Genetic testing and molecular biomarkers最新文献

Background: The nitric oxide (NO) synthase 3 (NOS3) 894G>T (p.Glu298Asp) variant has been associated with an elevated risk of neural tube defects (NTDs) in Caucasians. This association suggests a link between the NO and folic acid pathways. Aim: This study aimed to evaluate the NOS3 (p.Glu298Asp) variant as a potential genetic risk factor in infants with isolated open and closed NTDs (CNTDs) from Western Mexico. Materials and Methods: The studied population included 114 live-born infants with open and CNTDs (cases) and 155 neonates without major birth defects (controls). Genotyping of the NOS3 894G>T (p.Glu298Asp) variant was performed by PCR amplification and direct Sanger sequencing. Data were analyzed using logistic regression analysis. Results: The NOS3 894T allele (adjusted odds ratio [aOR] = 2.1; 95% confidence interval [95% CI]: 1.3-3.4), the 894GT (aOR = 2.3; 95% CI: 1.3-4.1), and the 894GT/TT (aOR = 2.6; 95% CI: 1.4-4.7) genotypes were significantly associated with open NTDs (ONTDs). There was no association between the NOS3 894G>T gene variants and CNTDs. Conclusions: This study indicates that the NOS3 894G>T (p.Glu298Asp) variant is associated with an increased risk of ONTDs in the studied Mexican patients.

Background: Endometrial cancer (EC) is a malignancy of the inner epithelial lining of the uterus, with an increasing incidence and disease-associated mortality worldwide. Inflammation and lipid metabolism contribute to EC risk. Materials and Methods: Differential expression genes (DEGs) in EC and normal samples were analyzed based on the TCGA-UCEC database, and DEGs associated with inflammation and lipid metabolism were screened out to be candidate genes. Prognosis-related genes were analyzed using Cox regression and LASSO regression, and a prognostic model was established. Receiver operating characteristic curves and Kaplan-Meier survival analysis were performed to assess the predictive performance of the prognostic model. Gene Set enrichment analysis, immune infiltration analysis, and gene set variation analysis were performed. Expression of prognostic genes in local tissues was examined by Reverse Transcription Quantitative PCR (RT-qPCR) and immunohistochemistry. Methylthiazolyldiphenyl-tetrazolium bromide assay, migration assay, and wound-healing assay were applied to examine the role of CKMT1B on cell proliferation and migration in EC cell lines. Results: A prognostic model based on six prognosis-related genes (CKMT1B, NTS, NSG2, H3C1, MAL, ELOA2) was established in EC, and this model had a favorable predictive performance. Respective different pathways and immune cell infiltration were associated with prognostic genes. 5/6 prognostic genes were highly expressed in local EC tissues compared with normal tissues. Knockdown of CKMT1B significantly suppressed cell proliferation and metastasis in EC cell lines. Conclusion: CKMT1B, NTS, NSG2, H3C1, MAL, and ELOA2 (especially CKMT1B) were important factors in human EC and could be potentially used for risk stratification and prognosis prediction in EC.

Background: Vitamin D deficiency influences the pathogenicity and severity of coronavirus disease 2019 (COVID-19), suggesting that polymorphisms in the vitamin D receptor may impact disease susceptibility and outcomes. This study aims to examine the relationship between the rs7975232 SNP and susceptibility to severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) infection. Materials and Methods: This study compared 138 COVID-19 patients with 136 healthy individuals at Shohada-ye Ashayer Hospital in Khorramabad. The PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) method was employed to ascertain the genotypes following the collection of blood samples. The results of PCR-RFLP method were confirmed by sequencing. IBM SPSS and SNPStats software were utilized to compare genotypes and allele frequencies, as well as to conduct odds ratio analysis. Results: This study's results did not demonstrate a significant association between the rs7975232 polymorphism and COVID-19 susceptibility (p = 0.58). Subsequent analysis revealed that individuals with low lymphocyte levels and the CC genotype exhibited increased susceptibility to COVID-19 (OR = 3.45, 95%CI: 1.18-10.11). A significant association was observed between creatinine (p < 0.0001), neutrophils (p = 0.02), and NLR (Neutrophil to Lymphocyte Ratio) (p = 0.0015) with rs7975232. In a comparison of AA/AC genotype cases, individuals with normal levels of ALT, CPK, creatinine, blood sugar, and hemoglobin exhibited an increased likelihood of infection. In CC genotype cases, individuals with normal neutrophil levels exhibited a reduced chance of COVID-19. Conclusion: The current study did not demonstrate a significant association between the examined SNP and COVID-19. The findings indicated that the standard levels of various laboratory parameters influence the likelihood of the disease. Additional studies involving larger and more diverse populations can yield more valid results.

Objective: To check the correlation between the MAGE Family Member C1 (MAGEC1) gene variant rs176036 and ovarian cancer risk among the Jammu and Kashmir population. Methodology: A case-control association study of the MAGEC1 gene variant rs176036 (G > A) and ovarian cancer. The variation was identified through whole exome sequencing, and the selected variant was genotyped in 111 patients with ovarian cancer and 107 healthy controls belonging to the Jammu and Kashmir region of North India using Sanger sequencing to confirm its association with the ovarian cancer. Odds ratio (OR) and other statistical values were calculated using standard tools. Results: The allelic frequency distribution was found to be similar between cases and controls, with the dominant allele (G) present in 89.6% of cases and 90.2% of controls (p = 0.84). The allelic OR for the dominant allele was 1.08 (0.55-2.11), which is nonsignificant (p = 0.83). Conclusion: The present study suggests that the rs176036 variant does not confer any increased risk of ovarian cancer among population of Jammu and Kashmir.

Aim: Genetic predisposition is an important factor related to the enhancement of inflammation or immune responses in COVID-19 patients. This study aimed to explore the association between the IL-6 (rs1800795) polymorphism and COVID-19 severity in the southwest of Iran. Methods: We evaluated these variants in 100 patients with moderate and 100 patients with severe COVID-19 using an (Amplification Refractory Mutation System Polymerase Chain Reaction) ARMS-PCR assay. In addition, we collected clinical characteristics of patients to assess their association with the severity of COVID-19. Statistically, the significance in the present evaluation was p < 0.05. Results: Our findings showed a significant association with the SNP-174G/C of the IL-6 gene between the moderate and severe groups of COVID-19 patients under the dominant and codominant genetic models (p = 0.02 and 0.03, respectively). The frequency of the G allele was notably higher in the severe group compared to the moderate group (p = 0.02). Also, the rs1800795 genotypes, as well as the patients' age and gender (p = 0.13 and 0.31, respectively), were detected. Additionally, we confirmed a significant correlation between clinical data known as risk factors for COVID-19 severity. Conclusion: Taken together, understanding the risk factors associated with the increased severity of COVID-19 may provide the opportunity for early and useful intervention in individuals at higher risk.

Background: Obstructive sleep apnea syndrome (OSAS) is a kind of sleep disturbance in which breathing is reduced or stopped for a short time and, if left untreated, can lead to long-term dangerous complications such as heart attack and obesity. Previous studies have shown that leptin receptor (LEPR) gene polymorphisms correlate with obesity and OSAS. This study aimed to measure the correlation of LEPR K109R and Q223R gene polymorphisms with OSAS in the Kurd population of Kermanshah, Iran. Materials and Methods: This study's population includes 100 patients with OSAS and 100 healthy individuals. Polysomnography diagnostic tests were performed on both patient and control groups. Polymerase chain reaction-restriction fragment length polymorphism was used to check the association between OSAS and LEPR gene polymorphisms. Results: Significant differences were observed in the allelic frequencies and genotype distributions of the LEPR K109R single nucleotide polymorphism (SNP) between the patients with OSAS and those of the healthy controls, whereas no such differences were found in the allelic and genotype frequencies of LEPR gene Q223R polymorphism. Additionally, the genotypic distribution of patients did not correspond to the severity of the disease. Conclusion: The results indicate an association between K109R and OSAS, with no such relation between Q223R and OSAS. Neither of the SNPs showed a link with the disease severity level.

Background: Gout is the most common arthritis, and it is associated with monosodium urate (MSU) crystal deposits in articulations, kidney, and soft tissue. The MSU crystal deposit initiates an inflammatory response, mediated by NLRP3 inflammasome, with the release of interleukin-1beta. Toll-like receptor 4 (TLR4) is involved in this response. The association of TLR4 single nucleotide polymorphisms (SNPs) and gout risk is controversial, with different results according to different populations. In the present study, we aimed to investigate the association between TLR4 gene rs2770150, rs4986790, rs4986791, and rs7873784 SNPs and hyperuricemia (HUA) and primary gout in males of Bai minority in Dali Prefecture, Yunnan Province, Southwest China. Methods: In total, 600 male patients with primary gout and 720 male patients with HUA of Bai minority were collected from the First Affiliated Hospital of Dali University and the Affiliated Hospital of Traditional Chinese Medicine of Dali University from 2022 to 2024. Nine hundred and eighty-eight men of Bai minority (without HUA and primary gout) received the health examination in the physical examination center of the hospital during the same period were recruited in the healthy control group. The four SNPs of rs2770150, rs4986790, rs4986791, and rs7873784 in TLR4 receptor were compared among the three groups. Results: There were no statistically significant differences in the genotype and allele frequency of rs4986790, rs4986791, and rs7873784 among the three groups (all p > 0.05). The difference in distribution of rs2770150 was statistically significant between HUA group and gout group (p < 0.05). There were 714 cases (99.2%) of AA type and 6 cases (0.8%) of GA type in HUA group, while there were 580 cases (96.7%) of AA type and 20 cases (3.3%) of GA type in primary gout group. Conclusion: Our study demonstrated that patients with HUA with TLR4 gene rs2770150 carrying GA type may be more likely to develop gout in males of Bai minority from Dali Prefecture of Yunnan Province, Southwest China.

Objectives: Investigating the molecular ABO blood group genotyping in specific populations helps improve our understanding of population genetics and its forensic applications. This study aimed to determine the genotypes and allele frequencies of ABO blood groups in the Minangkabau population. Materials and Methods: Blood samples were obtained from 200 participants (74 males and 126 females) using consecutive sampling. Only healthy, unrelated Minangkabau individuals with no history of interracial marriage of up to three generations were included. The polymerase chain reaction-restriction fragment length polymorphism technique was employed to amplify segments of the transferase gene, specifically nucleotide 261 in exon 6 and nucleotide 703 in exon 7 of the ABO gene locus, using the restriction enzymes Kpn1 and Alu1. Results: Phenotypic distribution revealed that 46.5% of participants were type A, 33% type B, 16% type O, and 4.5% type AB. The genotypes identified were 4.5% AA, 42% AO, 1.5% BB, 31.5% BO, 4.5% AB, and 16% OO. The gene frequencies calculated were 0.4 for the I^o allele, 0.39 for the I^a allele, and 0.21 for the I^b allele. Conclusions: These findings provide valuable insights into the genetic structure of the Minangkabau population and contribute to the understanding of ABO allele distributions in Southeast Asia, with potential applications in population genetics and forensic science.

Objective: We designed a prospective experiment to explore the whole promoter region of fibrinogen B β (FGB) with the intent to detect all single nucleotide polymorphisms (SNPs) in this region and their impact on the susceptibility of aseptic lower extremity superficial thrombophlebitis (STP). Methods: The experiment was conducted prospectively and randomized. Thirty-four idiopathic STP patients and 50 healthy people were recruited, respectively, as case and control groups. The whole FGB promoter was gene sequenced. Results: From upstream to downstream of the promoter, a totally 6 SNPs-rs1800789 (-1420G/A), rs2227389 (-993C/T), rs1800791 (-854G/A), rs1800790 (-455G/A), rs1800788 (-249C/T), and rs1800787 (-148C/T) were detected via gene sequencing. A statistical difference was found in the -455A allele (rs1800790) between the two groups (p < 0.05, odds ratio = 0.368, 95% confidence interval: 0.093 - 0.852), while no statistical difference as for the other five SNPs (all p > 0.05). Conclusions: The 455A allele may be a protective locus for the onset of STP. However, due to the low incidence of idiopathic STP, multiple verification tests are still needed.

Objective: Herein, we addressed the clinical challenge of high lymph node metastasis rates despite the lack of reliable diagnostic biomarkers in papillary thyroid carcinoma (PTC) by employing bioinformatics approaches to identify key biomarkers, aiming to provide new strategies for clinical diagnosis and treatment. Methods: Through bioinformatics analysis, plasminogen activator urokinase (PLAU) was identified as a key biomarker for lymph node metastasis in PTC. Immunohistochemistry (IHC) was performed to validate PLAU expression in tumor and adjacent normal tissues and its correlation with clinicopathological features. PLAU cellular expression was further confirmed by immunocytochemistry (ICC), Western blotting, and quantitative real-time PCR (qRT-PCR). Cell Counting Kit-8 and Transwell assays were used to assess its role in PTC tumor cell proliferation, migration, and invasion. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed on PLAU-related genes; immune cell infiltration in PTC was evaluated using the TIMER database and CIBERSORT algorithm. Results: Bioinformatics analysis showed that PLAU expression was significantly elevated in the PTC lymph node metastasis group [area under the receiver operating characteristic curve, 75.3%]. IHC results demonstrated significantly elevated PLAU expression in tumor tissues. Clinicopathological correlation analysis indicated that PLAU was associated with lymph node metastasis, particularly lateral cervical lymph node involvement. ICC, qRT-PCR, and Western blotting confirmed that PLAU was highly expressed in PTC tumor cells. After transient knockdown of PLAU, proliferation, migration, and invasion of PTC tumor cells were significantly reduced. GO and KEGG enrichment analyses showed that PLAU-related genes were primarily involved in signal transduction, inflammatory response, and P53, PI3K-Akt, and Mitogen-activated protein kinase (MAPK) signaling pathways. Immune cell infiltration was significantly higher in PTC tissues than in adjacent normal tissues; PLAU expression positively correlated with B and CD8⁺ T cell infiltration and Programmed cell death protein 1 (PD-1) and Cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) expression. Conclusions: PLAU enhances PTC cell proliferation, migration, and invasion while promoting immune escape through the Th1/Th2 imbalance and PD-1/CTLA-4 upregulation, serving as a potential biomarker for lymph node metastasis in PTC.