Biochemical Genetics最新文献

Diabetic foot ulcer (DFU) is one major, common and serious chronic complication of diabetes mellitus, which is characterized by high incidence, high risk, high burden, and high treatment difficulty and is a leading cause of disability and death in patients with diabetes. Long-term hyperglycemia can result in cellular dysfunction of fibroblasts, which play pivotal roles in wound healing. MicroRNAs (miRNAs) were reported to mediate the pathological processes of multiple diseases, including diabetic wound healing. This research aimed to investigate the functional role of miR-145-5p in high-glucose (HG)-exposed fibroblasts and in DFU mouse models. Human foreskin fibroblast cells (HFF-1) were stimulated by HG to induce cell injury. MiR-145-5p level in HG-stimulated HFF-1 cells was detected via RT-qPCR. The binding between miR-145-5p and PDGFD was validated by Luciferase reporter assay. The effects of the miR-145-5p/PDGFD axis on the viability, migration, and apoptosis of HG-exposed HFF-1 cells were determined by CCK-8, wound healing, and flow cytometry assays. DFU mouse models were subcutaneously injected at the wound edges with miR-145-5p inhibitor/mimics. Images of the wounds were captured on day 0 and 8 post-injection, and wound samples were collected after mice were sacrificed for histological analysis by H&E staining. HG decreased cell viability and increased miR-145-5p expression in HFF-1 cells in a dose- and time-dependent manner. MiR-145-5p downregulation promoted cell viability and migration and inhibited cell apoptosis of HG-stimulated HFF-1 cells, while miR-145-5p overexpression exerted an opposite effect on cell viability, migration, and apoptosis. PDGFD was a direct target gene of miR-145-5p, whose silencing reversed the influence of miR-145-5p downregulation on HG-induced cellular dysfunction of HFF-1 cells. Additionally, downregulating miR-145-5p facilitated while overexpressing miR-145-5p inhibited wound healing in DFU mouse models. MiR-145-5p level was negatively associated with PDGFD level in wound tissue samples of DFU mouse models. MiR-145-5p inhibition improves wound healing in DFU through upregulating PDGFD expression.

MicroRNAs could be promising biomarkers for various diseases, and small RNA drugs have already been FDA approved for clinical use. This area of research is rapidly expanding and has significant potential for the future. Fennel (Anethum foeniculum) is a highly esteemed spice plant with economic and medicinal benefits, making it an invaluable asset in the pharmaceutical industry. To characterize the fennel miRNAs and their Arabidopsis thaliana and Homo sapience targets with functional enrichment analysis and human disease association. A homology-based computational approach characterized the MiRnome of the Anethum foeniculum genome and assessed its impact on Arabidopsis thaliana and Homo sapience transcriptomes. In addition, functional enrichment analysis was evaluated for both species' targets. Moreover, PPI network analysis, hub gene identification, and MD simulation analysis of the top hub node with fennel miRNA were incorporated. We have identified 100 miRNAs of fennel and their target genes, which include 2536 genes in Homo sapiens and 1314 genes in Arabidopsis thaliana. Functional enrichment analysis reveals 56 Arabidopsis thaliana targets of fennel miRNAs showed involvement in metabolic pathways. Highly enriched human KEGG pathways were associated with several diseases, especially cancer. The protein-protein interaction network of human targets determined the top ten nodes; from them, seven hub nodes, namely MAPK1, PIK3R1, STAT3, EGFR, KRAS, CDC42, and SMAD4, have shown their involvement in the pancreatic cancer pathway. Based on the Blast algorithm, 21 fennel miRNAs are homologs to 16 human miRNAs were predicted; from them, the CSPP1 target was a common target for afo-miR11117a-3p and has-miR-6880-5p homologs miRNAs. Our results are the first to report the 100 fennel miRNAs, and predictions for their endogenous and human target genes provide a basis for further understanding of Anethum foeniculum miRNAs and the biological processes and diseases with which they are associated.

Data on the role of CYP2D6 and CYP3A4/5 polymorphisms in relation to risperidone (RIS) pharmacokinetics (PK) in children are relatively limited and inconsistent. This is partially attributable to the limited coverage of CYP2D6 and CYP3A4/5 metabolizer phenotypes, particularly those of poor and ultrarapid metabolizers (PMs and UMs), which has led to calls for studies of populations with a non-European background that may carry variants that are less frequent in Europeans. Children ≤ 18 years old with at least 8 weeks of a RIS-based regimen were recruited from three autism centers in Riyadh, Saudi Arabia. The primary outcomes measured were plasma concentrations of RIS and 9-hydroxyrisperidone (9-OH-RIS) and their dose-adjusted (C/D) ratios as a function of phenotypes and activity score (AS). For accurate DNA genotyping, targeted pharmacogenomic testing with the Axiom PharmacoFocus Array was performed via examination of a broad collection of probesets targeting CYP2D6 and CYP3A4/5 variants. The frequency of genotypes/phenotypes and the impact of their allele translation and phenoconversion-predicted enzyme activity were examined. The final cohort included 83 individuals. The most common CYP2D6 phenotype in our population was normal metabolizers (NMs, 66.3%). Inconsistent with some previous studies, the three phenotypes of intermediate metabolizers (IMs), NMs, and UMs were significantly different in terms of RIS concentration, the RIS/9-OH-RIS ratio, the RIS C/D ratio and the 9-OH-RIS C/D ratio. According to AS analyses, there were statistically significant differences in the RIS concentration (P = 0.013), RIS/9-OH-RIS ratio (P < 0.001) and RIS C/D ratio (P = 0.030) when patients were categorized into AS ≤ 1 vs. AS > 1. None of the CYP3A4/5 star allele translated phenotypes revealed a significant influence on any of the RIS PK parameters. Notably, neither CYP2D6 nor CYP3A4/5 phenotyping demonstrated a significant impact on the total active moiety, suggesting that other gene variants could modulate RIS PK. The study confirmed the previously reported partial impact of the CYP2D6 gene on RIS PK. However, future studies using contemporary genotyping techniques targeting a wide range of variants in other candidate genes must be conducted to further examine their interactive effects on RIS PK and the clinical response.

SLC4A4 variants are the etiologies of inherited proximal renal tubular acidosis (pRTA), which results in metabolic acidosis, hypokalemia, glaucoma, band keratopathy, and cataract. This study aims to characterize SLC4A4 variant and uniparental isodisomy of chromosome 4 in a patient, and analyse the functional characterization of SLC4A4 variants. This study analyzed renal tubular acidosis disease genes by whole exome sequencing (WES). H3M2 algorithm was used to analyze the run of homozygosity region in chromosomal regions in trio-WES data. The pathogenicity analysis of variants was performed using bioinformatics tools. Additionally, protein stability was analyzed by cycloheximide chase assay. Whole-cell patch clamping was used to examine the electrophysiological properties of NBCe1-A. A novel homozygous SLC4A4 variant was identified in the patient: a missense variant c.496C > T, p. Arg166Trp (NM_003759.4). But the father was heterozygous variant carrier, and the mother did not detect the variant. The H3M2 and UPDio algorithm revealed paternal uniparental isodisomy on chromosome 4 in the patient. SIFT, Poly Phen-2, FATHMM and Mutant Taster showed that the variant might be pathogenic. The tertiary structure analysis showed that the variant could cause structural damage to NBCe1 protein. Foldx results showed that the protein stability of the variant was slightly reduced. Cycloheximide chase assay demonstrated that the variant affects protein stability. The result of electrophysiological studies showed that the variant altered Na⁺/HCO₃^- cotransport activity of protein. In conclusion, the study is the first to report a pRTA patient with Arg166Trp variant with UPiD (4) pat and analyze the function of Arg166Trp variant.

The number of patients with COVID-19 caused by severe acute respiratory syndrome coronavirus 2 is still increasing. In the case of COVID-19 and tuberculosis (TB), the presence of one disease affects the infectious status of the other. Meanwhile, coinfection may result in complications that make treatment more difficult. However, the molecular mechanisms underpinning the interaction between TB and COVID-19 are unclear. Accordingly, transcriptome analysis was used to detect the shared pathways and molecular biomarkers in TB and COVID-19, allowing us to determine the complex relationship between COVID-19 and TB. Two RNA-seq datasets (GSE114192 and GSE163151) from the Gene Expression Omnibus were used to find concerted differentially expressed genes (DEGs) between TB and COVID-19 to identify the common pathogenic mechanisms. A total of 124 common DEGs were detected and used to find shared pathways and drug targets. Several enterprising bioinformatics tools were applied to perform pathway analysis, enrichment analysis and networks analysis. Protein-protein interaction analysis and machine learning was used to identify hub genes (GAS6, OAS3 and PDCD1LG2) and datasets GSE171110, GSE54992 and GSE79362 were used for verification. The mechanism of protein-drug interactions may have reference value in the treatment of coinfection of COVID-19 and TB.

The spotted pond turtle Geoclemys hamiltonii (Gray, 1830) is widely distributed in the Indus, Ganges, and Brahmaputra river basins. In this study, the complete mitochondrial genome (mitogenome) of G. hamiltonii was sequenced using the next-generation sequencing (NGS) and Sanger sequencing, and the essential characteristics, gene arrangement, and phylogenetic relationship were analyzed. The results showed that the G. hamiltonii mitogenome was 16,505 bp in length (A: 33.6%, C: 27.1%, G: 13.4%, T: 25.8%) and consisted of 22 tRNAs, 13 protein-coding genes, two ribosomal RNA genes, and a non-coding control region (GenBank accession ON243873). The genome composition of G. hamiltonii presented a slight A + T bias (59.4%), and showed a positive AT skew (0.131) and a negative GC skew (- 0.338). All tRNAs had the typical clover structure, except trnS1 (GCT). The gene order of the G. hamiltonii mitogenome was the same as other Geoemydidae mitogenomes. A phylogenetic analysis based on the complete mitogenome indicated that the G. hamiltonii grouped independently of other species in the family Geoemydidae, supporting the species' placement in the monotypic genus Geoclemys. Our results describe a novel genome at the species level. As the first complete mitogenome of G. hamiltonii, it provided valuable molecular information for phylogenetic and conservation genetics analyses of G. hamiltonii.

Osteoporosis (OP) has a significant detrimental impact on the health of the elder. Long-term clinical effectiveness of current drugs used for OP treatment is limited. Therefore, it is very important to explore novel treatment targets for OP. The expression of SNHG1, HMGB1, OCN and OPN in gene level was measured using RT-qPCR, and the protein expression was determined by Western blotting assay. The concentration of IL-1β and IL-18 in supernatant of the bone marrow mesenchymal stem cells (BMSCs) was measured by ELISA. The interaction between SNHG1 and HMGB1 was confirmed by RNA pull down. Besides, alizarin red staining was performed to evaluate the differentiation of BMSCs into osteoblast. SNHG1 and HMGB1 were found to be upregulated in the serum of OP patients. During the osteogenic differentiation of BMSCs, the expression of osteoblastogenesis markers (OCN and OPN) and the activity of ALP were upregulated, while the expression levels of SNHG1 and HMGB1 were decreased in a time-dependent manner. In addition, the interaction between SNHG1 and HMGB1, expression of pyroptosis-associated factors (caspase-1 p20 and GSDMD-N), and secretion of IL-1β and IL-18 were also decreased during osteogenic differentiation. Interestingly, increasing SNHG1 promoted HMGB1 expression, activated pyroptosis, but inhibited osteogenic differentiation. Silencing HMGB1 or inhibiting caspase-1 partially rescued the inhibitory effect of SNHG1 on osteogenic differentiation. Our findings indicate that SNHG1 suppresses the osteogenic differentiation of BMSCs by activating pyroptosis through interaction with HMGB1 and promotion of HMGB1 expression. Our work provides further evidence supporting SNHG1 acts as a potential target for OP treatment, and reveals for the first time that SNHG1 regulates osteogenic differentiation by affecting pyroptosis.

Rheumatoid arthritis (RA) is a common inflammatory autoimmune disease characterized by synovial inflammation and joint damage. Previous studies have shown that pyroptosis plays an important role in the pathogenesis of RA. In this study, the effects of circular RNA hsa_circ0000175 on pyroptosis and inflammation of RA were evaluated. Serum levels of circ_0000175 and miR-31-5p were determined by RT-qPCR, and the correlation between them was evaluated by Spearman correlation analysis. Fibroblast-like synoviocytes (FLSs) were extracted and prepared for in vitro study. The subcellular localization of circ_0000175 was detected by FISH assay. Pyroptosis and inflammatory cytokines interleukin (IL)-1β, IL-18 and IL-6 were measured by flow cytometry and ELISA, respectively. RNA pull-down and luciferase reporter assays verified the interaction between circ_0000175 and miR-31-5p. Western blot was used to detect the differential expression of pyroptosis-related factors (GSDME-N, GSDMD-N, cleaved caspase-1 and cleaved caspase-3). Circ_0000175 level was increased but miR-31-5p expression was decreased in PBMCs of RA patients and LPS/ATP-treated FLSs, companied with negative correlation. Moreover, miR-31-5p was a target of circ_0000175 in RA-FLSs. Silencing of circ_0000175 or overexpression of miR-31-5p significantly alleviated LPS/ATP-induced pyroptosis in FLSs through both caspase-1/GSDMD and caspase-3/GSDME pathways. Additionally, GSDME was identified as the target of miR-31-5p. The inhibitory effects of circ_0000175 depletion on pyroptosis and inflammation in RA-FLSs treated with LPS/ATP were strengthened by GSDME knockdown. Circ_0000175 can induce pyroptosis and trigger inflammatory response during the occurrence of RA through the miR-31-5p/GSDME axis, which provides a novel therapeutic target for RA treatment.

Background: Colorectal cancer (CRC) is a common gastrointestinal malignancy. Dysregulation of circular RNAs (circRNAs) is associated with the progression of CRC. However, the role of circ_0013339 (hsa_circ_0013339) in CRC is still not clear.

Methods: The levels of circ_0013339, miR-136-5p, and SRY-box transcription factor 9 (SOX9) in CRC were gauged by quantitative real-time polymerase chain reaction (qRT-PCR). Colony formation and 5-Ethynyl-2'-deoxyuridine (EdU) assays were used to detect cell proliferation. Cell counting kit-8 (CCK8) assay was used to measure cell viability. Western blot assay was performed to examine protein expression. The relationship between miR-136-5p and circ_0013339 or SOX9 was tested by dual-luciferase reporter assay. The effect of sh-circ_0013339 on tumor growth in vivo was examined by xenograft experiments.

Results: Circ_0013339 expression was elevated in CRC tissues and cells, and circ_0013339 knockdown diminished the growth of CRC cells. MiR-136-5p was regulated by circ_0013339. MiR-136-5p deficiency ameliorated the effects of circ_0013339 silencing on CRC cell malignant behaviors. Circ_0013339 modulated SOX9 expression through miR-136-5p. SOX9 addition reversed the effects of miR-136-5p overexpression on CRC cell behaviors. Moreover, silencing of circ_0013339 suppressed the growth of xenograft tumors in vivo.

Conclusion: Circ_0013339 regulates the progression of CRC through miR-136-5p-dependent regulation of SOX9, uncovering a novel regulatory mechanism of circ_0013339 in CRC.

The chemoattractant Receptor23 (ChemR23) plays an essential role in triggering and resolving acute inflammation. This study aimed to evaluate the association between four potentially functional SNPs of the chemR23 gene (rs4373981 G > C, rs73201532 C > T, rs35121177 G > A, and rs4964676 G > A) with susceptibility to Allergic rhinitis (AR). 130 patients with allergic rhinitis and 130 healthy individuals were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Our findings showed that genotypes and alleles frequencies were not significantly different between patient and control groups (p > 0.05). Furthermore, haplotype analysis (rs4373981, rs73201532, and rs4964676, respectively) revealed a protective effect of CTG, GTA, and GTG haplotypes against AR (p = 0.009, p = 0.0001, p = 0.001, respectively), and CCG, GCA, and GCG haplotypes of ChemR23 polymorphisms were associated with increased risk of AR (p = 0.03, p = 0.02, p = 0.0002, respectively). These findings suggested a possible role for ChemR23 in the pathogenesis of AR.