Molecular Biotechnology最新文献

Renal ischemia-reperfusion injury (RIRI) is a primary cause of acute kidney injury (AKI), frequently resulting in high mortality rates and progression to chronic kidney disease (CKD). This study aimed to investigate the therapeutic potential of total saponins from Panax notoginseng (PNS) in the context of RIRI. Utilizing a murine RIRI model, the efficacy of PNS was evaluated, demonstrating a significant reduction in renal inflammation and cellular pyroptosis. Furthermore, PNS was found to modulate the ROCK2/NF-κB signaling pathway, thereby attenuating the inflammatory response. Importantly, in vitro experiments with hypoxia/reoxygenation cell models corroborated these findings, showing that PNS inhibited pyroptosis and regulated the ROCK2/NF-κB pathway. This research underscores the therapeutic potential of PNS in the treatment of RIRI, providing a robust scientific basis for its consideration as a prospective clinical therapy.

Lung adenocarcinoma (LUAD) is a leading cause of cancer-related deaths worldwide, and there is an urgent need to develop personalized prognostic models for effective treatment strategies. The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathways has been confirmed to engage in multiple cancer progression, prognosis, and immunotherapy benefits. However, the prognostic significance and immunotherapy response of cGAS-STING pathway-associated genes (CSPAGs) in LUAD remain unclear. Herein, we aimed to establish a CSPAG-based prognostic signature for LUAD patients. A total of 139 CSPAGs derived from the GSEA website were enrolled for subsequent analysis. Univariate Cox regression analysis shows that 22 of 139 CSPAGs were associated with LUAD prognosis. Lasso analysis identified 6 CSPAGs (IFNE, NFKB2, POL3RG, TRAF2, TICAM1 and NLRC3) as the most significant prognostic CSPAGs with the best model efficacy. The CSPAG signature classified LUAD patients into low-risk (LR) and high-risk (HR) groups. Kaplan-Meier analysis demonstrated that patients in the LR group had significantly better overall survival (OS) than those in the HR group (p < 0.05 represents statistical significance), indicating the predictive power of the CSPAG signature in LUAD prognosis. The receiver operating characteristic (ROC) curve analysis showed that the area under the curve (AUC) values for the CSPAG signature were higher than those for other well-established predictive factors, suggesting that the CSPAG signature had a higher predictive efficacy. The CSPAG nomogram incorporating clinical factors such as age, TNM status and the CSPAG risk score accurately predicted the OS of LUAD patients at 1, 3, and 5 years, indicating its potential clinical application in LUAD prognosis. Furthermore, we investigated the expression pattern of the 6 signature CSPAGs in different LUAD subpopulations with distinct clinical features. The CSPAG risk score was increased in the immune-high groups, suggesting a positive correlation between immune infiltration degree and CSPAG risk score. There was a heterogenicity of somatic mutation landscape between the two groups. The LR group had a strong immune cell activity, and most immune checkpoints were significantly expressed in the LR group, implying that this group benefited from immune checkpoint blockade (ICB) therapy. In addition, we verified the high predictive accuracy of the CSPAG signature in the GSE31210 and GSE203360 datasets. Taken together, this study established a CSPAG-based prognostic signature for LUAD patients with high predictive efficacy and clinical relevance. The association between CSPAGs and immune infiltration, and ICB therapy response, highlights the potential of the CSPAG signature as a personalized treatment strategy for LUAD patients.

Aldose reductase is a reduced monomeric enzyme that utilizes NADPH as a cofactor to mediate the glucose reduction to sorbitol in the polyol pathway. Overexpression of aldose reductase has been observed to mediate pathologies associated with diabetes mellitus. Inhibition of aldose reductase thus seems promising to deal with these pathologies. Pineapple and its extract have been identified for its anti-diabetic effect due to the presence of effective bioactive agents. In the present study, the major bioactive compounds of pineapple have been studied for their potential to structurally inhibit aldose reductase. The ADMET analysis of lead bioactive compounds including myrcene, palmitic acid, limonene, n-decanal, beta-carophyllene, 1-cyclohexane-1-caboxaldehyde, and α-farnesene showed most of the compounds were non-toxic and have druglike properties with LD50 values of greater than 2000 mg/kg. Molecular docking of these compounds at the substrate binding site of the aldose reductase-NADPH complex disclosed effective binding with binding energy values of - 5.025 to - 8.003 kcal/mol. α-farnesene, known for its antibacterial, antiviral, and anti-inflammatory properties gave the highest binding energy of - 8.003 kcal/mol. The molecular dynamic simulation studies of α-farnesene-aldose reductase-NADPH ternary complex, aldose reductase-NADPH binary complex, and apo-aldose reductase revealed similar RMSD values with respect to time during the simulation trajectory indicating stable interaction of the compound with the enzyme. DFT analysis showed high reactivity of α-farnesene which favours its utilization as a drug for specific target protein. Therefore, this study provides an efficient natural aldose reductase inhibitor α-farnesene that can be further explored for its potential to develop an effective natural drug to treat diabetes.

The high frequency of genetic diseases compels the development of refined diagnostic and therapeutic systems. CRISPR is a precise genome editing tool that offers detection of genetic mutation with high sensitivity, specificity and flexibility for point-of-care testing in low resource environment. Advancements in CRISPR ushered new hope for the detection of genetic diseases. This review aims to explore the recent advances in CRISPR for the detection and treatment of genetic disorders. It delves into the advances like next-generation CRISPR diagnostics like nano-biosensors, digitalized CRISPR, and omics-integrated CRISPR technologies to enhance the detection limits and to facilitate the "lab-on-chip" technologies. Additionally, therapeutic potential of CRISPR technologies is reviewed to evaluate the implementation potential of CRISPR technologies for the treatment of hematological diseases, (sickle cell anemia and β-thalassemia), HIV, cancer, cardiovascular diseases, and neurological disorders, etc. Emerging CRISPR therapeutic approaches such as base/epigenetic editing and stem cells for the development of foreseen CRIPSR drugs are explored for the development of point-of-care testing. A combination of predictive models of artificial intelligence and machine learning with growing knowledge of genetic disorders has also been discussed to understand their role in acceleration of genetic detection. Ethical consideration are briefly discussed towards to end of review. This review provides the comprehensive insights into advances in the CRISPR diagnostics/therapeutics which are believed to pave the way for reliable, effective, and low-cost genetic testing.

Acer okamotoanum, a medicinally significant endemic plant of Korea, has seen limited genomic research. To address this gap, we conducted a comprehensive sequencing and analysis of its chloroplast genome. The assembled genome is 156,242 bp in length, with typical quadripartite structure, consisting of a large single-copy region, a small single-copy region, and two inverted repeat regions. It contains 130 genes, including 85 protein-coding, 37 tRNA, and 8 rRNA genes. Sixteen genes have a single intron, while clpP and ycf3 possess two introns each. Additionally, 17 genes are duplicated within the inverted repeat regions. The genome analysis revealed 92 Simple Sequence Repeats (SSRs), predominantly located in intergenic regions, with a bias toward A/T-rich codons. Comparative analysis with five closely related Acer species highlighted a highly conserved genomic structure, but also revealed differences in SSRs and repeat sequences. Hypervariable regions, such as rpl32-trnL and ycf1, were identified as potential molecular markers for phylogenetic and population studies. Phylogenetic analysis involving 37 chloroplast genomes confirmed the monophyly of the Acer genus and placed A. okamotoanum within the Platanoidea section, closely related to A. truncatum. This study improves the understanding of A. okamotoanum's genomic structure, offering insights for phylogenetic analysis, marker development, and conservation efforts.

Glucanases are widely applied in industrial applications such as brewing, biomass conversion, food, and animal feed. Glucanases catalyze the hydrolysis of glucan to produce the sugar hemiacetal through hydrolytic cleavage of glycosidic bonds. Current study aimed to investigate structural insights of a glucanase from Clostridium perfringens through blind molecular docking, site-specific molecular docking, molecular dynamics (MD) simulation, and binding energy calculation. Furthermore, we aimed to enhance structural stabilization through formation of hydrophobic interaction network. The molecular docking results illustrated that residues Glu222 and Asp187 may act as nucleophile acid/base catalyst. Moreover, the MM/PBSA results illustrated a high binding affinity of 108.71 ± 8.5 kJ/mol between glucanase and barely glucan during 100 ns simulation. The RMSF analysis illustrated a high flexible surface loop with the highest mobility at position D130. Therefore, the structural engineering was carried out through introducing a double-mutant S125Y/D130P, and the structural stability was improved by forming the hydrophobic interaction network and one π-π aromatic interaction. The spatial distance between the mutation sites and the catalytic pocket attenuates their direct impact on binding interactions within the catalytic pocket.

One kind of hydroxycinnamic acid is calceolarioside A. Plantago coronopus, Cassinopsis madagascariensis, and other organisms for whom data are available are known to have this naturally occurring compound. IC50 values of Calceolarioside A for ovarian cell lines (NIH-OVCAR-3, ES-2, UACC-1598, Hs832.Tc, TOV-21G, UWB1.289) were 24.42, 13.50, 9.31, 14.90, 20.07, and 16.18 µM, respectively. IC50 values were 19.83 and 73.48 µM for tyrosinase and HMG-CoA reductase enzymes. The chemical activities of Calceolarioside A against HMG-CoA reductase and tyrosinase were assessed by conducting the molecular docking study, MM/GBSA calculation, and molecular dynamics (MD) simulation. The anticancer activities of this compound were evaluated against some ovarian cancer cells, such as NIH-OVCAR-3, ES-2, UACC-1598, Hs832.Tc, TOV-21G, and UWB1.289 cell lines. The chemical activities of Calceolarioside A against some of the expressed surface receptor proteins (folate receptor, CD44, EGFR, Formyl Peptide Receptor-Like 1, M2 muscarinic receptor, and estrogen receptors) were investigated using computational methods. The results exhibited the interplay among atoms. The compound formed robust associations with both the enzymes and receptors. Calceolarioside A can hinder the functioning of these enzymes and the proliferation of malignant cells.

Quantitative polymerase chain reaction (qPCR) is a vital molecular technique for biomarker detection; however, its clinical application is impeded by the scarcity of robust biomarkers and the inherent limitations of the technology. This study conducted a bibliometric analysis of 4063 qPCR-based biomarker studies sourced from the Web of Science (WOS) database, employing VOSviewer and CiteSpace to generate multi-dimensional structural insights into this field. The results reveal a growing trend in research within this domain, with gene expression analysis playing a central role in the identification of potential biomarkers. Among these, cancer-related biomarkers are the most prominent, while research on biomarkers for other diseases remains limited. Liquid biopsy biomarkers, including microRNA (miRNA), circulating free DNA (cfDNA), and circulating tumor DNA (ctDNA), are increasingly being explored. The integration of bioinformatics, omics analysis, and high-throughput technologies with qPCR is accelerating biomarker discovery. Furthermore, large-scale parallel sequencing is emerging as a potential alternative to relative quantification and microarray techniques. Nevertheless, qPCR remains essential for validating specific biomarkers, and further standardization of its protocols is necessary to enhance reliability. This study provides a systematic analysis of qPCR-based biomarker research and underscores the need for future technological integration and standardization to facilitate broader clinical applications.

Mitochondrial ribosomal protein L21 (MRPL21) is essential for normal cell function and may play a significant role in cancer development. In this study, we performed a comprehensive pan-cancer analysis to explore MRPL21's function across different cancers, utilizing multiple online data platforms such as TCGA. Our analysis covered its clinical significance and biological functions, including expression levels, survival and diagnostic analysis, gene mutations, multidimensional immune-correlation analysis, tumor heterogeneity, and cancer-associated signaling pathways. Additionally, we constructed a prognostic nomogram for lung adenocarcinoma (LUAD) patients based on MRPL21 and validated its biological function through in vitro experiments. Our findings revealed that MRPL21 is commonly overexpressed in various cancers and is associated with poor prognosis. It significantly impacts cancer-related pathways, particularly those related to cell cycle activation. Moreover, MRPL21 is critical in the tumor microenvironment and is closely linked to immune infiltration across several cancer types. Its expression correlates with essential factors such as tumor mutational burden, microsatellite instability, immune checkpoint, and methylation patterns. In LUAD, MRPL21 was identified as an independent risk factor and demonstrated that MRPL21 promotes LUAD progression. Overall, MRPL21 holds potential as both a diagnostic and prognostic marker in cancer and could serve as a promising therapeutic target, particularly for LUAD.

Despite significant advancements in gene delivery and CRISPR technology, several challenges remain. Chief among these are overcoming serum inhibition and achieving high transfection efficiency with minimal cytotoxicity. To address these issues, there is a need for novel vectors that exhibit lower toxicity, maintain stability in serum-rich environments, and effectively deliver plasmids of various sizes across diverse cell types. In this study, to convert common polyethylenimine (PEI_1.8k) into high-performance DNA delivery vectors, an innovative multifunctional vector was constructed based on histidine linked to PEI_1.8k by redox-responsive disulfide bonds. Apart from highly efficient transfection of both small and large plasmids into HEK 293T (Human Embryonic Kidney 293T cells) with negligible cytotoxicity, PEI_1.8k-S-S-His showed great transfection potential even at low plasmid doses (0.5 µg), as well as at serum concentrations ranging from 5 to 30% into HEK 293T cells, and achieved excellent plasmid transfection into NIH/3T3 (Mouse Embryonic Fibroblast cells), and MCF7 (Human Breast Cancer cells). Additionally, several metals were tested (Co, Cu, Cd, Ni, Zn, and Mn) to promote the plasmid packaging functionality and improve transfection efficiency. We observed that, in comparison to PEI_1.8k-S-S-His, the manganese-functionalized nanocarrier (PEI_1.8k-S-S-His-Mn) could transfect a large plasmid with equal efficiency (~ 30%) into MSCs (Mesenchymal Stem Cells). Interestingly, PEI_1.8k-S-S-His-Mn showed higher transfection efficiency with the small plasmid (~ 90%) and the large one (~ 80%) into HEK 293T cells, even better than its backbone. We propose that the presence of metal-coordinated His ligand, redox-responsive S-S bonds, and the cationic polymer can synergistically provide robust DNA binding, efficient endosomal disruption, tolerance of serum protein adsorption, and low cytotoxicity. These new vectors could be promising for gene delivery and may be therapeutically relevant.