Single Nucleotide Polymorphisms In Genes Research Articles

Estrogen Receptor 1 Gene Polymorphism and its Association with Idiopathic Short Stature in a North Indian Population

In the hypothalamic-pituitary-gonadotrophin axis, estrogen plays a key role in the regulation of bone maturation and growth plate closure. This study was designed to explore the link between single nucleotide polymorphisms (SNPs) in the estrogen receptor 1 (ESR1) gene with idiopathic short stature (ISS) susceptibility in a North Indian population. Four SNPs of ESR1 (rs543650, rs6557177, rs2234693 and rs9340799) were genotyped by Sanger sequencing in ISS patients and controls. Linkage disequilibrium (LD) and haplotyping were done by SNPStat and SHEsisPlus software. The extent of LD was determined by calculating D’ and R2 values in SNP paired combinations. Fifty-two ISS patients were compared with 68 controls. A significant positive association was found between rs6557177 and rs543650 genotype and ISS susceptibility. The frequencies of the rs6557177 CC genotype [p=0.030; odds ratio (OR)=0.13; 95% confidence interval (CI): 0.01-1.10] and rs543650 genotype TT (p=0.043; OR=0.29; 95% CI: 0.09-0.92) were increased in the ISS group compared with controls. However, no significant correlation was observed between clinical parameters of patients and these SNPs. rs543650 showed strong LD with rs2234693 and rs9340799, similarly rs2234693 and rs9340799. Our study showed that the CC genotype at rs6557177 and TT genotype at rs543650 of ESR1 constituted a risk factor for developing ISS in North Indian children. These findings may lead to a better understanding of the SNPs associated with ISS susceptibility.

Machine learning-based prediction of rheumatoid arthritis with development of ACPA autoantibodies in the presence of non-HLA genes polymorphisms.

Machine learning (ML) algorithms can handle complex genomic data and identify predictive patterns that may not be apparent through traditional statistical methods. They become popular tools for medical applications including prediction, diagnosis or treatment of complex diseases like rheumatoid arthritis (RA). RA is an autoimmune disease in which genetic factors play a major role. Among the most important genetic factors predisposing to the development of this disease and serving as genetic markers are HLA-DRB and non-HLA genes single nucleotide polymorphisms (SNPs). Another marker of RA is the presence of anticitrullinated peptide antibodies (ACPA) which is correlated with severity of RA. We use genetic data of SNPs in four non-HLA genes (PTPN22, STAT4, TRAF1, CD40 and PADI4) to predict the occurrence of ACPA positive RA in the Polish population. This work is a comprehensive comparative analysis, wherein we assess and juxtapose various ML classifiers. Our evaluation encompasses a range of models, including logistic regression, k-nearest neighbors, naïve Bayes, decision tree, boosted trees, multilayer perceptron, and support vector machines. The top-performing models demonstrated closely matched levels of accuracy, each distinguished by its particular strengths. Among these, we highly recommend the use of a decision tree as the foremost choice, given its exceptional performance and interpretability. The sensitivity and specificity of the ML models is about 70% that are satisfying. In addition, we introduce a novel feature importance estimation method characterized by its transparent interpretability and global optimality. This method allows us to thoroughly explore all conceivable combinations of polymorphisms, enabling us to pinpoint those possessing the highest predictive power. Taken together, these findings suggest that non-HLA SNPs allow to determine the group of individuals more prone to develop RA rheumatoid arthritis and further implement more precise preventive approach.

Abstract 6130: Association of vitamin D-related genetic variants and prostate cancer risk in Black men

Abstract Background: What we know of the relationship between vitamin D status and prostate cancer has largely been characterized among men of European ancestry, hereafter referred to as “White”. Research among White men indicate positive associations between circulating vitamin D status, as measured by concentrations of 25-hydroxyvitamin D (25(OH)D), with prostate cancer risk, and that genetic scores based on genome-wide associated single nucleotide polymorphisms (SNPs) reflecting high vs. low 25(OHD) is positively associated with aggressive disease. Limited research exists elucidating this relationship among men of African ancestry, hereafter referred to as “Black”. This is despite the fact that Black populations experience chronically lower circulating 25(OH)D, and ancestry-specific differences in genetic variants in some vitamin D-related genes. Given the paucity of research in this area, we examined the role of genetic variants in six commonly studied genes in the vitamin D pathway involved in synthesis (CYP27A1 and CYP27B1), transport (GC), activity (VDR and RXR), and metabolism (CYP24A1) in relation to prostate cancer among Black men. Methods: We assessed a total of 78 candidate SNPs in six vitamin D pathway genes that were either previously associated with circulating 25(OHD) and/or associated with prostate cancer risk in studies of White men. We compared vitamin D gene SNP associations with prostate cancer in Black and White men using summary statistics from a large GWAS of over 10,000 prostate cancer cases and 10,000 controls among Black men and over 85,000 cases and 91,000 controls among White men. A statistical significance threshold of 0.00064 (0.05/78 candidate SNPs) was used to adjust for multiple comparisons. Results: None of the examined SNPs were significantly associated with prostate cancer risk among Black men after adjustment for multiple comparisons. However, four SNPs were nominally significant in Black men, including two in RXR [rs41400444 OR=1.09, 95% CI: 1.01-1.17, P = 0.024 and rs10881574 OR = 0.93, 0.867-0.999, P = 0.04556] and two in VDR [rs2853563 OR = 1.07, 1.012-1.13, P = 0.0173 and rs1156882 OR = 1.06, 1.00-1.12, P = 0.0495]. The latter SNP rs1156882 was also positively associated with prostate cancer risk in White men (OR = 1.035, 1.02-1.06, P = 0.00024), along with VDR SNP rs4516035 (OR = 1.027, 1.012-1.042, P = 0.00055), both after correction for multiple comparisons. Conclusions: We observed non-significant, though suggestive, associations between genetic variants in vitamin D pathway genes previously associated with prostate cancer or vitamin D levels in White populations and prostate cancer risk in Black men. Future research exploring the potential role of vitamin D pathway genes and prostate cancer in Black men – a population at high risk both for low circulating vitamin D and prostate cancer - will need to identify vitamin D-related genetic variants specific to carcinogenesis in Black men. Citation Format: Tracy M. Layne, Joseph H. Rothstein, Xiaoyu Song, Weiva Sieh, Robert J. Klein. Association of vitamin D-related genetic variants and prostate cancer risk in Black men [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6130.

Variación molecular de genes asociados a lipoxigenasas en grano de variedades de soya comercial mexicana

Lipoxygenase enzymes encoded by the Lox1, Lox2 and Lox3 genes play a crucial role in soybean grain, particularly in the development of off-flavors. Understanding molecular variation within Lox genes is essential for the improvement of soybean organoleptic traits. This study investigated the genetic variation in the internal regions of the Lox1, Lox2, and Lox3 genes in mature grain of commercially grown soybean cultivars in Mexico. Genomic DNA from a diverse panel of Mexican soybean cultivars was analyzed using resequencing techniques and in-silico analysis. Single nucleotide polymorphisms (SNP) within the Lox1, Lox2, and Lox3 genes were identified and characterized. The findings indicated that Lox3 gene displayed lower genetic variability compared to Lox1 and Lox2 genes, specifically, was identified a total of 26 SNPs in the Lox1 gene, 11 SNPs in the Lox2 gene, and 5 SNPs in the Lox3 gene among the examined cultivars. A non-synonymous SNP variant of the C/C genotype located in exon 6 of the Lox2 gene was associated with a destabilizing effect on the lipoxygenase 2 enzyme in the Guayparime S-10 and Huasteca 300 cultivars. These findings provide insights into the molecular variation of lipoxygenase-associated genes in Mexican soybean cultivars.

Protective Role of TRPC3 Gene Polymorphism (rs10518289) in Obstructive Sleep Apnea Hypopnea Syndrome Among Hypertensive Patients.

BACKGROUND Obstructive sleep apnea-hypopnea syndrome (OSAHS) presents a significant health concern, particularly among individuals with essential hypertension (EH). Understanding the genetic underpinnings of this association is crucial for effective management and intervention. We investigated the relationship between TRPC3 gene polymorphisms and susceptibility to OSAHS in patients with EH. MATERIAL AND METHODS We enrolled 373 patients with EH hospitalized at the First Affiliated Hospital of Xinjiang Medical University between April 2015 and November 2017. Patients were categorized into EH (n=74) and EH+OSAHS (n=299) groups according to the apnea-hypopnea index. Sequenom detection technology was used for TRPC3 gene single-nucleotide polymorphism genotyping, including genotypes at rs953691, rs10518289, rs2292232, rs4995894, rs951974, and rs4292355. RESULTS Sex, smoking history, alcohol history, hypertension duration, fasting blood glucose, urea, creatinine, total cholesterol, HDL-C, LDL-C, glycosylated hemoglobin, 24-h mean systolic BP, and 24-h mean diastolic BP were not significantly different between the 2 groups (P>0.05); however, age, BMI, triglyceride levels differed significantly (P<0.05). No significant difference was detected in distribution frequency of polymorphisms of TRPC3 gene between the 2 groups (P>0.05), while genotype, dominant genotype, and recessive genotype at rs10518289 and alleles at rs4292355 differed significantly (P<0.05). Logistic regression analysis showed age, BMI, and CG+GG genotypes at rs10518289 were risk factors for OSAHS in patients with EH. Interaction between TRPC3 (rs10518289) and obesity was not a risk of OSAHS with EH (P>0.05). CONCLUSIONS CC genotype of rs10518289 in the TRPC3 gene could be a protective genetic marker of OSAHS, and CG+GG genotype may be a risk genetic marker of OSAHS with EH.

Effects of pharmacogenetics on pharmacokinetics and toxicity of doxorubicin in Egyptian breast cancer patients

This study investigates the impact of single nucleotide polymorphisms in genes (SLC22A16 and CBR1) involved in the pharmacokinetics and toxicity of doxorubicin (DOX) in Egyptian female patients with breast cancer. Patients administered DOX (60 mg/m2) for 4 cycles every 3 weeks. The peak DOX plasma concentration was measured using a validated chromatographic method. The genotyping for the selected SNPs, SLC22A16 T > C (rs714368), and CBR1 C > T (rs20572), was performed by RT-PCR. Patients were monitored for hematological and cardiac toxicities. The variant carriers of CBR1 C > T (rs20572) exhibited significantly higher DOX concentration, but no significant association to DOX-induced hematological toxicity. On the other hand, SLC22A16 T > C (rs714368) had no significant influence on DOX plasma concentration, but was significantly correlated with lower risk of neutropenia (OR 0.31, 95% CI 0.12–0.75, p = 0.01) and leukopoenia (OR 0.18, 95% CI 0.07–0.5, p = 0.001). DOX-related cardiotoxicity was correlated with the cumulative dose of DOX (R = 0.238, p = 0.017), but not with any of the two examined SNPs. Genetic polymorphisms in SLC22A16 and CBR1 may explain the inter-individual variations in DOX pharmacokinetics and toxicity. Using pharmacogenetic testing is important to customise drug therapy for cancer patients treated with anthracyclines.

Effect of weekly vitamin D supplementation on the severity of atopic dermatitis and type 2 immunity biomarkers in children: A randomized controlled trial.

Vitamin D (VD) deficiency is common among patients with atopic dermatitis (AD) and often associated with severity. However, randomized trials of VD supplementation in AD have had equivocal results, and there is little information regarding the effect of VD supplementation on type 2 immunity in AD patients. To investigate the efficacy of VD supplementation to decrease severity of AD and to alter type 2 immunity biomarkers. We performed a randomized, double-blind, placebo-controlled trial. We randomly assigned 101 children with AD to weekly oral vitamin D3 (VD3) or placebo for 6 weeks. The primary outcome was the change in the Severity Scoring of AD (SCORAD). Mean age of subjects was 6.3 ± 4.0 years, and baseline SCORAD was 32 ± 29. At baseline, 57% of children were VD deficient, with no difference between groups. Change in 25(OH)D was significantly greater with VD3 than placebo (+43.4 ± 34.5 nmol/L vs. +2.3 ± 21.2 nmol/L, p < 0.001). SCORAD change at 6 weeks was not different between VD and placebo (-5.3 ± 11.6 vs. -5.5 ± 9.9, p = 0.91). There were no significant between-group differences in change of eosinophil counts, total IgE, Staphylococcal enterotoxin specific IgE, CCL17, CCL22, CCL27, LL-37 or Staphylococcus aureus lesional skin colonization. Vitamin D receptor (VDR) gene single nucleotide polymorphisms FokI, ApaI and TaqI did not modify subjects' response to VD supplementation. Among children with AD, weekly VD supplementation improved VD status but did not modify AD severity or type 2 immunity biomarkers compared to placebo (ClinicalTrials.gov NCT01996423).

Gene Polymorphisms of NLRP3 Associated With Plasma Levels of 4β-Hydroxycholesterol, an Endogenous Marker of CYP3A Activity, in Patients With Asthma.

Inflammation decreases the activity of cytochrome P450 3A (CYP3A). Nucleotide-binding oligomerization domain (NOD)-like receptor family pyrin domain containing 3 (NLRP3) is responsible for regulating the inflammatory response, and its genetic polymorphisms have been linked to inflammatory diseases such as asthma. However, there have been few studies on the effect of NLRP3 on CYP3A activity. We aimed to investigate the association between polymorphisms in the NLRP3 gene and plasma 4β-hydroxycholesterol (4βOHC), an endogenous marker of CYP3A activity, in patients with asthma. In this observational study including 152 adult asthma patients, we analyzed 10 NLRP3 gene single-nucleotide polymorphisms (SNPs). Plasma 4βOHC levels were measured by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The results showed that five SNPs were associated with significantly lower plasma 4βOHC concentrations. Among these SNPs, rs3806265, rs4612666, rs1539019, and rs10733112 contributed to a significant increase in plasma IL-6 concentrations. Moreover, a multivariate regression model showed that the rs3806265 TT, rs4612666 CC, rs1539019 AA, and rs10733112 TT genotypes were significant factors for decreased plasma 4βOHC, even after including patient background factors and CYP3A5*3 (rs776746) gene polymorphisms as covariates. These results were also observed when plasma 4βOHC concentrations were corrected for cholesterol levels. We conclude that NLRP3 gene polymorphisms are involved in increasing plasma IL-6 concentrations and decreasing plasma 4βOHC concentrations in patients with asthma. Therefore, NLRP3 gene polymorphisms may be a predictive marker of CYP3A activity in inflammatory diseases such as asthma.

Predicting early Alzheimer’s with blood biomarkers and clinical features

Alzheimer’s disease (AD) is an incurable neurodegenerative disorder that leads to dementia. This study employs explainable machine learning models to detect dementia cases using blood gene expression, single nucleotide polymorphisms (SNPs), and clinical data from Alzheimer’s Disease Neuroimaging Initiative (ADNI). Analyzing 623 ADNI participants, we found that the Support Vector Machine classifier with Mutual Information (MI) feature selection, trained on all three data modalities, achieved exceptional performance (accuracy = 0.95, AUC = 0.94). When using gene expression and SNP data separately, we achieved very good performance (AUC = 0.65, AUC = 0.63, respectively). Using SHapley Additive exPlanations (SHAP), we identified significant features, potentially serving as AD biomarkers. Notably, genetic-based biomarkers linked to axon myelination and synaptic vesicle membrane formation could aid early AD detection. In summary, this genetic-based biomarker approach, integrating machine learning and SHAP, shows promise for precise AD diagnosis, biomarker discovery, and offers novel insights for understanding and treating the disease. This approach addresses the challenges of accurate AD diagnosis, which is crucial given the complexities associated with the disease and the need for non-invasive diagnostic methods.

Influence of arsenic exposure and TGF-β gene single nucleotide polymorphisms (gene-environment interaction) on cardiovascular risk biomarkers levels in Mexican people from San Luis Potosi, Mexico

Influence of arsenic exposure and TGF-β gene single nucleotide polymorphisms (gene-environment interaction) on cardiovascular risk biomarkers levels in Mexican people from San Luis Potosi, Mexico

The impact of XPC gene single nucleotide polymorphism rs2228001 on head and neck cancer patients' response to radiotherapy treatment.

Head and neck squamous carcinoma (HNSC) is the sixth most common neoplasm, with a 40-50% overall survival rate. HNSC standard treatment depends on tumor size, metastasis or human papillomavirus (HPV) status including surgery, chemotherapy, and radiotherapy. The last two may lead to defects in the tumor microenvironment and cancer cell biology as disorders in DNA damage repair systems. Here, we evaluate the correlation between single nucleotide polymorphism (SNP) rs2228001 in the XPC gene with the early and late adverse effects of radiotherapy, determine the distribution of the SNP and post-treatment follow-up in HNSC patients. Head and neck cancer tissues and clinical data were obtained from 79 patients. The SNP of the XPC gene (rs2228001) was evaluated with polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP). The chi-square test was used to determine the correlation between mutation and adverse effects occurrence. Single nucleotide polymorphism rs2228001 in the XPC gene is correlated with the early adverse effect of skin reaction and the late adverse effect of elevated C-reactive protein (CRP) levels in the HNSC patients.

Single-Nucleotide Polymorphisms of Growth Hormone Gene and Its Relationship with Growth Traits in Black Bengal Goats.

The single-nucleotide polymorphisms (SNPs) of the growth hormone (GH) gene could be related to growth traits, particularly in farm animals. This study aimed to identify the SNPs of the GH gene (A781G and A1575G) in Black Bengal (BB) goats in Thailand. Seventy-seven BB goats of both sexes were recruited, and their genotypes were identified. Preweaning growth at birth (weight, W0; height, H0; length, L0; and chest girth, C0) and at 10 weeks postpartum (W10, H10, L10, and C10), including average daily gain (ADG) at 0-4 weeks (ADG0-4W), 4-8 weeks (ADG4-8W), and 8-12 weeks (ADG8-12W), was compared among the different genotypes in goats born from twin litter-size dams. The results showed one genotype, CC, for A1575G and three genotypes, AA, AB, and BB, for A781G. The AA gene had significantly higher W10 than AB (p < 0.05) and BB (p < 0.05). The AA had significantly higher L10 than AB (p < 0.05), while C10 was only higher in male goats (p < 0.01). The ADG4-8W of the AA genotype was significantly higher than the BB genotype (p < 0.01). We came to the conclusion that A781G is associated with growth traits during the preweaning period, while the AA genotype showed better performance than the other genotypes.

Iron-related gene mutations driving global Mycobacterium tuberculosis transmission revealed by whole-genome sequencing

BackgroundIron plays a crucial role in the growth of Mycobacterium tuberculosis (M. tuberculosis). However, the precise regulatory mechanism governing this system requires further elucidation. Additionally, limited studies have examined the impact of gene mutations related to iron on the transmission of M. tuberculosis globally. This research aims to investigate the correlation between mutations in iron-related genes and the worldwide transmission of M. tuberculosis.ResultsA total of 13,532 isolates of M. tuberculosis were included in this study. Among them, 6,104 (45.11%) were identified as genomic clustered isolates, while 8,395 (62.04%) were classified as genomic clade isolates. Our results showed that a total of 12 single nucleotide polymorphisms (SNPs) showed a positive correlation with clustering, such as Rv1469 (ctpD, C758T), Rv3703c (etgB, G1122T), and Rv3743c (ctpJ, G676C). Additionally, seven SNPs, including Rv0104 (T167G, T478G), Rv0211 (pckA, A302C), Rv0283 (eccB3, C423T), Rv1436 (gap, G654T), ctpD C758T, and etgB C578A, demonstrated a positive correlation with transmission clades across different countries. Notably, our findings highlighted the positive association of Rv0104 T167G, pckA A302C, eccB3 C423T, ctpD C758T, and etgB C578A with transmission clades across diverse regions. Furthermore, our analysis identified 78 SNPs that exhibited significant associations with clade size.ConclusionsOur study reveals the link between iron-related gene SNPs and M. tuberculosis transmission, offering insights into crucial factors influencing the pathogenicity of the disease. This research holds promise for targeted strategies in prevention and treatment, advancing research and interventions in this field.

Identification of single nucleotide polymorphisms (SNPs) in selected rice phosphate transporter (OsPHT) genes

Phosphorus (P) is one of the fundamental elements for plant growth and development. Due to the scarcity of viable P in the soil for plants, P deficiency was often the culprit that restrained plant’s wellbeing. Plasma membrane phosphate transporters (PHT) are a group of proteins responsible for phosphate (Pi) uptake from soil and further allocation to plant organs and tissues. The PHT can be further categorized into constitutively expressed low-affinity Pi transporter or high-affinity Pi transporter that are induced upon Pi starvation. Significant variability in P use efficiency has been observed among different rice varieties. Genotypic differences such as single nucleotide polymorphisms (SNPs) could be responsible for the variation observed aside from the well-studied phenotypic responses. Nevertheless, the occurrence of the SNPs in OsPHT genes remain unexplored. Therefore, the objective of this study was to analyse and profile the SNPs in five selected high affinity OsPHT genes which are responsible for P uptake under P deficiency. The SNPs mining was conducted using Rice SNP-Seek Database against 3024 rice varieties with Oryza sativa japonica cultivar Nipponbare as the reference sequence. Results showed that a total of zero, seven, three, one and ten non-synonymous SNPs was identified in OsPHT1;2, OsPHT1;3, OsPHT1;6, OsPHT1;9 and OsPHT1;10, respectively. A base substitution of C to A at position 16028497 of chromosome 10 of OsPHT1;3 was found to change tyrosine to a stop codon. This could result in a truncated protein which has only 213 amino acids as compared 526 amino acids in the complete protein. The large number of non-synonymous SNPs in OsPHT1;10 could explain the redundant function of this gene in the translocation and uptake of P in rice. In short, the identified SNPs especially the non-synonymous SNPs could potentially disrupt the biosynthesis of phosphate in rice which requires further investigation.

MISSENSE MUTATIONS IN THE IRAK1 GENE ARE ASSOCIATED WITH AN INCREASED RISK OF SYSTEMIC LUPUS ERYTHEMATOSUS

Single nucleotide polymorphisms (SNPs) are the most common form of genetic variation in humans. Missense SNPs can change protein structure and function. This study aimed to determine missense SNPs of the IRAK1 gene that can affect the amino acid sequence and lead to changes in protein structure and function, as well as their relationship as a risk factor for SLE. In this in silico method, several bioinformatics tools have been used to identify missense SNPs, including their properties and impacts, as well as their interaction networks with proteins. The tools used were PolyPhenv2, SIFT, PhD-SNP, PROVEAN, SNAP, Panthers, I-Mutant 3.0, and GeneMania. Four missense SNPs, rs11465830, rs1059702, rs1059703, and 10127175, were obtained from the NCBI SNP database. The SIFT test results showed that all the SNPs were tolerant. In the test results obtained using PolyPhen, the four SNPs were benign. The results of the probe test indicated that the four SNPs were neutral. When tested with SNAP, one SNP was neutral, and three others had an impact. In the PhD-SNP test, all SNPs were neutral. In the panther test, all SNPs were benign. The I-mutant assay showed that the four SNPs could decrease protein stability. Tests with GeneMania have reported that most interactions between genes were between IRAK1 and MYD88, and physical interactions were the most dominant form of interaction. Conclusion. rs10127175, rs11465830, rs1059702, and rs1059703 are missense SNPs in IRAK1, which can disrupt protein stability and be a risk factor for SLE. Keywords: IRAK1, SNP, Missense, Systemic Lupus Erythematosus

Association of three single nucleotide polymorphisms in the LPIN1 gene with milk production traits in cows of the Yaroslavl breed.

Lipin-1 is a member of the evolutionarily conserved family of proteins and is expressed predominantly in adipose tissue and skeletal muscle. On the one hand, lipin-1 is an enzyme that catalyzes the dephosphorylation of phosphatidic acid to diacylglycerol (DAG) and thus participates in the metabolic pathways of biosynthesis of storage lipids in the cell, membrane phospholipids, and intracellular signaling molecules. On the other hand, lipin-1 is able to be transported from the cytoplasm to the nucleus and is a coactivator of lipid metabolism gene transcription. It was shown, using the analysis of single nucleotide polymorphism (SNP) associations, that the lipin-1 coding gene (LPIN1) is a promising candidate gene for milk production traits in Holstein and Brown Swiss cows. However, it is unclear how much of its effect depends on the breed. The Yaroslavl dairy cattle breed was created in the 18-19 centuries in Russia by breeding northern Great Russian cattle, which were short and poor productive, but well adapted to local climatic conditions and bad food base. It was shown by whole genome genotyping and sequencing that the Yaroslavl breed has unique genetics compared to Russian and other cattle breeds. The aim of the study was to assess the frequency of alleles and genotypes of three SNPs in the LPIN1 gene and to study the association of these SNPs with milk production traits in Yaroslavl cows. Blood samples from 142 cows of the Yaroslavl breed were obtained from two farms in the Yaroslavl region. Genotyping of SNPs was carried out by polymerase chain reaction-restriction fragment length polymorphism method. Associations of SNPs with 305-day milk yield, fat yield, fat percentages, protein yield, and protein percentages were studied from the first to the fourth lactation. Statistical tests were carried out using a mixed linear model, taking into account the relationship between individuals. We identified three SNPs - rs110871255, rs207681322 and rs109039955 with a frequency of a rare allele of 0.042-0.261 in Yaroslavl cows. SNP rs110871255 was associated with fat yield during the third and fourth lactations. SNP rs207681322 was associated with milk yield for the second, third and fourth lactations, as well as protein yield for the third lactation. Thus, we identified significant associations of SNPs rs207681322 and rs110871255 in the LPIN1 gene with a number of milk production traits during several lactations in Yaroslavl cows.

ATP2B1 gene polymorphisms associated with resistant hypertension in the Japanese population.

Single-nucleotide polymorphisms (SNP) of ATP2B1 gene are associated with essential hypertension but their association with resistant hypertension (RHT) remains unexplored. The authors examined the relationship between ATP2B1 SNPs and RHT by genotyping 12 SNPs in ATP2B1 gene of 1124 Japanese individuals with lifestyle-related diseases. Patients with RHT had inadequate blood pressure (BP) control using three antihypertensive drugs or used ≥4 antihypertensive drugs. Patients with controlled hypertension had BP controlled using ≤3 antihypertensive drugs. The association between each SNP and RHT was analyzed by logistic regression. The final cohort had 888 (79.0%) and 43 (3.8%) patients with controlled hypertension and RHT, respectively. Compared with patients homozygous for the minor allele of each SNP in ATP2B1, a significantly higher number of patients carrying the major allele at 10 SNPs exhibited RHT (most significant at rs1401982: 5.8% vs. 0.8%, p=.014; least significant at rs11105378: 5.7% vs. 0.9%, p=.035; most nonsignificant at rs12817819: 5.1% vs. 10%, p=.413). After multivariate adjustment for age, sex, systolic BP, and other confounders, the association remained significant for rs2681472 and rs1401982 (OR: 7.60, p<.05 and OR: 7.62, p=.049, respectively). Additionally, rs2681472 and rs1401982 were in linkage disequilibrium with rs11105378. This study identified two ATP2B1 SNPs associated with RHT in the Japanese population. rs1401982 was most closely associated with RHT, and major allele carriers of rs1401982 required significantly more antihypertensive medications. Analysis of ATP2B1 SNPs in patients with hypertension can help in early prediction of RHT and identification of high-risk patients who are more likely to require more antihypertensive medications.

Effects of VDR and CYP24A1 gene polymorphisms on the outcome of supraglottic larynx cancer.

Vitamin D has been demonstrated to play a protective role in carcinogenesis. Polymorphisms of the vitamin D receptor (VDR) genes and 24-α-hydroxylase (encoded by CYP24A1) may affect the outcome of some cancers. This study examines the effects of the VDR gene and CYP24A1 single nucleotide polymorphisms on the outcome of supraglottic larynx cancer. Patients diagnosed with supraglottic larynx cancer between 2017 and 2022 were enrolled. Single nucleotide polymorphisms of the VDR gene (rs2228570, rs731236, rs7975232, rs11574113, rs11168267 and rs11168266) and CYP24A1 gene (rs4809960, rs6022999, rs6068816, rs2259735 and rs2296241) were investigated. All patients were followed up for any evidence of local recurrence, regional recurrence, distant metastasis, and second primary tumor development. Cox regression analysis was performed to evaluate the prognostic value of single-nucleotide polymorphisms (SNPs). Kaplan-Meier method was used for survival analysis. 87 patients were included. The mean follow-up time was 45.02±24.47 months. Cox regression analysis for locoregional recurrence revealed that the hazard ratio of rs731236 GG was 2.098 (95% CI, range: 1.047-4.202, p=0.037). Locoregional recurrence for rs731236 AA, AG, and GG were 38.6%, 23.1%, and 53.3%, respectively. In the presence of rs731236 GG polymorphism, disease-specific survival was significantly shorter (47.63±7.48 months, p=0.015), and disease-free survival (45.71±6.3 months) was significantly shorter (p=0.040). Rates of metastases and second primary tumors were not significantly different between SNPs. This study has demonstrated the possible effects of VDR rs731236 SNP on the locoregional recurrence and prognosis of supraglottic larynx cancer.

Role of polymorphism in vitamin D receptor gene on diabetic foot ulcer: A systematic review and meta-analysis

Context: Once vitamin D is converted to its active form, the molecule binds to its receptor (VDR) and performs its function as a transcription factor in modulating immune response, inflammation cascade, and insulin signaling. Among diabetic individuals, these activities are thought to be correlated with foot ulceration. Gene polymorphisms could change the function of VDR, thereby affecting the development of foot ulceration among individuals with diabetes. Aims: To construct evidence on the role of VDR gene variants or single nucleotide polymorphisms (SNPs) on diabetic foot ulcers. Methods: Records reporting the distribution of genotypes and/or alleles among diabetic foot ulcer (DFU) patients and published until 10 March 2023 were retrieved from 12 major databases using predetermined keywords. The original research articles included in the study were assessed for reporting quality using the Newcastle Ottawa Scale. The quality of genotypic and allelic data was appraised by Hardy-Weinberg equilibrium (HWE). A quantitative analysis-based fixed-effects model was performed to estimate the proportion of genotype and allele frequencies among DFU patients. Results: Three studies were included in the systematic review reporting the FokI (rs2228570), TaqI (rs731236), BsmI (rs1544410), and ApaI (rs7975232) SNPs. Based on pooled estimates, among DFU patients CC, CT, and TT genotypes of VDR FokI SNPs had a prevalence of 45%, 43%, and 12%, respectively, without significant heterogeneity found in the reported data (p-Het&lt;0.001; I2&gt;0%). ApaI and FokI were associated with DFU, while no association in all genotypic and allelic models was found between TaqI or BsmI and DFU. CC genotype of BsmI and T allele of FokI was associated with oxidative stress (one of the underlying factors in DFU). Conclusions: Certain genotypes and alleles of FokI and ApaI SNPs could act as the risk factor for foot ulceration among diabetic individuals. More high-quality studies are still needed to draw solid conclusions on the role of VDR SNPs among DFU patients.

Genetic risk score for insulin resistance based on gene variants associated to amino acid metabolism in young adults.

Circulating concentration of arginine, alanine, aspartate, isoleucine, leucine, phenylalanine, proline, tyrosine, taurine and valine are increased in subjects with insulin resistance, which could in part be attributed to the presence of single nucleotide polymorphisms (SNPs) within genes associated with amino acid metabolism. Thus, the aim of this work was to develop a Genetic Risk Score (GRS) for insulin resistance in young adults based on SNPs present in genes related to amino acid metabolism. We performed a cross-sectional study that included 452 subjects over 18 years of age. Anthropometric, clinical, and biochemical parameters were assessed including measurement of serum amino acids by high performance liquid chromatography. Eighteen SNPs were genotyped by allelic discrimination. Of these, ten were found to be in Hardy-Weinberg equilibrium, and only four were used to construct the GRS through multiple linear regression modeling. The GRS was calculated using the number of risk alleles of the SNPs in HGD, PRODH, DLD and SLC7A9 genes. Subjects with high GRS (≥ 0.836) had higher levels of glucose, insulin, homeostatic model assessment- insulin resistance (HOMA-IR), total cholesterol and triglycerides, and lower levels of arginine than subjects with low GRS (p < 0.05). The application of a GRS based on variants within genes associated to amino acid metabolism may be useful for the early identification of subjects at increased risk of insulin resistance.