Variant Genotypes Research Articles

Role of HIF1A gene polymorphisms with serum uric acid and HIF-1α levels in monosodium urate crystal-induced arthritis.

Gouty arthritis is a metabolic disease characterized by the deposition of monosodium urate crystals in the joints, which triggers the release of interleukin-1β (IL-β) by activating the NLRP3 inflammasome. Hypoxia-inducible factor-1α (HIF-1α) is a transcription factor involved in IL-β production and as a regulator of NLRP3. The aims were to analyze the association of HIF1A rs11549465, rs11549467, and rs2057482 variants in patients with gouty arthritis, and to evaluate the correlation between urate and HIF-1α levels according to the associated genotypes. Cases and controls were genotyped using TaqMan probes, and urate and HIF-1α levels were quantified. Data were analyzed using SPSS v21 software and P-values < 0.05 were considered statistically significant. Urate and HIF-1α levels were higher in patients than in controls (P < 0.05). Under the three inheritance models (codominant, dominant, and recessive), the AA genotype of the rs11549467 variant was associated with gout risk (OR = 5.74, P = 0.009, OR = 3.33, P = 0.024, and OR = 9.09, P = 0.003, respectively). There were significant differences in the distribution of serum levels of both HIF-1α (P < 0.0001) and urate (P = 0.016) according to the genotypes of the rs11549467 variant. These results suggest that the HIF1A rs11549467 variant may play a key role in the pathogenesis of gouty arthritis. Key Points • The pathogenesis of gouty arthritis involves the HIF1A gene. • In patients with gout, the AA genotype of the rs11549467 (HIF1A) variant is associated with increased serum levels of urate and HIF-1α. • HIF-1α is involved in the regulation of IL-1β and NLRP3.

Investigation of the α9-nicotinic receptor single nucleotide polymorphisms induced oncogenic properties and molecular mechanisms in breast cancer.

α9-nAChR, a subtype of nicotinic acetylcholine receptor, is significantly overexpressed in female breast cancer tumor tissues compared to normal tissues. Previous studies have proposed that specific single nucleotide polymorphisms (SNPs) in the CHRNA9 (α9-nAChR) gene are associated with an increased risk of breast cancer in interaction with smoking. The study conducted a breast cancer risk assessment of the α9-nAChR SNP rs10009228 (NM_017581.4:c.1325A > G) in the Taiwanese female population, including 308 breast cancer patients and 198 healthy controls revealed that individuals with the heterozygous A/G or A/A wild genotype have an increased susceptibility to developing breast cancer in the presence of smoking compared to carriers of the G/G variant genotype. Our investigation confirmed the presence of this missense variation, resulting in an alteration of the amino acid sequence from asparagine (N442) to serine (S442) to facilitate phosphorylation within the α9-nAchR protein. Additionally, overexpression of N442 (A/A) in breast cancer cells significantly enhanced cell survival, migration, and cancer stemness compared to S442 (G/G). Four-line triple-negative breast cancer patient-derived xenograft (TNBC-PDX) models with distinct α9-nAChR rs10009228 SNP genotypes (A/A, A/G, G/G) further demonstrated that chronic nicotine exposure accelerated tumor growth through sustained activation of the α9-nAChR downstream oncogenic AKT/ERK/STAT3 pathway, particularly in individuals with the A/G or A/A genotype. Collectively, our study established the links between genetic variations in α9-nAChR and smoking exposure in promoting breast tumor development. This emphasizes the need to consider gene-environment interactions carefully while developing effective breast cancer prevention and treatment strategies.

Relationship of EDNRA rs6842241 and MRAS rs9818870 polymorphic variants with predisposition to coronary artery disease and their effect on the lipid-lowering effect of rosuvastatin

Aim. To study the effect of EDNRA rs6842241 and MRAS rs9818870 polymorphic variants on the lipid-lowering effect of rosuvastatin in patients with coronary artery disease (CAD), and to determine the role of these loci in the development of CAD among Central Russia residents.Material and methods. The pharmacogenetic study involved 116 patients with class II-III stable angina. Patients received rosuvastatin with dose titration to achieve target low-density lipoprotein cholesterol (LDL-C) levels. The genetic and epidemiological study included DNA samples of 1960 Central Russia residents (1261 patients with CAD and 699 healthy individuals). Genotyping of polymorphic variants was performed on a MassARRAY-4 genomic mass spectrometer. Associations of polymorphisms with lipid changes for 1, 6 and 12 months of follow-up were calculated using linear regression analysis adjusted for sex, age, body mass index and rosuvastatin dose; associations with CAD risk — using logistic regression analysis adjusted for sex and age. The statistical significance of associations was calculated using the permutation test.Results. Carriage of the AA and CA genotypes of EDNRA rs6842241 variant was associated with a weakening of the rosuvastatin lipid-lowering effect in relation to total cholesterol (β=0,075, p=0,001) and LDL-C (β=0,145, p=0,017) at the end of the first month and 12 months of therapy (β=0,049, p=0,013 and β=0,072, p=0,040, respectively). Carriage of the AA genotype of EDNRA rs6842241 variant was associated with an increased CAD risk (odds ratio 5,36; 95% confidence interval 1,62-17,71, p=0,004). MRAS rs9818870 variant was not associated with rosuvastatin pharmacogenetics or with the CAD risk. Both polymorphic variants were not associated with lipid levels outside of lipid-lowering therapy, as well as with the triglyceride changes. High-density lipoprotein cholesterol levels during the entire follow-up period changed insignificantly.Conclusion. The EDNRA rs6842241 variant is associated with both a weakening of the lipid-lowering effect of rosuvastatin in CAD and an increased risk of its development in the population.

Genetic variants of interleukin-1α, interleukin-12β and matrix metalloproteinase-9 in oral cancer risk and progression

BackgroundCytokines and matrix metalloproteinases play an important role in inflammation and metastasis in the development of cancer. Single nucleotide polymorphisms in these genes may affect gene expression and protein activity and, therefore, may be associated with cancer predisposition. The study seeks to examine the correlation between single nucleotide polymorphisms in the cytokines (Interleukin-1α and Interleukin-12β) and Matrix metalloproteinase (MMP9) gene with oral cancer. The interplay of the genetic variants, Interleukin 1α -889 C/T (rs1800587), Interleukin 12β +1188A/B (rs3212227), and MMP9 R279Q (rs17576) with tobacco chewing and smoking habits is determined in patients with oral cancer and controls. The relationship between these genetic variations with the tumor size, lymph node involvement, and metastasis in oral cancer was studied. MethodCase-control research was implemented with a total of 150 participants, which includes 50 individuals who were diagnosed with oral cancer and 100 healthy volunteers. The study on Single Nucleotide Polymorphism (SNP) was performed using the Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP) technique. ResultsInterleukin-1α -889 C/T polymorphism was significantly associated with oral cancer. The heterozygous genotype (CT) IL-1α -899 C/T was most frequent in oral cancer patients with a p value of 0.000002 in the chi-square test with no node involvement or metastasis. No interaction with the smoking or tobacco chewing habit with the genotypes of any of the genes is observed. The genotype of the mutant (TT) was also significantly different among the two groups (p = 0.01, OR = 7.63, CI- 1.5–37.5). The distribution of the mutant RR genotype of MMP9 R279Q in oral cancer patients was statistically significant in comparison with healthy controls (p = 0.005, OR = 4.46, CI- 1.52–3.04). The genotypic variants of IL-12β +1188A/B were, however, not found to be associated with oral cancer risk. IL-1α-899 (CT) and MMP9R279Q (RR) genotypes were found to be significantly associated with tumor size. ConclusionThis finding indicates that the substitution of C to T at IL-1α-889 position and substitution of glutamine with arginine at amino acid position 279 in MMP9 due to single nucleotide polymorphism increases the risk of oral cancer. IL-12β +1188 polymorphism was not associated with oral cancer risk. Habit does not play any role in the interaction of these genes with oral cancer.

Diagnostic Impacts of Aldehyde Dehydrogenase 2 Genetic Variants on Hepatocellular Carcinoma Susceptibility.

The role of alcohol consumption and aldehyde dehydrogenase 2 (ALDH2) genotype in hepatocellular carcinoma (HCC) development remains uncertain. We conducted genotyping of the ALDH2 rs671 single nucleotide polymorphism in 298 patients with HCC and 889 non-cancerous healthy controls. We assessed associations stratified by sex and alcohol consumption status. Distribution of ALDH2 rs671 variant genotypes differed significantly between HCC patients and controls (ptrend=0.0311). Logistic regression analyses indicated that compared to the wild-type GG genotype, the heterozygous variant AG genotype and homozygous variant AA genotype conferred 1.22- and 1.77-fold increases in HCC risk (p=0.1794 and 0.0150, respectively). Allelic frequency analysis showed that the A allele was associated with a 1.29-fold increased HCC risk (p=0.0123). Additionally, AA genotype carriers had significantly higher HCC risk than GG genotype carriers among males (p=0.0145) and non-alcohol drinkers (p<0.001). HCC risk is influenced by ALDH2 genotype, with effects modified by sex and alcohol consumption. Particularly, individuals with the ALDH2 rs671 AA genotype should avoid alcohol consumption, especially males.

Association of vitamin D receptor gene polymorphisms, metabolic features and susceptibility to polycystic ovary syndrome: a preliminary study

Research questionAre the combined genotypes and haplotypes of VDR gene polymorphisms (FokI, ApaI, TaqI) associated with PCOS susceptibility and metabolic features of the disease? DesignWe performed a case-control study, including 46 women with PCOS and 48 controls. Genotypes of VDR genes were determined using the PCR-RFLP (restriction fragment length polymorphism) method. In all women, the waist circumference, parameters of lipid and glucose metabolism were evaluated. ResultsPCOS group presented higher waist circumference and visceral adiposity index (VAI) levels compared to controls. Total cholesterol, LDL-C and triglycerides had higher values in PCOS women. VDR-FokI C/C (F/F) genotype had significantly higher odds of PCOS (adjusted OR = 6.27, 95% CI: 1.53-25.65). VDR-Apal was associated with susceptibility to PCOS in the dominant model, the variant genotype (A/C-A/A) (A/a- a/a) had higher odds of PCOS than the wild genotype C/C (A/A) (adjusted OR = 3.15, 95% CI: 1.07-9.32). Haplotype analysis revealed that T-C- T (f-A-T) haplotype was statistically associated with lower odds of PCOS (adjusted OR = 0.10, 95% CI: 0.01-0.95). PCOS women with VDR-Fokl T/T (f/f) genotype had lower fasting glucose and higher VAI levels compared to C/T (Ff) or C/C (F/F) genotype. ConclusionThe present findings suggest the association between FokI and ApaI polymorphisms and PCOS susceptibility. Moreover, T/T (f/f) genotype of VDR-FokI could be a marker of decreased fasting glucose in PCOS. TaqI polymorphism did not reveal a relationship with PCOS susceptibility in our study population.

The Influence of OCT3 and MATE2 Genetic Polymorphisms in Poor Response to Metformin in Type 2 Diabetes Mellitus.

The response of patients with Type 2 diabetes mellitus (T2DM) to metformin may be a variation because of genetic differences in solute carrier (SLC) transporter proteins and other effect factors, which have an important effect on how metformin is processed in the body and its efficiency for glycaemic control. This study was conducted to investigate the impact of certain genetic variants of the organic cation transporter genes OCT3 (SLC22A3 rs12194182 and rs8187722) and MATE2 (SLC47A2 rs12943590) and their association with glycaemic parameters in patients with T2DM who respond poorly to metformin. This cross-sectional study involved 150 Iraqi cases with T2DM who were prescribed a daily dose of (1000 mg/day) metformin for a minimum of 3 months. Various parameters included are as follows: demographic data, glycaemic parameters and three SNPs: rs12943590 variant of SLC47A2, rs12194182 and rs8187722 variant of SLC22A3 using the standard PCR-sequencing technique. Thirty-nine patients (26.17%) were responders, whereas 111 patients (73.82%) could not respond to metformin treatment. Upon analysing the genotypes of the rs12943590 variants of SLC47A2, rs12194182 and rs8187722 SNPs of SLC22A3, the present findings revealed a nonsignificant association of genetic variations in all SNPs with metformin response. SLC47A2 (rs12943590) showed nonsignificant associations of the GG, AA and AG genotyping; SLC22A3 (rs12194182) showed nonsignificant associations of the TT, TC and CC genotyping; and SLC22A3 (rs8187722) showed nonsignificant associations of the AA, CC and AC genotyping between two groups. Variations in genes SLC22A3 and SLC47A2 did not have a significant role in the response of patients with T2DM to metformin (1000 mg/day).

CYP2D6, CYP2E1 Gene Polymorphisms and Gastrointestinal Cancer Risk in Rural Maharashtra: A Hospital Based Case-Control Study.

Cytochrome P450 (CYP) is a family phase I metabolizing enzymes important in xenobiotics metabolism. Genetic polymorphisms of CYPs have been comprehensively studied for their association with a range of diseases including cancer risk. In this study we assessed single nucleotide polymorphism (SNP) CYP2D6 and CYP2E1 genes and their role in gastrointestinal (GI) cancer susceptibility in the rural population of Maharashtra. Genotyping of CYP2D6*4, CYP2E1*5B, CYP2E1*6, CYP2E1*7B genes among 200 GI cancer cases and equal number of controls was studied by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The Odds ratio (OR) with 95% confidence interval and p-value were evaluated to get the level of association of polymorphisms with risk of GI cancer, where p ≤0.005 was considered as statistically significant. After the analysis of CYP2D6 and CYP2E1 gene polymorphisms, we noticed that CYP2D6*4 (rs3892097) with heterozygous genotype (G/C) showed negative association with GI cancer risk (OR=0.43, 95% CI: 0.25-0.74; p=0.002) and CYP2E1*6 (rs6413432) variant genotype showed positive association (OR=2.85, 95% CI: 1.40-5.81; p=0.003) showed positive association with GI cancer risk in studied population. The findings obtained from this study concluded that the polymorphic CYP2D6 was negatively associated; however CYP2E1*6 polymorphism was significantly associated with GI cancer risk in studied population.

Glucose-6-phosphate Dehydrogenase Variants: Analysing in Indian Plasmodium vivax Patients.

Primaquine (PQ) is recommended for radical cure of Plasmodium vivax (Pv) malaria, but its utilization is still limited due to high risk of severe haemolytic anaemia in patients with glucose-6-phosphate dehydrogenase deficiency (G6PD-d). The aim of the present study is to assess the different genotypic variants leading to G6PD-d in Delhi and Goa regions of India. A total of 46 samples (34 retrospective Pv-mono-infected samples and 12 Pv-uninfected samples) were included in the study. Various genetic variants leading to G6PD-d were analysed by PCR amplification and DNA sequencing of different targeted exons of G6PD gene. Molecular analysis showed presence of four mutations in study population viz. 1311C > T, 34.1% & IVSXI 93T > C, 45.5% and two novel mutations 1388G > T, 2.3% and 1398C > T, 2.3% (silent mutation). The bioinformatics and computational analysis demonstrate that the slight conformational changes caused by R643L mutation in protein are deleterious in nature. The observed mutations do not clarify the role or association between G6PD-d and Pv-infected cases. Further investigation is required in order to fully comprehend and analyse the precise role of these mutations with context to malaria infections.

Impact of Matrix Metalloproteinase-8 Polymorphisms on Nasopharyngeal Carcinoma Risk.

Upregulation of matrix metallo-proteinase-8 (MMP-8) serves as a protein-based indicator for predicting nasopharyngeal carcinoma (NPC) metastasis. Nevertheless, the role of MMP-8 genotypes in NPC has never been investigated. This study aimed to explore the involvement of MMP-8 genotypes in NPC development. We employed the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique to analyze MMP-8 genotypes, specifically C-799T (rs11225395), Val436Ala (rs34009635), and Lys460Thr (rs35866072), in a Taiwanese cohort comprising 208 NPC cases and 416 healthy controls. Individuals with either heterozygous or homozygous variant genotypes of MMP-8 rs11225395 showed no significant change in NPC risk compared to those with the wild-type genotype [odds ratio (OR)=0.97 and 0.79, 95% confidence intervals (95%CI)=0.68-1.38 and 0.46-1.36; p=0.9304 and 0.4736, respectively]. Similarly, there was no significant association between the heterozygous genotypes of MMP-8 rs34009635 and NPC risk (OR=0.66, 95%CI=0.24-1.84; p=0.5738). For MMP-8 rs35866072, all individuals in the study were of the TT genotype. Furthermore, the presence of variant alleles at MMP-8 rs11225395 or rs34009635 did not result in altered NPC risk (OR=0.91 and 0.66, 95%CI=0.71-1.16 and 0.24-1.84, p=0.4876 and 0.5769, respectively). Additionally, no significant association was observed between MMP-8 rs11225395 variant genotypes and NPC risk among individuals regardless of smoking, alcohol consumption, or betel quid chewing habits (all p>0.05). There was no association between the MMP-8 genotypes rs11225395, rs34009635, or rs35866072 and NPC risk among Taiwanese individuals. Moreover, no combined effects of MMP-8 genotype with smoking, alcohol consumption, or betel quid chewing habits on NPC risk were observed.

Association of a Promoter DNA Methyltransferase 3 Gene Variant with DNA Methylation and Anthropometrics in Children from 4 to 12 Years Old

The global prevalence of obesity among adults, adolescents, and children has increased to alarming levels, making this disease a serious public health problem. The etiology of obesity is complex and multifactorial. Currently, epigenetic alterations are being investigated to understand the mechanisms of interaction between genes and environmental and behavioral risk factors involved in the genesis of obesity. In this study, we examined the association of the DNA methyltransferase 3 (DNMT3B) gene-149 C&gt;T variant (rs2424913) genotypes with global DNA methylation and the changes in anthropometric parameters in a cohort of 171 children followed from birth to 12 years old. Genotypes were obtained using real-time polymerase chain reaction, and global DNA methylation was measured in blood samples collected at 4 years old through enzyme-linked immunosorbent assays. Our results showed that the TT genotype is associated with an increase in global methylation levels at 4 years old and higher changes in body mass index, waist circumference, subscapular subcutaneous fat, body fat mass, body lean mass, and basal metabolic rate from 4 to 12 years. Our results suggest that this promoter DNMT3B gene variant and DNA methylation can be factors relevant to the increased risk of children developing obesity at an early age.

Impacts of Matrix Metalloproteinase-2 Promoter Genotypes on Breast Cancer Risk.

Matrix metalloproteinase-2 (MMP-2) has been implicated in the pathogenesis of breast cancer (BC). However, there is limited research on the role of MMP-2 genotypes in BC risk. This study aimed to investigate the associations between two MMP-2 promoter polymorphisms, rs243865 and rs2285053, and BC risk. MMP-2 genotypes were analyzed using PCR-based RFLP methodology in a cohort comprising 1,232 BC cases and 1,232 controls. Genotypic frequencies of MMP-2 rs243865 and rs2285053 in controls were consistent with Hardy-Weinberg equilibrium (p=0.3702 and 0.2036, respectively). There were no significant differences in the distribution of rs243865 and rs2285053 genotypes between BC cases and controls (p for trend=0.1602 and 0.2170, respectively). Variant genotypes at rs243865 and rs2285053 appeared to confer a protective effect, although not statistically significant (all p>0.05). Similarly, the variant T allele at rs243865 and rs2285053 showed a non-significant trend towards decreased BC risk (OR=0.84 and 0.89, 95%CI=0.69-1.02 and 0.78-1.02, p=0.0811 and 0.1043, respectively). There was no interaction observed between MMP-2 rs243865 or rs2285053 genotypes and age. Stratified analysis did not reveal significant associations between MMP-2 rs243865 or rs2285053 genotypes and triple-negative breast cancer (TNBC) (p=0.6458 and 0.8745, respectively). Among both TNBC and non-TNBC cases, none of the variant genotypes at rs243865 or rs2285053 showed significant associations with TNBC (all p>0.05). MMP-2 rs243865 and rs2285053 genotypes appear to have a minimal impact on individual susceptibility to BC or TNBC.

CMAH Coding Sequence Variants in 15 Non-Domestic Felid Species Related to ABC Blood Group System.

Different blood group systems have been characterized in people and other mammals. In domestic cats, the ABC blood group system plays the most important clinical role and has been investigated extensively-from the phenotype to the molecular genetics. In non-domestic felids, phenotypic ABC blood typing has been performed by different methods to detect the antigens, but the four informative CMAH markers in domestic cats were not able to identify types B and C (AB) in non-domestic cats. In this study, 138 blood samples from 15 non-domestic (wild) felid species were investigated by CMAH exonic sequencing and genotyping for putative variants causing type B or C (AB) and correlation to the respective ABC blood phenotype. A total of 58 CMAH variants were found, including 15 missense and 43 synonymous CMAH variants. One variant (c.635G>C) was concordant with blood type B (and C) in cheetahs and type B in cougars, compared to blood type A in all other felid species (lion, tiger, Canada lynx, snow leopard, clouded leopard, serval, jaguar, fishing cat, Pallas cat, bobcat, black footed cat, leopard, and sand cat). Since cheetahs and cougars belong to the genera puma, it could not be determined if the common CMAH variant is either a marker for type B (or C) or is just common in pumas.

Uncovering molecular mechanisms for amelanotic/hypopigmented primary cutaneous melanoma.

A portion of approximately 2-20% of cutaneous melanoma (CM) are diagnosed as amelanotic/hypopigmented melanoma (AHM) and represent a challenge for early diagnosis. Since the degree to which somatic mutations and copy number aberrations (CNA) in genes associated with skin-lightening or albinism may contribute to the loss of tumour pigmentation in AHM samples has not yet been addressed, we have investigated loss of function mutations of key pigmentation genes in matched germline and AHM as well as pigmented melanoma (PM) tumour DNA samples. An analysis of clinical and histopathological characteristics together with whole exome sequencing data of 34 fresh frozen primary CM, graded according to the amount of pigmentation present was performed. Together with germline and somatic variant analysis, 30 samples were previously analysed for CNA changes. This study focussed on germline and somatic variants in the coding region of 16 genes known to be associated with albinism/hypopigmentation or variation in human pigmentation in all samples. Chromosomal regions encompassing these 16 genes were examined for DNA copy loss or gain. The finding that red hair related MC1R and TYR R402Q loss of activity gene variant alleles and genotypes are associated with AHM was validated in this study. Germline AHM-related gene variants were enriched in 70% (n=7 of 10) of AHM patients vs 8.3% (n=2 of 24) of PM patients. This surprisingly high frequency of rare germline variants in AHM patients constitutes the "first hit" and confirms that AHM patients are more likely to be albinism allele carriers than patients with PM. Next, in CNA analysis of each tumour sample, 50% (n=4 of 8) AHM samples with a pigmentation gene variant had LOH in the region containing the corresponding gene, and 25% (=2 of 8) had loss-of-heterozygosity (LOH) in chromosomal regions of two AHM-related genes. This study proposes that the likely molecular mechanism for development of amelanogenesis in AHM is carriage of an albinism/hypopigmentation allele followed by LOH of the corresponding gene in the tumour.

Mutagenicity and DNA damage assessment of locally produced nano-hydroxyapatite-silica-glass ionomer cement on human periodontal ligament fibroblasts using Ames and Comet assays

AimThis research assessed the mutagenicity and DNA damage of a novel type of nano-hydroxyapatite-silica glass ionomer cement (nano-HA-SiO2-GIC) and a conventional GIC (cGIC) using Ames and Comet assays. MethodsCell viability was tested on human periodontal ligament fibroblasts (HPLFs) using 3.125 mg/ml, 6.25, 12.5, 25, 50, 100 and 200 mg/ml, on both types of GICs employing MTT assay. For the Comet assay, HPLFs were treated with IC50, IC25 and IC10 of test materials and the tail moments were measured. In the Ames test, four genotypic variants of strains of Salmonella typhimurium (TA100, TA98, TA1537 and TA1535) and a strain of Escherichia coli (WP2 uvrA) were employed. The material tested was extracted using sterile distilled water (0.2 g per ml) at 37 °C for 72 h. This was considered as 100 %, which was diluted to 50, 25, 12.5 and 6.25 % utilizing sterile distilled water. These five concentrations were incubated with the bacterial strains with and without metabolic activation (S9), along with appropriate positive controls. The number of revertant colonies was used to evaluate the outcome. ResultsThe highest cell viability (159.4 %) for nano-HA-SiO2-GIC was noticed at 3.125 mg/ml, while the lowest (24.26 %) was observed at 200 mg per ml. IC50, IC25 and IC10 values were 95.27, 51.4 and 20.1 mg/ml for cGIC, 106.9, 55.8 and 22.9 mg/ml for nano-HA-SiO2-GIC, respectively. The IC10 of both test materials showed no significant DNA damage compared to that of the negative control based on the Comet assay. The plate treated with nano-HA-SiO2-GIC showed less than double the average number of revertant colonies compared to that of negative control with regard to the Ames test. ConclusionsIt can be concluded that nano-HA-SiO2-GIC is non-mutagenic based on the Ames test and did not cause DNA damage at the lowest concentration of IC10 based on the Comet assay.

Correlation between human BDNF rs6265 gene polymorphism and type-2 diabetes and diabetic peripheral neuropathy

Background &amp; objective: Diabetes mellitus is quite common and globally prevalent condition affecting patients’ quality of life. Patients who have type 2 diabetes mellitus (T2DM), are more likely to get diabetic peripheral neuropathy (DPN), which may affect feet, legs, hand, and arm. A BDNF gene rs6265 polymorphism in humans results in the substitution of valine with methionine at codon 66 (Val66Met). We aimed to find the possible link between human BDNF rs6265 gene polymorphism and T2DM with and without peripheral neuropathy and compare it with healthy subjects in Kirkuk City, Iraq. Methodology: One hundred subjects were chosen to participate in this research, aged from 35 to 75 y and divided into three groups: 35 DPN, 35 T2DM patients, and 30 healthy controls were selected randomly for BDNF gene rs6265 SNP screening by using conventional PCR with specific sets of primers. Products of PCR for patients and control groups were run on the gel electrophoresis to detect the SNP rs6265 fragment. A nerve-conducting study was used to examine DPN. Results: The observed results demonstrated the presence of two types of alleles identified as genotypic variants (GG and GA) among all participants in this investigation. By applying the Hardy-Weinberg Equilibrium principle (HWE) for both patient and control groups, the results proved that there was a statistically significant variance (P &lt; 0.05) in the genotypic frequencies between each of the groups that had been studied. The wild homozygous GG genotype in type 2 diabetic without neuropathy, with DPN, and healthy control group were 51.4%, 40% and 80% respectively. The heterozygous GA genotype were 48.6%, 60% and 20%, respectively in the three groups. Conclusion: The present study showed that the BDNF (Val66Met) rs6265 polymorphism is associated with type 2 diabetes mellitus and diabetic peripheral neuropathy in heterozygous allele G/A (Met/Met) and homozygous allele GG (Val/Val) genotype. Also, the current study found the absence of the mutant genotype AA, possibly due to the evidence that the distribution of the BDNF polymorphisms varies widely among different ethnic groups. Abbreviations: BDNF - Brain-derived neurotrophic factor; DPN - Diabetic peripheral neuropathy Keywords: Type2 diabetes mellitus; Diabetic peripheral neuropathy; Brain-Derived Neurotrophic Factor; BDNF rs6265 SNP; BDNF Val66Met polymorphism. Citation: Hamid R, Al-Wasiti E, Jabbar AM. Correlation between human BDNF rs6265 gene polymorphism and type-2 diabetes and diabetic peripheral neuropathy. Anaesth. pain intensive care 2024;28(4):752−756. DOI: 10.35975/apic.v28i4.2517 Received: March 08, 2024; Reviewed: April 20, 2024; Accepted: April 28, 2024

Drug Response of Iranian Alzheimer's Patients to Rivastigmine Concerning Their Genotype for VDR rs11568820 and MTHFR C677T Variants: A Pharmacogenetic and Association Study.

Alzheimer's disease is a neurodegenerative disorder with polygenic etiology. Genetic risk variants for Alzheimer's disease differ among populations. Thus, discovering them in each population is clinically important. A total of 118 patients and 97 controls for VDR rs11568820 and 88 patients and 100 healthy controls for MTHFR C677T polymorphism were genotyped to evaluate the association of these polymorphisms with late-onset Alzheimer's disease in the Iranian population, along with their impacts on the response to Rivastigmine treatment. The VDR C allele was significantly associated with Alzheimer's disease and provided protection against it (P = 0.003, RR = 1.14, 95% CI 1.04-1.24), while the T allele increased susceptibility (P = 0.003, RR = 1.93, 95% CI 1.23-3.02). These results were also considerable upon excluding the effect of APOE ε4 allele. The Prevalence-corrected Positive Predictive Value was 1.71% for the VDR CC genotype and 4% for the VDR CT genotype, indicating lower and almost twofold higher chances of developing Alzheimer's disease, respectively. No significant correlation was observed between MTHFR C677T and Alzheimer's disease. Based on our pharmacogenetic study, MTHFR T allele carriers lacking APOE ε4 allele showed a better response to Rivastigmine treatment after a 2-year follow-up. Moreover, patients with VDR CC genotype displayed milder Alzheimer's disease, particularly when coincided with the APOE ε4 allele. The VDR rs11568820 polymorphism affects both Alzheimer's disease risk and the response to Rivastigmine in Iranian patients. Also, MTHFR C677T polymorphism may play a role in the response to Rivastigmine, through a pathway that needs to be elucidated in future studies.

Polymorphisms in the Growth Hormone Gene and Their Association with Pre-pullet Body Weight in Kuttanad Ducks of Kerala, India

Background: Kuttanad ducks are dual purpose native ducks found in Kerala state of India. Identification of single nucleotide variations in candidate genes like growth hormone gene and exploring their association with body weight at grower and pre-pullet stages is essential for the marker assisted selection of breeder ducks for genetic improvement. Methods: Genomic DNA was extracted from blood samples collected from 101 Kuttanad ducks. PCR-amplification of two duck growth hormone gene (dGH) loci viz, exon 3 and partial intron 3 (227 bp), exon 5 and partial intron 4 (366 bp) were undertaken using custom-synthesised primers. The 366 bp region was genotyped using Single Strand Conformation Polymorphism. The 227 bp region was genotyped using DNA pooling assay to yield a 139 bp product for subsequent High-Resolution Melting analysis. The association of dGH genotypic variants for these loci with fortnightly body weight at pre-pullet stages up to 16 weeks of age was analysed. Result: In the 366 bp fragment, GG and GA genotypes were revealed with one novel SNP (g 74G greater than A). The GG homozygotes had significantly higher body weight at all stages from two to 14 weeks of age (p≤0.01). A novel SNP (g 71A greater than G) was revealed at the 139 bp locus within the 227 bp region with three genotypes viz., AA, AG and GG. The GG homozygotes had significantly higher body weight at six, 14 and 16 weeks of age (p≤0.05). The study revealed that dGH polymorphic loci have jointly contributed to the variation in growth and hence can be used as markers for the primary selection of growers at sixth week of age followed by their secondary selection at 14-16 weeks of age during the multi-stage selection programmes for breeder ducks.

The Effects of Two Selected Single Nucleotide Polymorphisms of the Fatty Acid Synthase Gene on the Fat Content and Fatty Acid Profile of Cow's Milk from the Polish Holstein-Friesian Red-and-White Breed versus Two Polish Red-and-White and Polish Red Conservation Breeds Kept in Poland.

Fatty acid synthase (FASN) is a metabolic enzyme responsible for the synthesis of fatty acids in milk and meat. The SNPs g.841G/C and g.17924A/G of the FASN gene significantly influence the fat and fatty acid content of milk from cows of various breeds. Therefore, these SNPs were selected for this study. This study aimed to analyze the relationship of SNPs and their genotypes with the fat content and fatty acid profile of milk from Polish Red-and-White (ZR), Polish Red (RP), and Polish Holstein-Friesian Red-and-White (RW) cows. Milk samples were obtained during a milking trial. SNP genotyping was performed using the real-time PCR (HRM) method. It was shown that SNPs (with specific genotypes) were significantly associated with the presence of fatty acids such as C18:1n9t and C18:2n6c in milk. In addition, it was found that the milk fat from the ZR (genotypic variant A/G, AA) and RP (genotypic variant GG, A/G) breeds often exhibited a more attractive fatty acids profile than the milk fat from RW cows. This information can be used by both cattle breeders and people interested in consuming functional foods.

RNA-DNA differences in variant calls from cattle tissues result in erroneous eQTLs

BackgroundAssociation testing between molecular phenotypes and genomic variants can help to understand how genotype affects phenotype. RNA sequencing provides access to molecular phenotypes such as gene expression and alternative splicing while DNA sequencing or microarray genotyping are the prevailing options to obtain genomic variants.ResultsWe genotype variants for 74 male Braunvieh cattle from both DNA (~ 13-fold coverage) and deep total RNA sequencing from testis, vas deferens, and epididymis tissue (~ 250 million reads per tissue). We show that RNA sequencing can be used to identify approximately 40% of variants (7–10 million) called from DNA sequencing, with over 80% precision. Within highly expressed coding regions, over 92% of expected variants were called with nearly 98% precision. Allele-specific expression and putative post-transcriptional modifications negatively impact variant genotyping accuracy from RNA sequencing and contribute to RNA-DNA differences. Variants called from RNA sequencing detect roughly 75% of eGenes identified using variants called from DNA sequencing, demonstrating a nearly 2-fold enrichment of eQTL variants. We observe a moderate-to-strong correlation in nominal association p-values (Spearman ρ2 ~ 0.6), although only 9% of eGenes have the same top associated variant.ConclusionsWe find hundreds of thousands of RNA-DNA differences in variants called from RNA and DNA sequencing on the same individuals. We identify several highly significant eQTL when using RNA sequencing variant genotypes which are not found with DNA sequencing variant genotypes, suggesting that using RNA sequencing variant genotypes for association testing results in an increased number of false positives. Our findings demonstrate that caution must be exercised beyond filtering for variant quality or imputation accuracy when analysing or imputing variants called from RNA sequencing.