Common gene polymorphism in ATP-binding cassette transporter A1 and coronary artery disease: A genetic association study and a structural analysis

Association of PADI4 Gene Polymorphisms With Susceptibility to Rheumatoid Arthritis: Evidence From 24 Case-Control Studies

This study aims to investigate the association of rs11203366, rs11203367, rs874881, rs2240340 and rs1748033 polymorphisms of protein-arginine deiminase type 4 (PADI4) gene with the risk of rheumatoid arthritis (RA) through a meta-analysis that was followed with a bioinformatics approach. The data were collected from reputable articles and underwent quantitative analysis, followed by in silico analysis using some bioinformatics tools. The results showed that rs874881 polymorphism in Latino (G vs. C: OR = 1.35, 95% CI = 1.11-1.65, p = 0.003; GG + CG vs. CC: OR = 2.02, 95% CI = 1.41-2.89, p = 0.0001; CG vs. CC + GG: OR = 1.38, 95% CI = 1.04-1.83, p = 0.027; GG vs. CC: OR = 2.09, 95% CI = 1.35-3.23, p = 0.001; CG vs. CC: OR = 1.98, 95% CI = 1.36-2.87, p = 0.00033) and rs1748033 in Caucasian population (T vs. C: OR = 1.25, 95% CI = 1.07-1.45, p = 0.005; TT vs. CT + CC: OR = 1.34, 95% CI = 1.09-1.64, p = 0.005, TT + CT vs. CC: OR = 1.26, 95% CI = 1.09-1.44, p = 0.001; TT vs. CC: OR = 1.59, 95% CI = 1.13-2.23, p = 0.007; CT vs. CC: OR = 1.20, 95% CI: 1.04-1.39, p = 0.015) are associated with increased risk of RA. Moreover, rs11203366 (G vs. A: OR = 1.46, 95% CI = 1.19-1.78, p = 0.0002, GG vs. AG + AA: OR = 1.42, 95% CI = 1.01-2.01, p = 0.043; GG + AG vs. AA: OR = 2.03, 95% CI = 1.45-2.86, p = 0.00004; GG vs. AA: OR = 2.29, 95% CI = 1.49-3.51, p = 0.0002; AG vs. AA: OR = 1.93, 95% CI = 1.35-2.76, p = 0.0003) and rs11203367 (T vs. C: OR = 1.50, 95% CI = 1.23-1.83, p = 0.00007; TT vs. CT + CC: OR = 1.56, 95% CI = 1.12-2.18, p = 0.009; TT + CT vs. CC: OR = 2.02, 95% CI = 1.43-2.84, p = 0.00007, TT vs. CC: OR = 2.43, 95% CI = 1.59-3.71, p = 0.0004; CT vs. CC: OR = 1.86, 95% CI = 1.30-2.68, p = 0.0007) had an impact in the Latino population. Bioinformatics tools showed the effect of these polymorphisms on gene function. These findings suggest that rs11203366, rs11203367, rs874881 and rs1748033 polymorphisms may be genetic risk factors for RA. Moreover, differences between populations suggest that ethnicity may play an important role in the effect of these polymorphisms on RA risk.

Association of Functional Genetic Variations in Uric Acid Transporters with the Risk of Idiopathic Male Infertility: A Genetic Association Study and Bioinformatic Analysis

Uric acid plays an important role in sustaining and improving sperm morphology, viability, and motility. It is known that SLC2A9 and ABCG2 protein are the main urate transporter and genetic variations in these genes could be associated with the levels of serum uric acid. This study aimed to investigate the association between single-nucleotide polymorphisms (SNPs) SLC2A9-rs16890979, SLC2A9-rs3733591, ABCG2-rs2231142, and ABCG2-rs2231137 with male infertility. Additionally, the correlation of these SNPs with the uric acid level in seminal plasma of infertile men was examined. Subsequently, an in silico analysis was performed. In a case-control study, 193 infertile and 154 healthy controls were recruited. After semen sample collection, the uric acid level of seminal plasma was measured by a commercial kit. After genomic DNA extraction from sperm samples, SNPs genotyping was performed by PCR-RFLP method. Lastly, the effects of SNPs on the SLC2A9 and ABCG2 gene function were evaluated by bioinformatics tools. The genetic association study revealed that there are significant associations between rs16890979, rs3733591, rs2231142, and rs2231137 genetic variations and increased risk of male infertility. Also, these variations were associated with oligozoospermia and teratozoospermia, and sometimes with asthenozoospermia. Also, we found that four studied SNPs could be associated with a decreased level of uric acid of seminal plasma in teratozoospermia and asthenozoospermia. Bioinformatic analysis revealed that the mentioned polymorphisms could affect molecular aspects of SLC2A9 and ABCG2 genes. In this preliminary study, the rs16890979, rs3733591, rs2231142, and rs2231137 genetic variations could be considered as genetic risk factors for male infertility by interfering with the uric acid level of seminal plasma.

Prominent genetic variants and epigenetic changes in post-traumatic stress disorder among combat veterans

Post-traumatic stress disorder (PTSD) is one of the most widespread and disabling psychiatric disorders among combat veterans. Substantial interindividual variability in susceptibility to PTSD suggests the presence of different risk factors for this disorder. Twin and family studies confirm genetic factors as important risk factors for PTSD. In addition to genetic factors, epigenetic factors, especially DNA methylation, can be considered as a potential mechanism in changing the risk of PTSD. So far, many genetic and epigenetic association studies have been conducted in relation to PTSD. In genetic studies, many single nucleotide polymorphisms have been identified as PTSD risk factors. Meanwhile, the variations in catecholamines-related genes, serotonin transporter and receptors, brain-derived neurotrophic factor, inflammatory factors, and apolipoprotein E are the most prominent candidates. CpG methylation in the upstream regions of many genes is also considered a PTSD risk factor. Accurate identification of genetic and epigenetic changes associated with PTSD can lead to the presentation of suitable biomarkers for susceptible individuals to this disorder. This study aimed to delineate prominent genetic variations and epigenetic changes associated with post-traumatic stress disorder in military veterans who have experienced combat, focusing on genetic and epigenetic association studies.

Identification of Important Genes Associated with the Development of Atherosclerosis

Atherosclerosis is one of the most important medical problems due to its prevalence and significant contribution to the structure of temporary and permanent disability and mortality. Atherosclerosis is a complex chain of events occurring in the vascular wall over many years. Disorders of lipid metabolism, inflammation, and impaired hemodynamics are important mechanisms of atherogenesis. A growing body of evidence strengthens the understanding of the role of genetic and epigenetic factors in individual predisposition and development of atherosclerosis and its clinical outcomes. In addition, hemodynamic changes, lipid metabolism abnormalities, and inflammation are closely related and have many overlapping links in regulation. A better study of these mechanisms may improve the quality of diagnosis and management of such patients.

The eNOS-G894T genetic polymorphism and risk of preeclampsia: A case-control study, an updated meta-analysis, and a bioinformatic assay

OBJECTIVES

Preeclampsia (PE) is a leading cause of maternal death worldwide and involves vascular endothelial dysfunction. The aim of this study was to investigate the association of the G894T polymorphism in the endothelial nitric oxide synthase (eNOS) gene and the risk of preeclampsia in a case-control design in an Iranian population, which was followed by a meta-analysis and an in silico approach.

METHODS

In the case-control study, 300 people including 135 pregnant women with preeclampsia and 165 healthy pregnant women were included. The genotype of G894T polymorphism was determined by the PCR-RFLP method. We searched authoritative scientific databases to find eligible studies for meta-analysis. The odds ratio with a 95% confidence interval was estimated to find the strength of the association of the mentioned polymorphism with the risk of preeclampsia. In addition, the effect of G894T transversion on eNOS gene function was evaluated by some bioinformatics tools.

RESULTS

Our case-control data showed that the G894T polymorphism is associated with an increased risk of preeclampsia. In the meta-analysis, 33 eligible studies were included, and the results showed that the G894T polymorphism is associated with an increased risk of preeclampsia in the overall analysis and some stratified analyses. In addition, the structural analysis showed that the G894T variant can affect the splicing process as well as the protein stability.

CONCLUSIONS

Based on the results, the aforementioned polymorphism may be a risk factor for preeclampsia and could be considered a potential molecular biomarker for screening susceptible individuals.

Administration of stem cells against cardiovascular diseases with a focus on molecular mechanisms: Current knowledge and prospects

Cardiovascular diseases (CVDs) are a serious global concern for public and human health. Despite the emergence of significant therapeutic advances, it is still the leading cause of death and disability worldwide. As a result, extensive efforts are underway to develop practical therapeutic approaches. Stem cell-based therapies could be considered a promising strategy for the treatment of CVDs. The efficacy of stem cell-based therapeutic approaches is demonstrated through recent laboratory and clinical studies due to their inherent regenerative properties, proliferative nature, and their capacity to differentiate into different cells such as cardiomyocytes. These properties could improve cardiovascular functioning leading to heart regeneration. The two most common types of stem cells with the potential to cure heart diseases are induced pluripotent stem cells (iPSCs) and mesenchymal stem cells (MSCs). Several studies have demonstrated the use, efficacy, and safety of MSC and iPSCs-based therapies for the treatment of CVDs. In this study, we explain the application of stem cells, especially iPSCs and MSCs, in the treatment of CVDs with a focus on cellular and molecular mechanisms and then discuss the advantages, disadvantages, and perspectives of using this technology in the treatment of these diseases.

Molecular mechanisms involved in anosmia induced by SARS-CoV-2, with a focus on the transmembrane serine protease TMPRSS2

Since 2020, SARS-CoV-2 has caused a pandemic virus that has posed many challenges worldwide. Infection with this virus can result in a number of symptoms, one of which is anosmia. Olfactory dysfunction can be a temporary or long-term viral complication caused by a disorder of the olfactory neuroepithelium. Processes such as inflammation, apoptosis, and neuronal damage are involved in the development of SARS-CoV-2-induced anosmia. One of the receptors that play a key role in the entry of SARS-CoV-2 into the host cell is the transmembrane serine protease TMPRSS2, which facilitates this process by cleaving the viral S protein. The gene encoding TMPRSS2 is located on chromosome 21. It contains 15 exons and has many genetic variations, some of which increase the risk of disease. Delta strains have been shown to be more dependent on TMPRSS2 for cell entry than Omicron strains. Blockade of this receptor by serine protease inhibitors such as camostat and nafamostat can be helpful for treating SARS-CoV-2 symptoms, including anosmia. Proper understanding of the different functional aspects of this serine protease can help to overcome the therapeutic challenges of SARS-CoV-2 symptoms, including anosmia. In this review, we describe the cellular and molecular events involved in anosmia induced by SARS-CoV-2 with a focus on the function of the TMPRSS2 receptor.

Genetic and Epigenetic Regulation of Lipoxygenase Pathways and Reverse Cholesterol Transport in Atherogenesis

Atherosclerosis is one of the most important medical and social problems of modern society. Atherosclerosis causes a large number of hospitalizations, disability, and mortality. A considerable amount of evidence suggests that inflammation is one of the key links in the pathogenesis of atherosclerosis. Inflammation in the vascular wall has extensive cross-linkages with lipid metabolism, and lipid mediators act as a central link in the regulation of inflammation in the vascular wall. Data on the role of genetics and epigenetic factors in the development of atherosclerosis are of great interest. A growing body of evidence is strengthening the understanding of the significance of gene polymorphism, as well as gene expression dysregulation involved in cross-links between lipid metabolism and the innate immune system. A better understanding of the genetic basis and molecular mechanisms of disease pathogenesis is an important step towards solving the problems of its early diagnosis and treatment.

A common genetic variation in paraoxonase 1 and risk of breast cancer: a literature review, meta-analysis, and in silico analysis

Paraoxonase 1 (PON1), an enzyme with multifactorial antioxidant activity, has a protective role against oxidative stress, which is supposed to contribute to the development of cancers including breast cancer. The aim of this study was to examine the correlation of PON1-L55M common genetic polymorphism with the risk of breast cancer in a meta-analysis approach which was followed by an in silico analysis. The eligible studies were collected from valid electronic databases such as Google Scholar, PubMed, Embase, and Web of Science. Quantitative synthesis was performed to report the strength of PON1-L55M polymorphism with breast cancer. Some bioinformatics tools were used to analyze the effects of L55M variation on PON1 gene function. The meta-analysis revealed that there are significant associations between the mentioned polymorphism and breast cancer in M vs. L, MM vs. LL, LM vs. LL, MM + LM vs. LL, and MM vs. LL + LM genetic models. Besides, similar results were observed in the stratified analyses based on ethnicity, genotyping method, Hardy-Weinberg equilibrium in control groups, and sample size. Bioinformatics analysis revealed that the PON1 could be damaging to the protein function. Our findings propose that the PON1-L55M genetic polymorphism might be a genetic risk factor for the risk of breast cancer.

Assessment of genetic polymorphism associated with ATP-binding cassette transporter A1 (ABCA1) gene and fluctuations in serum lipid profile levels in patients with coronary artery disease

Background

Coronary artery disease (CAD) is one of the common genetic and clinical risk factors associated with cardiovascular and multifactorial disorder. ATP-binding cassette transporter A1 (ABCA1) gene plays an important role in lipid metabolism and in multiple studies associated with CAD. However, more studies are needed to identify the exact role of single nucleotide polymorphisms which may cause CAD.

Objectives

The aim of this study is to investigate the genetic association of polymorphism g.1051G > A in the ABCA1 gene with CAD patients in the Saudi population.

Methods

We included 315 confirmed CAD cases, and 205 non-CAD or control subjects in this case-control study. DNA isolation was carried out for all registered participants and the polymorphism g.1051G > A was genotyped with Polymerase Chain Reaction followed by Restriction Fragment Length Polymorphism analysis with EcoNI restriction enzyme.

Results

Modifiable risk factors such as Body Mass Index, smoking and diabetes were strongly associated and non-modifiable risk factors such as hypertension (Systolic Blood Pressure and Diastolic Blood Pressure) and serum analysis such as Fasting Blood Glucose, Total cholesterol (TC), Triglyceride (TG) and LDL-c were significantly associated in CAD cases (p < 0.05). Allele (OR-1.73;95% CI:1.33–2.26; p = 0.0004), GA vs GG (OR-2.26; 95% CI: 1.53–3.35; p = 0.0003 and dominant inheritance pattern (OR-2.23; 95% CI:1.56–3.20; p = 0.00009 was strongly associated with CAD cases and control subjects. The frequency level of use of atorvastatin was significantly different among GG, GA and AA subjects. Additionally, TC and TG levels were influenced by the presence of g.1051G > A polymorphism.

Conclusion

The polymorphism g.1051G > A in the gene ABCA1 is closely associated with the existence of the CAD subjects. This polymorphism could also affect the serum levels of the lipid profile, suggesting a possible occurrence of CAD in the Saudi population.

Feature, Function, and Information of Drug Transporter-Related Databases

With the rapid progress in pharmaceutical experiments and clinical investigations, extensive knowledge of drug transporters (DTs) has accumulated, which is valuable data for the understanding of drug metabolism and disposition. However, such data are largely dispersed in the literature, which hampers its utility and significantly limits its possibility for comprehensive analysis. A variety of databases have, therefore, been constructed to provide DT-related data, and they were reviewed in this study. First, several knowledge bases providing data regarding clinically important drugs and their corresponding transporters were discussed, which constituted the most important resources of DT-centered data. Second, some databases describing the general transporters and their functional families were reviewed. Third, various databases offering transporter information as part of their entire data collection were described. Finally, customized database functions that are available to facilitate DT-related research were discussed. This review provided an overview of the whole collection of DT-related databases, which might facilitate research on precision medicine and rational drug use. SIGNIFICANCE STATEMENT: A collection of well established databases related to drug transporters were comprehensively reviewed, which were organized according to their importance in drug absorption, distribution, metabolism, and excretion research. These databases could collectively contribute to the research on rational drug use.

Association between the ABCA1 (R219K) polymorphism and lipid profiles: a meta-analysis

Conflicting evidence was found about the relationship between lipid profiles and R219K polymorphism in adenosine triphosphate-binding cassette exporter A1 (ABCA1) gene. In this study, four meta-analyses were conducted to assess the effect of R219K on lipid levels, including high-density lipoprotein cholesterol (HDLC), low-density lipoprotein cholesterol, total cholesterol, and triglycerides (TG). A total of 125 samples of 87 studies (about 60,262 subjects) were included. The effect of each study was expressed using the standard mean difference (SMD) and 95% confidence interval (95% CI) and pooled by meta-analysis in the random-effects model. Subgroup and meta-regression analyses were conducted to explore potential heterogeneity sources. The overall pooled effect showed the following results. (1) The R219K was significantly associated with HDLC level (SMD = - 0.25 mmol/L, 95%CI - 0.32 to - 0.18, z = - 6.96, P < 0.01, recessive genetic model). People with different genotypes had significantly different HDLC levels under the recessive, codominant and dominant genetic models (all Ps < 0.01). (2) A weak and indeterminate relationship between R219K and TG level was observed (SMD = 0.18 mmol/L, 95%CI 0.06-0.30, z = 3.01, P < 0.01, recessive genetic model). These findings suggested that R219K was associated with HDLC and TG levels, which might implicate a promising clinical application for lipid-related disorders, though the influences of race, health status, BMI, and other heterogeneity sources should be considered when interpreting current findings. The protocol was registered at PROSPERO (registration number: CRD42021231178).

Genetic variations as molecular diagnostic factors for idiopathic male infertility: current knowledge and future perspectives

INTRODUCTION

Infertility is a major health problem, worldwide, which affects 10-15% of couples. About half a percent of infertility cases are related to male-related factors. Male infertility is a complex disease that is the result of various insults as lifestyle issues, genetics, and epigenetic factors. Idiopathic infertility is responsible for 30% of total cases. The genetic factors responsible for male infertility include chromosomal abnormalities, deletions of chromosome Y, and mutations and genetic variations of key genes.

AREAS COVERED

In this review article, we aim to narrate performed studies on polymorphisms of essential genes involved in male infertility including folate metabolizing genes, oxidative stress-related genes, inflammation, and cellular pathways related to spermatogenesis. Moreover, possible pathophysiologic mechanisms responsible for genetic polymorphisms are discussed.

EXPERT OPINION

Analysis and assessment of these genetic variations could help in screening, diagnosis, and treatment of idiopathic male infertility.

Novel associations of SNPs MYLIP rs3757354 and ABCA1 2230806 gene with early-onset-preeclampsia: A case-control candidate genetic study

OBJECTIVE

To investigate the association between MYLIP rs3757354 and ABCA1 2230806 single nucleotide polymorphisms in women with preeclampsia in China.

STUDY DESIGN

The case-control study involved 205 patients with preeclampsia and 145 controls. All women with preeclampsia were divided into two groups: 78 patients with early-onset preeclampsia and 127 with late-onset preeclampsia.

MAIN OUTCOME MEASURE

MYLIP rs3757354 and ABCA1 rs2230806 SNPs were analyzed through multiplex PCR for targeted next-generation sequencing technology. A secondary outcome was lipid profile changes and liver function in women with PE.

RESULTS

Maternal age (OR: 1.073, 95% CI = 1.006-1.145), BMI (OR: 1.118, 95% CI = 1.040-1.201), TG/HDL-C (OR: 1.536, 95% CI = 1.080-2.183), and TT genotype of SNP rs3757354 (OR: 3.238, 95% CI = 1.313-7.990) were associated with EOPE risk. Our study found that patients with TT genotype of ABCA1 rs2230806 had more severe hepatic dysfunction and higher HDL levels in the EOPE group compared with CC/CT genotype. There was no association between rs2230806 and the risk of PE.

CONCLUSION

The polymorphisms of rs3757354 are associated with the risk of EOPE in Chinese pregnant women. The TT genotype in ABCA1 rs2230806 is a strong predictive risk for elevated aminotransferase levels in pregnant women with EOPE.

CYP1A1 and GSTs common gene variations and presbycusis risk: a genetic association analysis and a bioinformatics approach

Antioxidant enzymes such as glutathione S-transferases (GSTs) and cytochromes P450 (CYPs) are involved in the metabolism and detoxification of cytotoxic compounds, as well as the elimination of reactive oxygen species (ROS). Therefore, alterations in the structure of these enzymes could result in prolonged production of ROS with subsequent risk of development of disorders such as presbycusis. This study aimed to investigate the association between CYP1A1 (rs4646903, rs1048943) and GSTs (GSTM1-deletion, GSTT1-deletion, GSTP1-rs1695) with presbycusis risk in an Iranian population which was followed by an in silico approach. In a case-control study, 280 subjects including 140 cases with presbycusis and 140 healthy controls were enrolled. Genotypes of single-nucleotide polymorphisms (SNPs) were detected by PCR-RFLP method and the genotype of the above mentioned deletions was determined by touchdown PCR. Some bioinformatics tools were employed to evaluate the impact of SNPs on the gene function. SNP analysis revealed that there are significant associations between rs1048943 (AG vs. AA: OR = 2.46, 95%CI = 1.30-4.65, p = 0.006; GG + AG vs. AA: OR = 2.53, 95%CI = 1.36-4.69, p = 0.003; G vs. A: OR = 2.36, 95%CI = 1.33-4.17, p = 0.003) and rs4646903 (C vs. T: OR = 1.45, 95%CI = 1.02-2.06, p = 0.040) variations and increased risk of presbycusis. However, there was no significant association between rs1695 and presbycusis risk. Also, significant associations were observed between GSTM1 (OR = 4.28, 95%CI = 1.18-15.52, p = 0.027) and GSTT1 (OR = 1.64, 95%CI = 1.02-2.65, p = 0.041) deletions and elevated risk of presbycusis. Moreover, the combination analysis revealed a significant association between GSTM1+/GSTT1- genotype and presbycusis susceptibility (OR = 1.63, 95%CI = 1.00-2.67, p = 0.049). In silico analysis revealed that the rs1048943 SNP could influence significantly on the RNA structure of CYP1A1 (distance: 0.1454; p value: 0.1799). Based on our findings, the rs4646903, rs1048943 SNPs as well as GSTM1 and GSTT1 deletions could be considered as genetic risk factors for the development and progression of presbycusis.

Association Analysis of Methylenetetrahydrofolate Reductase Common Gene Polymorphisms with Breast Cancer Risk in an Iranian Population: A Case-Control Study and a Stratified Analysis

Genetic polymorphisms in the methylenetetrahydrofolate reductase (MTHFR) gene may alter the risk of breast cancer. This study aimed to investigate the association of MTHFR C677T and A1298C genetic polymorphisms with breast cancer risk in case-control studies which was followed by stratified analysis. In the case-control study, 300 subjects including 150 women with breast cancer and 150 healthy women were enrolled. After blood sample collection, the C677T and A1298C polymorphisms genotyping were done by the PCR-RFLP method. Our data revealed a significant association between MTHFR C677T and A1298C polymorphisms and breast cancer risk. But, as a preliminary study, stratified analysis revealed no significant association between C677T and A1298C polymorphisms and tumor size and also lymph node metastasis in breast cancer. According to the mentioned findings, the C677T and A1298C polymorphisms in the MTHFR gene could be molecular risk factors for breast cancer in our studied population. However, further studies with larger sample sizes are required to obtain a more accurate conclusion in stratified analysis.

Association of ApaI and TaqI polymorphisms in VDR Gene with Breast Cancer

Background:

Vitamin D inhibits cell proliferation via the vitamin D receptor (VDR), which may affect breast cancer risk. This study aimed to investigate the association of ApaI and TaqI polymorphisms of the VDR gene with breast cancer risk which followed by stratified analysis.

Materials and methods:

A case-control study was conducted on 150 breast cancer patients and 150 healthy controls. VDR ApaI and TaqI genotyping were performed by PCR-RFLP. Some demographic and pathologic features of patients were extracted from their archived files and then were analyzed by genotypes distributions.

Results:

For ApaI polymorphism, our data showed a significant difference between the patient and healthy groups for mutant allele carriers compared with those with AA genotype. Besides, statistical analysis showed that there was a significant association between the C allele and the increased risk of breast cancer. For TaqI polymorphism, statistical analysis revealed that there was a significant association between CC genotype and increased risk of breast cancer. Also, there was a significant association between the C allele and the increased risk of breast cancer. In a preliminary study, stratified analysis based on the size of tumor and lymph node metastasis revealed no significant association between two ApaI and TaqI variations and these parameters.

Conclusions:

Based on our results, the VDRApaI and TaqI variations could be considered as genetic risk factors for breast cancer. However, further studies with a larger sample size are required to obtain more accurate outcomes, especially in stratified analysis.