Genetic testing and molecular biomarkers最新文献

Objectives: Genetic polymorphisms in microRNA binding sites (mir-SNPs) may affect rheumatic diseases risk. We genotyped two mir-SNPs in the 3' UTR of SET8 (rs16917496) and KRT81 (rs3660) in ankylosing spondylitis (AS) patients to assess their association with AS risk. Methods: DNAs were extracted from blood samples for polymerase chain reaction analysis. Western blot was used to detect protein expression. Plasma reactive oxygen species (ROS) levels were measured by fluorescent probe technology. Results: We found that SET8 CC genotype had an increased chance of developing AS than the TT + CT genotype carrier (odds ratio, 5.378; 95% confidence interval, 1.130-25.593; p = 0.019). Moreover, the SET8 CC genotype displayed a lower expression of SET8 than the TT genotype. Additionally, increased ROS generation in AS patients was observed compared with controls (23859.055 ± 12283.038 vs. 14758.330 ± 5854.946, p < 0.001). Furthermore, the AS-susceptible CC genotype was associated with high ROS levels (35062.000 ± 17748.785 vs. 22629.463 ± 11002.181, p = 0.033). Conclusion: Our study revealed that the SNP rs16917496 located in the miR-502 binding site in the 3' UTR of SET8 could be used as a biomarker to predict AS risk. Importantly, SNP rs16917496 could participate in the pathogenesis of AS by regulating the expression of SET8, thereby promoting oxidative stress levels.

Background: This study aims to investigate whether elevated human neutrophil peptides 1-3 (HNP 1-3) levels in cerebrospinal fluid (CSF) are associated with disease severity and clinical outcomes in patients with intracerebral hemorrhage (ICH). Materials and Methods: HNP 1-3 levels were measured in CSF samples collected within 3 days after hemorrhage onset in ICH patients and control subjects. Results: HNP 1-3 levels were significantly higher in ICH patients with moderate-severe coma and hematoma volume >30 mL group. Univariate and multivariate logistic regression analyses demonstrated that CSF HNP 1-3 levels were associated with unfavorable outcomes. Receiver operating characteristic analysis revealed that CSF HNP 1-3 concentrations >466.95 ng/mL could distinguish ICH patients at risk for an unfavorable prognosis. Conclusions: HNP 1-3 exhibit satisfactory diagnostic efficiency for predicting the prognosis of ICH patients.

Background: Numerous genetic factors influence the severity and susceptibility to COVID-19. The renin-angiotensin system has a role in the genesis of COVID-19. This study aims to investigate the genetic polymorphisms of Angiotensin-Converting Enzyme Insertion/Deletion (ACE I/D) and ACE2 rs2285666 in patients with COVID-19 and their association with mild, severe, and critical disease symptoms. Materials and Methods: This study included 300 patients with COVID-19, categorized as mild, severe, and critical. Genotypes for the I/D polymorphism of ACE1 and the rs2285666 polymorphism of ACE2 were determined in all samples using polymerase chain reaction (PCR) and restriction fragment length polymorphism-PCR methodologies, respectively. Results: This study revealed a significant association between the ACEI/D genotype and the severity of COVID-19 (p < 0.001). A strong association was seen between the frequency of ACEI/D alleles and the severity of COVID-19, with the D allele being more prevalent in the severe and critical cohorts compared with the mild cohort (p < 0.001). A significant association was found between the ACE2 rs2285666 polymorphism and disease severity in both male and female groups (p < 0.05). The frequency of G/A alleles linked to the ACE2 polymorphism exhibited a significant association with disease severity, as the G allele was more common in the severe and critical groups than in the mild group (p = 0.004). Conclusion: Individuals with the homozygous ACE D/D genotype have an increased susceptibility to severe COVID-19, while the presence of allele I may provide a preventive advantage against severe disease symptoms. The ACE2 rs2285666 variant is associated with disease severity, while the ACE2 G/G genotype is linked to an increased severity of COVID-19.

Background: Pheochromocytoma and paraganglioma (PPGL) are rare neuroendocrine tumors with a high rate of germline predisposition. Although multigene panel testing (MGPT) using next-generation sequencing (NGS) is widely adopted globally, its clinical application in Japan remains limited. Methods: We developed a custom amplicon-based NGS panel targeting 12 established PPGL susceptibility genes. Germline analysis was performed in 23 Japanese patients with confirmed PPGL to evaluate sequencing quality and variant detection. Results: Sequencing quality was consistently high (Q30 > 96%, mapping rate >99%, on-target rate >80%), with nearly all exons (148/149) achieving >1,000× coverage. Pathogenic or likely pathogenic variants were found in 21.7% (5/23), including SDHB, VHL, and RET. In addition, variants of uncertain significance (VUS) were found in 17.4% (4/23), including novel missense variants in FH, SDHA, and MAX. Conclusions: This study demonstrates the feasibility and clinical utility of amplicon-based MGPT for PPGL in a real-world Japanese setting and highlights the importance of ongoing VUS reclassification to improve clinical interpretation. The findings support its diagnostic value, reflect underlying clinical demand, and contributed to its non-insured clinical adoption at certified laboratories in Japan.

Background: Coiled-coil-helix-coiled-coil-helix domain containing 1 (CHCHD1) is a mitochondrial protein involved in oxidative phosphorylation and mitochondrial protein synthesis. While its functions have been explored in basic mitochondrial biology, the role of this process in hepatocellular carcinoma (HCC) remains poorly understood. Materials and Methods: We performed transcriptomic analysis on 272 HCC and 50 normal liver tissue samples to assess CHCHD1 expression. Correlations with clinical features were analyzed using Pearson coefficients. Prognostic relevance was evaluated using receiver operating characteristic analysis. Functional studies in SMMC-7721 cells included transwell migration/invasion assays, as well as western blotting, to assess epithelial-mesenchymal transition (EMT) markers and transforming growth factor (TGF)-β1 signaling. Gene set enrichment analysis (GSEA), single-cell RNA sequencing (scRNA-seq), and immune infiltration analyses were conducted to investigate immunoregulatory functions. Results: CHCHD1 expression was significantly upregulated in HCC tissues (1.38-fold, p < 0.001) and correlated positively with tumor size (R = 0.45), vascular invasion (R = 0.56), and advanced Barcelona Clinic Liver Cancer stage (R = 0.62; all p < 0.001). High CHCHD1 predicted shorter progression-free survival (area under the curve = 0.938; 95% confidence interval 0.910-0.965; p = 0.039). Overexpression of CHCHD1 enhanced cell migration and invasion, promoted EMT (downregulation of E-cadherin and upregulation of vimentin), and activated TGF-β1 signaling. GSEA linked CHCHD1 to immune-related pathways. scRNA-seq localized CHCHD1 to myeloid-derived suppressor cells, showing potential interactions with TGF-β receptor 1. CHCHD1 expression correlated with Th2 cell infiltration (R = 0.57, p = 0.025) and programmed cell death 1 expression (p = 0.027). Conclusion: CHCHD1 promotes EMT and immune evasion in HCC via TGF-β1 signaling, implicating it as a promising biomarker and therapeutic target.

Introduction: Breast cancer is a common cancer in women, often linked to reduced survival in advanced stages. Recently, lncRNAs have gained attention as potential biomarkers for early detection. Among them, lncRNA AC073352.1 and its target protein Y-box 1 (YBX1) are associated with breast cancer progression and are promising diagnostic tools for early-stage detection. Materials and Methods: This study included 45 newly diagnosed breast cancer patients and 45 healthy controls from Shafa Hospital. Serum was separated from the collected blood samples, and total RNA was extracted and reverse-transcribed into cDNA. Expression levels of lncRNA AC073352.1 and YBX1 were quantified using SYBR Green-based real-time polymerase chain reaction. Their diagnostic performance was assessed by ROC curve analysis. Results: The study demonstrated that the expression levels of lncRNA AC073352.1 and YBX1 were significantly higher in breast cancer patients compared to the control group. ROC curve analysis indicated that AC073352.1 and YBX1 had suitable sensitivity and specificity for breast cancer detection. Additionally, a significant positive correlation was found between the expression of these two markers in patients, suggesting the possibility of a shared regulatory pathway. Conclusion: lncRNA AC073352.1 and YBX1 are promising biomarkers for early breast cancer detection, potentially enhancing diagnostic accuracy when used in combination with other methods.

Background: Male patients with prolactinomas exhibit greater invasiveness, resistance to dopamine agonists, making treatment more challenging. This study aims to explore the potential different genes contributing to sex disparities in prolactinomas. Materials and Methods: Weighted gene co-expression network analysis and differential expressed genes analysis were performed to identify sex-related hub genes. In addition, bioinformatics analyses were conducted to understand gene localization on chromosomes, gene regulatory networks, signaling pathways, and their relationship with immune function, which was verified in 21 human prolactinoma samples. Results: A total of 21 sex-related hub genes were identified. The hub genes in males included nine Y chromosome genes and six autosomal genes, while females had six specific genes. Further predictions using the NetworkAnalyst online tool suggested that transcription factors (REST, androgen receptor) and microRNAs (miR-27a-3p, miR-146a-5p) may be involved in regulating the above sex-related hub genes. CIBERSORT analysis revealed that prolactinomas in males showed significant infiltration of resting dendritic cells and naive CD4⁺ T cells. Correlation analysis between sex-related hub genes and immune checkpoint genes indicated that male hub genes were positively correlated with CD47 and CEACAM1, while showing a strong negative correlation with CD28, TNFSF14, and CD226. Finally, similar changes of gene expression in our surgical prolactinoma samples were confirmed by RT-qPCR. Conclusions: In prolactinomas, the male hub genes and female hub genes are identified by our bioinformatics analysis. Our findings suggest that KDM5D, PDCD1, ELOA3BP, XRRA1, and SIGLEC12 serve as potential biomarkers for male prolactinomas, while SOX3, DMGDH, and NPAS1 may serve as potential biomarkers for female prolactinoma, providing a theoretical basis for targeted therapy.

Objective: This study aimed to investigate the association between the KCNE1 single nucleotide polymorphism (SNP: rs1805127; T>C transition; S38G substitution) and atrial fibrillation (AF) in the Mazandaran population of northern Iran. Materials and Methods: To conduct this case-control study, 120 blood samples from healthy individuals and 120 from individuals with AF were collected over an 11-month period. All participants underwent electrocardiogram analysis by a cardiologist. In addition, they completed a questionnaire that included questions about their medical history, lifestyle factors, and current medications. Genotyping of KCNE1-rs1805127 was performed using the restriction fragment length polymorphism method. The impact of KCNE1-rs1805127 on protein stability, function, and mRNA secondary structure was assessed using SIFT, I-Mutant, MetaRNN, and RNAsnp servers. Results: The results revealed a significant association of the CC genotype and C allele with AF (CC genotype: p value = 0.035; C allele: p value = 0.042). Furthermore, an association was observed between smoking (p value = 0.018), hypertension (p value = 0.046), and thyroid disorders (p value = 0.040) and AF. in silico predictions indicated that KCNE1-rs1805127 may impair protein function, reduce stability, and alter mRNA secondary structure. Conclusions: Based on the results obtained, KCNE1-rs1805127 may increase the risk of AF, particularly in the presence of risk factors such as smoking, hypertension, and thyroid disorders. Notably, in silico predictions from computational tools validate this observed impact. Given the role of the KCNE1 gene in modulating ion channels and cardiac electrophysiology, we suggest that further research on KCNE1 and its SNPs could provide valuable insights into its role in the pathogenesis of cardiac arrhythmias, particularly AF.

Objective: Genetic variations of long noncoding RNAs are potential biomarkers for gastric cancer (GC). However, reports on the association between single nucleotide polymorphisms (SNPs) in antisense noncoding RNA in the INK4 locus (ANRIL) and GC risk are few. This case-control study aimed to evaluate the association between SNPs in ANRIL, GC risk, and subgroups in a Korean population. Methodology: The TaqMan genotyping assay of six SNPs in ANRIL was performed in 419 patients with GC and 348 controls. Results: After adjusting for age and gender, the following significant associations were identified: rs2157719 in the dominant model (TC+CC vs. TT) with decreased GC risk in the lymph node metastasis (LNM)-negative subgroup (p = 0.045, adjusted odds ratio [AOR] = 0.65, 95% confidence interval [CI] = 0.43-0.99); rs1333040 in the recessive model (CC vs. TT+TC) with increased risk in the undifferentiated subgroup (p = 0.032, AOR = 1.92, 95% CI = 1.06-3.50); and rs4977574 in the dominant model (AG+GG vs. AA) with decreased risk in the LNM-positive, tumor stage III (A+B+C), and undifferentiated subgroups (p = 0.007, AOR = 0.58, 95% CI = 0.39-0.86; p = 0.028, AOR = 0.63, 95% CI = 0.42-0.95; and p = 0.049, AOR = 0.63, 95% CI = 0.40-1.00, respectively). Conclusion: Our findings suggest that these SNPs in ANRIL are associated with GC risk and influence GC development. Further studies are needed to confirm our results in different ethnic groups and larger populations.