Genetic testing and molecular biomarkers最新文献

Background: Colorectal cancer is a prevalent malignancy with high incidence and poor prognosis. This study explores the clinical significance of 5-methylcytosine RNA modification factors, specifically the NOP2/Sun RNA Methyltransferase (NSUN) family, in colorectal cancer. Methods: Utilizing data from The Cancer Genome Atlas database, we analyzed the expression levels of NSUN family members in tumor tissues, their prognostic relevance, and their relationship with immune cell infiltration. To further investigate, paraffin-embedded cancer tissue microarrays were used to assess the expression of NOP2 Nucleolar Protein (NOP2) and NSUN6 in colorectal cancer tissues and adjacent normal tissues. The correlation between the expression of these genes and patient prognosis was also examined. Results: Bioinformatic analysis revealed that NOP2 is highly expressed in tumors, whereas NOP2/Sun RNA Methyltransferase 6 (NSUN6) is linked to poor prognosis. Immune infiltration analysis demonstrated that NOP2 expression is significantly correlated with varying levels of immune cell infiltration, including a positive association with myeloid-derived suppressor cells (MDSCs), M1 macrophages, and natural killer cells and a negative correlation with regulatory T cells and M2 macrophages. NSUN6 expression showed a significant positive correlation with MDSC infiltration. Clinical sample analysis indicated that NOP2 expression is strongly associated with tumor grade and nerve invasion, whereas NSUN6 is significantly related to nerve invasion. Survival analyses revealed that high levels of NOP2 and NSUN6 are linked to shorter overall survival. Notably, NSUN6 expression, vascular invasion, and T stage emerged as key predictors of colorectal cancer patient survival. Conclusions: These findings suggest that NOP2 and NSUN6 may serve as valuable molecular markers for predicting poor prognosis in colorectal cancer, with potential applications in clinical decision-making.

Background: Neurofibromatosis is an autosomal dominant genetic disease caused by the abnormal development of neural crests due to genetic defects and is difficult to treat. Patients have a characteristic phenotype with neurofibromas as the main features in different forms, which are accompanied by multisystem involvement. The clinical symptoms of this disease vary greatly, making the treatment more difficult. Methods: Preimplantation genetic testing (PGT) is a useful technique to prevent chromosomal aneuploidies and other genetic disorders in origin. PGT for monogenic diseases (PGT-M) is now widely used as an effective strategy to screen embryos for monogenic or chromosomal diseases before implantation. In this study, PGT-M was performed in a family history of hereditary with neurofibromatosis type 1 (NF1) to prevent the offspring from inheriting disease-causing gene variant from their parents. Trio-based whole-exome sequencing was used to identify potential pathogenic variants associated with NF1. Blastocyst biopsy was performed on embryos obtained by intracytoplasmic sperm injection. Single-cell amplification of biopsied cells was performed for targeted next-generation sequencing. Single nucleotide polymorphism markers on both sides of NF1 were selected to identify disease-carrying haplotypes in each embryo. Results: A novel heterozygotic frameshift pathogenic variant, c.2033_2034delinsA(p.P678Qfs*10), was identified in the NF1 gene in the proband. A total of five blastocysts were biopsied, and the PGT results showed that only one blastocyst was unaffected and was euploid, and the remaining four blastocysts were all carrying paternal pathogenic variants. The only one normal blastocyst was transferred in a frozen-thawed embryo transfer cycle, and a live singleton pregnancy was successfully achieved. At 18 weeks, the amniocentesis test revealed normal karyotype, and the variant carried by the proband was not detected. At 40 weeks, the proband's wife successfully delivered a healthy baby naturally. Conclusion: PGT is an effective method to detect chromosome copy number variation and gene variant sites in embryos, and it provides suggestions for possible innovations to block the transmission of single-gene genetic diseases to offspring, thereby preventing the occurrence of birth defects.

Background: Cervical cancer (CC) is the most prevalent gynecological tumor among women. Cyclin-dependent kinase 8 (CDK8), which plays a crucial role in cellular transcriptional processes and various signaling pathways, has been identified as a key oncogenic factor in numerous cancers. However, limited data exists on the correlation between CDK8 and CC. The objective of our study was to investigate whether there is an association between CDK8 gene polymorphisms and the development of CC in Han women from Southwest China. Materials and methods: A total of 300 unrelated CC patients and 335 healthy controls from Southwest China were included in the study. The polymerase chain reaction-restriction fragment length polymorphism analysis was used to genotype the two tag single nucleotide polymorphisms (SNPs) of CDK8 gene (rs17083838 and rs7992670), and the relationship between the two tag SNPs and CC incidence was analyzed by SNPstats software. Multifactor dimensionality reduction (MDR) was used to analyze the interaction of multiple polymorphisms of the CDK8 gene. The false-positive report probability (FPRP) was used to verify the effective correlation. Results: The frequency of the A allele of CDK8 rs17083838 in the CC group was significantly higher than that in the control group (25% vs. 12%, p < 0.0001, odds ratio (OR): 0.42, 95% confidence intervals [CI]: 0.31-0.58). The frequency of the A allele at rs7992670 was higher in the CC group than that in the control group (52% vs. 45%, p = 0.026, OR: 0.78, 95% CI: 0.63-0.97). MDR analysis showed that rs17083838 and rs7992670 as the overall model was the best model, the detection accuracy was 0.6157, and the cross-validation consistency was 10/10 (p < 0.0001). In addition, 22 valid FRPR values were verified by using the FPRP detection method. Conclusion: The two SNPs of the CDK8 gene may be associated with the increased risk of CC in the Han population in Southwest China.

Background: Infertility affects 10-15% of couples worldwide, with male factors accounting for half of cases. Environmental, behavioral, and genetic problems contribute to spermatogenic failure in 30% of idiopathic male infertility cases. Other factors, such as oxidative stress (OS), cause impaired spermatogenesis, abnormal sperm morphology, and reduced motility, eventually triggering male infertility. In the male reproductive tract, glutathione S-transferase (GST) family antioxidants are essential for preventing OS, detoxification, and DNA damage protection. Methods: GSTP1 isoenzyme, one of GST members, has previously been linked to male infertility, and this case-control study is the first to assess the possible association of GSTP1 gene polymorphisms (rs1695 and rs1138272) with nonobstructive azoospermia and severe oligospermia within 300 patients and 300 controls from the Moroccan population using an allele-specific PCR. The statistical analysis was performed with the R programming language. Results: Genotyping of GSTP1 polymorphisms fitted the Hardy-Weinberg equilibrium in both cases and controls (p > 0.05), but no significant association was found in rs1695 (odds ratio [OR] = 1.238, 95% confidence interval [CI] = 0.855 to 1.794, p = 0.258, power = 0.204) and in rs1138272 (OR = 1.192, 95% CI = 0.852 to 0.1668, p = 0.304, power = 0.176). Likewise, results from haplotype analysis (OR = 1.25, 95% CI = 0.61 to 2.57, p = 0.537) and SNP-SNP interactions (OR = 1.522, 95% CI = 0.838 to 2.762, p = 0.166) demonstrated no correlation with the risk of male infertility. Conclusion: The two SNPs (rs1695 and rs1138272) of the GSTP1 gene loci are not associated with male infertility susceptibility in Moroccan subjects. Yet, future investigations with a larger sample size may conclusively help to confirm this association.

Background: Ankylosing spondylitis (AS) is a chronic inflammatory disorder with a significant genetic predisposition. Genome-wide association studies (GWAS) have identified immune-related loci, including the G Protein-Coupled Receptor 35 (GPR35) gene, as potential contributors to AS pathogenesis. This study aimed to evaluate the association between the rs4676410 polymorphism in the GPR35 gene and both AS susceptibility and disease activity in a Turkish population. Methods: This case-control study included 200 participants (100 AS patients and 100 healthy controls). DNA was isolated from blood samples, and the rs4676410 polymorphism was analyzed using real-time polymerase chain reaction (PCR). Disease activity in AS patients was assessed using the Bath AS Functional Index (BASFI), Bath AS Disease Activity Index (BASDAI), and disease activity scores including C-reactive protein (ASDAS-CRP) scores. Statistical analyses were conducted using IBM SPSS 26. Results: The rs4676410 polymorphism was significantly associated with AS susceptibility. The AA genotype and A allele were more prevalent in AS patients, indicating an increased risk of developing AS. Among disease activity measures, ASDAS-CRP scores were significantly higher in patients with the AA genotype (p = 0.043), while no significant differences were observed for BASFI and BASDAI scores across genotypes. Conclusion: The findings suggest that the rs4676410 polymorphism in the GPR35 gene is associated with AS susceptibility and may influence disease activity through elevated inflammatory responses. These results highlight the potential of the AA genotype and A allele as genetic markers for AS and underscore the importance of integrating genetic insights into personalized treatment approaches.

Background: Fanconi anemia (FA) is a rare genetic disorder that affects multiple systems in the body and is the most prevalent congenital syndrome, leading to bone marrow failure. Twenty-two genes have been identified as contributors to the disease. Significant advancements have been made in the past 2 decades in understanding the genetic and pathophysiological processes involved. Whole exome sequencing (WES) is employed to diagnose rare Mendelian disorders when standard tests fail to provide a definitive pathological diagnosis. However, WES has the potential to reveal pathogenic variants that may complicate the diagnostic process. In this study, the method was chosen to examine SLX4/FANCP. Aims: The goal of our research was to suggest that the new potentially harmful genetic mutation, c.4921dup A>AC (p.Val1641GlyfsTer15), could lead to the development of FA. Methods and Result: This patient was analyzed by performing the WES test, and a homozygous pathogenic variant in the SLX4 gene (c.4921dupA>AC - chr16-3633329-p.Val1641GlyfsTer15) was identified in this patient. The candidate variant was confirmed by Sanger sequencing. The parent of the patient and the fetus of this family were also examined using Sanger sequencing, and they were determined to be carriers and heterozygous. Conclusion: Our research has uncovered a new form of pathogenic genetic variation in the SLX4 gene, providing new insights into the molecular causes of this condition. To date, the c.4921dup A>AC (p.Val1641GlyfsTer15) pathogenic variant has not been observed or reported worldwide. These findings could be valuable for investigating the mechanisms of FA and may offer insights for preventing, diagnosing, and managing the risks associated with this disease.

Purpose: Periodontal disease worsens glycemic control due to the bidirectional link between periodontitis and type 2 diabetes mellitus (T2DM), involving inflammatory markers such as soluble tumor necrosis factor-like weak inducer of apoptosis (sTWEAK), tumor necrosis factor-α (TNF-α), and omentin-1. However, their combined role in T2DM with periodontitis has not been studied. This study aimed to evaluate the levels of these biomarkers in periodontitis patients with T2DM before and after nonsurgical periodontal therapy (NSPT). Materials and Methods: Sixty subjects were divided into four groups (15 each): Group I (systemically and periodontally healthy), Group II (systemically healthy with periodontitis), and Groups III and IV (periodontitis with T2DM, exhibiting good glycemic control [hemoglobin A1c (HbA1c) <7%] and poor control [HbA1c >8%]), respectively. Periodontal parameters such as plaque index, bleeding index, probing pocket depth, and clinical attachment level were assessed. Serum samples were collected at baseline and 3 months to measure sTWEAK, omentin-1, and TNF-α levels using ELISA. HbA1c levels were evaluated at baseline and 3 months. Results: TNF-α was significantly elevated in all groups compared with sTWEAK and omentin-1. However, omentin-1 levels were higher in the healthy group compared with all other groups. Periodontal parameters and biomarker levels showed significant improvement across all groups after 3 months post-NSPT. Conclusion: TNF-α and sTWEAK may serve as diagnostic markers, while omentin-1 can be a reliable prognostic marker for evaluating NSPT effects in T2DM patients with periodontitis and varying glycemic control.

Background: The main objective of this prospective, multicenter study (REVEAL-CP) was to test children with cerebral palsy-like signs and symptoms for raised 3-O-methyldopa (3-OMD) blood levels, a biomarker for aromatic L-amino acid decarboxylase deficiency (AADCd). A secondary objective was to characterize the molecular basis for the defective aromatic L-amino acid decarboxylase (AADC) gene product. Methods: Patients were identified in pediatric secondary and tertiary care hospitals through database searches and personal communication. 3-OMD concentrations from Guthrie card tests were determined using liquid chromatography/mass spectrometry. If 3-OMD was raised, cerebrospinal fluid analysis and dopa decarboxylase (DDC) gene sequencing were performed. An in-silico mutagenesis analysis was carried out to model altered AADC enzymes. Results: In total, 166 patients were enrolled in this study. The median age was 8 years. Sixty-six patients (39.8%) had a diagnosis of cerebral palsy, with the most common type being "mixed" (n = 42; 25.3%). One patient (0.6%), an 11-month-old boy from Italy, was diagnosed with AADCd caused by a homozygous, pathogenic DDC variant (c.749C>T; p.Ser250Phe). Three-dimensional modeling of the Ser250Phe AADC enzyme variant revealed its destabilization. Conclusions: A Guthrie card test for 3-OMD is a recognized screening technique for AADCd. If universal newborn screening for this metabolic disease is not available, children with signs and symptoms of a movement disorder should be investigated for AADCd.

Background: Tetralogy of Fallot (TOF) is the most common cyanotic heart defect in newborns, with a complex etiology and genetic variation considered to be one of the main pathogenic factors. Identifying genetic variations associated with TOF has important clinical value for understanding its pathogenesis, patient susceptibility, and prognosis of patients with TOF. Therefore, this study aimed to identify potential pathogenic genes of TOF through comprehensive genetic analysis. Materials and Methods: In this study, we employed whole exome sequencing (WES) of the DNA of 47 Chinese children who received surgical TOF treatment at the Children's Hospital of Zhejiang University of Medicine and processed for DNA extraction and quantification of the DNA following WES using the Illumina NovaSeq platform. WES data undergo strict quality control and analysis processes including alignment, postprocessing, variant calling, annotation, and prioritization. Key tools, such as GATK's haplotype calling module and Annotate Variation, were used for variant annotation. In addition, by combining bioinformatics tools such as SIFT, Polyphen2, and Clin Pred, we evaluated the potential impact of nonsynonymous mutations on protein function and referred to relevant literature to support our prediction. Results: Comprehensive data analysis and quality assessment analysis corroborated the data generated from the WES dataset of 47 patients with TOF. Interpreting variants from the perspective of clinical pathogenicity results revealed a novel polymorphism and variant associated with TOF. The identified genetic results revealed evidence for a major contribution of MUTYH, RARB, GFM1, PDZD2, CEP57, DCPS, POMT2, BUB1B, CYP19A1, MAZ, USP10, and TCF3 and provided novel findings for functionally interacting proteins associated with the pathomechanism of TOF. Seven pathogenic variants related to TOF were detected, most of which were previously unreported in this cohort. Conclusions: The genetic variations discovered in this study emphasize the importance of genetic factors in the pathogenesis of TOF, revealing its complex molecular pathways and protein-protein interactions. The study of genetic diversity provides a new perspective for understanding the etiology of TOF and promotes an in-depth exploration of its pathological mechanisms. These findings lay the foundation for subsequent clinical research and the development of treatment strategies.