Genetic testing and molecular biomarkers最新文献

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.

Background: Gene variants of ICAM1 (rs1799969), ADD1 (rs4961), NPPA (rs5065), and NOS3 (rs1799983) have been proposed as possible genetic risk factors for vascular compromise in gastroschisis. However, this interpretation is questionable because the vascular disruption theory is now considered unlikely. According to current knowledge, gastroschisis is caused by a separation of the umbilical ring. Aim: This study reevaluated the gene variants of ICAM1 (rs1799969), ADD1 (rs4961), NPPA (rs5065), and NOS3 (rs1799983) as potential genetic risk factors for gastroschisis. Materials and Methods: The study involved a cohort of 151 live-born patients with gastroschisis (cases) and 229 controls from Western Mexico. We used Sanger sequencing to investigate the potential influence of risk alleles for the ICAM1 (rs1799969), ADD1 (rs4961), NPPA (rs5065), and NOS3 (rs1799983) gene variants. Data were analyzed using logistic regression analysis. Results: The risk of gastroschisis increased in relation to the frequency of homozygosity for the ICAM1 778G>A (rs1799969) variant among cases and controls (6% vs. 2.6%, respectively, adjusted odds ratio = 3.2, 95% confidence interval 1.0-10.1). For the ADD1 1378G>T (rs4961), NPPA 553T>C (rs5065), and NOS3 894G>T (rs1799983) gene variants, the adjusted odds ratios did not show an association with the risk of gastroschisis. Conclusions: Although the number of identified homozygotes was small, our results suggest that the ICAM1 778AA (gly241arg) genotype is associated with an increased risk of gastroschisis. This gene variant is discussed in relation to the pathogenesis of amniotic damage in gastroschisis.

Background: Rheumatoid arthritis (RA) is a chronic inflammatory disease, presenting with joint inflammation and its progressive destruction, affecting a range of about 0.24-1% of the population in different parts of the world. It is one of the major disabling conditions among middle-aged and older women. In this study, the association between five single nucleotide polymorphisms (SNPs) of the CTLA4 gene and RA was investigated. Materials and Methods: The study group included 200 patients with RA and 184 healthy individuals from the Iranian population as a control group. Results: After PCR and genotyping, 4 of the 5 SNPs studied showed a significant association with RA. Also, an association between specific haplotypes with RA was determined. Conclusion: Based on the results, it can be said that some SNPs of the CTLA4 gene may serve as genetic markers for predicting RA susceptibility or progression and using personalized treatment, lead to improved outcomes among patients with RA.

Background: Inherited hearing loss is an extremely heterogeneous and often ethnicity-specific disorder, with more than 150 genes identified to date. Thus, clinical diagnosis is challenging, particularly because of the thousands of different severe causal mutations between populations. Materials and methods: In this study, we aimed to identify the mutational spectra associated with hearing loss in 89 Southwestern Chinese families. We used a hearing loss-targeted panel to sequence 163 genes known to cause or be candidate genes for hearing loss. The targeted panel was implemented to 89 families with syndromic or nonsyndromic hearing loss. Results: Of the total 89 patients, 55 patients carried 101 pathogenic/likely pathogenic alleles, providing a genetic diagnosis in 61.80%. GJB2 variants were predominant, with a frequency of 43.6% among all variants, followed by variants of SLC26A4 (31.7%), MYO15A (5.9%), and MT-RNR1 (5%). These 4 genes accounted for 80.56% (87/108) of all identified alleles. Furthermore, 3 of the 89 patients carried 7 alleles of unknown significance. In total, 45 variants were identified, including 35 variants reported in the Human Gene Mutation Database Professional and 10 novel variants that had not been previously reported. Conclusion: Our findings provide a survey of the mutation spectrum in patients with hearing loss from Southwestern Chinese families. This highlights the fact that genomic sequencing with a selected gene panel specific to hearing loss is effective for its genetic diagnosis.

Background: Aplasia cutis congenita and ectrodactyly skeletal syndrome (ACCES) is caused by heterozygous variants in the UBA2 gene, with phenotypic heterogeneity encompassing a range of diverse skeletal, dermatological, and neurological features. Aims: The goal of our research was to suggest that pathogenic frameshift variant c.52_58dupGGCCGGG p.(Val20Gfs*31) could lead to the development of ACCES and also to review the literature to document phenotypic variability among individuals with UBA2 variants, providing further insights into this ultrarare syndrome. Methods and Result: We report a case of a 7-year-old male presenting with cutis aplasia congenita, syndactyly, preaxial polydactyly, and severe hypospadias. Exome sequencing (ES) identified a heterozygous frameshift variant c.52_58dupGGCCGGG p.(Val20Gfs*31) in the UBA2 gene. This variant is absent in gnomAD and is predicted to cause a premature stop codon with consequent protein truncation and/or nonsense-mediated decay. Initially classified as a variant of uncertain significance, this frameshift variant was reclassified as pathogenic following a comprehensive reassessment post-enrollment of the patient in the Undiagnosed Rare Disease Clinic of Indiana University School of Medicine. Conclusion: This study illustrates the critical role of ongoing genomic data reevaluation, particularly in unsolved cases, where variant reclassification has the potential to impact diagnostic precision, targeted treatment planning, and family counseling. The clinical variability observed among reported cases, spanning mild to severe presentations, underscores the complexity of UBA2-related disorders. This variability suggests an interplay of genetic modifiers, epigenetic influences, and environmental factors, highlighting the need for further research into the mechanisms driving this heterogeneity.

Slow transit constipation (STC) is a complication of depression that can negatively impact patient prognosis and quality of life. Nonetheless, the pathogenesis of STC is unclear. In this work, colon tissues from STC and non-STC patients were utilized to determine transcriptome expression patterns (messenger ribonucleic acids [mRNAs], Long noncoding RNAs [lncRNAs], and Circular RNAs [circRNAs]) via high-throughput sequencing. We found that 4430 mRNAs, 984 lncRNAs, and 2152 circRNAs exhibited substantial variations in expression patterns in the colon tissues of STC and non-STC patients. Next, we constructed a protein-protein interaction network and identified three significant elements, namely, POLR2B, SRSF1, and SUMO1, which attracted our interest. Utilizing the data of 6 upregulated circRNAs and 10 downregulated circRNAs, we created a competing endogenous RNA network. Subsequently, we found that hsa_circ_0000994 and hsa_circ_0008699 were significantly enriched in the upregulated and downregulated networks, respectively. The coexpression network analysis suggested that circRNAs and lncRNAs might exert control over mRNAs by influencing the neural functions of STC. According to the results of the integrated circRNA-miRNA-mRNA network, circRNA-regulated mRNAs were linked to both the transforming growth factor-β (TGF-β) and Notch signaling pathways. Our findings could provide new perspectives for identifying potential prognostic markers in STC. Targeting SUMO1 may present a promising approach to address colonic motility disorders in STC therapy.

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.