Genetic testing and molecular biomarkers最新文献

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes a respiratory disorder responsible for the global pandemic and widespread mortality. Circular RNAs (circRNAs), one of the newest forms of noncoding RNAs (ncRNAs), are important regulators of the host immune response and viral replication through sponging of microRNAs (miRNAs). This work aims to look at the expression and functions of hsa_circ_0009910/hsa-miR-145-5p/IFN beta 1 (IFNB1) in SARS-CoV-2-related infection and the molecular mechanisms that underpin them. In the experimental phase of the study, total RNA was isolated from the peripheral blood mononuclear cells (PBMCs) of 48 patients with symptomatic COVID-19, 48 patients with nonsymptomatic COVID-19, and 48 negative controls, and then cDNA was synthesized. Next, the expression of these genes was examined with quantitative real-time PCR (qRT-PCR). A receiver operating characteristic (ROC) curve was created to assess each gene's potential as a biomarker. The interactions of hsa_circ_0009910, hsa-miR-145-5p, and IFNB1, also the functional and pathway enrichment analyses, were detected by bioinformatics analysis. When compared with the negative control group, the expression of hsa_circ_0009910 in both symptomatic and nonsymptomatic groups, and IFNB1 in the symptomatic group was higher in the COVID-19 patients. Furthermore, the relative expression of hsa-miR-145-5p in the symptomatic and nonsymptomatic groups was lower than that in the negative control group. In addition, there was a positive correlation between hsa_circ_0009910 and IFNB1 expression, as well as a negative correlation between hsa-miR-145-5p, hsa_circ_0009910, and IFNB1 expressions. hsa-miR-145-5p has a higher area under the curve and may be a more effective biomarker to distinguish COVID-19 patients from the healthy controls, based on ROC curve study, but further study is needed. In conclusion, our data show that the hsa_circ_0009910/hsa-miR-145-5p/IFNB1 triple network may play a role in the pathogenesis of COVID-19 and can be considered a therapeutic target in COVID-19 patients.

Background: Autoimmune thyroid diseases (AITDs), including Hashimoto's thyroiditis and Graves' disease, are characterized by aberrant immune responses influenced by both genetic predisposition and environmental triggers. Genetic association studies have identified several candidate loci that may contribute to the onset and progression of these conditions. The present study investigates the potential impact of specific genetic polymorphisms in interleukin genes (IL17A, IL1B, IL18) and CTLA-4 on thyroid peroxidase antibody (TPOAb) levels in individuals from northwest Iran. Results: A total of 82 individuals with elevated TPOAb levels and 82 antibody-negative controls were genotyped for single nucleotide polymorphisms using the tetra-primer amplification refractory mutation system polymerase chain reaction. The analysis revealed significant associations between specific genetic variants and TPOAb levels. Notably, the AG genotype of IL17A rs4711998 was associated with a protective effect, whereas the AA genotype of IL1B rs16944 was correlated with elevated antibody levels, suggesting a potential role in enhancing autoimmune responses. Conclusions: These findings underscore the contribution of genetic variations in interleukin genes to the pathogenesis of AITDs in the northwest Iranian population. Elucidating these associations may enhance our understanding of disease mechanisms and contribute to the development of targeted therapeutic strategies.

Background: Familial exudative vitreoretinopathy (FEVR) is a rare inherited ocular disorder characterized by abnormal peripheral retinal vascular development. KIF11 variants are known to cause autosomal dominant FEVR, but novel pathogenic variants remain to be identified. Objective: This study aimed to identify a novel causative variant of FEVR and provide evidence for genetic counseling. Methods: Whole-exome sequencing was performed on members of a Chinese family with FEVR. Rare variants with a gnomAD allele frequency <0.1% in East Asian and general populations were prioritized. Sanger sequencing was used for validation, and bioinformatic analyses (including Combined Annotation Dependent Depletion [CADD] score and cross-species conservation analysis) were conducted to assess pathogenicity. Results: A novel heterozygous frameshift variant KIF11 c.1239_1240del (p.V414Sfs*9) was identified in the proband, his brother, and his mother. This variant, absent from public databases (1000 Genomes, ExAC, gnomAD), had a CADD score of 26.9 and affected a highly conserved residue, suggesting disruptive effects on protein structure. The proband's mother showed macular involvement. Conclusions: The novel KIF11 frameshift variant (c.1239_1240del p.V414Sfs*9) identified in a Chinese family expands the mutation spectrum of autosomal dominant FEVR, with macular involvement aiding clinical prognostic assessment.

Background: Methyltransferase proteins, including SET Domain Containing 7 (SETD7), play an important role in the initiation of carcinogenesis through epigenetic mechanisms. Due to the reduced chance of survival in colorectal cancer (CRC), it is necessary to find molecular methods to detect CRC in the early stages. This study aimed to investigate the expression of SETD7 in metastatic and nonmetastatic tumor tissues in CRC compared with healthy tissue in order to evaluate its potential as a biomarker for the diagnosis of CRC in the early stages. Methods: In this study, the expression level of the SETD7 gene in primary colon adenocarcinoma was analyzed using the UALCAN database. To confirm the bioinformatics data, SETD7 gene expression was investigated in 80 colorectal tumor tissues (metastatic and nonmetastatic) and adjacent normal tissues using RT-qPCR. Results: According to the results obtained from the UALCAN database, SETD7 expression is significantly increased in tumor tissues compared with normal tissues, which was confirmed by the RT-qPCR results. We showed that although the SETD7 expression level in colorectal tumor tissues was higher than in adjacent normal tissues (p = 0.0001), this increase was only statistically significant in nonmetastatic tumor tissues (p = 0.0001). Based on receiver operating characteristic (ROC) analysis, increased SETD7 gene expression can be used as a good biomarker to distinguish tumor tissue from normal tissue in the early stages (area under the ROC curve = 0.85). Conclusion: Increased SETD7 gene expression can be used as an epigenetic marker in tissue-based prognosis and screening of CRC in the early tumor stages.

Noncoding RNAs (ncRNAs) comprise a significant portion of the transcriptome and contribute to various cellular and molecular processes and disease development. Although many functional roles for ncRNAs have been discovered, the regulatory functions of many require further elucidation. Intervertebral disk degeneration (IDD) is a leading cause of lower back pain and represents a major social and financial challenge worldwide. This review summarizes the literature on long ncRNAs and circular RNAs as novel regulators in IDD development. IDD diminishes quality of life, underscoring the importance of research on its pathogenesis and the identification of novel therapeutic targets. The definitive cellular and molecular mechanisms underlying IDD pathogenesis remain unidentified, and no effective treatment is available. Both genetic and environmental or lifestyle factors are associated with IDD development. Therefore, understanding the exact molecular mechanisms of IDD could yield novel therapeutic targets.

Background: Postaxial polydactyly (PAP) is characterized by the development of extra digits at the fifth finger. It can occur as an isolated disease or a part of a syndrome. The genetic basis of nonsyndromic PAP has been linked to sequence variants in different genes. The aim of the present study was to identify the causative genetic variants in four Pakistani families demonstrating PAP. Methods: Causative genetic variants were identified using whole-exome sequencing and microsatellite mapping, followed by validation through Sanger sequencing. Further analysis was carried out through conservation, structural modeling, and 100-ns molecular dynamic simulations of GLI1. Results: Whole-exome and targeted sequencing in four families (A, B, C, and D) identified novel variants in the GLI1 (c.1013G>T; p.Cys338Phe), and GLI3 (c.2003C>T; p.Pro668Leu and c.4564delG; p.Ala1522ProfsTer2), and a recurrent variant in IQCE genes (c.895_904del; p.Val301SerfsTer8) linked to 7p22.3. All the variants were highly conserved across different species. Comparative analysis of the GLI1^WT and GLI1^Cys338Phe proteins revealed domain fluctuations leading to the loss of structurally and functionally important inter- and intramolecular interactions. The three-dimensional structural analysis of the GLI3 protein showed that the missense variant p. (Pro668Leu) disturbed the protein folding and intra-residue interaction, while the frameshift variant p. (Ala1522ProfsTer2) led to the loss of the C-terminus of the protein. Similarly, the IQCE structural analysis confirmed the loss of protein function due to frameshift and C-terminal deletion. Conclusion: This study has broadened the phenotypic and allelic spectrum of the genes associated with isolated PAP and strengthened the role of these genes in regulating limb development.

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.