTB susceptibility. Among PTB patients, the frequencies of rs17524572 TT genotype, T allele were significantly associated with drug-induced liver injury, and rs1230358, rs2549782, rs2549794 polymorphisms were linked to the occurrence of fever. Haplotype analysis of ERAP2 gene suggested that the frequency of CTGGT haplotype was higher, while the frequency of CTGTT haplotype was lower in PTB patients. When compared with controls, the ERAP1 methylation level was lower in PTB patients, while the ERAP2 methylation level was significantly increased. Moreover, rs1230358 polymorphism was found to affect the ERAP2 methylation level.ConclusionThe ERAP2 rs2549782 variant and altered methylation levels of ERAP1, ERAP2 genes were related to susceptibility to PTB.

5,10-methylenetetrahydrofolate reductase C677T gene polymorphism as a risk factor for premature coronary artery disease in patients with type 2 diabetes mellitus.

Africa, like the rest of the world, is experiencing an increasing prevalence of diabetes mellitus. Diabetes increases the risk for coronary artery disease (CAD) by fourfold compared to people without diabetes. C677T polymorphism in methylenetetrahydrofolate reductase (MTHFR) and hyperhomocysteinemia were reported by many studies as risk factors for CAD among patients with type 2 diabetes mellitus (T2DM). Early detection of modifiable risk factors for CAD is an important aspect of management of diabetes. This is the only study in Sudan which investigates the association between MTHFR genotypes and plasma homocysteine levels, and their role in premature CAD (PCAD) among patients with T2DM. This study is a comparative study. We enrolled 226 Sudanese patients with T2DM, age range 25-60 years, recruited from Alshaab and Omdurman teaching hospitals in Khartoum State. 113 patients had CAD confirmed by angiography and electrocardiography (ECG) and 113 had no evidence of CAD. Polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP), using Hinf1 restriction enzyme, were used to determine MTHFR genotypes. Plasma homocysteine levels were determined by enzymatic assay on the Hitachi Cobas Integra® 400 plus. Data was analyzed using statistical package for Social Sciences (SPSS) 23, using Mann-Whtney U test, general linear model, Chi-square test and logistic regression analysis. The frequencies of TT, CT, and CC genotypes were 16,40 and 44% among T2DM patients with PCAD. In T2DM patients without PCAD, the frequencies of TT, CT, and CC genotypes were 00,19 and 83%. The T allele showed strong association with PCAD among T2DM patients, p <0.001, odds ratio (OR) 6.2, 95% CI (3.4-11.6). Patients with PCAD showed higher plasma homocysteine levels than patients without PCAD (13.5 µmol/L versus 10 µmol/L, p < 0.001). The T allele had significant effect on homocysteine level, (p <0.001). Plasma homocysteine levels were higher in individuals with TT genotype than those with CT or CC genotypes in patients with PCAD (16.2+5.3, 14.3+5.7 and 12.9+5.02 µmol/L, p=0.017). Homocysteine levels showed a significant association with CAD, p<0.001, OR 3.2, 95% CI (1.9-5.5). Our study suggests that C677T polymorphism of MTHFR gene and hyperhomocysteinemia are risk factors for PCAD in Sudanese population with T2DM.

Missense mutation 1234C&gt;T of TOLL-like receptor 3 gene in ulcerative colitis

Maintenance of intestinal homeostasis suggests dynamic interaction between the host immune system and local microbiota. Impaired immune response, genetic predisposition and changes in microbiota composition lead to chronic gut inflammation, which is the basis for the development of immune pathology accompanying inflammatory bowel disease (IBD). Resident enteric viruses also have immunomodulatory effects in IBD. Toll-like receptors recognizing PAMPs penetrating intestinal barrier are an important component of the inflammatory process in ulcerative colitis (UC). Viral double-stranded RNA is recognized by endosomal TLR3. Our goal was to identify the association between alleles, genotypes of the TLR3 gene and its haplotypes formed with TLR2 genes, TLR1, TLR6, and UC in Russian population of the Chelyabinsk Region. The study groups included 96 patients with UC and 86 healthy individuals. DNA was isolated from whole blood using a column method, polymorphic gene regions were amplified using allele-specific PCR and RFLP, amplification products were detected by gel electrophoresis in a 3% agarose with UV-visualization. The SNP 1234CT (Leu412Phe) of the TLR3 gene were typed. Linkage disequilibrium parameters were evaluated for the mentioned TLR3 SNP and other SNPs, i.e., 1805TG (Ser602Ile) in TLR1 gene, 2258GA (Arg753Gln) in TLR2 gene, 745CT (Ser249Pro) in TLR6 gene. The frequency analysis of alleles and genotypes of TLR3 SNP 1234CT showed a statistically significant increase of the mutant T allele frequency (p = 0.019; OR = 1.72; 95% CI: 1.09-2.71), and higher frequency of homozygous TT genotype among the patients with UC (p = 0.011; OR = 4.72; 95% CI: 1.31-17.05). By assessing the parameters of linkage disequilibrium, two haplotypes were discovered that may be predisposition factors for UC, i.e., haplotype 1234*T~2258*A, with linkage of mutant alleles of SNPs 1234CT TLR3 and 2258GA TLR2 (p = 0.006; OR = 12.42; 95% CI: 1.61-95.97), as well as haplotype 1234*T~1805*T, with linkage of the mutant allele of SNP 1234CT TLR3 to wild allele of SNP 1805TG TLR1 (p = 0.009; OR = 2.94; 95% CI: 1.35-6.42).

Genetic Polymorphism of Interferon-Gamma +874T/A as a Risk Factor for Pulmonary Tuberculosis in Cirebon, Indonesia

Background: Tuberculosis (TB) is one of the leading causes of death globally, caused by Mycobacterium tuberculosis. With 10% of all cases worldwide in 2022, Indonesia is the second-largest contributor of tuberculosis cases. IFN-γ gene polymorphism is one of the factors that have been studied extensively for its association with TB. Aims: To analyze IFN-γ +874T/A gene polymorphism as a risk factor for pulmonary tuberculosis in Cirebon. Methods: Observational analysis with case control design was used in this study. Thirty-two tuberculosis patients as cases and 32 healthy controls at RSUD Waled were collected and performed DNA extraction to evaluate the polymorphism by using Amplification-refractory mutation system–polymerase chain reaction (ARMS–PCR). Statistical comparison was performed by using Pearson Chi-square and Kruskal Wallis test. Mann-Whitney U test was done for post hoc test. Odds ratio was calculated to see the risk of the assessed variables, including genotype, allele frequency, and the presence of polymorphism. Results: In the case group, the frequency of TT genotype was 3 (9.4%), TA genotype was 26 (81.3%), AA genotype was 3 (9.4%). In the control group, the frequency of TT genotype was 12 (37.5%), TA genotype was 17 (53.1%), AA genotype was 3 (9.4%). A significant difference (p=0.034) was found among 3 genotype groups. Post hoc test revealed that TT and TA was the pair with significant difference (p=0.007). In addition, TA polymorphism was significantly associated (p=0.004) with tuberculosis (OR=6.614; CI95% = 1.660-26.349). Conclusion: IFN-γ +874 TA gene polymorphism is associated with pulmonary tuberculosis in the population of Cirebon, West Java, Indonesia. Received: 25 September 2024 | Reviewed: 23 October 2024 | Revised: 10 November 2024 | Accepted: 30 November 2024

Investigating the Rrelationship between polymorphisms pd1.9 and rs7421861 of PD1 gene with breast cancer

IntroductionPD1 molecule is a regulatory protein in the immune system that is responsible for the negative induction of active T cells. The PD1 gene has many single nucleotide polymorphisms. In this study, the association of polymorphisms in the pd1.9 and rs7421861 positions of the PD1 gene with breast cancer was investigated in women with breast cancer. Materials and methodsThis experimental study was done in healthy (n = 110) and breast cancer (n = 110) women. First, 2 ml of blood were taken from groups, and the genome of white blood cells (WBCs) was extracted using a DNA extraction kit. The genotype of samples was determined in pd1.9 and rs7421861 region of PD1 gene with the help of PCR-RFLP technique. Data analysis was done by SPSS software version 19. ResultsThe analysis of the data about pd1.9 polymorphism genotypes demonstrated that the frequency of CC genotype in the control group was equal to 92.7 %; while this amount was reported as 80 % in the patient group. Regarding the CT genotype, its frequency was 19.1 % in the patient group, while this rate was 7.3 % in the control group. Also, the data showed that the frequency of TT allele is 0.9 % in the patient group and 0 % in healthy people. In the case of rs7421861, the frequency of TT genotype in the control group was equal to 56.4 %, while this rate was equal to 41.8 % in the patient group. Regarding the CT genotype, its frequency in the patient group was 48.2 %, while this rate was 36.4 % in the control group. The frequency of CC allele is 10 % in the patient group and 7.3 % in healthy people. ConclusionThe results showed that polymorphism of pd1.9 and rs7421861 in PD1 gene cannot be related to breast cancer. Therefore, determining the genotype of polymorphism in these gene regions will not be useful for screening affected people.

MIR27A rs895819 CC Genotype Severely Reduces miR-27a Plasma Expression Levels.

Background/Objectives:MIR27A rs895819 polymorphism has emerged as a potential additional pharmacogenomic marker of fluoropyrimidine response. Current evidence on its potential effect on miR-27a expression, which represses DPD activity, leading to DPD deficiency and increased fluoropyrimidine-associated toxicity risk, is scarce and inconsistent. We have analyzed the effect of MIR27A rs895819 polymorphism on miR-27a-3p plasma expression levels under different models of inheritance to contribute further evidence on its plausible biological role in miR-27a expression. Methods: A total of 59 individuals with no medical history of cancer were included in this study. MIR27A rs895819 genotyping and miR-27a-3p expression were analyzed by using predesigned TaqMan assays. Results: The frequency of TT, TC, and CC genotypes was present at a prevalence of 50.8%, 44.1%, and 5.1%, respectively. Individuals carrying the CC genotype presented with decreased miR-27a-3p expression (0.422 fold-change versus TT, p = 0.041; 0.461 fold-change versus TC, p = 0.064), whereas no differences were present between TT and TC individuals (1.092 fold-change, p = 0.718). miR-27a-3p expression was decreased in CC individuals under a recessive model of inheritance (0.440 fold-change, p = 0.047). No differences were found in dominant (TT vs. TC+CC, 0.845 fold-change, p = 0.471) or over dominant (TT+CC vs. TC, 0.990 fold-change, p = 0.996) models of inheritance. Conclusions:MIR27A rs895819CC genotype leads to severely reduced miR-27a-3p expression in plasma. Further study of this association is warranted in cancer patients to apply MIR27A genotyping in therapeutics to identify fluoropyrimidine-treated patients who are at a decreased risk of experiencing fluoropyrimidine-induced severe toxicity.

Association between TERT gene polymorphisms (rs2736100 and rs2736109) and breast cancer risk in the Iranian population: A case-control study

BackgroundThe level of hormones and genetic predispositions increase the risk of breast cancer. Genetic variations in the genes of the telomere pathway, which can influence the activity of telomerase, may be decisive for the development of breast cancer. Due to a lack of studies on TERT gene polymorphisms (rs2736100 and rs2736109) in the Iranian population, in this study we investigated the association of these polymorphisms with breast cancer in the Iranian population. Patients & methodsA total of 300 individuals participated in this research, which included 150 breast cancer patients and 150 healthy controls. Participants' blood samples were collected before the beginning of treatment. The RFLP-PCR procedure was used for the genotyping of TERT gene rs2736109 and rs2736100 polymorphisms. ResultsThere are statistically significant differences in the age of menarche and the age of menopause (P-value <0.05). For rs2736100, the frequency of TT genotype in the case and control groups was 22.7 % and 16.7 %, respectively. However, these differences were not statistically significant (P-value >0.05). For rs2736109, the frequency of the AA genotype was lower in the case group (12.0 % vs. 19.3 %). These differences reach a statistically significant level (P-value = 0.012). Individuals carrying AA genotype have a lower risk of suffering from breast cancer (odds ratio = 0.403, 95 % CI: 0.196–0.827). ConclusionOur findings suggest that the rs27326109 polymorphism in the TERT gene is associated with a decreased risk of breast cancer. Also this study reveals that age of menarche and age of menopause are associated with risk of this disease.

Association Between the Risk of Dental Caries and DLX3 Gene Polymorphisms in Chinese Children.

To explore the association between the risk of dental caries and distal-less homeobox 3 (DLX3) gene in Chinese children. Based on the decayed, missing, and filled teeth (dmft) score, the children were divided into a control group (dmft &#61; 0) and a case group (dmft ≥ 1). DLX3 gene (rs11656951 and rs2278163) polymorphisms were genotyped by polymerase chain reaction (PCR) and Sanger sequencing methods. Possible association of DLX3 gene (rs11656951 and rs2278163) polymorphisms with dental caries risk was assessed using the chi-squared test. Subgroup analysis of association was assessed by logistic regression analysis for the potential risk factors. The age at which toothbrushing was started, the brushing frequency, brushing with fluoride toothpaste, and regular dental visits were statistically significantly different between case and control groups (p 0.05). The frequencies of rs11656951 TT genotype and T allele were statistically significantly higher in the control group than in the case group. The chi-squared test showed that CT genotype (p &#61; 0.026, OR &#61; 0.613, 95%CI &#61; 0.398-0.944) and TT genotype (p &#61; 0.001, OR &#61; 0.378, 95%CI &#61; 0.212-0.673) were negatively correlated with caries susceptibility. The T allele of rs11656951 was more frequently discovered in the control group, and was statistically significantly associated with decreased caries susceptibility (p &#61; 0.001, OR &#61; 0.636, 95%CI &#61; 0.486-0.831). The G allele of rs2278163 was obviously correlated with elevated caries susceptibility (p &#61; 0.049, OR &#61; 1.314, 95%CI &#61; 1.000-1.725). DLX3 gene rs11656951 TT genotype was a protective factor for caries susceptibility in the subgroups gender, sweets intake, eating before sleep, brushing frequency, brushing with fluoride toothpaste, and dental visits. The GG genotype of rs2278163 was a risk factor for caries in subgroups eating before sleep, brushing without fluoride toothpaste, and regular dental. The TT genotype of rs11656951 was dramatically correlated with reduced caries risk in low (p &#61; 0.004, OR &#61; 0.387, 95%CI &#61; 0.202-0.742) and moderate/high (p &#61; 0.016, OR &#61; 0.360, 95%CI &#61; 0.154-0.840) groups. DLX3 gene rs11656951 TT genotype is a protective factor and rs2278163 GG genotype is a risk factor for caries susceptibility, especially in low and moderate/high subgroups.

Relationship between polymorphism of GDF5 and CAPN1 genes in kalmyk breed cattle with economic and biological traits

The article presents the results of polymorphism of the GDF5 and CAPN1 genes in cattle of the Kalmyk breed, owned by the agricultural production company “Plodovitoe” of the Maloderbetovsky district of the Republic of Kalmykia, in the amount of 60 heads. DNA samples were isolated from whole blood taken from the jugular vein by an automatic extraction method. A real-time polymerase chain reaction was carried out to determine the polymorphism T586C of the GDF5 gene and C316G of the CAPN1 gene. In the studied herd of cattle, animals with the TT genotype predominate - 68.3 % of the population, the number of animals with the TC and CC genotypes is 21.7 % and 10 %. When studying the polymorphism of the CAPN1 gene, it was revealed that 23.3 % of the bulls of the studied population of Kalmyk cattle have the desired genotype CC, while the heterozygous genotype is present in 16.7 %, and the recessive genotype GG is present in 60 % of animals. The frequency of occurrence of the T allele of the GDF5 gene is 0.792, which exceeds the indicator of the C allele (0.208) by 58.2 %, the observed frequency of TT and CC genotypes exceeds the expected indicator by 5.6 and 5.7 %, respectively, while the indicator of the TC genotype is lower than the expected frequency by 11.2 %. The frequency of occurrence of the G allele (0.683) is 36.6 % higher than that of the C allele (0.317) of the CAPN1 gene. It is noted that the GG genotype with an index of 0.600 occurs with the highest frequency, while the CG genotype has a frequency of 0.167 (43.3 % less), the CC genotype – 0.233 (36.7 % less). The indicators of the observed frequency of the CC and GG genotypes are 13.3% higher than expected, the heterozygous genotype has an excess of the expected frequency by 26.6 %. Bulls with the TT genotype of the GDF5 gene outperformed their peers with the TC and CC genotypes in all measurements. When studying the live weight of Kalmyk cattle at the age of 15 months, a positive effect of the CC genotype of the CAPN1 gene was revealed. Thus, the group of animals with this genotype had the largest live weight and surpassed their peers with the genotypes CG (by 9.9 %) and GG (by 11.1 %).

Associations of the TNFSF11 gene polymorphisms with knee osteoarthritis in post-menopausal women

Objective: to determine the role of the TNFSF11 gene polymorphisms rs9594738 and rs9594759 in the development of knee osteoarthritis in postmenopausal women. Material and methods. The case-control study included 483 postmenopausal women. Of these 157 were diagnosed with primary knee osteoarthritis. The remaining 326 women without signs of joint disease were included in the control group. Molecular genetic studies included determination of TNFSF11 rs9594738 and TNFSF11 rs9594759 gene polymorphisms using the real-time polymerase chain reaction. Results. Analysis of genetic markers distribution in two groups of women showed a decrease in the frequency of rs9594738 polymorphism TT genotype among the patients with osteoarthritis (odds ratio 0.59; 95% confidence interval 0.36-0.97; p=0.049). The distribution of this polymorphism alleles, as well as alleles and genotypes of TNFSF11 rs9594759 gene polymorphism in the group of women with osteoarthritis did not differ significantly from the results of the control group (p&gt;0.05). Conclusion. An association of TNFSF11 rs9594738 gene polymorphism with knee osteoarthritis in postmenopausal women has been established. Further research of TNFSF11 gene polymorphic variants role in the knee osteoarthritis etiopathogenesis are needed to develop individual approaches to the prevention and treatment of the above disease.

TaqI polymorphism of VDR gene in colorectal cancer and Crohn’s disease patients

To study the relation of TaqI polymorphism of VDR gene with age, sex and the disease phenotype in patients with colorectal cancer (CRC) and Crohn’s disease (CD) from western regions of Ukraine. Fifty six patients with CRC, 46 patients with CD and 65 control individuals were included in this research. Assessment of TaqI polymorphism was performed using PCR-RFLP method. The genotype-phenotype association for this polymorphism was analyzed. The frequency of tt genotype in patients with CRC is 0.107 and among the control group is 0.138, OR (95% CI 0.248-2.246). The ratio of genotypes TT:Tt:tt in patients with CRC and in control was 37.5%:51.8%:10.7% and 44.6%:41.6%:13.8%. In men with Tt genotype the average age of CRC onset was 57.6 ± 3.6 years, in women with TT genotypethe mean age of the disease onset was 54.5 ± 4.5 years. The frequency of tt genotype in the patients with CD is 0.217 and among the control group is 0.138, OR (95% CI 0.640–4.666). The Tt genotype was detected in a half of patients with CD and TT genotype was found more frequently in control.The ratio of genotypes in men and women with CD was 38.0%:38.0%:24.0% and 20.0%:60.0%:20.0%. Among patients with CD, who underwent surgery, 33.3% individuals were carriers of tt genotype. It was confirmed no statistically significant difference in the allele frequencies and genotype distributions of Taq1 mutation in patients with CRC and CD in comparison to control group. The ratio of men and women with Tt genotype by groups of B1-B3 forms of CD behaviour according to the Montreal classification is differs, in particular, women with Tt genotype are four times more likely to have the B1 form. A study of Taq1 mutation might contribute to the identification of the groups that are at the greatest risk of severe form of CD.

Identification of the association of the GH, IGF-I and Pit-I gene polymorphism with growth traits in Saanen, Alpine and Boer goat breed

This study aims to determine an effect between GH, IGF-I, and Pit-I gene polymorphisms and growth traits such as body weight, heart girth, body length, height at wither, and chest width in Saanen, Alpine, and Boer goat breeds. The polymorphism was identified using the PCR-RFLP technique. GH/HaeIII gene polymorphism results identified two alleles (A and B) and two genotypes (AB and BB). A and B allele frequencies for Saanen, Alpine, and Boer goat breeds were found to be 0.438 and 0.562, 0.444 and 0.556, and 0.197 and 0.803, respectively. AB and BB genotype frequencies were found to be 0.876 and 0.124, 0.889 and 0.111, and 0.394 and 0.606, respectively. IGF-I/HaeIII gene polymorphism results identified two alleles (A and B) and three genotypes (AB, BB, and AA). A and B allele frequencies for the Saanen, Alpine, and Boer breeds were found to be 0.191 and 0.809, 0.173 and 0.827, and 0.182 and 0.818, respectively. The AB, BB, and AA genotype frequencies were found to be 0.315, 0.652, and 0.033 for Saanen, 0.247, 0.704, and 0.049 for Alpine, and 0.242, 0.697, and 0.061 for Boer, respectively. Regarding Pit-I/PstI gene polymorphism, T and C allele frequencies were determined as 0.921 and 0.079, 0.988 and 0.012, and 0.985 and 0.015 for Saanen, Alpine, and Boer breeds, respectively. TT and TC genotype frequencies were found to be 0.843 and 0.157, 0.975 and 0.025, and 0.970 and 0.030 in Saanen, Alpine, and Boer goats, respectively. An association was found between GH polymorphism and chest width in Saanen and Alpine goats and between body weight and heart girth in Boer goats. Additionally, an association was identified between IGF-I polymorphism and body weight in Alpine and chest width in Boer. There was also an association between Pit-I polymorphism and body weight in Alpine goats.

Correlation Analysis between STING Promoter Polymorphism and Susceptibility to Infection after Chemotherapy for Multiple Myeloma

To investigate the correlation between the stimulator of interferon genes (STING ) promoter polymorphism and the susceptibility to infection after chemotherapy for multiple myeloma. A total of 102 patients who had undergone chemotherapy for multiple myeloma in our hospital from January 2016 to July 2022 were selected. Depending on the presence or absence of infection after chemotherapy, the enrolled patients were divided into infection group (53 cases) and non-infection group (49 cases). The infection sites and distribution characteristics of pathogenic bacteria of the infection group were analyzed. The genotype distribution of STING gene promoter rs587777609 was compared between the two groups, and the risk factors of infection after chemotherapy for multiple myeloma were analyzed. For infection site, digestive system, respiratory system, urinary system, skin and mucous membranes accounted for 43.40%, 26.42%, 20.75%, and 9.43%, respectively. For pathogenic bacteria, Gram-negative bacteria, Gram-positive bacteria and fungi accounted for 57.14%, 26.98%, and 15.87%, respectively. The CC genotype frequency of STING gene rs587777609 locus in the infection group was lower than that in the non-infection group, while the TT genotype frequency was higher than that in the non-infection group (P < 0.05). The proportions of patients with diabetes, chronic obstructive pulmonary disease, renal insufficiency, serum albumin level< 35 g/L, ISS stage III, mechanical ventilation, and indwelling catheter in the infection group were higher than those in the non-infection group (P < 0.05). Multivariate logistic regression analysis showed that diabetes (OR =1.992), serum albumin level< 35 g/L (OR =2.782), ISS stage III (OR =2.707), mechanical ventilation (OR =3.031), and TT genotype (OR =2.401) were risk factors of infection after chemotherapy for multiple myeloma (P < 0.05). There is a correlation between STING promoter polymorphism and the susceptibility to infection after chemotherapy for multiple myeloma, and patients with TT genotype have a higher risk of infection.

Comparing vitamin D receptor gene polymorphisms in rs11568820, rs7970314, rs4334089 between COVID-19 patients with mild and severe symptoms: a case control study

The associations of vitamin D receptor (VDR)- single nucleotide polymorphisms (SNPs) with the symptoms of COVID-19 may vary between patients with different severities of COVID-19. Therefore, in the present study, we aim to compare VDR polymorphisms in severe and mild COVID-19 patients. In this study, a total number of 85 hospitalized patients and 91 mild/moderate patients with COVID-19 were recruited. SNPs in VDR genes were determined using ARMS and then confirmed by sanger sequencing. The mean (SD) age of participants in hospitalized and non-hospitalized group was 59.0 (12.4) and 47.8 (14.8) years, respectively. Almost 46% of participants in hospitalized and 48% of participant in non-hospitalized group were male. The frequency of TT genotype of SNP rs11568820 was significantly lower in hospitalized than non-hospitalized group (3.5% vs. 17.6%; P = 0.018). However, there was no significant differences between genotypes of SNPs rs7970314 and rs4334089 and also alleles frequencies in all SNPs of two groups. The genotype of rs11568820 SNP had an inverse association with hospitalization of patients with COVID-19 after adjustment for comorbidities [OR 0.18, 95% CI 0.04, 0.88; P = 0.034]. While, there was no relationship between genotypes of SNPs rs7970314 and rs4334089 and hospitalization. The TT genotype of rs11568820 plays protective role in sever COVID-19 and hospitalization. Further studies with a large sample size which consider various confounding factors are warranted to confirm our results.

Screening of single nucleotide polymorphism in matrix metalloproteinase-2 (MMP2) and tetraspanin CD63 genes in Chlamydia trachomatis-infected tubal ectopic pregnancy patients.

Tubal ectopic pregnancy (EP) is a leading cause of maternal morbidity and mortality. Studies have suggested that infection-induced inflammatory responses are major risk factors for EP. The aim of the present study was to find an association between MMP2 and CD63 gene variants and risk of EP during Chlamydia trachomatis infection in an Indian population. Fallopian tube samples of 120 EP and 120 tubal ligation women were collected. C. trachomatis was detected by PCR. The genotyping of MMP2 (rs17859882 G/T, rs7201A/C) and CD63(rs2231464 C/T, rs376086542 A/G) gene variants was done by qualitative real-time PCR using allelic discrimination method (VIC- and FAM-labeled). The frequency of GG or GT genotype of MMP2 G/T polymorphism (rs17859882) was 66.6% in infected EP and 36.7% in uninfected EP and 22% in tubal ligation controls (P < 0.0001), while the frequency of AC or CC genotype of MMP2 A/C polymorphism (rs7201) was 66.6% in infected EP and 20.6% in uninfected EP and 13.5% in tubal ligation controls (P < 0.0001). The frequency of CT or TT genotype of CD63 C/T polymorphism (rs2231464) was 74% in infected EP and 21.8% in uninfected EP and 11.8% tubal ligation controls (P < 0.0001), while the frequency of AG or GG genotype of CD63 A/G polymorphism (rs376086542) was 48.1% in infected EP and 41.3% in uninfected EP and 18.6% tubal ligation controls (P < 0.0001). The present study revealed a strong association between the presence of gene variants MMP2 (rs17859882 G/T, rs7201A/C) and CD63 (rs2231464 C/T, rs376086542 A/G) and risk of tubal EP during C. trachomatis infection.

Prognostic significance of &lt;I&gt;TLR3&lt;/I&gt; and &lt;I&gt;TLR9&lt;/I&gt; gene polymorphism in assessing the severity of COVID-19

Objective: to study polymorphic variants of TLR3 (rs3775291) and TLR9 (rs352140) genes in patients with COVID-19 depending on the severity of the disease and their significance for determining the risk of severe course of COVID-19.Materials and Methods: genetic analysis of polymorphism of TLR3 (rs3775291) and TLR9 genes (rs352140) was performed in 164 patients with COVID-19, who were divided by degree of severity into three groups: Group 1 with mild, Group 2 with moderate and Group 3 with severe and extremely severe degrees of severity. The control group consisted of 40 healthy donors. Statistical processing of the obtained results was carried out using STATISTICA 12.0 programs (Stat Soft, USA). To assess the difference of groups by qualitative characteristics, the χ2 criterion with Yates correction was used, and in case of violation of its conditions, the χ2 criterion was applied. Yates correction, and if the conditions of its applicability were violated, the two-sided Fisher’s two-sided criterion (RF). The difference between the groups was considered statistically significant at р&lt;0,05. The strength of associations was evaluated in the values of the odds ratio index odds ratio (OR) and 95% confidence interval.&gt; ˂ 0,05. The strength of associations was evaluated in the values of the odds ratio index odds ratio (OR) and 95% confidence interval.Results: the frequency of the ST genotype was significantly higher and the frequency of the TT genotype of the rs3775291 allele of the TLR3 gene was significantly lower in patients with the manifest form of COVID-19 compared with the control group. Frequency analysis of TLR9 (rs352140) in COVID-19 patients showed significantly higher values of the ST genotype and lower values of the CC genotype compared to healthy individuals. Comparative analysis between groups of hospitalized patients depending on severity revealed higher frequency of ST genotype and lower frequency of TT genotype of TLR3 (rs3775291) and TLR9 (rs352140) genes in patients with severe and extremely severe condition.Conclusion: reliable differences in the frequency of occurrence of genotypes of TLR3 (rs3775291) and TLR9 (rs352140) genes in patients with the manifest form of COVID-19 compared to healthy people were revealed. The analysis of nucleotide sequence variants of the studied genes in hospitalized patients depending on the degree of severity also showed significant differences in the frequency of genotypes. Thus, in patients with severe and extremely severe COVID-19, a significant difference in the frequency of occurrence of ST and TT genotypes of TLR3 (rs3775291) and TLR9 (rs352140) genes was revealed compared to patients with mild and moderate COVID-19, which may further have prognostic value in assessing the severity of the disease.

Exploring the Relationship Between Growth Hormone Secretagogue Receptor (GHSR) Gene and Body Proportions in Bangkok Chickens: Insights from DNA Sequencing and Hin6I Enzyme-Restricted PCR-RFLP Analysis

The purpose of this study was to determine the diversity of the growth hormone secretagogue receptor (GHSR) gene and also to analyze the association of the GHSR gene with the body proportions of Bangkok chickens. A total of 125 Bangkok chickens were reared, and blood samples were taken. Bangkok chickens were kept in colony cages with ad libitum feeding and drinking. The GHSR gene polymorphism was determined using the PCR-RFLP method. The restriction enzyme used in this study was Hin6I. The data analyzed were indicators of body proportions, which included data on body weight, carcass weight, and commercial cut weight. Single nucleotide polymorphism (SNP) identification using the Molecular Evolutionary Genetics Analysis 7 program with reference number AB095994.1. Allele frequency values, genotype frequencies, and Hardy-Weinberg balance values were also analyzed. The association between the GHSR gene and the traits observed in Bangkok chickens was analyzed using the T-test. The results of the study showed that the GHSR gene in Bangkok chickens had two genotypes, namely TT and CT. The values for Ho and He were 0.224 and 0.198, respectively. The genotype frequencies of TT and CT were 0.776 and 0.224, respectively. The two genotypes were associated with body weight, carcass weight, and commercial weight (p &lt; 0.05). For all measured criteria, the TT genotype showed a higher weight value than the CT genotype. The GHSR gene has the potential to be used as a genetic marker for the selection process on body weight, carcass weight, and commercial weight traits.

Association of ABCB1(Rs10276036, C/T) Gene, IL-18, and TNFα as Risk Factors for Nephrotic Syndrome Incidence.

The most common cause of Nephrotic Syndrome (NS) in children is idiopathic NS, also called nephrosis. The most prominent clinical signs are hyperlipidemia, severe proteinuria, edema, swelling of body tissues, and an increased risk of infection. The object of this study was to examine the correlation of the ABCB1 gene (rs10276036, C > T), IL-18, and TNFα to the prevalence of NS among Egyptian children having NS. This study included 100 participants with NS and 100 healthy controls. To analyze the ABCB1 gene (rs10276036 C >T) variant PCR technique was used. IL-18 and TNF levels were estimated using Enzyme-Linked Immunosorbent Assay (ELISA). Increased frequency of CT and TT genotypes of the ABCB1 gene (rs10276036 C / T) in NS patients compared to controls, with p-value = 0.001, OR = 2.270, CI = (1.550-3.327) for CT genotype and p-value = 0.001, OR = 5.070, CI = (2.463-10.438) for TT genotype. The frequencies of ABCB1 (rs10276036 C >T) genotypes were statistically significant in the dominant model (OR 2.560; p< 0.001) and in the recessive model OR, 3.231; p= 0.001). Significantly high levels of both IL-18 and TNFα were found in NS patients compared to controls. The ABCB1gene (rs10276036 C/T), IL-18, and TNFα are associated with the prevalence of NS in Egyptian children and might be considered as independent risk factors for its incidence.

Interleukin 1 Alpha Gene Polymorphism in Breast Cancer After Chemotherapy Treatment

Abstract Background: The interleukin 1 (IL-1) family of cytokines is essential for triggering and controlling immunological and inflammatory responses. We believe the levels of these cytokines in breast tumor homogenates relate to other known prognosticators of patient survival. Objectives: The association between the risk of breast tumors and the IL-1 alpha −889 C&gt;T Promoter Primer polymorphism has been established. Interleukin 1 alpha −889 C&gt;T Promoter Primer has been proven to influence breast tumor susceptibility. Our research aimed to determine whether the IL-1 alpha −889 C&gt;T Promoter Primer gene polymorphism and susceptibility to Breast cancers (BCs) are related. Materials and Methods: The genotype frequencies of the IL-1 alpha −889 C&gt;T Promoter Primer polymorphism were compared between 100 BC cases and 50 controls with the assistance of polymerase chain reaction and restriction fragment length polymorphism techniques. Additional multivariate binary logistic regression analyses were carried out to determine the level of IL-1 in patients’ blood and to examine the association between the IL-1 alpha −889 C&gt;T Promoter Primer polymorphism and BC risk utilizing the ELISA technique after therapy. Results: The concentration of CA 15-3 in patients with BC was 101.107 increase significantly compare with mean of control group was 62.802, in chemotherapy patients genotype frequencies of TT, CT, CC of IL-1 alpha −889 C&gt;T gene polymorphism where it patients with genotype TT were affected by breast tumors approximately one time comparison with patients having genotype CT (odd ratio = 1.50 and 0.91). Conclusion: Concentration of CA 15-3 increase in patients after chemotherapy compared with healthy, The IL-1 alpha −889 C&gt;T polymorphism affects breast tumors in women.

MiR-4716–3p and the target AKT2 Gene/rs2304186 SNP are associated with blood cancer pathogenesis in Pakistani population

AKT2 is crucial for cancer cells' invasion, metastasis, and survival. It is a possible downstream gene target of cancer glycolysis-related microRNAs. The study investigated the role of miRNA-4716–3p, rs2304186, and the AKT2 gene in blood cancer pathogenesis. RT-qPCR was used to analyze AKT2 gene mRNA and miRNA-4716–3p expression in 200 blood cancer samples and 200 healthy controls. Furthermore, Tetra-ARMS PCR was used to examine the rs2304186 AKT2 SNP in 300 patients and 290 control samples. miRNA-4716–3p was shown to be significantly downregulated (p = 0.0294), whereas mRNA expression of the AKT2 gene was found to be significantly upregulated (p = 0.0034) in blood cancer patients compared to healthy individuals. miRNA-4716–3p downregulation (p = 0.0466) was more pronounced, while AKT2 upregulation was non-significant (p = 0.1661) in untreated patients compared to chemotherapy-treated patients. Blood cancer risk was significantly associated with the rs2304186 GT genotype (p = 0.0432), TT genotype (p = 0.0502), and mutant allele (T) frequency (p = 0.0008). Polymorphism rs2304186 was associated with an increased risk of blood cancer in dominant (p = 0.0011), recessive (p = 0.0502), and additive (p = 0.0008) genetic models. The results suggested that the rs2304186 and the deregulated expression of miRNA-4716–3p and AKT2 gene at the mRNA level may significantly increase the incidence of blood cancer, particularly in the Pakistani population. Therefore, these may function as suitable biomarkers for blood cancer diagnosis and prognosis. Additional, larger-scale investigations may be required to affirm these results.