Biochemistry Research International最新文献

Juvenile dermatomyositis (JDM) is a rare autoimmune disease primarily affecting children, characterized by muscle weakness and skin lesions. This study identifies 145 genes significantly associated with JDM through differential gene expression analysis, weighted gene coexpression network analysis (WGCNA), protein-protein interaction network analysis, and miRNA and transcription factor (TF) prediction, using blood and muscle microarray sequencing datasets. Functional enrichment analysis indicates that these genes are involved in crucial biological processes, including cytokine-mediated signaling, extracellular matrix organization, and immune response. Further analysis reveals key TFs (e.g., STAT1 and NFKB1) and miRNAs (e.g., hsa-miR-127-3p and hsa-miR-17-5p) that may regulate the expression of these critical genes in JDM. The findings provide new insights into the molecular mechanisms of JDM and offer potential targets for future diagnostic and therapeutic strategies.

Bromelain is one of the protease enzymes found in all parts of pineapple (Ananas comosus (L.) Merr.), including the crown and peel. This enzyme has been widely used in various fields of life, including the food industry, health, pharmaceuticals, and cosmetics. However, pineapple processing often focuses on the flesh of the fruit, leaving behind substantial agricultural waste, such as crown and peel waste. The waste is often collected and stored before being used, causing the bromelain enzyme to decrease or even dissipate. Therefore, this study aims to determine the effect of time and the condition of storage of pineapple crown and peel waste on total protein content and protease activity. The extracted bromelain was precipitated with ethanol and then dried, and total protein content and protease activity were determined. The results showed that pineapple crown and peel waste can be stored for 7 days at 29 ± 1°C and humidity of 70 ± 2% and 20 days at 4 ± 0.5°C and humidity of 40 ± 2%, respectively. The total protein content and protease activity were 169.94 ± 2.68 μg/mL and 46.35 ± 0.69 IU/mg for crown bromelain, while those for peel bromelain were 229.75 ± 15.61 μg/mL and 29.10 ± 1.98 IU/mg, respectively. In conclusion, pineapple crown waste has the potential to be developed as a source of bromelain.

Background and objective: Renal clear cell carcinoma (RCCC) stands out as a prevalent and aggressive subtype of kidney cancer characterized by a challenging prognosis. The need to enhance patient outcomes in RCCC underscores the significance of identifying prognostic biomarkers and therapeutic targets. MicroRNAs (miRNAs) and the signaling pathways orchestrating RCCC pathogenesis emerge as promising candidates for such endeavors.

Methods: This study utilized publicly available gene expression data to compare miRNA profiles in nine RCCC and 11 normal kidney tissues. Rigorous bioinformatics analyses were employed to identify differentially expressed miRNAs and their associated gene targets. Prognostic significance was assessed, and a protein-protein interaction network was constructed to highlight pivotal RCCC hub genes. The expression and prognostic value of key hub genes and miRNAs were further validated in independent cohorts, including the GEO dataset GSE76351 and the TCGA-KIRC cohort via the Kaplan-Meier plotter. Expression of RUNX2 was confirmed using real-time PCR in five cancer and five normal renal tissues.

Results: Fifteen DEMs were identified alongside 74 hub genes. The downregulation of miR-26a-1-3p, miR-144-3p, and miR-144-5p was associated with a poorer prognosis in RCCC. The overexpression of CDK1 and RUNX2 was validated in an independent GEO dataset and correlated with decreased patient survival in the TCGA-KIRC cohort. Furthermore, a statistically significant but modest inverse association was observed between miR-26a-1-3p and RUNX2 expression, indicating a possible miRNA-mRNA relationship. Significant enrichment was observed in pathways related to PI3K-Akt, MAPK, apoptosis, and cell cycle. The overexpression of RUNX2 was confirmed in our patient samples (p value< 0.05).

Conclusion: This multistep validation study confirms that specific miRNAs and hub genes, particularly the miR-26a-1-3p/RUNX2 axis, are potential prognostic indicators in RCCC. A comprehensive understanding of these biomarkers and their enriched signaling pathways provides deeper insight into the molecular underpinnings of RCCC, uncovering potential therapeutic opportunities.

Background: Malaria remains a significant and worldwide health threat with increasing resistance to current treatments, stimulating the demand for innovative approaches in pursuing drug discovery. This systematic review integrates the progress made from 2014 through 2024 regarding molecular methods like gene expression profiling, molecular docking and machine learning to understand the biology of Plasmodium and identify new drug targets and compounds, focusing on herbal remedies and computational methods.

Methodology: Several studies were found using a PRISMA-guided search of PubMed, Scopus and Web of Science (64 studies found). The data extracted were gene expression outcomes, docking affinities, ML models and experimental validations (in vitro/in vivo).

Results: Molecular docking emerged as the dominant technique (32.37%), followed by in vitro antiplasmodial assays (14.39%), ADMET profiling (10.79%) and gene expression studies (3.60%). RNA-seq analysis revealed key host and parasite genes modulated by herbal treatments, including those involved in apoptosis and inflammation. Notably, compounds like isorhamnetin and myricetin 3-O-glucoside showed exceptionally high binding affinities to Plasmepsin II and Plasmodium falciparum lactate dehydrogenase (PfLDH) (ΔG < -13 kcal/mol). ML models like random forest and support vector machine (SVM) exhibited high predictive results (AUC value up to 0.87) for bioactivity and resistance patterns that showed flavonoids (quercetin) and terpenoids (eugenol) as good candidates. Pathways that are often attacked are haemoglobin degradation, glycolysis, pyrimidine metabolism and protein synthesis.

Conclusion: Multiomics, docking and ML integration improve the target identification and prioritise the compounds. This review illustrates the great potential of molecular techniques for the development of drugs against antimalarial helicases that are not resistant to drug therapy. However, in vivo data holes and methodology inconsistency limit clinical translation. Future work should include standardisation of protocols and studies of synergistic combinations of phytochemicals.

Type 2 diabetes mellitus (T2DM) is a state where the body's glucose metabolism is compromised. AMP-activated protein kinase, or AMPK, has an important part to play in glucose metabolism, and the liver kinase B1 (LKB1) protein functions as a major upstream kinase for AMPK activation, thereby making it appealing therapeutic targets for treating and preventing T2DM. Drug resistance cases for biguanides like metformin is a serious concern and pose great threat to treatment success for diabetic patients. Thus, the hunt for biguanide-like small molecules with enhanced insulin sensitizing potentials is necessary. In the present study, interaction between LKB1 and biguanides such as phenformin, metformin, and buformin has been thoroughly assessed using computational tools. Ligand-based pharmacophore mapping of 29,000 phytochemicals collected from NPASS database was carried out. The screening was conducted to hunt novel antidiabetic compounds targeting LKB1 pathway to improve insulin sensitivity in T2DM. Molecular docking of 31 phytochemicals with good pharmacophore fit scores was then carried out to identify hit compounds. ADMET analysis was also utilized to screen down compounds. dragmacidin D, dioncopeltine A, saussureamine C, and agelastatin D have good binding affinities and acceptable ADMET parameters. Molecular dynamics simulation was carried out to confer the stability of ligand-protein complex under simulated human body conditions. After 100 nanoseconds molecular dynamics simulation, the LKB1 protein complexed with compounds (saussureamine C and agelastatin D) was found to be stable. The results of the current study can be useful in developing antidiabetic medications with enhanced insulin sensitization activates superior to those available in market.

During tumorigenesis and metastasis, cancer cells initiate antioxidant defense mechanisms to prevent irreversible damage, thereby sustaining tumor growth. The functionality of reactive oxygen species (ROS)-scavenging proteins is dependent on nicotinamide adenine dinucleotide phosphate (NADPH), which is regulated by specific metabolic enzymes, which are described as potential biomarkers of cancer aggressiveness. Immunohistochemistry (IHC) is one of the most accessible and widely utilized techniques to augment the pathological diagnosis of cancer. Hence, this review addresses the protein expression of NADPH-related enzymes, as assessed by IHC, and their associations with human cancer progression factors (overall survival, tumor staging, metastasis, and recurrence). Studies indicate that glucose-6-phosphate dehydrogenase (G6PD), along with malic enzymes and methylenetetrahydrofolate dehydrogenase 2 (MTHFD2), represents the most pertinent enzymes examined through IHC concerning cancer aggressiveness. The immunolabeling method produced consistent results for this group of enzymes, which might lead to successful application in predicting tumor prognosis. Other NADPH-related enzymes, such as glutamate dehydrogenase (GDH), aldehyde dehydrogenase 1 (ALDH1), and dihydrofolate reductase (DHFR), deserve more extensive investigation to elucidate their potential as cancer biomarkers via IHC.

High-density lipoproteins (HDLs) are deeply implicated in atherosclerosis. HDL, myeloperoxidase (MPO), and paraoxonase-1 (PON1) form a functional ternary complex where PON1 partially inhibits the MPO activity, and MPO in turn partially inactivates PON1. The activity of MPO is dependent on the concentration of hydrogen peroxide, but the extremely low concentrations of hydrogen peroxide in serums severely constrain MPO activity. PON1 has the activities of organophosphatase, arylesterase, and thiolactonase, but these hydrolase activities are extraneous to antioxidative stress. Thus, we proposed that MPO and PON1 may be involved in atherosclerosis by acting as proteins, rather than enzyme activities. Cholesterol efflux assay, ATP-binding cassette transporter A1 (ABCA1)-dependent cholesterol efflux, and LCAT activity assay were performed. The effect of MPO, PON1, and serums from the individuals with ASCVD and healthy individuals on cholesterol efflux of human acute monocytic leukemia cell line (THP-1 cells) was compared. Noncatalytic functions of MPO and PON1 were analyzed using recombinant proteins and neutralizing antibodies. Wound healing assay and tube formation assay were used to analyze noncatalytic functions of MPO and PON1 in modulating the involvement of human umbilical vein endothelial cells (HUVECs). We found that MPO protein decreased the cholesterol efflux; by contrast, PON1 protein increased the cholesterol efflux of THP-1 cells. Importantly, MPO antibody partially restored cholesterol efflux, but PON1 antibody partially reduced cholesterol efflux of THP-1 cells. Moreover, ABCA1 was necessary for controlling the involvement of MPO and PON1 in modulating cholesterol efflux of THP-1 cells. There existed the confrontations between the noncatalytic functions of PON1 and MPO in migration of endothelial cells. Instead, MPO protein enhanced the expression of intercellular adhesion molecule-1 (ICAM-1) and E-selectin of HUVECs; nonetheless, PON1 protein reduced the expression of these adhesion molecules. Of note, PON1 protein was unable to balance out the induction of MPO protein for these adhesion molecules in that the expression of these adhesion molecules generated by the combination of MPO protein and PON1 protein was similar to that of MPO. The activation of THP-1 cells induced by MPO protein directly impaired in vitro microvascular structure via increasing the expression of IL-6 and TNFα regulated by NF-κB p65 of THP-1 cells. Together, the noncatalytic functions entail MPO and PON in modulating the involvement of monocytes and endothelial cells in atherosclerosis.

Background: Crohn's disease (CD) is a chronic, complex inflammatory condition that can affect the entire digestive tract, most commonly the terminal ileum. The exact cause of CD remains unknown. Bioinformatics was used in this study to identify the differentially expressed genes (DEGs) and microRNAs (miRNAs) that show potential as diagnostic and therapeutic agents in treating CD.

Materials and methods: Datasets were downloaded from the Gene Expression Omnibus database and filtered. DEGs between CD samples and healthy control samples were identified using the GEO2R tool (including GEOquery and Linear Models for Microarray Analysis), and Kyoto Encyclopedia of Genes and Genomes/Gene Ontology enrichment analyses were conducted as part of the study to gain deeper insights into the data. A network depicting protein-protein interactions was established and visualized using the STRING database and Cytoscape software, and hub genes were identified and extracted utilizing the cytoHubba program. Cytoscape and miRTarBase were used to construct the miRNA-hub gene regulatory network and predict the potential miRNAs associated with the DEGs. The hub genes were analyzed further using ROC curves and combined ROC curve analyses of the GSE179285, GSE186582, and GSE112366 datasets. A regularized LASSO regression model was constructed to reduce the risk of overfitting.

Results: Three datasets (GSE179285, GSE186582, and GSE112366) were selected. A comprehensive analysis of the three datasets revealed 60 DEGs that showed significantly altered expression levels, including 44 upregulated genes and 16 downregulated genes. Ten different algorithms were randomly used, and three hub genes (CXCL1, CXCL2, and CXCR2) were identified. Based on the miRNA-hub gene regulatory network, hsa-miR-1-3p and hsa-miR-335-5p were recognized as potentially vital miRNAs.

Conclusion: Three hub genes (CXCL1, CXCL2, and CXCR2) and two miRNAs (hsa-miR-1-3p and hsa-miR-335-5p) are postulated to play a role in the initiation and progression of CD, thereby offering potential as biomarkers for this condition.

Introduction: Compensated cirrhosis carries a significant risk of progression to decompensation, which substantially worsens prognosis. Accurate prediction of decompensation events is critical for guiding surveillance, optimizing intervention timing, and improving patient outcomes. Although many prognostic biomarkers have been studied, findings remain heterogeneous. This umbrella review synthesizes evidence from systematic reviews and meta-analyses to identify and appraise biomarkers predicting decompensation in alcoholic and nonalcoholic compensated cirrhosis.

Methods: PubMed, Scopus, and Web of Science were searched to August 15, 2025, for English-language systematic reviews and meta-analyses. From the included meta-analyses, prognostic performance, heterogeneity, and publication bias were recorded.

Results: Four systematic reviews were included, two with meta-analyses. Strong predictors across reviews were serum albumin, INR, bilirubin, platelet count, and liver stiffness measurement. HVPG remained a robust invasive predictor, while emerging biomarkers-interleukin-6, keratin-18, and extracellular vesicles-were associated with an increased risk of decompensation, although the certainty of evidence was limited by heterogeneity and methodological constraints. Composite scores enhanced predictive accuracy. AMSTAR 2 ratings ranged from high to low, with common reporting limitations. Overlap analysis indicated moderate redundancy among primary studies.

Conclusions: Both established and emerging biomarkers predict decompensation in compensated cirrhosis. Integrated multidomain models combining clinical, biochemical, and imaging-derived measures may provide the greatest predictive value for guiding clinical decision-making.

Whey, a by-product of the cheese manufacturing industry, represents one of the most abundant and polluting effluents in the global food industry. Despite traditionally being underutilized and often discarded, its rich nutrient profile, particularly protein and lactose, has increasingly sparked an interest in its value within biotechnological processes. This review analyses the potential of whey as a sustainable substrate for the microbial production of value-added bioproducts, focussing on L-threonine production as a strategic case study, while addressing the environmental impact of inadequate disposal and current utilization strategies. A comparative analysis with other agroindustrial waste demonstrates whey's competitive advantages in terms of composition, cost-effectiveness and sustainability metrics. Furthermore, L-threonine biological and industrial importance, and the most relevant advances in metabolic engineering, optimized fermentation and emerging tools such as optogenetics and machine learning are discussed, as they facilitate enhanced L-threonine yields through the creation of robust, high-producing strains. Technoeconomic analysis at pilot scale (33.8 tons/year) indicates that whey-based production offers a comparative cost advantage of 7.4% over glucose-based processes (20.55 USD/kg vs. 22.20 USD/kg). While absolute costs at pilot scale exceed current industrial market prices (1.31-1.66 USD/kg)-reflecting typical scale effects-the demonstrated comparative advantage and substantial environmental benefits (waste valorization, elimination of disposal costs and circular economy alignment) position whey-based L-threonine production as a strategic biorefinery opportunity with significant potential for industrial-scale implementation. This cost benefit is primarily driven by the lower market price of whey compared to commercial glucose substrates, which compensates for the slightly higher downstream processing costs (5.90 vs. 5.40 USD/kg) required for complex matrices. Downstream processing considerations, including recovery, purity requirements and economic viability, are comprehensively addressed. This review concludes that whey, far from being merely a pollutant, has the characteristics required to become an asset for biotechnology. Utilizing whey as a culture medium for L-threonine production by E. coli in bioreactors not only offers a solution to mitigate a significant environmental issue but also opens a path for the cost-effective, sustainable production of a globally high-demand amino acid. Whey represents a strategic biorefinery platform with potential for industrial-scale implementation. Continued research and development in this area are fundamental to fully realizing this potential.