Pub Date : 2025-11-29DOI: 10.1016/j.meomic.2025.100051
Kifle Jilo Jego , Legesse Adane , Fillipo Tamiru
Euphorbia candelabrum is a medicinal plant traditionally used for treating coughs, tuberculosis, malaria, wound healing, and various skin conditions. This study aimed to analyze the secondary metabolites present in its root extract and evaluate its antioxidant and antibacterial properties. Samples were collected from Sika Kebele in the Gedeo Zone of Southern Ethiopia, air-dried, and then extracted using hexane, dichloromethane, a methanol:dichloromethane mixture (1:1 v/v), and methanol. Phytochemical analysis revealed the presence of alkaloids, flavonoids, phenolics, glycosides, terpenoids, tannins, and saponins in the dichloromethane, methanol:dichloromethane 1:1 mixture, and methanol extracts. In contrast, the hexane extract contained only alkaloids, terpenoids, and steroids. Notably, the methanol:dichloromethane extract yielded flavonoids (10.47 mg QE/g), phenolics (13.4 mg GAE/g), alkaloids (1.426 mg AE/g), and steroids (2.91 mg DME/g). The methanol extract demonstrated higher levels of flavonoids (11 mg QE/g) and phenolics (19 mg GAE/g). Antibacterial activity was assessed against E. coli, P. aeruginosa, S. aureus, and S. pyogenes using the disc diffusion method. The isolated compounds exhibited greater antibacterial activity than crude extracts, with compound KJ-3 showing greater activity against all tested strains, slightly less than tetracycline. These findings suggest that the root of Euphorbia candelabrum may serve as a promising source for the development of new antibacterial agents.
{"title":"Phytochemical analysis, evaluation of antioxidant activity, and investigation of antibacterial activity in euphorbia candelabrum root extracts","authors":"Kifle Jilo Jego , Legesse Adane , Fillipo Tamiru","doi":"10.1016/j.meomic.2025.100051","DOIUrl":"10.1016/j.meomic.2025.100051","url":null,"abstract":"<div><div>Euphorbia candelabrum is a medicinal plant traditionally used for treating coughs, tuberculosis, malaria, wound healing, and various skin conditions. This study aimed to analyze the secondary metabolites present in its root extract and evaluate its antioxidant and antibacterial properties. Samples were collected from Sika Kebele in the Gedeo Zone of Southern Ethiopia, air-dried, and then extracted using hexane, dichloromethane, a methanol:dichloromethane mixture (1:1 v/v), and methanol. Phytochemical analysis revealed the presence of alkaloids, flavonoids, phenolics, glycosides, terpenoids, tannins, and saponins in the dichloromethane, methanol:dichloromethane 1:1 mixture, and methanol extracts. In contrast, the hexane extract contained only alkaloids, terpenoids, and steroids. Notably, the methanol:dichloromethane extract yielded flavonoids (10.47 mg QE/g), phenolics (13.4 mg GAE/g), alkaloids (1.426 mg AE/g), and steroids (2.91 mg DME/g). The methanol extract demonstrated higher levels of flavonoids (11 mg QE/g) and phenolics (19 mg GAE/g). Antibacterial activity was assessed against E. coli, P. aeruginosa, S. aureus, and S. pyogenes using the disc diffusion method. The isolated compounds exhibited greater antibacterial activity than crude extracts, with compound KJ-3 showing greater activity against all tested strains, slightly less than tetracycline. These findings suggest that the root of Euphorbia candelabrum may serve as a promising source for the development of new antibacterial agents.</div></div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"16 ","pages":"Article 100051"},"PeriodicalIF":0.0,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145694764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-24DOI: 10.1016/j.meomic.2025.100050
Salman Khan , Ishaq Khan , Arshad Iqbal , Syed Shujait Ali , Nisar Ahmad , Sami Ullah , Liaqat Ali , Sajjad Ahmad
Background
Ebola virus (EBOV), a member of the Filoviridae family, is a highly lethal disease that has caused multiple outbreaks primarily in Central Africa. According to the World Health Organization (WHO) report, the Ebola Virus Disease death rate in 2019 was around 67 %. Specifically, Bundibugyo Ebolavirus (BEBOV) has a relatively lower pathogenic mortality rate, estimated at 37 %. Previous epidemics have seen varying death rates ranging from 25 to 95 % due to the lack of effective medicines and immunizations.
Objectives
This study aimed to design a multi-epitope vaccine against BEBOV using immunoinformatics to induce robust immune responses.
Methods and results
T-cell (CTL and HTL) and linear B-cell epitopes from spike glycoprotein and nucleoprotein were identified and screened for antigenicity (VaxiJen score: 0.6488), allergenicity, and immunogenicity. Selected epitopes were combined into a vaccine construct with beta-defensin as an adjuvant. The vaccine exhibited favorable physicochemical properties and solubility (0.863482). Molecular docking and dynamics simulations revealed strong binding to TLR-3 (docking score: −354.13 kcal/mol). Codon optimization and in silico cloning suggested efficient expression in Escherichia coli.
Conclusion and future recommendation
The designed multi-epitope vaccine demonstrates promising immunogenic potential against BEBOV. Experimental validation is required to confirm efficacy and safety, and further studies should focus on optimization and clinical evaluation for potential outbreak prevention.
{"title":"Design of a novel multi-epitope-based vaccine against Bundibugyo Ebolavirus using computational approach","authors":"Salman Khan , Ishaq Khan , Arshad Iqbal , Syed Shujait Ali , Nisar Ahmad , Sami Ullah , Liaqat Ali , Sajjad Ahmad","doi":"10.1016/j.meomic.2025.100050","DOIUrl":"10.1016/j.meomic.2025.100050","url":null,"abstract":"<div><h3>Background</h3><div>Ebola virus (EBOV), a member of the Filoviridae family, is a highly lethal disease that has caused multiple outbreaks primarily in Central Africa. According to the World Health Organization (WHO) report, the Ebola Virus Disease death rate in 2019 was around 67 %. Specifically, Bundibugyo Ebolavirus (BEBOV) has a relatively lower pathogenic mortality rate, estimated at 37 %. Previous epidemics have seen varying death rates ranging from 25 to 95 % due to the lack of effective medicines and immunizations.</div></div><div><h3>Objectives</h3><div>This study aimed to design a multi-epitope vaccine against BEBOV using immunoinformatics to induce robust immune responses.</div></div><div><h3>Methods and results</h3><div>T-cell (CTL and HTL) and linear B-cell epitopes from spike glycoprotein and nucleoprotein were identified and screened for antigenicity (VaxiJen score: 0.6488), allergenicity, and immunogenicity. Selected epitopes were combined into a vaccine construct with beta-defensin as an adjuvant. The vaccine exhibited favorable physicochemical properties and solubility (0.863482). Molecular docking and dynamics simulations revealed strong binding to TLR-3 (docking score: −354.13 kcal/mol). Codon optimization and in silico cloning suggested efficient expression in Escherichia coli.</div></div><div><h3>Conclusion and future recommendation</h3><div>The designed multi-epitope vaccine demonstrates promising immunogenic potential against BEBOV. Experimental validation is required to confirm efficacy and safety, and further studies should focus on optimization and clinical evaluation for potential outbreak prevention.</div></div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"16 ","pages":"Article 100050"},"PeriodicalIF":0.0,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145750170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01DOI: 10.1016/j.meomic.2025.100049
Shabiha Afroj Heeamoni, Safayat Mahmud Khan, Md. Omar Faruk, Md. Ismail Hosen
Bladder cancer is a common urological malignancy with poor prognosis, underscoring the need for robust prognostic biomarkers. This study investigated gene expression profiles of 194 epithelial-mesenchymal transition (EMT) hallmark genes in 411 muscle-invasive bladder cancer patients from The Cancer Genome Atlas (TCGA). Non-negative matrix factorization identified two subtypes (C1 and C2) with distinct prognostic, clinical, and immunological characteristics. C2 was enriched in EMT-related pathways, including extracellular matrix and structure organization. Differential expression analysis revealed 1,514 prognosis-associated genes. A four-gene prognostic signature—SIGLEC6, NEFL, NTNG1, and FOXC2—was constructed using univariate, LASSO, and multivariate Cox regression models. Patients were stratified into high- and low-risk groups, with the signature demonstrating predictive value in survival analysis and ROC curves. External validation was performed using GEO data. This EMT-based four-gene signature offers a promising prognostic tool for bladder cancer patient stratification and potential therapeutic targeting.
{"title":"Identification of a prognostic signature for bladder cancer associated with the epithelial-mesenchymal transition hallmark pathway using the TCGA Database","authors":"Shabiha Afroj Heeamoni, Safayat Mahmud Khan, Md. Omar Faruk, Md. Ismail Hosen","doi":"10.1016/j.meomic.2025.100049","DOIUrl":"10.1016/j.meomic.2025.100049","url":null,"abstract":"<div><div>Bladder cancer is a common urological malignancy with poor prognosis, underscoring the need for robust prognostic biomarkers. This study investigated gene expression profiles of 194 epithelial-mesenchymal transition (EMT) hallmark genes in 411 muscle-invasive bladder cancer patients from The Cancer Genome Atlas (TCGA). Non-negative matrix factorization identified two subtypes (C1 and C2) with distinct prognostic, clinical, and immunological characteristics. C2 was enriched in EMT-related pathways, including extracellular matrix and structure organization. Differential expression analysis revealed 1,514 prognosis-associated genes. A four-gene prognostic signature—<strong>SIGLEC6, NEFL, NTNG1,</strong> <!-->and<!--> <strong>FOXC2</strong>—was constructed using univariate, LASSO, and multivariate Cox regression models. Patients were stratified into high- and low-risk groups, with the signature demonstrating predictive value in survival analysis and ROC curves. External validation was performed using GEO data. This EMT-based four-gene signature offers a promising prognostic tool for bladder cancer patient stratification and potential therapeutic targeting.</div></div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"15 ","pages":"Article 100049"},"PeriodicalIF":0.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145529487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-24DOI: 10.1016/j.meomic.2025.100048
Oluwasayo P. Abodunrin , Olayinka F. Onifade , P.M. Osamudiamen , Zacchaeus S. Ololade , Esther O. Abam , Somto O. Otega , Faith O. James , Benjamen O. Okunlola
Introduction
Nonsteroidal anti-inflammatory drugs (NSAIDs) are widely used for pain relief and anti-inflammatory effects but can cause significant liver damage and oxidative stress. Mezoneuron benthamianum, a plant with medicinal properties, has been traditionally used for various treatments.
Methods
This study evaluates the hepatoprotective and antioxidant effects of Mezoneuron benthamianum leaves extract against NSAID-induced toxicity in albino rats. Rats were divided into five groups: control, indomethacin-treated, Mezoneuron benthamianum extract-treated, indomethacin and Mezoneuron benthamianum co-treated, and indomethacin and methyl gallate co-treated. The extract’s biochemical composition was analyzed using GC–MS, and liver function biomarkers (ALT, AST, ALP) and biochemical markers (MDA, SOD, CAT, GSH) were measured.
Results and discussion
Results showed that the indomethacin-treated group had significantly increased ALT, AST, and ALP levels, elevated MDA levels, and reduced SOD, CAT, and GSH activities, indicating liver damage and oxidative stress. Treatment with Mezoneuron benthamianum extract significantly reduced these biomarkers and restored antioxidant enzyme activities. Histopathological analysis confirmed reduced liver damage in the extract-treated group, with similar protective effects observed in the indomethacin and methyl gallate co-treated group. The concentration of Cd marginally exceeded WHO’s limit (0.3412 mg/kg vs. 0.3 mg/kg) whereas concentrations of Fe, Mn, and Cu were well below the thresholds. The hepatoprotective and antioxidant effects of Mezoneuron benthamianum extract might be partially mediated through interactions with essential trace elements, such as Fe, Cu, and Mn.
Conclusion
The study reveals that Mezoneuron benthamianum extract attenuated liver damage by restoring antioxidant enzymes (SOD, CAT, GSH) and reducing oxidative stress markers (MDA). Molecular docking suggested PPAR-α activation as a potential mechanism, though further validation is needed. The study highlights its hepatoprotective potential but warrants dose-response studies for clinical translation.
非甾体抗炎药（NSAIDs）广泛用于缓解疼痛和抗炎作用，但可能导致严重的肝损伤和氧化应激。benthamium是一种具有药用价值的植物，传统上用于各种治疗。方法研究本品对非甾体抗炎药（nsaid）致白化大鼠的肝保护和抗氧化作用。将大鼠分为5组：对照组、吲哚美辛组、苯并咪唑脲提取物组、吲哚美辛与苯并咪唑脲共处理组、吲哚美辛与没食子酸甲酯共处理组。采用GC-MS分析提取物的生化成分，测定肝功能生物标志物（ALT、AST、ALP）和生化标志物（MDA、SOD、CAT、GSH）。结果与讨论结果显示，吲哚美辛治疗组大鼠ALT、AST、ALP水平显著升高，MDA水平升高，SOD、CAT、GSH活性降低，提示肝损伤和氧化应激。用苯达胺提取物处理可显著降低这些生物标志物并恢复抗氧化酶活性。组织病理学分析证实，提取物处理组肝损伤减轻，吲哚美辛和没食子酸甲酯共处理组也有类似的保护作用。镉的浓度略高于世卫组织的限值（0.3412 mg/kg vs. 0.3 mg/kg），而铁、锰和铜的浓度远低于阈值。benthamium Mezoneuron benthamium提取物的肝保护和抗氧化作用可能部分通过与必需微量元素（如Fe、Cu和Mn）的相互作用介导。结论本品提取物通过恢复抗氧化酶（SOD、CAT、GSH）和降低氧化应激标志物（MDA）来减轻肝损伤。分子对接提示PPAR-α激活是潜在的机制，但需要进一步验证。该研究强调了其肝保护潜力，但需要进行临床转化的剂量反应研究。
{"title":"Mezoneuron benthamianum attenuates indomethacin-induced toxicity: Design, synthesis, elemental analysis, in vivo and in silico studies","authors":"Oluwasayo P. Abodunrin , Olayinka F. Onifade , P.M. Osamudiamen , Zacchaeus S. Ololade , Esther O. Abam , Somto O. Otega , Faith O. James , Benjamen O. Okunlola","doi":"10.1016/j.meomic.2025.100048","DOIUrl":"10.1016/j.meomic.2025.100048","url":null,"abstract":"<div><h3>Introduction</h3><div>Nonsteroidal anti-inflammatory drugs (NSAIDs) are widely used for pain relief and anti-inflammatory effects but can cause significant liver damage and oxidative stress. <em>Mezoneuron benthamianum,</em> a plant with medicinal properties, has been traditionally used for various treatments.</div></div><div><h3>Methods</h3><div>This study evaluates the hepatoprotective and antioxidant effects of <em>Mezoneuron benthamianum</em> leaves extract against NSAID-induced toxicity in albino rats. Rats were divided into five groups: control, indomethacin-treated, <em>Mezoneuron benthamianum</em> extract-treated, indomethacin and <em>Mezoneuron benthamianum</em> co-treated, and indomethacin and methyl gallate co-treated. The extract’s biochemical composition was analyzed using GC–MS, and liver function biomarkers (ALT, AST, ALP) and biochemical markers (MDA, SOD, CAT, GSH) were measured.</div></div><div><h3>Results and discussion</h3><div>Results showed that the indomethacin-treated group had significantly increased ALT, AST, and ALP levels, elevated MDA levels, and reduced SOD, CAT, and GSH activities, indicating liver damage and oxidative stress. Treatment with <em>Mezoneuron benthamianum</em> extract significantly reduced these biomarkers and restored antioxidant enzyme activities. Histopathological analysis confirmed reduced liver damage in the extract-treated group, with similar protective effects observed in the indomethacin and methyl gallate co-treated group. The concentration of Cd marginally exceeded WHO’s limit (0.3412 mg/kg vs. 0.3 mg/kg) whereas concentrations of Fe, Mn, and Cu were well below the thresholds. The hepatoprotective and antioxidant effects of <em>Mezoneuron benthamianum</em> extract might be partially mediated through interactions with essential trace elements, such as Fe, Cu, and Mn.</div></div><div><h3>Conclusion</h3><div>The study reveals that <em>Mezoneuron benthamianum</em> extract attenuated liver damage by restoring antioxidant enzymes (SOD, CAT, GSH) and reducing oxidative stress markers (MDA). Molecular docking suggested PPAR-α activation as a potential mechanism, though further validation is needed. The study highlights its hepatoprotective potential but warrants dose-response studies for clinical translation.</div></div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"15 ","pages":"Article 100048"},"PeriodicalIF":0.0,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145580411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-01DOI: 10.1016/j.meomic.2025.100047
Ali Khan, Sara Khan, Muhammad Rahiyab, Salman Khan, Zabih Ullah, Syed Shujait Ali
Bovine alphaherpesvirus 2 (BoHV-2), a major pathogen in cattle, belongs to the Herpesviridae family. In this work, we designed a vaccine against BoHV-2 using its envelope glycoprotein B (gB) and glycoprotein H. In this work, computational methods were utilized for predicting the B and T lymphocyte epitopes with striking results in their antigenicity and low allergenicity. Thereafter, the vaccine design stability tests showed that it was physicochemically stable. Molecular docking and molecular dynamics simulation analyses validated its further efficacy. The docking results demonstrated 11 hydrogen bonds coupled with one salt bridge between the vaccine and TLR3 while PRODIGY analysis suggested a binding free energy (ΔG) of −10.7 kcal/mol alongside a dissociation constant (kDa) of 1.5e-08. In silico cloning demonstrations showed effective expression levels together with immune simulation predictions, suggesting robust immunological responses. However, this study has certain limitations, such as the experimental validation. Future in vivo and in vitro studies are required to confirm the immunogenicity and safety of the in-silico designed vaccine construct.
{"title":"Designing a highly antigenic multi epitope subunit vaccine against Bovine alpha herpes virus 2 targeting glycoprotein B and H: A reverse vaccinology approach","authors":"Ali Khan, Sara Khan, Muhammad Rahiyab, Salman Khan, Zabih Ullah, Syed Shujait Ali","doi":"10.1016/j.meomic.2025.100047","DOIUrl":"10.1016/j.meomic.2025.100047","url":null,"abstract":"<div><div>Bovine alphaherpesvirus 2 (BoHV-2), a major pathogen in cattle, belongs to the <em>Herpesviridae</em> family. In this work, we designed a vaccine against BoHV-2 using its envelope glycoprotein B (gB) and glycoprotein H. In this work, computational methods were utilized for predicting the B and T lymphocyte epitopes with striking results in their antigenicity and low allergenicity. Thereafter, the vaccine design stability tests showed that it was physicochemically stable. Molecular docking and molecular dynamics simulation analyses validated its further efficacy. The docking results demonstrated 11 hydrogen bonds coupled with one salt bridge between the vaccine and TLR3 while PRODIGY analysis suggested a binding free energy (ΔG) of −10.7 kcal/mol alongside a dissociation constant (kDa) of 1.5e-08. In silico cloning demonstrations showed effective expression levels together with immune simulation predictions, suggesting robust immunological responses. However, this study has certain limitations, such as the experimental validation. Future <em>in vivo</em> and <em>in vitro</em> studies are required to confirm the immunogenicity and safety of the in-silico designed vaccine construct.</div></div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"14 ","pages":"Article 100047"},"PeriodicalIF":0.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144925352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-07-08DOI: 10.1016/j.meomic.2025.100046
Yanjun Liang , Xiao Zhu
Alternative splicing (AS) is pivotal in gene expression regulation and protein diversity generation. Suppression of aberrant AS holds promise in cancer management. Utilizing zebrafish-human homologous genes, we investigated AS events across 33 tumor types from TCGA, employing Cox regression analyses to identify prognostic AS events. A risk-scoring model distinguished high and low-risk groups, revealing differences in survival, tumor microenvironment, and immune cell infiltration. Notably, Complement C1q C Chain (C1QC), DENND5A, HP, IRF5, and LRP1 were associated with poor prognosis and immune infiltration. Mendelian randomization confirmed the protective role of C1QC across cancers, further supported by Bayesian Weighted Mendelian Randomization. Leveraging zebrafish homologs enhances our understanding of AS mechanisms and potential therapeutic targets in cancer biology.
{"title":"Analysis of zebrafish homologs within the human genome provides valuable insights into exploring pan-cancer alternative splicing events as prognostic markers and therapeutic targets","authors":"Yanjun Liang , Xiao Zhu","doi":"10.1016/j.meomic.2025.100046","DOIUrl":"10.1016/j.meomic.2025.100046","url":null,"abstract":"<div><div>Alternative splicing (AS) is pivotal in gene expression regulation and protein diversity generation. Suppression of aberrant AS holds promise in cancer management. Utilizing zebrafish-human homologous genes, we investigated AS events across 33 tumor types from TCGA, employing Cox regression analyses to identify prognostic AS events. A risk-scoring model distinguished high and low-risk groups, revealing differences in survival, tumor microenvironment, and immune cell infiltration. Notably, Complement C1q C Chain (C1QC), DENND5A, HP, IRF5, and LRP1 were associated with poor prognosis and immune infiltration. Mendelian randomization confirmed the protective role of C1QC across cancers, further supported by Bayesian Weighted Mendelian Randomization. Leveraging zebrafish homologs enhances our understanding of AS mechanisms and potential therapeutic targets in cancer biology.</div></div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"14 ","pages":"Article 100046"},"PeriodicalIF":0.0,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144680574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-26DOI: 10.1016/j.meomic.2025.100045
Xiao Zhu , Zhuolong Xiong
Background
Lung adenocarcinoma (LUAD) is characterized by low overall survival rates. This research aims to explore the association between long non-coding RNAs (lncRNAs) and chromatin histone methylation/demethylation modifiers in LUAD.
Methods
Datasets from The Cancer Genome Atlas (TCGA), Molecular Signatures Database (MSigDB), and IEU Open genome-wide association studies (GWAS) database were analyzed. A prognostic risk model for LUAD was developed based on 32 lncRNAs linked to histone modification. The relationship between lncRNAs and the high-risk group of lung cancer was evaluated, and GO/KEGG analysis was conducted to investigate the connection between chromatin histone modification-related lncRNAs and biological processes/pathways. Mendelian Randomization methods, including Inverse Variance Weighted (IVW) and Bayesian Weighted Mendelian Randomization (BWMR), were employed to validate the GO/KEGG results. MR-Egger intercept test, Cochran’s Q test, and leave-one-out Analysis were utilized to assess the sensitivity of Mendelian Randomization analysis. Tumor mutation burden (TMB) analysis was performed to evaluate the prognostic impact of high-risk patients with high TMB.
Results
Identified lncRNAs, including AC025741.1 and NHS-AS1, demonstrated strong associations with the high-risk group. GO/KEGG analysis revealed significant correlations between chromatin histone modification-related lncRNAs and microtubule-based movement and cytochrome enzyme P450. Response to the renin-angiotensin agents is a protective factor for lung cancer, while response to glucocorticoids is a risk factor for lung cancer. Immunomarkers MDSC, CAF, and Exclusion showed positive correlations with the risk score, and the combined effects of CAF and MDSC were found to play a pivotal role in LUAD development and progression.
Conclusion
Our study not only establishes a promising LUAD prognostic risk model with potential implications for immunotherapy but also identifies lncRNAs as immune markers for LUAD immunotherapy. Additionally, we validate the causal relationship between chromatin histone methylation-related pathways and lung cancer, bolstering our understanding from a genetic perspective and opening avenues for targeted interventions in LUAD treatment.
{"title":"Multi-omics integration reveals chromatin-associated lncRNA prognostic model in lung adenocarcinoma: Bridging GWAS, transcriptome and clinical outcomes","authors":"Xiao Zhu , Zhuolong Xiong","doi":"10.1016/j.meomic.2025.100045","DOIUrl":"10.1016/j.meomic.2025.100045","url":null,"abstract":"<div><h3>Background</h3><div>Lung adenocarcinoma (LUAD) is characterized by low overall survival rates. This research aims to explore the association between long non-coding RNAs (lncRNAs) and chromatin histone methylation/demethylation modifiers in LUAD.</div></div><div><h3>Methods</h3><div>Datasets from The Cancer Genome Atlas (TCGA), Molecular Signatures Database (MSigDB), and IEU Open genome-wide association studies (GWAS) database were analyzed. A prognostic risk model for LUAD was developed based on 32 lncRNAs linked to histone modification. The relationship between lncRNAs and the high-risk group of lung cancer was evaluated, and GO/KEGG analysis was conducted to investigate the connection between chromatin histone modification-related lncRNAs and biological processes/pathways. Mendelian Randomization methods, including Inverse Variance Weighted (IVW) and Bayesian Weighted Mendelian Randomization (BWMR), were employed to validate the GO/KEGG results. MR-Egger intercept test, Cochran’s Q test, and leave-one-out Analysis were utilized to assess the sensitivity of Mendelian Randomization analysis. Tumor mutation burden (TMB) analysis was performed to evaluate the prognostic impact of high-risk patients with high TMB.</div></div><div><h3>Results</h3><div>Identified lncRNAs, including AC025741.1 and NHS-AS1, demonstrated strong associations with the high-risk group. GO/KEGG analysis revealed significant correlations between chromatin histone modification-related lncRNAs and microtubule-based movement and cytochrome enzyme P450. Response to the renin-angiotensin agents is a protective factor for lung cancer, while response to glucocorticoids is a risk factor for lung cancer. Immunomarkers MDSC, CAF, and Exclusion showed positive correlations with the risk score, and the combined effects of CAF and MDSC were found to play a pivotal role in LUAD development and progression.</div></div><div><h3>Conclusion</h3><div>Our study not only establishes a promising LUAD prognostic risk model with potential implications for immunotherapy but also identifies lncRNAs as immune markers for LUAD immunotherapy. Additionally, we validate the causal relationship between chromatin histone methylation-related pathways and lung cancer, bolstering our understanding from a genetic perspective and opening avenues for targeted interventions in LUAD treatment.</div></div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"14 ","pages":"Article 100045"},"PeriodicalIF":0.0,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144604159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alzheimer’s disease (AD) is a neurodegenerative disorder responsible for 70–80 % of dementia cases. Aluminum, a neurotoxicant, accelerates AD progression through oxidative stress and neuroinflammation. Many phytochemicals have shown promise as alternative AD therapies. This study investigated the therapeutic effects of Persea americana (PA) and Tabebuia rosea (TR) ethanolic leaf extracts in aluminum chloride (AlCl3)-induced AD in male rats. GC–MS analysis identified phytocompounds in the extracts. Forty-two male rats (70–100 g) were divided into six groups: control, AlCl3-only, TR-treated, PA-treated, combined extracts, and donepezil-treated (standard AD drug) groups. Biochemical and histopathological analyses were conducted on brain tissues. In silico analysis docked Beta-secretase (BACE1) against Elenbecestat and extracted phytochemicals. AlCl3 exposure significantly increased acetylcholinesterase (AChE) activity and malondialdehyde (MDA) levels while reducing glutathione (GSH) levels, with notable brain histopathology. PA and TR treatment reversed these effects, lowering AChE and MDA levels while increasing GSH. In silico analysis revealed that ethyl (9E,12E)-octadeca-9,12-dienoate and 9-octadecenoic acid, ethyl ester, exhibited superior docking scores and binding energies compared to Elenbecestat. These findings suggest PA and TR extracts as potential alternative treatments for AD.
{"title":"Neuroprotective effects of Persea americana and Tabebuia rosea ethanolic extracts against aluminum chloride-induced Alzheimer’s disease in rat model","authors":"Olayinka Fisayo Onifade , Oluwasayo Peter Abodunrin , Esther Omolara Oyeneye , Ebubechukwu Goodness Chigozie , Abdusalam Gbemisola Arafa , Benjamen Olujide Okunlola","doi":"10.1016/j.meomic.2025.100044","DOIUrl":"10.1016/j.meomic.2025.100044","url":null,"abstract":"<div><div>Alzheimer’s disease (AD) is a neurodegenerative disorder responsible for 70–80 % of dementia cases. Aluminum, a neurotoxicant, accelerates AD progression through oxidative stress and neuroinflammation. Many phytochemicals have shown promise as alternative AD therapies. This study investigated the therapeutic effects of <em>Persea americana</em> (PA) and <em>Tabebuia rosea</em> (TR) ethanolic leaf extracts in aluminum chloride (AlCl<sub>3</sub>)-induced AD in male rats. GC–MS analysis identified phytocompounds in the extracts. Forty-two male rats (70–100 g) were divided into six groups: control, AlCl<sub>3</sub>-only, TR-treated, PA-treated, combined extracts, and donepezil-treated (standard AD drug) groups. Biochemical and histopathological analyses were conducted on brain tissues. <em>In silico</em> analysis docked Beta-secretase (BACE1) against Elenbecestat and extracted phytochemicals. AlCl<sub>3</sub> exposure significantly increased acetylcholinesterase (AChE) activity and malondialdehyde (MDA) levels while reducing glutathione (GSH) levels, with notable brain histopathology. PA and TR treatment reversed these effects, lowering AChE and MDA levels while increasing GSH. <em>In silico</em> analysis revealed that ethyl (9E,12E)-octadeca-9,12-dienoate and 9-octadecenoic acid, ethyl ester, exhibited superior docking scores and binding energies compared to Elenbecestat. These findings suggest PA and TR extracts as potential alternative treatments for AD.</div></div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"14 ","pages":"Article 100044"},"PeriodicalIF":0.0,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144535115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-03-01DOI: 10.1016/j.meomic.2025.100041
Xiaohui Shi , Xiao Zhu , Dongpei Li
Background
Epigenetic reprogramming plays a crucial role in the progression of uveal melanoma (UM). RNA methylation constitutes more than 60% of all RNA modifications, with N6-methyladenosine (m6A) being the most prevalent RNA modification in higher organisms. This study aimed to investigate the construction of the m6A regulatory factor modification model and its assessment of UM clinical prognosis.
Methods
The expression levels of 23 m6A regulators in The Cancer Genome Atlas (TCGA) were analyzed, and the survival rate was assessed based on TCGA clinicopathological data. Consistent cluster analysis was performed to evaluate different m6A scores in tumor mutation burden (TMB) and to predict the correlation between m6A scores and UM prognosis.
Results
Various expression patterns of m6A regulators were observed in UM tumors, and multiple m6A genes were found to be correlated with prognosis. Through consistent cluster analysis, three distinct m6A modification patterns were identified. The overlapping differentially expressed genes (DEGs) among the three m6A clusters were screened, leading to the establishment of three different subgroups. Among these subgroups, cluster B exhibited the most favorable prognosis. Based on the m6A score derived from DEGs, UM patients could be categorized into high-scoring subgroup and low-scoring subgroup subgroups. Importantly, patients with higher m6A scores demonstrated prolonged survival and improved clinical characteristics. Furthermore, the study established an association between the m6A score and TMB, suggesting that the m6A score may serve as a potential prognostic predictor for UM patients.
Conclusion
We conducted a screening of DEGs from the m6A cluster and categorized them into three distinct clusters for analysis of m6A scores. Subsequently, we developed a highly predictive model with prognostic value. This study will contribute to our understanding of the overall impact of m6A modification patterns on the progression of UM.
{"title":"Omics-based evaluation of m6A modification patterns in uveal melanoma and their prognostic implications","authors":"Xiaohui Shi , Xiao Zhu , Dongpei Li","doi":"10.1016/j.meomic.2025.100041","DOIUrl":"10.1016/j.meomic.2025.100041","url":null,"abstract":"<div><h3>Background</h3><div>Epigenetic reprogramming plays a crucial role in the progression of uveal melanoma (UM). RNA methylation constitutes more than 60% of all RNA modifications, with N6-methyladenosine (m6A) being the most prevalent RNA modification in higher organisms. This study aimed to investigate the construction of the m6A regulatory factor modification model and its assessment of UM clinical prognosis.</div></div><div><h3>Methods</h3><div>The expression levels of 23 m6A regulators in The Cancer Genome Atlas (TCGA) were analyzed, and the survival rate was assessed based on TCGA clinicopathological data. Consistent cluster analysis was performed to evaluate different m6A scores in tumor mutation burden (TMB) and to predict the correlation between m6A scores and UM prognosis.</div></div><div><h3>Results</h3><div>Various expression patterns of m6A regulators were observed in UM tumors, and multiple m6A genes were found to be correlated with prognosis. Through consistent cluster analysis, three distinct m6A modification patterns were identified. The overlapping differentially expressed genes (DEGs) among the three m6A clusters were screened, leading to the establishment of three different subgroups. Among these subgroups, cluster B exhibited the most favorable prognosis. Based on the m6A score derived from DEGs, UM patients could be categorized into high-scoring subgroup and low-scoring subgroup subgroups. Importantly, patients with higher m6A scores demonstrated prolonged survival and improved clinical characteristics. Furthermore, the study established an association between the m6A score and TMB, suggesting that the m6A score may serve as a potential prognostic predictor for UM patients.</div></div><div><h3>Conclusion</h3><div>We conducted a screening of DEGs from the m6A cluster and categorized them into three distinct clusters for analysis of m6A scores. Subsequently, we developed a highly predictive model with prognostic value. This study will contribute to our understanding of the overall impact of m6A modification patterns on the progression of UM.</div></div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"13 ","pages":"Article 100041"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144169424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-03-01DOI: 10.1016/j.meomic.2025.100042
Yaqi Huang , Xiao Zhu , Dongpei Li
The development and prognosis of acute myeloid leukemia (AML) are influenced by multiple factors. This study utilized bioinformatics analysis to explore differentially expressed genes (DEGs) in acute myeloid leukemia (AML) and non-tumor tissues, evaluating their prognostic significance. Target gene data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases were extracted for analysis. Over 100 DEGs were identified, with MIR9-1 exhibiting downregulated expression in AML. Survival analysis revealed significant differences in overall survival rates between subgroups, with Cluster 2 showing better outcomes. Notable DEGs, including DEFA1B, FLT3LG, CUX1, and ZMYM2, were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis highlighted relevant signaling pathways. Mendelian Randomization (MR) analysis unveiled a negative correlation between the “transcriptional misregulation in cancer pathway” and “hypermethylation of CpG island pathway” with AML. Sensitivity analysis demonstrated no heterogeneity or pleiotropy. Bayesian Weighted Mendelian Randomization (BWMR) validated MR results. Overall, this study identified potential therapeutic targets like FLT3LG, elucidated key genes for AML prognosis, and revealed protective roles of pathways through comprehensive bioinformatics analysis and Mendelian randomization.
{"title":"Uncovering prognostic markers and therapeutic targets in acute myeloid leukemia: Insights from differential gene expression and Mendelian randomization analysis","authors":"Yaqi Huang , Xiao Zhu , Dongpei Li","doi":"10.1016/j.meomic.2025.100042","DOIUrl":"10.1016/j.meomic.2025.100042","url":null,"abstract":"<div><div>The development and prognosis of acute myeloid leukemia (AML) are influenced by multiple factors. This study utilized bioinformatics analysis to explore differentially expressed genes (DEGs) in acute myeloid leukemia (AML) and non-tumor tissues, evaluating their prognostic significance. Target gene data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases were extracted for analysis. Over 100 DEGs were identified, with MIR9-1 exhibiting downregulated expression in AML. Survival analysis revealed significant differences in overall survival rates between subgroups, with Cluster 2 showing better outcomes. Notable DEGs, including DEFA1B, FLT3LG, CUX1, and ZMYM2, were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis highlighted relevant signaling pathways. Mendelian Randomization (MR) analysis unveiled a negative correlation between the “transcriptional misregulation in cancer pathway” and “hypermethylation of CpG island pathway” with AML. Sensitivity analysis demonstrated no heterogeneity or pleiotropy. Bayesian Weighted Mendelian Randomization (BWMR) validated MR results. Overall, this study identified potential therapeutic targets like FLT3LG, elucidated key genes for AML prognosis, and revealed protective roles of pathways through comprehensive bioinformatics analysis and Mendelian randomization.</div></div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"13 ","pages":"Article 100042"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144184894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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