Current Medicinal Chemistry - Online First
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101 - 150 of 182 results
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Capsid Assembly Modulators: A Promising Curative Regimen for Chronic Hepatitis B
Authors: Chunhua Ma, Xiaoyan Zhang, Junbiao Chang and Bin YuAvailable online: 23 May 2025More Less 
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Betanin, a Natural Product from Red Beets, Improves Endothelial Dysfunction through Activation of Autophagy
Authors: Junpei Li, Luyan Xu, Duoduo Zha, Yixiong Zhan, Yijia Wu, Xianxian Mao, Li Zuo, Xinyan Bai, Linsiqi Wang, Kunhua Chen, Jinghua Luo and Yisong QianAvailable online: 22 May 2025More LessObjectiveEndothelial dysfunction is the altered pathological ability of endothelial cells to modulate the passage of cells and solutes across vessels, which underlies the development of inflammatory diseases. Betanin (betanidin-5-O-β-glucoside), a natural product rich in red beets, is a water-soluble nitrogen-containing pigment, and its potential protective effects on cardiovascular disease have been reported. In this study, we investigated the protective role of betanin in vascular endothelial dysfunction induced by TNFα and explored potential mechanisms.
MethodsWe modelled endothelial dysfunction through TNFα stimulation in human umbilical vein endothelial cells (HUVECs) and examined the role of betanin and its possible mechanism of action by MTT assay, Western blotting, and immunofluorescence staining. A systemic inflammation model of mice was built through LPS to investigate the protective roles of betanin.
ResultsBetanin pre-treatment increased cell viability, inhibited the expression of intercellular cell adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1), and improved endothelial tight junction by upregulating the expression of occludin and zonula occludens-1 (ZO-1) after TNFα stimulation in HUVECs. In terms of endothelial-mesenchymal transition, betanin up-regulated the expression of endothelial phenotypes VE-cadherin and CD31, whereas it inhibited the expression of mesenchymal phenotype N-cadherin, indicating that betanin reduced endothelial-mesenchymal transition in TNFα-stimulated HUVECs. In addition, betanin increased the expression of LC3 and decreased the expression of p62, two central proteins in autophagy. Betanin also reversed the abnormal autophagic flux after TNFα exposure. However, the specific autophagy inhibitor, 3-methyladenine, blocked the protective effect of betanin. Finally, betanin was found to greatly decrease ICAM-1 and VCAM-1 expression, and upregulate occludin and ZO-1 levels in a systemic inflammation model of mice.
ConclusionThe above results collectively suggested that betanin may improve endothelial dysfunction by promoting autophagy, thus exerting beneficial effects on cardiovascular health.
 
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Construction of PANoptosis-related LncRNA Prognostic Signature and Functional Analysis of AC034229.4 in Hepatocellular Carcinoma
Authors: Rui He, Ningning Wang, Xiujuan Zheng, Baiming Jin, Xuying Li, Mingqi Li, Shijing Nian and Kewei WangAvailable online: 22 May 2025More LessAimsThis study aimed to establish a PANoptosis related prognostic signature and identify potential prognostic markers and therapeutic targets for HCC.
BackgroundHepatocellular carcinoma (HCC) is one of the most common malignant tumors worldwide. The survival rate of patients with HCC remains relatively low. PANoptosis can be mediated by lncRNA to involve the pathophysiology of HCC, but the mechanism is still unclear.
ObjectiveTCGA and GEO hepatocellular carcinoma databases and previous research results were used to construct the PANoptosis related risk model.
MethodsBased on the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database, this study identified long non-coding RNAs (lncRNAs) associated with PANoptosis in HCC. Univariate, LASSO-Cox, and multivariate COX analyses were employed to gradually screen prognostic lncRNAs and construct prognostic models. Further analysis was conducted on the core lncRNA-AC034229.4.
ResultsA total of 8 differentially expressed lncRNAs closely correlated with HCC prognosis were discovered. A prognostic model comprising 6 lncRNAs (AC090192.2, LINC01703, AC034229.4, AC073352.1, AC004816.1, and AL136162.1) was established demonstrating good predictive ability for prognosis. Moreover, this prognostic model exhibited close associations with tumor immune microenvironment and immune checkpoints. Subsequent investigations revealed that AC034229.4 independently influenced HCC prognosis by regulating cell cycle progression and inhibiting the immune microenvironment response. Drug sensitivity analysis indicated that AC034229 .4 displayed sensitivity to various anticancer drugs as well. In addition, inhibition of AC034229 .4 expression suppressed HCC migration and invasion abilities.
ConclusionThis study generated a novel and efficient prognostic signature model while identifying AC034229 .4 as a promising diagnostic and prognostic biomarker in HCC.
 
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Relationship between 21 Medications and Negative Emotions: A Mendelian Randomization Analysis in Asian Populations
Authors: Xiaotong Wang, Yuhan Wei, Xi Nie, Yuchuan Zhang, Lan Yang, Weiting Zeng, Kexin Shi and Haixiong LinAvailable online: 19 May 2025More LessObjectiveNegative emotional states, such as nervousness, anxiety, depression, and tension, exert profound detrimental effects on an individual's quality of life and overall health. Although certain widely prescribed medications have been observed to modulate these emotional states, the existing body of research in this domain remains insufficient. To address this gap, Mendelian randomization (MR) methodologies, leveraging large-scale datasets, were employed to investigate the causal relationships between 21 commonly utilized medications and the manifestation of negative emotions.
MethodsThe inverse variance weighting (IVW) method was employed as the primary analytical strategy to analyze causal relationships. MR-Egger, weighted mode, and weighted median approaches were utilized to enhance the robustness of the results. Sensitivity analyses were conducted to assess the stability of the data.
ResultsAgents acting on the renin-angiotensin system, β-blocking agents, antithrombotic agents, and salicylic acid and derivatives could reduce the risk of nervousness, anxiety, tension, or depression (OR = 0.61, 95% CI 0.37 to 0.99, p = 0.047; OR = 0.59, 95% CI 0.36 to 0.98, p = 0.041; OR = 0.55, 95% CI 0.34 to 0.88, p = 0.013; OR = 0.61, 95% CI 0.40 to 0.95, p = 0.030), with no heterogeneity, horizontal pleiotropy, or reverse causation (p > 0.05).
ConclusionThis study revealed four medications associated with reducing the risk of negative emotions, providing clinicians with a scientific basis for medication selection to better assist patients in alleviating psychological issues and improving their quality of life.
 
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Cholesteatoma: An Updated Review of Molecular Pathogenesis and Potential Therapeutic Directions
Authors: Bingwen Xing, Yalong Dang and Kai XiAvailable online: 19 May 2025More LessCholesteatoma, an abnormal accumulation of keratinized squamous epithelium in the middle ear, occurs as a locally invasive but histologically benign lesion. Its capacity for bone erosion leads to significant complications, including hearing loss, facial nerve paralysis, and intracranial infections. Chronic inflammation is central to its pathogenesis, with proinflammatory mediators like TNF-α, IL-1β, and IL-6 activating signaling pathways, such as NF-κB, JAK/STAT, and MAPK. These pathways contribute to epithelial hyperproliferation and extracellular matrix degradation mediated by Matrix Metalloproteinases (MMPs). Dysregulation of epithelial cell behavior, involving altered keratinocyte function and reduced E-cadherin-mediated adhesion, may facilitate lesion formation and expansion. Furthermore, aberrant signaling involving growth factors (e.g., EGF, TGF-β) and dysregulation of osteoclast activity via the RANKL pathway contribute to enhanced bone erosion and tissue invasion. Emerging research highlights potential roles of the c-MYC proto-oncogene, microRNAs, and Sonic hedgehog signaling in disease progression, offering deeper insights into the pathogenesis. Current management primarily involves surgical excision, yet high recurrence rates emphasize the need for adjunctive therapeutic strategies. Potential future directions include modulating key pathways, such as NF-κB, MMP activity, and RANKL signaling, as well as exploring interventions related to growth factors and cell adhesion. Integrating molecular insights with clinical research is essential for developing strategies to reduce recurrence and improve patient outcomes.
 
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Emerging New Treatments for Colon Cancer
Authors: Sheu Ibrahim Adedayo and Eva Sonnenberg-RiethmacherAvailable online: 16 May 2025More LessColorectal cancer includes cancer of the rectum and colon. It is the primary cause of cancer-related deaths among men under 50 years of age. In 2022, over 1.9 million cases of CRC were reported, resulting in approximately 904,000 deaths worldwide. Factors like smoking, alcohol consumption, obesity, familial history, and inflammation significantly contribute to the risk of CRC development. Additionally, bacterial infections from organisms like Bacteroides fragilis, Fusobacterium nucleatum, and Helicobacter pylori also play a role in increasing this risk. Conventional treatment methods for CRC typically involve surgery/polypectomy, chemotherapy, and radiotherapy. Because of limitations like lack of target specificity, the risk of tumor relapse, and the potential for tumor resistance, there is a growing necessity for more individually tailored treatment strategies to improve the outcomes of patients with CRC. As such, emerging treatments like cancer vaccine, (CAR) T-cells, CAR-NK cells, macrophages, and stem cell engineering (particularly mesenchymal stem cells), dendritic vaccine, siRNA, and miRNA, hold significant promise in enhancing outcomes for CRC patients. Moreover, specific gut microbiomes like Bacteroides fragilis, Streptococcus gallolyticus, Enterococcus faecalis, and Escherichia coli, linked to CRC development, have been identified. Hence, modulating the gut microbiome to potentially enhance responses to CRC in high-risk populations could be a new line of treatment. This modulation can be accomplished through dietary interventions, prebiotics, probiotics, postbiotics, antibiotics, and fecal microbiota transplantation (FMT). This review summarizes the most promising new emerging treatments in the fight against colon cancer.
 
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A Neuroendocrine Differentiation-related Molecular Model for Prognosis Prediction in Prostate Cancer Patients
Authors: Yong Wei, Jiang-Bo Sun, Qian-Ren-Shun Qiu, Yu-Xuan Zhao, Qing-Shui Zheng, Xiong-Lin Sun, Ning Xu and Xue-Yi XueAvailable online: 15 May 2025More LessPurposeThe purpose of this study is to construct and validate a neuroendocrine differentiation-related molecular model for predicting prognosis in patients with prostate cancer (PCa).
Materials and MethodsTranscriptome data for PCa were collected from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) websites. Differentially expressed neuroendocrine differentiation related genes (NDGs) were identified. By utilizing multivariate Cox analysis, a neuroendocrine differentiation-related molecular model for predicting prognosis was constructed and validated. The study investigated the novel model’s association with the tumor immune microenvironment, clinicopathological characteristics, tumor stemness, and anticancer treatment sensitivity. Additionally, preliminary experimental verifications of Diencephalon / Mesencephalon Homeobox 1 (DMBX1) were conducted.
ResultsFinally, we identified a total of 19 differentially expressed NDGs. A neuroendocrine differentiation-related molecular model was established and successfully validated both internally and externally. The high-risk group exhibited significantly poorer biochemical recurrence-free survival (BCRFS) in the training, testing, and validating cohorts. The areas under the receiver operating characteristic curves for the training, testing, and validating cohorts were 0.825, 0.719, and 0.729, respectively. The tumor immune microenvironment, clinicopathological features, tumor stemness, and anti-cancer drug sensitivity was significantly different between high and low-risk patients. Preliminary experiments revealed that higher expression of DMBX1 significantly enhanced the proliferation, migration, and neuroendocrine differentiation of PCa cells.
ConclusionThis research developed a unique neuroendocrine differentiation-related molecular model that is highly suitable for predicting BCRFS. High DMBX1 expression may promote the development and neuroendocrine differentiation of prostate cancer.
 
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Next-generation Approaches in Targeting Polycystic Ovarian Syndrome: Innovative Strategies
Available online: 12 May 2025More LessPolycystic Ovary Syndrome (PCOS) is a complex endocrine disorder that affects millions of women worldwide and is characterized by ovarian dysfunction, hyperandrogenism, and metabolic abnormalities. The traditional diagnostic and therapeutic approaches often fail to address the multifaceted nature of PCOS. Recent advancements in next-generation sequencing (NGS), bioinformatics, and precision medicine have paved the way for innovative research and therapeutic strategies that promise to revolutionize PCOS management. This review focuses on exploring the genetic and molecular mechanisms of PCOS using innovative methodologies, such as genome-wide association studies (GWAS), transcriptomics, and computational approaches. Integrating big data analytics and machine learning algorithms enhances the predictive accuracy of PCOS diagnoses and treatment outcomes. In addition, the emergence of personalized medicine has enabled tailored therapeutic interventions based on individual genetic profiles and phenotypic expression. Furthermore, we explored the development of novel pharmacological agents and combinational therapies to enhance the understanding of PCOS pathophysiology. These approaches also focus on reducing inflammation, improving insulin sensitivity, and optimizing hormonal balance to achieve optimal health outcomes. The potential of digital health tools, including mobile applications and wearable technologies, to support self-monitoring and patient engagement in PCOS management is also highlighted. In conclusion, the integration of next-generation technologies and innovative research is necessary to transform the field of PCOS diagnosis and treatment, offering hope for more effective and individualized care. These underscore the importance of continued investment in advanced research methodologies and the adoption of personalized therapeutic strategies to address the complexities of PCOS.
 
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Binding Specificity and Local Frustration in Structure-based Drug Discovery
Authors: Zhiqiang Yan, Yuqing Li, Ying Cao, Xuetao Tao, Jin Wang and Yongsheng JiangAvailable online: 12 May 2025More LessEvolution has optimized proteins to balance stability and function by reducing unfavorable energy states, leading to regions of flexibility and frustration on protein surfaces. These locally frustrated regions correspond to functionally important areas, such as active sites and regions for ligand binding and conformational plasticity. Typical strategies of structure-based drug discovery primarily concentrate on enhancing the binding affinity during compound screening and target identification. However, this often overlooks the binding specificity, which is critical for distinguishing specific binding partners from competing ones and avoiding off-target effects. According to the energy landscape theory, optimization of the intrinsic binding specificity involves globally minimizing the frustrations existing in the biomolecular interactions. Recent studies have demonstrated that identifying local frustrations provides a promising approach for screening more specific compounds binding with targets, and quantifying binding specificity complements typical strategies that focus on binding affinity only. This review explores the principles and strategies of computationally quantifying the binding specificity and local frustrations and discusses their applications in structure-based drug discovery. Moreover, given the advancements of artificial intelligence in protein science, this review aims to motivate the integration of AI and available approaches in quantifying the binding specificity and local frustration. We expect that an AI-powered prediction model will accelerate the drug discovery process and improve the success rate of hit compounds.
 
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Nanomaterial Enhances the Performance of Amyloid-beta Biosensing for Alzheimer’s Disease Diagnosis
Authors: Zhong Zhao, Wenli Chen, Hao Tang, Xiaoyan Wang, Wenjiao Huang, Subash C.B. Gopinath and Shu YangAvailable online: 07 May 2025More LessBackgroundHighly sensitive, accurate, and low-cost detection systems are gaining interest for early intervention in the progression of Alzheimer's disease (AD). Amyloid-beta (Aβ), a peptide highly involved in the progression of AD, is found in abundance in patients with severe AD.
ObjectiveThis research focused on developing an Aβ oligomer (AβO) biosensor using a single-walled carbon nanotube-modified (SWCN) interdigitated electrode (IDE) sensor.
MethodsThe SWCN was functionalized onto the sensor surface through an amine linker, followed by the attachment of an aptamer-gold nanoparticle (GNP) complex, which was used to capture the AβO.
ResultsThe GNP-aptamer was saturated at 500 nM on the SWCN surface, and AβO was detected using a sandwich consisting of aptamer-AβO-antibody. The SWCN modification increased the number of aptamer attachment sites on the IDE, while the aptamer and antibody conjugation with GNP enhanced AβO interaction. This sandwich assay detected AβO at concentrations as low as 10 fM, with a linear regression coefficient (y = 2.9189x - 2.076; R2 = 0.9544). Furthermore, AβO-spiked artificial CSF was detected without interference, as confirmed by the increased current responses. No significant changes were recorded with control proteins, including α-synuclein, IgG antibody, and a complementary aptamer, indicating specific AβO detection.
ConclusionThis SWCN modified IDE-based sandwich detects AβO at its lower level and contributes to the early diagnosis of AD.
 
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Icaritin Attenuates HSC Activation by Down-regulating the HIF-1α and TGF-β/Smad Signaling Pathways to Ameliorate Liver Fibrosis
Authors: Keping Feng, Qiaoman Fei, Na Huang, Ke Du, Chengbo Zhang, Yudan Fan, Ying Zhou, Yaping Zhao, Pengfei Liu and Zongfang LiAvailable online: 05 May 2025More LessIntroductionIcaritin is a bioactive flavonol isolated from the Chinese medicinal herb Epimedium. The comprehensive understanding of antifibrotic effects and associated molecular mechanisms of icaritin remains incomplete. This study aims to explore the protective effects of icaritin against liver fibrosis and to further elucidate the mechanisms involved.
MethodsHuman hepatic stellate LX-2 cells stimulated with TGF-β1 and a carbon tetrachloride (CCl4)-induced liver fibrosis mouse model were employed. In vitro assays were carried out to evaluate collagen type I (COL I) and α-smooth muscle actin (α-SMA) expression, while in vivo studies assessed fibrosis alleviation. Molecular mechanisms were explored via analysis of TGF-β1, phosphorylated Smad2/3, and HIF-1α protein levels using Western blotting.
ResultsIcaritin suppressed TGF-β1-induced COL I and α-SMA expression in LX-2 cells and ameliorated liver fibrosis in CCl4-treated mice. Mechanistically, it significantly reduced TGF-β1 levels, inhibited Smad2/3 phosphorylation, and downregulated HIF-1α protein expression in LX-2 cells.
ConclusionIcaritin attenuated experimental liver fibrosis through the inhibition of the TGF-β/Smad and HIF-1α signaling pathways, highlighting its therapeutic potential for fibrotic liver diseases.
 
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Genetic Studies on Multiple Consanguineous Families Segregating Diverse Phenotypes of Microphthalmia Identified Novel and Recurrent Mutations
Available online: 05 May 2025More LessIntroductionAnophthalmia/microphthalmia (A/M) and anterior segment dysgenesis (ASD) are severe ocular anomalies impacting eye morphology, occurring in 30 per 100,000 live births. Genetic research has identified over 30 genes linked to A/M anomalies, with their products mainly involved in eye organogenesis.
Aims and ObjectivesThis study examined two consanguineous A/M families to identify disease-associated pathogenic mutations and predict their functional impact.
MethodologyPatients were clinically examined using A-scan and ophthalmic ultrasonography. Whole exome sequencing (WES) identified candidate pathogenic variants validated through Sanger sequencing. Computational analyses assessed the impact of these mutations on protein structure and function.
ResultsThe clinical diagnosis of family A revealed microphthalmia with ASD, while family B presented with an A/M phenotype. Exome analysis of family A identified a novel missense variant, NM_012293:c.A3742G [p.(Arg1248Gly)], in the peroxidasin (PXDN) gene (ClinVar ID: VCV001333267.1). At the cellular level, PXDN is involved in establishing sulfilimine bonds in collagen IV, a component of the basement membrane, suggesting that ocular defects may result from impaired integrity of the basement membrane in the developing eye. In contrast, Family B exhibited a nonsense variant NM _012186:c.720C>A (p.Cys240*) in the FOXE3 gene. This variant has been previously reported in other South Asian populations, suggesting a founder effect in subcontinent populations. Structural modeling and simulation analysis of mutant proteins revealed altered properties, thus corroborating the pathogenicity of the identified mutation.
ConclusionOur findings may contribute to the elucidation of genotype-phenotype correlations, potentially facilitating the molecular diagnosis of microphthalmia and ASD.
 
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Spinosin Suppresses RANKL-induced Osteoclastogenesis and Alleviates LPS-induced Cranial Osteolysis: A Study based on Network Pharmacology and Experimental Validation
Authors: Qi Meng, Yang Su, Shankun Dong, Jianxun Ge, Lei Tian and Shui SunAvailable online: 05 May 2025More LessAimInflammatory osteolysis often characterizes many orthopedic diseases, with an important role played by the overactivity of osteoclasts. This research endeavoured to investigate the effects of spinosin, a potent ingredient in traditional Chinese medicine, on Lipopolysaccharide (LPS)-induced osteoclast activity and formation to alleviate osteolysis.
MethodsBased on the molecular structure of spinosin, network pharmacology was used to predict its primary targets and mechanisms. LPS was used to stimulate pre-osteoclasts and to simulate an inflammatory environment. The effect of spinosin on osteoclast biology was subsequently examined via morphological study, qPCR, and Western blot (WB). Moreover, LPS-induced cranial osteolysis mice were utilized, followed by micro-CT analysis, to reveal the curative effects in vivo.
ResultsNetwork pharmacology and molecular docking suggested that EGFR and Akt might be the key targets for the efficacy of spinosin in inflammatory osteolysis. The results of in vitro experiments demonstrated that spinosin significantly inhibited osteoclast function and activity in the inflammatory environment, and this effect might be achieved through regulating EGFR-Akt signaling. The results of animal experiments also showed spinosin-protected mice against LPS-induced bone loss.
ConclusionSpinosin can inhibit EGFR-mediated Akt phosphorylation, which in turn negatively affects downstream Nfatc1-mediated osteoclast-associated gene expression and subsequent osteoclast formation and functionality, mitigating the LPS-induced osteolysis. Our study proves that spinosin holds the promise of being an innovative drug to prevent inflammatory osteolysis.
 
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Identification and Validation of BATF3 as a Promising Biomarker Gene for Peripheral T-cell Lymphoma
Authors: Yidong Zhu, Jun Liu and Ting ZhangAvailable online: 02 May 2025More LessBackgroundPeripheral T-cell lymphoma (PTCL) is a rare and heterogeneous group of hematological malignancies. Treatment options are limited and often unsatisfactory, leading to a poor prognosis in most subtypes.
ObjectiveThis study aimed to identify potential biomarker genes for PTCL and to explore the underlying mechanisms by integrating machine learning, Mendelian Randomization (MR), and experimental validation.
MethodsMicroarray datasets (GSE6338, GSE14879, and GSE59307) were downloaded from the Gene Expression Omnibus database. Differential expression analysis was conducted to identify the Differentially Expressed Genes (DEGs) between patients with PTCL and controls. A machine learning algorithm was then used to further refine the selection of characteristic genes for PTCL. We integrated genome-wide association studies data with expression quantitative trait loci data to identify genes with potential causal relationships to PTCL. Functional analysis was performed to explore underlying mechanisms. Finally, the identified gene was validated in clinical samples from patients with PTCL and controls.
ResultsBased on 60 DEGs, the least absolute shrinkage and selection operator algorithm identified nine characteristic genes for PTCL. MR analysis revealed 203 genes with causal effects on PTCL, ultimately identifying one co-expressed gene: Basic Leucine Zipper ATF-like Transcription Factor 3 (BATF3). It demonstrated good predictive performance across various PTCL subtypes, with AUC values ranging from 0.7 to 1. Functional analysis suggested that BATF3 may play a role in PTCL through immune-related pathways. Experimental validation using clinical samples further suggested the potential of this biomarker gene in PTCL.
ConclusionBy combining machine learning, MR, and experimental validation, we identified and validated BATF3 as a promising biomarker of PTCL. These findings provide insights into the molecular mechanisms underlying PTCL and may inform the development of effective treatment strategies for this disease.
 
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Identification and Experimental Validation of Tumor Antigens and Hypoxia Subtypes of Osteosarcoma for Potential mRNA Vaccine Development
Authors: Chunnian Ren, Dawei He and Quan WangAvailable online: 29 April 2025More LessBackgroundOsteosarcoma is the most common primary malignant bone tumor in children and adolescents. The aim of this study was to explore the possibility of OS hypoxia subtype for anti-OS mRNA vaccine development and select suitable patients for precision therapy.
MethodsWe comprehensively explored hypoxia-related genes (HRGs) as potential sources of tumor neoantigens in OS patients. Gene set enrichment analysis algorithm and consensus clustering analysis were used to determine immune subtypes and evaluate tumor microenvironment. Estimation of stromal and immune cells in malignant tumour tissues using expression data algorithm was used to assess tumour immune activity. The OS hypoxia landscape was visualized using dimensionality reduction analysis based on the DDRTree algorithm. Assessment of clinical samples and molecular experiments were performed to verify the determined tumor antigens.
ResultsFour overexpressed and mutated tumor antigens associated with prognosis and infiltration of antigen-presenting cells were identified and verified by clinical samples and molecular experiments. Furthermore, OS patients were stratified into two OS hypoxia subtypes. Interestingly, patients with the OS hypoxia subtype 1 tumor had a superior survival than those with the OS hypoxia subtype 2 tumor. Distinct expressions of immune checkpoint proteins (ICPs) and immunogenic cell death (ICD) modulators were observed in different immune subtype tumors. Finally, the immune landscape of OS showed a high degree of heterogeneity between individual patients.
ConclusionThis study identified potential antigens for the anti-OS mRNA vaccine as well as different OS hypoxia subtypes, guiding more effective immunotherapeutic strategies and selecting appropriate patients for tumor vaccine therapy.
 
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The Pre-metastatic Niche-related Index Reveals the Immune Signature and Immunotherapy Response in Lung Adenocarcinoma
Authors: Weichang Yang, Zhijian Wu, Shanshan Cai, Jiajia Xiang and Xiaoqun YeAvailable online: 29 April 2025More LessBackgroundMetastasis is the leading cause of death in lung cancer patients. Pre-metastatic niche (PMN) plays an important role in pre-metastatic tumors. However, the development of clinical applications of PMN is still limited.
MethodsExpression data for lung adenocarcinoma (LUAD) patients and PMN-related genes were downloaded from the UCSC Xena website and GeneCards database, respectively. Multiple combinations based on machine learning algorithms were used to screen signature genes and construct a PMN-associated index. Spearman analysis explored the correlation between the PMN-associated index and immune cell infiltration. In addition, we analyzed the clinical value of the PMN-associated index based on drug sensitivity analysis and TIDE scores.
ResultsThe enrichment analyses suggested that PMN-related genes were mainly enriched in the PI3K-Akt and HIF-1 signaling pathways. We chose random survival forest, Lasso, and multivariate Cox regression analyses to construct the PMN-associated index based on the results of multiple machine learning algorithms. Six signature genes (SNAI2, CXCR4, TNFSF11, ENG, TIMP1, and PDGFB) were screened to construct the PMN-associated index. KM analysis suggested that the survival probability was greater in the low PMN-associated index group than in the high PMN-associated index group. In addition, we confirmed that LUAD patients with a low PMN-associated index were more likely to benefit from immunotherapy.
ConclusionWe confirmed that the PMN-associated index is a valid predictor of prognosis, immune characteristics, and antitumor therapy efficacy in LUAD patients, which provides additional evidence for the potential clinical value of PMN development.
 
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Melittin Inhibits Ovarian Cancer Cell Growth by Downregulating MMP9 Expression via the JAK2-STAT3 Signaling Pathway
Authors: Hongyi Sun, Jie Ding, Yujia Jiang, Danying Zhang, Jin Yu, Shuai Sun, Jing Zhou and Chaoqin YuAvailable online: 29 April 2025More LessObjectiveThis study aimed to investigate the target sites, core pathways, and mechanisms of action of melittin in treating ovarian cancer through network pharmacology, molecular docking, and experimental verification.
MethodsPotential targets for melittin in ovarian cancer treatment were predicted using databases, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. The binding of the drug to these targets was confirmed through molecular docking. The core targets and pathways were experimentally validated. A tumor-bearing nude mouse model was established, with the mice randomly divided into treatment and control groups. The treatment group received 5 mg/kg of melittin by intraperitoneal injection, whereas the control group received saline injections. Changes in mouse weight and tumor volume were monitored, and protein expression in mouse tumor tissues was assessed via immunohistochemistry and Western blotting at the end of the experiment.
ResultsFifty-three common targets between melittin and ovarian cancer were identified in the SEA and GeneCards databases. The Protein-Protein Interaction (PPI) analysis highlighted core targets, including MMP9, STAT3, MMP2, STAT6, FURIN, and BRCA1. The GO enrichment results were related mainly to the metabolic processes of collagen degradation, extracellular matrix disassembly, external encapsulating structures, and phospholipase C-activated G-protein-coupled receptor signaling pathways. The KEGG pathway analysis revealed the enrichment of genes related to estrogen signaling, necroptotic apoptosis, the FoxO signaling pathway, microRNAs in cancer, the JAK-STAT signaling pathway, proteoglycans in cancer, and receptor-mediated carcinogenesis. Cell Counting Kit-8 (CCK8) assays, scratch wound healing tests, and Transwell invasion assays demonstrated that melittin significantly inhibited the proliferation, migration, and invasion of ovarian cancer cells. The Western blot results indicated that melittin downregulated the levels of p-JAK2, p-STAT3, and MMP9 in ovarian cancer cells. Molecular docking demonstrated that melittin bound stably to MMP9 and STAT3. The results of animal experiments indicated that melittin suppressed the growth of ovarian tumors in nude mice and significantly downregulated the expression of MMP9, p-JAK2, and p-STAT3 in tumor tissues (p<0.05).
ConclusionMelittin may inhibit the growth of ovarian cancer cells by downregulating MMP9 expression via the JAK2-STAT3 signaling pathway, thus exerting a therapeutic effect.
 
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Integrating Transcriptomic Data and Mendelian Randomization Analyses Reveals Potentially Novel Sepsis-related Targets
Authors: Wenting Tao and Liang ChenAvailable online: 29 April 2025More LessBackgroundSepsis remains a leading cause of global morbidity and mortality.
ObjectiveTo identify candidate biomarkers that may be mechanistically related to the pathogenesis of sepsis.
MethodsThe Gene Expression Omnibus database was leveraged to identify differentially expressed genes (DEGs) between the healthy control and septicemia groups. Genes causally related to sepsis were probed through the integration of GWAS and expression quantitative trait loci (eQTL) data in a two-sample Mendelian randomization (MR) analysis. A set of key sepsis-related genes was then selected based on the overlap between these putative causal genes and the DEGs. These genes were then subjected to enrichment analyses, testing set validation, and analyses of their expression dynamics in clinical samples.
ResultsAn examination of the overlap between 228 sepsis-related DEGs identified in the training dataset and 275 candidate causal genes linked to sepsis derived from the MR analysis led to the selection of four overlapping (SLC22A15, IL5RA, HDC, and SLC46A2) that may play a key role in sepsis. Enrichment analyses indicated that these genes were involved in the regulation of histidine metabolism and immune/inflammatory responses. In immune cell infiltration analyses, these genes were positively correlated with inflammatory response activation and the suppression of adaptive immunity. Consistent findings were obtained through qPCR verification in clinical samples.
ConclusionThese results offer potential insight into the mechanisms that govern septicemia and thus suggest a promising series of candidates that may be amenable to targeting to prevent or treat sepsis more effectively.
 
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Sulfur and Selenium Modifications at Phosphorus Atom in Nucleoside Monophosphates, Activity and Potential Applications
Available online: 28 April 2025More LessNucleotides and nucleosides play an essential role in many cellular processes but have low physiological stability, which limits their usefulness. Nucleosides modified with chalcogen at the phosphorus atom are more stable in body fluids and tissues. They can act as activators or inhibitors in many processes, including signal transduction through receptors and intracellular signaling. Some of them are also used as drugs or prodrugs that can serve as potential therapeutics in cancer and other diseases. This review focuses primarily on the activity and potential application of the nucleoside monophosphates modified with sulfur and selenium at the phosphorus atom, such as nucleoside 5’-O-phosphorothioate and 5’-O-phosphoroselenoates as well as adenosine cyclic 5’, 3’- monothiophosphate and guanosine cyclic 5’, 3’-monothiophosphate.
 
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Variants of Visceral Adipocytokine Genes in Obesity and Coronary Atherosclerosis: A Review
Available online: 23 April 2025More LessAdipocytokines secreted by adipokines can have both direct and indirect effects on the development of atherosclerosis progression. Research using modern high-tech methods of molecular genetic analysis, which make it possible to identify the influence of certain variants of regulatory genes on the course of the atherosclerotic process, is becoming increasingly relevant. The review examines variants of genes (ADIPOQ, RETN, ITLN1, PBEF1, SCT, LEP, and GHRL) associated with obesity and metabolic disorders, as well as atherosclerosis-associated cardiovascular diseases. The review also addresses the mechanisms underlying various variants of visceral adipocytokine genes, as well as the translational potential of understanding these variants for therapeutic advances. The variants studied in the context of obesity, metabolic disorders, and atherosclerosis-associated cardiovascular diseases included rs1501299 (276G/T), rs2241766 (45G/T), rs74577862, rs182052, and rs266729 for ADIPOQ gene; rs1862513 (-420C/G), rs3745367 (299 G/A) for RETN gene; rs2274907 (326A/T) for ITLN1 gene; rs1319501 (G-948T), rs2302559, rs1215113036, rs11977021 (−3187G>A), rs4730153, and rs9770242 for PBEF1 gene; rs7799039 (G2548A), rs2167270 G>A, rs12112075 (G-2548A) for LEP gene; rs696217 (+408C>A, c.214G>T, p.Leu72Met), rs27647 (A-604G) for GHRL gene. The missense variant rs376423879 in the SCT gene was the only variant that has been studied in association with overweight. The contribution of gene variants to the development of obesity, metabolic disorders, and CVD depends on many factors, including lifestyle, nutrition, and other genetic and environmental factors. For a more accurate understanding of the role of the genes presented in the review, more research is needed in different populations, both in terms of the nature of the variation of genes predisposing to diseases associated with overweight, dyslipidemia, and atherosclerosis and in terms of the characteristics of their phenotypic manifestation.
 
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Regulatory Relationships between DNA Methylation and Long Non- coding RNAs in Neuroblastoma
Authors: Yuan Fang, Fei Xu, Rui Dong, Lian Chen and Yizhen WangAvailable online: 23 April 2025More LessObjectivesNeuroblastoma (NB) is a prevalent pediatric solid malignancy associated with significant morbidity and mortality, largely driven by epigenetic alterations. This review aims to identify novel biomarkers related to long non-coding RNAs (lncRNAs) and DNA methylation in NB to enhance prognostic capabilities.
MethodsWe conducted a detailed analysis of the interplay between lncRNAs and DNA methylation in NB, focusing on regulatory variations and their implications for disease progression. Key lncRNAs, including GTL2/MEG3, DALI, NBAT-1, and DLX6-AS1, were examined for their regulation by DNA methylation through cis- and trans-methylation mechanisms.
ResultsThere are clinical and biological implications of lncRNAs in NB and related cancers. Notably, GTL2 and its alias MEG3 are implicated in tumorigenesis through epigenetic modifications, such as hypermethylation, leading to the loss of gene expression and aggressive tumor behavior. Similarly, the interactions of DALI with adjacent genes illustrate the crucial role lncRNAs play in neuronal differentiation and tumor progression, suggesting their potential to impact prognosis through regulatory effects. Furthermore, NBAT-1 emerges as a promising tumor suppressor with strong correlations to NB prognosis, where its methylation-induced silencing is associated with negative outcomes. DLX6-AS1 is also linked to increased NB risk, with expression patterns correlating to disease stage and survival rates; however, more extensive survival data are required to establish its prognostic value.
ConclusionThis review highlights the potential of lncRNAs as prognostic indicators in NB, emphasizing the need for further research to elucidate their roles and validate them as biomarkers for improved patient outcomes.
 
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Exploring Therapeutic Strategies against Monkeypox Virus Through Network Pharmacology and Bioinformatics Analysis
Authors: Zafer Saad Al Shehri, Faez Falah Alshehri and Abdur RehmanAvailable online: 23 April 2025More LessIntroductionThe emergence of the monkeypox virus (MPXV) as a zoonotic threat has necessitated the development of effective treatments, particularly after it spread to regions outside of Central and Western Africa, such as the 2003 outbreak in the United States. Our groundbreaking study identifies CDK1 and TOP2A as key proteins in the pathogenesis of MPXV infection, utilizing network pharmacology to target these proteins for the first time. CDK1 and TOP2A, previously known for their roles in cell reprogramming, emerge as critical targets in our strategy to combat the virus.
MethodsBy targeting CDK1 and TOP2A, proteins integral to cell reprogramming, with small molecules identified in our study, such as carnosic acid, rosmarinic acid, and coclaurine, we propose a novel method not only to inhibit the replication of the monkeypox virus but also to harness cellular plasticity for therapeutic purposes. The identification and targeting of these proteins with specific compounds disrupt the virus's life cycle and simultaneously enhance the efficiency of cell reprogramming.
ResultsThis dual-action approach leverages the inherent plasticity of cellular reprogramming processes to combat the virus, showcasing a pioneering step in the use of regenerative medicine principles for antiviral strategies. Moreover, molecular docking and dynamic simulations strengthen our findings by demonstrating a strong binding affinity between TOP2A and CDK1, validating the synergistic effects of our identified small molecules.
ConclusionOur research thus opens new avenues for addressing viral threats like monkeypox, utilizing the convergence of virology, network pharmacology, and cellular reprogramming to pave the way for innovative treatments.
 
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Erbin Inhibited Angiogenesis in vitro with the Inhibition on the STAT3 Pathway in Breast Cancer Cells
Authors: MingZhen Zhao, HaiLan Xu, Yu Sun, XinYang Li, LingLing Wang, Xing Zhao, Die Mu, YaLei Li and LiXin SunAvailable online: 23 April 2025More LessBackgroundAngiogenesis plays an important role in progression of tumors including breast cancer, which accounts for the vast majority of women's malignant tumors globally, to meet the excessive requirement of oxygen and nutrition for growth, metastasis, and invasion of the tumor. Therefore, targeting tumor angiogenesis has turned into a significant target for cancer therapy. Erbin has a significant effect on the initiation and progression of cancer, including breast cancer, but its role in inhibiting vascular endothelial cell proliferation and angiogenesis by breast cancer cells remains unclear.
MethodsIn this study, human SKBR3 and MCF-7 breast cancer cells were used and transfected with the plasmid and siRNA for overexpression and silence of Erbin, respectively. Western blot, qRT-PCR, CLEIA, CCK-8 and Matrigel Tube Formation Assay were used for the proteins detection, mRNAs detection, detection of VEGF in the culture supernatants, detection of cell proliferation and detection of the angiogenic ability of HUVECs in vitro, respectively.
ResultsIt was shown that the expression of both Erbin protein and mRNA in SKBR3 cells was lower compared to that in MCF-7 cells (p < 0.05). While the expression of VEGF protein was higher in SKBR3 cells than that in MCF-7 cells (p < 0.05). Furthermore, the VEGF protein and mRNA in the cells, VEGF protein in the culture supernatant, HUVEC proliferation in the conditioned medium at 16 h and 24 h, the total length of tube formation in the conditioned medium, and pSTAT3 protein in the cells, were downregulated by transfection of Erbin gene in SKBR3 cells and upregulated (excluding HUVEC proliferation at 16 h) by transfection of Erbin siRNA in MCF-7 cells compared with their NC cells (p < 0.05).
ConclusionIt can be concluded that Erbin, with inhibiting the STAT3 pathway, suppresses the proangiogenic effects of breast cancer cells, thereby suggesting its potential as a therapeutic target for breast cancer.
 
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Protective Effects of Ginsenosides on Drug-induced Cardiotoxicity: A New Therapeutic Approach with Focus on Molecular Mechanisms in Cardio-oncology Field
Available online: 17 April 2025More LessPanax ginseng (PG), a staple in traditional medicine in Korea and China, holds a rich history of application for various diseases. Notably, its primary active components, ginsenosides, exhibit diverse therapeutic effects. Chemotherapy-induced side effects pose significant challenges to the treatment outcomes of cancer patients. Current strategies for managing the adverse effects of chemotherapy exhibit limited efficacy and have the potential to induce various detrimental side effects. In the realm of complications, cardiotoxicity poses a serious threat, ranking as the second major contributor to illness and death in individuals suffering cancer. It is linked to various cellular mechanisms such as oxidative stress, inflammation, apoptosis, autophagy, endoplasmic reticulum stress, and aberrant myocardial energy metabolism. Both in vivo and in vitro experiments confirm that ginsenosides undeniably present non-toxic and efficacious alternatives for addressing chemotherapy-induced side effects, including cardiotoxicity, neurotoxicity, nephrotoxicity, hepatotoxicity, immunotoxicity, and hematopoietic inhibition. Hence, there is a need to produce novel and potent drugs sourced from natural, non-toxic compounds to address the side effects induced by chemotherapy. The emphasis should be on the underlying mechanisms targeting mentioned cellular pathways. In this comprehensive review, we consolidate current knowledge and summarization with this aim and shed light on the future research of PG in cardio-oncology.
 
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Mechanisms and Characteristics of Chronic Pain in Alzheimer’s Disease: A Narrative Review
Authors: Roman Konovalov, Mina Aubakirova and Dmitriy VidermanAvailable online: 15 April 2025More LessAlzheimer’s disease is a neurodegenerative illness that significantly diminishes patients’ quality of life. Chronic pain remains a major contributor to exacerbating patients’ well-being. This comprehensive review aims to explore the mechanisms underlying pain perception in AD as well as identify potential targets and future considerations for pain relief. AD causes structural and functional alterations in the affected brain, including shrinkage of gray matter volume and disruptions in brain network connectivity. Besides memory loss, pain is a significant yet often neglected symptom. Effective pain management in AD is challenged by the adverse effects of pain-relief medications and communication difficulties, especially as the disease progresses. Both non- and pharmacological interventions are currently used to alleviate pain in AD. Pharmacological options include opioids, nonsteroidal anti-inflammatory drugs, paracetamol/acetaminophen, and adjuvant pain relievers like antidepressants and antiepileptic medications, though these are not officially approved for pain relief in AD. Non-pharmacological strategies, such as exercise therapy, music therapy, Reiki, reflexology, and behavioral therapy, are preferred to prevent the side effects of medication. However, the use of these methods is limited due to a lack of high-quality research. The review highlights a crucial link between neurological changes in AD and the perception of pain, underscoring the need for customized pain management approaches for this population. Emphasizing non-pharmacological interventions could potentially improve pain management in AD patients, provided that further research supports their effectiveness.
 
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lncRNAs and circRNAs: Emerging Players in Pediatric Medulloblastoma Pathology
Authors: Ozal Beylerli, Elmar Musaev, Tatiana Ilyasova and Albert SufianovAvailable online: 15 April 2025More LessMedulloblastomas (MBs) are the most common malignant brain tumors in children, marked by aggressive growth, molecular heterogeneity, and a high propensity for cerebrospinal dissemination. Despite advancements in conventional treatments - surgery, chemotherapy, and radiation therapy—substantial challenges persist, including debilitating long-term toxicities and emerging resistance to therapy. This review examines the multifaceted roles of non-coding RNAs (ncRNAs) - particularly long non- coding RNAs (lncRNAs) and circular RNAs (circRNAs) - in pediatric medulloblastoma pathogenesis, diagnosis, and therapeutic targeting. NcRNAs exert robust regulatory effects on gene expression by modulating signaling pathways, acting as miRNA sponges, and controlling the expression of oncogenic or tumor-suppressive genes. In this study, we focus on notable examples of lncRNAs (e.g., HOTAIR, TP73-AS1) and circRNAs (e.g., circ-SKA3, circ_63706) implicated in fundamental oncogenic processes, such as cell proliferation, apoptosis, metastasis, and stem cell maintenance. We also discuss their subgroup-specific roles, emphasizing high-risk groups, such as Sonic Hedgehog (SHH) and Group 3 medulloblastomas. In parallel, we explore the potential of ncRNAs to serve as diagnostic/prognostic biomarkers, given their tissue-specific expression, stability, and detectability in biological fluids like the Cerebrospinal Fluid (CSF). Finally, we review emerging therapeutic strategies, including antisense oligonucleotides, RNA sponges, and CRISPR-based editing, aimed at disrupting oncogenic ncRNA functions or reinforcing tumor-suppressive pathways. While these strategies hold promise, major hurdles include functional redundancy, optimizing in vivo delivery, and mitigating off-target effects. By detailing these challenges and outlining future research directions, this review underscores the revolutionary potential of ncRNA-focused diagnostics and therapies for managing pediatric medulloblastomas, offering new paths for improving survival outcomes and quality of life in affected children.
 
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TGF-β: The Molecular Mechanisms of Atherosclerosis - insights into SMAD Pathways and Gene Therapy Prospects
Available online: 15 April 2025More LessAtherosclerosis, a leading cause of global morbidity and mortality, is characterized by plaque formation resulting from the accumulation of fibrous elements, lipids, and calcification in arteries, leading to complications such as ischemic stroke, coronary artery disease, and myocardial infarction. Traditional treatments primarily address symptoms but fail to target underlying causes, prompting exploration of novel approaches like gene therapy. The TGF-β family, encompassing TGF-β1, TGF-β2, and TGF-β3, plays a critical role in cellular processes including proliferation, apoptosis, and migration, with its dysregulation strongly linked to cardiovascular diseases. In atherosclerosis, TGF-β influences key factors, such as macrophage cholesterol regulation, plaque stability, and vascular smooth muscle cell function, while also contributing to endothelial dysfunction-an early stage in disease development. Personalized medicine has highlighted the importance of tailoring therapies to genetic profiles, particularly regarding TGF-β pathway variations such as SNPs in TGF-β1 and TGFBR2, which could inform more precise interventions. Emerging technologies like CRISPR-Cas9 and RNA-based therapies enable targeted modulation of these genetic factors, offering new avenues to mitigate disease progression. CRISPR-Cas9 allows direct editing of gene loci linked to atherosclerosis, potentially correcting mutations or modulating expression levels, while RNA-based therapies, including siRNAs and antisense oligonucleotides, provide additional precision tools for addressing dysregulated genes. This review focuses on identifying key genes and additional molecular players involved in or regulated by the TGF-β pathway that may serve as precise targets for gene therapy intervention in atherosclerosis and related cardiovascular diseases. By targeting genes involved in cholesterol metabolism, inflammation, and endothelial function, gene therapy offers a targeted strategy to ameliorate the genetic drivers of these conditions. In summary, modulation of TGF-β signaling by gene therapy has the potential to revolutionize the treatment of atherosclerosis and other cardiovascular diseases while shedding light on the underlying genetic mechanisms of these disorders.
 
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COL4A1 Promotes Gastric Cancer Progression by Regulating Tumor Invasion, Tumor Microenvironment and Drug Sensitivity
Authors: Xiaojun Qian, Wei Jia, Yuntian Li, Jian Chen, Jinguo Zhang and Yubei SunAvailable online: 07 April 2025More LessBackgroundCollagen type IV alpha 1 chain (COL4A1), which has been proven to be a potential biomarker in Gastric Cancer (GC), but its role in tumors and the tumor microenvironment (TME) needs further explanation.
MethodsWe analysed the relationship between COL4A1 and clinical characteristics based on The Cancer Genome Atlas (TCGA) database and verified by tissue microarrays as well as GC cell lines using immunohistochemistry, Q-PCR, Western blot, cell proliferation assays, colony formation assays, cell invasion and migration assays. The immune infiltration and drug sensitivity information between high and low COL4A1 expression were analysed by R package and pRRophetic package. Finally, we established a nomogram based on COL4A1 expression using the bootstrap method.
ResultsCOL4A1 was overexpressed in gastric carcinoma compared with normal gastric tissue, indicating a poor prognosis of GC patients in the TCGA database which were also validated by GC tissue microarrays. GO, KEGG and hallmark enrichment analyses indicated that COL4A1 was mainly associated with the extracellular matrix than malignant proliferation. By siRNA transfection, we found that COL4A1 knockdown inhibited cell colony formation, invasion and migration but did not affect cell proliferation, similar to previous results. Immune infiltration and drug sensitivity analysis showed that COL4A1 was negatively correlated with antitumor immunity and positively correlated with multidrug resistance. By developing a nomogram model based on 8 risk factors, including COL4A1, patients with better clinical outcomes could be accurately distinguished.
ConclusionCOL4A1 is identified as a prognostic marker and potential therapeutic target in gastric cancer. Its overexpression correlates with poor prognosis, tumor invasion, and immunosuppression. A nomogram based on COL4A1 can predict patient outcomes. Future research should validate these findings and explore targeted therapies.
 
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Development of Potential Pharmacological Targets to Normalize Gene Expression in Islets of Type 2 Diabetic Patients
Available online: 07 April 2025More LessBackgroundType 2 diabetes (T2D) is a disease of high prevalence that is expected to continue increasing despite the pharmacological treatments available; in most cases, it is difficult to control. Therefore, more research on experimental drugs is necessary to propose better treatments.
ObjectiveThis study aimed to identify the molecular alterations of pancreatic islets in type 2 diabetes through multi-omics data integration and possible pharmacological targets using bioinformatics methods.
MethodsIn this study, the OmicsNet tool was used to integrate the multi-omics data associated with T2D, and the protein-protein interaction was visualized. Then, gene ontology and KEGG pathways analyses were carried out. Using the DrugRep server, the hub genes obtained underwent a virtual screening with experimental drugs, and twelve experimental drugs were selected to execute the molecular docking by CB-Dock2. Finally, the interactions were displayed in BIOVIA software.
ResultsOur results showed that the main molecular alterations of pancreatic islets in T2D were enzyme binding, mitochondrial metabolism, transcription factors, etc. They were involved in glucose uptake, receptor insulin signaling, and secretion. The molecular docking showed that SRC, AKT1, CREBBP, and HSP90AA1 were therapeutic targets for DB02729, DB04877, DB07970, DB07789, and DB03373.
ConclusionWe identified some alterations in the pancreas of patients with T2D, ten hub genes, and five experimental drugs that could potentially correct gene expression abnormalities. However, further studies are required to validate these results.
 
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Mapping the Multifaceted Roles of ZNF280A: Insights into Prognosis, Immunity, and Function Across Pan-Cancer
Authors: Xiong Qin, Boyuan Qiu, Kai Xiong, Chuangming Huang, Xi Xie, Dejie Lu and Bo ZhuAvailable online: 07 April 2025More LessIntroductionZNF280A, a pivotal member of the zinc finger protein family, is significantly involved in vital cellular functions including cell proliferation, programmed cell death, cellular invasion, metastasis, and resistance to therapeutic drugs across various malignancies. However, its comprehensive role in pan-cancer has not been thoroughly investigated.
MethodsThis research aims to elucidate the oncogenic and immunological functions of ZNF280A across different types of cancer. We conducted an extensive analysis of ZNF280A expression levels, prognostic significance, functional pathways, methylation status, and interactions with immune cells, while also examining immune infiltration patterns and responses to immunotherapy using diverse databases.
ResultsOur findings reveal that ZNF280A expression is significantly upregulated in numerous cancers, correlating with adverse patient prognosis. This association appears to be linked to its involvement in key cancer-related pathways, including the Ras signaling pathway, and its correlation with ZNF280A methylation levels, microsatellite instability (MSI), tumor mutational burden (TMB), and the dynamics of immune cells. Notably, ZNF280A seems to undermine anti-tumor immunity and the effectiveness of immunotherapeutic approaches by promoting the infiltration of immune cells and compromising the functionality of cytotoxic T lymphocytes.
ConclusionThese findings suggest that ZNF280A holds promise as a valuable indicator for forecasting patient outcomes and assessing the effectiveness of immunotherapy, thereby opening avenues for further exploration into targeted therapeutic approaches.
 
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In Silico ADMET Studies, Molecular Docking and Molecular Dynamics Simulation of Thiadiazole Derivatives for the Identification of Putative HsaA Monooxygenase Inhibitors
Available online: 03 April 2025More LessIntroductionThe rise of drug-resistant strains of Mycobacterium tuberculosis (Mtb) represents a substantial public health challenge. Current TB treatments involve the combination of several antibiotics and other agents. However, the development of drug resistance, reduced bioavailability, and elevated toxicity have rendered most of the drugs less effective.
MethodsTo resolve this problem, the identification of novel anti-tuberculosis agents with novel mechanisms of action is the need of the hour. HsaA monooxygenase is an enzyme involved in cholesterol metabolism, particularly in certain strains of Mycobacterium bacteria. This research focuses on discovering new inhibitors for HsaA from a pool of 40 compounds using computational techniques like molecular docking and Molecular Dynamics (MD) simulations along with comparing it with GSK2556286.
ResultsDocking studies revealed that AK05 and AK13 showed good binding affinity as compared to GSK2556286. The docking scores of AK05, AK13, and GSK2556286 are -9.4, -9.0, and -8.9 kcal/mol, respectively. ADMET studies showed that these thiadiazole derivatives can be investigated as lead molecules for the development of novel antituberculosis drugs. MD simulation studies showed that both of the compounds AK05 and AK13 were stable at the binding site with RMSD below 0.25 nm.
ConclusionAll these findings demonstrated that AK05 and AK13 could be used as potent compounds for the development of HsaA monooxygenase inhibitors.
 
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Immunogenic Cell Death-relevant Molecular Patterns, Prognostic Genes, and Implications for Immunotherapy in Ovarian Cancer
Authors: Pijun Gong, Jia Li, Yinbin Zhang and Shuqun ZhangAvailable online: 03 April 2025More LessBackgroundOvarian cancer (OV) is one of the deadliest gynecologic cancers, and approximately 75% of serous ovarian cancer (SOC) patients are diagnosed at advanced stages due to the lack of effective biomarkers.
ObjectiveImmunogenic cell death (ICD) has been investigated in many comprehensive studies, and the role of ICD in ovarian cancer and its impact on immunotherapy is not yet known.
MethodsThe NMF clustering analysis was employed to categorize OV samples into different subgroups. Survival, mutation, and CNV analyses were performed in these clusters. ESTIMATE, CIBERSORT, TIDE, and drug sensitivity analyses (based on GDSC) were also performed on the subtypes. Then, differentially expressed immunogenic cell death genes (DE-ICDGs) in OV were obtained by crossing the DEGs between cluster3 vs. cluster1, DEGs from the TCGA-GTEx dataset, and DEGs from the GSE40595 dataset. Functional enrichment analysis of DE-ICDGs was then performed. The signature genes related to the prognosis of OV in three OV datasets were excavated by drawing Kaplan-Meier curves. Finally, quantitative real-time PCR (qRT-PCR) was performed to verify the expression trends of the signature genes.
ResultsThe NMF clustering analysis categorized OV samples into three distinct groups according to the expression levels of ICDGs, with differential analysis indicating that Cluster3 represented the subgroup with high ICD expression. Mutation and CNV analysis did not differ significantly between clusters, but Amp and Del's numbers did. Immuno-infiltration analysis revealed that cluster3 showed significant differences from cluster1 and cluster2. Immunotherapy and drug sensitivity analysis showed differences in immunotherapy and chemotherapy sensitivity between the clusters. The DEGs in cluster3 vs. cluster1, TCGA-GTEx dataset and GSE40595 dataset were intersected to obtain a total of 71 DE-ICDGs, and functional enrichment result suggested that the DE-ICDGs were significantly correlated with inflammatory response, complement system and positive regulation of cytokine production. 2 DE-ICDGs (FN1 and LUM) were identified that were associated with OV prognosis and were validated significantly down-regulated in the SOC group with PCR.
ConclusionWe identified ICD-associated subtypes of OV and mined 2 OV prognostic genes (FN1 and LUM) associated with ICD, which may have important implications for OV prognosis and therapy.
 
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Decoding Colorectal Cancer: Key Genes and Pathways in the Chinese Population Revealed
Authors: Dongbing Li and Guizhen LyuAvailable online: 03 April 2025More LessBackgroundAs the leading cause of cancer-related deaths globally, colorectal cancer (CRC) ranks third in prevalence. Gene Expression Omnibus (GEO) offers clinicians and bioinformaticians an accessible platform for genomic research across various cancer types, with a particular emphasis on CRC.
ObjectiveWe aim to uncover key genes and pathways in the Chinese CRC population.
MethodsWe identified differentially expressed genes (DEGs) in CRC utilizing four microarray datasets sourced from the GEO database, all specifically from the Chinese population. Functional enrichment analysis was conducted to uncover the molecular mechanisms at play in CRC. The PPI network and CytoHubba tools were employed to identify key genes linked to CRC, with further validation through databases such as Gene Expression Profiling Interactive Analysis (GEPIA), ONCOMINE, and the Human Protein Atlas (HPA).
ResultsOur analysis identified 188 DEGs with overlapping significance, comprising 97 up-regulated and 91 down-regulated genes. Gene Ontology (GO) analysis indicated that up-regulated DEGs were predominantly involved in the extracellular space. In contrast, the down-regulated ones were linked to bicarbonate transport and extracellular exosomes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis highlighted the involvement of up-regulated DEGs in cytokine-cytokine receptor interactions and the TNF signaling pathway. In contrast, the down-regulated genes were associated with nitrogen metabolism and bicarbonate reclamation in the proximal tubule. Notably, the transcriptional levels of CCL20, CDC20, CXCL1, CXCL2, CXCL5, NEK2, and PPBP were elevated in CRC tissues compared to normal tissues. In addition, CXCL12 showed a decreased expression. Additionally, the translational levels of CDC20 and PPBP were found to be higher in CRC tissues.
ConclusionEight genes (CCL20, CDC20, CXCL1, CXCL12, CXCL2, CXCL5, NEK2, and PPBP) were identified as potential diagnostic indicators for CRC. The identified pathways, such as cytokine-cytokine receptor interactions and TNF signaling, along with nitrogen metabolism and bicarbonate reclamation in the proximal tubule, are hypothesized to have a role in the genesis and progression of CRC. This study provides unique insights into the etiology and progression of CRC within the Chinese population.
 
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Target Selectivity of Cysteine Protease Inhibitors: A Strategy to Address Neglected Tropical Diseases
Available online: 25 March 2025More LessNeglected tropical diseases (NTDs) are a group of infectious diseases that mainly affect the population living in poverty and without basic sanitation, causing severe damage to countries' economies. Among them, Leishmaniasis, Chagas disease, sleeping sickness, and related diseases such as Malaria stand out, which, despite being well known, have limited treatments based on old drugs and have high rates of parasite resistance. In addition, current drugs have an uncertain mechanism of action, and there is a need to identify new mechanisms to overcome problems related to side effects and resistance. In a sense, exploring cysteine proteases (CPs) may be a promising alternative that can lead to discovering innovative drugs that may be useful against these diseases. However, exploring CPs in drug discovery should be a cautious and rational process since parasitic CPs show a high degree of homology with human CPs, raising the need to identify increasingly specific patterns of target selectivity to identify safer drugs with fewer side effects. Finally, in this review, we present the main aspects related to the design of CP inhibitor drugs, highlighting structural features of ligands and targets that can be used in the design of new compounds against Leishmaniasis (LmCPB), Chagas disease (Cruzain), sleeping sickness (rhodesain) and malaria (falcipain). We hope our findings can guide researchers in searching for an innovative drug that can be used against these diseases that threaten the world population's health.
 
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Identification of a Protein-truncating Variant in SCAPER Gene Causing Syndromic form of Intellectual Disability
Available online: 25 March 2025More LessBackgroundIntellectual disability (ID) is characterized by impairments in cognitive functioning and adaptive behavior. Globally, it affects 1-3% of the general population, with an increased prevalence in consanguineous families. It is a clinically heterogeneous disorder that can manifest as a variable phenotype. Intellectual developmental disorder and retinitis pigmentosa (IDDRP) is a rare syndrome in which patients present with both ID and retinitis pigmentosa.
Aims and ObjectivesThis study examined a consanguineous family to identify disease-associated pathogenic mutations and elucidate their potential functional impact in patients with IDDRP.
MethodologyClinical assessment of the patients revealed characteristics consistent with both intellectual disability (ID) and retinitis pigmentosa. Individuals affected by IDDRP were subjected to whole exome sequencing (WES), and the identified candidate pathogenic variants were validated by Sanger sequencing. Computational analyses were conducted to evaluate the impact of these mutations on the protein structure and function.
ResultsWES identified a protein-truncating variant, c.2605A>T (p.Lys869Ter), in the S-phase cyclin A-associated protein in the endoplasmic reticulum (SCAPER) gene. SCAPER has previously been reported to cause IDDRP. In silico analyses revealed structural and interactional alterations in the SCAPER protein. This variant is novel in the Pakistani population and has not been previously reported. This variant exhibits an autosomal recessive mode of inheritance and segregates among the investigated affected and unaffected family members.
ConclusionThe present study expands the spectrum of disease-causing variants in SCAPER and will contribute to a better understanding of the genetic etiology of IDDRP.
 
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The Protective Effects of Ferula assa-foetida L. oleo-gum Resin on Diabetic Neuropathy in Animal Models
Available online: 18 March 2025More LessBackgroundFerula assa-foetida L. has traditionally been used to treat various diseases, including infections, asthma, stomach aches, and flatulence. Previous studies have highlighted its anti-inflammatory, anti-oxidative, anti-diabetic, neuroprotective, and nerve-stimulating properties.
ObjectiveThis study aimed to evaluate the therapeutic effects and molecular mechanisms of action of the oleo-gum resin from Ferula assa-foetida L. in an animal model of diabetic neuropathy (DN).
MethodsThe essential oil of oleo-gum resin from Ferula assa-foetida L. was analyzed using Gas Chromatography-Mass Spectrometric Analysis. Forty-two male Wistar rats were included in the study, with diabetes induced via streptozotocin (STZ) injection. The rats were randomly assigned to seven groups (n=6 per group) and treated with different doses of Ferula assa-foetida L. extract (100, 200 mg/kg/day) or oil (10, 20 mg/kg/day), alongside appropriate control groups. After a five-week treatment period, samples of dorsal root ganglia (DRG), pancreatic tissue, and blood were collected. Key parameters assessed included blood glucose and insulin levels, motor function tests, oxidative stress protein generation, pro-inflammatory cytokine gene expression, and histopathological analyses.
ResultsTreatment with various doses of Ferula assa-foetida L. extract or oil, as well as gabapentin, led to significant improvements. These included reduced blood sugar levels, increased insulin levels, and improved glycemic control. Motor function was enhanced, while the expression of pro-inflammatory cytokines and oxidative stress markers was significantly reduced.
ConclusionThese findings indicate a promising therapeutic approach for managing DN. Further studies are warranted to elucidate the underlying mechanisms of Ferula assa-foetida L.'s beneficial effects in DN.
 
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Prognostic Role of Global DNA Methylation in Renal Cancer Reveals Decitabine Treatment Benefit
Authors: Wei Wu, Bin Huang, Peng Xia, Quanzhong Liu, Jin Yi, Ruohan Zhang and Qianghu WangAvailable online: 12 March 2025More LessBackgroundRenal cancer presents a significant global health challenge due to its rising incidence and mortality rates. Often undetected in early stages, it complicates diagnosis and treatment. Current therapies face resistance and limited effectiveness, especially in advanced stages. The diverse subtypes of renal cancer highlight the need for new biomarkers and risk assessment tools for targeted treatments.
ObjectiveThis study aims to assess the prognostic significance of global DNA methylation (GM) levels in renal cancer, identify new biomarkers, and evaluate the therapeutic potential of the DNA methyltransferase inhibitor decitabine.
MethodsData on RNA sequencing, gene mutations, DNA methylation, and clinical outcomes were collected from TCGA and GEO databases. We calculated global DNA methylation scores (GMS) and categorized patients into high, intermediate, and low GMS groups. Survival analysis and genomic analyses were conducted to explore the relationships between GMS, clinical outcomes, and tumor characteristics.
ResultsHigher GMS was identified as an independent prognostic factor associated with worse outcomes in renal cancer. Patients with elevated GMS showed increased mutations, copy number variations, and a more aggressive tumor phenotype. Treatment with decitabine was observed to reduce tumor hypermethylation and downregulate cell cycle pathway activity, indicating potential therapeutic benefits.
ConclusionGlobal DNA methylation plays a significant role in renal cancer prognosis. GMS may serve as valuable biomarkers for prognosis and personalized treatment strategies. Decitabine shows potential efficacy for high GMS patients, particularly through its impact on cell cycle regulation, underscoring the importance of personalized approaches in cancer treatment.
 
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Near-infrared (NIR) Fluorophores in Cancer Bioimaging and Therapy
Authors: Libo Yan, Weiming Zhang, Daogang Wang, Min Zhang, Ning Xu, Mengzhe Yang and Tao RenAvailable online: 12 March 2025More LessThe development of multiple fluorescent agents has contributed to cancer diagnosis and therapy. Near-infrared (NIR) dyes have already been well studied and displayed significant potential in cancer bioimaging and therapy due to their unique characteristics. In the present literature, we illustrated the updated NIR classification and characteristics as well as their applications in (pre-) clinical cancer imaging and treatment. The NIR-based photodynamic therapy (PDT) and photothermal therapy (PTT) were also discussed, including their present limitations. Taken together, the future development of NIR fluorophores would greatly improve cancer precision diagnosis and targeted therapy as one of the promising approaches in this field.
 
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The Role of MicroRNAs in Mitochondrial Homeostasis and their Involvement in the Pathogenesis of Obesity and Metabolic Syndrome: A Focus on MicroRNAs
Available online: 07 March 2025More LessThe maintenance of the functional potential of mitochondria is directly related to epigenetic factors, microRNAs (miRs), and mitomicroRNAs (mitomiRs). An important role in the development of metabolic syndrome (MetS)/obesity is attributed to miRs, which have pro-inflammatory or anti-inflammatory potential and can penetrate the mitochondrial matrix. Deciphering the mechanisms responsible for the transport of miRs into the mitochondria would, we believe, allow us to use the knowledge obtained to build designs for the transport of drugs/mitomiRs into cells/mitochondria with low toxicity. A thorough understanding of the polyfunctionality/versatility of individual mitomiRs in specific cells (cell cultures, tissues: adipocytes, brain cells) will allow targeting cellular metabolism to comprehensively block the central link in disease pathogenesis with low potential side effects of this treatment. In this review, we have attempted to identify the key miRs/mitomiRs associated with MetS that affect mitochondrial function. In our opinion, further research should focus specifically on the miR/mitomiRs described here and further investigate their potential in the development of MetS and its components.
 
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Development of an Inflammation-related Gene-based Diagnostic Risk Model and Immune Infiltration Analysis in Bipolar Disorder
Available online: 05 March 2025More LessObjectiveThis study aimed to construct a diagnostic risk model for Bipolar Disorder (BD) using inflammation-related genes (IRGs) and to explore the role of immune cell infiltration in BD pathogenesis.
MethodsBD datasets (GSE23848, GSE124326, GSE39653, and GSE46449) were retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified using the edgeR package. The intersection of DEGs and IRGs was defined as differentially expressed IRGs. A LASSO regression model was used to identify optimal biomarkers, which were then utilized to construct a diagnostic risk model. Receiver operating characteristic (ROC) curves were used to evaluate the diagnostic accuracy of the biomarkers. Internal validation was performed with GSE124326, while external validation utilized GSE23848, GSE39653, and GSE46449. The xCell module in the IOBR package was employed to assess immune cell infiltration proportions. The relationship between IRGs, the diagnostic risk model, and immune cell dynamics was further analyzed.
ResultsA total of 2345 DEGs were identified in GSE124326. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses indicated that inflammatory pathways are critically involved in BD pathogenesis. A total of 69 BD-related IRGs were identified. Six key IRGs (IL33, DNASE1L3, IL2RA, CD70, CLEC5A, and SLPI) were identified through LASSO regression analysis and used to develop a diagnostic risk model. Internal and external validations confirmed the robust diagnostic performance of the risk model. Immuno-infiltration analysis showed significant differences in immune cell infiltration between BD patients and healthy controls. The diagnostic risk model and four potential biomarkers (DNASE1L3, IL2RA, CD70, and SLPI) showed strong correlations with various immune cell types.
ConclusionA diagnostic risk model for BD was constructed based on IRGs, highlighting the critical role of immune cell infiltration in BD pathogenesis.
 
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The Role of Lipid Rafts in the Mitogen-Activated Protein Kinase Signaling in Cancer
Available online: 03 March 2025More LessSpecific regions of plasma membrane enriched with cholesterol and sphingolipids, recognized as lipid rafts or membrane rafts, play an essential part in cell signal transduction. The ability to actively utilize or exempt signaling proteins for the reinforcement or inactivation of specific signaling pathways is the prominent characteristic of lipid rafts, enabling them to act as lipid-based units that can affect signal transduction and cell activity. A connection between lipid raft structure changes and enhancement of the mitogen-activated protein kinase (MAPK) pathway has been reported. Moreover, alteration in lipid raft construction in cancer has also been confirmed. Thus, this review aimed to study the relationship between lipid rafts and the MAPK signaling pathway in a variety of cancer types.
 
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Molecular and Biochemical Evidence of Edaravone's Impact on Dasatinib-induced AGS Cell Senescence: A Promising Strategy for Gastric Cancer Therapy
Available online: 24 February 2025More LessIntroductionInternal or external stress can induce cellular senescence, which reduces cell division. These metabolically active cells contribute to medication resistance. We examined the potential for edaravone (Eda) to cause apoptosis in dasatinib (Das)-induced senescent gastric adenocarcinoma cells (AGS). Our goal was to develop a new stomach cancer treatment.
MethodsAll Eda doses evaluated were nontoxic to cells. Das decreased AGS cell survival in a dose-dependent manner. The study found that Das (5-10 μM) and Eda (100 μM) caused cell senescence in AGS cells. This was shown by increased β-galactosidase enzyme activity and reactive oxygen species levels and decreased telomerase enzyme activity. These are the biggest signs of aging.
ResultsThis combination therapy also upregulated the expression of cell-senescence genes p53, p16, p21, and p38. This resulted in increased expression of inflammation genes such as TNF-α, IL-1β, and IL-6.
ConclusionThe scratch assay showed that this combination medication down-regulated the cell migration-regulating matrix metalloproteinase-2 (MMP2) gene. Both Das and Eda decreased AGS cell proliferation, suggesting treatment with Eda may prevent metastasis.
 
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Therapeutic Effect of Rosolic Acid against Endothelial Dysfunction in Diabetic Wistar Rats
Authors: Karan Naresh Amin and Kunka Mohanram RamkumarAvailable online: 24 February 2025More LessIntroductionEndothelial dysfunction (ED) results from impaired vascular endothelial cell function, disrupting key processes such as hemostasis, vascular tone regulation, vasculogenesis, angiogenesis, and inflammation. These processes are mediated by a complex signaling network involving hormones, cytokines, and chemokines. ED is recognized as a major contributor to the onset and progression of several micro- and macrovascular diseases, including diabetes. Our previous study demonstrated that the polyphenol Rosolic acid (RA) protects against endoplasmic reticulum (ER) stress-induced ED in vitro by activating nuclear factor erythroid 2-related factor 2 (Nrf2). Additionally, RA enhanced the proliferation and survival of pancreatic β-cells in a co-culture model with endothelial cells under ER stress conditions.
MethodsIn this study, we investigated RA's protective effects against diabetes-induced ED using high-fat diet (HFD)-fed and streptozotocin-induced type-2 diabetic rat models. We evaluated RA’s impact on vascular function and metabolic parameters in these models.
ResultsRA significantly mitigated diabetes-induced ED in the aortic tissues of HFD-fed diabetic Wistar rats. RA treatment improved glucose tolerance and reduced hyperlipidemia, showing efficacy comparable to the anti-diabetic drug Gliclazide. Moreover, RA elevated Nrf2 levels and its downstream target genes in aortic tissues while reducing ED markers such as Intercellular Adhesion Molecule 1 (ICAM1), vascular cell adhesion molecule 1 (VCAM1), and endothelin-1.
ConclusionThese findings highlight RA as a promising therapeutic agent for diabetes and its associated vascular complications, with potential for broader clinical applications.
 
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HER3-targeting Antibody-drug Conjugates Therapy for Solid Tumors: Recent Advances and Future Potentials
Authors: Xuerui Wang, Linlin Zhao, Fangfang Gao, Yuan Meng, Jie Yang, Meiying Zhu, Dongying Liao, Yingjie Jia and Fanming KongAvailable online: 24 February 2025More LessIn most advanced cancers, standard medical treatments are generally employed. With the emergence of Antibody-Drug Conjugates (ADCs), more optimal therapeutic methods have become available for treating tumors. ADC is composed of a monoclonal antibody that targets a specific antigen and a cytotoxic payload, which conjugates via the synthetic linkers. Therefore, ADC combines the accurate targeting of monoclonal antibodies with the potent efficacy of cytotoxic chemotherapy drugs while circumventing systemic toxicity. Besides, the epidermal growth factor receptor (EGFR) family, expressing differently between tumors and normal tissues, is one of the most frequently targeted antigens for ADC therapy, which mainly encompasses EGFR1/ERBB1, human epidermal growth factor receptor 2/ epidermal growth factor receptor 2 (HER2/ERBB2), HER3/ERBB3, and HER4/ERBB4. In contrast to other targets, HER3 stands out as a promising one, closely associated with the pathogenesis of treatment resistance in several cancers. Moreover, solid tumors, which are more prevalent than hematological malignancies, present a vast field of opportunities for the development of HER3-targeting ADCs. However, research on HER3-targeting ADCs treating solid tumors remains insufficient. Therefore, it is imperative for researchers to gather more clinical trial data and continue to elucidate the efficacy and safety of HER3-ADCs in solid tumors. This review summarizes recent advances and future potentials, aiming to provide insights into targeted therapy. We hope that this review will provide useful information to physicians in the field.
 
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DDX59-AS1: A Novel Prognostic Biomarker and Immunotherapy Predictor in Lung Adenocarcinoma
Authors: Yanli Wang, Wei Li, Su Wei, Lixi Zhang, Dongbing Li and Xu QiAvailable online: 18 February 2025More LessBackgroundThe precise function of DDX59 Antisense RNA 1 (DDX59-AS1) in lung adenocarcinoma (LUAD) has yet to be fully elucidated.
ObjectiveThis study uses bioinformatics analysis and experimental validation to investigate the association between DDX59-AS1 and LUAD.
MethodsThis study uses statistical analysis and database interrogation to investigate the potential association between DDX59-AS1 expression and various clinical characteristics, prognostic factors, regulatory networks, and immune infiltration in LUAD. The quantification of DDX59-AS1 expression in LUAD cell lines is conducted through the use of quantitative real-time polymerase chain reaction (qRT-PCR).
ResultsDDX59-AS1 showed significantly elevated levels of expression in patients with LUAD. High levels of DDX59-AS1 expression were found to be significantly associated with poorer overall survival (OS) in patients with LUAD (p = 0.024). Furthermore, an independent correlation was observed between high DDX59-AS1 expression (p = 0.037) and OS in LUAD patients. DDX59-AS1 was found to be involved in various pathways, including glutathione metabolism, proteasome function, and the cytosolic DNA sensing pathway, among others. A significant correlation was observed between the expression levels of DDX59-AS1 and immune cell infiltration in the context of LUAD. Notably, elevated expression of DDX59-AS1 was observed in LUAD cell lines compared to the non-cancerous Beas-2B cell line.
ConclusionA significant correlation was observed between elevated DDX59-AS1 expression in patients with LUAD and adverse prognosis, alongside increased immune infiltration. These results indicate that DDX59-AS1 may function as a prognostic marker for LUAD and a potential predictor of immunotherapy response.
 
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Bibliometric Analysis of Research on Traditional Chinese Medicine Treatment of Myocardial Infarction from 2007 to 2024 Based on the Web of Science Database
Authors: Qi Lan, Hao Wu, Ming-Tai Chen, Jin-Yi Xue, Maryam Mazhar, Zi-Wen Deng, Yuan Zou, Ping Liu, Gang Luo, Li Dong and Meng-Nan LiuAvailable online: 18 February 2025More LessBackgroundMyocardial infarction (MI) is a common critical syndrome in the late development of cardiovascular diseases (CVDs), and traditional Chinese Medicine (TCM) treatment has become an essential branch in this field.
ObjectiveThis study aimed to use bibliometric methods to examine the research trajectory of TCM treatment of MI from 2007 to 2024 from a multidimensional perspective and analyse its characteristics, hotspots, and frontiers.
MethodsThis study used the search formula TS OR TI OR AB OR A (“traditional Chinese medicine” or “Chinese medicine” or “TCM” or “traditional medicine, Chinese” or ” Chinese traditional medicine” or “Chinese medicine, traditional”) AND TS OR TI OR AB OR AK (“myocardial infarction” or “myocardial infarctions” or ” infarction, myocardial” or “infarctions, myocardial” or “myocardial infarct” or “MI”) to find the Web of Science Core Collection (WOSCC) of relevant studies from 01/01/2007 to 04/29/2024. Target literature records were analysed and graphed using CiteSpace, VOSviewer, and Scimago Graphica.
ResultsA total of 754 records were obtained and 399 records were finally retained after screening. Countries, institutions, authors, and journals were visually analyzed. The current research hotspots and frontiers included Salvia miltiorrhiza, ischemia-reperfusion injury, pathway, molecular docking, and network pharmacology.
ConclusionThis research study would enrich the researchers' understanding of the existing research methodology and future development trends and provide a more efficient research methodology for the research on the mechanism of action of TCM for the treatment of MI and its clinical trials.
 
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Identification of Ferroptosis-Related Prognostic Models and FDFT1 as a Potential Ferroptosis Driver in Colorectal Cancer
Authors: Lili Duan, Lu Cao, Jinqiang Liu, Zixiang Wang, Jie Liang, Fan Feng, Jian Zhang, Liu Hong and Jianyong ZhengAvailable online: 13 February 2025More LessAimsWe aimed to develop Ferroptosis-Related Gene (FRG) signatures to predict overall survival (OS) along with disease-free survival (DFS) in individuals with colorectal cancer (CRC).
BackgroundPrediction of CRC prognosis is challenging. Ferroptosis constitutes a newly reported kind of cell death, and its association with CRC prognosis remains unexplored.
ObjectiveThis research endeavored to establish a prognostic risk signature for colorectal cancer by leveraging ferroptosis-related genes (FRGs), with the objective of refining prognostic precision in clinical settings.
MethodsThe clinical data and mRNA expression profiles were obtained from The Cancer Genome Atlas (TCGA) colorectal cancer cohorts. The Lasso algorithm was employed to develop the overall survival (OS) and disease-free survival (DFS) prediction models. These models were subsequently validated using independent data from GSE38832.
ResultsOur research unveiled a significant difference in the expression levels of 85% of ferroptosis-related genes (FRGs) between CRC tissues and paracancer tissues. Out of these, 11 prognostic genes were pinpointed through univariate Cox analysis. By employing two models, patients were stratified into low- and high-risk groups based on predicted risk scores, which were subsequently validated as independent prognostic factors via multivariate Cox analysis. The robustness of these models was further confirmed through Receiver Operating Characteristic (ROC) curve analysis. Functional enrichment analysis indicated a predominance of cancer-associated pathways in the high-risk group, including WNT signaling, along with variations in immune status between the two risk categories. Leveraging the Connectivity Map (CMap) database, a total of sixteen potential therapeutic drugs were identified. Additionally, in vitro experiments corroborated that Farnesyl-Diphosphate Farnesyltransferase 1 (FDFT1) was underexpressed in CRC and exhibited tumor suppressive properties. More specifically, FDFT1 may augment ferroptosis in CRC by modulating the expression of the Iron-Sulfur Cluster Assembly Enzyme (ISCU).
ConclusionOur study highlighted the significance of ferroptosis-related genes in the pathogenesis of CRC and underscored the potential of ferroptosis-related gene-based risk signatures as valuable tools for improving prognostic accuracy and tailoring therapeutic strategies. However, the validity of these predictive models required further validation through real-world studies to ensure their reliability and applicability.
 
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The Pathophysiological Role of Mitochondria-associated Membranes in Coronary Artery Disease and Atherosclerosis
Authors: Junyan Zhang, Zhongxiu Chen, Li Rao and Yong HeAvailable online: 12 February 2025More LessMitochondria-associated membranes (MAMs) are pivotal in cellular homeostasis, mediating communication between the endoplasmic reticulum and mitochondria. They are increasingly recognized for their role in atherosclerosis and coronary artery disease (CAD). This review delves into the cellular perspective of MAMs' impact on atherosclerosis and CAD, highlighting their influence on disease progression and the potential for therapeutic intervention. MAMs are implicated in key pathophysiological processes such as the generation of reactive oxygen species, calcium homeostasis, myocardial ischemia-reperfusion injury, autophagy, lipid synthesis and transport, and energy metabolism—fundamental to the development and progression of atherosclerosis and CAD. The complex interplay of MAMs with these pathological processes underscores their potential as therapeutic targets. This review synthesizes current understanding and emphasizes the need for further research to elucidate the multifaceted roles of MAMs in atherosclerosis and CAD, offering avenues for developing novel strategies aimed at improving mitochondrial health and mitigating the impact of these conditions.
 
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New Advancements in Prognostic Biomarkers for Upper Tract Urothelial Carcinoma
Authors: Xiaotong Shi and Guodong ZhuAvailable online: 07 February 2025More LessAs research on upper tract urothelial carcinoma (UTUC) has deepened, the value of biomarkers in the prognostic evaluation of UTUC has been gradually highlighted. As a high-grade epithelial tumor derived from the renal pelvis or ureter, UTUC has a significant prognostic challenge to patients, given its high invasiveness and recurrence rate for the formation of post-operative bladder cancer. To better predict the recurrence and metastasis risk of UTUC, this article provides a comprehensive review of hematologic, urologic, genetic, and histologic biomarker studies on the prognostic assessment of UTUC. This study covers a broad range of different kinds of biomarkers, as shown in the graphical abstract. By systematically analyzing these biomarkers, we will have a better understanding of the biological features of UTUC, and it will provide more comprehensive and accurate information for its prognostic assessment. This will not only help clinicians develop more precise treatment strategies, but also provide patients with more personalized rehabilitation recommendations.
 
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The Role and Molecular Mechanism of Icaritin in the Treatment of Alzheimer's Disease
Authors: Chong-Bo Zheng, Li-Zhen Wu, Wan-Ying Song, Liang Luo, Jia-Ting Cai, Zhi-Hua Huang and Ke-Qiang TianAvailable online: 07 February 2025More LessAlzheimer's disease (AD), a degenerative disease of the central nervous system, affects approximately 70 million individuals worldwide. As the number of elderly in the population increases, the prevalence and incidence of AD are increasing annually. Although the drugs are currently used to alleviate certain cognitive symptoms, their overall therapeutic efficacy remains unclear. Consequently, there is significant societal demand for safe and effective therapeutic options. Icaritin (ICT), a bioactive compound derived from Epimedium brevicornu Maxim, has anti-apoptotic, antioxidant, anti-neuroinflammatory, anti-aging, and neuroprotective properties. In recent years, it has garnered significant interest because of its potential preventative and therapeutic effects in the context of AD. In this review, we analyze the therapeutic effects of ICT on AD, namely the inhibition of neuroinflammation, effects against oxidative stress and apoptosis, and promotion of cellular autophagy. The aim of this review was to provide a general reference for the research and development of new drugs, in particular ICT, for the prevention and treatment of AD.
 
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