Single Nucleotide Polymorphisms In Genes Research Articles

Association of CTLA4 and NOD2/CARD15 (N852S) Genes Single Nucleotide Polymorphisms with Inflammatory Bowel Disease in Iraqi Patients

Association of CTLA4 and NOD2/CARD15 (N852S) Genes Single Nucleotide Polymorphisms with Inflammatory Bowel Disease in Iraqi Patients

Association of Genetic Polymorphisms in SLC45A2, TYR, HERC2, and SLC24A in African Women with Melasma: A Pilot Study

Melasma is a chronic skin disorder characterized by hyperpigmentation, predominantly affecting women with darker skin types, including those of African descent. This study investigates the association between genetic variants in SLC45A2, TYR, HERC2, and SLC24A5 genes and the severity of melasma in women of reproductive age. Forty participants were divided into two groups: twenty with facial melasma and twenty without. Deoxyribonucleic acid (DNA) was extracted from blood samples and genotyped using TaqMan assays to identify allele frequencies and genotype distributions. Significant associations were observed for the TYR gene (rs1042602), HERC2 gene (rs1129038), and SLC24A5 gene (rs1426654) polymorphisms, highlighting their potential roles in melasma susceptibility. For example, the rs1042602 Single Nucleotide Polymorphisms (SNP) in the TYR gene showed a strong association with melasma, with the AA genotype conferring a markedly increased risk. Similarly, the rs1129038 SNP in the HERC2 gene and the rs1426654 SNP in the SLC24A5 gene revealed significant genetic variations between groups in women of African descent. These findings underscore the influence of genetic polymorphisms on melasma’s pathogenesis, emphasizing the need for personalized approaches to its treatment, particularly for women with darker skin types.

MiR-423 Coding Region Genetic Polymorphism rs8067576 May Associate With the Risk of Developing Recurrent Spontaneous Abortion: A Case-Control Study in a Chinese Han Population.

Our previous study has identified an association of a single nucleotide polymorphism (SNP) in the miR-423 gene with recurrent spontaneous abortion (RSA). The presence of additional RSA-linked SNPs in the miR-423 gene remains unclear. We evaluated polymorphisms in the coding region of miR-423 in Han Chinese women with unexplained RSA (URSA). Significant differences were observed in the genotype and allele distribution of miR-423 rs8067576 between patients with RSA and control subjects. A robust association was found between an elevated RSA incidence and the presence of A/T heterozygosity in miR-423 rs8067576, with an odds ratio (OR) of 1.76 (95% confidence interval [CI]: 1.26 to 2.47, p = 0.000292). The rare allele T in the pre-miR-423 sequence was shown to cause a discernible structural change and a reduced ΔG value. Compared with the A allele, the rare T allele promoted cell proliferation. Furthermore, compared with the T allele, the A allele in the rs8067576 polymorphism exhibited a greater ability to inhibit the translation of proliferation-associated 2 group 4 (Pa2g4), which is the functional target of miR-423. The T allele in the rs8067576 polymorphism was also found to be more susceptible to the inhibition of cell proliferation induced by mifepristone. The rs8067576 A > T polymorphism in the miR-423 gene may serve as a genetic susceptibility locus for RSA. This polymorphism appears to contribute to an increased risk of acquiring URSA in humans by destroying mature miR-423.

Genetic Polymorphism of Zinc Transporter-8 Gene (SLC30A8), Serum Zinc Concentrations, and Proteome Profiles Related to Type 2 Diabetes in Elderly

Background and Aims: Older adults are particularly susceptible to type 2 diabetes mellitus (T2DM) due to factors such as age-related insulin resistance, decreased physical activity, and deficiency of micronutrients, especially zinc. Studies have suggested that the risk allele of the zinc transporter 8 gene (SLC30A8) single-nucleotide poly-morphism (SNP) rs13266634 may contribute to T2DM susceptibility in addition to the complex protein interactions and alterations in the protein expressions and modifications associated with T2DM. This study was implemented to study the associations between SLC30A8 polymorphism, serum zinc levels, and the profiles of proteins differentially expressed in nondiabetic (n = 116) and prediabetic/diabetic (n = 149) subjects. Methods: SNP genotyping using TaqMan® assay and proteomic analysis by LC-MS/MS were performed in each group. Results: The results showed a higher risk of diabetes in individuals with the risk genotype CC accompanied by a low serum zinc level than in those with other genotypes. Profiles of proteins differentially expressed between the groups were identified and shown to be particularly associated with zinc-related functions, zinc transporter 8, and glucose metabolism. Proteins exclusively expressed in prediabetes/diabetes were assigned to a Reactome pathway related to zinc transporter and insulin processing. Conclusions: Our findings suggest that individuals carrying at least one copy of SLC30A8 rs13266634 accompanied by a low serum zinc level might be susceptible to T2DM, which could be due to alterations in insulin signaling and zinc metabolism. Understanding this relationship deepens our understanding of the genetic and molecular mechanisms underlying T2DM risk, offering potential targets for therapeutic intervention and prevention strategies.

P1143 Impact of vitamin D metabolism gene polymorphisms on therapeutic efficacy of vedolizumab and ustekinumab in Inflammatory Bowel Disease

Abstract Background Vitamin D (VD) is a crucial biological agent with immunoregulatory and anti-inflammatory properties. There is growing interest in identifying genes regulated by VD to explore its therapeutic potential in various diseases, including Inflammatory Bowel Disease (IBD). Understanding single nucleotide polymorphisms (SNPs) and genotypes of VD-associated genes is essential for predicting therapeutic outcomes of biologic treatments and personalizing IBD management. This study aimed to evaluate the role of VD-related genetics in predicting the clinical response of patients with Crohn's disease (CD) and ulcerative colitis (UC) to biologics vedolizumab (VDZ) and ustekinumab (UST) after 12 months of therapy (T12), and to assess the achievement of fecal calprotectin (FC) levels <250 mg/kg, a surrogate marker for mucosal healing. Methods A prospective study was conducted including 103 patients (67 with CD, 36 with UC) treated with VDZ (40/103) and UST (63/103). SNPs of the genes CYP24A1, GC, CYP27B1, VDR ApaI, VDR Cdx2, VDR BsmI and VDR TaqI were analyzed using polymerase chain reaction (PCR) and correlated with clinical and laboratory outcomes through contingency tables and univariate logistic regression analysis for each SNP. Results UST therapy showed a higher clinical response rate at T12 than VDZ (85.7% vs. 67.5%, OR 2.89, 95% CI 1.10-7.60, p=0.03). A significant association was observed between response at T3 and T12 (p=0.0002, OR 6.91, 95% CI: 2.48-19.30). The GC 1296 AC polymorphism was a negative predictor of response at T12, with 63.6% of non-responders carrying this genotype. Treatment stratification confirmed that in VDZ-treated patients, AC heterozygotes were less likely to achieve the primary outcome (46.7%), with an OR of 4.57 (95% CI: 1.12-18.73, p=0.04). CYP24A1 8620 AG was a statistically significant negative predictor for achieving FC levels < 250 mg/kg (p=0.045). Moreover, CYP24A1 22776 CT and VDR Cdx2 GG were associated with a higher likelihood of presenting with CD rather than UC (OR = 3.40, 95% CI: 1.35 - 8.52, p-value = 0.009 and OR = 3.74, 95% CI = 1.02-13.77, p-value = 0.047, respectively). In addition, SNPs in the CYP27B1 gene, -1260 GT and +2838 CT, were significantly associated with non-ileal CD (non-L1 CD), increasing the probability of non-L1 presentation by 3-fold (OR = 3.13, 95% CI: 0.98-10.01, p-value = 0.054) and 7-fold (OR = 7.02, 95% CI: 1.44-34.25, p-value = 0.01), respectively. Conclusion In conclusion, this study identifies associations between polymorphisms in the vitamin D pathway and clinical and laboratory responses to VDZ or UST after 12 months of therapy, IBD phenotype, and CD localization. Further research is needed to validate these findings and to develop personalized IBD treatment strategies.

Vitamin D Binding Protein Gene Polymorphisms (rs4588 and rs7041) and VDBP Levels in Total Hip Replacement Outcomes

Background: Total hip replacement (THR) significantly improves patients’ quality of life; however, prosthesis loosening remains a significant complication. Vitamin D, essential for calcium homeostasis and bone mineralization, is transported and stabilized by vitamin D binding protein (VDBP). Common single nucleotide polymorphisms (SNPs) in the VDBP gene, rs4588 and rs7041, may influence serum vitamin D levels and potentially impact THR outcomes. This study aimed to analyze the association between these SNPs, serum levels of VDBP and 25(OH)D, and their potential roles in THR outcomes. Methods: The study included three patient groups: (1) patients undergoing arthroscopy after a THR without prosthesis loosening (CA—Control Arthroplasty), (2) patients with hip prosthesis loosening (L—Loosening), and (3) a control group (C—Control). Genotyping of rs4588 and rs7041 in the VDBP gene was conducted using PCR-RFLP and TaqMan Genotyping real-time PCR. Serum levels of VDBP and 25(OH)D were measured using ELISA. Comparisons between groups were performed using statistical analyses, including odds ratios (OR) and significance testing (p-values). Results: There are significant differences in VDBP concentrations between the groups: L vs. CA (p < 0.0001), L vs. C (p = 0.0118), L vs. L + CA (p = 0.0013), CA vs. C (p < 0.0001), and CA vs. L + CA (p < 0.0001), and in 25(OH)D concentrations between groups: L vs. C (p < 0.0001), CA vs. C (p = 0.0008), and C vs. L + CA (p < 0.0001). Conclusions: The study findings suggest a protective role of 25(OH)D against prosthesis loosening in THR. The rs4588 SNP in the VDBP gene may increase the risk of loosening, while differences in VDBP and 25(OH)D concentrations between patient groups highlight their potential importance in THR outcomes.

Impact of single nucleotide polymorphisms (SNPs) in antioxidant-enzyme genes on the concentrations of folate, homocysteine and glutathione in plasma from healthy subjects after folic acid supplementation – a randomized controlled crossover trial

BackgroundOne-carbon metabolism links folate and methionine metabolism and this is essential for nucleotide synthesis in the cells. Alterations in one-carbon metabolism are associated with cardiovascular disease (CVD), type 2 diabetes and cancer. Our aim was to investigate whether SNPs in antioxidant-enzyme genes impact the concentrations of folate in serum (s-folate), plasma total homocysteine (p-tHcy) and total glutathione in plasma (p-tGSH) in healthy subjects after supplementation with folic acid.MethodsIn a randomized, double blind, crossover study, healthy subjects received 0.8 mg folic acid per day or a placebo for two weeks. Twenty-four male, and sixty-seven female subjects participated in this study. Participants were aged 36.4 ± 14.8 years (mean ± SD). We studied SNPs in six genes by PCR methods. The concentrations of s-folate, p-tHcy and p-tGSH were measured in fasting samples with Cobas and an HPLC-fluorescence method. Student T-tests and ANOVA were used for the statistical calculations.Main findingsThe subjects with SNP (rs4880) in superoxide dismutase (SOD2) gene (CC) allele had higher concentrations of s-folate and lower concentrations of p-tHcy than subjects with (CT + TT) alleles, (p = 0.014 and p = 0.012). Contrary to SOD2 (CC) allele, the subjects with SNP (rs1001179) catalase (CAT) CC allele had lower concentrations of s-folate (p = 0.029), higher concentrations of p-tGSH (0.017) and higher concentrations of p-tHcy before and after folic acid supplementations (p = 0.015, p = 0.017) than the subjects with (CT + TT) allele. Glutathione transferase (theta)1 (GST-T1) genotype was associated with higher concentrations of s-folate than GST-T0 before (p = 0.025) and after folic acid supplementation (p = 0.047). SNP (rs1050450) in glutathione peroxidase (GPX1) had also impact on the concentrations of p-tGSH (p = 0.011) in healthy subjects.ConclusionSNPs in SOD2 (rs4880), CAT (rs1001179), and GST1 impact the concentrations of s-folate, and p-tHcy in healthy subjects before and after folic acid supplementation. Our findings suggest that SNPs in antioxidant-genes have a role in health and disease by impacting the concentrations of s-folate, p-tHcy and p-tGSH.

Serum levels of Wnt5a in Egyptian women with obesity and their association with toll like receptor 2 Arg753Gln gene polymorphism in a pilot case control study of obesity as a state of metaflammation

Female obesity is a worldwide health issue linked to chronic metabolic low-grade inflammation (metaflammation) causing multiple obesity-related co-morbid conditions. We aimed to assess the serum levels of wingless integration site family member 5 A (Wnt5a), leptin, and tumor necrosis factor-alpha (TNF-α) as markers of obesity-associated metaflammation and investigate the association with toll-like receptors2 (TLR2) gene (Arg753Gln) single nucleotide polymorphism (SNP) among Egyptian females. The study included 60 females with obesity and 30 matched controls. Serum levels of Wnt5a, leptin, and TNF-α were assessed by ELISA, while TLR2 (Arg753Gln) genotyping was done by PCR-RFLP. Serum Wnt5a, leptin, and TNF-α showed significantly higher levels in females with obesity than controls and a significant increase with higher classes of obesity. They showed significant positive correlations with each other. Only TNF-α and leptin were associated with metabolic syndrome (MetS) among the obesity group. According to TLR2 (Arg753Gln) SNP, the homozygous GG genotype was associated with elevated levels of Wnt5a, leptin, and TNF-α compared to the AA + GA model carriers. No significant differences were found in the distribution of TLR2 Arg753Gln (rs5743708) genotypes and alleles according to obesity or MetS, and the regression analysis showed no significant risk association. Serum Wnt5a, leptin, and TNF-α levels increase in women with obesity and the A allele of TLR2 (Arg753Gln) SNP could be protective against obesity-associated metaflammation.

Analysis of the association of influenza clinical course with single nucleotide polymorphisms in genes affecting the interferon-λ3 production

Analysis of the association of influenza clinical course with single nucleotide polymorphisms in genes affecting the interferon-λ3 production

Identification of the Highly Polymorphic Prion Protein Gene (PRNP) in Frogs (Rana dybowskii).

Prion diseases are fatal neurodegenerative diseases that can be transmitted by infectious protein particles, PrPScs, encoded by the endogenous prion protein gene (PRNP). The origin of prion seeds is unclear, especially in non-human hosts, and this identification is pivotal to preventing the spread of prion diseases from host animals. Recently, an abnormally high amyloid propensity in prion proteins (PrPs) was found in a frog, of which the genetic variations in the PRNP gene have not been investigated. In this study, genetic polymorphisms in the PRNP gene were investigated in 194 Dybowski's frogs using polymerase chain reaction (PCR) and amplicon sequencing. We carried out in silico analyses to predict functional alterations according to non-synonymous single nucleotide polymorphisms (SNPs) using PolyPhen-2, PANTHER, SIFT, and MutPred2. We used ClustalW2 and MEGA X to compare frog PRNP and PrP sequences with those of prion-related animals. To evaluate the impact of the SNPs on protein aggregation propensity and 3D structure, we utilized AMYCO and ColabFold. We identified 34 novel genetic polymorphisms including 6 non-synonymous SNPs in the frog PRNP gene. The hydrogen bond length varied at codons 143 and 207 according to non-synonymous SNPs, even if the electrostatic potential was not changed. In silico analysis predicted S143N to increase the aggregation propensity, and W6L, C8Y, R211W, and L241F had damaging effects on frog PrPs. The PRNP and PrP sequences of frogs showed low homology with those of prion-related mammals. To the best of our knowledge, this study was the first to discover genetic polymorphisms in the PRNP gene in amphibians.

Impact of Genetic Variants on Vitamin E Levels in an Italian Cohort of Bariatric Surgery Patients: A Focus on SNPs Involved with Transport and Bioavailability.

Obesity is a global epidemic associated with chronic inflammation, oxidative stress, and metabolic disorders. Bariatric surgery is a highly effective intervention for sustained weight loss and the improvement of obesity-related comorbidities. However, post-surgery nutritional deficiencies, including vitamin E, remain a concern. This study investigates the role of single-nucleotide polymorphisms (SNPs) in genes related to vitamin E transport and bioavailability in determining vitamin E levels post bariatric surgery. A cohort of 140 patients with obesity undergoing bariatric surgery was analyzed. Serum vitamin E levels were measured before and one year after surgery, and SNPs in genes associated with vitamin E transport and metabolism were genotyped using PCR, DHPLC, and sequencing methods. Associations between SNPs, haplotypes, and vitamin E levels were statistically evaluated. Significant associations were observed between the APOE rs7412 SNP and serum vitamin E levels. The rare T allele was linked to lower vitamin E levels post surgery, with an increased frequency in patients with severe deficiency (<11.6 μmol/L). Haplotype analysis of APOE revealed that the ε2 haplotype (T-T) was strongly associated with vitamin E deficiency. Other SNPs, including CD36 rs1761667, SCARB1 rs4238001, and ABCA1 rs4149314, were also linked to changes in vitamin E levels, suggesting that an impaired bioavailability and transport can be the reason for low vitamin E levels post surgery. Genetic polymorphisms in APOE, CD36, SCARB1, and ABCA1 significantly influence vitamin E status after bariatric surgery. These findings highlight the importance of personalized supplementation strategies considering patients' genetic profiles to mitigate the risk of vitamin E deficiency and related complications.

Relationship Between an Interleukin 6 SNP and Relapse After Allogeneic Bone Marrow Transplantation.

Background/Objectives: Unrelated bone marrow transplantation (BMT) is a curative treatment for hematological malignancies. While HLA mismatch is a recognized risk factor in unrelated BMT, the significance of non-HLA single nucleotide polymorphisms (SNPs) remains uncertain. Cytokines play key roles in several aspects of unrelated BMT. Although the relationship between cytokine gene SNPs and BMT outcomes has been examined, the findings obtained have been inconsistent; therefore, further investigations in additional cohorts are warranted. Methods: Four SNPs in the IL2, IL6, IFN-gamma, and TGF-beta1 genes were retrospectively genotyped in 822 malignant patients and their corresponding donors who received unrelated BMT through the Japan Marrow Donor Program with compatibility at minimum HLA-A, -B, and -DRB1. The relationships between these SNP genotypes and BMT outcomes were statistically analyzed. Results: The donor interleukin-6 (IL6) SNP, rs1800796, also known as -572G>C and -634C/G, was associated with the relapse of the original disease in both univariable and multivariable regression analyses (minimum p-value = 0.0013), and the cumulative incidence curve analysis identified CC as a risk genotype (p-value = 0.0012). None of these SNPs correlated with overall survival. Conclusions: The donor IL6 SNP, rs1800796, may serve as a useful predictor of tumor relapses if validated.

Single-Nucleotide Polymorphisms in MMP3, TIMP1, and MTR Genes are Associated With Delayed Deciduous Tooth Eruption.

To analyze whether the single-nucleotide polymorphisms (SNPs) in Matrix metalloproteinases 2, 3, and 9 (MMP2, MMP3, and MMP9), Tissue Inhibitor of Metalloproteinases 1 and 2 (TIMP1 and TIMP2), methionine synthase (MTR) and methionine synthase reductase (MTRR) influence delayed deciduous tooth eruption (DDTE). This cross-sectional study included 1060 biologic unrelated children (aged between 6 and 36months) of both sexes, selected from 25 public schools in Nova Friburgo, Rio de Janeiro, Brazil. Oral examination was conducted and DDTE was defined by the absence of gingival eruption according to a chronology based on the Brazilian population. Genotyping of selected SNPs (rs243847, rs52261, rs17576, rs4898, rs7501477, rs1805087, and rs1801394) was performed using TaqMan real-time PCR with genomic DNA extracted from buccal cells. The association between genotypes and DDTE was evaluated using univariate and multivariate analyses (p < 0.05). A total of 224 children and caregivers were included after the eligibility criteria. The heterozygous genotype for the SNPs MTR (rs11805087) was associated with DDTE in both the univariate (p = 0.004) and multivariate (p < 0.001) codominant models, as well as in the univariate (p = 0.010) and multivariate (p = 0.001) recessive models. TIMP1 (rs4898) and MMP3 (rs522616) were associated with DDTE only in the univariate model (p < 0.05). The SNPs in MTR (rs11805087), MMP3 (rs522616) and TIMP (rs4898) genes are associated with DDTE. The factors affecting the chronology of deciduous tooth eruption has been insufficiently studied. This article brings novel knowledge regarding the role of genetics polymorphisms on timing variation of deciduous tooth eruption. Understanding the factors that impact tooth eruption is crucial for the fields of pediatric dentistry and orthodontics.

Genetic signatures of ERCC1 and ERCC2 expression, along with SNPs variants, unveil favorable prognosis in SCLC patients undergoing platinum-based chemotherapy.

Platinum chemotherapy (CT) remains the backbone of systemic therapy for patients with small-cell lung cancer (SCLC). The nucleotide excision repair (NER) pathway plays a central role in the repair of the DNA damage exerted by platinum agents. Alteration in this repair mechanism may affect patients' survival. We conducted a retrospective analysis of data from 38 patients with extensive disease (ED)-SCLC who underwent platinum-CT at the Clinical Oncology Unit, Careggi University Hospital, Florence (Italy), from 2015 to 2020. mRNA expression analysis and single nucleotide polymorphism (SNP) characterization of three NER pathway genes-namely ERCC1, ERCC2, and ERCC5-were performed on patient tumor samples. Overall, elevated expression of ERCC genes was observed in SCLC patients compared to healthy controls. Patients with low ERCC1 and ERCC5 expression levels exhibited a better median progression-free survival (mPFS = 7.1 vs. 4.9 months, p = 0.39 for ERCC1 and mPFS = 6.9 vs. 4.8 months, p = 0.093 for ERCC5) and overall survival (mOS = 8.7 vs. 6.0 months, p = 0.4 for ERCC1 and mOS = 7.2 vs. 6.2 months, p = 0.13 for ERCC5). Genotyping analysis of five SNPs of ERCC genes showed a longer survival in patients harboring the wild-type genotype or the heterozygous variant of the ERCC1 rs11615 SNP (p = 0.24 for PFS and p = 0.14 for OS) and of the rs13181 and rs1799793 ERCC2 SNPs (p = 0.43 and p = 0.26 for PFS and p = 0.21 and p = 0.16 for OS, respectively) compared to patients with homozygous mutant genotypes. The comprehensive analysis of ERCC gene expression and SNP variants appears to identify patients who derive greater survival benefits from platinum-CT.

Use of Oral Rub and Rinse Technique for Oral Cancer Screening: Results from a Community-based Program in an LMIC.

Oral cancer screening programs can aid in the early identification of potentially malignant oral lesions. The objective of the present study was to evaluate the effectiveness of the Oral Rub and Rinse (ORR) technique as an oral cancer screening tool and to test its potential in detecting genetic alterations in exfoliated cells obtained through ORR. The screening programs were conducted in rural Dakshina Kannada and Udupi districts in Karnataka. All adults with red and/or white lesions were included in the study. Samples were collected using the ORR technique, and smears were prepared. In parallel, Conventional Exfoliative cytology (CEC) smears were also prepared. ORR samples and tissue biopsy were obtained from Classes III, IV, and V cases. Seven Oral Squamous Cell Carcinoma (OSCC) tissue samples, 7 OSCC ORR samples, and five control samples were randomly selected. The presence of single nucleotide polymorphisms (SNP) in USP9X and DDX3X were checked through Sanger sequencing. Diagnostic agreement between the ORR and CEC technique was assessed using the McNemar test. A total of 2514 individuals were screened, of which 217 patients with red/ white lesions were included in the study. There was good agreement between the exfoliative cytology and ORR. The sensitivity of the ORR was 84.54%, specificity 85.83%, positive predictive value 82.83%, and negative predictive value 87.29%. Overall, the diagnostic accuracy of the ORR technique was 85.25%. Although none of the samples showed the presence of target SNPs in USP9X and DDX3X genes, the utility of the ORR technique as a tool for conventional and molecular studies was confirmed. The present study highlights the usefulness of the ORR technique as an effective tool in population-based oral cancer screening programs. Further, the cells obtained from ORR are an excellent source of DNA and can potentially identify genetic alterations with high accuracy.

Detecting CYP2C19 genes through an integrated CRISPR/Cas13a-assisted system.

CYP2C19 gene single nucleotide polymorphisms (SNPs) should be considered in the clinical use of clopidogrel as they have important guiding value for predicting the risk of bleeding and thrombosis after clopidogrel treatment. The CRISPR/Cas system is increasingly used for SNP detection owing to its single-nucleotide mismatch specificity. Simultaneous detection of multiple SNPs for rapid identification of the CYP2C19 genotype is important, but there is no method to detect a wide variety of CYP2C19 SNPs. This study proposes a new integrated system that integrates the PCR reaction and CRISPR/Cas detection of three CYP2C19 genes on a device, achieving rapid, sensitive, and specific detection. In our design, magnetic beads with three different sizes capture target nucleic acid from the sample, which are dragged through different areas by magnetic force, for PCR amplification reaction and CRISPR/Cas13a detection of CYP2C19*2, CYP2C19*3 and CYP2C19*17 genes. Note that magnetic beads were sorted via microporous PC membranes of different apertures. This study exhibits a broad clinical application prospect and provides a favorable tool for clinical clopidogrel administration.

Association Between Single-Nucleotide Polymorphisms in Toll-like Receptor 3 (tlr3), tlr7, tlr8 and tirap Genes with Severe Symptoms in Children Presenting COVID-19.

The global number of COVID-19 deaths has reached 7 million, with 4% of these deaths occurring in children and adolescents. In Brazil, around 1500 children up to 11 years old died from the disease. The most common symptoms in children are respiratory, potentially progressing to severe illnesses, such as severe acute respiratory syndrome (SARS) and MIS-C. Studies indicate that comorbidities and genetic factors, such as polymorphisms in immune response genes, can influence the severity of COVID-19. This study investigates the occurrence of single-nucleotide polymorphisms (SNPs) in innate immune response genes in children with COVID-19. Seventy-three samples were analyzed from children under 13 years old hospitalized at João Paulo II Children's Hospital due to COVID-19. The evaluated SNPs were tlr8 (1) (rs3764879), tlr8 (2) (rs2407992), tlr7 (rs179008), tlr3 (rs3775291), tirap (rs8177374), and mcp-1 (rs1024611), considering four categories of severity: mild, moderate, severe, and critical COVID-19. To identify the SNPs, PCR and sequencing were performed. The frequencies of the SNPs obtained were not discrepant when compared to the frequencies described in the Global ALFA, Global 1000 Genomes, Global gnomAD, American 1000 Genomes, and American gnomAD databases, except for the SNP in TLR7. Comparing severe and critical cases to mild and moderate cases, we found a higher relative risk associated with mutations in tlr8 (1), tlr7, tlr3, and tirap (p < 0.05). No association was found for SNPs in tlr8 (2) and mcp-1. Our analyses suggest an association between SNPs in innate immune response genes and severity of symptoms in children with COVID-19 (or SARS-CoV-2 infected children).

Unveiling DENND2D as a Novel Prognostic Biomarker for Prostate Cancer Recurrence: From Gene to Prognosis.

Background: Prostate cancer is a major global health burden, with biochemical recurrence (BCR) following radical prostatectomy affecting 20-40% of patients and posing significant challenges to prognosis and treatment. Emerging evidence suggests a critical role for differentially expressed in normal and neoplastic cell (DENN) domain-containing genes in oncogenesis; however, their implications in prostate cancer and BCR risk remain underexplored. Methods: This study systematically evaluated 151 single-nucleotide polymorphisms in DENN domain-containing genes in 458 patients with prostate cancer and BCR, followed by validation in an independent cohort of 185 patients. Results: Multivariate Cox regression analyses identified DENND2D rs610261 G>A as significantly associated with improved BCR-free survival in both cohorts (adjusted hazard ratio = 0.39, 95% confidence interval = 0.23-0.66, p = 0.001). Functional analysis revealed rs610261's regulatory potential, with the protective A allele correlating with increased DENND2D expression in various human tissues. Compared to normal prostate tissues, DENND2D expression was reduced in prostate cancer, with higher expression being linked to favorable patient prognosis (p = 0.03). Gene set enrichment analysis revealed an association between DENND2D expression and the negative regulation of MYC target genes, including MAD2L1, ERH, and CLNS1A, which are overexpressed in prostate cancer and associated with poor survival. Furthermore, the elevated DENND2D expression promotes immune infiltration in prostate cancer, supporting its role in immune modulation. Conclusions:DENND2D is a prognostic biomarker for BCR in prostate cancer and offers new avenues for personalized treatment strategies.

SNPs in GPCR Genes and Impaired Osteogenic Potency in Osteoporotic Patient Lines-Based Study.

G-protein-coupled receptors (GPCRs) have emerged as critical regulators of bone development and remodeling. In this study, we aimed to identify specific GPCR mutations in osteoporotic patients via next-generation sequencing (NGS). We performed NGS sequencing of six genomic DNA samples taken from osteoporotic patients and two genomic DNA samples from healthy donors. Next, we searched for single-nucleotide polymorphisms (SNPs) in GPCR genes that are associated with osteoporosis. For three osteoporotic patients and one healthy donor, bone biopsies were used to generate patient-specific mesenchymal stem cell (MSC) lines, and their ability to undergo osteodifferentiation was analyzed. We found that MSCs derived from osteoporotic patients have a different response to osteoinductive factors and impaired osteogenic differentiation using qPCR and histochemical staining assays. The NGS analysis revealed specific combinations of SNPs in GPCR genes in these patients, where SNPs in ADRB2 (rs1042713), GIPR (rs1800437), CNR2 (rs2501431, rs3003336), and WLS (rs3762371) were associated with impaired osteogenic differentiation capacity. By integrating NGS data with functional assessments of patient-specific cell lines, we linked GPCR mutations to impaired bone formation, providing a foundation for developing personalized therapeutic strategies. SNP analysis is recognized as a proactive approach to osteoporosis management, enabling earlier interventions and targeted preventive measures for individuals at risk. Furthermore, SNP analysis contributes to the development of robust, holistic risk prediction models that enhance the accuracy of risk assessments across the population. This integration of genetic data into public health strategies facilitates healthcare initiatives. This approach could guide treatment decisions tailored to the patient's genetic profile and provide a foundation for developing personalized therapeutic strategies.

Genomic Comparison of Reoccurring, Emerging, and Persistent (REP) Shiga Toxin-Producing Escherichia coli O157:H7.

Escherichia coli O157:H7 strains associated with several recent (2017-2020) multi-state outbreaks linked to leafy green vegetables have been characterized as "reoccurring, emerging, and persistent" (REP). Our recent unpublished work demonstrated that the REP strains had significantly enhanced potential for biofilm formation. In this study, comparative genomic analyses were conducted for a better understanding of the mechanisms behind the enhanced biofilm formation, and thereby potentially increased environmental fitness, by the REP strains. Phylogenetically, the recent outbreak strains formed two distinct clusters represented by REPEXH01 and REPEXH02. Compared with EDL933 and other previous outbreak reference strains, the REP strains (clustering with REPEXH02) exhibiting strong biofilm formation were found to have acquired two genes encoding proteins of unknown functions (hypothetical proteins) and lost certain prophage-related genes. In addition, several single nucleotide polymorphisms in genes related to biofilm formation were identified.