Biochemical Genetics最新文献

This study evaluated talin1 expression in platelets and platelet-derived microvesicles (PMVs) from nonvalvular atrial fibrillation (NVAF) patients. Meanwhile, this study analyzed the impacts of talin1 expression in PMVs on platelet activation. Twelve healthy controls and 38 NVAF patients were recruited in this study. The levels of talin1 and RAP1B activation were observed in the platelets and PMVs from the participants, and their levels were significantly increased in the NVAF patients compared to the healthy controls (P < 0.01). Talin1 silence in MEG-01 cells was obtained by transfecting talin1 siRNA, and the cells were stimulated by thrombin receptor-activating peptide 6 (TRAP-6) to induce platelet-dense granule secretion. TRAP-6 stimulation increased the talin1 expression and RAP1B activation in the platelet-like particles from MEG-01 cells, but talin1 silence suppressed the TRAP-6-stimulated RAP1B activation and CD62p expression in the platelet-like particle. Moreover, the platelets from healthy donors were activated by the PMVs from the TRAP-6-stimulated MEG-01 cells. However, the decreased talin1 level in the PMVs from MEG-01 cells weakened the platelet activation. This study suggested that talin1 expression in the PMVs affected platelet activation in patients with NVAF.

Drug resistance resulting from mutations in Plasmodium falciparum, that caused the failure of previously effective malaria drugs, has continued to threaten the global malaria elimination goal. This study describes the profiles of P. falciparum chloroquine resistance transporter (Pfcrt) and P. falciparum multidrug resistance 1 (Pfmdr1), the genetic markers associated with 4-aminoquinoline resistance, among P. falciparum isolates from Lagos, Nigeria. Genomic DNA was extracted from the dried blood spot samples obtained from individuals with microscopically confirmed P. falciparum infection in health facilities and communities in Lagos State, Nigeria. The DNA was amplified using nested polymerase chain reaction, and sequence analysis was performed to identify single nucleotide polymorphisms in the pfcrt and pfmdr1 genes. The study showed that 82.4% (178) of the isolates had pfmdr1 wild-type, while mutations were observed at codons N86Y (11.6%) and D1246Y (3.2%). Other mutations seen were at codons Y23S (0.5%), E130K (2.3%), and S149P (0.5%). 30.8% (64) of the isolates had pfcrt wild-type (CVMNK), while 62.0% (129) had CVIET (mutant) haplotype. Other pfcrt haplotypes detected include; CVIDT (1.9%); CVMDT (1.4%); CVIKT (1.0%); CVINT (0.5%); CVMET (0.5%); CVMKT (0.5%); CVMNT (1.0%); and CVMEK (0.5%). The findings underscore the presence of uncommon pfcrt haplotypes and a high prevalence of drug-resistant pfcrt haplotypes (CVIET), alongside a high prevalence of wild-type pfmdr in Lagos. This study highlights the need for ongoing surveillance of these genetic markers to provide data that can inform decisions on malaria case management and preserve the efficacy of artemisinin combination therapies (ACTs) in Nigeria.

Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by intestinal inflammation and autoimmune responses. This study aimed to identify diagnostic biomarkers for UC through bioinformatics analysis and machine learning, and to validate these findings through immunofluorescence staining of clinical samples. Differential expression analysis was conducted on expression profile datasets from 4 UC samples. Key biomarkers were selected using LASSO logistic regression, SVM-RFE, and Random Forest algorithms. The diagnostic performance of these biomarkers was evaluated using receiver operating characteristic (ROC) curves. Functional enrichment analysis assessed the biological functions of these biomarkers. The CIBERSORT algorithm was used to analyze immune cell infiltration. Regulatory networks for diagnostic markers were constructed. Additionally, immunofluorescence staining was performed on clinical samples to validate the expression levels of key biomarkers. Differential analysis identified 199 significantly differentially expressed genes. SLC6A14 was selected as a key diagnostic biomarker, demonstrating excellent diagnostic performance in training and validation sets (AUC values: 0.973, 0.984, and 0.970). Immune cell infiltration analysis revealed significant increases in Neutrophils and activated Mast cells in UC samples, whereas resting Mast cells were relatively downregulated. Furthermore, SLC6A14 showed strong correlations with various immune cells. The ceRNA network identified 22 lncRNAs and 10 miRNAs associated with SLC6A14. Immunofluorescence staining of clinical samples confirmed that SLC6A14 expression is significantly higher in UC patients compared to normal intestinal mucosa, and its expression increases with UC activity. SLC6A14 has been confirmed as a key diagnostic marker for UC, validated both through bioinformatics analysis and immunofluorescence staining of clinical samples. It maintains regulatory relationships with various non-coding RNAs and plays a significant role in the pathogenesis of UC through its interactions with immune cells.

Genetic variations in the lipoprotein lipase (LPL) gene including the HindIII polymorphism (rs320) have been reported to modify fat metabolism, adiposity, and body weight. However, little attention has been given to the African population. The present study aimed to investigate the relationship between the rs320 gene polymorphism and a number of metabolic and anthropometric parameters in a sample of the Nigerian population. We recruited 236 participants for the study. The participants were required to sign informed consent forms after which information related to their calorie intake and utilization as well as anthropometric measurements were recorded. Plasma metabolic parameters were subsequently determined using an autoanalyzer. Genotyping for HindIII polymorphism was performed using the PCR-RFLP method. The frequencies (n) of T and G alleles were 0.841 (397) and 0.158 (75), while the frequencies (n) of TT, TG, and GG were 0.691(163), 0.301(71), and 0.01(2), respectively. The population was not in Hardy-Weinberg equilibrium (χ² = 3.717, df = 1, p = 0.841). The anthropometric parameters, the fasting blood glucose, and low-density lipoprotein cholesterol showed no association with the alleles, while plasma high-density lipoprotein cholesterol and total cholesterol were significantly higher among the G allele carriers. However, triglyceride and total protein were significantly higher among the non-G allele carriers. The LPL HindIII gene polymorphism is associated with changes in plasma lipid profile in a sample of the Nigerian population.

Sepsis, a life-threatening condition characterized by a systemic inflammatory response, leads to organ dysfunction and high mortality rates. Honeysuckle, a traditional herbal remedy, has shown promise in attenuating organ damage and inhibiting pro-inflammatory factors in sepsis. However, the underlying molecular mechanisms remain unclear. We employed a multi-omics approach to elucidate honeysuckle's potential therapeutic effects in sepsis. RNA sequencing was performed on blood samples from 22 sepsis patients and 10 healthy controls to identify differentially expressed genes. Network pharmacology was utilized to predict effective ingredients and therapeutic targets of honeysuckle in sepsis. Meta-analysis compared gene expression between sepsis survivors and non-survivors. Single-cell RNA sequencing was employed to localize target gene expression at the cellular level. We identified 1328 differentially expressed genes in sepsis, with 221 upregulated and 1107 downregulated. Network analysis revealed 15 genes linked to 12 honeysuckle components. Four genes-DPP4, CD40LG, BCL2, and TP53-emerged as core therapeutic targets, showing decreased expression in non-survivors but upregulation in survivors. Single-cell analysis demonstrated that these genes were primarily expressed in T cells and other immune cells, suggesting their role in regulating immune response and inflammation. This study uses single-cell RNA sequencing and network analysis to identify DPP4, CD40LG, BCL2, and TP53 as key regulatory targets in sepsis, providing insights into disease mechanisms and potential therapeutic interventions. Network pharmacology analysis suggests possible interactions with honeysuckle compounds, though experimental validation is needed.

Atherosclerosis is the main cause of coronary artery disease (CAD), and it is not easy to be detected at the early stage. To mine biomarkers for early diagnosis of CAD. Potential molecular mechanism was mined using the biological databases. The qPCR and western blotting were used to detect the expression of LINC01220, hsa-miR- 6727 - 5p, and FBLN5. Dual-luciferase report assay and overexpression experiment were used to explore the regulation among LINC01220, hsa-miR- 6727 - 5p, and FBLN5. The cell viability, migration, apoptosis, and senescence were evaluated by CCK- 8, transwell, Annexin V/PI staining, and detection of aging markers. The differentiation of human bone marrow monocytes (HBMMs) was evaluated by detecting the expression of CD68, CD86, and iNOS. The clinical analysis was performed based on the blood samples from healthy individuals and asymptomatic CAD patients. The receiver operating characteristic (ROC) curve and logistic regression analysis were used to evaluate the diagnostic value of LINC01220/hsa-miR- 6727 - 5p/FBLN5 in CAD. Overexpression of LINC01220 promoted FBLN5 expression by down-regulating hsa-miR- 6727 - 5p. LINC01220 rescued human aortic endothelial cell (HAEC) viability injury, apoptosis, and senescence induced by oxidized low-density lipoprotein (ox-LDL), and inhibited HBMM migration and differentiation, by regulating hsa-miR- 6727 - 5p/FBLN5. The area under curve (AUC) of the LINC01220/hsa-miR- 6727 - 5p/FBLN5 axis in diagnosing CAD was 0.954 (0.919-0.990), with sensitivity of 91.9% and specificity of 91.7%. LINC01220 may hinder CAD progression by negatively regulating hsa-miR- 6727 - 5p which targeted FBLN5, and they were potential biomarkers of CAD.

Intrauterine adhesions (IUA) is one of the most prevalent gynecological conditions affecting women of childbearing age. The active ingredient curcumin (CUR), derived from turmeric, is a promising candidate for the treatment of IUA. Nevertheless, the mechanism of action remains undetermined. This study investigates the role and mechanism of CUR in the treatment of IUA through network pharmacology, molecular docking, and molecular biology experiments. IUA-related targets were sourced from the GeneCards database. CUR-related targets were obtained from Herb and SwissTarget Prediction. Cytoscape version 3.10.2 was employed to construct PPI networks and to identify core targets. GO and KEGG enrichment analyses were conducted using the DAVID database. Additionally, molecular docking was employed to evaluate the interaction between CUR and core targets. Finally, the mechanism and targets of CUR in IUA were validated through animal experiments. A total of 122 common target points for CUR and IUA were identified. Topological analysis and KEGG analysis identified 20 core target points, encompassing multiple pathways, including inflammation and the PI3K/AKT signaling pathway. Molecular docking results demonstrated that CUR exhibits a strong binding affinity for the core target points. In vivo experiments indicate that CUR significantly alleviates the fibrosis and epithelial-mesenchymal transition (EMT) processes of the endometrium in IUA rats while inhibiting the overexpression of TGF-β1 in the uterine tissue of IUA rats and the activation of the PI3K/AKT and TLR4/NLRP3 signaling pathways. CUR can inhibit fibrosis and the EMT process in the endometrium of IUA rats, and its mechanism may be associated with the inhibition of the PI3K/AKT and TLR4/NLRP3 signaling pathways.

NASH poses a significant threat to human health and is recognized as the leading contributor to HCC. In this study, we leveraged publicly accessible datasets to identify novel differentially expressed genes that may serve as potential targets in NASH or potentially NASH-induced HCC. The publicly available datasets were obtained from the GEO. Differential gene expression analysis and enrichment analysis was performed. Subsequently, WGCNA and PPI network were constructed. Lastly, machine learning was employed to identify key feature genes. Utilizing the integrated GEO database, we identified 446 genes exhibiting differential expression. Enrichment analysis indicated that these genes are predominantly associated with glucose and lipid metabolism and inflammatory processes. Through WGCNA, three modules were identified that demonstrated a significant correlation with NASH. Furthermore, core genes among the differentially expressed genes were extracted via protein and protein interaction analysis. Ultimately, machine learning techniques were employed, leading to the identification of three genes: FosB, Fos, and SOCS3. Notably, FosB exhibited consistent expression across various datasets, demonstrated strong predictive capabilities for NASH, and was associated with improved prognostic outcomes in hepatocellular carcinoma by data from TCGA. Additionally, in vitro immunohistochemistry experiments revealed significant reduction of FosB expression in NASH. Bioinformatics analyses conducted on various datasets, along with in vitro immunohistochemistry experiments, revealed significant downregulation of FosB in NASH. It indicates that FosB plays a critical role in the pathogenesis of NASH, and its expression is associated with the prognosis of patients with HCC. Further experimental studies are required to investigate the potential targeting of FosB in NASH and NASH-induced HCC.

Common bean (Phaseolus vulgaris) anthracnose, caused by Colletotrichum lindemuthianum affects and decreases its yield substantially. Fifty Simple Sequence Repeat (SSR) markers were used to analyze the genetic and genotypic variation among 36 C. lindemuthianum isolates. Among the 50 SSRs, 24 were polymorphic and amplified 66 alleles. Most of the SSRs had polymorphic information content (PIC) values > 0.30, indicating their strong discriminative competence. Distance based dendrogram analysis and population structure analysis divided 36 C. lindemuthianum isolates into three clusters. Analysis of molecular variance at spatiotemporal levels showed high genetic variation among the populations. The six C. lindemuthianum subpopulations had high Shannon-Wiener indices. The multilocus genotype and genetic diversity indices show that C. lindemuthianum populations in Kashmir are diverse. The three geographic subpopulations of C. lindemuthianum rejected the null hypothesis of linkage equilibrium (p = 0.001). Before this study, all PCR based genetic diversity studies on C. lindemuthianum relied on dominant markers. This study is the first to identify 24 robust SSRs, which can be utilized to elucidate the population structure of the common bean anthracnose pathogen.

SATB2-associated syndrome (SAS) is a multisystemic disorder characterized by developmental delay, moderate to profound intellectual disability, speech delay and/or absent speech, behavioral issues such as autistic tendencies, agitation or aggressive outbursts, self-injury, impulsivity, hyperactivity, anxiety and sleeping difficulties. Alterations in the SATB2 gene have been identified as pathogenic causes of SAS. No formal clinical diagnostic criteria have been established for SAS, and molecular disruption of SATB2 is necessary to confirm the diagnosis. To investigate the molecular pathogenesis of five sporadic patients with intellectual disability, and to delineate the comprehensive clinical characteristics of SAS patients. Whole-exome sequencing analysis was performed in five unrelated patients, and RNA analysis was employed to validate the impact of genetic variation on aberrant splicing. Five SATB2 variants were identified, three of which were novel, including three frameshift variants, one nonsense variant, and a missense variant resulting in aberrant splicing was verified by RNA analysis. A comparative analysis was conducted between the clinical features of our patients and those reported in the literature. In addition to intellectual disability and impaired speech, abnormalities in palmar creases and postnatal growth delay were highlighted as clinically significant features for the diagnosis of SAS. Language regression, as well as joints and fingers abnormalities were also observed in our cohort. Our findings demonstrate that effective mRNA analysis is helpful for understanding the pathogenic mechanisms of novel variants. This study broadens the genetic and phenotypic spectrum of SAS and enhances our knowledge to facilitate accurate genetic counseling and appropriate treatment options.